Jan 202007
 

Definitions:

Common descent is the idea that two populations or species share a common ancestral species, and are both descended from that ancestor by normal processes of replication. This is a fairly commonplace notion. The theory of common descent states that all species (on Earth, at least) share common ancestors, back to a single common ancestor of all life.

The mechanisms that produce diversity from common ancestors are those of the Theory of Evolution.

Is above definition correct?

Anyone bother to give Common design definition so we can start debate?  Preferably by one who opposes the concept.

  223 Responses to “Common descent vs Common design”

  1. I have been and will continue to use common descent to mean specifically that all organisms are descended from a single or very limited number of organisms (and for convenience I will say it is a single ancestor). No one is disputing that every breed of dog has a common ancestor.

    The theory of evolution is just one way that we could have common descent; common descent is not restricted to that (afterall Behe and Denton accept common descent). Common descent is neutral on the mechanism of evolution.

    I suggest some one who believes in common design define it. I am bound to get accused of misrepresention.

  2. Hi Pixie,

    Thank you man. I think you give us your definition and than we can modify it if necessary. No need to accuse anyone of anything here. We are just debating things in a friendly manner, I hope.

    Don’t understand what do you mean by “Common descent is neutral on the mechanism of evolution.” Will you please explain.

  3. Okay then…

    Common Design

    Let us suppose YEC for a moment. The idea behind commin design is that all the archetypes created by God have varying trait in common because there was a single designer who used the same design module across a variety of archetypes. He started with a basic body plan of two fore limbs and two hind limbs, and modified that conceptual design to produce the design for a bird. The desigm for a bird was then further refined to give the actualised designs for chickens and eagles.

    I guess common design is not restricted to YEC. The design event could have happened at the Cambrian explosion, for example, or frequent invervals over the last 4 billion years. It is a creationist theory (though not necessarily a Biblical creationist theory) because it claims each archetype is created in isolation.

    An analogy to human design is apparent. Although every model of washing machine is created in isolation, the design will take features found in many other washing machines, such as a spinning drum, a control mechanism, a water heater, a timer. Models of dish washers will show the same pattern, where most of the features are pretty similar. Furthermore, we can see a relationship – but a more “distant” one – between the dish washer and the washing machine, as both have control mechanisms, water heaters and timers. We could look at freezers, and see a rather different set of design features for a rather different job, but there are still some common features even here. Thus, we could build a hierarch of kitchen appliances.

    Common Descent

    Common descent, in contrast, is not a creationist theory (the common ancestor could have been created by God, but I still would not call it a creationist theory. Common descent says that species have evolved, that is changed by small amounts over numerous generations. The changes have to be small to keep the continuity; all the way from “molecules to man” or “goo to you” there are no sudden jumps where you might be sure this generation is one species, the next generation is a new species. It is all gradual change (even for punctuated equilibrium, the change is small). Quite how that change happens is not a part of common descent. I believe it is through a process of variation and selection, but other people (bertvan and mturner at ARN) say the organism itself is intelligently designing the changes to the species. It could be God directing the mutations. It could be something else. Common descent is neutral on the mechanism of evolution.

    Comments by the IDists

    Evolution is a controversial topic, so it is necessary to address a few basic questions at the beginning of the book. Many people think that questioning Darwinian evolution must be equivalent to espousing creationism. As commonly understood, creationism involves belief in an earth formed only about ten thousand years ago, an interpretation of the Bible that is still very popular. For the record, I have no reason to doubt that the universe is the billions of years old that physicists say it is. Further, I find the idea of common descent (that all organisms share a common ancestor) fairly convincing, and have no particular reason to doubt it.

    Behe, M.J., “Darwin’s Black Box: The Biochemical Challenge to Evolution,” Free Press: New York NY, 1996, pp.5-6

    Dembski from here:

    Indeed, intelligent design is perfectly compatible with common descent.

    Dembski from here:

    More significantly for the educational curriculum, however, is that intelligent design has no stake in living things coming together suddenly in their present form. To be sure, intelligent design leaves that as a possibility. But intelligent design is also fully compatible with large-scale evolution over the course of natural history, all the way up to what biologists refer to as “common descent” (i.e., the full genealogical interconnectedness of all organisms). If our best science tells us that living things came together gradually over a long evolutionary history and that all living things are related by common descent, then so be it. Intelligent design can live with this result and indeed live with it cheerfully.

    Denton from here:

    It is important to emphasize at the outset that the argument presented here is entirely consistent with the basic naturalistic assumption of modern science – that the cosmos is a seamless unity which can be comprehended ultimately in its entirety by human reason and in which all phenomena, including life and evolution and the origin of man, are ultimately explicable in terms of natural processes. This is an assumption which is entirely opposed to that of the so-called “special creationist school”. According to special creationism, living organisms are not natural forms, whose origin and design were built into the laws of nature from the beginning, but rather contingent forms analogous in essence to human artifacts, the result of a series of supernatural acts, involving the suspension of natural law. Contrary to the creationist position, the whole argument presented here is critically dependent on the presumption of the unbroken continuity of the organic world – that is, on the reality of organic evolution and on the presumption that all living organisms on earth are natural forms in the profoundest sense of the word, no less natural than salt crystals, atoms, waterfalls, or galaxies.

    I started a thread at ARN about the evidence for common descent, by the way. There was not much response, but admittedly ARN is pretty quiet these days.

  4. I was expecting this to get a bit more lively.

    Something I missed on the ARN page was the issue of biogeography; the distribution of different species.

    Here:

    How can we make intelligible the colossal diversity of living beings and the existence of such extraordinary, seemingly whimsical creatures as the fungus, beetle, and fly described above? And why are island groups like the Galopagos so often inhabited by forms similar to those on the nearest mainland but belonging to different species? Evolutionary theory explains that biological diversity results from the descendants of local or migrant predecessors becoming adapted to their diverse environments. This explanation can be tested by examining present species and local fossils to see whether they have similar structures, which would indicate how one is derived from the other. Also, there should be evidence that species without an established local ancestry had migrated into the locality.
    Wherever such tests have been carried out, these conditions have been confirmed. A good example is provided by the mammalian populations of North and South America, where strikingly different native organisms evolved in isolation until the emergence of the isthmus of Panama approximately 3 million years ago. Thereafter, the armadillo, porcupine, and opossum–mammals of South American origin–migrated north, along with many other species of plants and animals, while the mountain lion and other North American species made their way across the isthmus to the south.
    The evidence that Darwin found for the influence of geographical distribution on the evolution of organisms has become stronger with advancing knowledge. For example, approximately 2,000 species of flies belonging to the genus Drosophila are now found throughout the world. About one-quarter of them live only in Hawaii. More than a thousand species of snails and other land mollusks also are found only in Hawaii. The biological explanation for the multiplicity of related species in remote localities is that such great diversity is a consequence of their evolution from a few common ancestors that colonized an isolated environment. The Hawaiian Islands are far from any mainland or other islands, and on the basis of geological evidence they never have been attached to other lands. Thus, the few colonizers that reached the Hawaiian Islands found many available ecological niches, where they could, over numerous generations, undergo evolutionary change and diversification. No mammals other than one bat species lived in the Hawaiian Islands when the first human settlers arrived; similarly, many other kinds of plants and animals were absent.
    The Hawaiian Islands are not less hospitable than other parts of the world for the absent species. For example, pigs and goats have multiplied in the wild in Hawaii, and other domestic animals also thrive there. The scientific explanation for the absence of many kinds of organisms, and the great multiplication of a few kinds, is that many sorts of organisms never reached the islands, because of their geographic isolation. Those that did reach the islands diversified over time because of the absence of related organisms that would compete for resources.

  5. Have some problems with the spam filter, so breaking up my post…

    Here:

    A. The total number of species on oceanic islands is small compared to the number on an equal area of continent
    B. Proportion of endemic species is very high
    C. Oceanic islands are missing entire Classes
    D. Endemic species often possess characters that are adaptive elsewhere, but are useless characters on the island
    E. Endemic species often show (new) adaptive traits not possessed by any of their relatives
    F. Batrachians are universally absent (except one frog in New Zealand)
    G. Terrestrial mammals are not found on any island >300 miles from mainland
    H. But arial mammals are found on such islands, and many of these are endemic
    I. Also a correlation between the depth of the sea separating islands inhabited by mammals and the degree of “affinity” (classification) between these species
    J. “The most striking and important fact” (p. 397) is the affinity of these island species to those of the nearest mainland, without being actually the same species
    K. Within an archipelago, species are more closely related to each other than to those on the mainland (but still distinct from each other)
    L. The principle applies widely that island inhabitants are most closely related to the inhabitants of a region from which colonization is possible
    M. According to this principle, it must be the case that at some former time, a single parental species covered both ranges (i.e., the migration event itself)
    N. Darwin draws a parallel between Time and Space in the “Laws of Life” (p. 409)

  6. Here:

    Another clue to patterns of past evolution is found in the natural geographic distribution of related species. It is clear that major isolated land areas and island groups often evolved their own distinct plant and animal communities. For instance, before humans arrived 60-40,000 years ago, Australia had more than 100 species of kangaroos, koalas, and other marsupials such as dogs, cats, bears, horses. Land mammals were entirely absent from the even more isolated islands that make up Hawaii and New Zealand. Each of these places had a great number of plant, insect, and bird species that were found nowhere else in the world. The most likely explanation for the existence of Australia’s, New Zealand’s, and Hawaii’s mostly unique biotic environments is that the life forms in these areas have been evolving in isolation from the rest of the world for millions of years.

  7. A. Madagascar
    Madagascar is a large island that is actually a piece of a continent (not like Hawaii which is created by volcanoes) that is separated from other land masses. It has the highest level of endemism (i.e., organisms that only live there) on earth. For example of the 150 amphibians present there 148 are only found in Madagascar. 90% of all the reptiles and 100% of the rodents are only found in Madagascar. Lemurs are only found in Madagascar.
    Why might this be so? Plate tectonic theory says that Madagascar used to be part of India and Antarctica and so the animals at that time were able to rove back and forth between these land masses. When Madagascar separated from India and Antarctica, the animals were isolated and since that time (when they had a common ancestor with Indian and Antarctican animals) they have evolved to look very different. This would also explain the presence of fossils on Madagascar that are related to the living animals there now.
    B. The Hawaiian Islands
    Like Madagascar, the plants and animals on Hawaii are almost completely different from anywhere else on earth. Unlike Madagascar, Hawaii is a set of volcanic islands. The animals and plants almost certainly came there from another continent. Yet they clearly have changed since arriving. Even on the islands, the species are often different from one island to another. Thus we can see that evolution has happened even between islands.
    Consistent with the idea that the animals and plants have their common ancestors on the mainland, there is only one mammal native to Hawaii – the bat. Only the bat has been able to get to Hawaii. There are NO native reptiles, as no reptiles have been able to get across the over 1000 miles of open ocean to the islands.

  8. Here:

    The trees on the remote island of St. Helena are unlike the trees anywhere else on earth. Sunflowers are the closest relative to the strange gumwood tree and to the various cabbage-trees. And, the most closely related sunflower is the local sunflower. The scientific explanation is that this volcanic island was originally formed far away from any continent, and therefore started out with no land plants. Eventually, some sunflower seeds managed to get there. Since no one else was filling the role of “tree”, the largest plants on the island – some of the sunflowers – took the job. Transformed by time and competition and by the demands of their role, they now look like trees.
    Every other remote island has its own examples. In the Galapagos, the role of woodpecker is taken by a finch. Or rather, it’s mostly a finch, but it has a beak specialized for the woodpecker role. Apparently, the only land bird which got to the Galapagos was a finch, so all the land birds there are modified finches. (DNA studies prove the relationship.)
    In Hawaii, the role of woodpecker was taken by a modified honeycreeper bird. Again, every land bird in Hawaii is a modified honeycreeper. There’s a honeycreeper “parrot” too.
    Most remote islands had flightless birds, such as the Dodo. There is an obvious evolutionary explanation for why these existed on islands, but not on continents. Birds could get to islands, and ground animals couldn’t. So, the role of ground animal was available, and on each island, some bird took on the role. From this explanation, we can predict that each island would have its own unique species of flightless bird. And that is a correct prediction.
    Because of Australia, South America, and the various remote islands, it’s easy to come up with a really long list. For example, South American tropical species are more closely related to South American desert species than they are to African tropical species. Australia’s marsupials took on the roles of predator (Tasmanian Wolf), mouse, mole, wolverine (Tasmanian Devil), and anteater.

    It is probably worth mentioning that evidence in geology indicates that Antartica, South America, Australia and New Guinea were all part of one large continent at one time, so today we see some marsupials in South America (and into North America by migration) and in New Guinea. The only placental mammals in Australia before the arrival of Europeans were bats and dingos; the former flew, the latter descended from dogs brough by man.

  9. Pixie and others you all seem to be busy posters in the past few days.

    Pixie,

    Common descent is neutral on the mechanism of evolution.

    I think I know what you mean but it is unnecessarily obscurant. You should really phrase it in accordance by how ID theorists and Darwinists understand these mechanisms — although I am not sure what a mechanism is, from an ID perspective. The mechanisms for common descent from ID and Darwinian evolution perspectives are mutually exclusive therefore it can’t be neutral.

    Your quotes from Behe and Dembski only add to the confusion when you’ve conflated the idea of common ancestry with “mechanisms” . Common descent is an inference from the data but have no influence on the data itself. Where as the mechanism does not only evaluate the data but also may be the data. e.g. genetic drift, information theory, irreducible complexity.

    Let me also just say that while I respect and agree with other IDists on the core tenets of ID; I am a Creationists that accepts the universe to be billions of years in age and reject common descent, so Behe is wrong in is characterization of Biblical Creationists.

    How can we make intelligible the colossal diversity of living beings and the existence of such extraordinary, seemingly whimsical creatures as the fungus, beetle, and fly described above?

    Isn’t this merely an argument from ignorance? Like so many of the criticisms of ID, the idea that we can’t “imagine” why the designer did it this way or we don’t know the teleology of certain artifacts, therefore it must be random and unguided Darwinism. Why aren’t Darwinians more critical of their own argument from ignorance.

    And why are island groups like the Galopagos so often inhabited by forms similar to those on the nearest mainland but belonging to different species?

    What I don’t understand is why do Darwinians continue to think that by pulling out examples of microevolution would be enough to fool people who are knowledgeable about macroevolution?

    Here:

    This can hardly be considered as real scientific evidence let alone for macroevolution or common descent. While none of the points qualifies as empirical evidence for macroevolution, other lines of evidences can certainly falsify them. e.g. Convergent evolution from the Anolis lizards, wolves, sandlance and chameleon eyes, and numerous examples of common morphology from differing environments. Darwinian macroevolution and common descent is also falsified at the molecular level with molecular convergence or more accurately molecular common design.

    The most likely explanation for the existence of Australia’s, New Zealand’s, and Hawaii’s mostly unique biotic environments is that the life forms in these areas have been evolving in isolation from the rest of the world for millions of years.

    This has actually an interesting question. I’ve been pondering on this for some time. Maybe you can help me understand how does Darwinian evolution create a snake in a 10my old island like Hawaii?

    Australia’s marsupials took on the roles of predator (Tasmanian Wolf), mouse, mole, wolverine (Tasmanian Devil), and anteater.

    As I said this is evidence against Darwinian evolution and common descent because of convergence.

    so today we see some marsupials in South America

    This is also another interesting problem for Darwinian (CD). How is it possible for species like the marsupial opossiums in South America to remain relatively unchanged for over 100mya? I though the Darwinian theory was suppose to predict that isolation should produce unique and new macro species changes?

  10. Teleologist

    The mechanisms for common descent from ID and Darwinian evolution perspectives are mutually exclusive therefore it can’t be neutral.

    ID could be true, and could include common descent. Darwinism could be true, and includes common descent. So common descent does not side with either one, it is neutral. Conversely, if we knew for a fact that common descent was true, we could not reject ID on that basis, and we could not reject Darwinism.

    Isn’t this merely an argument from ignorance? Like so many of the criticisms of ID, the idea that we can’t “imagine” why the designer did it this way or we don’t know the teleology of certain artifacts, therefore it must be random and unguided Darwinism. Why aren’t Darwinians more critical of their own argument from ignorance.

    I think there is a fundamental difference in that scientists are actively working to combat our ignorance about how evolution happened, and indeed creationist will argue from their own ignorance about issue scientists already have explanations for.

    On the other hand, ID forbids imagining how or why the designer did certain things. Inunison called me presumptuous for doing so, and it is well known that ID shies away from any qustion about the designer.

    What I don’t understand is why do Darwinians continue to think that by pulling out examples of microevolution would be enough to fool people who are knowledgeable about macroevolution?

    Then explain the distribution of placentals and marsupials.

    This has actually an interesting question. I’ve been pondering on this for some time. Maybe you can help me understand how does Darwinian evolution create a snake in a 10my old island like Hawaii?

    The brown tree snake was introduced by man in the 1950s apparently. Is this the species you are thinking about?

    As I said this is evidence against Darwinian evolution and common descent because of convergence.

    Convergence gives us a strong prediction. According to common descent, features that animal share because of shared ancestry will be due to the same underlying genetic code. Features shared due to convergence will not. The prediction from common design should be that all shared features have the same underlying genetic code.

    This is also another interesting problem for Darwinian (CD). How is it possible for species like the marsupial opossiums in South America to remain relatively unchanged for over 100mya? I though the Darwinian theory was suppose to predict that isolation should produce unique and new macro species changes?

    There is nothing in common descent that says a species cannot “remain relatively unchanged for over 100mya” (same for Darwinism, but let us stick to common descent for this thread).

    By the way, I am not seeing any evidence for common design, or any attempt to explain anything using common design so far, only supposed evidence against common descent.

  11. Hi The Pixie,

    Your post confirms that you think Common Design denies evolution, and that is not true. What you presented here shows that species can change but that does not entail Common Descent. Also you need to get away from Theological arguments for Common Descent. Because if you use them it will only show that Common Descent is based on one’s particular view on Creator – religion.

    I will start with claims for Common Descent:

    A: THE FUNDAMENTAL UNITY OF LIFE
    1. If universal common ancestry is true, then all organisms will have one or more traits in common.
    2. All organisms have one or more traits in common.

    B: A “NESTED” HIERARCHY OF SPECIES
    1. If universal common ancestry is true, then organisms will be classifiable in a nested hierarchy.
    2. Organisms are classifiable in a nested hierarchy.

    C: CONVERGENCE OF INDEPENDENT PHYLOGENIES
    1. If universal common ancestry is true, then phylogenies constructed from any comparisons of organisms will “converge” on the standard phylogenetic tree.
    2. Phylogenies constructed from comparisons of certain biological molecules in organisms “converge” on the standard phylogenetic tree.

    D: POSSIBLE MORPHOLOGIES OF PREDICTED COMMON ANCESTORS
    1. If universal common ancestry is true, then all fossilized animals will “conform” to the standard phylogenetic tree.
    2. All fossilized animals “conform” to the standard phylogenetic tree.

    E: CHRONOLOGICAL ORDER OF PREDICTED COMMON ANCESTORS
    1. If universal common ancestry is true, then fossil intermediates will appear in the “general chronological order” reflected in the standard phylogenetic tree;
    2. Fossil intermediates appear in the “general chronological order” reflected in the standard phylogenetic tree;

  12. There is more but lets debate these first 5.

    I’ll start with problems that I have with above predictions/fulfillments:

    A:

    – The biochemical similarity of living things fits easily within a design framework.  One can just easily say that all life was constructed to look like the unified work of a single designer

    – The fact that some leading evolutionists believe early life forms were biochemically distinct from modern forms confirms that evolution does not predict biologic universals.

    – What if plants, animals, and bacteria all had different codes (traits)?  Such a finding would not falsify evolution; rather, it would be incorporated into the theory.  For if the code is arbitrary, why should there be just one?  The blind process of evolution would explain why there are multiple codes.

    – The claim that all organisms have one or more traits in common is true in the sense that all living things necessarily have the traits by which life is defined, but that is simply a tautology– living things all have the traits of living things.

    Will continue later with the rest.  Sorry The Pixie this is coming along too slow.

  13. B:

    – It is not a corollary of the hypothesis of common descent that organisms will have features by which they can be classified as groups within groups. Common descent can explain or accommodate nested hierarchy (though not without difficulty in the specific case of Neo-Darwinism), but it does not predict it. There are mechanisms of descent from a common ancestor that would yield a different pattern. If common descent can yield either nested hierarchy or something else, then the presence of nested hierarchy does not count as evidence of common descent.

    – The pattern of descent depends on the extent that evolved characters are later lost. Suppose losses are significant, and characters are replaced at a high rate. Then there is no reason to expect a nested pattern. Descendants could be totally different from their distant ancestors and sister groups, with little or no semblance of nested similarities linking them. Simple processes of loss, replacement, anagenesis, transposition, unmasking, or multiple biogenesis would prohibit such a pattern. Since hierarchical patterns (such as cladograms or phenograms) are not predicted by common descent they are not evidence for common descent.

    – There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process. If the hierarchy suggests any model of nature it is typology and not common descent.

    – The notion that the nested hierarchy of organisms is incompatible with design is based, not on science, but on the unprovable theological assumption that if God created life he would do it in some other way. As we could see in large measure by recent posts.

    – It may be that the nested hierarchy of living things simply is a reflection of designer’s orderliness. Accordingly, it is not evidence for or against either theory.

    – Any set of objects, whether or not they originated in an evolutionary process, can be classified hierarchically. Chairs, for instance, are independently created; they are not generated by an evolutionary process: but any given list of chairs could be classified hierarchically, perhaps by dividing them first according to whether or not they were made of wood, then according to their color, by date of manufacture, and so on. The fact that life can be classified hierarchically is not, in itself, an argument for common descent.

  14. C:

    – There is an obvious disconnect between the alleged prediction and fulfillment. The fulfillment refers to only one basis of comparison (biological molecules), not all bases of comparison, and it refers to only some comparisons on the selected basis (some biological molecules), not all comparisons.

    – The important point is that it is not a prediction of the hypothesis of common ancestry that phylogenies constructed from comparisons of biological molecules will match phylogenies constructed from comparisons of morphology. This is obvious from the fact molecular and morphological phylogenies often are inconsistent, and yet the hypothesis of common descent is not considered falsified. The discordant data are simply accommodated by the theory.

  15. ID could be true, and could include common descent. Darwinism could be true, and includes common descent.

    I accept this, but I was contesting your statement that ” Common descent is neutral on the mechanism of evolution” , which I do not believe to be true.

    I think there is a fundamental difference in that scientists are actively working to combat our ignorance about how evolution happened, and indeed creationist will argue from their own ignorance about issue scientists already have explanations for.

    You may believe what you said here but it doesn’t make it true. Creationists do not argue from ignorance but rather we are skeptical and dispute the fairy tale stories by Darwinians as science, Creationists are strict empirical evidentialists.

    But your spin to trot out this tired attack on ID completely evaded my point that ID critics are arguing from ignorance. Can you give another argument from these scientists other than we can’t “imagine” why the designer did it this way or we don’t know the teleology of certain artifacts; therefore it must be random and unguided Darwinism? Why aren’t Darwinians more critical of their own argument from ignorance?

    ID forbids imagining how or why the designer did certain things

    Again you are wrong about what ID forbids. inunison is right, it is presumptuous to speculate on how or why the designer created certain things. We are still in the identification stage. Science can’t be expected to answer all the questions at the beginning of a theory. e.g. If you find a crystal based fusion engine, the first task is to identify if it is designed or if it is a natural phenomenon. It is only after an artifact has been identified as designed do we speculate on how it is designed. ID scientists are working hard to build a working theory on design detection and a library of artifacts that can be accepted by the scientific community. To insist that ID must know everything about an artifact, Darwinists are embellishing an argument from ignorance.

    Then explain the distribution of placentals and marsupials.

    What is there to explain? Every species migrates and adapt within limits to their environments to create microevolutionary uniqueness. Some of the isolation and uniqueness are due to the supercontinent theory. Distribution is not a problem for ID. Can you explain how distribution is evidence for macroevolution?

    The brown tree snake was introduced by man in the 1950s apparently. Is this the species you are thinking about?

    No. There is only one species of snake in Hawaii, the Brahminy Blind Snake, presumably introduced to the islands from Asia. I have not seen any definitive evidence of this. If you can I would appreciate it. The problem for the Darwinists is that there is no evidence to explain all the different indigenous species of birds and insects on the island. I don’t know of any diligent scientists that you speak of, who are actually trying to find the precise genesis of these indigenous species, other than taking the easy presupposed Darwinian fairy tale that it must have migrate to the island somehow.

    Features shared due to convergence will not. The prediction from common design should be that all shared features have the same underlying genetic code.

    Really? Let me get this straight, are you saying that morphology and phenotype have no genetic basis? Can you give some evidence that any convergent expressions have different genetic compositions?

    My prediction is that common design does have similar underlying genetic codes for those phenotypic features.

    There is nothing in common descent that says a species cannot “remain relatively unchanged for over 100mya” (same for Darwinism, but let us stick to common descent for this thread).

    This is why Darwinian evolution is not science, isn’t it, because it can’t be tested. Darwinian evolution can’t have speciation and stasis as a result of mutation and selection. I am talking about common descent. Why don’t you explain how common descent is possible if species stay in stasis through mutation and selection pressures over such long periods of time?

    By the way, I am not seeing any evidence for common design

    What are you talking about? I gave you 2 links to examples of evidence for design, Convergent evolution and molecular convergence. Convergence makes no sense under the mechanisms of Darwinian evolution. It only makes sense under the design paradigm where a designer can utilize existing designs to build similar and identical new forms in disparate environments and independent of prior forms. This is exactly what we see in nature.

  16. Inunison

    Your post confirms that you think Common Design denies evolution, and that is not true. What you presented here shows that species can change but that does not entail Common Descent. Also you need to get away from Theological arguments for Common Descent. Because if you use them it will only show that Common Descent is based on one’s particular view on Creator – religion.

    Well I did say someone else should define common design. I look forward to seeing your definition.

    What do you mean by the “Theological arguments for Common Descent”?
    A:

    The biochemical similarity of living things fits easily within a design framework. One can just easily say that all life was constructed to look like the unified work of a single designer

    It is compatible with common design, but required by common descent.

    The fact that some leading evolutionists believe early life forms were biochemically distinct from modern forms confirms that evolution does not predict biologic universals.

    I had not heard of that. Can you be more specific? It is always helpful to provide quotes and links when you make claims like this.

    What if plants, animals, and bacteria all had different codes (traits)? Such a finding would not falsify evolution; rather, it would be incorporated into the theory. For if the code is arbitrary, why should there be just one? The blind process of evolution would explain why there are multiple codes.

    Codes or traits? A single ancestor suggests one basic system of inheritance; I do not think it requires it.

    The claim that all organisms have one or more traits in common is true in the sense that all living things necessarily have the traits by which life is defined, but that is simply a tautology– living things all have the traits of living things.

    I think there are more traits that those required by the definition of life. There is no reason that all living things have the same fundamental biochemistry (DNA/RNA plus infrastructure, same 20 amino acids)… except that they are all related, of course.
    B:

    It is not a corollary of the hypothesis of common descent that organisms will have features by which they can be classified as groups within groups. Common descent can explain or accommodate nested hierarchy (though not without difficulty in the specific case of Neo-Darwinism), but it does not predict it. There are mechanisms of descent from a common ancestor that would yield a different pattern. If common descent can yield either nested hierarchy or something else, then the presence of nested hierarchy does not count as evidence of common descent.

    Could you give an illustration of how common descent could give something other than a nested hierarchy? Something along the lines of species A gives species B and C, species B gives… It is easy to make this claim, but I think you will find it difficult to give that illustration.

    The pattern of descent depends on the extent that evolved characters are later lost. Suppose losses are significant, and characters are replaced at a high rate. Then there is no reason to expect a nested pattern. Descendants could be totally different from their distant ancestors and sister groups, with little or no semblance of nested similarities linking them. Simple processes of loss, replacement, anagenesis, transposition, unmasking, or multiple biogenesis would prohibit such a pattern. Since hierarchical patterns (such as cladograms or phenograms) are not predicted by common descent they are not evidence for common descent.

    No, this is wrong. The hierarchy would still exist, it would just be very difficult to determine.

    However, I stated earlier (post 3) that evolution is a slow process. There are no sudden jumps, no point when you can say this generation was this species, the next generation was another species. This is a strawman argument; it is not what common descent is claiming.

    There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process.

    Another vague assertion. Come on! Explain what you mean. Give examples or links to back it up. What facets? What does “flow naturally” mean?

    The notion that the nested hierarchy of organisms is incompatible with design is based, not on science, but on the unprovable theological assumption that if God created life he would do it in some other way. As we could see in large measure by recent posts.

    Sure, God could have designed life last Thursday to make it appear that common descent was true. Are you arguing that there is no evidence conceiveable that would support common descent but refute common design?

    Perhaps you should define common design, eh?
    C:

    There is an obvious disconnect between the alleged prediction and fulfillment. The fulfillment refers to only one basis of comparison (biological molecules), not all bases of comparison, and it refers to only some comparisons on the selected basis (some biological molecules), not all comparisons.

    Where do you get that from? Common descent was originally derived from the morphological similarities. The molecular similarities are now taken as more reliable, but the agreement is very good.

    The important point is that it is not a prediction of the hypothesis of common ancestry that phylogenies constructed from comparisons of biological molecules will match phylogenies constructed from comparisons of morphology. This is obvious from the fact molecular and morphological phylogenies often are inconsistent, and yet the hypothesis of common descent is not considered falsified. The discordant data are simply accommodated by the theory.

    You say “often are inconsistent”. How often is that? Like a fifty times out of a hundred, or fifty times out of ten million? Here again a quote and a link might go a long way to supporting your claims.

    From here:

    Well-determined phylogenetic trees inferred from the independent evidence of morphology and molecular sequences match with an extremely high degree of statistical significance. Many genes with very basic cellular functions are ubiquitous– they occur in the genomes of most or all organisms. An oft-cited example is the cytochrome c gene. Since all eukaryotes contain the gene for this essential protein, neither its presence nor its function correlates with organismal morphology. Additionally, because of the fact of DNA coding redundancy, parts of certain DNA sequences have absolutely no correlation with phenotype (e.g. certain introns or the four-fold degenerate third-base position of most DNA codons). Due to these two aspects of certain DNA sequences, ubiquity and redundancy, DNA sequences can be carefully chosen that constitute completely independent data from morphology. (See point 17 and 18 for more background about the molecular sequence evidence and for more detail about how it is independent of morphology.) The degree of phylogenetic congruence between these independent data sets is nothing short of incredible.

  17. I accept this, but I was contesting your statement that ” Common descent is neutral on the mechanism of evolution” , which I do not believe to be true.

    I suspect we are using the word “mechanism” differently.

    But anyway, you think it is not true. Argue the case then.

    I think there is a fundamental difference in that scientists are actively working to combat our ignorance about how evolution happened, and indeed creationist will argue from their own ignorance about issue scientists already have explanations for.

    You may believe what you said here but it doesn’t make it true. Creationists do not argue from ignorance but rather we are skeptical and dispute the fairy tale stories by Darwinians as science, Creationists are strict empirical evidentialists.

    This is joke right? “Creationists are strict empirical evidentialists”?

    What scientists do is hypothosise about what might be, given the observations available and a background knowledge of how the univese works. This is true for evolution, forensic science, chemistry, whatever. They then go looking for supporting evidence. Once a fair amount of evidence has been collected, they publish their tentative claims. Creationist, when it suits them, like to label these claims as “just-so” stories. “just-so” stories are tentative, but supported ideas about evolution that disagree with the Bible. It is spin; a way to pretend that the claim is just made up, without having to bother with the evidence that supports it.

    It is the antithesis of empirical evidentialism!

    But your spin to trot out this tired attack on ID completely evaded my point that ID critics are arguing from ignorance. Can you give another argument from these scientists other than we can’t “imagine” why the designer did it this way or we don’t know the teleology of certain artifacts; therefore it must be random and unguided Darwinism? Why aren’t Darwinians more critical of their own argument from ignorance?

    Sure, here is another argument. The MET claims are science. The claims are based ob observationsd, make predictions and those predictions have been tested.

    Can you point to a “risky” prediction from creationism – or more specifically, from common design? By “risky”, I mean a prediction that disagrees with the established paradigm, i.e., common descent. If not, you have no science.

    Again you are wrong about what ID forbids. inunison is right, it is presumptuous to speculate on how or why the designer created certain things. We are still in the identification stage. Science can’t be expected to answer all the questions at the beginning of a theory. e.g. If you find a crystal based fusion engine, the first task is to identify if it is designed or if it is a natural phenomenon. It is only after an artifact has been identified as designed do we speculate on how it is designed. ID scientists are working hard to build a working theory on design detection and a library of artifacts that can be accepted by the scientific community. To insist that ID must know everything about an artifact, Darwinists are embellishing an argument from ignorance.

    Oh, that tired refrain. Imagine next week on CSI (the TV show, not the dubious ID claim), the forensic scientists say, well we have determined that the death was caused by an intelligent agent. Hopefully by the end of the day we can give you some information about how it was done, like whether he was shot or stabbed.

    It does not happen like that. The reality is that any evidence for design also gives clues about the design process, the designer and the purpose.

    The reality is that ID makes a political decision to avoid the designer question, to distance itself from creationism. Do you honestly believe otherwise?

    What is there to explain? Every species migrates and adapt within limits to their environments to create microevolutionary uniqueness. Some of the isolation and uniqueness are due to the supercontinent theory. Distribution is not a problem for ID. Can you explain how distribution is evidence for macroevolution?

    We are talking about common design, which is a creationist theory, not ID.

    Now, from the claims of common design, how do you explain the distribution of placental and marsuial mammals?

    The brown tree snake was introduced by man in the 1950s apparently. Is this the species you are thinking about?

    No. There is only one species of snake in Hawaii, the Brahminy Blind Snake, presumably introduced to the islands from Asia. I have not seen any definitive evidence of this. If you can I would appreciate it. The problem for the Darwinists is that there is no evidence to explain all the different indigenous species of birds and insects on the island. I don’t know of any diligent scientists that you speak of, who are actually trying to find the precise genesis of these indigenous species, other than taking the easy presupposed Darwinian fairy tale that it must have migrate to the island somehow.

    As opposed to the creationist fairy tale that God put them there?

    I did find that all Brahminy Blind Snakes are female; they reproduce a sexually. So you only need one to float over at some point, rather than a breeding pair.

    Really? Let me get this straight, are you saying that morphology and phenotype have no genetic basis?

    For convergent evolution, yes.

    This is why Darwinian evolution is not science, isn’t it, because it can’t be tested. Darwinian evolution can’t have speciation and stasis as a result of mutation and selection. I am talking about common descent. Why don’t you explain how common descent is possible if species stay in stasis through mutation and selection pressures over such long periods of time?

    Why is that a problem? Sorry, I cannot see why a very slow evolution is a problem.

    Pix: By the way, I am not seeing any evidence for common design
    Tel: What are you talking about? I gave you 2 links to examples of evidence for design, Convergent evolution and molecular convergence. Convergence makes no sense under the mechanisms of Darwinian evolution. It only makes sense under the design paradigm where a designer can utilize existing designs to build similar and identical new forms in disparate environments and independent of prior forms. This is exactly what we see in nature.

    What was I talking about? I was talking about this thread on common descent vs common design. As this was your first post, I think maybe you had not given any links.
    Wrt molecular convergence evidence against Darwinian evolution:
    Here:

    Apolipoprotein(a) [apo(a)] is the distinguishing protein component of lipoprotein(a), a major inherited risk factor for atherosclerosis. Human apo(a) is homologous to plasminogen. It contains from 15 to 50 repeated domains closely related to plasminogen kringle four, plus single kringle five-like and inactive protease-like domains. This expressed gene is confined to a subset of primates. Although most mammals lack apo(a), hedgehogs produce an apo(a)-like protein composed of highly repeated copies of a plasminogen kringle three-like domain, with complete absence of protease domain sequences. Both human and hedgehog apo(a)-like proteins form covalently linked lipoprotein particles that can bind to fibrin and other substrates shared with plasminogen. DNA sequence comparisons and phylogenetic analysis indicate that the human type of apo(a) evolved from a duplicated plasminogen gene during recent primate evolution. In contrast, the kringle three-based type of apo(a) evolved from an independent duplication of the plasminogen gene approximately 80 million years ago. In a type of convergent evolution, the plasminogen gene has been independently remodeled twice during mammalian evolution to produce similar forms of apo(a) in two widely divergent groups of species.

    The hedgehog apo(a)-like gene apparently was derived by remodeling the kringle 3 domain of plasminogen, in a process distinct from the derivation of the human apo(a) gene from plasminogen kringle 4, kringle 5, and protease domains (6). Both the UPGMA alignments using total nucleotide sequences (data not shown) and using only the absolutely conserved residues (Fig. 2A) suggest that the ancestor of hedgehog apo(a) arose in the line leading to placental mammals after the separation from marsupials, with the latter analysis placing it closest to hedgehogs.

    Here:

    Apo(a) is virtually confined to primates, and the gene may have arisen during primate evolution. One exception is the occurrence of an Lp(a)-like particle in the hedgehog. Cloning of the hedgehog apo(a)-like gene shows that it is distinctive in form and evolutionary history from human apo(a), but that it has acquired several common features. It appears that the primate and hedgehog apo(a) genes evolved independently by duplication and modification of different domains of the plasminogen gene, providing a novel type of “convergent” molecular evolution.

    So eviolution hit upon the same (more or less) protein twice. Convergent evolution. The prediction from common descent is that the underlying genetic code will be different, while common design says the same. Guess what? The articles say they are different.

  18. What scientists do is hypothosise about what might be, given the observations available and a background knowledge of how the univese works. This is true for evolution

    No this is not true for Darwinian evolution. I would say Darwinists have not provide a SINGLE piece of empirical evidence that macroevolution has ever taken place. Can you show me a single piece of empirical evidence that has been “collected” that demonstrates the hypothesis that a bacterium turned into a fish into an amphibian into a reptile into etc, etc. All we ever get from Darwinians are fairy tale stories of disparate fossil of alleged common descent.

    Creationists are strict evidentialists when it comes to science because we understand what science is. When we make a hypothesis, we must be able to test the premise of that hypothesis through repeatable observation and predictions. Darwinism fails in both counts.

    Sure, here is another argument. The MET claims are science. The claims are based ob observationsd, make predictions and those predictions have been tested.

    I’ve been asking you and other Darwinists for a long time now. Show us just one example of this prediction of common ancestry with empirically tested results, no putative hand waiving from scattered fossils which disproves your prediction.

    Can you point to a “risky” prediction from creationism – or more specifically, from common design?

    I just gave you one i.e., convergence in phenotypical features from diverse environments have similar genetic design. Here is another one, IC could not be derived from random and unguided processes.

    Oh, that tired refrain. Imagine next week on CSI (the TV show, not the dubious ID claim),

    The only problem is that you want to stop the science and investigation at the first 5 minutes of the show because they don’t give you all the answers. Darwinists are anti-science.

    The reality is that ID makes a political decision to avoid the designer question

    Now you are misrepresenting ID again! There is no political factor involved with ID when it comes to the designer. It is a non-starter. ID does not address and I suspect will never be able to address the designer question. We might be able to address the design process but never the designer unless the designer decides to show up. Just as Darwinism and archaeology will never be able to address the designer question when it comes to Stonehenge, unless the designer shows up.

    We are talking about common design, which is a creationist theory, not ID.

    Wrong again. Common design can be a part of ID. You might be thinking about Biblical Creationist who are against common ancestry, which is not a part of ID.

    Now, from the claims of common design, how do you explain the distribution of placental and marsuial mammals?

    I just gave that to you, why don’t you tell me what specifically is the problem with what I’ve said so I can understand what it is that you are looking for.

    As opposed to the creationist fairy tale that God put them there?

    Don’t put words in my mouth. I’ve never said that. I am only raising the questions that Darwinists must answer if Darwinian evolution is to be viewed as a viable scientific theory.

    I did find that all Brahminy Blind Snakes are female; they reproduce a sexually. So you only need one to float over at some point, rather than a breeding pair.

    This is a joke. This is exactly the kind of fairy tale stories from Darwinists I am talking about. 2500 miles of ocean surround the Hawaiian Islands. It is beyond credulity that a tiny snake can float all that distance.

    For convergent evolution, yes.

    Can you tell me what is the underlying cause for the phenotype expressions, if it is not genetics?

    Why is that a problem?

    This is the problem if you can’t see why the same Darwinian prediction produces two opposite results given the same conditions.

    So eviolution hit upon the same (more or less) protein twice.

    That is the point. Even at a 50% identify the probability of in hitting that convergence would be 4.75 X 101865. It is not believable with those odds.

    The prediction from common descent is that the underlying genetic code will be different, while common design says the same. Guess what? The articles say they are different.

    You don’t understand what the article is saying. It inferred that Apo(a) was homologous to the common plasminogen 90mya. At that time plasminogen diverged and became two different proteins but somehow 90my later they end up at a different protein Apo(a) with 50% identity performing essentially the same function. No, common descent do not make these predictions, but common design does.

  19. Teleologist

    It is interesting and of course not surprising that you ducked defining what exactly the theory of common design is claiming. The last thing you want is to be pinned down to specifics. I am curious how long you can keep avoiding that.

    Creationists are strict evidentialists when it comes to science because we understand what science is. When we make a hypothesis, we must be able to test the premise of that hypothesis through repeatable observation and predictions. Darwinism fails in both counts.

    Could you point to a web site that you think is both good science and creation science; somewhere with some substance (Walt Brown’s web site for example has plenty of substance). We could then look at how truthful this claim is. I find it surprising, to say the least. You might want to start a new thread.

    Pix: Can you point to a “risky” prediction from creationism – or more specifically, from common design?
    Tel: I just gave you one i.e., convergence in phenotypical features from diverse environments have similar genetic design.

    And how exactly do you test that prediction? You cannot. It is not falsifiable. Not so very risky then.

    Here is another one, IC could not be derived from random and unguided processes.

    How is IC a necessary consequence of common design?

    The way this scienmce thing works is that you infer a hypothesis from observations. Then you suppose the hypothesis is true, and consider what the necessary consequences are for that hypothesis. These are the predictions. You then go and test those predictions. This makes the hypothesis falsifiable. If the predictions are risky, are not what the current theory predicts and turn out to be correct, you publish.

    IC is not a necessary prediction of common design or ID. And “convergence in phenotypical features from diverse environments have similar genetic design” is not testable.

    The only problem is that you want to stop the science and investigation at the first 5 minutes of the show because they don’t give you all the answers. Darwinists are anti-science.

    Not so. Darwinists are the ones actually doing the science, remember!

    Now you are misrepresenting ID again! There is no political factor involved with ID when it comes to the designer. It is a non-starter. ID does not address and I suspect will never be able to address the designer question. We might be able to address the design process but never the designer unless the designer decides to show up. Just as Darwinism and archaeology will never be able to address the designer question when it comes to Stonehenge, unless the designer shows up.

    We know plenty about the designers of stone henge. How many eyes they have, what they eat (we can even say exactly which 20 amino acids they require in their diet), etc. Sure, there are some details, but we have a pretty good idea.

    Wrong again. Common design can be a part of ID. You might be thinking about Biblical Creationist who are against common ancestry, which is not a part of ID.

    Oh, no! Common design says something about how the creator created. Ergo, not ID remember.

    Pix: Now, from the claims of common design, how do you explain the distribution of placental and marsuial mammals?
    Tel: I just gave that to you, why don’t you tell me what specifically is the problem with what I’ve said so I can understand what it is that you are looking for.

    What I was hoping for was some explanation or rationalisation for why placental mammals are distributed in one way, and marsuial mammals another way. Why are they not all mixed in together. Check back and see what I did if you are not sure what an “explanation” is.

    Pix: As opposed to the creationist fairy tale that God put them there?
    Tel: Don’t put words in my mouth. I’ve never said that. I am only raising the questions that Darwinists must answer if Darwinian evolution is to be viewed as a viable scientific theory.

    Are you honestly saying you do not believe God put them there? You are on record on this site as a creationist!

    That is the point. Even at a 50% identify the probability of in hitting that convergence would be 4.75 X 101865. It is not believable with those odds.

    Can you walk me through the maths here (and the English)?

    Pix: The prediction from common descent is that the underlying genetic code will be different, while common design says the same. Guess what? The articles say they are different.
    Tel: You don’t understand what the article is saying. It inferred that Apo(a) was homologous to the common plasminogen 90mya. At that time plasminogen diverged and became two different proteins but somehow 90my later they end up at a different protein Apo(a) with 50% identity performing essentially the same function. No, common descent do not make these predictions, but common design does.

    It is you getting it wrong. From the second article “duplication and modification of different domains of the plasminogen gene“. Different mutations to different parts of the plasminogen gene, i.e., different genetic code.

  20. The distribution of eyes is another puzzle for common design. The reverse-wired eye of vertebrates is common to sharks, eagles and man. The obverse-eye is, of course found in cephalopods, such as squid. Common descent says that they are distributed thus because the shark, eagle and man (together with all other vertebrates) share a common ancestor that happened to evolve the reverse wired eye, while the cephapods are not, but are instead descended from some ancestor with the first obverse-wired eye.

    The prediction from common design should be that we each get the eye best suited to our environment and life style, regardless of any passing similarity in our morphology. Sure, fish have a backbone like us, as well as several other features in common, but living underwater, they will be better served by the obverse-wired eye, like the squid (or the squid would be better served by the reverse-wired eye). What you expect from common design is that each “kind” has the features that suits it best. If the obverse eye works best in this situation, then every beast in that situation should have it.

  21. It is interesting and of course not surprising that you ducked defining what exactly the theory of common design is claiming.

    Now that is funny, because I was not that I am required to give a definition. Honestly, I have not thought about it in terms of some formal theory or hypothesis, but I will take a stab at it if it makes you happy. I look at common design in the sense that Darwinists look at common descent. Where a Darwinist sees similar features and attribute those similarities to common ancestry, I see a designer using the same features in different biological organisms.

    Could you point to a web site that you think is both good science and creation science; somewhere with some substance (Walt Brown’s web site for example has plenty of substance).

    Oh I can do much better than Walt Brown’s web site. Would you consider the prestigious Journal Nature good science? How about the Science Magazine, PloS and PNAS? There is no difference between “good science” and “creation science” . Every day these prestigious scientific publications inform us about how new experiments have failed to provide any empirical evidence for the Darwinian claim of macroevolution. And sometimes I find stories like the one I cited above that shows why a design inference is much more plausible than an unguided and random process. I don’t think we need to start a thread about the truthfulness of these prestigious publications, do you?

    And how exactly do you test that prediction? You cannot. It is not falsifiable.

    Of course you can, maybe not at our level of science today but maybe soon. e.g. Create a life from scratch, allow it to randomly mutate in different environments and see if it will randomly arrive at similar morphologies, and that would falsify common design. There are a lot of other ways to falsify common designs. Another method that is within our capabilities now is to take 2 diverse species and randomly mutate them and observe to see if they can produce the similar complexity as the paper I cited above.

    How about you, do you know of a way to falsify common descent other than finding a fossil rabbit?

    The way this scienmce thing works is that you infer a hypothesis from observations. Then you suppose the hypothesis is true, and consider what the necessary consequences are for that hypothesis. These are the predictions. You then go and test those predictions. This makes the hypothesis falsifiable.

    We all know what these things are. Save us some time and instead of talking about it show us some empirical evidence of these predictions that proves your hypothesis. Common design is a proven fact e.g. GMO and gene therapy. There is no doubt that design can and are reused in biological systems. The question now is can we completely rule out RM&NS. The answer seems to be a firmer yes every day.

    IC is not a necessary prediction of common design or ID. And “convergence in phenotypical features from diverse environments have similar genetic design” is not testable.

    Originally I mentioned IC in response to your question about creation or design from my POV. But now I don’t know why it can’t be a part of common design. Blood clotting is universal similar in all animals throughout the history of life. If common descent is true and it can turn a fish into a fox like mammal and turn it back to a water dwelling mammal, I would think there should be equal diversity on how blood clotting works. Nope, common design is a better inference for IC to me.

    Not so. Darwinists are the ones actually doing the science, remember!

    How can I forget. You Darwinists spend all you time telling us that you are doing science, but all you ever produce are fairy tales. I remember.

    We know plenty about the designers of stone henge. How many eyes they have, what they eat (we can even say exactly which 20 amino acids they require in their diet), etc.

    There you go again spinning fairy tales. Prove it! Show me the evidence. Are there inscription on Stonehenge? Do you have pictures of the construction? The fact to the matter is that you don’t know anything about the designers but you somehow can infer that Stonehenge must be designed. Imagine that, what a quaint idea.

    Oh, no! Common design says something about how the creator created. Ergo, not ID remember.

    Can you tell me how does it show “how” the creator created?
    Common design can be a part of ID, remember?

    What I was hoping for was some explanation or rationalisation for why placental mammals are distributed in one way, and marsuial mammals another way. Why are they not all mixed in together.

    Huh? What part of the supercontinent theory did you not understand? Check wiki if you need help.

    Check back and see what I did if you are not sure what an “explanation” is.

    It seems all you did was to throw out a bunch of quotes. Why don’t you remind me?

    Are you honestly saying you do not believe God put them there? You are on record on this site as a creationist!

    Huh? I am a creationist but why would that make it necessary for me to conclude that God put the snake and all the insects and birds in Hawaii? There is no theological reason for me to do so and I do not yet have scientific reason either. I am skeptical of the Darwinian explanations and find it very unconvincing. Care to give another try other than floating?

    Can you walk me through the maths here (and the English)?

    Please read the post for the detail.

    It is you getting it wrong. From the second article “duplication and modification of different domains of the plasminogen gene”. Different mutations to different parts of the plasminogen gene, i.e., different genetic code.

    The problem appears to be that you don’t understand about genetics. The reason why they can even consider it as homologous is because the 2 proteins perform the same function and are inordinately similar.

  22. Hi The Pixie,

    Your post #20 is another one that uses Theological argument for Common Descent. And I am asking you again to refrain from doing so. For the simple reason that I can give you numerous Theological Design arguments as to why distribution of eyes points to a single Creator. However as you are well aware none of these can be scientifically evaluated. But I am prepared to concede to your point if you can tell us what special insight you have into the mind of The Designer.

  23. The distribution of eyes is another puzzle for common design.

    On the contrary, I say this is a much bigger problem for Darwinian evolution. Doesn’t Darwinian evolution say that we are in a biological arms race? Isn’t differential survival supposed to select out those organisms with less favorable phenotypes to their environments? Why would evolution continue to pass on these disadvantageous genes?

    As inunison has said we can go back and forth with this all day, but I’ve given you my best empirical evidences for common design. Why don’t you answer my request and give me the best empirical evidence that you have for common descent. Please do not tell me that shark — mammal eye thing is the best empirical evidence that you have for common descent.

  24. Teleologist

    Now that is funny, because I was not that I am required to give a definition. Honestly, I have not thought about it in terms of some formal theory or hypothesis,

    Really? This thread is about comparing one to the other. How can we do that properly without a formal statement of exactly what is entailed in each?

    … but I will take a stab at it if it makes you happy. I look at common design in the sense that Darwinists look at common descent. Where a Darwinist sees similar features and attribute those similarities to common ancestry, I see a designer using the same features in different biological organisms.

    The theory of common descent says life started a little under 4 billion years ago, and has been slowly evolving (by whatever mechanism) ever since, in numerous directions.
    Does common design make any estimate about when species were created? For example, could there have been a single design event in the Cambrian, and all species we see to day evolved from then? I get the impression that the answer is no, but the last thing I want is to be accused of misrepresenting you guys. How much evolution does common design allow? To quantify that, does common design allow a lion to be related to a tiger (which many would call micro-evolution), a house cat, a dog (certainly macro-evolution), etc.

    Oh I can do much better than Walt Brown’s web site. Would you consider the prestigious Journal Nature good science? How about the Science Magazine, PloS and PNAS? There is no difference between “good science” and “creation science”. Every day these prestigious scientific publications inform us about how new experiments have failed to provide any empirical evidence for the Darwinian claim of macroevolution. And sometimes I find stories like the one I cited above that shows why a design inference is much more plausible than an unguided and random process. I don’t think we need to start a thread about the truthfulness of these prestigious publications, do you?

    I would not call any of them creation science. Creation science – as if you did not know – makes some very clear claims about the world, claims that contradict mainstream science. If creation scientists are the strict empiricalist that you claim they are, you should be able to point me to sites that have creation science and we can judge the truth of your claim.

    From the way you are blatently dodging, I think we both know you cannot.

    Of course you can, maybe not at our level of science today but maybe soon. e.g. Create a life from scratch, allow it to randomly mutate in different environments and see if it will randomly arrive at similar morphologies, and that would falsify common design.

    No, that would only show it could be common descent, not that it could not be common design. And then there is the issue of running the experiment for billions of years, making it effectively impossible, and hence the claim unfalsifiable.

    There are a lot of other ways to falsify common designs. Another method that is within our capabilities now is to take 2 diverse species and randomly mutate them and observe to see if they can produce the similar complexity as the paper I cited above.

    Again, this would only show common descent was possible, not that common design was impossible.

    As usual for ID/creationism, what you are really arguing for is anti-evolution. You can find nothing to support your own hypothesis, only to test ours.

    How about you, do you know of a way to falsify common descent other than finding a fossil rabbit?

    Very similar genetic sequences in distantly related organisms, but absent in closely related organisms.

    We all know what these things are.

    You seem to believe that you do, and yet when asked, you can offer no predictions that necessarily follow from your hypothesis. Time and again you show that actually you do not know it.

    Start by stating your theory in as much detail as you can. Then think about what the necessary consequences are – if you theory is true, then logically these consequences must be true. See if you can explain why they must be true in that case. If you cannot, they are not predictions.

    Then think about when it is actualy possible to run an experiment to confirm or deny the prediction.

    Save us some time and instead of talking about it show us some empirical evidence of these predictions that proves your hypothesis. Common design is a proven fact e.g. GMO and gene therapy.

    This is sadly a common trick in these debates – though the first time I have seen it at this site. Sometimes design means what the creator did, sometimes it includes what man has done. Be honest; is the theory of common design really about GMO and gene theory?

    What is interesting about genetic engineering by mankind is that you find genetic sequences from one organism in a completely unrelated organism.

    There is no doubt that design can and are reused in biological systems.

    And there are clear signs of it when mankind reuses the genes from one organism in another. It sticks out like a sore thumb. Because it is against the natural pattern of genetic sequences, where that kind of reuse is not seen.

    Pix: IC is not a necessary prediction of common design or ID. And “convergence in phenotypical features from diverse environments have similar genetic design” is not testable.
    Tel: Originally I mentioned IC in response to your question about creation or design from my POV. But now I don’t know why it can’t be a part of common design. Blood clotting is universal similar in all animals throughout the history of life. If common descent is true and it can turn a fish into a fox like mammal and turn it back to a water dwelling mammal, I would think there should be equal diversity on how blood clotting works. Nope, common design is a better inference for IC to me.

    So? IC is not a prediction of common design. Common design could be true, but IC structures could still be absent from the universe, if the designer created life like that.

    There you go again spinning fairy tales. Prove it! Show me the evidence. Are there inscription on Stonehenge? Do you have pictures of the construction? The fact to the matter is that you don’t know anything about the designers but you somehow can infer that Stonehenge must be designed. Imagine that, what a quaint idea.

    It is actually pretty well established that stone henge was built by stone age man. Not a proven fact – you do not get them in science – but well established nevertheless.

    Can you tell me how does it show “how” the creator created?
    Common design can be a part of ID, remember?

    Common design says the creator used design features

    What I was hoping for was some explanation or rationalisation for why placental mammals are distributed in one way, and marsuial mammals another way. Why are they not all mixed in together.

    Huh? What part of the supercontinent theory did you not understand? Check wiki if you need help.

    It was the part that fits with the theory of common design.Does the Wiki entry mention common design? Somehow I doubt.

    Another explanation dodged.

    Huh? I am a creationist but why would that make it necessary for me to conclude that God put the snake and all the insects and birds in Hawaii? There is no theological reason for me to do so and I do not yet have scientific reason either. I am skeptical of the Darwinian explanations and find it very unconvincing. Care to give another try other than floating?

    Why not give your explanation? Oh, wait, this thread is about you avoiding explanations.

    Please read the post for the detail.

    There you go again. You just cannot explain anything. It seems almost pathelogical.

    The problem appears to be that you don’t understand about genetics. The reason why they can even consider it as homologous is because the 2 proteins perform the same function and are inordinately similar.

    But are coded from different sequences of DNA. As predicted by common descent.

    On the contrary, I say this is a much bigger problem for Darwinian evolution. Doesn’t Darwinian evolution say that we are in a biological arms race? Isn’t differential survival supposed to select out those organisms with less favorable phenotypes to their environments? Why would evolution continue to pass on these disadvantageous genes?

    But I gave an explanation of how it happened, given common descent. You as usual can give no explanation.

    As inunison has said we can go back and forth with this all day, but I’ve given you my best empirical evidences for common design. Why don’t you answer my request and give me the best empirical evidence that you have for common descent. Please do not tell me that shark — mammal eye thing is the best empirical evidence that you have for common descent.

    I have yet to see anything on this thread that resembles evidence for common design, just evidence you think opposes common descent. I have yet to see anyone attempt to show how common design can explain the features I have brought up. Indeed, inunison’s atest post seems to be arguing that we are not even allowed to do so!

    Is anyone prepared to argue for common design? Or are we wasting our time?

  25. I would not call any of them creation science. Creation science – as if you did not know – makes some very clear claims about the world, claims that contradict mainstream science. If creation scientists are the strict empiricalist that you claim they are, you should be able to point me to sites that have creation science and we can judge the truth of your claim.

    I disagree. All science is Creation science. Darwinians would like to make a distinction between Creation science with “science” . In truth Creation science is antithetical to Darwinian science, but then again Darwinian science isn’t real science so we don’t have a problem.

    From the way you are blatently dodging, I think we both know you cannot.

    If you want to call it dodging that is fine. I’ve given you is what I believe to be the best empirical evidences for common design and against common descent. If you want to call the articles and web sites I referenced as not science or dodging, go right ahead. BTW, what is the best empirical evidence you have for common descent?

    No, that would only show it could be common descent, not that it could not be common design.

    Er”, that’s what I am saying. You confidently declared common design is not falsifiable but now you confidently declared that it is falsifiable. Hmm”.

    Again, this would only show common descent was possible, not that common design was impossible.

    That may be true but I would be left without my best empirical evidence for common design. As an empirical evidentialist, unlike Darwinian storytellers, I have to follow the evidence. I can understand how this might not be a problem for you.

    what you are really arguing for is anti-evolution. You can find nothing to support your own hypothesis, only to test ours.

    Are you experiencing some self induced cognitive dissonance?

    Very similar genetic sequences in distantly related organisms, but absent in closely related organisms.

    Duh. Isn’t this circular reasoning? How do Darwinians classify phylogeny? You stack the deck and classify organisms as close or distant relative by your perceived sequences and then you want people to disprove it by finding outgroups? But even if I find evidence that this is indeed case would that change you mind? I don’t think so. You know like the purple sea urchin, which has more homology to us than flies or worms.

    Start by stating your theory in as much detail as you can.

    Please stop being a bombastic popinjay and explain what theory am I suppose to explain to you.

    Then think about when it is actualy possible to run an experiment to confirm or deny the prediction.

    Oh you mean like the details that you’ve been giving on the empirical experiments to test the predictions of your Darwinian hypothesis?

    This is sadly a common trick in these debates

    Empirical evidence is a common trick. Now that is a Darwinian for you.

    What is interesting about genetic engineering by mankind is that you find genetic sequences from one organism in a completely unrelated organism.

    Oh you mean like in the case of convergent evolution, with thylacine-wolf, sandlance-chameleon, marsupial-placental counterparts, crustacean-dragonfly eyes, hedgehog-human Apo(a), etc” Don’t let these empirical evidence fool you it is just a debate trick.

    Because it is against the natural pattern of genetic sequences, where that kind of reuse is not seen.

    If you haven’t noticed these patterns have been set for millions and even billions of years ago. So to claim the current static pattern as evidence for no design is ludicrous. That would be analogous to saying a computer has always been the nature order of things and any redesign of it now does not prove that it was once designed.

    So? IC is not a prediction of common design.

    I never said that it was a prediction. I said it is a part of common design.

    It is actually pretty well established that stone henge was built by stone age man. Not a proven fact – you do not get them in science – but well established nevertheless.

    I understand that as a Darwinian you are not interested in empirical sciences but just for kicks how do you know that Stonehenge was built by humans? Please layout your evidence.

    What I was hoping for was some explanation or rationalisation for why placental mammals are distributed in one way, and marsuial mammals another way. Why are they not all mixed in together.

    I get it now. This is that theological question that inunison was talking about. As an empirical evidentialist, I have no idea why. But then again I have no idea why Stravinsky would compose the Rite of Spring the way he did either. It doesn’t mean that isn’t a reason for it but I just don’t know. Is that allowed in science, I don’t know?

    It was the part that fits with the theory of common design.Does the Wiki entry mention common design? Somehow I doubt.

    No of course not wiki is a Darwinian propaganda machine why would they say anything positive about common design. But I just want to make sure you understand the supercontinent theory and why animals are isolated.

    Another explanation dodged.

    Another explanation that Pixie failed to understand.

    But are coded from different sequences of DNA. As predicted by common descent.

    Duh of course they were from 2 different sequences of DNA that is why Darwinians call it Convergence. This is also the reason why it is evidence for common design and not common descent.

    BTW, where, who and how was this prediction made before this study?

    There you go again. You just cannot explain anything. It seems almost pathelogical.

    Funny you should mention pathological because I don’t remember you giving any empirical evidence for common descent. OTOH, you been attacking the empirical evidences that I’ve offered for common design. Isn’t that interesting?

    Is anyone prepared to argue for common descent?

  26. Is anyone prepared to argue for common descent?

    Hi teleologist, that would be me, see post #11. As time permits I will continue.

    Hi The Pixie,

    It is here, that we can learn an extremely valuable lesson in the design/descent controversy. That lesson is this: rarely is it the data that are in dispute– it is the interpretation placed on the data that is in dispute. We both have access to the same data. You, however, look at the data and say that is proof of common ancestry. Me, on the other hand, examine the exact same data and suggest that is evidence of design. In essence, a stalemate exists. We both have an answer to the data at hand. And in many instances, either explanation might appear legitimate. However, the evolutionists’ argument works only if certain portions of the data for common descent are presented. If all the available data are allowed full exposure, then the inference from data fails.

    Evidence for common descent entails too many anomalies, too many counter-instances, far too many phenomena which simply do not fit easily into the orthodox picture The proof of that lies in an examination of the data that have become available during the past several years. For example, Wysong provided an extensive list of such data, among which were the following examples:

    # The octopus eye, pig heart, Pekingese dog’s face, milk of the ass, and the pronator quadratus muscle of the Japanese salamander are all very similar to analogous human structures. Do these similarities show evolutionary relationships?
    # The weight of the brain in proportion to body weight is greater in the dwarf monkey of South America, the marmoset, than in man. Since this proportion is used to show relationship between primates and man, is the marmoset, therefore, more evolved than man?
    # The plague bacterium (Pasteurella pestis [now designated as Yersinia pestis– BT/BH]) afflicts only man and rodent. Does this similarity show close relationship?
    # Plant nettle stings contain acetylcholine, 5-hydroxytryptamine and histamine. These chemicals are also found in man. Are man and plant closely related?
    # The root nodules of certain leguminous plants and the crustacean, Daphnia, contain hemoglobin, the blood pigment found in man. Are these organisms closely related to man?
    # If certain specific gravity tests are run on the blood of various animals, the frog and snake are found to be more similar to man than the monkey is to man.
    # If the concentration of red blood cells in animals is compared (millions per cubic millimeter of blood), man is more similar to frogs, fish, and birds than he is to sheep.
    # Since bones are often used to show relationships, bone chemistry should be useful in this regard. If the calcium/phosphorus ratio is plotted against bone carbonate, man proves to be close to the turtle and elephant, the monkey close to the goose, and the dog close to the horse but distant from the cat.
    # The tetrapyrole chemical ring is found in plant chlorophyll, in hemoglobin and other animal respiratory pigments, sporadically as a coloring pigment in molluscan shells, and also in the feathers of some bird species. How does tetrapyrole similarity speak for relationships

    When someone– like Philip Gingerich– picks up two bones, concludes that they very likely came from an organism like an antelope, and then assigns them to a “four-legged whale,” that is not homology at work. Nor is it good science at work. It is sheer imagination and wishful thinking!

  27. Teleological

    I disagree. All science is Creation science. Darwinians would like to make a distinction between Creation science with “science” . In truth Creation science is antithetical to Darwinian science, but then again Darwinian science isn’t real science so we don’t have a problem.

    Okay, okay, you want to go down the road of sematic squabbling and cheap sniping. I guess that is no surprise.

    So I will ask the question differently. Given your claim that creationist are “strict empiricalist”, can you point me to a web site that discusses the claims of the creation event in a strictly empirical way?

    If you want to call it dodging that is fine. I’ve given you is what I believe to be the best empirical evidences for common design and against common descent. If you want to call the articles and web sites I referenced as not science or dodging, go right ahead. BTW, what is the best empirical evidence you have for common descent?

    But I have seen no attempt at any evidence for common design, only evidence you think is against common descent.

    Pix: No, that would only show it could be common descent, not that it could not be common design.
    Tel: Er”, that’s what I am saying. You confidently declared common design is not falsifiable but now you confidently declared that it is falsifiable. Hmm”.

    So you are making the assumption that if common descent is not true, then it necessarily follows that common design is true?

    Do you think that is a reasonable assumption? I can think of a third possibility; that life on Earth was designed by a number of creators working in isolation. No common descent, no common design. Maybe you want to argue for the validity of your assumption, but to leave it unspoken is not the way to win an honest argument.

    Duh. Isn’t this circular reasoning? How do Darwinians classify phylogeny? You stack the deck and classify organisms as close or distant relative by your perceived sequences and then you want people to disprove it by finding outgroups? But even if I find evidence that this is indeed case would that change you mind? I don’t think so. You know like the purple sea urchin, which has more homology to us than flies or worms.

    Actually the relatedness of organisms was originally based on the cladogram devised by Linneaus, a creationist.

    Please stop being a bombastic popinjay and explain what theory am I suppose to explain to you.

    That would be the one you are arguing for. Check the thread title. If still in doubt I will tell you, it is the theory of common design.

    I will get back to you on the rest of your post when you have explained what you theory – yes, the theory of common design still – actually says. Because right now I get the feeling you really want to avoid doing that. And if that is the case, I really cannot be bothered debating with you.

  28. Inunison

    I am sorry, but I get the same feeling from you. Again, no attempt to say what the theory of common design actually says, or to explain the data using common design.

    Here we are considering the relative merits of two different theories. As a working scientist, I judge a theory by how useful it is. At the end of the day, we have no way of know what is actually right and wrong, all we can say is this theory explains the data well, this theory does not. So when we look at the data, let us see which theory explains it and which does not.

    Early, I mentioned the distribution of placental and marsupial mammals. I said how common descent explains the distribution. No one here has attempted to show how common design explains the data. One-nil to common descent. I mentioned the distribution of obverse- and reverse-wired eyes, and I said how common descent explains the distribution. No one here has attempted to show how common design explains the data. Two-nil to common descent. In your latest post you have presented a list of supposed problem for common descent, but again no attempt to show how common design explains the data. I am already winning the explanations contest, so at this point I feel I can sit back and relax. Once you guys come up with some explanations, and level the score, I will get back to your list.

    Back in your post 13, you made the claim “Common descent can explain or accommodate nested hierarchy…, but it does not predict it. There are mechanisms of descent from a common ancestor that would yield a different pattern.” I challenged you to show how common descent can fail to produce a nested hierarchy in post 16. Have you looked at this? Have you found an example of common descent that does not produce a nested hierarchy? If you are going to make claims like this, you should be prepared to back them up or admit you were wrong. If your claim is true, it should be easy to find that different pattern (you made the claiming knowing what you were talking about right?). So I will keep mentioning this until you address it by the way, to make sure it does not get forgotten.

  29. Hi The Pixie,

    The question of origins is plainly a matter of science history– not the domain of applied science. Contrary to the unilateral denials of many evolutionists, one’s worldview does indeed play heavily on one’s interpretation of scientific data, a phenomenon that is magnified in matters concerning origins, where neither repeatability, nor observation, nor measurement– the three immutable elements of the scientific method– may be employed. The fact is many proponents of evolutionism nevertheless persist in claiming exclusive “scientific” status for their popularized beliefs, while curtly dismissing (if not angrily deriding) all doubters. So you as a working scientist you should be aware that “explanations” you refer to are speculations or “just so” stories. The sad part is many scientist accept these as some kind of religious dogma.

    Your “explanation” of distribution of placental and marsupial mammals is case in point. The fact is distribution of marsupials is not well answered by evolutionary theories. According to Michael Pitman, “the most diverse fossil assemblies have been obtained from South America and, later (Pliocene), Australia” (Pitman, Michael (1984), Adam and Evolution (London: Rider).). That is, according to the fossil record, the marsupials already were well defined as a distinct group before the alleged separation of Australia from other continents. Thus, geographic separation cannot be as significant to their development as evolutionists like to think (or as they would like everyone else to think).

    There also are numerous other facts in regard to the distribution of living (and/or fossil) organisms. For example, evolutionists are forced to admit that marsupials once lived in Europe, Asia, and in abundance in North America, yet now are largely absent (except for opossums in the Americas). The Pixie, consider the following revealing admission from two evolutionists:

    Living marsupials are restricted to Australia and South America (which were part of the supercontinent Gondwana); North American opossums are recent immigrants to the continent. In contrast, metatherian fossils from the Late Cretaceous are exclusively from Eurasia and North America (which formed the supercontinent Laurasia). This geographical switch remains unexplained (Cifelli, R.L. and B.M. Davis (2003), “Marsupial Origins,” Science, 302:1899–1902, December 12.).

    I quite understand that you are upset (for the want of better word) because we are giving you facts showing your “explanations” to be plain speculations based on your particular view of what God (gods, aliens, agents…who ever) could and could not do.

  30. I challenged you to show how common descent can fail to produce a nested hierarchy in post 16

    It is quite evident that careful reading of my post #13 gives you an answer to which you replied:

    No, this is wrong. The hierarchy would still exist, it would just be very difficult to determine.

    To me it looks like desperate attempt to salvage your pet theory.

    I also said that nested hierarchy is not evidence for or against either theory and I explained the reasons why I think so.

    You might also want to read Denton, “Evolution: The Theory in Crisis” p 136,137 (I believe you have his book) and also article by Patterson, “Cladistics”, Biologist, 27:234-240 and Thompson, “A Radical Look at Fish-Tetrapod Relationships”, Paleobiology, 7: 153-156. Thoughts of this last two scientists you can also find in Denton’s book.

    There is inherent contradiction between an orderly hierarchic pattern and random evolutionary process to top it up. Design, being non random event better explains data than common descent.

  31. Inunison

    The question of origins is plainly a matter of science history– not the domain of applied science. Contrary to the unilateral denials of many evolutionists, one’s worldview does indeed play heavily on one’s interpretation of scientific data, a phenomenon that is magnified in matters concerning origins, where neither repeatability, nor observation, nor measurement– the three immutable elements of the scientific method– may be employed.

    Do you think the same is true of archeology or forensic science? I think that in all three cases scientists observe the evidence there today from events in the past. Chemists cannot see electrons, but still observe their effects, still measure their effects, still expect repeatability in those measurements. Forensicscientists cannot see the murder, but they still observe the effects, still measure those effects, still expect repeatability in those measurements. Biologists cannot see the evolution of the diversity of life we see today, but they still observe the effects, still measure those effects, still expect repeatability in those measurements.

    The fact is many proponents of evolutionism nevertheless persist in claiming exclusive “scientific” status for their popularized beliefs, while curtly dismissing (if not angrily deriding) all doubters.

    And rightly so! When the theory of common design gets stated in sufficient detail that you can draw predictions about what evidence will be around today, and then test those predictions, and show them to be consistently better than the predictions for common descent, then you can claim science.

    That has happened for common descent, but not for common design. So scientists will inevitably persist in claiming exclusive “scientific” status for common descent. And the more IDists try to pass off common design as science, as equivalent to common descent, without actually bothering to do the first step and stating exactly what that claim consists of, the more derision you will receive.

    The ball is in your court. Do the science. The first step is to clearly state what it is you are claiming. What is the theory of common design? When did the design happen? What is related to what? Etc.

    So you as a working scientist you should be aware that “explanations” you refer to are speculations or “just so” stories. The sad part is many scientist accept these as some kind of religious dogma.

    They start as speculations, then scientists think about the necessary consequences, and what would be expected in the world today, then look for confirming (or refuting) evidence. That is science. Same for biology, geology, physics.

    Then the creationists decide they do not like that science because it contradicts their interpreation of the Bible, so they label it a “just-so” story. That is dogma.

    Your “explanation” of distribution of placental and marsupial mammals is case in point. The fact is distribution of marsupials is not well answered by evolutionary theories. According to Michael Pitman, “the most diverse fossil assemblies have been obtained from South America and, later (Pliocene), Australia” (Pitman, Michael (1984), Adam and Evolution (London: Rider).). That is, according to the fossil record, the marsupials already were well defined as a distinct group before the alleged separation of Australia from other continents. Thus, geographic separation cannot be as significant to their development as evolutionists like to think (or as they would like everyone else to think).

    Pitman is then ignorant of the claims of common descent. Marsupials arose on the supercontinent that consisted of Australia, South America and Antartica (as I said in post 8). So their fossils are found in Australia, South America and Antartica. They were geologically separate from the rest of the world. See here for example (you will probably want to dismiss that as a “just-so” story, but please at least acknowledge that common descent does have an explanation).

    Now, how about that common design explanation?

    There also are numerous other facts in regard to the distribution of living (and/or fossil) organisms. For example, evolutionists are forced to admit that marsupials once lived in Europe, Asia, and in abundance in North America, yet now are largely absent (except for opossums in the Americas). The Pixie, consider the following revealing admission from two evolutionists:
    Living marsupials are restricted to Australia and South America (which were part of the supercontinent Gondwana); North American opossums are recent immigrants to the continent. In contrast, metatherian fossils from the Late Cretaceous are exclusively from Eurasia and North America (which formed the supercontinent Laurasia). This geographical switch remains unexplained (Cifelli, R.L. and B.M. Davis (2003), “Marsupial Origins,” Science, 302:1899–1902, December 12.).

    So you do know that Australia and South America were joined, but you still quoted Pitman, who thinks that marsupials in South America are a problem. The site I linked to before does explain this observation. Marsupials appeared on the northern supercontinent first, and migrated south; placentals later appeared in the north, and out competed the marsupials there, but could not migrate south as the continents had moved apart. Yes, another speculation (or, as it opposes a literal interpretation of the Bible, a “just-so” story). But a speculation that is supported by the placement of the fossils, that fits with the findings in geology about the movement of tectonic plates.

    As opposed to the deafening silence we get from the common design proponents when asked to explain this observation.

    I quite understand that you are upset (for the want of better word) because we are giving you facts showing your “explanations” to be plain speculations based on your particular view of what God (gods, aliens, agents”who ever) could and could not do.

    What I am highlightong is that your theory does not allow you make speculations! This is why it is not science. This is why it is not useful. This is why scientists will stick with common descent. A theory that makes predictions and gets them right 90% of the time and can explain 90% of what we observe is far superior to a theory that gives no predictions and offers no explanations at all.

  32. There is inherent contradiction between an orderly hierarchic pattern and random evolutionary process to top it up. Design, being non random event better explains data than common descent.

    If the contradiction is real, you could devise a random evolutionary process, and show that it produces a pattern that is not a nested hierarchy. Is it really that difficult to find one single example of common descent that does not give a nested hierarchy? You seem very sure of yourself, so must think it is possible? Simple even?

    But you cannot do it! Instead you refer me to books where other people make the same claim. Why should I believe them? Have any of them got an example? One, just one example of common descent not giving a nested hierarchy will prove you right, and me (and all the evolutionists) wrong. But I bet Denton did not do that.

    Have a go. Indeed, anyone reading this, have a go. Can anyone out there in ID-land find me an example of common descent that does not give a nested hierarchy?

    I will get the ball rolling, shall I? (the blog s/w removes leading spaces and backslashes for some reason from preformated text, so it looks a bit odd)

    ..A
    ..|
    ..B
    ./.*
    C…D

    Here we have three tiers, the top tier consists of all the animals descended from the first colony of species A (that is A, B, C and D), the second tier is all the animals descended from the first colony of species B (that is B, C and D), while the bottom tier is all the animals descended from the first colony of species C (that is just C), and an equivalent group for species D. Groups C and D nested inside group B, while group B nests inside group A. A nested hierarchy.

    A
    |
    B
    |
    C

    Here we have three tiers again, the top tier consists of all the animals descended from the first colony of species A (that is A, B and C), the second tier is all the animals descended from the first colony of species B (that is B and C), while the bottom tier is all the animals descended from the first colony of species C (that is just C). Group C nested inside group B, while group B nests inside group A. A nested hierarchy. Again.

    ….A
    …/.*
    ..B…D
    ./…/.*
    C…E…F

    Here we have three tiers again, the top tier consists of all the animals descended from the first colony of species A (that is A, B, C, D, E and F), the second tier is all the animals descended from the first colony of species B (that is B and C) and a second group descended from D (that is D, E and F), while the bottom tier has groupings for C, E and F. Groups E and e nested inside group D, group C nested inside group B, while groups B and D nest inside group A. A nested hierarchy. Again.

    So now it is your turn. See what you can do. Read what Denton says, surely that will lead you to the answer. Roll dice if you want it random.

    But do not expect to be taken too seriously until you have had a go!

    As an aside, the second law of thermodynamics ultimately comes down to the fact that energy is distrubuted at random. A law that covers all physics, chemistry and biology without exception, based on randomness. How about that for an inherent contradiction!

  33. Hi The Pixie,

    What I am highlightong (sic) is that your theory does not allow you make speculations! This is why it is not science. This is why it is not useful.

    Now this sounds like a cheap propaganda that is often encountered debating these issues. I am disappointed that you are using it as well.

    You often claim that the concept of design has never been useful in science. You are plain wrong. A nice example that demonstrates this comes from William Harvey, who employed teleological reasoning to uncover the circulation of blood. Teleology played a crucial role in providing the motivation for doing science.

    Do you think The Pixie that this world is governed by haphazard and chance? Or rather do you believe that it is ruled by reason? Is not the core of reality based on reason? Modern science is premised on the faith that reality is rational and coherent and it owes this faith to the teleologists and not the materialists.

    Even Kant admits great respect for the argument because of its stimulus to scientific enquiry: he realizes that many biological investigations have been motivated by the expectation of purpose in organic structures.

    Kant writes of Design:

    “It enlivens the study of nature. . . . It suggests ends and purposes, where our observation would not have detected them by itself, and extends our knowledge of nature by means of the guiding concept of special unity, the principle of which is outside Nature.”

    Kant’s notion of teleology had an enormous influence on the work of German biologists in the first half of the nineteenth century. Like Kant, for the most part these biologists did not regard teleology and mechanism as polar opposites, but rather as explanatory modes complementary to each other. Mechanism was expected to provide a completely accurate picture of life at the chemical level, without the need to invoke ‘vital forces.’ Indeed, Kant and many of the German biologists were strongly committed to the idea that all objects in Nature, be they organic or inorganic, are completely controlled by mechanical physical laws. These scientists had no objection to the idea that living beings are brought into existence by the mechanical action of physical laws. What they objected to was the possibility of constructing a scientific theory, based on mechanism alone, which described that coming into being, and that could completely describe the organization of life. . . . In Kant’s view, a mechanical explanation”could be given only when there is a clear separation between cause and effect. In living beings, causes and effects are inextricably mixed. . . . ultimate biological explanations require a special non-mechanical notion of causality – teleology – in which each part is simultaneously cause and effect. Parts related to the whole in this way transcend mechanical causality.

    It is clear to many that biology has long been drawing from teleology to succeed. Although it officially denies teleology, biology works only because it relies on teleology. The illusion is that biology’s success has been guided by the assumptions of materialism and Darwinian evolution. Yet materialism cannot justify the constant reference to intelligent design concepts and language so ubiquitous in biology and Darwinian evolution is more like icing on a cake than any kind of core ingredient.

    It will take only a slight nudge to shift the hidden teleology of biology out into the open. That is, ID researchers can easily do all that science has done and perhaps more by simply viewing a protein as a sensor rather than being like a sensor. Science is built upon the faith that reality is rational and ID can take this faith into the realm of biology, where thus far, the discovery of the irrational has become the stop point at the hands of the irrational blind watchmaker.

  34. Check the thread title. If still in doubt I will tell you, it is the theory of common design

    I know what the problem is, Pixie can’t read. The title of this thread does not say THEORY of common design. And he can’t read what I said as in comment #21. ” Honestly, I have not thought about it in terms of some formal theory or hypothesis” .

    I don’t know of a “theory of common design” , but then again I don’t consider the “theory of common descent” (according to Pixie) is a theory either.

    Do you think the same is true of archeology or forensic science? I think that in all three cases scientists observe the evidence there today from events in the past. ” Biologists cannot see the evolution of the diversity of life we see today, but they still observe the effects, still measure those effects, still expect repeatability in those measurements.

    Not only does this demonstrate ignorance of science, it is down right silly. In archaeology we can test the digs, radiometric date the finds. We can study the culture through the tools, art and writings from the past. We can test every one of these aspects of a civilization with our experiences today. We can’t do that with Darwinian evolution. When Darwinists claim that a major taxonomic form mutated into another sometime in the distant past. Can we reproduce that event or a similar event today? To make this comparison is ludicrous. Next thing Pixie will be telling us that Darwinian evolution is as well tested as gravity.

    When the theory of common design gets stated in sufficient detail that you can draw predictions about what evidence will be around today, and then test those predictions, and show them to be consistently better than the predictions for common descent, then you can claim science.

    That has happened for common descent

    Who are you trying to kid? I’ve asked you repeatedly to provide what you consider as the strongest empirical evidence for common descent and up to now you still have not shown any, why?

    Marsupials appeared on the northern supercontinent first, and migrated south; placentals later appeared in the north, and out competed the marsupials there, but could not migrate south as the continents had moved apart. Yes, another speculation (or, as it opposes a literal interpretation of the Bible, a “just-so” story).

    Pixie don’t let you religious Atheism get in the way of science. Yes, you are promoting a just-so story because you have no empirical evidence to support this fairy tale. When Darwinists don’t know the answer you always fall back to that tired diatribe about survival of the fittest. There is absolutely no evidence that selection and environment have anything to do with the extinction of marsupial in the northern hemisphere.

    Do you know when the marsupial and placental lines first appeared? What sorts of animals were competing with each other? What was the environment that caused the fitness? How strong was the selection coefficient? What about the great extinction event, could that have anything to do with their extinction? You don’t know any hard evidence to make that conclusion, yet you sit there nonchalantly and declare the placental out competed the marsupial because it fits your Darwinian fairy tale. Go ahead but don’t expect rational people to accept it.

  35. Hi The Pixie,

    Your post #32 does not show that common descent predicts nested hierarchy. We are going in circles here but let me repeat from post #13:

    Any set of objects, whether or not they originated in an evolutionary process, can be classified hierarchically. Chairs, for instance, are independently created; they are not generated by an evolutionary process: but any given list of chairs could be classified hierarchically, perhaps by dividing them first according to whether or not they were made of wood, then according to their color, by date of manufacture, and so on. The fact that life can be classified hierarchically is not, in itself, an argument for common descent.

    Which makes your challenge “Can anyone out there in ID-land find me an example of common descent that does not give a nested hierarchy?” nonsensical.

    There are various ways in which existing organisms could descend from a common ancestor and not exhibit a nested hierarchy. Anagenesis, loss of characters, replacement of characters, transposition of characters, atavism (masking and unmasking), and convergence all work against a hierarchical pattern, and the bare hypothesis of universal common ancestry says nothing about the rate or prevalence of those processes. They can be invoked in whatever blend is necessary to explain whatever pattern is found. Therefore, the claim that the hypothesis of universal common ancestry makes a falsifiable prediction that organisms will exhibit a pattern of nested hierarchy is incorrect. In short, nested hierarchy is not a falsifiable prediction of common ancestry because the theory includes without restriction processes that work against that pattern. Those processes can be invoked in any blend to account for any non-nested pattern that is observed.

  36. Inunison

    Teleology played a crucial role in providing the motivation for doing science.

    Sure. But not actually in the science itself.

    Do you think The Pixie that this world is governed by haphazard and chance? Or rather do you believe that it is ruled by reason? Is not the core of reality based on reason? Modern science is premised on the faith that reality is rational and coherent and it owes this faith to the teleologists and not the materialists.

    Now this sounds like a cheap propaganda that is often encountered debating these issues. I am disappointed that you are using it as well.

    If you stop to actually think for a moment, it might cross your mind that science is all about reason, laws and cause and effect. It also acknowledges that there are random elements too (see quantum mechanics for that).

    Even Kant … blind watchmaker.

    Great. So you can find an example of how the theory of common design has been used then? Oh, no, to do that you might have to let me into the secret of exactly what the theory of common design actually is.

    Your post #32 does not show that common descent predicts nested hierarchy. We are going in circles here but let me repeat from post #13:

    No, it only shows that – despite the supposed inherent contradiction – common descent can give a nested hierarchy. But the point was to show that it really is not that difficult to present a pattern of comon descent on this thread. So how come you cannot?

    Any set of objects, whether or not they originated in an evolutionary process, can be classified hierarchically. Chairs, for instance, are independently created; they are not generated by an evolutionary process: but any given list of chairs could be classified hierarchically, perhaps by dividing them first according to whether or not they were made of wood, then according to their color, by date of manufacture, and so on. The fact that life can be classified hierarchically is not, in itself, an argument for common descent.
    Which makes your challenge “Can anyone out there in ID-land find me an example of common descent that does not give a nested hierarchy?” nonsensical.

    Oh, please, the desparation to avoid the issue! Any set of objects can be classified hierarchically. But we are talking about a nested hierarchy. Something you said is not always the case for common descent: “Common descent can explain or accommodate nested hierarchy (though not without difficulty in the specific case of Neo-Darwinism), but it does not predict it. There are mechanisms of descent from a common ancestor that would yield a different pattern.”

    So come on! Find one of these “mechanisms of descent from a common ancestor that would yield a different pattern”. You said they exist. Was this just a hope, a faith that they do? Were you just bluffing? Frankly, I am not going to believe what you say unless you can back up this claim.

  37. Teleologist

    Ah, more of the semantic squabbling. Just tell me what you mean by “common design”, if “theory of common design” confuses you so.

    Not only does this demonstrate ignorance of science, it is down right silly. In archaeology we can test the digs, radiometric date the finds. We can study the culture through the tools, art and writings from the past. We can test every one of these aspects of a civilization with our experiences today. We can’t do that with Darwinian evolution. When Darwinists claim that a major taxonomic form mutated into another sometime in the distant past.

    Wow, what an ignorance of biology you are displaying. This may surprise you but biologist look at things called “fossils”, which, like archaeological evidence, are buried in the ground. They can even be radiodated, just like archaeological finds (the dates contradict the Bible, so you will want to discredit them, but this is what biologists do). And do you know what? Biologists also test their theories with out observations of species alive today too!

    Who are you trying to kid? I’ve asked you repeatedly to provide what you consider as the strongest empirical evidence for common descent and up to now you still have not shown any, why?

    I have decided to debate the ID way, which is to just rubbish the opposition’s theory, and say nothing at all about mine. There is lots of evidence for common descent, and it explains everything we see in nature. In contrast, common design has many facets that do not make sense or just contradict what we see.

    Easy.

  38. Hi The Pixie,

    So come on! Find one of these “mechanisms of descent from a common ancestor that would yield a different pattern” . You said they exist. Was this just a hope, a faith that they do? Were you just bluffing? Frankly, I am not going to believe what you say unless you can back up this claim.

    I have had no illusions that you would believe me, as you reject anything that does not fit your understanding of origins and evolution, even papers coming from evolutionary scientists you outright reject.

    So come on! Find one of these “mechanisms of descent from a common ancestor that would yield a different pattern” . You said they exist. Was this just a hope, a faith that they do? Were you just bluffing? Frankly, I am not going to believe what you say unless you can back up this claim.

    You read my posts selectively as well.

    …shows that – despite the supposed inherent contradiction – common descent can give a nested hierarchy.

    Common descent can give nothing, it is just an metaphysical idea derived by inference from existing data and yes, it can explain nested hierarchy and also non-nested non-hierarchy. Hence it is devoid of meaning and usefulness for science.

  39. This may surprise you but biologist look at things called “fossils” , which, like archaeological evidence, are buried in the ground. They can even be radiodated, just like archaeological finds

    Pixie, your ignorance is beyond help but I will point this out for the reader in case some might be confused by your misdirection. Pixie is a master of obfuscation and equivocation. What he did was to conflate what these other branches of sciences are trying to prove with Darwinian evolution. e.g. When an archaeologist looks at a pottery his task is to place that pottery in a historical context. He uses radiometric dating to fix a date on that artifact, that’s his end objective. A Darwinian evolutionist when they look at a fossil they need to know how that species originated from common descents POV. So when he says biologists also radiometrically date the fossil, this has absolutely no relevance to common descent. Fixing a date is the end objective for the archaeologist. Fixing a date for a Darwinian is only the beginning. This kind of ignorance can only be found in Darwinists like Pixie.

  40. Hi The Pixie

    These ideas might interest you and relate to some issues in theoretically exploring design

    Introduction

    Intelligent design is a unique conjoining of scientific, mathematical, and investigative disciplines. Mathematics is utilized principally for probabilistic calculations of events. Knowledge from physics and chemistry enables observational accounts to correspond with empirical data. Special sciences such as archeology and forensics provide foundations for design criteria, while psychology and neuroscience lend premises for understanding intelligence. The observational method of investigation employed by intelligent design is derived from time-tested scientific methodology:

    Causality

    Intelligent design employs the principal of causality, or cause and effect, to study specific phenomena. The effects observed are design, with intelligence inferred as the cause.

    Induction

    Intelligent design operates by an inductive procedure of inquiry wherein science explores new areas of knowledge by moving from facts and data that are well-established, and extrapolating from those areas of knowledge into the obscure knowledge that is being pursued. More specifically, ID makes retrodictive inferences about the past from present evidence.

    The purpose of using inductive reasoning by intelligent design is to formulate general principles based on specific observations of recurring patterns in samples. So, samples used in an inductive proposition must share one or a subset of designated properties. The induction holds if
    1)the examples share the designated properties, and
    2)the dissimilarities do not make a relevant difference to the property(ies) one wishes to explain.

    So, how does ID utilize inductive reasoning when it proposes that the characteristic of design, or a purposeful arrangement of parts, is found in phenomena? Design can be found in phenomena we factually know were intelligently designed, and design can also be found in phenomena where the cause is not known, e.g. specific microbiological components, certain aspects of the universe, and the universe as a whole.

    When considering the biological and microbiological realm, ID proposes that specific features of living cells and features of man-made machines share the characteristic of design, or a purposeful arrangement of parts.

    The likenesses between man-made information structures and bio-informational structures are so strong, that they are by definition the same type of phenomena. Additionally, the likenesses between man-made mechanical structures and bio-molecular machines are so strong, indeed, the likenesses are so close; by definition they are the same type of phenomena.

    When considering the universe, ID proposes that specific cosmological features have the characteristic of purposeful arrangement of parts, since the multitude of natural forces, universal constants, and fundamental characteristics are supremely fit for the purpose of allowing life to exist.

    Uniformity

    ID is an application of the principle of uniformity to observed phenomena which have the characteristic of design.

    The basis used in this observation is the verifiable fact that intelligent agents use building techniques that:

    * infuse large amounts of information into data structures at one time
    * develop complex communication systems
    * make production capabilities based on informatic code
    * channel energy through nonrandom pathways
    * involve very complicated development processes
    * bring about results that are of infinitesimally small probability
    * utilize high quantity and quality of coordinated parts

    These are capabilities we see intelligent agents employing, and these capabilities are exactly what we see in living systems.

    Uniform sensory experience

    Another aspect of uniformity utilized by empirical science is the uniform experience of the senses.
    ID employs uniform sensory experience by noting that that certain effects, especially functional information, have only one repeatedly and uniformly observed cause; intelligence.

    Statistical probability

    Intelligent design premises are based on a statistical warranted inference, called the Design Inference. This probabilistic inference is being developed by a mathematician and philosopher named William Dembski, who has named the main premise of the inference Specified Complexity. Specified Complexity probabilistically sifts through possible causal explanations, eliminating non-teleological causes that do not work towards an intended goal, leaving the researcher to a statistically warranted inference to design.

    Causal adequacy

    ID proposes that specific natural phenomena that give the appearance of design may have a fundamentally intelligent cause. By inductive logic, intelligence is proposed as the cause for the characteristic of design in specific phenomena.

    * There is no observational or verifiable scientific evidence for an ateleological origin of designed phenomena. The insistence that designed objects in nature have an ateleological origin rests on metaphysical arguments, not scientific ones. In addition to this complete lack of evidence, it is extremely improbable that chance and necessity gave rise to these designed phenomena.
    * However, there is reliable and verifiable evidence demonstrating that intelligence can form these structures, making intelligent design a viable explanatory option.

    Interpretation

    In interpretation, it is a purely a posteriori and inductive argument based on the repeated application of the cause and effect between the well-established effects of intelligent causes and specific attributes of phenomena in nature.

    If you are so inclined you may also want to check this paper:

    The origin of biological information and the higher taxonomic categories

    This is also very relevant and relates to some questions that are important to those interested in ID and to those interested in understanding the world from a neo–Darwinian viewpoint

  41. Inunison

    … it can explain nested hierarchy and also non-nested non-hierarchy.

    Then show us one example of how common descent can give a non-nested non-hierarchy.

    I can only think of one reason for you not doing so and that is that you are unable to do so. And if you cannot do so, then you know this claim is false. And if you are knowingly making false claims, I have no desire to continue debating with you.

    Support your claim, find just one example of how common descent can give something other than a non-nested non-hierarchy, one of these “mechanisms of descent from a common ancestor that would yield a different pattern” and I will look at the other points you make.

  42. When an archaeologist looks at a pottery his task is to place that pottery in a historical context.

    And when a biologist looks at a fossil, his task is to place the fossil in an evolutionary context. Kind of similar so far.

    He uses radiometric dating to fix a date on that artifact, that’s his end objective.

    And the biologist uses radiometric dating to fix a date on the fossil. And like the archaeologist, the biologist uses that information to build a picture of how the universe works. For the biologist, that means how evolution has happened, for the archaeologist, that means how history happened. This may surprise you but there is more to archaeology than just finding out the dates!

    A Darwinian evolutionist when they look at a fossil they need to know how that species originated from common descents POV.

    And the archaeologist needs to know how the artifact originated, and how the culture that built the artefact originated.

    So when he says biologists also radiometrically date the fossil, this has absolutely no relevance to common descent.

    What? Of course it does, it places the organism in the “tree of life” that is common descent. The height in the tree is the date of the fossil. It is directly relevant.

    Fixing a date is the end objective for the archaeologist.

    This kind of ignorance can only be found in IDists like Teleologist!

  43. Hi The Pixie,

    Really don’t like repeating myself, so hopefully now you can stop with your mantra

    There are various ways in which existing organisms could descend from a common ancestor and not exhibit a nested hierarchy. Anagenesis, loss of characters, replacement of characters, transposition of characters, atavism (masking and unmasking), and convergence all work against a hierarchical pattern, and the bare hypothesis of universal common ancestry says nothing about the rate or prevalence of those processes. They can be invoked in whatever blend is necessary to explain whatever pattern is found. Therefore, the claim that the hypothesis of universal common ancestry makes a falsifiable prediction that organisms will exhibit a pattern of nested hierarchy is incorrect

  44. Common design: shared design as determined by anomalies to the application of natural selection. They would include the concept of front loading, origin of life and DNA repair mechanisms. All three entail challenges to selection and provide a basis for a design alternative.

  45. Inunison

    Really don’t like repeating myself, so hopefully now you can stop with your mantra

    I am not asking you to repeat the same assertion again and again and again. I am asking you to think about that claim, and show how it can possibly be true. Show an example. If your assertion was true, why would that be difficult? I believe either you know no example is possible, or you do not understand what it is you are posting. Either way, why should I want to debate with someone who posts stuff like that?

    How Common Descent Works

    Imagine it is the year 2200, and you are sitting up in heaven, looking down at your descedants. There are your children (perhaps in heaven with you too by now), your grandchildren, you great grandchildren, and so on. Each of your great grandchildren is, of course, the child of one of your grandchildren, so you could group all your great grandchildren in terms of which of your grandchildren is their parent. But wait. Each of those great grandchildren is a grand child of your children, so you might want to group all your great grandchildren in terms of which of your children is their grandparent. Then again, you just say they are all your great grandchildren, one big happy group.

    And do you know what? The first set of groups (great grandchildren who share a parent) nests entirely inside the second group (great grandchildren who share a grandparent), and the second group nests entirely within the third group (great grandchildren who share a great grandparent). And that has to be true.

    Let us now pick out a few descendants. The person at the top is you, the common ancestor. Let us suppose you have a child called Brian, Brian has a child that I will call Charlie, and Charlie has a child called David. For this to be nested hierarchy, it must be true that any grouping that is lower in the hierarchy must nest entirely within groups higher up the hierarchy. In this case we have a grouping that is “Charlie’s descendants”, so for this to be a nested hierarchy it must always be the case that the “Charlie’s descendants” group nests completely within the “Brian’s descendants” group, and also, higher up the hierarchy, within the “Inunison’s descendants”.

    So is this necessarily the case? Yes! If David and his siblings are all descendants of Charlie, and if Charlie is a descendant of Brian, then it must also be true that David and his siblings are also descendants of Brian; that is, it must be true that any member of the “Charlie’s descendants” group is also a member of the “Brian’s descendants” group. Or to put it aother way, it is necessarily true that the “Charlie’s descendants” group nests completely within the “Brian’s descendants” group.

    The only possible problem arises if there is incest. If you were a Brahminy Blind Snake, which reproduces asexually, that would be impossible, and the nested hierarchy would be a certainty.

    Evolution is like the Brahminy Blind Snake; a new species evolves from a single earlier species. It is not possible for two species to come together to form a third – species can be defined as animals unable to breed, so that excludes any coming together.

    How any Pattern of Common Descent can be Assigned to a Nested Hierarchy

    I challenged Inunison to produce some pattern of common descent, some mechanism that will not produce a nested hierarchy knowing that it is not possible. Whatever pattern of descent he comes up with, if every organism can be traced back to the common ancestor, and each species has evolved from a single previous species – the requirements of common descent – then here is what I shall do…

    Let me first assume that Inunison’s diagram has the single common ancestor at the top, and all the species extant today at the bottom, as I did earlier. If not, we could just turn his diagram so it is, and this allows me to explain better.

    I draw two horizontal lines, the first about a third of the way down, the second two thirds of the way down. These present points in time; for real evolution they might be two billion years ago and one billion years ago. They let us see what species were alive at that time. Let us say these were time t1 and t2. The bottom of the diagram I will call t3 (today), and the top, representing when life began, t0.

    And now it is just like before. All the species at the bottom, at t3, are like the great grandchildren. They can all be grouped by which species at t2 they are descended from, just as the great grandchildren could be grouped by the grandchildren they are descended from. Or they can be grouped by which species at t1 they are descended from, just as the great grandchildren could be grouped by the children they are descended from.

    Let us now pick out a few species. The organism at the top I will call alpha. Alpha has a descendant alive at time t1 called beta, beta has a descendant alive at time t2 that I will call gamma, and gamma has a descendant still aline today (time t3) called delta. For this to be nested hierarchy, it must be true that any grouping that is lower in the hierarchy must nest entirely within groups higher up the hierarchy. In this case we have a grouping that is “gamma’s descendants”, so for this to be a nested hierarch it must always be the case that the “gamma’s descendants” group nests completely within the “beta’s descendants” group, and also, higher up the hierarchy, within the “alpha’s descendants”.

    So is this necessarily the case? Yes! If the species delta and the closely related species are all descendants of species gamma, and if species gamma is a descendant of species beta, then it must also be true that species delta and the closely related species are also descendants of species beta, that is, it must be true that any member of the “gamma’s descendants” group is also a member of the “beta’s descendants” group. Or to put it aother way, it is necessaril true that the “gamma’s descendants” group nests completely within the “beta’s descendants” group.

    No Discernable Nested Hierarchy?

    Despite the above, it could still be the case that the nested hierarchy cannot be reconstructed. It could be that changes are too frequent for long distance relationships to be established. The nested hierarchy still exists, but we cannot see it properly.

    Inunison clings to the following claim (repeating it as a mantra, without actually understanding what it means I suspect):

    There are various ways in which existing organisms could descend from a common ancestor and not exhibit a nested hierarchy. Anagenesis, loss of characters, replacement of characters, transposition of characters, atavism (masking and unmasking), and convergence all work against a hierarchical pattern, and the bare hypothesis of universal common ancestry says nothing about the rate or prevalence of those processes. They can be invoked in whatever blend is necessary to explain whatever pattern is found. Therefore, the claim that the hypothesis of universal common ancestry makes a falsifiable prediction that organisms will exhibit a pattern of nested hierarchy is incorrect.

    Perhaps this is clever, because if challenged, the author can say he only meant no discernableThe Challenge

    Unfortunately, Inunison has fallen for it, and makes some rather stronger claims (post 13):

    Common descent can explain or accommodate nested hierarchy (though not without difficulty in the specific case of Neo-Darwinism), but it does not predict it. There are mechanisms of descent from a common ancestor that would yield a different pattern. If common descent can yield either nested hierarchy or something else, then the presence of nested hierarchy does not count as evidence of common descent.

    I challenge Inunison to support these claims. All he has to do is provide one single example of common descent that does not give a nested hierarchy, just on of these “mechanisms of descent from a common ancestor that would yield a different pattern”. Unfortunately for Inunison, this will require that he actually thinks about what he is posting, rather than repeating the same claim again and again. If the claim was true, and if Inunison actually understood what he claims, this would be easy. He could prove me wrong with no trouble at all.

    But if I am right, he will not find that one example, and instead will dodge the issue, as he has studiously done up to now.

  46. Bradford

    Welcome to the debate, and thank you for being brave enough to define common design for us. I will wait and see if the others agree with you before commenting further.

  47. Strict Empirical Evidentialists
    Back in post 15, Teleoloist made the extraordinary claim:

    Creationists are strict empirical evidentialists

    In post 18, he elaborates:

    Creationists are strict evidentialists when it comes to science because we understand what science is. When we make a hypothesis, we must be able to test the premise of that hypothesis through repeatable observation and predictions.

    Frankly, I do not believe that. So I challenged Teleologist to back up that claim. For a couple of posts he pretended that all science is creation science – despite the obvious fact that nearly all scientists reject creationism! For example, in post 21 he says:

    Oh I can do much better than Walt Brown’s web site. Would you consider the prestigious Journal Nature good science? How about the Science Magazine, PloS and PNAS? There is no difference between “good science” and “creation science” .

    Does he really think anyone will believe that the journal Nature is full of examples of creationist making hypotheses, testing the premise of that hypothesis through repeatable observation and predictions?

    So in post 27 I rephrase the question, to give him less room to wriggle his way out of it:

    So I will ask the question differently. Given your claim that creationist are “strict empiricalist” , can you point me to a web site that discusses the claims of the creation event in a strictly empirical way?

    The response? Ignore the question!

    There seems to be a common tactic here. Just as with the claim by Inunison that common descent need not produce nested hiarachy, Teleologist seems to think it is reasonable to, well, make stuff up! And if your opponent calls your bluff, just avoid giving a proper answer for a few posts and hope he forgets. And as I said in my post to Inunison, I see no point debating with someone who is in the habit of just making stuff up.

    So I challenge Teleologist to support his claim: “Creationists are strict evidentialists when it comes to science because we understand what science is. When we make a hypothesis, we must be able to test the premise of that hypothesis through repeatable observation and predictions.”

  48. Hi The Pixie,

    Instead of throwing challenge after challenge you need to go back to posts and actually read what I presented or linked to. I gave you the list of evolutionary mechanisms that do give other pattern than nested hierarchy, than I gave you examples that cannot be explained using common descent. On top of all that I gave you links to evolutionary literature that has huge reserves regarding common ancestry and classifications that is done according to orthodox Darwinism. With the slight of hand you rejected all of that but still keep on asking for mechanisms and examples.

  49. I threw you exactly one challenge, hardly “throwing challenge after challenge”. And that challenge was to substantiate what you posted. After three days, you cannot find that one example of common descent that is not a nested hierarchy. Just one trivial thing to do to prove me wrong – well, trivial if all that stuff you posted and linked to actually meant something. I know it did not; I know you cannot do it, of course. Instead, you have descended to accusing me of “slight of hand”, and making a vague claims that you have already fulfilled the challenge. I salute you audacity!

    I gave you the list of evolutionary mechanisms that do give other pattern than nested hierarchy, than [then?] I gave you examples that cannot be explained using common descent.

    Good for you. But the challenge was about common descent giving a pattern other than a nested hierarchy. What you seem to be saying is that you listed evolutionary mechanisms that do not involve common descent. So as examples of common descent not giving a nested hierarchy… well, they are not really going to cut it, are they?

    Actually, I would be interested to know which post has that list, I do not remember it. Odd that you somehow neglected to tell us all which post you did that in, making it difficut to go back and check.

    So to recap, the challenge revolves around your claim in post 13 (by the way, do you see what I am doing here? I am quoting an earlier post by you, to support what I am saying. If you want people to believe you have already answered the challenge, you might want to do that):

    Common descent can explain or accommodate nested hierarchy (though not without difficulty in the specific case of Neo-Darwinism), but it does not predict it. There are mechanisms of descent from a common ancestor that would yield a different pattern. If common descent can yield either nested hierarchy or something else, then the presence of nested hierarchy does not count as evidence of common descent.

    The claim is about these “mechanisms of descent from a common ancestor that would yield a different pattern”. The challenge, to show us one of those mechanisms with an example of common descent not giving a nested hierarchy. One challenge. But an impossible one, admittedly.

  50. Hi The Pixie,

    You are telling me that I am making it difficult for you to check my previous posts? Come now. If you read them in the first place instead of just following you own train of thoughts, you would be able to find my thoughts on your challenge. My post #43 repeats main point. If you want details from evolutionary literature go to these papers/articles:

    Bushes in the Tree of Life

    Pegasoferae, an unexpected mammalian clade revealed

    Platypus sex is XXXXX-rated

    the eyeless, earless sea urchin has genes that in humans are involved in detecting sight and sound

    spindle cell neurons in whales, which are only found in primates

  51. Inunison, I know what post 43 says. I believe it is wrong (further, I guess it is based on what Denton said in his first book, and refuted in his second). I believe if you actually try to look for that example of common descent that produces something other than a nested hierarchy, you will discover that true. I urge anyone who is interested in the truth to do this for themselves. At this point, Inunison, sadly I do not count among those interested in the truth. Either you have tried to find this example and failed, but do not have the honesty to admit it; or you are so entrenched in dogma, you will not even try.

    I will quickly respond to the links. The first is highly supportive of comon descent, its point being that the tree of life is harder to discern the further you go back in time. This is common in any historical research. Perhaps you find that a convincing argument for common design, but of course you could not actually explain why, so perhaps not. Explanations are not exactly forcoming from your side, are they?

    The article on Pegasaferae is interesting, and again highlights that our knowledge is incomplete. But so what? Nothing in the paper argues against common descent or a nested hierarchy.

    The platypus sex gene is perfectly compatible with common descent. Some mutations happened after the marsupials and placentals split off from the monotremes, and the mutations gave some complicated sex genes. The mutation is neatly nested inside one branch of the tree, just as one would expect. On the other hand, what was the designer thinking? Why make platypus sex so unnecessarily complicated? Here we have “common design” across all mammals except these few. Why would that be? Oh, wait, I remember the ID answer: It is presumptuous to question God. Which is basically an excuse for why explanations are not forcoming from your side.

    You need a subscription for the fourth.

    The fifth is like the paper you found earlier with the protein found in hedgehogs; basically convergent evolution. Again, the test would be whether the genetic sequence that codes for these neurons is the same – common descent predicts no. What is curious from a common design perspective is why bottlenose dolphins – considered to be more intelligent than humpback whales – do not have them. Why is this design not common to them too? Or am I being presumptuous again?

  52. Hi The Pixie,

    I can also say that the one who is not interested in truth is you, just because you don’t or will not see data in the way I see it. But I will not claim that. The message for common ancestor you convinced yourself is there in the observed data is simply not in that data.

    And you are still missing the point. Let me try again. Because descent from a common ancestor does not necessarily result in a pattern of nested hierarchy, the hypothesis of common ancestry would not be falsified if organisms did not fit that pattern. That is, a nonhierarchical pattern could be explained consistently with common ancestry by appeal to processes that work against a nested hierarchy. Hence, the claim that the hypothesis of universal common ancestry makes a falsifiable prediction that organisms will exhibit a pattern of nested hierarchy is incorrect.

    So it is irrelevant if I or anybody else, can give you example of common descent that produces something other than a nested hierarchy. The fact is that finding such example would not falsify the hypothesis of universal common ancestry. The discovery could be accommodated by the theory in several ways.

  53. Inunison

    I can also say that the one who is not interested in truth is you, just because you don’t or will not see data in the way I see it.

    Perhaps if you could have a go at explaining exactly what common design is, what it predicts, how it explains the evidence, I might see the data your way. But you seem overly reluctant to do that. Bradford kindly offered a definition of comon design before; I was hoping you would comment on it. Here it is again:

    Common design: shared design as determined by anomalies to the application of natural selection. They would include the concept of front loading, origin of life and DNA repair mechanisms. All three entail challenges to selection and provide a basis for a design alternative.

    I find it interesting that he includes front-loading, which I would consider a common descent theory. Does this mean common design and common descent are not mutually exclusive? Odd then that your attempt to prove common design seem to come down to refuting common descent. Personally, I was imagining common design was a bit more specific; frankly this sounds as vacuous as ID itself.

    Your post 11, you said “I will start with claims for Common Descent“, and I was hopeful then that you would go onto the claims for common design in as much detail. That never happened. You have never stated the any such claims, so it would be bizarre if I found them convincing, surely?

    And you are still missing the point. Let me try again. Because descent from a common ancestor does not necessarily result in a pattern of nested hierarchy,…

    Again, the assertion and the failure to find a single example of common descent not resulting in a nested hierarchy!

    See, this is why I, well, do not believe your claims about evidence for common design. You are happy to make claims, and when challenged, cannot back them up.

    So it is irrelevant if I or anybody else, can give you example of common descent that produces something other than a nested hierarchy. The fact is that finding such example would not falsify the hypothesis of universal common ancestry. The discovery could be accommodated by the theory in several ways.

    Wrong. If you can give that one, single example of common descent that produces something other than a nested hierarchy it would:

    * Prove you were capable of supporting your assertions, giving you credibility
    * Prove I was wrong (surely reason enough)

    But the thing about the nested hierarchy is that it is a necessary prediction of common descent. Remember that science revolves around testing predictions. If common descent predicts a nested hierarchy, and a nested hierarchy is what we find, then common descent has scientific support (there may be other things, but this is the big one). If you can prove that common descent does not predict a nested hierarchy, then you take away that scientific support, and common descent is then no better than common design.

    All you need is that one, single, solitary example of common descent that produces something other than a nested hierarchy, and you remove that scientific support! Could a creationists hope to do any more than that?

  54. Hi The Pixie,

    Few comments:

    Prove I was wrong (surely reason enough)

    That is not my purpose in corresponding with you here.

    If common descent predicts a nested hierarchy…

    Nested hierarchy is not a prediction of common descent, and can not be used as evidence of common descent. This is not a prediction, but rather an accommodation (yet again) by it. True common descent would be much better represented by a continuous, blurred line with no nests at all.

    All you need is that one, single, solitary example of common descent that produces something other than a nested hierarchy, and you remove that scientific support!

    I am not that naive. Even the discovery of an organism having no similarity to any known life would not falsify common descent, because evolution does not predict its absence. Evolutionary theory would be immediately adjusted to allow for two systems of life. Some mechanism or just-so story can alway be invoked to explain data away and accommodate it to fit (as you did it in your post #51). It makes common descent unfalsifiable. And that’s where science of it ends.

    Some more for you to explain away: Phylogenetic Classification and the Universal Tree

    what common design is, what it predicts, how it explains the evidence

    Continuing on my post #40 (that I assume you have not read) here are some mechanisms inherent within the theory. Only from our observations about how intelligent agents operate when designing, can we understand how or in what specific ways intelligent designers act when designing:

    (1) Take many parts and arrange them in highly specified and complex patterns which perform a specific function.
    (2) Rapidly infuse any amounts of genetic information into the biosphere, including large amounts, such that at times rapid morphological or genetic changes could occur in populations.
    (3) ‘Re-use parts’ over-and-over in different types of organisms (design upon a common blueprint).
    (4) Be said to typically NOT create completely functionless objects or parts (although we may sometimes think something is functionless, but not realize its true function).

    We can then use this understanding of the mechanisms of intelligent design to make a few predictions:

    (1) High information content machine-like irreducibly complex structures will be found.
    (2) Forms will be found in the fossil record that appear suddenly and without any precursors.
    (3) Genes and functional parts will be re-used in different unrelated organisms.
    (4) The genetic code will NOT contain much discarded genetic baggage code or functionless “junk DNA”.

    Now lets compare Design vs Descent.

    In The Methodological Equivalence of Design & Descent: Can There Be a Scientific “Theory of Creation”?, philosopher of science Stephen C. Meyer frames this question as “design versus descent,” in a competition of which best qualify as strong scientific theories. Meyer uses the term “descent” to refer to all theories of origins which uphold the claim that all-life arose from non-life and is interrelated through ancestry through a purely unbroken naturalistic chain of events (one example is Darwinian evolution). Meyer finds that any argument used against design to disqualify it as a scientific theory can also be used against descent, or some other scientific theory and concludes that a consistent philosophy of science must allow design as a scientific theory, or else allow for the exclusion of other theories currently considered scientific–including descent!

    Common descent also makes predictions which are mutually exclusive with the predictions of design. In other words, descent often predicts the exact opposite of what one would expect from design:

    1. High information content machine-like irreducibly complex structures will NOT be found.
    2. Forms will appear in the fossil record as a gradual progression with transitional series.
    3. Genes and functional parts will reflect those inherited through ancestry, and are only shared by related organisms.
    4. The genetic code discarded genetic baggage code or functionless “junk DNA”.

    Each of the predictions of design will now be tested against the predictions of descent.

    1. The origin of irreducibly complex systems

    Darwin himself realized that there were certain types of biological structures which Darwinian evolution simply couldn’t create. Darwinian evolution works by a process called the mutation-selection mechanism. Purely random mutations in the DNA create new types of organisms, and those organisms which are better at surviving and reproducing tend to leave more offspring. Over time, populations of organisms change as those which are best suited to the environment get “selected” (i.e. they survive and reproduce better). The catch to all of this is that changes must occur at a very slow pace, one little mutation at a time. Also, biological systems produced by evolution must be functional (i.e. confer some benefit to the organism) at every little step along their evolutionary path.

    In his book Darwin’s Black Box, Michael Behe noted that:
    In The Origin of Species Darwin stated:

    ‘If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.’

    A system which meets Darwin’s criterion is one which exhibits irreducible complexity. By irreducible complexity I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.
    Behe then shows that there are a host of biochemical systems which function much like machines and exhibit this sort of “irreducible complexity”. These machines work only if all the necessary parts are present for if one part is removed, the entire machine breaks down. These systems defy an evolutionary origin, because they cannot be built up in a step-by-step manner. Examples Behe gives include the bacterial flagellum, the blood clotting mechanism, and the biochemical processes behind vision. It just so happens that these machine-like “irreducibly complex” structures also contain just the sort of high specified complex information we would expect to be produced by intelligent action.

    Yet evolutionists do not admit that their theory is falsified by the presence of these unevolvable structures. Instead they turn to explanations of gene duplication and co-optation to build these complex structures. While these sorts of explanations still leave the details to the dice and lack strong explanatory power, it should be noted that evolutionists have not allowed their theory to be falsified. As long as there is some protein with some homology to some part in the irreducibly complex structure, evolutionists believe it could have been put their through some combination of gene duplication, co-optation, and micromutation. Thus, evolution makes essentially untestable claims of high improbability to explain the origin of irreducibly complex systems.

    In intelligent design, irreducible complexity is merely a special case of “specified complexity”

    One hot area of research in biology relevant to looking for “specified complexity” is investigating protein specificity. Many new articles have been published in recent years, and many new research groups are beginning to ask questions about how specific biological parts must be in order to function. Three mainstream articles include:

    # “Exploring the Conformational Properties of the Sequence Space between two proteins with different folds: An Experimental Study” by F. Blanco, I. Angrand, and L. Serrano in Journal of Molecular Biology (1999) 285:741-753
    # “Estimating the Entropy of DNA Sequences” by A. Schmitt and H. Herzel in Journal Theoretical Biology (1997) 1888:369-377
    # “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors” by Douglas D. Axe in Journal Molecular Biology (2000) 301:585-595

    Each article concludes that proteins and thus DNA are highly specified in the function they perform. This sort of research is on its way to detecting specified complexity, and affirming a design inference, and is an active area of research for intelligent design theorists. As far as the flagellum goes, it almost looks as if the design inference is on its way to being made, as one biologist said in a major mainstream biology journal, Cell, “[m]ore so than other motors, the flagellum resembles a machine designed by a human.”

    2. The fossil record and transitional forms

    Darwin himself realized that his theory predicted that fossils indicating transitionss from one form to another should be found in the fossil record. For this reason, Darwin asked the question:

    … The number of intermediate varieties, which have formerly existed on the earth, (must) be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory.

    Without getting too deep into the complexities of this issue, the fossil record by and large only very rarely provides anything resembling a plausible transitional form:

    The absence of fossil evidence for intermediary stages between major transitions in organic design, indeed our inability, even in our imagination, to construct functional intermediates in many cases, has been a persistent and nagging problem for gradualistic accounts of evolution.

    Gould wrote this over 120 years after Darwin wrote Origin of Species, a time when the fossil record was much better understood. Yet evolutionary theory was not falsified due to the lack of fossil evidence. Instead, paleontologists took hold of a theory proposed by Gould called “punctuated equilibrum”. This theory predicts that modes of transformation (i.e. speciation) would take place in small isolated populations where transitional forms would not have the chance to be fossilized. Therefore, with regards to the fossil record, descent is put in an unfalsifiable position: it predicts that confirming evidence of evolution (change) will not be found.

    3. Darwinian trees and molecular evolution

    “Family Trees” (called “phylogenetic trees”) based off of DNA sequences in genes should make nice neat “Darwinian Trees” if common ancestry is true. However, it is well recognized in the field of classification (systematics) that very often phylogenetic trees based upon one gene or protein sequence, will lead to one tree, while a tree based upon some other biomolecule will look quite different. Molecular biologist W. Ford Doolittle wrote, “[m]olecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.” Yet, evolution predicts that molecular data should allow a phylogenetic “tree of life” to be reconstructed. Descent, apparently, has been falsified.

    As Doolittle indicates, from the base of the tree of life, it is not “tree-like.” In the “bush” below, it is impossible to reconstruct such trees, as the observed distribution of characters create something which looks more like a tangled thicket or a bush. The three major “domains” of life–Bacteria, Archaea, and Eukarya have a distribution of characteristics which does not allow a tree to be constructed to describe their alleged ancestral relationships. This is due to a character distribution which is not what one would predict if they inherited their genes through common ancestry:

    1. Ribosomal genes in archaea are similar to those found in eukaryotes
    2. Morphology of archea is much more similar to bacteria.
    3. Eukaryote “operational” genes (those involved with amino acid synthesis and metabolism) seem to be most similar to those found in bacteria.
    4. Eukaryote “informational” genes (those involved with cell replication) seem to be most similar to those found in Archaea.

    Though some have envisioned the origin of Eukaryotes as a symbiotic fusion of members of archaea with members of bacteria, this simple “symbiosis hypothesis” has been recently challenged after it was found that eukaryotes contain over 300 proteins which do not bear any resemblance to any proteins in their supposed bacteria and archaea ancestors. The researchers suggest that a hypothetical pre-cursor cell type–the chronocyte–merged with members of both the archea and bacteria domains to provide these extra genes, making the an evolutionary symbiotic origin of eukaryotes a much more complicated and much less elegant theory. The tree of life, at its base, is nothing of the sort, and predictions from descent have failed.

    Many defenders of descent have argued that gene sharing, differing rates of evolution, or even convergent evolution among microorganisms is perhaps a plausible explanation for the lack of consensus among trees. But regardless, a prediction of the descent hypothesis has again failed, and we are left with an “epicycle”. Descent-based theories become so plastic that they can potentially explain any dataset, and there is no way to falsify the theory as it loses explanatory value. Just as the case with punctuated equilibrium, descent becomes unfalsifiable with respect to molecular phylogenetic trees.

    The father of molecular systematics Carl Woese found that conflicts in phylogenies are present not only at the base of the tree, saying, “[p]hylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, form its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.” For example, de Jong noted that,”the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows.” Another recent study entitled “Widespread horizontal transfer of mitochondrial genes in flowering plants” invoked the gene-swapping mechanism to explain the fact that some plant mitochondrial genes are distributed in patterns strongly at odds with expectations from common descent. At least one study would argue that horizontal gene transfer isn’t even possible in advanced Eukaryotes like plants. Cao et al. found that molecular-based phylogenies conflicted sharply with previously established phylogenies of major mammal groups, such as ferungulates, rodents, and primates.

    Some studies have tried to analyze the general relationships between animals and vertebrate groups through molecular data. One study analyzed molecular data from 10 different vertebrates and found that using different mitochondrial genes, twenty different disagreeing phylogenetic trees were produced, which differed at both recent and ancient divergence points. Brown and Naylor found that trees based off of entire mitochondrial DNA genomes for 19 multicellular (metazoan) organsism did not match the previously accepted phylogeny for chordates, or within chordates, for vertebrates. Finally, a study which compared many proteins in humans, nematodes, arthropods, and yeast found that 2 starkly different trees were produced, depending on which genes were used. This pattern of different genes yielding very different phylogenetic trees is very common in the scientific literature, and shows that molecular data fail to give a consistent picture of the alleged common descent ancestry of organisms.

    It has also been recognized that various genes distributed in organisms often do not match predictions of Darwinism. Schwabe and Warr found that proteins such as relaxin, insulins, adrenocorticotropic hormone, somatostatin, histocompatability antigens, neural glycoproteins and microglobulin are distributed in both animal and non-animal groups in ways which differ markedly from predictions of common descent.

    Another prediction of descent is that molecular data should verify phylogenetic trees based upon “macro-morphology” (larger structural features of biological organisms) in both living and fossil organisms. However, molecules and morphology often strongly disagree, and as one researcher put it, this causes ‘evolution wars’:
    When biologists talk of the ‘evolution wars’, they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species’ morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history.
    A recent study of the primate “family tree” found that the morphological evidence is irreconcilable with the molecular data, as a review article reported, “no matter how the computer analysis was run, the molecular and morphological trees could not be made to match.” There are also conflicts between the alleged ancestry of whales, depending on if evolutionists look at molecules or morphology. In fact, classifying the different types of whales within their own monophyletic group has proven difficult, as some toothed sperm whales seem to be more genetically similar to baleen whales. Finally, another study found that traditional “family trees” for reptiles based off of morphology differ sharply than those based upon DNA similarity.

    Systematist Colin Patterson also did a review of congruence between trees generated by morphology and trees created by molecular data and found that “congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology.” His study concluded that after reviewing trees based off of molecular and morphological data, their hopes of verifying morphologically derived trees were “dampened,” disconfirming their expectations from descent-based hypotheses.

    Some have hoped that over time, as more data is accumulated by finding more fossils and determining more DNA sequences, that apparent contradictions between the molecular and morphologically-based trees would be resolved. However, a recent study reported that, “our ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years” and that, “[d]espite increasing methodological sophistication, phylogenies derived from morphology, and those inferred from molecules, are not always converging on a consensus.”

    Despite 100 years of intense and disconfirming research, the study attributed the contradictions to a lack of data. Molecular-based trees are often at odds with trees created by the fossil record, or from structural characteristics of organisms. This is a serious problem for “descent,” because it shows that evidence for common ancestry (the idea that all life-forms are related through ancestry) is not supported or flatly contradicted by molecular data. Proponents of descent invent a number of “ad hoc” hypotheses to explain away the inconsistencies (gene sharing, changing rates of evolution, convergent evolution, lack of data) however descent has now been placed in an unfalsifiable position also with respect to molecular data.

    4. Allegedly “Junk DNA” or “non-functional DNA.”

    # Ever since scientists began to understand the working of genetics, it became apparent that only about 3% of our DNA is composed of genes that code for proteins. Many evolutionists have claimed that the rest of the DNA is “junk-DNA,” an evolutionary relic of ancient discarded genes. Not only do they claim it is a fulfilled prediction of evolution, but it is seen as a non-functional product that an intelligent designer wouldn’t create. Yet, in recent years, more and more types of “junk-DNA’ have been found to have function. If this trend continues, perhaps eventually most DNA will be found to have function (though probably not all as some information loss has undoubtedly occurred whether it was originally designed or not). Consider the following examples:

    # UCSD and Japanese researchers have found functionality for a pseudogene in a mouse. A Nature news story notes that evolution has led researchers to believe that “‘[p]seudogenes’ are produced from functional genes during evolution, and are thought to be simply molecular fossils” and that the evolutionary expectation that they are functionless makes this an “unexpected discovery of a biological function for one pseudogene [that] challenges popular belief.” This “pseudogene” apparently regulates regulation of messenger-RNA on a different chromosome. The article ends with a profound question that both evolutionists and design theorists ought to take seriously: “Might the pseudogene copies of other functional genes be similarly useful?”

    # The NY Times reported that “huge stretches of DNA that do not contain protein-coding genes and have been considered “junk” actually hold the code for some of this RNA” which apparently plays a large role in gene regulation. (RNA Trades Bit Part for Starring Role in the Cell, 1/20/03).

    # With the recent sequencing of the mouse genome, the Washington Post reported that 3% of non-gene portions of the human and mouse genomes seem to be highly “conserved” or similar, implying functionality. These similarities come from portions of the genome which do NOT code for genes, and were previously thought to be functionless “junk-DNA”. The article speculated these portions may regulate growth or gene expression and quoted one of the leading scientists who sequenced the mouse genome saying, “My goodness, there’s a lot more that matters in the human genome than we had realized.” A report on the mouse genome was published in Nature.

    # Another study found similarity in introns among distantly related organisms. This blow to “junk DNA” came from Harvard microbiologists who found that as much as 20% of introns in plants, animals, and fungi are found at similar chromosomal loci. Under the evolutionary interpretation, this implies these introns have persisted in similar locations for many hundreds of millions of years in the ancestors, which is extremely unlikely to have occurred if these non-coding introns truly are purely functionless and randomly-inserted pieces of so-called junk-DNA.

    # Essential Cell Division “Zipper” Anchors to So-Called Junk DNA: Mechanism May Provide Insights Into Development and Cancer. Previously thought “genetic junk,” ALU sequences appear to have some functionality providing anchoring points for chromosomes to link to one-another during mitosis (cell duplication). The article reports that a full report is was published in Nature. Additionally. ALU sequences can allow for different genes to be spliced together to create many versions of a similar protein. This has been cited as the solution to the recently discovered question as to why where are so few genes in the human genome.

    # A press release, Parasite or partner? Study suggests new role for junk DNA, discussed how transposable L1, or LINE-1, elements, typically thought to be non-coding “junk DNA,” comprise 17% of our DNA and seem to have a newfound purpose, as they have the ability to repair DNA breaks in chromosomes. The article noted a full report was published in Nature Genetics.

    # A large number of studies have suggested that many types of noncoding “Junk DNA” helps regulating gene expression (see http://www.psrast.org/junkdna.htm for a list of references).

    # One study found that noncoding DNA could actually provide necessary structural material to physically maintain a larger size for a cell.

    An extensive discussion of examples of functionality of previously alleged “Junk DNA” can be found at When “Junk” DNA Isn’t Junk (http://www.godandscience.org/evolution/junkdna.html).

    It should be noted that various types of DNA persist whose functions are not yet known. However, given the current trend that as we increase understanding of genetics, many many more types of previously thought “junk-DNA” is found to be functional, one might expect that in time, many, if not all types of DNA might be found to have function. In the end, perhaps it will turn out that expectations from evolutionary theory that the genome should be full of relic “junk-DNA” might have actually hindered and slowed our investigation and understanding of many types of DNA.

    It should also be noted that intelligent design theory only predicts original functionality, and allows for loss of function, where something was originally designed functional, but perhaps function was lost due to various environmental factors. This could be seen as analogous to leaving brand new car out on a mountaintop. 500 years later, natural forces leave parts of it non-functional, although it was designed as initially functional.

    It is also possible that a designer might have, in some instances, pre-programmed diversity as “dormant genes” which might have been unexpressed in the past, or expressed in the past but unexpressed in the present. This “pre-programmed diversity” could account for some redundant, but functional-gene-like components of “junk-DNA” whose functions are currently unknown, as is the case with some pseudogenes. Thus “functionless DNA” might be designed to be only “temporarily functionless” and not the permanently functionless evolutionary relic that evolutionists mistake them to be. Expectations and predictions of design seem to be yielding much more fruit in this area of research than are predictions of descent via neo-Darwinian processes.

    Since the time of Darwin, evolutionists have known about the weaknesses of the theory of evolution and descent with modification. Yet, they have not abandoned it simply because they say, “it’s the best theory we’ve got”. Descent, through these “ad hoc” hypotheses, has been forced into an unfalsifiable position, lest it be falsified. Today, biologists have a new and growing theory of life’s origin: intelligent design. As intelligent design theory matures and develops as a scientific theory, evolution may not be the “best” any longer, and the “design hypothesis” may once again be considered as a viable explanation for the origins of lifeforms on earth.

    Line of Evidence: Biochemical complexity.
    Prediction of descent: High information content machine-like irreducibly complex structures will NOT be found.
    Prediction from design: High information content machine-like irreducibly complex structures will be found.
    Data: High information content machine-like irreducibly complex structures are commonly found.
    Best explaining theory: Design

    Line of Evidence: Fossil Record.
    Prediction of descent: Forms will appear in the fossil record as a gradual progression with transitional series.
    Prediction from design: Forms will appear in the fossil record suddenly and without any precursors.
    Data: Forms tend to appear in the fossil record suddenly and without any precursors.
    Best explaining theory: Design

    Line of Evidence: Distribution of Molecular and Morphological Characteristics.
    Prediction of descent: Genes and functional parts will reflect those inherited through ancestry, and are only shared by related organisms.
    Prediction from design: Genes, DNA sequences, and functional parts will be re-used in different unrelated organisms.
    Data: Genes and functional parts often are not distributed in a manner predicted by ancestry, and are often found in clearly unrelated organisms.
    Best explaining theory: Design

    Line of Evidence: Biochemical Functionality.
    Prediction of descent: The genetic code will contain much discarded genetic baggage code or functionless “junk DNA.”
    Prediction from design: The genetic code will NOT contain much discarded genetic baggage code or functionless “junk DNA.”
    Data: Increased knowledge of genetics has created a strong trend towards functionality for “junk-DNA”; examples of DNA of unknown function persist, but function may be expected or explained under a design paradigm.
    Best explaining theory: Design

    Evolutionists currently resolve the discrepancies between its predictions and the data through “ad hoc” hypotheses. However, if evolution cannot explain the data over time, then there is nothing wrong with appealing to a theory which can.

    Thus, it can be seen from this that intelligent design theory makes empirically-based predictions, which are matched in the data.

    Until the time that biologists are ready to admit design into their picture, the quirks and counter-evidences to evolution, and the auxiliary hypotheses of descent-based theories may increase, and the data may become increasingly inconsistent with evolution. Descent has failed each of these tests, yet it has been retained by scientists as a valid scientific description of the history and origins of life on earth. Hopefully, at some point, science will consider design.

  55. Inunison

    Nested hierarchy is not a prediction of common descent, and can not be used as evidence of common descent. This is not a prediction, but rather an accommodation (yet again) by it. True common descent would be much better represented by a continuous, blurred line with no nests at all.

    Again with the same old same old. But can you support it? No!

    I am not that naive. Even the discovery of an organism having no similarity to any known life would not falsify common descent, because evolution does not predict its absence.

    But that was not what I said you had to find. Find one single example of common descent not giving a nested hierarchy.

    The real problem here is that if such an example existed, the creationists would have been touting it for 150 years.

    Some more for you to explain away.

    I have yet to see you explain the distribution of marsupials and placentals using common design. I have yet to see you explain the distribution of reverse- and obverse-wired eyes using common design. So really at this stage I feel no great need to explain the problems you think exist for common descent.

    Continuing on my post #40 (that I assume you have not read)…

    Well, I read it, but I found nothing to indicate what the theory actually is, i.e., what it claims actually happened.

    (1) High information content machine-like irreducibly complex structures will be found.

    Why is this a prediction. Is it not at least possible that the designer created life with low information content, that is not machine-like and with no IC structures?

    (2) Forms will be found in the fossil record that appear suddenly and without any precursors.

    Again, why is this a necessary prediction? Is it inconceiveable that life was created incrementally, a series of design experiments perhaps.

    (3) Genes and functional parts will be re-used in different unrelated organisms.

    That wuld be like the fish and the squid have obverse wired eyes, I guess?

    (4) The genetic code will NOT contain much discarded genetic baggage code or functionless “junk DNA” .

    Bradford said earlier that front-loading was a common design possibility (and nothing you have presented suggests otherwise). That would surely lead to the prediction that they was plenty of discarded genetic baggage code. Again, I do not see why this is a necessary prediction.

    Meyer finds that any argument used against design to disqualify it as a scientific theory can also be used against descent, or some other scientific theory and concludes that a consistent philosophy of science must allow design as a scientific theory, or else allow for the exclusion of other theories currently considered scientific–including descent!

    Then give us a design theory. One with substance, that actually makes some claims about what happened. Then you can go test the predictions, and maybe it will turn out to be science. There is nothing in your posts that I have noticed that even states whether you are claiming life is 100 years old or a trillion years old. That sort of fence-sitting is what gets you disqualified as science.

    1. High information content machine-like irreducibly complex structures will NOT be found.

    That is not a prediction from common descent. Bear in mind common descent allows for genetic tinkering by a designer, and such a designer could periodically introduce high information content, IC structures (if we allow for a moment that IC structures even exist, and Darwinian evolution cannot produce information).

    2. Forms will appear in the fossil record as a gradual progression with transitional series.

    The fosil record is incomplete, so this is not a prediction of comon descent (thouigh plenty of sequences do exist, of course).

    3. Genes and functional parts will reflect those inherited through ancestry, and are only shared by related organisms.

    Genes yes, functional parts no. Again your genetic tinkerer might decide he wants platypi and ducks to have the same bills.

    4. The genetic code discarded genetic baggage code or functionless “junk DNA” .

    Okay. So the prediction is that there are sections of DNA that can be scrambled, without affecting the organism. I think that would be an interesting experiment, though I guess scientists would wait until they had a better idea of the genome first.

    A system which meets Darwin’s criterion is one which exhibits irreducible complexity. By irreducible complexity I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning

    I think Behe has been forced to change this definition…

    This sort of research is on its way to detecting specified complexity, and affirming a design inference, and is an active area of research for intelligent design theorists.

    Which IDists are involved in this research? What experiments are they doing?
    From here:

    This is about enzymes, and their ability to catalyze different reactions with different substrates, even those that aren’t found in nature. It’s a property known as “promiscuity” , one that’s being increasingly recognized as important in enzymology and enzyme evolution.

    I really cannot be bother to go through the rest, some of which I have already addressed. Sure, you have a lot there; you have made a big effort (er, maybe not). Odd then that you cannot do that one little thing, conjure up a pattern of common descent leading to something other than a nested hierarchy – a specific example, to show that the mechanisms you claim are real and not phantoms.

    By the way, unless you are Casey Luskin, you are guilty of plagarism. Personally, I think it is morally wrong to copy a large tract of text, without crediting the real author. For anyone else, here is where Inunison stole it from.

  56. Hi The Pixie,

    Of course I paste it from Casey Luskins’ article, so what. If I was dishonest and tried to claim authorship, do you think I would make it so obvious. But that is beside the point. The fact is that all you do is waving your hands and repeating your old mantra instead of addressing the issues. But that is to be expected.

  57. ALL “evidence” for Common Descent is circumstantial. We cannot even objectively test the premise that chimps and humans shared a common ancestor. That is because we have no idea whether or not any mechanism can account for the physiological and anatomical differences observed between the two populations.

    Nested hierarchy is not a prediction of Common Descent because Common Descent is NOT a racheting process with respect to traits and characteristics. And it is via traist and characteristics that nested hierarchies are derived. So if all the alleged transitionals and intermediates were still alive we would see a blend of traits and characteristics-> mammal-like reptiles and reptile-like mammals- with nothing that stops either from reverting back to some ancestral form. Overlapping is not allowed in a nested hierachy scheme. And if is wasn’t for a few fortunate extinction events we wouldn’t observe NH to the extent that we do.

    NH is NOT observed with single-celled organisms. And as such if metazoans “evolved” from them we wouldn’t expect to see it with metazoans either.

    the Pixie:
    Then give us a design theory.

    Many people ask if there is a theory of Intelligent Design. To which I respond, “Is there a theory of Archaeology?”

    Intelligent Design, also called the design inference, is just that, a reasoned inference from the data.

    IOW ID is an observation, which can be used as an underlying assumption from which to start the research. And as we all (should) know, it does make a difference to an investigation whether or not the object(s) in question arose via an intelligent cause or via nature, operating freely.

    “Thus, Behe concludes on the basis of our knowledge of present cause-and-effect relationships (in accord with the standard uniformitarian method employed in the historical sciences) that the molecular machines and complex systems we observe in cells can be best explained as the result of an intelligent cause.
    In brief, molecular motors appear designed because they were designed” Pg. 72 of “Dawinism, Design and Public Education”

    We already have processes in place that we use to detect design:

    Del Ratzsch in his book Nature, Design and Science discusses “counterflow as referring to things running contrary to what, in the relevant sense, would (or might) have resulted or occurred had nature operated freely.”

    Anthropologists use this type of process when detecting artifacts. Markings (marking does not pertain to the sound made by dogs with a harelip) on a rock that are contrary to what scientists deem nature acting alone could/ would not do, as compared to what we know intelligent agencies have done and can do is what determines the categorization of an object- artifact or just another rock.
    Archaeologists checking for inscriptions would employ similar methodology- as Del puts it “an artifact is anything embodying counterflow.”

    (Paraphrasing Del)If you come upon a group of trees in exact rows, each row the same distance from the next and each tree in the row the same distance from the next tree in the row, although nature acting alone could have produced such a pattern, our minds would instinctively infer the pattern was the result of intentional design.

    Sometimes design is mind correlative. That is when what we observe fits some identifiable/ recognizable pattern- Nasca, Peru. (Or in organisms, the presence of the insulin protein in bacteria.)

    Using the Explanatory Filter is also a good tool for a starting inference. (We know science is not about proof. The EF is not about proving design. The EF is about the design inference. As with any inference the design inference can be falsified. Pulsars were once thought to be signals from ETs. Further research falsified that inference. The properly applied DEF would have not allowed design to be the initial inference.) The EF can give initial false negatives. IOW something that is designed can fall into the categories of chance and/ or law. That is why design theorists don’t say just give up once design is or isn’t the initial inference. And with all inferences future research can either confirm it or refute it.

    The ONE alleged false positive I have read was from Del’s aforementioned book pertaining to a tumbleweed getting blown across the road directly through a hole in a fence. Wind currents explain that phenomenon. IOW the DEF was not properly applied.

    So the question is what is it that prevents tried-n-true design detection techniques from being applied to biological organisms?

    Is there a theory of sheer dumb luck? Because in the materialistic anti-ID world that is all you have. SDL that the proto-Earth was struck by a giant impactor at just the right angle to impart a rotation, at just the right time in plantary devo, at just the right speed, etc., to leave us with a large stabilizing Moon. One that just happens to be 400x smaller than the Sun, which just happens to be 400x farther away. This gives us the amazing coincidence of having the only habitable planet or moon in the olar system that also has total solar eclipses and just at the time when there are intelligent observers to best appreciate and use them to better understand the universe.

  58. Joe G

    ALL “evidence” for Common Descent is circumstantial.

    Of course it is! No one was around to watch it happen. All the evidence for the Roman empire is circumstantial. Sure, we would love to have direct evidence, but we work with what we have.

    Nested hierarchy is not a prediction of Common Descent because Common Descent is NOT a racheting process with respect to traits and characteristics. And it is via traist and characteristics that nested hierarchies are derived. So if all the alleged transitionals and intermediates were still alive we would see a blend of traits and characteristics-> mammal-like reptiles and reptile-like mammals- with nothing that stops either from reverting back to some ancestral form. Overlapping is not allowed in a nested hierachy scheme. And if is wasn’t for a few fortunate extinction events we wouldn’t observe NH to the extent that we do.

    Then perhaps you can succeed where Inunison has failed. Give us one example of a tree of life, with common descent, that does not give a nested hierarchy. You might like to look at my post 32 to see a couple of examples of trees that do give nested hierarchies (and yes, I know that does not prove common descent has to give a nested hierarchy, but it does prove people can draw patterns of common descent on this thread).

    Just one example will prove you are right, and I am wrong. Thankfully, I know it is impossible.

    NH is NOT observed with single-celled organisms. And as such if metazoans “evolved” from them we wouldn’t expect to see it with metazoans either.

    Can you support that claim?

    Many people ask if there is a theory of Intelligent Design. To which I respond, “Is there a theory of Archaeology?”
    Intelligent Design, also called the design inference, is just that, a reasoned inference from the data.

    So no. By the way, I think there are numerous theories in archaeology.

    Can you tell me what the claims of “common design” are?

    IOW ID is an observation, which can be used as an underlying assumption from which to start the research. And as we all (should) know, it does make a difference to an investigation whether or not the object(s) in question arose via an intelligent cause or via nature, operating freely.

    Okay. But please do not call ID science until that research has been done, and the predictions shown to good.

    (Paraphrasing Del)If you come upon a group of trees in exact rows, each row the same distance from the next and each tree in the row the same distance from the next tree in the row, although nature acting alone could have produced such a pattern, our minds would instinctively infer the pattern was the result of intentional design.

    Sure. It is much more likely that a physical, intelligent agent lined the trees up. We know such agents exist, and we know they occasionally line up treees. Circumstantial evidence of course…

    Using the Explanatory Filter is also a good tool for a starting inference.

    You can generate a starting inference anyway you want. “I wonder if…” is good enough. The important part for science is what you do next. Generate predictions, and test them.

    (We know science is not about proof. The EF is not about proving design. The EF is about the design inference. As with any inference the design inference can be falsified. Pulsars were once thought to be signals from ETs. Further research falsified that inference. The properly applied DEF would have not allowed design to be the initial inference.)

    Science is about supporting or refuting, not proving. Once you have your starting inferece, you cannot prove it, but you can support it by showing that the predictions are good. And if you cannot support it you have no business claiming it is science. While you are testing the predictions you can claim to be doing scientic research, but do not kid yourself that ID has any place in the body of knowledge that is science until it has done the reseach.

    Is there a theory of sheer dumb luck? Because in the materialistic anti-ID world that is all you have. SDL that the proto-Earth was struck by a giant impactor at just the right angle to impart a rotation, at just the right time in plantary devo, at just the right speed, etc., to leave us with a large stabilizing Moon. One that just happens to be 400x smaller than the Sun, which just happens to be 400x farther away. This gives us the amazing coincidence of having the only habitable planet or moon in the olar system that also has total solar eclipses and just at the time when there are intelligent observers to best appreciate and use them to better understand the universe.

    Given the number of stars out there, I do not see it as that unlikely that it happened somewhere.

  59. The fact that all the evidence for Common Descent is circumstantial means that it is NOT open to objective testing and as such it does NOT belong in a science classroom.

    the Pixie:
    Give us one example of a tree of life, with common descent, that does not give a nested hierarchy.

    Umm demonstrate that the tree of life arose by Common Descent. Also the examples I provided of reptile-like mammals a mammal-like reptiles demonstrates that NH is NOT expected.

    Also I already provided the science that shows NH is not observed in single-celled organisms and why that is so.

    the Pixie:
    But please do not call ID science until that research has been done, and the predictions shown to good.

    But the MET doesn’t have that- research nor predictions.

    the Pixie:
    Science is about supporting or refuting, not proving.

    Umm THAT is what I said.

    the Pixie:
    Given the number of stars out there, I do not see it as that unlikely that it happened somewhere.

    You aren’t a scientist. I will side with the science and reality on this one.

    I would also be interested in those theories in archaeology. I would bet they are similar to what is in ID.

    Obviously the Pixie does NOT understand the rules of hierarchy- even though I posted them here before…

  60. The fact that all the evidence for Common Descent is circumstantial means that it is NOT open to objective testing

    Well how does that follow?

    Umm demonstrate that the tree of life arose by Common Descent. Also the examples I provided of reptile-like mammals a mammal-like reptiles demonstrates that NH is NOT expected.

    Actually the reptile-like mammals and mammal-like reptiles all nest inside groups. All reptiles, mammals and birds are in one large group. There is a smaller group of mammals, reptile-like mammals and mammal-like reptiles nested inside that. There is a smaller group of mammals and reptile-like mammals nested inside that. Then there is a smaller group of mammals nested inside that, then there is a smaller group of placental mammals nested inside that. And so on.

    Also I already provided the science that shows NH is not observed in single-celled organisms and why that is so.

    No, you asserted an opinion. If there was any real science you would be able to draw a diagram for that one elusive example.

    But the MET doesn’t have that- research nor predictions.

    Of course it does.

    Pixie: Science is about supporting or refuting, not proving.
    Joe G: Umm THAT is what I said.

    Great! So show me IDists researching the support for an ID theory.

    You aren’t a scientist. I will side with the science and reality on this one.

    Well actually I am a scientist. But talk us through the science, Joe. What is the probability and how was it determined?

    I would also be interested in those theories in archaeology. I would bet they are similar to what is in ID.

    See Wiki for a starting point. Not too like ID as far as I can see…

    Obviously the Pixie does NOT understand the rules of hierarchy- even though I posted them here before”

    Hmm, maybe I do not, I would hate to be dogmatic about it. Do you understand them? If so, it should be trivial to give one example of common descent not giving a nested hierarchy. I mean, come on, Joe. You understand common descent, right? You understand what Denton was talking about right? How hard can it be? Have you even tried? Surely the hope of proving me wrong would be enough to get one of you guys to have a go.

    Or perhaps you have all secretly tried and failed?

  61. Hi The Pixie,

    Thankfully, I know it is impossible.

    If I ever seen dogmatic statement this is one and ultimate science stopper to boot. Is that why you will not accept data that shows your faith wrong? And on top of everything there comes Dr. Theobald. You need to find more credible witness The Pixie.

    Then perhaps you can succeed where Inunison has failed.

    That is dead wrong. You were given examples that you explained away using various evolutionary mechanisms and thus shown that your pet theory is unfalsifiable.

  62. The MET cannot be objectively tested because we don’t even know whether or not any mechanism can account for the physiological and anatomical differences observed between chimps and humans. We don’t even know what makes a chimp a chimp and a human a human.

    Also I already provided the science that shows NH is not observed in single-celled organisms and why that is so.

    the Pixie:
    No, you asserted an opinion.

    Here it is AGAIN:

    Can evolution make things less complicated?
    Scientists suggest cell origins involved a forward-and-backward process

    then we have:

    Antonis Rokas & Sean B. Carroll, “Bushes in the Tree of Life,” PLOS Biology, Vol 4(11):1899-1904 (November, 2006)

    Which is included in:

    “The Phylogenetic Tree Topples”

    But the MET doesn’t have that- research nor predictions.

    the Pixie:
    Of course it does.

    Name the research and name some predictions. We will see if they are from the MET or not.

    An example of Common Descent not leading to NH would be reptiles, giving rise to mammal-like reptiless, which gave rise to reptile-like mammals, (all the while including trait reversals), which then reversed the trend back to reptiles.

    IDists researching for ID support- Minnich, Behe, Axe, Gonzalez, just to name 4 right off the top of my head.

    Now how about any scientists researching the premise that chimps and humans shared a common ancestor?

  63. Common Design:

    Of Newton, Kepler, & Galileo in the book Mathematics: The Loss of Certainty by Morris Kline, Kline states that these scientist-mathematicians believed that “God had designed the universe, and it was to be expected that all phenomena of nature would follow one master plan. One mind designing a universe would almost surely have employed one set of basic principles to govern all related phenomenon.”

    Duane Gish explains:

    A creationist would also expect many biochemical similarities in all living organisms. We all drink the same water, breathe the same air, and eat the same food. Supposing, on the other hand, God had made plants with a certain type of amino acids, sugars, purines, pyrimidines, etc.; then made animals with a different type of amino acids, sugars, purines, pyrimidines, etc.; and, finally, made man with a third type of amino acids, sugars, etc. What could we eat? We couldn’t eat plants; we couldn’t eat animals; all we could eat would be each other! Obviously, that wouldn’t work. All the key molecules in plants, animals, and man had to be the same. The metabolism of plants, animals, and man, based on the same biochemical principles, had to be similar, and therefore key metabolic pathways would employ similar macromolecules, modified to fit the particular internal environment of the organism or cell in which it must function.

    and then even more “rules”:

    Unified physics theory explains animals’ running, flying and swimming

    Also pertaining to nested hierarchy- only descent WITH divergence would give any branching pattern. Evolution doesn’t predict neither divergence nor convergence.

    and Denton in that chapter 6:

    In the final analysis the hierarchic pattern is nothing like the straightforward witness for organic evolution that is commonly assumed. There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process. If the hierarchy suggests any model of nature it is typology and not evolution. How much easier it would be to argue the case for evolution if all nature’s divisions were blurred and indistinct, if the systema naturalae was largely made up of overlapping classes indicative of sequence and continuity.

  64. Inunison

    That is dead wrong. You were given examples that you explained away using various evolutionary mechanisms and thus shown that your pet theory is unfalsifiable.

    Look at my post 32. I give some simple examples of comon descent giving a nested hierarchy. All you have to do is provide one single diagram like that, where there is no nested hierarchy, but we can see common descent, and you prove me wrong. Instead, what I was given was vague hand-waving and a misunderstood example of reptiles-to-mammals. If the example exists, show it! What could be easier?

  65. The MET cannot be objectively tested because we don’t even know whether or not any mechanism can account for the physiological and anatomical differences observed between chimps and humans. We don’t even know what makes a chimp a chimp and a human a human.

    Here is some news for you… MET involves more than just the mechanism that accounts for the physiological and anatomical differences observed between chimps and humans.

    Can evolution make things less complicated?
    Scientists suggest cell origins involved a forward-and-backward process

    So what? Why is this a problem for common descent? Why does this upset the nested hierarchy? Remember that going down the tree of life is the passing of time. It is not possible for evolution to go back in time! Certainly you can have loss of function (front-loading assumes a huge loss of information), but you are still looking at one species going to a second, going to a third, going to a fourth. It does not matter that the third is a simpler organism that the second or fourth.

    From “The Phylogenetic Tree Topples” article on your blog:
    From the article by Margulis: “From these facts Darwin correctly inferred that life “descended with modification” from common ancestors. Overwhelming evidence for this fact (and none against) comes from, e.g., animal behavior, biochemistry, comparative anatomy, ecology, genetics, geochronology, microbiology, physiology, paleobotany, sedimentary geology, virology and zoology, amplifying Darwin’s insight.” I guess I must be missing something here, because it seems to me that Margulis is arguing for me, not you. Did you read the article, or just the title?

    “Two biologists from Canada and the United Kingdom were brave …” What they are saying is that the evidence from any one molecular study is not enough to determine the tree of life, that you have to correlate the evidence from multiple studies. And the reason for that is that the technique is dependant on random mutations.

    The third and fourth are talking about what happened billions of years ago. It becomes harder and harder to determine the tree of life the further back you go. That would seem obvious. Historians have a similar problem – the further back in time they go, the less reliable the evidence tends to be.

    An example of Common Descent not leading to NH would be reptiles, giving rise to mammal-like reptiless, which gave rise to reptile-like mammals, (all the while including trait reversals), which then reversed the trend back to reptiles.

    As I said last time: Actually the reptile-like mammals and mammal-like reptiles all nest inside groups. All reptiles, mammals and birds are in one large group. There is a smaller group of mammals, reptile-like mammals and mammal-like reptiles nested inside that. There is a smaller group of mammals and reptile-like mammals nested inside that. Then there is a smaller group of mammals nested inside that, then there is a smaller group of placental mammals nested inside that. And so on.

    A creationist would also expect many biochemical similarities in all living organisms. We all drink the same water, breathe the same air, and eat the same food. Supposing, on the other hand, God had made plants with a certain type of amino acids, sugars, purines, pyrimidines, etc.; then made animals with a different type of amino acids, sugars, purines, pyrimidines, etc.; and, finally, made man with a third type of amino acids, sugars, etc. What could we eat? We couldn’t eat plants; we couldn’t eat animals; all we could eat would be each other! Obviously, that wouldn’t work. All the key molecules in plants, animals, and man had to be the same. The metabolism of plants, animals, and man, based on the same biochemical principles, had to be similar, and therefore key metabolic pathways would employ similar macromolecules, modified to fit the particular internal environment of the organism or cell in which it must function.

    So nothing specific like when the design was done. Not surprised.

    In the final analysis the hierarchic pattern is nothing like the straightforward witness for organic evolution that is commonly assumed. There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process. If the hierarchy suggests any model of nature it is typology and not evolution. How much easier it would be to argue the case for evolution if all nature’s divisions were blurred and indistinct, if the systema naturalae was largely made up of overlapping classes indicative of sequence and continuity.

    So read what Denton says about these facets, and use one to draw that elusive diagram. You know the one. The impossible one. A specific example of common descent, not giving a nested hierarchy. You can do it with the reptiles if you want, but you would have to draw it out. Something like this perhaps:
    …………….First life
    ………………..|
    …………..Early Reptiles
    ……………/……….|
    ..Mammal-like reptiles….Other reptiles
    ……….|
    ..Reptile-like mammals
    ……….|
    …..Early Mammals
    ……/……..|
    ..Monotemes….Placentals
    See, these diagrams are not that difficult. At least, not if you do not mind ending up with a nested hierarchy. Bit more tricky if you want to avoid that…

  66. the Pixie:
    Here is some news for you” MET involves more than just the mechanism that accounts for the physiological and anatomical differences observed between chimps and humans.

    I know what it involves and I know that it cannot be objectively tested.

    Can evolution make things less complicated?
    Scientists suggest cell origins involved a forward-and-backward process

    the Pixie:
    So what? Why is this a problem for common descent? Why does this upset the nested hierarchy?

    It isn’t an issue for Common Descent but it is an issue for NH for the reasons already provided- reversal of traits.

    the Pixie:
    From “The Phylogenetic Tree Topples” article on your blog:
    From the article by Margulis: “From these facts Darwin correctly inferred that life “descended with modification” from common ancestors. Overwhelming evidence for this fact (and none against) comes from, e.g., animal behavior, biochemistry, comparative anatomy, ecology, genetics, geochronology, microbiology, physiology, paleobotany, sedimentary geology, virology and zoology, amplifying Darwin’s insight.” I guess I must be missing something here, because it seems to me that Margulis is arguing for me, not you. Did you read the article, or just the title?

    You have serious issues Pixie. Nothing in what Margulis said supports that Common Descent expects NH. As a matter of fact what she states contradicts you.

    the Pixie:
    As I said last time: Actually the reptile-like mammals and mammal-like reptiles all nest inside groups. All reptiles, mammals and birds are in one large group. There is a smaller group of mammals, reptile-like mammals and mammal-like reptiles nested inside that. There is a smaller group of mammals and reptile-like mammals nested inside that. Then there is a smaller group of mammals nested inside that, then there is a smaller group of placental mammals nested inside that. And so on.

    I know what you said and it is wrong.

    the Pixie:
    So nothing specific like when the design was done. Not surprised.

    LoL! Your position is totally VOID of specifics.

    And obviously you don’t understand hierarchy principles even though I posted a link- so here it is again:

    Summary of the Principles of Hierarchy Theory

    With trait reversals we would have an overlap no matter how much you wave your arms.

    It was also nice of you to ignore this:’

    Also pertaining to nested hierarchy- only descent WITH divergence would give any branching pattern. Evolution doesn’t predict neither divergence nor convergence.

  67. It would also be nice if the Pixie could provide ANY data which demonstrates a population of reptiles could “evolve” into a population of something other than reptiles.

    Please don’t forget the specifics…

  68. It would also be nice if the Pixie could provide ANY data which demonstrates a population of reptiles could “evolve” into a population of something other than reptiles.

    Dream on! I’ve been asking Darwinists that since the ARN day, years ago.

  69. Hi The Pixie,

    See, these diagrams are not that difficult.

    Of course they are not, because they are product of your imagination as they are arbitrary. You can easily accommodate several phylogenies as easily. Hypothesis of universal common ancestry is too amorphous to be falsified by the discovery of an organism that does not conform to the standard phylogeny as Re Mine correctly noted. He says the following about evolution (which determines phylogeny):

    The central illusion of evolution lies in making a wide array of contradictory mechanisms look like a seamless whole. There is no single evolutionary mechanism — there are countless. Evolutionary theory is a smorgasbord: a vast buffet of disjointed and conflicting mechanisms waiting to be chosen by the theorist. For any given question, the theorist invokes only those mechanisms that look most satisfying. Yet, the next question elicits a different response, with other mechanisms invoked and neglected.

    Evolutionary theory has no coherent structure. It is amorphous. It is malleable and can readily adjust to disparate patterns of data. Evolution accommodates data like fog accommodates landscape. In fact, evolutionary theory fails to clearly predict anything about life that is actually true.

    And you The Pixie proved him correct by invoking one of evolutionary mechanisms to explain away examples that I gave you. And true to Darwinian logic, when you don’t have an answer you are ready to invoke some fictional future discovery, not understanding that data available now question grand evolutionary claims in principle.

    The view that living things in all the major kingdoms are modified descendants of a common ancestor (described in the pattern of a branching tree) has been challenged in recent years by discrepancies in the molecular evidence (e.g. differences in relatedness inferred from sequence studies of different proteins) previously thought to support that view.

    see scientific evidence here starting from page 9

  70. Hi teleologist,

    But of course the answer lies in a question. Who designed the Designer? Once you IDiots answer that question proof of evolution will be self evident. So the Darwinian logic goes. And if you don’t like it, you simply don’t understand how science works. There!

  71. Joe G

    It isn’t an issue for Common Descent but it is an issue for NH for the reasons already provided- reversal of traits.

    No, you assert it is a problem, which is a bit different. Explain how “reversal of traits” upsets a nested hierarchy. Could you even do the impossible and illustrate it with a diagram that shows common descent not giving a nested hierarchy and prove me wrong?

    You have serious issues Pixie. Nothing in what Margulis said supports that Common Descent expects NH. As a matter of fact what she states contradicts you.

    And yet you cannot quote anything to support your claim. Just assertions again and again.

    I know what you said and it is wrong.

    But you cannot explain why, can you? All you can do is assert it.

    LoL! Your position is totally VOID of specifics.

    Not true. Scientists have a pretty good idea of when life appeared, and when individual species appeared. ID does not.

    And obviously you don’t understand hierarchy principles even though I posted a link- so here it is again:

    So give the diagram that prove me wrong. You know the one, I mention it severaltimes each post. And still you fail!

    With trait reversals we would have an overlap no matter how much you wave your arms.

    Why do you think that is true? And if it really is true, why can you not give the diagram that would prove you right and me wrong?

    Also pertaining to nested hierarchy- only descent WITH divergence would give any branching pattern. Evolution doesn’t predict neither divergence nor convergence.

    Where do you get that from? Of course evolution predicts branching. Surely if you must accept that branching occurs during microevolution!

    It would also be nice if the Pixie could provide ANY data which demonstrates a population of reptiles could “evolve” into a population of something other than reptiles.

    Goalpost shift! I thought we were arguing about whether the reptile to mammal lineage fitsa nested hierarchy. When I show it does, suddenly I am expected to “demonstrates a population of reptiles could “evolve” into a population of something other than reptiles”. Actually this is just a labelling issue. By convention we consider mammals to be separate to reptiles, but we are all descended from the first reptiles, so in a sense we are still reptiles. We could say Dalmations are not dogs, and lo-and-behold, something not a dog has been breed from a dog. You will probably think that is a dodge, but a dodge seems a reasonable response to a goalpost shift.

    Please don’t forget the specifics”

    That is a joke right? You make a post full of assertions, unable even to quote Margulis, despite a link from your own blog to the paper, and you demand I provide specifics about an issue that is just you shifting the goalposts? Well it made me laugh.

    So still no diagram of common descent giving something other than a nested hierarchy.

  72. Hi Inunison

    Of course they are not, because they are product of your imagination as they are arbitrary.

    The ones in post 32 are, yes. And I invite you to provide your own arbitrary diagram, from your own imagination, to support your claim that common descent need not give a nested hierarchy.

    The diagram with reptile to mammal evolution is not arbitary. From the fossil record, reptiles appeared, then mammal-like reptiles, then reptile-like mammals, then mammals. My diagram reflects that. Also, please note that mammal-like reptiles are more like reptiles than mammals, so are nearer to the reptiles, while the reptile-like mammals are more mammal like. What we are seeing is transitionals. Also, I am supposing mammals descended from reptile-like mammals rather than other reptiles, because again mammals more closely resemble the reptile-like mammals. So no, not arbitrary.

    You can easily accommodate several phylogenies as easily.

    I do not get your point.

    Hypothesis of universal common ancestry is too amorphous to be falsified by the discovery of an organism that does not conform to the standard phylogeny…

    Probably true, I imagine that would cause a restructuring of the tree only. But it would be falsified by large numbers of such organisms.

    … as Re Mine correctly noted. He says the following about evolution (which determines phylogeny):

    I do not think ReMine’s comments have anything to do with common descent.

    And you The Pixie proved him correct by invoking one of evolutionary mechanisms to explain away examples that I gave you. And true to Darwinian logic, when you don’t have an answer you are ready to invoke some fictional future discovery, not understanding that data available now question grand evolutionary claims in principle.

    Ah, you demand omniscience from science, anything less and the theory must be rejected. Do you demand the same from ID? Would you reject ID if, say, it could not say if life started 4 billion years ago or 6000?

    And still no diagram of common descent giving something other than a nested hierarchy.

  73. Hi The Pixie,

    The diagram with reptile to mammal evolution is not arbitary. From the fossil record, reptiles appeared, then mammal-like reptiles, then reptile-like mammals, then mammals. My diagram reflects that. Also, please note that mammal-like reptiles are more like reptiles than mammals, so are nearer to the reptiles, while the reptile-like mammals are more mammal like. What we are seeing is transitionals. Also, I am supposing mammals descended from reptile-like mammals rather than other reptiles, because again mammals more closely resemble the reptile-like mammals. So no, not arbitrary.

    You are not even wrong!

    The ease with which this arbitrary adjustment could occur was illustrated two decades ago, when the reality of the ‘mammal-bird,’ a hypothetical common ancestor of birds and mammals, was a contentious issue in modern systematics. You can read more about it in Benton, Mike. 1984. Is a Dog More Like a Lizard or a Chicken? New Scientist 103:18-19.

    In this light ReMine comment is relevant to the issue. It shows that CD + NH is not falsifiable.

    The view that living things in all the major kingdoms are modified descendants of a common ancestor (described in the pattern of a branching tree) has been challenged in recent years by discrepancies in the molecular evidence (e.g. differences in relatedness inferred from sequence studies of different proteins) previously thought to support that view.

    See scientific evidence here starting from page 9

    Any set of objects, whether or not they originated in an evolutionary process, can be classified hierarchically. Chairs, for instance, are independently created; they are not generated by an evolutionary process: but any given list of chairs could be classified hierarchically, perhaps by dividing them first according to whether or not they were made of wood, then according to their colour, by date of manufacture, and so on. The fact that life can be classified hierarchically is not, in itself, an argument for evolution.

    Above quote stolen from Mark Ridley: The Problems of Evolution. Oxford University Press, New York 1985

  74. Hi The Pixie,
    The diagram with reptile to mammal evolution is not arbitary. From the fossil record, reptiles appeared, then mammal-like reptiles, then reptile-like mammals, then mammals. My diagram reflects that. Also, please note that mammal-like reptiles are more like reptiles than mammals, so are nearer to the reptiles, while the reptile-like mammals are more mammal like. What we are seeing is transitionals. Also, I am supposing mammals descended from reptile-like mammals rather than other reptiles, because again mammals more closely resemble the reptile-like mammals. So no, not arbitrary.
    You are not even wrong!

    The ease with which this arbitrary adjustment could occur was illustrated two decades ago, when the reality of the ‘mammal-bird,’ a hypothetical common ancestor of birds and mammals, was a contentious issue in modern systematics. You can read more about it in Benton, Mike. 1984. Is a Dog More Like a Lizard or a Chicken? New Scientist 103:18-19.

    Sure, there are contentious issues in the details, but the basics were laid down before Darwin. I would be interested to read what Benton said; do you have a link?

    In this light ReMine comment is relevant to the issue. It shows that CD + NH is not falsifiable.

    No it does not. See, I can make unsupported assertions just as well as you. You think ReMine supports your case, explain why.

    The view that living things in all the major kingdoms are modified descendants of a common ancestor (described in the pattern of a branching tree) has been challenged in recent years by discrepancies in the molecular evidence (e.g. differences in relatedness inferred from sequence studies of different proteins) previously thought to support that view.

    The molecular evidence is due to random mutations. Nevertheless it is good enough for Sal to describe it as a “jewel of perfection”, and ReMine holds up this perfection as a message from God, as I understand it (based on what Sal has said at ARN).

    Above quote stolen from Mark Ridley: The Problems of Evolution. Oxford University Press, New York 1985

    It is stolen if you reproduce it without crediting the author or linking to the source. What you are doing here is called “citing”.

    Still cannot find that one example of common descent but no nested hierachy, eh? Are you beginning to wonder yet if it is possible?

  75. Hi The Pixie,

    Still cannot find that one example of common descent but no nested hierachy (sic), eh? Are you beginning to wonder yet if it is possible?

    Thankfully, I know it is impossible not to be possible. Hence I and JoeG gave you examples that you simply ignore or wave off. But hey there is more here showing contradictory evolutionary diagrams and you can choose any chimeric or mosaic creature in the fossil record, it will show you full extent of your not even wrong claim.

    I am just wondering if you are ignoring our examples because you know it is impossible to refute your claim or because Dr. Theobald told you so?

  76. the Pixie:
    Scientists have a pretty good idea of when life appeared, and when individual species appeared.

    Nope- all they have is speculation based on an assumption.

    the Pixie:
    Where do you get that from? Of course evolution predicts branching. Surely if you must accept that branching occurs during microevolution!

    That is false. All Common Descent predicts is a linear pattern. Nothing to say that one part of a population will diverge from another. And evolution just “predicts” change or stasis. That’s it. Common Descent would be just fine if one population evolved and left nothing behind to diverge from.

    I know that branching occurs. I also know what a prediction is. Neither Common Descent nor the MET predicts branching.

    And one more time-

    We start with a population that has traits WXYZ. That “evolves” into a population with traits WXYZa.

    So we have:

    WXYZ
    |
    WXYZa (then a gets lost)
    |
    WXYZ (then Z gets lost)
    |
    WXY (then a reappears)
    |
    WXYa (then Z reappears)
    |
    WXYZa

    So when we look at the populations we wouldn’t be able to determine what was descended from what.

    Did read the link that explains how hierarchy works?

    the Pixie:
    By convention we consider mammals to be separate to reptiles, but we are all descended from the first reptiles, so in a sense we are still reptiles.

    There isn’t any genetic or biological data that would demonstrate such a transformation is even possible, ie the premise is unscientific.

    As for specifics- no that isn’t a joke. Evolutionists have had a monopoly for decades and they hgaven’t provided anything- nothing, nada, zip, zilch.

    We do not know what makes a human a human or a chimp a chimp. We do not know whether or not any mechanism can do what believers of Common Descent require.

    reptiles
    |
    reptile-like mammals
    |
    mammal-like reptiles
    |
    reptile-like mammals
    |
    reptiles

    Common Descent without a resulting NH from that descent.

  77. We have populations A, B, C, D (possessing unique character traits 1 2 3 4 5 6 7)

    They are all nested under hypothetical population Z (acquired trait 1) with A & B being under hypothetical population X (acquired 2) and C & D being under hypothetical population Y (acquired 3). So draw Z diverging into X & Y with X diverging into A & B with Y diverging into C & D

    A B C D
    124 125 136 137

    Nice neat nested hierarchy.

    NH based on Common Descent depends on immutable characteristics. IOW there wasn’t anything preventing the following:

    A B C D
    124 24 36 137

    What happened to the nested hierarchy? (keep reading and feel free to sing along)

    Nah nah nah nah
    nah nah nah nah
    heeeeyyyyheyyyayyy goo-ood bye (to the argument that Common Descent predicts NH)

    Everybody join in-

    Nah nah nah nah
    nah nah nah nah
    Heeeyyyyheeeyyyayy go-ood bye

    You people in Kansas-

    Nah nah nah nah
    nah nah nah nah
    Heeeyyyyheeeyyyayy goo-ood bye

    the ACLU-

    Nah nah nah nah
    nah nah nah nah
    Heeeyyyyheeeyyyayy goo-ood bye

    Judge Jones III-

    Nah nah nah nah
    nah nah nah nah
    Heeeyyyyheeeyyyayy good bye

    (fade-their comin to take me away haha hoho heehee)

  78. Oops the formatting is a little off

    first run:
    A- 124
    B- 125
    C- 136
    D- 137

    second run:
    A- 124
    B- 25
    C- 36
    D- 137

  79. Credit to Denton Chapter 6 of “Evolution: A Theory in Crisis” pages 134-35 (I just fired my proof reader)

  80. JoeG, stop gloating! 😛

  81. Hi Inunison

    Thankfully, I know it is impossible not to be possible. Hence I and JoeG gave you examples that you simply ignore or wave off. But hey there is more here showing contradictory evolutionary diagrams and you can choose any chimeric or mosaic creature in the fossil record, it will show you full extent of your not even wrong claim.

    No, what this shows is that it can be difficult or even impossible to determine the tree of life (and therefore the true nested hierarchy), not that the nested hierarchy does not exist. Do you even understand the difference?

    You might like to look back at my post 45, the bit under the heading No Discernable Nested Hierarchy?, where I say “Despite the above, it could still be the case that the nested hierarchy cannot be reconstructed. It could be that changes are too frequent for long distance relationships to be established. The nested hierarchy still exists, but we cannot see it properly.”

  82. Joe G

    Well done! At last someone has had the gumption to try to prove me wrong. I was beginning to think you either suspected I was right or just had no clue how to do it. And all you had to do was look it up in Denton’s book, as I suggested way back in post 32, two weeks ago!

    We start with a population that has traits WXYZ. That “evolves” into a population with traits WXYZa.
    So we have:
    WXYZ
    |
    WXYZa (then a gets lost)
    |
    WXYZ (then Z gets lost)
    |
    WXY (then a reappears)
    |
    WXYa (then Z reappears)
    |
    WXYZa
    So when we look at the populations we wouldn’t be able to determine what was descended from what.
    Did read the link that explains how hierarchy works?

    The way the hierarchy works is that species earlier in time define larger groups. So there is the big group, defined by WXYZ(1), containing all the organisms. Nested inside that is a subgroup defined by WXYZa(1), which contains all the organisms except WXYZ(1). Nested inside that is the subgroup defined by WXYZ(2), which includes all the organisms descended from WXYZ(2) and WXYZ itself, and so on. You have six groups, each defined by one of the entries on your list above, each containing that organism and all those below it, and each neatly nested inside the grouping above. That is a nested hierarchy.

    Let me just anticipate two things. You might object that WXYZ(1) is the same as WXYZ(2). Well, it is not. The population of WXYZ(1) was made up of a group of individuals that lived before the individuals in the population of WXYZ(2). Even if we are talking about bacteria, and genetically they are identical, they are still not the same individuals; they exist at different times and places (just as twins are genetically identical, but two separate people). Furthermore, from the diagram it is clear that they have different evolutionary histories, despite the identical genome.

    The second objection might be that we cannot tell WXYZ(1) from WXYZ(2), and so cannot reconstruct the tree of life and the nested hierarchy. I accept that. I am not claiming the nested hierarchy can necessarily be reconstructed, as I just said to Inunison (and said prevously in post 45). What I am saying is that it is there, whether we can detect it or not.

    We have populations A, B, C, D (possessing unique character traits 1 2 3 4 5 6 7)
    They are all nested under hypothetical population Z (acquired trait 1) with A & B being under hypothetical population X (acquired 2) and C & D being under hypothetical population Y (acquired 3). So draw Z diverging into X & Y with X diverging into A & B with Y diverging into C & D
    A B C D
    124 125 136 137
    Nice neat nested hierarchy.
    NH based on Common Descent depends on immutable characteristics. IOW there wasn’t anything preventing the following:
    A B C D
    124 24 36 137
    What happened to the nested hierarchy?

    What has happened is that the hierarchy is identical. A and B still nest inside X, C and D still nest inside Y, A, B, C, D, X, and Y still nest inside Z. Nice neat nested hierarchy. Sure, the second run gives a nested hierarchy that is harder to reconstruct, but I am not claiming that the nested hierarchy can always be determined. Again, see that bit in my post 45.

    Good try, but perhaps the gloating was a bit premature. But do not be discouraged; have another go. Reread Denton, surely the answer is somewhere in there… Though of course Denton does now accept common descent, so maybe not.

  83. Research in ID and MET

    Joe, back in post 62 you asked about MET research. I found a few research groups looking at the very specific area of MET that is the chimp-human split, as you requested.

    Lars Feuk, Jeffrey R MacDonald, Terence Tang, Andrew R Carson, Martin Li, Girish Rao, Razi Khaja, and Stephen W Scherer have an article published, from the abstract:

    With a draft genome-sequence assembly for the chimpanzee available, it is now possible to perform genome-wide analyses to identify, at a submicroscopic level, structural rearrangements that have occurred between chimpanzees and humans.

    Nick Patterson, Daniel J. Richter, Sante Gnerre, Eric S. Lander and David Reich at Harvard and MIT have an article published, from the abstract:

    The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human–chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human–chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.

    In Germany, there is the Max Planck Institute for Evolutionary Anthropology. From the web site:

    The Institute unites scientists with various backgrounds (natural sciences and humanities) whose aim is to investigate the history of humankind from an interdisciplinary perspective with the help of comparative analyses of genes, cultures, cognitive abilities, languages and social systems of past and present human populations as well as those of primates closely related to human beings.

    Led by Svante Po?o?bo, the Department of Evolutionary Genetics studies the genetic history of humans, apes and other organisms. We are interested both in the forces that affect the genome directly, such as mutation and recombination, and in the effects of selection and population history.
    The Department of Human Evolution, led by Jean-Jacques Hublin, primarily studies fossil hominids and aims at reconstructing their biology, behavior and cultural evolution. The department is interdisciplinary with three areas represented: Palaeoanthropologists, who study fossil material with a special emphasize on the use of 3D imaging to assess phylogenetic reconstructions, brain development and analysis of the growth processes. Archaeological scientists, who undertake biochemical analyses of fossils to study dietary adaptations and migrations, as well as dating the ages of sites and fossils. And, Palaeolithic archaeologists who study the cultural adaptation of hominids to their environment. The three groups are involved in the development of international field projects.

    See also here:

    The Human Evolution Research Center (HERC), at the University of California Berkeley, is dedicated to the study of human origins and evolution. HERC represents an international focal point for field and laboratory research and education. It is a center for the study of the process and products of human evolution.

    See also here:

    The Institute of Human Origins (IHO) conducts, interprets and publicizes scientific research on the human career. IHO’s unique approach brings together scientists from diverse disciplines to develop integrated, bio-behavioral investigations of human evolution. Through research, education, and the sponsorship of scholarly interaction, IHO advances scientific understanding of our origins and its contemporary relevance. Combining interdisciplinary expertise and targeted funding, IHO fosters the pursuit of integrated solutions to the most important questions regarding the course, cause and timing of events in human evolution.

    See also here:

    The Center for Human Evolutionary Studies (CHES) at Rutgers, The State University of New Jersey, constitutes one of the world’s leading research, teaching, and training programs in the study of the evolution of human behavior.

    Our strengths lie in our multidisciplinary approach to this study, our world-class faculty and research associates, and our highly competitive graduate and undergraduate students, including a number of foreign students from the countries in which some of our research projects are based.

    We also enjoy access to some of the world’s premier localities for the study of our closest living primate relatives, and for the investigation of the fossilized remains and archaeological traces of our early human ancestors.

    A Goggle search of academic websites mentioning human evolution (site:edu “human evolution”), gave over 300,000 hits! So yes, there are a few research groups actively involved in research into the chimp-human split, nevermind the rest of MET. And you found four ID researchers?

    IDists researching for ID support- Minnich, Behe, Axe, Gonzalez, just to name 4 right off the top of my head.
    Scott Minnich’s home page

    Research Interests:

    Selected Publications :
    V. Kapatral , J. W. Campbell, S. A. Minnich, N. R. Thomson, P.
    Matsumura and B. M. Pruess. 2004. Gene array analysis of Yersinia
    enterocolitica FlhD and FlhC: regulation of enzymes affecting
    synthesis and degradation of carbamoylphosphate.
    Microbiology 150: p. 2289-2300.

    Monday S.R., Minnich S.A., Feng PC. 2004. A 12-base-pair deletion in
    the flagellar master control gene flhC causes nonmotility of the
    pathogenic German sorbitol-fermenting Escherichia coli O157:H-
    strains.
    J Bacteriol. 186:2319-27.

    Yoon J.W., Minnich S.A., Ahn J.S., Park Y.H., Paszczynski A., Hovde
    C.J. 2004. Thermoregulation of the Escherichia coli O157:H7 pO157 ecf
    operon and lipid A myristoyl transferase activity involves
    intrinsically curved DNA.
    Mol. Microbiol. 51:419-35.

    Ely B., Ely T.W, Crymes W.B. Jr, Minnich S.A. 2000. A family of six
    flagellin genes contributes to the Caulobacter crescentus flagellar
    filament.
    J. Bacteriol. 182:5001-4.

    Rohde J.R., Luan X.S., Rohde H., Fox J.M., Minnich S.A. 1999. The
    Yersinia enterocolitica pYV virulence plasmid contains multiple
    intrinsic DNA bends which melt at 37 degrees C.
    J Bacteriol 181:4198-204

    You will have to explain to me how these are ID research. Again, I see no sign of intelligence or design.

    Here is a review (by an MET supporter) of Behe’s research output from 1994 to 2004.

    Examination of Behe’s homepage at Lehigh indicates no new paper since 1998 (though he seems to have had time to include a link to the recently formed ISCID). While it is no sin for an academic not to have an up-to-date webpage, it is becoming increasingly unusual for scientific researchers not to make reprints and preprints freely available online. That being said let’s look elsewhere ”
    According to PubMed, since 1994, Behe has published five papers, none of which appear to have any relevence to his career as an ID theorist;

    Behe’s faculty home page is here, and has been updated to 2005, and he does have things published that actually mention intelligent design. Whether he has actually done research or is just reviewing what other people have said I do not know. These are two book chapters, published in 2003:

    Behe, M.J. 2003. “Design in the Details: The Origin of Biomolecular Machines.” In Darwinism, Design & Public Education, Campbell, J.A. and Meyer, S.C. eds., Michigan State University Press, pp. 287-302.

    Behe, M.J. 2003. “The Modern Intelligent Design Hypothesis: Breaking Rules.” In God and Design: The Teleological Argument and Modern Science , Neil Manson, ed., Routledge, pp. 277-291.

    Has anyone read them? Is there any experimental detail in there?

    I hope I got the right Gonzalez; Guillermo, an astrophysicist at the Iowa State University. If so, here is the university web page about him.

    Research Interests: Dr. Gonzalez is primarily interested in studying the late stages of stellar evolution through the use of spectroscopic observations. Recent work includes spectroscopic abundance analysis of post-AGB supergiants and RV Tau variables. He has also undertaken a study of the parent stars of the recently discovered extra-solar planetary systems. The results indicate that these stars have anomalous chemical abundances, suggesting some sort of unusual formation history.

    That does not sound like ID research either!

    With regards to Axe, I found this (by IDists):

    Axe’s Paper 1:
    “Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors” Journal of Molecular Biology, vol 301, p 585.
    What it reports: “Inducing multiple mutations in a bacterial enzyme causes it to lose its ability to perform its role as an antibiotic disabler.” Because such mutations destroy “the possibility of any functioning” in the enzyme, it could not have arisen via “Darwinian pathways” (William Dembski, from Debating Design: From Darwin to DNA, Cambridge University Press, p 327).
    Axe’s Paper 2:
    “Estimating the prevalence of protein sequences adopting functional enzyme folds” Journal of Molecular Biology, vol 341, p 1295.
    What it reports: “Calculates the probability that a random sequence of amino acids will result in the folded shape that a protein needs to function as an enzyme.” The probability of creating a functioning protein fold “at random” is very low, making “appeals to chance absurd, even granting the duration of the entire universe” (Stephen Meyer, Proceedings of the Biological Society of Washington, vol 117, p 213).

    Again, no intelligence, no design. Sure, an argument against evolution, but ID is not anti-evolution.

    So where is the ID research? I was thinking of insisting that you find me researchers working on a specific aspect of ID, as you did for me, insisting I find people researching specifically the human-chimp split. But it looks like you will have enough of a job finding actual real research for ID at all!

  84. the Pixie:
    What has happened is that the hierarchy is identical.

    Only if one doesn’t understand nested hierarchy, which it appears you do not.

    The Pixie:
    A and B still nest inside X, C and D still nest inside Y, A, B, C, D, X, and Y still nest inside Z.

    Umm on the second run B would not even be considered part of Z! And neither would C!

    the Pixie:
    Sure, the second run gives a nested hierarchy that is harder to reconstruct, but I am not claiming that the nested hierarchy can always be determined.

    THAT is the WHOLE point! If nested hierarchy can’t always be determined and Common Descent is OK with that then NH is NOT a prediction of Common Descent!

    And one more time- just because someone accepts Common Descent does NOT mean that it predicts nested hierarchy!

    People can accept Common Descent without NH because they understand Common Descent does NOT predict NH- that is it can live with it or without it.

    and the following is just nonsense:

    the Pixie:
    You might object that WXYZ(1) is the same as WXYZ(2). Well, it is not. The population of WXYZ(1) was made up of a group of individuals that lived before the individuals in the population of WXYZ(2).

    Umm if both populations were still around we wouldn’t be able to tell which came first. Especially if there wasn’t any fossil evidence or the only fossils were of the teeth, which remained the same.

  85. To finish with NH- in comment 77 we have populations A B C D. Now in the second run pops B & C lose characteristic trait 1. Now without any first-hand/ direct observation of this Cladists would group pops B & C outside of pop Z, not nested under it.

  86. With a draft genome-sequence assembly for the chimpanzee available, it is now possible to perform genome-wide analyses to identify, at a submicroscopic level, structural rearrangements that have occurred between chimpanzees and humans.

    This assumes the MET, ie Common Descent is real. Also to be indicative of the MET is has to talk about the mechanism- culled genetic accidents.

    The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human–chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human–chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.

    Ditto- it assumes that the divergence occurred. It does not verify that such a transformation is possible.

    The Human Evolution Research Center (HERC), at the University of California Berkeley, is dedicated to the study of human origins and evolution. HERC represents an international focal point for field and laboratory research and education. It is a center for the study of the process and products of human evolution.

    What are they doing? We still don’t know what makes a chimp a chimp or a human a human.

    And again- the debate at this time is just about being able to conduct SCIENTIFIC research and draw a design inference IF that is what the data affords.

    And nothing in what you posted states anything about a mechanism. And in a debate about mechanisms that is a key element. You do realize that if something was designed to evolve that is ID…

    Nice try and better luck next time.

  87. Hi The Pixie,

    No, what this shows is that it can be difficult or even impossible to determine the tree of life (and therefore the true nested hierarchy), not that the nested hierarchy does not exist. Do you even understand the difference?

    The Pixie, if it is impossible to determine true nested hierarchy what makes you believe it exists? However I think nested hierarchy is evident but does not provide evidence for common descent because it is always arbitrary.

    What I am saying is that it is there, whether we can detect it or not.

    I admire your faith The Pixie.

  88. Joe’s problem is that he doesn’t actually know what constitutes a nested hierarchy. We agreed to a definition based in sets, A nested hierarchy is an ordered set such that each subset is strictly contained within its superset.“, but Joe’s knowledge Set Theory is somewhat limited, even though I do think he has an intuitive understanding.

    This was the outline of the argument I have repeatedly attempted to make with Joe.
    1. Nature of sets.
    2. Nature of nested hierarchy.
    3. Taxonomy based on independently derived characteristics.

    And only then attempt to study the particulars of biology. However, we could never get past step 1.

    A nested hierarchy pattern *of hereditary relationships* is the expected result of descent along uncrossed lines. This is a mathematical truism whether or not it results in a discernable pattern of morphology or genomics. Joe needs to understand this basic concept.

  89. To reiterarte:

    first run:
    A- 124
    B- 125
    C- 136
    D- 137

    second run:
    A- 124
    B- 25
    C- 36
    D- 137

    All we have are populations A B C D to observe. XYZ were hypothetical/ alleged ancestral populations. Therefore it is obvious that in the second run population B would NOT be grouped together with A under X. The same goes for C and D under Y. And neither B nor C would be considered under Z.

    the Pixie:
    Well done! At last someone has had the gumption to try to prove me wrong. I was beginning to think you either suspected I was right or just had no clue how to do it.

    LoL!!! Denton’s book came out in 1985.

  90. JoeGfirst run:
    A- 124
    B- 125
    C- 136
    D- 137

    second run:
    A- 124
    B- 25
    C- 36
    D- 137

    Of course, if a third of a genome is mutated each generation, then any hierarchical pattern of hereditary relationships may not be discernable. Of course, as you actually constructed the sequence, you *know* that it is, in fact, a hereditary relationship.

    Now, you are using this extreme example to argue that a nested hierarchy of genomic pattern is not a prediction of common descent. I would be happy to discuss that issue in detail, but we need to make sure we understand the terms of the debate. In this case, the hereditary relationships of your example DO form a nested hierarchy — by design! — even though that relationship may not be apparent from examination of the end-points of that descent.

    So, for instance, a paternal family tree is a nested hierarchy, as are the twigs of a typical tree grouped by branch, though it may not be readily discernable by merely examining the sons or twigs.

  91. Umm on the second run B would not even be considered part of Z! And neither would C!

    Of course they would. They both have Z as an ancestor!

    Pix: Sure, the second run gives a nested hierarchy that is harder to reconstruct, but I am not claiming that the nested hierarchy can always be determined.
    Joe: THAT is the WHOLE point! If nested hierarchy can’t always be determined and Common Descent is OK with that then NH is NOT a prediction of Common Descent!

    Hmm, so how come you did not say anything when I pointed this out before, in particular post 45? Sounds almost as though you only just thought of it…

    and the following is just nonsense:

    But you cannot explain why. Wonder why.

    And nothing in what you posted states anything about a mechanism. And in a debate about mechanisms that is a key element. You do realize that if something was designed to evolve that is ID”
    Nice try and better luck next time.

    You claimed there were no people investigating the split between chimps and humans. When I find several research groups doing just that, you naturally change the goal posts.

  92. Hi Inunison

    The Pixie, if it is impossible to determine true nested hierarchy what makes you believe it exists? However I think nested hierarchy is evident but does not provide evidence for common descent because it is always arbitrary.

    This confuses three arguments.
    * I have been claiming that any pattern of common descent must necessarily lead to a nested hierarchy, whether the hierarchy can be reconstructed or not.
    * I believe that broadly the nested hierarchy of life has been determined, and is well-supported by both morphology (as originally done by Linnaeus, before Darwin) and by the molecular evidence, even though there are some discrepancies
    * I believe the nested hierarchy is not arbitrary, that the currently accepted hierarchy is well supported as the correct one and statistical testing has confirmed this.

  93. So if you guys are claiming that the nested hierarchy is not necessarily discernnable, does that mean you agree with me that it is necessarily present in any hypothetical common descent scenario, even if we cannnot always detect it? Somehow, I doubt anyone will want to comment on that. No one wants to agree with the atheist, but if you disagree, you are back to square one. But we shall see.

    With regards to whether my position supports MET, consider a forensic scientist investigating a murder. The forensic scientist suspects the victim died from a gunshot wound. This hypothesis makes the necessary prediction that there is a bullet somewhere that passed through the victim. Note, the hypothesis predicts the existence of the bullet, not that the bullet will be found. Finding the bullet supports the hypothesis.

    Any one here familiar with the Java programming language? Java is object-orientated, and – like evolution — the class structure has a single common ancestor, java.lang.Object, and all Java classes are descended from this one.

    Also like evolution, Java only allows single inheritance, that is each class has one and only one immediate superclass, from which it inherits. A section of the class tree can be seen here (which has the top of the tree to the left!). So at the top there is java.lang.Object, which has many subclasses including java.awt.Component, from which we get java.awt.Container, then javax.swing.JComponent and javax.swing.JLabel. Each of these defines a nested group. javax.swing.JComponent has numerous classes below it, all of which nest inside javax.swing.JComponent’s super class, java.awt.Component. No one has designed the Java class structure to be a nested hierarchy, that is a necessary consequence of inheritance from a single ancestor, with each node having exactly one parent.

    In contrast, C++ allows multiple inheritance; each class can have multiple parents. In C++ a nested hierarch is not predicted.

  94. So if you guys are claiming that the nested hierarchy is not necessarily discernnable, does that mean you agree with me that it is necessarily present in any hypothetical common descent scenario, even if we cannnot always detect it? Somehow, I doubt anyone will want to comment on that. No one wants to agree with the atheist, but if you disagree, you are back to square one. But we shall see.

    =================================================

    With regards to whether my position supports MET, consider a forensic scientist investigating a murder. The forensic scientist suspects the victim died from a gunshot wound. This hypothesis makes the necessary prediction that there is a bullet somewhere that passed through the victim. Note, the hypothesis predicts the existence of the bullet, not that the bullet will be found. Finding the bullet supports the hypothesis.

    =================================================

    Any one here familiar with the Java programming language? Java is object-orientated, and – like evolution — the class structure has a single common ancestor, java.lang.Object, and all Java classes are descended from this one.

    Also like evolution, Java only allows single inheritance, that is each class has one and only one immediate superclass, from which it inherits. A section of the class tree can be seen here (which has the top of the tree to the left!). So at the top there is java.lang.Object, which has many subclasses including java.awt.Component, from which we get java.awt.Container, then javax.swing.JComponent and javax.swing.JLabel. Each of these defines a nested group. javax.swing.JComponent has numerous classes below it, all of which nest inside javax.swing.JComponent’s super class, java.awt.Component. No one has designed the Java class structure to be a nested hierarchy, that is a necessary consequence of inheritance from a single ancestor, with each node having exactly one parent.

    In contrast, C++ allows multiple inheritance; each class can have multiple parents. In C++ a nested hierarch is not predicted.

  95. So if you guys are claiming that the nested hierarchy is not necessarily discernnable, does that mean you agree with me that it is necessarily present in any hypothetical common descent scenario, even if we cannnot always detect it? Somehow, I doubt anyone will want to comment on that. No one wants to agree with the atheist, but if you disagree, you are back to square one. But we shall see.

    *

    With regards to whether my position supports MET, consider a forensic scientist investigating a murder. The forensic scientist suspects the victim died from a gunshot wound. This hypothesis makes the necessary prediction that there is a bullet somewhere that passed through the victim. Note, the hypothesis predicts the existence of the bullet, not that the bullet will be found. Finding the bullet supports the hypothesis.

    *

    Any one here familiar with the Java programming language? Java is object-orientated, and – like evolution — the class structure has a single common ancestor, java.lang.Object, and all Java classes are descended from this one.

    Also like evolution, Java only allows single inheritance, that is each class has one and only one immediate superclass, from which it inherits. A section of the class tree can be seen here (which has the top of the tree to the left!). So at the top there is java.lang.Object, which has many subclasses including java.awt.Component, from which we get java.awt.Container, then javax.swing.JComponent and javax.swing.JLabel. Each of these defines a nested group. javax.swing.JComponent has numerous classes below it, all of which nest inside javax.swing.JComponent’s super class, java.awt.Component. No one has designed the Java class structure to be a nested hierarchy, that is a necessary consequence of inheritance from a single ancestor, with each node having exactly one parent.

    In contrast, C++ allows multiple inheritance; each class can have multiple parents. In C++ a nested hierarch is not predicted.

  96. So who thinks the NH must be there, even even we cannot see it?

    So if you guys are claiming that the nested hierarchy is not necessarily discernnable, does that mean you agree with me that it is necessarily present in any hypothetical common descent scenario, even if we cannnot always detect it? Somehow, I doubt anyone will want to comment on that. No one wants to agree with the atheist, but if you disagree, you are back to square one. But we shall see.

    An analogy from forensic science

    With regards to whether my position supports MET, consider a forensic scientist investigating a murder. The forensic scientist suspects the victim died from a gunshot wound. This hypothesis makes the necessary prediction that there is a bullet somewhere that passed through the victim. Note, the hypothesis predicts the existence of the bullet, not that the bullet will be found. Finding the bullet supports the hypothesis.

    Common descent in Java

    Any one here familiar with the Java programming language? Java is object-orientated, and – like evolution — the class structure has a single common ancestor, java.lang.Object, and all Java classes are descended from this one.

    Also like evolution, Java only allows single inheritance, that is each class has one and only one immediate superclass, from which it inherits. A section of the class tree can be seen here (which has the top of the tree to the left!). So at the top there is java.lang.Object, which has many subclasses including java.awt.Component, from which we get java.awt.Container, then javax.swing.JComponent and javax.swing.JLabel. Each of these defines a nested group. javax.swing.JComponent has numerous classes below it, all of which nest inside javax.swing.JComponent’s super class, java.awt.Component. No one has designed the Java class structure to be a nested hierarchy, that is a necessary consequence of inheritance from a single ancestor, with each node having exactly one parent.

    In contrast, C++ allows multiple inheritance; each class can have multiple parents. In C++ a nested hierarch is not predicted.

  97. Umm on the second run B would not even be considered part of Z! And neither would C!

    the Pixie:
    Of course they would. They both have Z as an ancestor!

    Yes they would but we wouldn’t have any way to make that determination (XYZ are no longer around). To us A would not have any relation to B and B would be placed in a clad outside of Z. The same goes for C.

    Pix: Sure, the second run gives a nested hierarchy that is harder to reconstruct, but I am not claiming that the nested hierarchy can always be determined.

    Joe: THAT is the WHOLE point! If nested hierarchy can’t always be determined and Common Descent is OK with that then NH is NOT a prediction of Common Descent!

    the Pixie:
    Hmm, so how come you did not say anything when I pointed this out before, in particular post 45? Sounds almost as though you only just thought of it”

    I have pointed it out so many times in my life I can’t keep track. And if you pointed it out before then why are you still arguing about it?

    As for grandparents, parents, children etec- that does not form a nested hierarchy. Why? Because it does NOT conform to the rules of hierarchy. The rules I linked to.

    and the following is just nonsense:

    the Pixie:
    But you cannot explain why. Wonder why.

    I did explain:

    Umm if both populations were still around we wouldn’t be able to tell which came first. Especially if there wasn’t any fossil evidence or the only fossils were of the teeth, which remained the same.

    Try to follow along.

    the Pixie:
    You claimed there were no people investigating the split between chimps and humans.

    Now how about any scientists researching the premise that chimps and humans shared a common ancestor?

    From what you posted all anyone is doing is to assume the split occurred, observe what’s left and make their speculation. No one is looking into whether or not such a transformation is even possible. Please take what I post in context. Thanks.

  98. the Pixie:
    I have been claiming that any pattern of common descent must necessarily lead to a nested hierarchy, whether the hierarchy can be reconstructed or not.

    That is almost too funny. The sad part is you really mean it.

    Too bad that Denton refuted this premise over 20 years ago- see my example above in 77.

  99. So who thinks the NH must be there, even even we cannot see it?

    So if you guys are claiming that the nested hierarchy is not necessarily discernnable, does that mean you agree with me that it is necessarily present in any hypothetical common descent scenario, even if we cannnot always detect it? Somehow, I doubt anyone will want to comment on that. No one wants to agree with the atheist, but if you disagree, you are back to square one. But we shall see.

  100. An analogy from forensic science

    With regards to whether my position supports MET, consider a forensic scientist investigating a murder. The forensic scientist suspects the victim died from a gunshot wound. This hypothesis makes the necessary prediction that there is a bullet somewhere that passed through the victim. Note, the hypothesis predicts the existence of the bullet, not that the bullet will be found. Finding the bullet supports the hypothesis.

  101. Common descent in Java

    Any one here familiar with the Java programming language? Java is object-orientated, and – like evolution — the class structure has a single common ancestor, java.lang.Object, and all Java classes are descended from this one.

    Also like evolution, Java only allows single inheritance, that is each class has one and only one immediate superclass, from which it inherits. A section of the class tree can be seen here (which has the top of the tree to the left!). So at the top there is java.lang.Object, which has many subclasses including java.awt.Component, from which we get java.awt.Container, then javax.swing.JComponent and javax.swing.JLabel. Each of these defines a nested group. javax.swing.JComponent has numerous classes below it, all of which nest inside javax.swing.JComponent’s super class, java.awt.Component. No one has designed the Java class structure to be a nested hierarchy, that is a necessary consequence of inheritance from a single ancestor, with each node having exactly one parent.

    In contrast, C++ allows multiple inheritance; each class can have multiple parents. In C++ a nested hierarch is not predicted.

  102. Well it looks like Joe pre-emptied my comment in post 93.

    Pix: I have been claiming that any pattern of common descent must necessarily lead to a nested hierarchy, whether the hierarchy can be reconstructed or not.
    Joe: That is almost too funny. The sad part is you really mean it.
    Too bad that Denton refuted this premise over 20 years ago- see my example above in 77.

    So Joe really is claiming that there is some pattern of common descent that does not lead to a nested hierarchy, and he is not just talking about whether it can be reconstructed or not. So the challenge is still out there, Joe. Show me that one example. The Z->X,Y->A,B,C,D one fails because the nested hierarchy is still there, it just cannot be reconstructed.

  103. Hi The Pixie,

    Sorry but your posts #81 and #90 taken together make no sense to me. As JoeG put it, if nested hierarchy can’t always be determined and Common Descent is OK with that then NH is NOT a prediction of Common Descent!

    …you agree with me that it is necessarily present in any hypothetical common descent scenario, even if we cannnot (sic) always detect it?

    But this does not follow, if you cannot detect it how is it necessarily present? Your analogy does not apply as we know exactly how the bullet wound look like. Finding the bullet is a nice bonus. Unless you are saying that nested hierarchy determines common descent.

    You should be aware that:

    1. relationships based on molecules are
    often different from those based on anatomy

    2. and relationships based on one molecule may be
    different from those based on other molecules

    3.even worse, different analysis of the same molecule
    may produce different relationships

    So again, the inconsistencies in relationships that are based on molecular comparisons must be explained away to reconcile the data with common ancestry. They do not provide evidence for common ancestry.

    So how is nested hierarchy not arbitrary?

  104. the Pixie:
    So who thinks the NH must be there, even even we cannot see it?

    No one should expect NH from Common Descent. And that is for all the reasons provided by Denton.

    the Pixie:
    The Z->X,Y->A,B,C,D one fails because the nested hierarchy is still there, it just cannot be reconstructed.

    That is false. The nested hierarchy is not there. It cannot be reconstructed because it isn’t there. Z is a hypothetical ancestor. If B does not have trait 1 then there would be no reason to think it evolved from population Z. One would think it evolved from some population prior to Z. Only if one had direct observation of the divergence could one properly catergoize the populations. But the rules of hierarchy would have to be thrown out first.

    That is like saying if verts gave rise to inverts, inverts would still be nested under verts. And that doesn’t make any sense at all.

    the Pixie:
    With regards to whether my position supports MET, consider a forensic scientist investigating a murder.

    That is wrong. Forensic scientists determine murder or not (and perhaps the method). Dectives do the investigating.

    the Pixie:
    The forensic scientist suspects the victim died from a gunshot wound.

    There would be evidence of such a wound. Evidence that can be observed and investigated. But even that evidence is not evidence for a murder.

    What type of bullet? What if the perp used an ice bullet?

    Let’s say someone is murdered by someone intentionaly dropping a 5 lb block of ice from 20 stories. No one sees it happen. When someone does show up all they see is a dead person with a crushed skull and a little bit of water around the area. If it is raining they (forensics) are out of luck.

  105. inunison: if nested hierarchy can’t always be determined and Common Descent is OK with that then NH is NOT a prediction of Common Descent!

    You are confusing two related statements. The nested hierarchy is the inevitable outcome of heredity along uncrossed lines, such as the twigs and branches of a typical tree. Whether this creates a nested hierarchy pattern of morphology is another question entirely. For instance, if differential morphological traits are not inherited, then the nested hierarchy of heredity (perhaps from careful observation of each generation) would still exist.

    Consider a tree with its limbs, branches and twigs. From the definition of a nested hierarchy, we can group the twigs into a nested hierarchy by association with their limbs and branches. However, the twigs may be identical in all other respects and we might be unable to reconstruct the original nested hierarchy if the twigs are cut from the tree. But it was still a nested hierarchy growth pattern.

    It is important to grasp this concept if you want to understand why the vast majority of biologists and geneticists consider the nested hierarchy to be such important evidence of common descent.

  106. Zachriel:
    Joe’s problem is that he doesn’t actually know what constitutes a nested hierarchy.

    Zachriel’s problem is that he doesn’t actually know what constitutes a nested hierarchy. Even after I posted all the rules of NH he is still clueless.

    Zachriel:
    A nested hierarchy pattern *of hereditary relationships* is the expected result of descent along uncrossed lines.

    That is not so. And all you did was to copy what Wiki stated and change it a little. Too bad in Common Descent we can and do have crossed lines!

    Paternal family trees are NOT an example of NH. Paternal family trees are decided by “who’s your daddy?” which is not a characteristic trait.

    With a paternal family tree the sets are determined by ONE AND ONLY ONE criterion- “who’s your daddy?”

    Hierarchical levels: levels are populated by entities whose properties characterize the level in question.

    Note the word “properties”.

    Level of organization: this type of level fits into its hierarchy by virtue of set of definitions that lock the level in question to those above and below.

    Note the words “set of definitions”

    The ordering of levels: there are several criteria whereby other levels reside above lower levels.

    Note the words “several criteria”.

    Set theory and NH:
    When talking about set theory any sets and subsequent subsets, apart from nested hierarchy, you can have items from one set by included with items from another set on the same level.

    With set theory in general anything can be a set. Just put whatever you want in {} and you have a set. Or if you can’t find {} just declare what you want to be in a set. Then all subsets are just that set and/ or that set minus any number of items.

    For example with Zachriel’s paternal family tree I can make a set of {Sharif Hussein bin Ali, Abdul Ilah,Faisal}. A subset would then be {Sharif Hussein bin Ali, Failsal}. It is a valid set and it is a valid subset. However neither make sense in a nested hierarchy.

    In a nested hierarchy we can NOT have two sets on the same level that contain items that can exist in either set. Also all subsets must be strictly contained within the set above it.

    In nested hierarchy each set and each level are specifically defined by several criteria. This is done such that a person can pick an item from one set, hand it to another person, and from the specifications be able to replace the item in its original set.

    That is why when you are talking about nested hierarchy and someone tries to divert the attention to set theory they are up to nothing but deception.

    the rules that Zachriel and the Pixie are ignoring can be read HERE– for all those interested in reality…

  107. JoeGSo we have:

    WXYZ
    |
    WXYZa (then a gets lost)
    |
    WXYZ (then Z gets lost)
    |
    WXY (then a reappears)
    |
    WXYa (then Z reappears)
    |
    WXYZa

    So when we look at the populations we wouldn’t be able to determine what was descended from what.

    In your rather unlikely scenario, we would not be able to determine after the fact the pattern of descent, but because you actually watch it happen, you could. And if there was branching of uncrossed lineages, it would form a nested hierarchy — by definition. This is true regardless of what pecularities you think might occur to the sequences you have in mind. Of course, in biology, it is relatively easy to reconstruct many nested hierarchies, but we will get to that once you admit the distinction between a nested hierarchy of *heredity* (e.g. paternity, bacteria observed in a petri dish, branches on a tree), and a nested hierarchy inferred from morphological or genetic characteristics.

    You can use this simulation to experiment with nested hierarchies of heredity using letters.
    http://www.zachriel.com/nested/

  108. Twigs on a tree’s branch do not for a nested hierarchy. IOW one cannot take 20 twigs from different branches, hand them to someone else and have that person put them back on the proper branch. With a properly formatted NH one can take 20 populations and have someone put them back where they belong based on the definitions of that NH.

    Zachriel:
    It is important to grasp this concept if you want to understand why the vast majority of biologists and geneticists consider the nested hierarchy to be such important evidence of common descent.

    But the vast majority don’t consider NH to be importatnt evidence for Common Descent. I have looked in several university level biology books and nested hierarchy isn’t even mentioned!

    I would say the vast majority understand we should see a web or bush- neither which makes a nested hierarchy.

  109. Zachriel:
    In your rather unlikely scenario, we would not be able to determine after the fact the pattern of descent, but because you actually watch it happen, you could.

    The scenario isn’t unlikely. Also a pattern of descent should never be confused with the pattern of nested hierarchy.

    And again there isn’t anything in Common Descent that says the lines will remain uncrossed. Nothing, nada, zip, zilch. As a matter of fact we see trait reversals- it is an observed fact (trait reversals = crossed lines).

  110. A nested hierarchy is an ordered set such that each subset is strictly contained within its superset.

    Zachriel: A nested hierarchy pattern *of hereditary relationships* is the expected result of descent along uncrossed lines.

    JoeG: That is not so.

    Sure it is, JoeG. You can keep saying otherwise, but all you demonstrate is that you don’t know what a nested hierarchy is. The twigs on a tree form a nested hierarchy. If you don’t understand that, then try and refer back to the definition.

    JoeG: Too bad in Common Descent we can and do have crossed lines!

    That is sometimes true, but there is little point moving on to that aspect of the discussion when you keep misstating what constitutes the set-relation of a nested hierarchy.

    JoeG: “With a paternal family tree the sets are determined by ONE AND ONLY ONE criterion- ‘who’s your daddy?’

    Male descendency.

    JoeG: “For example with Zachriel’s paternal family tree I can make a set of {Sharif Hussein bin Ali, Abdul Ilah,Faisal}. A subset would then be {Sharif Hussein bin Ali, Failsal}. It is a valid set and it is a valid subset. However neither make sense in a nested hierarchy.

    Of course, you violated the rule you just stated. Here are the are properly constituted sets according to the rule of paternity. (“Sons” means male descendents of.)

    Sons of Abdullah = {Neyef, Talal, Hussein I, Muhammad, El Hassan, Abdullah, Ali, Faisal, Hashim, Hamzah}
    Sons of Talal = {Hussein I, Muhammad, El Hassan, Abdullah, Ali, Faisal, Hashim, Hamzah}
    Sons of Hussein I = {Abdullah, Ali, Faisal, Hashim, Hamzah}
    http://www.internationalspecialreports.com/middleeast/99/jordan/8-1.gif

    And so on. As each subset is a strictly contained within its superset, this constitutes a nested hierarchy according to the definition. We can’t necessarily reconstruct this nested hierarchy only by looking at the individuals. But we can by using your own rule: ‘Who’s your daddy?

  111. JoeG: “But the vast majority don’t consider NH to be importatnt evidence for Common Descent.

    Nested hierarchy is the general mathematical relationship. In biology, it’s called the phylogenetic tree, or cladistics. I would be happy to discuss the phylogenetic tree once you have grasped the basic concepts of a containment or nested hierarchy, and how we use independently derived traits to classify objects.

    JoeG: “Also a pattern of descent should never be confused with the pattern of nested hierarchy.

    That’s right. Not all descendent patterns form nested hierarchies. For instance, while a paternal family tree is necessarily a nested hierarchy, a complete family tree of a sexually reproducing organism does not. Such a descent represents a great many crossings between lineages.

  112. I will post these points as I have time:

    1) Paternal family trees are NOT based on independent observation. Therefore to even attempt to include them in any scientific discussion is deceptive at best.

    2) Paternal family trees relies on ONE and ONLY ONE dependent critereon.

    3) Did I mention that hierarchy requires multiple definitions?

    4) In the “tree of life” the lines MAY be drawn straight and neat, but “evolution” could take a route similar to that of the flight of the bumble-bee.

    5) In the “tree of life” all we have are the tips to examine. The lines, if filled in correctly, would be a series of populations, with every generation (and even every individual) capable of being a branching node.

    6) If we still had all those populations, imagine how many tips we would have and how messy that would be.

    Zachriel:
    The twigs on a tree form a nested hierarchy. If you don’t understand that, then try and refer back to the definition.

    The principles of hierarchy demonstrates that you are wrong. I will side with the accepted rules. But thank you for the entertainment. But the misunderstandings are all yours.

  113. Zachriel:
    … a complete family tree of a sexually reproducing organism does not. Such a descent represents a great many crossings between lineages.

    Does anyone else see the contradiction?

    We shouldn’t expect a nested hierarchy with sexually reproducing populations. Therefore Common Descent does not predict NH as there will be a great many crossings…

  114. 1. You continue to misues the term “nested hierarchy”. This is a term defined in terms of sets. Like all mathematics, it may be used in science, but is not science. Until you exhibit some understanding of how these terms are used, there is little point moving onto how we use independently derived traits to classify objects.

    2,3. The nested hierarchy is defined in terms of sets. Any well-defined rule of rules can be used to classify objects. In taxonomy, it is independently derived traits.

    4. Tree branches are not generally straight. They can often be quite tangled, as well.

    5. That would make for an interesting discussion. So please try to come to grips with the distinction between a nested hierarchy of hereditary relationships and a nested hierarchy derived from traits.

    6. That would make for an interesting discussion, but without a foundation in the mathematics of pattern you will not be able to understand how scientists sort through such issues.

  115. JoeG: We shouldn’t expect a nested hierarchy with sexually reproducing populations. Therefore Common Descent does not predict NH as there will be a great many crossings”

    A nested hierarchy is only expected with descent along uncrossed lines. As sexually reproducing populations have crossed lines, we would not expect a nested hierarchy. (However, the maternal and paternal lines do form nested hierarcies. This fact is often used in genealogical research.) And if populations diverge through a process of reproductive isolation, then they would form a nested hierarchy of descent. This is regardless of any possible morphological differences.

    The separate problem is taking the descendents and using morphological traits to try and determine the pattern of descent after the fact. Before taxonomy, we need to have a clear understanding of sets, and in particular, the nested hierarchy.

  116. And there is more:

    Pattern pluralism and the Tree of Life hypothesis

    Abstract: Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.

    (HT to ARN’s finest)

    Zachriel:
    You continue to misues the term “nested hierarchy” .

    Zachriel you are clueless and as such don’t get to tell anyone they misuse anything.

    Zachriel:
    The nested hierarchy is defined in terms of sets.

    A summary of the principles of hierarchy theory can be found by reading the article linked to. Obviously Zachriel, having an issue with reality, chooses to ignore those rules. Then he will use himself as a reference by just repeating what has already been refuted.

    Zachriel:
    A nested hierarchy is only expected with descent along uncrossed lines.

    Nested Hierarchy

    In fact, a nested hierarchy is the almost inevitable result of descent with modification, if no transfer of traits between branches of descent is possible.

    Not quite the same. And even though Wiki isn’t an authority they are more so than you are.

    And considering the original point concerns sexually reproducing organisms, therefore Common Descent does NOT predict a nested hierarchy- by YOUR words- any further discussion is nothing more than childish whining. Then again THAT is your forte…

  117. Did everyone get that?:

    This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation.

    It is a sad day when alleged anti-evolutionists have to show evolutionists what they support is not expected to produce what they insist it should.

    How are we supposed to tell them about ID when they can’t even grasp their position?

    Unfortunately I am sure more flailing will follow…

  118. I note you completely ignored my points about the distinction between constructing a nested hierarchy based on heredity or growth and one based on traits.

    EvoWiki: In fact, a nested hierarchy is the almost inevitable result of descent with modification, if no transfer of traits between branches of descent is possible.

    EvoWiki’s qualified statement is correct.

    Doolittle and Bapteste: …incorporation of prokaryotes into the TOL is especially problematic

    This is also a correct statement. Common Descent does not properly apply to the early evolutionary history of cellular life.

  119. JoeG quoting approvingly: This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms…

    Ok, then. That settles that.

  120. JoeG quoting approvingly: This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms”

    Zachriel:
    Ok, then. That settles that.

    What does that settle?

    EvoWiki: In fact, a nested hierarchy is the almost inevitable result of descent with modification, if no transfer of traits between branches of descent is possible.

    Zachriel:
    EvoWiki’s qualified statement is correct.

    Who qualified it? You? LoL!!!! Did you notice the “almost inevitable”- and even then it wouldn’t qualify under the rules provided.

    Doolittle and Bapteste which Joe G also approved: “incorporation of prokaryotes into the TOL is especially problematic

    Zachriel:
    This is also a correct statement. Common Descent does not properly apply to the early evolutionary history of cellular life.

    It is a good thing that the paper is about ALL organisms in the tree of life (TOL).

    Zachriel:
    I note you completely ignored my points about the distinction between constructing a nested hierarchy based on heredity or growth and one based on traits.

    At this stage I consider all of your points akin to Monty Python’s Black Knight wanting to continue the fight after already losing all of his limbs.

  121. I would wager that the majority of biologists and geneticists would agree with Doolittle and Bapteste.

    If Zachriel comes back for more his new nickname will be “Timex” (for obvious reasons)

  122. EvoWiki: In fact, a nested hierarchy is the almost inevitable result of descent with modification, if no transfer of traits between branches of descent is possible.

    Zachriel: EvoWiki’s qualified statement is correct.

    JoeG: Who qualified it? You? LoL!!!! Did you notice the “almost inevitable” – and even then it wouldn’t qualify under the rules provided.

    They qualified it because there are a variety of factors that might preclude a discernable phylogenetic tree. But again, you’re not up to that subject. You still claim that the branching pattern of a tree doesn’t constitute a nested hierarchy. There is no more fundamental example. Consequently, any argument that follows from your misunderstanding of the nested hierarchy is simply not supported.

    JoeG: It is a good thing that the paper is about ALL organisms in the tree of life (TOL).

    You cite an article from the peer literature. The authors clearly accept “evolutionary mechanisms” as an explanation for organic variation. They discuss that different evolutionary models are required to explain the divergence of different taxa, and point to prokaryotes in particular. We’ve discussed this many times before, but it’s as if you keep forgetting. Vertebrates evolved by divergence from a common ancestor, but there is substantial evidence that the original cellular life evolved by a process akin to endosymbiosis.

    I always find it amusing when you quote from scientists who directly contradict your claim.

    I know you’re not interested, but perhaps other are. Larry Moran a Professor of Biochemistry blogged on Three domain Hypothesis, The Three Domain Hypothesis is Dead.

    If anyone would like to discuss the phylogenetic tree who has a simple grasp of the nested hierarchy and how we use independently derived traits to classify objects, I would be happy to oblige.

  123. JoeG: I would wager that the majority of biologists and geneticists would agree with Doolittle and Bapteste.

    That is becoming the consensus view in biology. Most life is known to have evolved from common ancestors. However, as we have pushed back the veil on early evolution, it has been found that the original cellular life evolved by a complex process of endosymbiosis (and possibly other mechanisms). For instance, the genetic material in mitochondria have a strong resemblance to bacteria. But again, it is impossible to have a reasonable discussion of common descent, and where it applies, if you don’t understand the primary evidence. Google Scholar lists over 50,000 articles on the “phylogenetic tree”

  124. Zachriel:
    You still claim that the branching pattern of a tree doesn’t constitute a nested hierarchy.

    It doesn’t for the many reasons already provided. IOW it doesn’t follow the rules of hierarchy.

    That you keep trying to pass it off does say quite a bit about your dishonesty. I am sure it isn’t lost on the readers and participants of this blog.

    Zachriel:
    You cite an article from the peer literature. The authors clearly accept “evolutionary mechanisms” as an explanation for organic variation.

    And that is irrelevant. But it does support my claim that Common Descent and the MET can live with or without NH. But I wouldn’t expect you to understand that.

    Zachriel:
    Vertebrates evolved by divergence from a common ancestor,

    Unsupported speculation. And as far as I know at least most verts reproduce sexually.

    Zachriel:
    I always find it amusing when you quote from scientists who directly contradict your claim.

    And I always find it amusing that your inferences are always incorrect. IOW there isn’t anything that I quoted that contradicts anything that I have claimed. You are just twisted.

    And it is hilarious that you would speak about “independently derived traits” and yet use trees and paternal family trees as examples. You contradict yourself. You don’t need anyone else around.

    Also it is impossible having any discussion with you. That is because you aren’t interested in reality.

    And phylogenetic trees can exist in the absence of an overall nested hierarchy. As for “primary evidence” please wake me when you have some. As I have stated many times- all you can muster is speculation based on the assumption.

    BTW it hasn’t been found that original cellular life evolved by endosymbiosis- that is just speculation, and it remains untested- objectively. For all we know bacteria are the discards of euks- at least that is what one team of scientists has proposed…

  125. JoeG cites

    W. Ford Doolittle: Our research focuses on the evolution of genes and genomes.

    W. F. Doolittle’s Laboratory: For most of this lab’s thirty-year history, we’ve subscribed to the belief that nothing in biology makes sense except in the light of evolution.

    Doolittle is widely published and cited in scientific journals with titles that include the word “evolution”.

  126. I KNOW who Doolittle is. Also “evolution” isn’t being debated. And if Doolittle could substantiate his beliefs in Common Descent then we wouldn’t be having this debate.

    IOW I do NOT care what ANYONE accepts.

    I care about what they can scientifically substantiate. And I have told you that on many occasions.

    But that just helps confirm my point- that you just don’t listen.

    I show that scientists say that NH is NOT expected. And they do it in a peer-reviewed venue. THAT has been my point. IOW I am confirmed and you & the Pixie are refuted by someone you think is inferior.

    And now look at what you are relegated to.

    Zachriel is that WWII Japanese soldier on some very remote outpost still fighting after every one else has settled the matter.

  127. A nested hierarchy is an ordered set such that each subset is strictly contained within its superset.

    JoeG: And if Doolittle could substantiate his beliefs in Common Descent then we wouldn’t be having this debate.

    Geez, Joe. You’re the one who cited Doolittle. I checked into his research, and you simply don’t understand the meaning of the article you cited, or the import of his findings. Doolittle has determined through his own extensive research (which is also the consensus view of the biological community), that most taxa are related by common descent, but that common descent breaks down in the very early evolution of life.

    But you’re still stuck on trying to understand the nested hierarchy. The twigs on a tree constitute a nested hierarchy *defined* by their respective branches. A paternal family tree is a nested hierarchy *defined* by male descendents. Vertebrates form a nested hierarchy *defined* by morphological traits. On the other hand, motorized vehicles do not form a unique nested hierarchy based on independently derived traits.

  128. Just to move half-a-step ahead. Once you understand what constitutes a nested hierarchy, then we can discuss how we can classify objects by observed traits.

    Then-and-only-then can we have a reasonable discussion as to the *observation* of the nested hierarchy in most taxa and how we can use this observation to make strong predictions of new phenomena based on the Theory of Common Descent.

  129. Zachriel:
    A nested hierarchy is an ordered set such that each subset is strictly contained within its superset.

    Right- ordered by a specified set or sets of definitions. I never said, thought nor implied otherwise.

    YOU on the other hand, have difficulty comprehending ordered by a specified set or sets of definitions.

    I know I cited Doolittle. And this:

    Doolittle has determined through his own extensive research (which is also the consensus view of the biological community), that most taxa are related by common descent, but that common descent breaks down in the very early evolution of life.

    has NOTHING to do with why he was cited. He was cited not because of Common Descent but because of nested hierarchy. That is nested hierarchy is NOT expected in a Common Descent scenario.

    Zachriel:
    But you’re still stuck on trying to understand the nested hierarchy.

    Reality demonstrates that is and always has been YOUR problem. That is you just don’t know what the heck you are talking about.

    When faced with the data you just ignore it and repeat your mistakes as if that lends credence to them.

    Zachriel:
    The twigs on a tree constitute a nested hierarchy *defined* by their respective branches.

    That is close to imbecilic. And it is sad that you are serious.

    Is that it? Are you now looking for pity?

    Do you have kids that “mumble dogface in the onion patch”? (Steve Martin)

    And what you say about predictions is in contradiction to Denett and the NCSE- both support the premise that there is no way to predict what will be selected for at any point in time. And that is what one would expect from a process that can resemble the flight of a bumble-bee.

    Zachriel:
    Once you understand what constitutes a nested hierarchy, then we can discuss how we can classify objects by observed traits.

    I had been waiting for you to get to that point, but I got tired of waiting and refuted the premise without you.

    Zachriel:
    A paternal family tree is a nested hierarchy *defined* by male descendents.

    Since when is “who’s your daddy?” an independenly derived trait? And how can a paternal family tree be an example of NH when it violates the very principles of hierarchy? It can’t be!

    IOW only someone very dishonest or very stupid would continue to use that example in light of the fact that you have been made aware of the principles of hierarchy theory.

    Zachriel:
    Vertebrates form a nested hierarchy *defined* by morphological traits.

    Which was used as scientific evidence for Common Design until the intellectually bankrupt bullies of evolutionary dogma stole the concept. Then they stole genetics and natural selection. All they “added” was genetic accidents.

  130. Zachriel: A nested hierarchy is an ordered set such that each subset is strictly contained within its superset.

    JoeG: Right- ordered by a specified set or sets of definitions.

    Zachriel: The twigs on a tree constitute a nested hierarchy *defined* by their respective branches.

    JoeG: That is close to imbecilic. And it is sad that you are serious.

    It’s not that hard to figure out, JoeG. We will construct “specified sets”. Notice that each twig is attached to only a single immediate branch. And each branch is attached in only one way to its super-branch or limb. And each limb is attached in only one way to the trunk. We can group the twigs into sets and supersets by their respective branches. If you like, we can give the twigs names, like Abdullah, Ali, Faisal, Hashim and Hamzah, and the branch they attach to we can call Hussein I, the superbranch Talal, the limb Abdullah, and the trunk Sharif Hussein bin Ali. Other twigs and branches trace different paths to the trunk. It doesn’t really matter what we call them, but they group into strictly nested sets as defined by their respective branches. If we cut a branch, then any sub-branch or twig attached to that branch is cut off from the trunk.

    Compare to a spider’s web. If we cut an arbitrary strand, it will probably have little effect on the rest of the web. A spider’s web is not a nested hierarchy and each thread is connected to other threads in multiple ways.

    The tree is such an archetypical image of a nested hierarchy that I have trouble believing that you retain your position.

  131. Inunison

    For reference, I am replying here to your post 103.

    As JoeG put it, if nested hierarchy can’t always be determined and Common Descent is OK with that then NH is NOT a prediction of Common Descent!

    I am saying that any hypothetical “tree of life” that has a single common ancestor, and each species has a single parent species must always result in a nested hierarchy. I have repeatedly challenged you guys to find a single exception to that. Do you believe such an exceptin is possible, or are you saying that I am right, but your point is that a detectable nested hierarchy is not inevitable?

    So then we have the second issue, of whether this can be called a prediction if it is not necessarily detectable. What I mean by prediction here is whether the nested hierarchy is a necessary consequence that is actually, rather than a prophesy of what will be seen in the future. The nested hierarchy had already been detected before Darwin proposed common descent. No one is saying that Darwin was looking into the future, claiming that if he was right, then this is what he predicted we would see. Rather I am saying that the observed nested hierarchy supports common descent, because a nested hierarchy is a necessary consequence of common descent.

  132. Joe G

    In your discussion with Zachriel (welcome to the discussion, Zachriel, by the way; good to have someone else on my side), you talk a lot about exactly what a nested hierarchy is:

    Post 106: In nested hierarchy each set and each level are specifically defined by several criteria. This is done such that a person can pick an item from one set, hand it to another person, and from the specifications be able to replace the item in its original set.
    That is why when you are talking about nested hierarchy and someone tries to divert the attention to set theory they are up to nothing but deception.
    the rules that Zachriel and the Pixie are ignoring can be read HERE– for all those interested in reality”

    This is not quite right, and I wonder if that is intentional? The problem is “each set and each level are specifically defined by several criteria”. Fortunately, we can go to that web page to see what they say (unfortunately, I really need to quite quite a chunk):

    Hierarchies occur in social systems, biological structures, and in the biological taxonomies. Since scholars and laypersons use hierarchy and hierarchical concepts commonly, it would seem reasonable to have a theory of hierarchies. Hierarchy theory uses a relatively small set of principles to keep track of the complex structure and a behavior of systems with multiple levels. A set of definitions and principles follows immediately:
    Hierarchy: in mathematical terms, it is a partially ordered set. In less austere terms, a hierarchy is a collection of parts with ordered asymmetric relationships inside a whole. That is to say, upper levels are above lower levels, and the relationship upwards is asymmetric with the relationships downwards.
    Hierarchical levels: levels are populated by entities whose properties characterize the level in question. A given entity may belong to any number of levels, depending on the criteria used to link levels above and below. For example, an individual human being may be a member of the level i) human, ii) primate, iii) organism or iv) host of a parasite, depending on the relationship of the level in question to those above and below.

    Nested and non-nested hierarchies: nested hierarchies involve levels which consist of, and contain, lower levels. Non-nested hierarchies are more general in that the requirement of containment of lower levels is relaxed. For example, an army consists of a collection of soldiers and is made up of them. Thus an army is a nested hierarchy. On the other hand, the general at the top of a military command does not consist of his soldiers and so the military command is a non-nested hierarchy with regard to the soldiers in the army. Pecking orders and a food chains are also non-nested hierarchies.

    That first definition mentions mathematical sets. A mathematic set has to have at least one defining property, but no more than that. The set of even numbers has the single defining property “divizible by two”. I see nothing else there to suggest that each set or each level must be “defined by several criteria”.

    Post 104: That is false. The nested hierarchy is not there. It cannot be reconstructed because it isn’t there. Z is a hypothetical ancestor. If B does not have trait 1 then there would be no reason to think it evolved from population Z. One would think it evolved from some population prior to Z. Only if one had direct observation of the divergence could one properly catergoize the populations. But the rules of hierarchy would have to be thrown out first.

    Well we can compare this to the rules of hierarchy that you provided. We have clearly defined sets, “descended from or is Z”, “descended from or is X”, etc. The sets have specific critera, and from what you have written, anyone can readily decide what goes into what set. I think it is clear that B goes into the “descended from or is Z” set, the “descended from or is X” set and the “”descended from or is B” set. Please note that I agree that if all we have to look at is A, B, C and D then we cannot reconstruct the hierarchy, nevertheless the hierarchy is there.

    In this case, we do have direct observation of the divergence, because you told us what happened. We know exactly how to categorise the populations, and they readily fall into a nested hierarchy, conforming to the rules above.

    Post 113: We shouldn’t expect a nested hierarchy with sexually reproducing populations. Therefore Common Descent does not predict NH as there will be a great many crossings”

    There is only a problem if animals breed between species. Any pattern of descent that allows only a single parent (eg evolution of the Java class structure) will give a nested hierarchy. As I said in post 45: “Evolution is like the Brahminy Blind Snake; a new species evolves from a single earlier species. It is not possible for two species to come together to form a third – species can be defined as animals unable to breed, so that excludes any coming together.”

    By the way, I was having problems with the anti-spam software yesturday, and posted the same stuff several times with slight differences; I see they are all there. I apologise for the multiple postings.

  133. Looking at your cite, and after talking to Prof. Allen,

    Timothy F. Allen: example, an army consists of a collection of soldiers and is made up of them. Thus an army is a nested hierarchy. On the other hand, the general at the top of a military command does not consist of his soldiers and so the military command is a non-nested hierarchy with regard to the soldiers in the army.

    Hence, George Pickett is not a nested hierarchy, but Pickett’s Division is a nested hierarchy. The placement of individuals within a typical military hierarchy into Brigades and Regiments is arbitrary. The differences are not taxonomic, but artificial (in the Civil War loosely based on customary regional relationships, in other wars completely arbitrary, hence GI’s in WWII). We define them so by ordering who is to be in Garnett’s Brigade or Baker’s Regiment. And Pickett’s Division is itself contained with the nested hierarchy of the Army of Northern Virginia.

    In biology, we use taxonomy to classify organisms. When we do, we find they form a natural nested hierarchy.

  134. Zachriel,

    Until one can take twigs from several branches, as well as several branches, off of the tree, and have someone else correctly replace them, there isn’t any specified defintions for either- twigs or branches.

    Zachriel:
    I am saying that any hypothetical “tree of life” that has a single common ancestor, and each species has a single parent species must always result in a nested hierarchy.

    That is false. Nesated Hierarchy relies on characteristic traits which must allow for independent observation to place them in their proper sets. No one could do that in your scenario.

    Zachriel:
    Rather I am saying that the observed nested hierarchy supports common descent, because a nested hierarchy is a necessary consequence of common descent.

    THAT CONTRADICTS what you already stated about sexually reproducing populations and crossing lines.

    IOW if lines can be crossed, which they can be in sexually reproducing populations then nh is NOT a necessary consequence of Common Descent.

    What part about that don’t you understand?

  135. Yes the Pixie I am more than well aware of the contents of the page I linked to. I have used it enough to refute Zachriel’s nonsense.

    the Pixie:
    I see nothing else there to suggest that each set or each level must be “defined by several criteria” .

    Get new reading glasses:

    Level of organization: this type of level fits into its hierarchy by virtue of set of definitions that lock the level in question to those above and below.

    And again the Pixie in my second run (seee comment 77) we would NOT place B under population Z. We WOULD NOT know who descended from what.

    We shouldn’t expect a nested hierarchy with sexually reproducing populations. Therefore Common Descent does not predict NH as there will be a great many crossings”

    the Pixie:
    There is only a problem if animals breed between species.

    That is false. You and Zachriel need to get on the same page as he has already agreed that crossings will occur in sexually reproducing populations. He agrees with it because that is what the data shows.

    BTW the definition of species is bogus.

    Zachriel:
    In biology, we use taxonomy to classify organisms. When we do, we find they form a natural nested hierarchy.

    We know that. What is being debated is whether or not Common Descent expects such a pattern.

    BTW Zachriel, I used the military example months ago.

    Do you remember this:

    The nested hierarchy is a pattern. Like all patterns, it can be defined mathematically and exists outside of biology. A nested hierarchy is an ordered set such that each subset is strictly contained within its superset.

    You provided that on my blog. Notice “exists outside of biology”- notice it does not say “also”. Most likely because without a few well-placed extinction events we wouldn’t observe it because we would see a blending of characteristic traits.

    I have provided a peer-reviewed article that demonstrates NH is NOT expaected from Common Descent.

    Neither the Pixie nor Zachriel has offered anything other than continued babbling. Gee I wonder why that is…

  136. JoeG: Until one can take twigs from several branches, as well as several branches, off of the tree, and have someone else correctly replace them, there isn’t any specified defintions for either- twigs or branches.

    The rule is based on their associated branch.

    JoeG: Nested Hierarchy relies on characteristic traits which must allow for independent observation to place them in their proper sets. No one could do that in your scenario.

    Clearly not. They were called GI’s in WWII because they were stamped out Government Issue. They are arranged arbitrarily into Divisions, Companies and Platoons, etc. Unless we put labels on them, there is no way to tell the archetypical GI’s apart.

    JoeG: THAT CONTRADICTS what you already stated about sexually reproducing populations and crossing lines. IOW if lines can be crossed, which they can be in sexually reproducing populations then nh is NOT a necessary consequence of Common Descent.

    I would be happy to discuss this issue, but that requires some modicum of facility with nested sets. But I agree that a sexually reproducing population does not form a nested hierarchy. But then, on one claims they do.

    the Pixie: There is only a problem if animals breed between species.

    JoeG: That is false. You and Zachriel need to get on the same page as he has already agreed that crossings will occur in sexually reproducing populations. He agrees with it because that is what the data shows.

    Try not to misrepresent the views of others. Though a single population of sexually reproducing organisms does not form a nested hierarchy, if a population diverges through a process of reproductive isolation, the descendant populations (species) will form a nested hierarchy. This is regardless of any morphological distinctions.

    JoeG: And again the Pixie in my second run (seee comment 77) we would NOT place B under population Z. We WOULD NOT know who descended from what.

    Sure we would, because you apparently observed the process and noted which were which. However, if all we had were the descendents, and most of the sequence is mutated in each generation, we might not be able to reconstruct the pattern of descent. This is a separate question. We know they descended from a common ancestor. You told us they did, and provided us the lineage.

    JoeG: What is being debated is whether or not Common Descent expects such a pattern.

    Well, first demonstrate you understand what constitutes such a pattern.

    JoeG: I have provided a peer-reviewed article that demonstrates NH is NOT expaected from Common Descent.

    You misrepresent the article. The evidence indicates that the origin of cellular life does not necessarily involve common descent, but endosymbiosis. The lack of a clear nested hierarchy between the various kingdoms, especially with regards to prokaryotes, and the similarity of certain organelles in eukaryotes to bacteria strongly indicates a different mechanism that what might apply to other taxa, and that “different evolutionary models and representations of relationships will be appropriate” for different taxa.

    There may not be a single universal common ancestor of all life, as Darwin himeself pointed out.

    Darwin: There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

  137. Zachriel: The nested hierarchy is a pattern. Like all patterns, it can be defined mathematically and exists outside of biology. A nested hierarchy is an ordered set such that each subset is strictly contained within its superset.

    JoeG: You provided that on my blog. Notice “exists outside of biology” – notice it does not say “also” . Most likely because without a few well-placed extinction events we wouldn’t observe it because we would see a blending of characteristic traits.

    That would make an interesting discussion. Do you have enough understanding of the nested hierarchy to engage such a discussion? The twigs on a branching tree form a nested hierarchy. An archtypical army is a nested hierarchy. A paternal family tree is a nested hierarchy. And the morphology of land vertebrates form a nested hierarchy.

    Are we ok with this so far?

  138. From a peer-reviewed article:

    This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation.

    JoeG: Nested Hierarchy relies on characteristic traits which must allow for independent observation to place them in their proper sets. No one could do that in your scenario.

    Zachriel:
    Clearly not. They were called GI’s in WWII because they were stamped out Government Issue. They are arranged arbitrarily into Divisions, Companies and Platoons, etc. Unless we put labels on them, there is no way to tell the archetypical GI’s apart.

    Your stupidity never ceases to amaze me.

    JoeG: THAT CONTRADICTS what you already stated about sexually reproducing populations and crossing lines. IOW if lines can be crossed, which they can be in sexually reproducing populations then nh is NOT a necessary consequence of Common Descent.

    Zachriel:
    I would be happy to discuss this issue, but that requires some modicum of facility with nested sets.

    Right and you are very defficient in that area.

    Zachriel:
    But I agree that a sexually reproducing population does not form a nested hierarchy. But then, on one claims they do.

    More babbling.

    Zachriel:
    Though a single population of sexually reproducing organisms does not form a nested hierarchy, if a population diverges through a process of reproductive isolation, the descendant populations (species) will form a nested hierarchy. This is regardless of any morphological distinctions.

    That is false because we could have a crossing or two of characteristic traits of the diverged populations. Claasification is based on those traits- not who is descended from who.

    JoeG: And again the Pixie in my second run (seee comment 77) we would NOT place B under population Z. We WOULD NOT know who descended from what.

    Zachriel:
    Sure we would, because you apparently observed the process and noted which were which.

    Talk about misrepresentation! Go seek professional help Zach. You need it. What part of independent observation don’t you understand? That is your tree example fails and why your paternal family tree example fails. And perhaps why you flail.

    JoeG: I have provided a peer-reviewed article that demonstrates NH is NOT expaected from Common Descent.

    Zachriel:
    You misrepresent the article.

    Wrong again, as usual.

    Zachriel:
    There may not be a single universal common ancestor of all life, as Darwin himeself pointed out.

    And as I have told you many times now if there wasn’t a single common ancestor to all living organisms then one would NOT expect a nested hierarchy from their descendents. Logic 101

  139. JoeG: Nested Hierarchy relies on characteristic traits which must allow for independent observation to place them in their proper sets. No one could do that in your scenario.

    Your own cite indicates that soldiers in a military organization form a nested hierarchy, and confirmed with the author.

    JoeG: Your stupidity never ceases to amaze me… More babbling… And perhaps why you flail… Wrong again, as usual.

    Those are not arguments, JoeG.

    Zachriel: Though a single population of sexually reproducing organisms does not form a nested hierarchy, if a population diverges through a process of reproductive isolation, the descendant populations (species) will form a nested hierarchy. This is regardless of any morphological distinctions.

    JoeG: That is false because we could have a crossing or two of characteristic traits of the diverged populations.

    If they cross, then they are not reproductively isolated. Please reread what I wrote. “If a population diverges through a process of reproductive isolation…”

    JoeG: Claasification is based on those traits- not who is descended from who.

    You are a bit old-fashioned. Taxonomic categorization has been largely updated over the last generation to properly reflect descendent relationships. There are entire scientific journals and research facilities dedicated to making these determinations.

    JoeG: And as I have told you many times now if there wasn’t a single common ancestor to all living organisms then one would NOT expect a nested hierarchy from their descendents.

    That’s correct. But let’s make sure you understand the pattern at issue first.

    A nested hierarchy is an ordered set such that each subset is strictly contained within its superset.

    According to your own cite, otherwise identical soldiers in a military organization form a nested hierarchy. Are you ok with this?

  140. As for predictions- If scientific predictions are based on scientific observation and scientific testing, then what can be predicted based on the following”:

    Sexuality has brought joy to the world, to the world of the wild beasts, and to the world of flowers, but it has brought an end to evolution. In the lineages of living beings, whenever absent-minded Venus has taken the upper hand, forms have forgotten to make progress. It is only the husbandman that has improved strains, and he has done so by bullying, enslaving, and segregating. All these methods, of course, have made for sad, alienated animals, but they have not resulted in new species. Left to themselves, domesticated breeds would either die out or revert to the wild state– scarcely a commendable model for nature’s progress.

    (snip a few paragraphs on peppered moths)

    Natural Selection, which indeed occurs in nature (as Bishop Wilberforce, too, was perfectly aware), mainly has the effect of maintaining equilibrium and stability. It eliminates all those that dare depart from the type– the eccentrics and the adventurers and the marginal sort. It is ever adjusting populations, but it does so in each case by bringing them back to the norm. We read in the textbooks that, when environmental conditions change, the selection process may produce a shift in a population’s mean values, by a process known as adaptation. If the climate turns very cold, the cold-adapted beings are favored relative to others.; if it becomes windy, the wind blows away those that are most exposed; if an illness breaks out, those in questionable health will be lost. But all these artful guiles serve their purpose only until the clouds blow away. The species, in fact, is an organic entity, a typical form, which may deviate only to return to the furrow of its destiny; it may wander from the band only to find its proper place by returning to the gang.

    Everything that disassembles, upsets proportions or becomes distorted in any way is sooner or later brought back to the type. There has been a tendency to confuse fleeting adjustments with grand destinies, minor shrewdness with signs of the times.

    It is true that species may lose something on the way– the mole its eyes, say, and the succulent plant its leaves, never to recover them again. But here we are dealing with unhappy, mutilated species, at the margins of their area of distribution– the extreme and the specialized. These are species with no future; they are not pioneers, but prisoners in nature’s penitentiary.– geneticist Giuseppe Sermonti in “Why is a Fly Not a Horse?”

    “seeing that it is based on scientific observation and scientific testing?

    and this before I go-

    JoeG: That is false because we could have a crossing or two of characteristic traits of the diverged populations.

    Zachriel:
    If they cross, then they are not reproductively isolated.

    Tell us Zachriel, what is it that prevents diverged populations that get reproductively isolated, from reclaiming the identity, genetic and morphologic, of the original pre-split parent population?

    Also we may and can have many splits- at each generation, as well as the parent population virtually staying the same.

    Has anyone seen a drawing of a configured star network? It is a central hub or server branching out in all directions. With Common Descent that is what we can see with respect to characteristic traits.

    And Zachriel, I understand EVERYTHING on the summary of the principles of hierachy theory page. However it is more than obvious that you don’t comprehend it with the possible exception tiny bits and pieces seem to have made through to you. So there is some slight glimmer of hope.

    Good luck with that…

  141. JoeG, I asked you if otherwise identical soldiers in an archtypical army form a nested hierarchy. Could you answer that please. The cite you have repeated many times on many different forums says it does.

    JoeG: Tell us Zachriel, what is it that prevents diverged populations that get reproductively isolated, from reclaiming the identity, genetic and morphologic, of the original pre-split parent population?

    In fact, natural selection is known to cause diverged populations to have similar morphological characteristics. E.g., fish and cetaceans have similar (but not identical) hydrodynamic shapes. We can discuss whether the morphological characteristics of vertebrates form a nested hierarchy — once we have some understanding of what that means.

    JoeG: Has anyone seen a drawing of a configured star network? It is a central hub or server branching out in all directions. With Common Descent that is what we can see with respect to characteristic traits.

    In a typical star network every node is directly connected to the hub. This is not the pattern seen in biology, which is a tree topology. See here:
    http://fcit.usf.edu/network/chap5/chap5.htm

    JoeG: I understand EVERYTHING on the summary of the principles of hierachy theory page.

    Great. Then you won’t mind answering a question. Do otherwise identical soldiers in an archtypical army form a nested hierarchy?

    Prof. Allen: “Thus an army is a nested hierarchy.”

  142. Level of organization: this type of level fits into its hierarchy by virtue of set of definitions that lock the level in question to those above and below.

    So what? You are basing your claim that “several” criteria are necessary for a set based on the above using the plural for definition? Or is there more to your claim?

    Why am I even asking. Your argument is based on unsupported assertions, spinked with the odd quote that you seem unable to explain the relevance of.

    And again the Pixie in my second run (seee comment 77) we would NOT place B under population Z. We WOULD NOT know who descended from what.

    So we might not be able to reconstruct it. I keep saying I accept that. And you still seem to be claiming there is no underlying nested hierarchy.

    That is false. You and Zachriel need to get on the same page as he has already agreed that crossings will occur in sexually reproducing populations. He agrees with it because that is what the data shows.

    I very much doubt e agrees with that (indeed, he says “Try not to misrepresent the views of others” in response to this claim). I also very much doubt you can show the data. On the other hand, you probably will claim you have already given the data, but without giving us any clue where. Just a guess mind.

    BTW the definition of species is bogus.

    Evolution predicts it will be difficult to define species.

  143. Hi Zachriel, welcome to Teleological.

    If anyone would like to discuss the phylogenetic tree who has a simple grasp of the nested hierarchy and how we use independently derived traits to classify objects, I would be happy to oblige.

    Assuming you have a simple grasp of the nested hierarchy (NH) maybe you can help me out here. Isn’t the NH just a classification system? And isn’t this classification system based on the assumption that common ancestry is true? It would seem that NH is nothing more than one giant circular argument. Let me use a simplified tree to make an illustration.

    In this NH for example fishes A-D are claimed to have a common ancestor from a bacterium. However, NH is a contrived classification system that has no empirical evidences. IOW, ancestral relationships are based on comparison and differentiation of similar and unique traits. By building such a tree by assuming common ancestry you then go back and use the tree as evidence for common ancestry is circular reasoning.

    What I would like to know is that are there any real empirical evidence outside of your NH tree that indicates common ancestry. For instance, if Homo sapiens share a common ancestor with the chimps then Darwinists should provide detail evidence for this common descent. And I don’t mean just click off a few distant fossils like Australopithecus or Orrorin. I am talking about the most recent common ancestor for Homo sapiens that is even more recent than Neanderthal, which have been shown to not have been the direct ancestor to humans. Where is that direct lineage that we can trace this common ancestry to the divergence between humans and apes? What were the genetic differences? How many genes are required to change from one ancestral form to the next? What were the selection factors and pressure and for how long?

    If Darwinists want to be taken seriously as science then do some real science for a change. Do you smoke and mirror like this bogus contrive gimmick of nested hierarchy and pretend that is evidence.

  144. teleologist: Isn’t the NH just a classification system?

    The nested hierarchy is a pattern. There are a variety of ways to classify objects. In biology, it is based on specific traits. It is observed that the process of classifying organisms leads naturally to a nested hierarchy. (This symmetry exists regardless of the explanation.) This underlying symmetry is explained by common descent (much like the underlying symmetry in the periodic table is explained by atomic theory), and then new predictions are made to test this explanation.

    teleologist: In this NH for example fishes A-D are claimed to have a common ancestor from a bacterium.

    Your cladogram is faulty. Modern bacterium are as much derived from their ancestors as are fish or humans. Nor did humans evolve from modern mice, but both evolved from a common vertebrate ancestor.

    teleologist: By building such a tree by assuming common ancestry you then go back and use the tree as evidence for common ancestry is circular reasoning.

    The nested hierarchy is observed across a large number of taxa. The inference of common ancestry is a theoretical explanation that leads to predictions of novel observations. Each time these predictions are confirmed, it adds confidence to the Theory of Common Descent. Anomalies, such as in the origin of cellular life, lead to modifications or the discarding of a theory. In this case, the domain of applicability of Theory of Common Descent has been narrowed somewhat by modern research. But remember, it took 150 years to determine whether common ancestry started with, in Darwin’s words, “a few forms or into one”.

    teleologist: What I would like to know is that are there any real empirical evidence outside of your NH tree that indicates common ancestry.

    Well, it would be nice of you to inform JoeG of the existence of the nested hierarchy within many taxa.

    teleologist: For instance, if Homo sapiens share a common ancestor with the chimps then Darwinists should provide detail evidence for this common descent. And I don’t mean just click off a few distant fossils like Australopithecus or Orrorin.

    Because you don’t like the evidence, so you simply disregard it? Homo erectus is very similar to modern humans, and you would have to know what to look at to know the difference. Think about it. It’s not a modern human, but it walked up right and made stone tools. This is exactly what we would expect from the Theory of Common Descent.

    Consider Donald Johanson. From other scientific evidence, including homo erectus, Johanson knew that humans diverged from other apes about 3-4 million years ago and probably in Africa. He looked in strata dated by geologists as of being the appropriate age and pulled out the fossil of a small ape with arm-leg length, gait and braincase intermediate between Pan and Homo. (Other examples of Australopithecus have since been found.) To think that this is just luck is the essence of handwaving.

    teleologist: If Darwinists want to be taken seriously as science then do some real science for a change.

    Making predictions, mounting expeditions to distant places, spending months in the field, publishing for your peers to review, having others replicate your findings, IS “real science”.

  145. In fact, natural selection is known to cause diverged populations to have similar morphological characteristics. E.g., fish and cetaceans have similar (but not identical) hydrodynamic shapes.

    Hi Zachiel,

    Do you have any empirical evidence to support this claim? By pointing out fish and cetaceans have hydrodynamic shapes is not empirical evidence for natural selection. Empirical evidence is to take a form that does not have hydrodynamic shapes and observe the affects of RM&NS change that shape into a hydrodynamic shape.

  146. Zachriel:
    In fact, natural selection is known to cause diverged populations to have similar morphological characteristics. E.g., fish and cetaceans have similar (but not identical) hydrodynamic shapes.

    Umm they are only similar if one looks through very blurry glasses. However thanks to science we have a good idea why some forms are similar(HINT- it has nothing to do with biology):

    Unified physics theory explains animals’ running, flying and swimming

    JoeG: Has anyone seen a drawing of a configured star network? It is a central hub or server branching out in all directions. With Common Descent that is what we can see with respect to characteristic traits.

    Zachriel:
    In a typical star network every node is directly connected to the hub. This is not the pattern seen in biology, which is a tree topology.

    Why am I NOT surprised that you missed the point entirely? With Common Descent a star pattern is as likely as any other pattern. THAT is what the science has told us.

    To the Pixie:

    YOU don’t even have an argument!
    cut and paste from my blog:

    The point about traits being gained and lost is key because it is via traits that we classify organisms.

    Again from Denton:

    “Biological classification is basically the identification of groups of organisms which share certain characteristics in common and its beginnings are therefore as old as man himself. It was Aristotle who first formulated the general logical principles of classification and founded the subject as science. His method employed many of the principles which are still used by biologists today. He was, for example, well aware of the importance of using more than one characteristic as a basis for identifying classes, and he was also aware of the difficult problem which has bedeviled taxonomy ever since: that of selecting the characteristics to be used and weighing their relative significance.” (bold added)

    This is all relevant because my debate with Zachriel is with biological classification and biological classification alone.

    It is amazing that is lost on both the Pixie and Zachriel. And yes the Pixie definitions is plural and “who’s your daddy?” is NOT a characteristic trait- besides the fact that it is the SOLE definition used in the paternal family tree nonsense.

    And again the Pixie in my second run (seee comment 77) we would NOT place B under population Z. We WOULD NOT know who descended from what.

    the Pixie:
    So we might not be able to reconstruct it. I keep saying I accept that. And you still seem to be claiming there is no underlying nested hierarchy.

    If we are unable to reconstruct it there would be no reason to infer any underlying hierarchy. And if we did construct it based on the observation of those 4 populations alone, it wouldn’t look anything like reality.

  147. Nested Hierarchy of living organsims is built on shared similarities. It will NEVER be evidence for Common Descent because it does not explain the DIFFERENCES. It just notes that they exist.

    Any theory of Common Descent must explain the differences- as in the physiological and anatomical differences observed between chimps and humans- or any other populations with alleged common ancestors.

    However in almost 150 years “On the Origins of Species…” was published we still don’t have a clue as to whether or not any mechanism can account for those differences!

    IOW just as I have been saying for decades the MET is no more than untestable speculations based on untestable assumptions.

  148. Hi Zachiel,

    The nested hierarchy is a pattern.

    Precisely, a pattern that is confer to a set of data by human minds. It is an idea not physical.

    It is observed that the process of classifying organisms leads naturally to a nested hierarchy.

    Whether or not it lead to a NH is irrelevant. The organization of data itself is not evidence for common descent.

    Your cladogram is faulty. Modern bacterium are as much derived from their ancestors as are fish

    What is that ancestor? Does it actually exist? My point for the diagram is to use as a marker for illustration. Your response actually shows the flaw in Darwinian science. What you are doing is to point to an unspecified common ancestor without giving the detail of what it is and how it evolved into its progeny.

    Let me give you another example.

    In a classification system, it would be just as valid to take the example from Scenario A and rearrange it to Scenario B & C. From an observational point of view there is no difference, except that Scenario B and C do not share a common ancestor.

    The inference of common ancestry is a theoretical explanation that leads to predictions of novel observations. Each time these predictions are confirmed, it adds confidence to the Theory of Common Descent. Anomalies, such as in the origin of cellular life, lead to modifications or the discarding of a theory.

    You can build a complex theory from ouija board but it does not make it science. I just have to reemphasize the fact that a classification system is not a substitute for real evidences.

    teleologist: What I would like to know is that are there any real empirical evidence outside of your NH tree that indicates common ancestry.

    Zachiel :Well, it would be nice of you to inform JoeG of the existence of the nested hierarchy within many taxa.

    So you don’t have any empirical evidence then.

    Because you don’t like the evidence, so you simply disregard it? Homo erectus is very similar to modern humans, and you would have to know what to look at to know the difference. Think about it. It’s not a modern human, but it walked up right and made stone tools. This is exactly what we would expect from the Theory of Common Descent.

    First, I did not disregard anything because of personal preference. Neanderthal was discarded as a direct descendent of humans by Darwinists.

    Second, let me make sure I understand what you are saying. Are you saying that Homo erectus is a direct ancestor of Homo sapiens?

    He looked in strata dated by geologists as of being the appropriate age and pulled out the fossil of a small ape with arm-leg length, gait and braincase intermediate between Pan and Homo. (Other examples of Australopithecus have since been found.) To think that this is just luck is the essence of handwaving.

    You are right, this is handwaving. You are still appealing to an idea and not hard evidence i.e., hey they look similar so they must be related. This is a conclusion based on a preconceive assumption, not science.

    Making predictions, mounting expeditions to distant places, spending months in the field, publishing for your peers to review, having others replicate your findings, IS “real science” .

    What prediction? Darwinian evolution has no scientific predictions. It is a farce to claim that it is a prediction, if we will find an amphibian fossil between the fossil of a fish and a reptile. A scientific prediction is the ability to find the exact characteristics of a platypus before it was found.

  149. Zachriel:
    Well, it would be nice of you to inform JoeG of the existence of the nested hierarchy within many taxa.

    I have never doubted that.

    It would be nice if Zachriel actually deals with reality. That nested hierarchies are observed (or exist) does not mean they were expected.

    Zachriel:
    From other scientific evidence, including homo erectus, Johanson knew that humans diverged from other apes about 3-4 million years ago and probably in Africa.

    Umm there isn’t any scientific evidence that shows such a transformation is even possible.

    Also if all the alleged transitionals and intermediates were still alive we would see a BLEND of characteristic traits. A blend would cause overlapping and overlapping is NOT allowed in NH.

    And it should be noted that not one of Zachriel’s predictions includes a mechanism. It should also be noted that other models could make the same predictions and yet have an entirely different PoV.

  150. Zachriel:
    JoeG, I asked you if otherwise identical soldiers in an archtypical army form a nested hierarchy. Could you answer that please. The cite you have repeated many times on many different forums says it does.

    If you want to discuss the principles of hierarchy then start at the BEGINNING and work your way down. I know that will be an issue for you because that will force you to discuss those valid and important principles that you have ignored for perhaps your entire life.

  151. Joe G

    I have only got a few moments, but just want to pick up on this:

    It is amazing that is lost on both the Pixie and Zachriel. And yes the Pixie definitions is plural and “who’s your daddy?” is NOT a characteristic trait- besides the fact that it is the SOLE definition used in the paternal family tree nonsense.

    Okay, so you argue “definitions” must mean several definitions. I disagee. In set theory a single crietierium is sufficient to define a single set, so I am interested in whether you can actually justify this.

    Do you have any other objection to the “who’s your daddy?” definition? I will agree that for reconstructing the biological tree of life, but surely that is about collecting evidence to determine who is that daddy.

  152. the Pixie:
    In set theory a single crietierium is sufficient to define a single set, so I am interested in whether you can actually justify this.

    I wasn’t talking about set theory. In set theory a set is anything one wants it to be- just put whatever between {} and you have a set. That is why set theory is irrelevant when discussing nested hierarchy. Fom comment 106:

    Set theory and NH:
    When talking about set theory any sets and subsequent subsets, apart from nested hierarchy, you can have items from one set by included with items from another set on the same level.

    With set theory in general anything can be a set. Just put whatever you want in {} and you have a set. Or if you can’t find {} just declare what you want to be in a set. Then all subsets are just that set and/ or that set minus any number of items.

    For example with Zachriel’s paternal family tree I can make a set of {Sharif Hussein bin Ali, Abdul Ilah,Faisal}. A subset would then be {Sharif Hussein bin Ali, Failsal}. It is a valid set and it is a valid subset. However neither make sense in a nested hierarchy.

    In a nested hierarchy we can NOT have two sets on the same level that contain items that can exist in either set. Also all subsets must be strictly contained within the set above it.

    In nested hierarchy each set and each level are specifically defined by several criteria. This is done such that a person can pick an item from one set, hand it to another person, and from the specifications be able to replace the item in its original set.

    That is why when you are talking about nested hierarchy and someone tries to divert the attention to set theory they are up to nothing but deception.

    Any questions?

    Set up a paternal family tree using mitochondrial DNA and get back to me…

  153. JoeG: That nested hierarchies are observed (or exist) does not mean they were expected.

    The nested hierarchy (morphological traits in organisms) was observed long before Darwin. The movement of planets was observed long before Newton. However, the theoretical explanations of these observations allows predictions of novel observations.

    Zachriel: From other scientific evidence, including homo erectus, Johanson knew that humans diverged from other apes about 3-4 million years ago and probably in Africa.

    JoeG: Umm there isn’t any scientific evidence that shows such a transformation is even possible.

    The ability to make novel predictions IS scientific evidence. Johanson specifically looked in 3-4 million year old strata in Africa and found a new organism with arm-leg length, braincase, hand structure, gait, intermediate between humans and other apes, and that this ape fills an early gap in the expected transition. Think about it. A new organism. He didn’t find it in his backyard, or some random strata.

    JoeG: A blend would cause overlapping and overlapping is NOT allowed in NH.

    You are conflating the nested hierarchy of descendent relationships with the nested hierarchy of discernable taxonomic differences. Without your being able to comprehend a nested hierarchy, you probably will continue to not recognize the distinction.

    JoeG: And it should be noted that not one of Zachriel’s predictions includes a mechanism.

    That’s correct. We can’t discuss a mechanism of evolutionary divergence if you refuse to acknowledge the existence of that divergence.

    JoeG: If you want to discuss the principles of hierarchy then start at the BEGINNING and work your way down. I know that will be an issue for you because that will force you to discuss those valid and important principles that you have ignored for perhaps your entire life.

    That’s exactly where we will start then. A nested hierarchy is an ordered set such that each subset is strictly contained within its superset. From this definition, it is clear that the twigs on a tree can be grouped into nested sets according to their associated branches. We could call the trunk of this tree Sharif Hussein bin Ali. The soldiers in an army form a nested hierarchy.

    JoeG: In nested hierarchy each set and each level are specifically defined by several criteria. This is done such that a person can pick an item from one set, hand it to another person, and from the specifications be able to replace the item in its original set.

    Your reference to “specifications” is ambiguous, but you probably mean by physically discernable differences. Your own cite indicates that an army is a nested hierarchy. There is no way to tell which platoon a soldier is in unless you put a label on them. However, an army is a nested hierarchy.

    Zachriel: JoeG, I asked you if otherwise identical soldiers in an archtypical army form a nested hierarchy. Could you answer that please. The cite you have repeated many times on many different forums says it does.

    I have asked you several times. You have refused to answer. Your own statements are in direct contradiction to your own cited authority.

  154. JoeG: Set up a paternal family tree using mitochondrial DNA and get back to me”

    As mitochondrial DNA is inherited from the mother, a maternal family tree can be constructed. This is a common methodology in modern genealogical research. It’s a wonderful thing.

  155. JoeG: For example with Zachriel’s paternal family tree I can make a set of {Sharif Hussein bin Ali, Abdul Ilah,Faisal}. A subset would then be {Sharif Hussein bin Ali, Failsal}. It is a valid set and it is a valid subset. However neither make sense in a nested hierarchy.

    A = {Sharif Hussein bin Ali, Abdul Ilah, Faisal}
    B = {Sharif Hussein bin Ali, Faisal}

    B is a strict subset of A. We can arrange elements into any number of patterns. We can arrange them into nested hierarchies. We can arrange them into non-nested hierarchies. We can arrange them into a square for a dance.

    The question isn’t whether we can arbitrarily arrange objects into various patterns. We can! But whether a paternal descendency constitutes a nested hierarchy.

    With “Sons” meaning “all the male descendents”, form a set of the Sons of Sharif Hussein bin Ali, and the set of Sons for each of his male descendents. What pattern do they form? If you guessed a nested hierarchy, you are right!!
    http://www.internationalspecialreports.com/middleeast/99/jordan/8-1.gif

  156. This is just lovely:

    JoeG: Set up a paternal family tree using mitochondrial DNA and get back to me”

    Zachriel:
    As mitochondrial DNA is inherited from the mother,

    Is that a prediction of the MET or Common Descent? And does that mean you cannot do what was requested? Typiical.

    Zachriel:
    a maternal family tree can be constructed.

    Construct a maternal family tree using only the Y chromosome and get back to me.

    Zachriel:
    This is a common methodology in modern genealogical research. It’s a wonderful thing.

    It’s a good thing that modern genetics has nothing to do with Common Descent.

    Umm, that patterns can be drawn that resemble a nested hierarchy does NOT mean said pattern represents a nested hierarchy. And that nested hierarchuies can be drawn to resemble a branching tree does not mean that all branching trees depict a nested hierarchy.

    Those concepts appear to confuse you. As does “independent observation” and “character traits”. “All male descendents” is not a character trait” and male descendents would NOT be possible without female involvement.

    Never mind the arbitrary starting point.

  157. Zachriel:
    The nested hierarchy (morphological traits in organisms) was observed long before Darwin.

    I already told you that. What’s your point?

    Zachriel:
    However, the theoretical explanations of these observations allows predictions of novel observations.

    But we have already been told that in your scenario there is no way to predict what will be selected for at any point in time.

    Zachriel:
    A nested hierarchy is an ordered set such that each subset is strictly contained within its superset.

    And AGAIN – it IS THAT plus much more.

    Zachriel:
    From this definition, it is clear that the twigs on a tree can be grouped into nested sets according to their associated branches.

    From the accepted principles of hierarchy theory that example doesn’t stand a chance. You have major issues and I thank you for exposing them here.

    JoeG: In nested hierarchy each set and each level are specifically defined by several criteria. This is done such that a person can pick an item from one set, hand it to another person, and from the specifications be able to replace the item in its original set.

    Zachriel:
    Your reference to “specifications” is ambiguous,

    Umm EVERYTHING you post is ambiguous. And if you don’t understand what I posted then there is absolutely no hope in a meaningful discussion with you. But we already knew that, didn’t we?

    Zachriel:
    but you probably mean by physically discernable differences.

    I mean specifically defined characteristic traits. You know like Aristotle knew thousands of years ago and scientists still employ.

    Zachriel:
    Your own cite indicates that an army is a nested hierarchy. There is no way to tell which platoon a soldier is in unless you put a label on them. However, an army is a nested hierarchy.

    The nested hierarchy of an army is specified regardless of the individual. The levels are specifically defined. What it takes to be in a specific set or subset is specifically defined.

    IOW if someone hands you a platoon sgt, if properly trained, you should be able to take an individual with those specified qualifications and plug him in to any platoon sgt’s role.

    And soldiers are labeled. That’s what makes them soldiers.

    I take it you have had absolutely no involvement with any regular military. Unfortunately for you, I have.

  158. JoeG: Set up a paternal family tree using mitochondrial DNA and get back to me”

    Zachriel: As mitochondrial DNA is inherited from the mother, a maternal family tree can be constructed. This is a common methodology in modern genealogical research. It’s a wonderful thing.

    JoeG: Is that a prediction of the MET or Common Descent?

    It’s an observation.

    JoeG: Construct a maternal family tree using only the Y chromosome and get back to me.

    As the Y-chromosome is inherited from the father, a paternal family tree can be constructed. This is a common methodology in modern genealogical research. It’s a wonderful thing.

    The rest of your post makes very little sense. You insist that a nested hierarchy include what you call “character traits” a concept which is nowhere to be found on your cited definition. Finally, after numerous requests, you admit that soldiers in an army constitute a nested hierarchy, but there is nothing about a soldier which tells us which company or platoon to place them in (e.g. all platoon sargents are functionally equivalent) which is even more arbitrary than associating twigs with branches.

  159. JoeG: IOW if someone hands you a platoon sgt, if properly trained, you should be able to take an individual with those specified qualifications and plug him in to any platoon sgt’s role.

    Actually, it can be done in a completely arbitrary manner. Someone is a platoon sergeant because that is his assigned role. Whether he is “properly trained” or not is irrelevant to his rank in the command hierarchy.

  160. Joe G

    Pix: In set theory a single crietierium is sufficient to define a single set, so I am interested in whether you can actually justify this.
    Joe: I wasn’t talking about set theory. In set theory a set is anything one wants it to be- just put whatever between {} and you have a set. That is why set theory is irrelevant when discussing nested hierarchy. Fom comment 106:

    So you say (1) you were not talking about set theory and set theory is irrelevant and (2) here is the post where you talk about set theory. Curious.

    Set theory is the starting point for the web page you linked to about NH, so set theory IS relevant. As you said “With set theory in general anything can be a set.” A nested hierarchy is a load of sets that conform to additional rules. As you said: “In a nested hierarchy we can NOT have two sets on the same level that contain items that can exist in either set. Also all subsets must be strictly contained within the set above it.” All well and good.

    The sleight hand appears in the next bit: “In nested hierarchy each set and each level are specifically defined by several criteria.” Basically, you seem to be making up the requirement for several criteria, because that suits your purpose. There is nothing in set theory requiring that, and nothing in the web page you linked to to support it either. It is just that your argument falls apart if the group can be defined by a single criterium.

    The web page you linked to mentions an army as an example of a nested hierarchy. I would suggest that squad, regiment and army are NOT “specifically defined by several criteria”

  161. The Pixie: The web page you linked to mentions an army as an example of a nested hierarchy. I would suggest that squad, regiment and army are NOT “specifically defined by several criteria”

    And to help Joe out a bit — in case he is actually interested — a archtypical army is a completely arbitrary nested hierarchy of otherwise identical soldiers; in WWII parlance, GI’s, Government Issue. The nested hierarchy of twigs on a tree are not arbitrary, but simply defined by their natural growth pattern, that is, by their associated branches. The nested hierarchy of a paternal family tree is inevitable when grouping male descendents into sets.

    Now, if you are ok with that, I would be happy to move on to discussing how we might non-arbitrarily classify objects by independently derived traits. Your mention of multiple criteria makes sense within taxonomy, even crucial. You will then see that the majority of taxa form a nested hierarchy of morphology, biogeography, fossils in time, embryonics, genomics, etc.

    Then, and only then, is it reasonable to discuss a theory of explanation for the observed pattern. (It really shouldn’t be this hard.)

  162. Zachriel:
    Someone is a platoon sergeant because that is his assigned role.

    Wrong. Not just anyone can be “assigned” to be a platoon sgt.

    Zachriel:
    You insist that a nested hierarchy include what you call “character traits” a concept which is nowhere to be found on your cited definition.

    Hierarchical levels: levels are populated by entities whose properties characterize the level in question.

    Note the word PROPERTIES- plural.

    Level of organization: this type of level fits into its hierarchy by virtue of set of definitions that lock the level in question to those above and below.

    Note the words set of definitions– also plural

    The ordering of levels: there are several criteria whereby other levels reside above lower levels.

    Note the words several criteria

    the Pixie:
    So you say (1) you were not talking about set theory and set theory is irrelevant and (2) here is the post where you talk about set theory. Curious.

    The curious part is you. I talk about set theory to demonstrate it is irrelevant when discussing NH. I made that very clear. That you refuse to grasp that simple point says quite a bit about you.

    the Pixie:
    Set theory is the starting point for the web page you linked to about NH, so set theory IS relevant.

    That’s false. True it talks about sets but NOT in the context of set theory.

    the Pixie:
    As you said “With set theory in general anything can be a set.” A nested hierarchy is a load of sets that conform to additional rules.

    Exactly! Do you see the difference?

    the Pixie:
    Basically, you seem to be making up the requirement for several criteria, because that suits your purpose.

    I take it you either can’t read or you just can’t comprehend what you read.

    Hierarchical levels: levels are populated by entities whose properties characterize the level in question.

    Note the word PROPERTIES- plural.

    Level of organization: this type of level fits into its hierarchy by virtue of set of definitions that lock the level in question to those above and below.

    Note the words set of definitions– also plural

    The ordering of levels: there are several criteria whereby other levels reside above lower levels.

    Note the words several criteria

    the Pixie:
    It is just that your argument falls apart if the group can be defined by a single criterium.

    Not at all. These criteria often run in parallel, but sometimes only one or a few of them apply.

    the Pixie:
    I would suggest that squad, regiment and army are NOT “specifically defined by several criteria”

    I would suggest that you don’t know what you are talking about.

  163. Zachriel:
    And to help Joe out a bit — in case he is actually interested — a archtypical army is a completely arbitrary nested hierarchy of otherwise identical soldiers

    Umm the NH of an army is not arbitrary at all.

    Zachriel:
    You will then see that the majority of taxa form a nested hierarchy of morphology, biogeography, fossils in time, embryonics, genomics, etc.

    That is irrelevant. What I have been discussing is whether or not Common Descent expects such a pattern. And as the scientific data shows, it does NOT.

    This is where character traits comes into play. Common Descent would be OK without NH because those character traits which define the levels and the sets can be reversed. IOW lines can be crossed! And they can be recrossed or merge!

    At ANY generation or any individual a population can start to diverge. And diverge just means split. To diverge does NOT confer a direction. And therefore the pattern can NOT be predicted by what exists. A pattern only forms when HUMANS make things nice and neat with the drawing of forward moving straight lines- even though the actual path could have resembled the flight of the bumble-bee.

    I guess I will just have to keep re-posting this until it sinks in (for Zachriel and the Pixie):

    The point about traits being gained and lost is key because it is via traits that we classify organisms.

    Again from Denton:

    “Biological classification is basically the identification of groups of organisms which share certain characteristics in common and its beginnings are therefore as old as man himself. It was Aristotle who first formulated the general logical principles of classification and founded the subject as science. His method employed many of the principles which are still used by biologists today. He was, for example, well aware of the importance of using more than one characteristic as a basis for identifying classes, and he was also aware of the difficult problem which has bedeviled taxonomy ever since: that of selecting the characteristics to be used and weighing their relative significance.” (bold added)

    This is all relevant because my debate with Zachriel is with biological classification and biological classification alone.

    And THAT is why Zachriel’s continued false use of trees and paternal family trees is nothing but a dishonest attempt to distract from the fact that he is totally clueless as to classification.

  164. JoeG: Umm the NH of an army is not arbitrary at all.

    Of course it is. A prototypical soldier can be placed anywhere in the hierarchy. He can be reassigned at any time. The whole point of the phrase “GI” encapsulates this idea, but it pervades history. A centuria is about a hundred (80) Roman legionaries. You don’t need to know their names, and they can be reassigned to other centuria at will. A cohort is about half a dozen centuria. The centuria can be reassigned at will. They form a nested hierarchy.

    On the other hand, the twigs on a tree can be grouped uniquely by a simple rule, by their associated branches.

    JoeG: That is irrelevant. What I have been discussing is whether or not Common Descent expects such a pattern. And as the scientific data shows, it does NOT.

    Until you indicate some understanding of the nested hierarchy, there is no point discussing the implications of such a pattern. You still claim that descent along uncrossed lines does not result in a nested hierarchy of hereditary relationships. As this follows directly from the definition, it means you are still confused.

    JoeG: This is where character traits comes into play.

    Sorry, JoeG. You haven’t graduated. You’re still stuck on nested hierarchies as a set pattern. Mostly because you can’t apply a simple definition. Any advancement in the discussion would only result in further conflation. Please try to comprehend this aspect of the discussion so that we may progress. If it confuses you, don’t call it a “nested hierarchy”. Call it “Bob”. A “Bob” is the pattern as found on twigs on a tree (associated by branch), or soldiers in an army (as assigned into units), or of descent along uncrossed lines. If you can grasp this, then we can progress to classification.

  165. Joe G

    The ordering of levels: there are several criteria whereby other levels reside above lower levels

    So how many criteria do you need? What is the minimum number, below which it does not count as a hierarch?

    And why?

  166. Zachriel:
    Sorry, JoeG. You haven’t graduated.

    That is because I never joined your school of dishonesty and deception.

    JoeG: Umm the NH of an army is not arbitrary at all.

    Zachriel:
    Of course it is. A prototypical soldier can be placed anywhere in the hierarchy.

    Pure nonsense. The hierarchy of an army exists regardless of the individuals who occupy the sets/levels.

    IOW a sgt will ALWAYS be above a corporal and always be below a Lt.

    Zachriel:
    On the other hand, the twigs on a tree can be grouped uniquely by a simple rule, by their associated branches.

    But if I pulled twigs from branches you wiouldn’t be able to put them back in their proper places. I will always be able to put soldiers back in their proper order- just by the definitions.

    Zachriel:
    You still claim that descent along uncrossed lines does not result in a nested hierarchy of hereditary relationships. As this follows directly from the definition, it means you are still confused.

    Two things- It does NOT follow from the definition and the “authority” that you stole and revised that from disagrees with you. Go figure..

    And finally I will again leave you with this:

    The point about traits being gained and lost is key because it is via traits that we classify organisms.

    Again from Denton:

    “Biological classification is basically the identification of groups of organisms which share certain characteristics in common and its beginnings are therefore as old as man himself. It was Aristotle who first formulated the general logical principles of classification and founded the subject as science. His method employed many of the principles which are still used by biologists today. He was, for example, well aware of the importance of using more than one characteristic as a basis for identifying classes, and he was also aware of the difficult problem which has bedeviled taxonomy ever since: that of selecting the characteristics to be used and weighing their relative significance.” (bold added)

    This is all relevant because my debate with Zachriel is with biological classification and biological classification alone.

    IOW we have known for thousands of years of the IMPORTANCE of using MORE THAN ONE CHARACTERISTIC.

    That you two keep avoiding THAT reality demonstrates you are not interested in science. That neither of you understands that those same characteristics which are used to define sets and levels can be reversed, and therefore foul any NH, says quite a bit about your agenda.

    And finally that both of you continue to ignore the peer-reviewed article that refutes you and supports myself, inunison and teleologist, exposes your dishonesty. That neither of you can reference any peer-review that supports you also says quite a bit.

  167. This just in:

    I have been handed an envelope. I am tearing it open and reading the contents.

    Folks we have a TIE! Zachriel and the Pixie win! It has been determined that they are the BIGGEST LOSERS!

    Let’s give them a round of applause…

  168. JoeG: IOW a sgt will ALWAYS be above a corporal and always be below a Lt.

    You again show that you don’t understand a nested hierarchy. You are confusing the military hierarchy with the nested hierarchy of soldiers. A sargeant does not consist of his soldiers. From your cite: “nested hierarchies involve levels which consist of, and contain, lower levels… For example, an army consists of a collection of soldiers and is made up of them. Thus an army is a nested hierarchy. On the other hand, the general at the top of a military command does not consist of his soldiers and so the military command is a non-nested hierarchy with regard to the soldiers in the army.”

    However, we will use a new term. A “Bob” is an ordered set such that each subset is strictly contained within its superset. This is an arbitrary “Bob” using numbers per our definition:

    {1,2,3,4,5,6}
    {1,2,4} {5,6}
    {1,4} {6}
    {4}

    The twigs on a tree, when naturally grouped by associated branches is a “Bob”, as are the soldiers in an army, as are patterns of descent without crossed lines. It’s really too bad mathematicians don’t have a term to describe sets strictly contained within supersets. Anyway, Linnaeus determined, well before Darwin, that when grouping organisms by specific morphological features, that they group naturally into a “Bob”.

  169. This just in:

    I have been handed an envelope. I am tearing it open and reading the contents.

    Folks we have a TIE! Zachriel and the Pixie win! It has been determined that they are the BIGGEST LOSERS!

    Let’s give them a round of applause”

    How old are you, Joe?

  170. And MORE support for my position:

    Dr. N Wells:

    The thing is that the textbook definition is better than the dictionary definition (with respect to biological usage and the ToE) precisely because it does not imply any direction to the change. Darwin’s phrase “descent with modification” does not imply direction, just change. Biologists have found that what you might consider increases in complexity and decreases in complexity can both be beneficial to an organism, or disadvantageous, entirely depending on circumstances, and that the explanations for increases and decreases are exactly the same. Most evolutionary change, in fact probably almost all of it, consists of fluctuations back and forth with no net change. Net change in one direction can happen when the organism’s environment or ecology changes in one specific direction, such as an island drifting into a new climatic zone, or the immigration or extinction of a particular predator, parasite, or food species.

    IOW just as I had mentioned earlier the pattern formed by descent with modification can resemble that of a star network.

    Zachriel:
    You again show that you don’t understand a nested hierarchy.

    Your continued projection is duly noted.

    Take heed of your words “morphological features”. You say it but it is obvious you cannot grasp the concept.

    And AGAIN:

    Zachriel continually confuses a pattern, that of a tree, with nested hierarchy. That NH can be drawn as a branching tree in NO WAY means that a tree forms a nested hierarchy. That a paternal family tree can be drawn as a pattern similar to NH does not mean it is NH.

    In order to be a nested hierarchy it must conform to the rules. That Zachriel refuses to follow those rules is strong evidence that he either doesn’t understand them or he is flat outr dishonest. (it could be a combo)

    The Pixie:
    How old are you, Joe?

    Old enough to know that you don’t know what you are talking about.

  171. Zachriel:
    A sargeant does not consist of his soldiers.

    I NEVER said, thought nor implied otherwise. And actually I flat out stated the hierarchy does NOT depend on individuals. I see you’re still having reading problems.

    When one makes up a hierarchy for the military it is specified before-hand. My example was of the US Army scheme- Sgts are ALWAYS above Corporals and ALWAYS below Lts. THAT is the hierarchy REGARDLESS of the individual who occupies that rank. And even if there aren’t any Sgts the hierarchy is still there.

    Military hierarchy would be- Theater, Army Group, Army, Corps, Division, Brigade and so on down the line. A Theater is made up of Army Groups, which is made up of Armies, which has its Corps, which are split in to Divisions and so on.

    Then we have the hierarchy of rank. Each rank is specified before-hand. The rank exists regardless of the person occupying it. And the hierarchy is alwqays there.

  172. Did everyone notice this from N wells:

    “Most evolutionary change, in fact probably almost all of it, consists of fluctuations back and forth with no net change.”

    N Wells on the ARN discussion board

    What type of pattern does a series of left turns make? How about a series of right turns? Now do that using Zachriel’s “uncrossed lines”. What pattern do you have?

    Or take a line from a starting population straight to the left, then back. then straight to the right, then back. Repeat for millions of generations. What does it look like?

  173. JoeG: IOW just as I had mentioned earlier the pattern formed by descent with modification can resemble that of a star network.

    Wells does not describe a star network, but an oscillation.

    A single node of descent may form a star network, e.g. a father and his sons is a star network of paternity. But a general lineage of descent is not a star network, but a tree, a nested hierarchy. In evolution, it is called adaptive radiation, and even then, it typically exhibits all the properties of a general nested hierarchy.

    JoeG: Zachriel continually confuses a pattern, that of a tree, with nested hierarchy. That NH can be drawn as a branching tree in NO WAY means that a tree forms a nested hierarchy. That a paternal family tree can be drawn as a pattern similar to NH does not mean it is NH.

    That just indicates you don’t know what a nested hierarchy is. I even offered to use a special definition of the pattern at issue, but as is usual when confronted with something that might lead to an actual discussion, you ignored it.

    This is the general definition of a nested hiearchy, an ordered set such that each subset is strictly contained within its superset.

    We can construct a completely arbitrary nested hierarchy, such as this:

    {1,2,3,4,5,6}
    {1,2,4} {5,6}
    {1,4} {6}
    {4}

    Or we can take functionally identical Roman legionaries and group them into centuria and cohorts and legions.

    Or we can take a simple rule, such as twigs on a tree, associated by their branches, and see that they fit the definition given above. They do.

    Or we can take a lineage of uncrossed descent and see that the hereditary pattern inevitably forms an ordered set such that each subset is strictly contained within its superset.

    Or we can look closely at biological taxa and see if there is a pattern. There is, but we can’t have that discussion of pattern until you understand what that pattern is. The entire discussion of common descent depends on understanding the nested hierarchy. If you want to call it something else, that’s fine. We’ll call it the pattern of interest. Start with the definition.

    The pattern of interest is an ordered set such that each subset is strictly contained within its superset.

    Then all you have to do is understand how to construct sets. You had difficulty with this previously, but you might try simple set construction. Consider the sons of a father. Consider the legionaries of a centuria. Consider the twigs on a single stem of a tree. These can all be considered as sets. Now, take the sons of the sons, or a cohort of centuria, or the twigs on a tree. These sets of sets form the pattern of interest. And if the pattern of interest is acceptable, we can then discuss the evidence for common descent.

  174. JoeG quoting Wells for the umpteenth time: “Most evolutionary change, in fact probably almost all of it, consists of fluctuations back and forth with no net change.”

    It doesn’t form a star network, but a random walk. See RANDOM WALKERS

    JoeG: Did everyone notice this from N wells: “Most evolutionary change, in fact probably almost all of it, consists of fluctuations back and forth with no net change.”

    Also from N.Wells,

    The fossil record provides evidence for evolution by a) demonstrating pervasive change in the biota over time, b) demonstrating diversification and radiation time and time again, c) providing many examples of likely ancestors and descendents in appropriate chronological sequence (involving both increasing complexity, decreasing complexity, and change with no particular net gains or losses in complexity), and d) providing many examples of the sorts of intermediate forms that provide plausible intermediates from one set of organisms to a significantly different set.

  175. Sorry, I confused two different Wells. I’m not sure that JoeG has quoted N.Wells before.

  176. Sorry, teleologist. I had missed this comment. I found it when I referenced to your previous comment. (I inverted your comments below.)

    teleologist: Empirical evidence is to take a form that does not have hydrodynamic shapes and observe the affects of RM&NS change that shape into a hydrodynamic shape.

    Empirical evidence can take many forms.

    teleologist: Do you have any empirical evidence to support this claim? By pointing out fish and cetaceans have hydrodynamic shapes is not empirical evidence for natural selection.

    Yes it is, but not in isolation from all the other evidence. We need to establish Common Descent before attempting to find an explanation for the divergence and adaptation.

  177. Zachriel:
    It doesn’t form a star network,

    Please learn how to read. This is what I said can resemble that of a star network.

    Zachriel:
    Wells does not describe a star network, but an oscillation.

    He also says that there isn’t any direction. That is the part where the star network comes in.

    As for oscillation – I know. I posted that in this thread plus several times on my blog- wobbling stability.

    Zachriel:
    But a general lineage of descent is not a star network, but a tree, a nested hierarchy.

    That is very false. General descent with lineage, in which the pattern is determined by characteristic traits, can form almost any pattern. That we observe NH is not evidence for Common Descent- especially when NH can also be used as strong evidence for Common Design.

    JoeG: Zachriel continually confuses a pattern, that of a tree, with nested hierarchy. That NH can be drawn as a branching tree in NO WAY means that a tree forms a nested hierarchy. That a paternal family tree can be drawn as a pattern similar to NH does not mean it is NH.

    Zachriel:
    That just indicates you don’t know what a nested hierarchy is.

    Let’s review- I go by the rules of hierarchy. Zachriel goes by his own rules.

    Reality demonstrates you don’t know what you are talking about.

    Zachriel:
    This is the general definition of a nested hiearchy, an ordered set such that each subset is strictly contained within its superset.

    That is false. NH is much more than that as I have demonstrated. That you continually ignore the accpeted rules of hierarchy for some simpleton version which you think you can exploit says quite a bit about you.

    And if you want to establish Common Descent start by scientifically explaining the physiological and anatomical differences observed between alleged closely related populations- like chimps and humans.

    However it is obvious from Doolittle et al., Margulis, Carroll et al., and now N Wells that Common Descent and NH do not belong together.

    As for the fossil record as evidence for evolution- that’s just wishful thinking.

  178. JoeG: He also says that there isn’t any direction. That is the part where the star network comes in.

    A star network is highly ordered and has every element directly attached to the hub. A father and sons is a star network. A meandering evolutionary history is not a star network. Adaptive radiation might resemble a star network.

    JoeG: General descent with lineage, in which the pattern is determined by characteristic traits, can form almost any pattern.

    Not “any pattern”. If the rate of change is very rapid, the traits will quickly decouple from the heredity lines. If the mutation rate is very slow, there may be no appreciable evolution. Neither of these represent “any pattern”.

    In any case, we’re not up to examining traits. We need to finally dispense with the issue of the pattern of interest. The pattern of hereditary relationships of descent along uncrossed lines forms the pattern of interest. Each family of descendents has one and only one ancestor and is a subset of the descendents of the family of that ancestor.

    The pattern of interest is an ordered set such that each subset is strictly contained within its superset.

  179. JoeG: NH is much more than that as I have demonstrated. That you continually ignore the accpeted rules of hierarchy for some simpleton version which you think you can exploit says quite a bit about you.

    The pattern of interest is an ordered set such that each subset is strictly contained within its superset.

    So the twigs on a tree, a cohort of Roman legionaries, descendents of an uncrossed lineage, are all examples of the pattern of interest. Are we ok with this? If so, we can proceed to discuss how we might classify objects by independently derived traits, and whether or not they form the same pattern of interest as do descendents of an uncrossed lineage.

    {1,2,3,4,5,6}
    {1,2,4} {5,6}
    {1,4} {6}
    {4}

    (Too bad mathematicians don’t have a name for such a hierarchical arrangement of subsets strictly contained within supersets.)

  180. JoeG: NH is much more than that as I have demonstrated. That you continually ignore the accpeted rules of hierarchy for some simpleton version which you think you can exploit says quite a bit about you.

    Zachriel:
    The pattern of interest is an ordered set such that each subset is strictly contained within its superset.

    The patern is NOT of interest. How that pattern was achieved is.

    Twigs on a tree can form many patterns. Those patterns are NOT defined before the tree arises from the ground.

    And Zachriel I am not OK with 99% of the pap you post. To summarize:

    You refuse to go by the accepted rules of hierarchy.

    You refuse to listen to evolutionary scientists.

    And you refuse to listen to reality.

    ZAchriel:
    If so, we can proceed to discuss how we might classify objects by independently derived traits,

    Been there, done that- got tired of waiting for your dribble to end.

    Evolutionary scientists have already determined that NH is not a “pattern of interest” for Common Descent. That is adequate to satisfy my requirement.

    Is there ANY part of those last two sentences that you DON’T understand?

    We can only continue if you answer that question.

  181. Zachriel:
    A star network is highly ordered and has every element directly attached to the hub.

    Yes, I know. I have designed and installed many.

    Zachriel:
    A father and sons is a star network.

    No. The sons can only “radiate” from the father in ONE direction. A star network pattern better resembles an asterisk.

    Zachriel:
    A meandering evolutionary history is not a star network.

    I NEVER said, thought nor implied that it was.

    Zachriel:
    Adaptive radiation might resemble a star network.

    It might.

    JoeG: General descent with lineage, in which the pattern is determined by characteristic traits, can form almost any pattern.

    Zachriel:
    Not “any pattern” .

    I said “almost”. What is your problem?

    Zachriel:
    If the rate of change is very rapid, the traits will quickly decouple from the heredity lines. If the mutation rate is very slow, there may be no appreciable evolution. Neither of these represent “any pattern” .

    If you had any reasoning abilities AT ALL, you would see the flaws in your argument. You are taking me out-of-context and inserting your inferences in for what I actually stated. IOW you have erected a strawman (typical) and then destroyed it. Do you feel better?

    Zachriel:
    In any case, we’re not up to examining traits.

    YOU’RE not. I have already passed that. And that is because THAT IS THE ONLY THING THAT SHOULD BE DISCUSSED. ANYTHING ELSE IS A DISHONEST DISTRACTION.

    Evolutionary scientists have already determined that NH is not a “pattern of interest” for Common Descent. That is adequate to satisfy my requirement.

    Is there ANY part of those last two sentences that you DON’T understand?

    We can only continue if you answer that question.

  182. This thread was established to pose the argument for Common Descent (and Common Design). Making that argument requires having a shared vocabulary.

    Pattern X = an ordered set such that each subset is strictly contained within its superset.

    JoeG: Twigs on a tree can form many patterns. Those patterns are NOT defined before the tree arises from the ground.

    The twigs of a tree can be grouped by their associated branches. This association creates Pattern X. This is inevitable from the growth pattern of trees. You might try actually examining a tree.

  183. JoeG: Evolutionary scientists have already determined that NH is not a “pattern of interest” for Common Descent.

    That is incorrect. However, we are not discussing your misunderstandings of the nested hierarchy. We are discussing Pattern X. From a discussion of this pattern, we can demonstrate the evidence for Common Descent.

    Pattern X = an ordered set such that each subset is strictly contained within its superset.

  184. JoeG: Evolutionary scientists have already determined that NH is not a “pattern of interest” for Common Descent. That is adequate to satisfy my requirement. Is there ANY part of those last two sentences that you DON’T understand?

    I fully understand your statements.

    JoeG: And you can’t correct me because there is no way I will ever listen to what you say.

  185. Zachriel:
    You might try actually examining a tree.

    I have and THAT is why I know you are wrong in trying to say that trees form a nested hierarchy. But in the end it isn’t the trees, it is the RULES OF HIERARCHY that demonstrate that trees are not NH.

    Evolutionary scientists have already determined that NH is not a “pattern of interest” for Common Descent.

    Zachriel:
    That is incorrect.

    That is a fact. And I fact I have substantiated in this thread. That you refuse to accept the facts says quite a bit about you. But it is obvious that you don’t care any more.

    Zachriel:
    From a discussion of this pattern, we can demonstrate the evidence for Common Descent.

    That is false. The ONLY way you can “demonstrate” evidence for Common Descent is to have data that explains the DIFFERENCES (all of them) observed between alleged closely related populations.

    JoeG: Evolutionary scientists have already determined that NH is not a “pattern of interest” for Common Descent. That is adequate to satisfy my requirement. Is there ANY part of those last two sentences that you DON’T understand?

    Zachriel:
    I fully understand your statements.

    (references an out-of-context quote)

    Thanks again for demonstrating your dishonesty!

    Prediction fulfilled- Zachriel needs to get a life:

    Let’s look at the content:

    Zachriel is relegated to quote-mining for out-of-context soundbites:

    Look what Joe G said

    It is true- that I will not listen to blipey. The reasoning is sound- time and again blipey has demonstrated that he is dishonest. Not only that but the best he can do is to pick on non-existent mistakes in my posts.

    And yes Zachriel- it applies to you too and for the SAME reasons.

    However if Zachriel could EVER find some scientist or peer-reviewed article that supports his PoV I will read what they have to say. Dr Theobald has come up but he has already been refuted.

    Zachriel claims:
    Pattern X = an ordered set such that each subset is strictly contained within its superset.

    Why do you continue to push a simpleton’s version? Is that because that is all you can understand? Are the REAL RULES and definitions too complicated for you?

    Too bad. Go get an education and come back when you are old enough to buy a vowel.

  186. Zachriel claims: Pattern X = an ordered set such that each subset is strictly contained within its superset.

    It’s not a claim, JoeG. It’s called a definition.

    JoeG: Why do you continue to push a simpleton’s version? Is that because that is all you can understand?

    It’s not a “version”. It’s a definition. Do you have a valid issue with the definition? Or any problem with understanding how elements can be grouped into sets? These are example of Pattern X: twigs on a tree associated by branch, Roman legionaries in centurias and cohorts, descendents of an uncrossed lineage. That’s because each of these examples meets the definition of Pattern X.

    {1,2,3,4,5,6}
    {1,2,4} {5,6}
    {1,4} {6}
    {4}

    Ok so far?

  187. Zachriel claims: Pattern X = an ordered set such that each subset is strictly contained within its superset.

    Zachriel:
    It’s not a claim, JoeG. It’s called a definition.

    It’s a simpleton’s definition if it is trying to define nested hierarchy- which I infer it does because that is how you have been using it.

    JoeG: Why do you continue to push a simpleton’s version? Is that because that is all you can understand?

    Zachriel:
    It’s not a “version” . It’s a definition.

    It is version of the PROPER definition.

    Zachriel:
    Do you have a valid issue with the definition?

    Other than the valid issues I have already presented?

    If Zachriel wants to discuss nested hierarchy I suggest he use the PROPER and ACCEPTED DEFINITIONS already provided:

    A SUMMARY OF THE PRINCIPLES OF HIERARCHY THEORY:

    The Hierarchy theory is a dialect of general systems theory. It has emerged as part of a movement toward a general science of complexity. Rooted in the work of economist, Herbert Simon, chemist, Ilya Prigogine, and psychologist, Jean Piaget, hierarchy theory focuses upon levels of organization and issues of scale. There is significant emphasis upon the observer in the system.

    Hierarchies occur in social systems, biological structures, and in the biological taxonomies. Since scholars and laypersons use hierarchy and hierarchical concepts commonly, it would seem reasonable to have a theory of hierarchies. Hierarchy theory uses a relatively small set of principles to keep track of the complex structure and a behavior of systems with multiple levels. A set of definitions and principles follows immediately:

    Hierarchy: in mathematical terms, it is a partially ordered set. In less austere terms, a hierarchy is a collection of parts with ordered asymmetric relationships inside a whole. That is to say, upper levels are above lower levels, and the relationship upwards is asymmetric with the relationships downwards.

    Hierarchical levels: levels are populated by entities whose properties characterize the level in question. A given entity may belong to any number of levels, depending on the criteria used to link levels above and below. For example, an individual human being may be a member of the level i) human, ii) primate, iii) organism or iv) host of a parasite, depending on the relationship of the level in question to those above and below.

    Level of organization: this type of level fits into its hierarchy by virtue of set of definitions that lock the level in question to those above and below. For example, a biological population level is an aggregate of entities from the organism level of organization, but it is only so by definition. There is no particular scale involved in the population level of organization, in that some organisms are larger than some populations, as in the case of skin parasites.

    Level of observation: this type of level fits into its hierarchy by virtue of relative scaling considerations. For example, the host of a skin parasite represents the context for the population of parasites; it is a landscape, even though the host may be seen as belonging to a level of organization, organism, that is lower than the collection of parasites, a population.

    The criterion for observation when a system is observed, there are two separate considerations. One is the spatiotemporal scale at which the observations are made. The other is the criterion for observation, which defines the system in the foreground away from all the rest in the background. The criterion for observation uses the types of parts and their relationships to each other to characterize the system in the foreground. If criteria for observation are linked together in an asymmetric fashion, then the criteria lead to levels of organization. Otherwise, criteria for observation merely generate isolated classes.

    The ordering of levels: there are several criteria whereby other levels reside above lower levels. These criteria often run in parallel, but sometimes only one or a few of them apply. Upper levels are above lower levels by virtue of: 1) being the context of, 2) offering constraint to, 3) behaving more slowly at a lower frequency than, 4) being populated by entities with greater integrity and higher bond strength than, and 5), containing and being made of – lower levels.

    Nested and non-nested hierarchies: nested hierarchies involve levels which consist of, and contain, lower levels. Non-nested hierarchies are more general in that the requirement of containment of lower levels is relaxed. For example, an army consists of a collection of soldiers and is made up of them. Thus an army is a nested hierarchy. On the other hand, the general at the top of a military command does not consist of his soldiers and so the military command is a non-nested hierarchy with regard to the soldiers in the army. Pecking orders and a food chains are also non-nested hierarchies.

    Duality in hierarchies: the dualism in hierarchies appears to come from a set of complementarities that line up with: observer-observed, process-structure, rate-dependent versus rate-independent, and part-whole. Arthur Koestler in his “Ghost in The Machine” referred to the notion of holon, which means an entity in a hierarchy that is at once a whole and at the same time a part. Thus a holon at once operates as a quasi-autonomous whole that integrates its parts, while working to integrate itself into an upper level purpose or role. The lower level answers the question “How?” and the upper level answers the question, “So what?”

    Constraint versus possibilities: when one looks at a system there are two separate reasons behind what one sees. First, it is not possible to see something if the parts of the system cannot do what is required of them to achieve the arrangement in the whole. These are the limits of physical possibility. The limits of possibility come from lower levels in the hierarchy. The second entirely separate reason for what one sees is to do with what is allowed by the upper level constraints. An example here would be that mammals have five digits. There is no physical reason for mammals having five digits on their hands and feet, because it comes not from physical limits, but from the constraints of having a mammal heritage. Any number of the digits is possible within the physical limits, but in mammals only five digits are allowed by the biological constraints. Constraints come from above, while the limits as to what is possible come from below. The concept of hierarchy becomes confused unless one makes the distinction between limits from below and limits from above. The distinction between mechanisms below and purposes above turn on the issue of constraint versus possibility. Forget the distinction, and biology becomes pointlessly confused, impossibly complicated chemistry, while chemistry becomes unwieldy physics.

    Complexity and self-simplification: Howard Pattee has identified that as a system becomes more elaborately hierarchical its behavior becomes simple. The reason is that, with the emergence of intermediate levels, the lowest level entities become constrained to be far from equilibrium. As a result, the lowest level entities lose degrees of freedom and are held against the upper level constraint to give constant behavior. Deep hierarchical structure indicates elaborate organization, and deep hierarchies are often considered as complex systems by virtue of hierarchical depth.

    Complexity versus complicatedness: a hierarchical structure with a large number of lowest level entities, but with simple organization, offers a low flat hierarchy that is complicated rather than complex. The behavior of structurally complicated systems is behaviorally elaborate and so complicated, whereas the behavior of deep hierarchically complex systems is simple.

    Hierarchy theory is as much as anything a theory of observation. It has been significantly operationalized in ecology, but has been applied relatively infrequently outside that science. There is a negative reaction to hierarchy theory in the social sciences, by virtue of implications of rigid autocratic systems or authority. When applied in a more general fashion, even liberal and non-authoritarian systems can be described effectively in hierarchical terms. There is a politically correct set of labels that avoid the word hierarchy, but they unnecessarily introduce jargon into a field that has enough special vocabulary as it is.

    Now if Zachriel cannot follow those then I suggest he discuss something else. Something that he can comprehend would be nice.

  188. It is not unusual to use specific definitions for scientific discussions. Pattern X is a definition of a particular pattern of sets. It applies to trees and it applies to descent along uncrossed lines. That makes it relevant.

    We were asked to provide the evidence for common descent, and that evidence is based in the patterns found in nature. If you refuse to have this discussion, that is your choice. I have seen that when pressed you usually try to end a discussion.

    Pattern X is an ordered set such that each subset is strictly contained within its superset. This pattern is found in the twigs on a tree associated by branch, Roman legionaries in centurias and cohorts, descendents of an uncrossed lineage. Are we ok so far with the definition and its application to these examples?

  189. Zachriel:
    It is not unusual to use specific definitions for scientific discussions.

    And I gave you the specific definitions that apply to this scientific discussion.

    Zachriel:
    We were asked to provide the evidence for common descent, and that evidence is based in the patterns found in nature.

    Funny because we were also asked to provide the evidence for Common Design, and THAT evidence is based in the patterns found in natutre.

    Zachriel:
    If you refuse to have this discussion, that is your choice.

    I just refuse to follow you down a one-way, dead-end street.

    Umm I live pretty much in the woods. Trees form a branching pattern but that pattern is nothing like Roman legions or descendants of any kind.

    AND none of that has anything to do with evidence for Common Descent which requirres an explanation of the differences observed. That you refuse to address that reality- well we have seen that when pressed you usually resort to deception and dishonesty- No that is wrong- deception and dishonesty is all you have.

  190. JoeG: And I gave you the specific definitions that apply to this scientific discussion… I just refuse to follow you down a one-way, dead-end street.

    You are not required to participate in any such discussion. But, in order to follow my argument, you’ll have to, well, follow my argument. If it reaches a dead-end, that will be clear soon enough. My argument begins with a definition of a particular pattern, Pattern X.

    JoeG: Umm I live pretty much in the woods. Trees form a branching pattern but that pattern is nothing like Roman legions or descendants of any kind.

    Then you are lacking the ability to observe. Because if we group twigs by their associated branches, we get the same pattern as we get when we group descendents of non-crossed lineage. In fact, twigs ARE descendents of non-crossed lineage. Think JoeG. Think!

    So, to begin again. Pattern X is an ordered set such that each subset is strictly contained within its superset. This pattern is found in the twigs on a tree associated by branch, Roman legionaries in centurias and cohorts, descendents of an uncrossed lineage. Are we ok so far with the definition and its application to these examples?

  191. It seems that we’ve exhausted the arguments on this subject. May I suggest, if it is agreeable with inunison, that JoeG and Zachriel each prepare a closing post to be posted at noon PST on Mon. 2/12. I will lock this thread 3 minutes past noon. This will prevent any attempt to have the last word.

    I think it is safe to say we would never see eye to eye in these debates. We do not seek to convert or convince but our objective should be for a clarification of each side’s argument.

  192. teleologist: It seems that we’ve exhausted the arguments on this subject.

    Actually, we haven’t even started it. Is there a reason why you are protecting JoeG in this manner? If it is only because of the length of the thread, I would be happy to move this discussion to a new thread. Otherwise, people might think that JoeG can’t follow an argument and has to be saved by the moderation bell.

    Pattern X is an ordered set such that each subset is strictly contained within its superset. This pattern is found in the twigs on a tree associated by branch, Roman legionaries in centurias and cohorts, descendents of an uncrossed lineage. Are we ok so far with the definition and its application to these examples?

    In fact, twigs ARE descendents of non-crossed lineage. Think JoeG. Think!

  193. Umm twigs are NOT descendents. Twigs are part of a tree unless they fall off.

    Zachriel:
    But, in order to follow my argument, you’ll have to, well, follow my argument.

    If you had an argument to follow that would be one thing. However it is obvious that you do not.

    And in order to follow my argument one requires a brain- oops that leaves you out.

    Zachriel:
    Otherwise, people might think that JoeG can’t follow an argument and has to be saved by the moderation bell.

    Anyone who thinks that by following this thread is as dense as you are and therefore their opinions on the matter don’t matter.

    “The absence of any overlapping classes implies the absence of any sort of natural sequential relationships among the objects grouped by such a scheme.” Denton in “Evolution: A Theory in Crisis”

    “Yet, direct evidence for evolution only resides in the existence of unambiguous sequential arrangements, and these are never present in ordered hierarchic schemes.” Ibid

    The point being that any normal person interested in reality understands what Denton said.

    I have said my piece and substantiated my claims. I have nothing left to do, except perhaps to sit back and enjoy Zachriel’s continued flailing.

  194. Actually, we haven’t even started it. Is there a reason why you are protecting JoeG in this manner?

    I don’t know what could have given you the impression that I need to protect JoeG from you. Frankly I find your argument repetitive and you’ve failed to address many of the points that JoeG is making. That is the reason for my suggestion.

  195. teleologist: Frankly I find your argument repetitive and you’ve failed to address many of the points that JoeG is making. That is the reason for my suggestion.

    I haven’t made an argument. We quibbled over the definition of a nested hierarchy, and when that was fruitless, I presented a specific definition of Pattern X. From there I intended to argue for Common Descent. You might have helped the situation by explaining why the definition is faulty (e.g. ambiguous) — it is not — or by prodding JoeG to accept the definition so that we could discuss first the process of classification and then what would be expected to observe with a hypothetical line of descent.

    Such patterns are at the very root of every argument on Common Descent since Darwin up to modern cladistics and systematics. If a valid definition is handwaved away, then of course, no reasonable discourse can occur. I would really like to discuss the details of common descent. However, when such fundamentals are misunderstood, then progressing the argument will just result in conflation. I would be happy to discuss the fundamentals of Common Descent in any open forum.


    When I use a word,’ Humpty Dumpty said, in a rather scornful tone,’ it means just what I choose it to mean, neither more nor less.’
    The question is,’ said Alice, ‘whether you can make words mean so many different things.’

    The question is,’ said Humpty Dumpty, ‘which is to be master – that’s all.’

    Lewis Carroll

  196. I haven’t made an argument. We quibbled over the definition of a nested hierarchy, and when that was fruitless, I presented a specific definition of Pattern X.

    The problem as I see it, is that JoeG has made some very good points with Doolittle, Margulis and discrepancies between different lines of evidences. If you want to move the argument forward then address those specifics of JoeG’s argument. I just get tired of 20 different ways of repeating the same thing over and over again.

  197. teleologist : If you want to move the argument forward then address those specifics of JoeG’s argument.

    I would be happy to. Do we then have an agreed definition of Pattern X, an ordered set such that each subset is strictly contained within its superset? Because, again, this pattern is at the very heart of all arguments about Common Descent since Darwin, including Doolittle and Margulis. And just so you know, I have posted on JoeG’s own blog nearly a year ago that Common Descent does not apply to the evolutionary origin of the cellular kingdoms. Why? Because the nested hierarchy, er, Pattern X does not seem to quite apply to the very trunk of the tree of cellular life — even though it strongly applies to nearly all other levels of classification.

    (If we can dispense with this issue, I might suggest that we that we start a new thread. This one is getting quite long.)

  198. Patterns and trees? Did someone say something about patterns and trees?

    Well take a look at these!:

    What pattern do you see?

    this pattern?

    how about a quad
    ?

    and now what do you see?

    and now?

    almost over

    pretty neat

    patterns and trees

    And that Zachriel posted the following is totally messed up considering it is he who refuses to accept valid definitions:

    If a valid definition is handwaved away, then of course, no reasonable discourse can occur.

    And there you have it. There can be “no reasonable discourse” with Zachriel as he just handwaves away the VALID definitions of hierarchy theory.

    And again until one can scientifically explain the DIFFERENCES there aren’t any fundamentals to discuss.

  199. Zachriel:
    And just so you know, I have posted on JoeG’s own blog over a year ago that Common Descent does not apply to the evolutionary origin of the cellular kingdoms.

    But if Common Descent doesn’t apply to the evolutionary origin of the celular kingdom (whatever that means), it shouldn’t apply anything that evolved from that. And just so you know I told you that on my blog at that time.

    Zachriel:
    Because, again, this pattern is at the very heart of all arguments about Common Descent since Darwin and including Doolittle and Margulis.

    Doolittle and Margulis disgree with you. And Darwin disagreed with you. He had to resort to mental gymnastics in order to explain the observed pattern. The very pattern that was used to explain Common Design. He understood that it took some nicely timed extinction events to provide what we do observe. For without those events we would see what Denton stated.

    Patterns and trees? Did someone say something about patterns and trees?

    Well take a look at these!:

    http://my.opera.com/Bjork/albums/showpic.dml?album=75883&picture=954663

    http://my.opera.com/Bjork/albums/showpic.dml?album=75883&picture=954662

    http://my.opera.com/Bjork/albums/showpic.dml?album=75883&picture=954659 (quad)

    http://my.opera.com/Bjork/albums/showpic.dml?album=75883&picture=954658

    http://my.opera.com/Bjork/albums/showpic.dml?album=75883&picture=954660

    http://my.opera.com/Bjork/albums/showpic.dml?album=75883&picture=954661

    http://my.opera.com/Bjork/albums/showpic.dml?album=75883&picture=954664

    http://my.opera.com/Bjork/albums/showpic.dml?album=75883&picture=954665

  200. Zachriel:
    And just so you know, I have posted on JoeG’s own blog nearly a year ago that Common Descent does not apply to the evolutionary origin of the cellular kingdoms. Why? Because the nested hierarchy, er, Pattern X does not seem to quite apply to the very trunk of the tree of cellular life — even though it strongly applies to nearly all other levels of classification.

    And as I told you at the time what applies to one applies to all. That is because if NH does not apply to the trunk there would be no reason to expect NH from that. Out of chaos, order? No Zachriel, that is just plain stupid, just like I told you on my blog.

    Zachriel:
    If a valid definition is handwaved away, then of course, no reasonable discourse can occur.

    Then I suggest that YOU stop handwaving away the valid definitions of hierarchy- they ALL apply.

  201. JoeG: That is because if NH does not apply to the trunk there would be no reason to expect NH from that.

    Observation, JoeG. It is observed that most taxa form a nested hierarchy, er, Pattern X. But it is also observed that the pattern does not quite apply to the origin of the cellular domains. As these are observations, they are not optional.

  202. That is because if NH does not apply to the trunk there would be no reason to expect NH from that.

    Zachriel:
    Observation, JoeG.

    As you have been told- what we observe has NOTHING to do with what was expected.

    Zachtiel:
    It is observed that most taxa form a nested hierarchy,…

    The discussion is not about what we observe but what we would expect given the mechanism(s) involved.

    Zachriel:
    But it is also observed that the pattern does not quite apply to the origin of the cellular domains.

    And therefore that the pattern is observed in other taxa that allegedly evolved from cellular domains means it was not expected. IOW the observation has been accomodated into the theory. The theory does not expect it.

  203. Here is a pattern (that no one expected) formed by a tree:

    Cool

    And there are more patterns (that aren’t expected) made by trees – just use the “next” or “previous” buttons on the right side of the page.

    Seeing that trees CAN and DO form many different patterns, what does that do to Zachriel’s argument?

  204. hi teleologist I agree and this is last from me to those who still re-digest 19th century science (stolen from David Tyler):

    No phylogeny estimation is assumption free

    The nested hierarchies that emerge from taxonomical studies have often been used as evidence supporting the concept of common descent (i.e. all organisms have evolved from an ancestral single cell). Hierarchies emerge from studies of morphology, from genetic similarities and from other data. However, as has recently been pointed out, “to create an evolutionary tree of relationships, one must make assumptions about the evolutionary process that produced the observed data.” This highlights one of the major problems we have in the field of evolutionary biology: the assumptions are so deeply embedded that any alternative approach that seeks to stand outside the conventional paradigm is regarded with suspicion. This research paper has the merit of exploring these issues, although it does so without challenging the evolutionary mindset of phylogenetics. To those who doubt the claim that “No phylogeny estimation is assumption free”, this paper deserves their close attention. Once it is recognised that “assumptions” are critical for the production of phylogenies, the evidences against common descent, identified by some (but not all) ID advocates, can then be considered on their merits. This is a scientific issue, worthy of wider debate.

    Model use in phylogenetics: nine key questions
    Scot A. Kelchner and Michael A. Thomas
    Trends in Ecology & Evolution, Volume 22, Issue 2 , February 2007, Pages 87-94

    and second article already quoted 2 or 3 times before but it’s implications ignored:

    The Tree of Life: “we do not need this ladder anymore”

    Darwin’s one illustration in “On the Origin of Species” was of a branching “Tree of Life” (TOL). This has entered the mindset of evolutionary biologists and there has been a very real danger of confusing concept with reality. The authors of a discussion paper suggest that this concept has acted like a ladder to climb over an obstacle. “The TOL was thus the ladder that helped the community to climb the wall of acceptance and understanding of evolutionary process. But now that we have climbed it, we do not need this ladder anymore.” Not only do we not need it, we are better off without it! “Holding onto this ladder of pattern is an unnecessary hindrance in the understanding of process (which is prior to pattern) both ontologically and in our more down-to-earth conceptualization of how evolution has occurred.”
    How can this be? Do the authors not know how important the TOL concept is to evolutionary biologists? They do. But they also know that it cannot be justified using empirical data. “The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree.”
    But some argue that the nested hierarchy branching pattern is a proof of Darwinism. These people have something to learn from the authors, who write: “The notion that a tree pattern is the product of induction, obvious to any intelligent observer, is belied by most of the early history of systematics, during which quite different schemes seemed fully defensible.” Also, that “hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so.” For more on this, go here.
    None of this, in the authors view, is to undermine evolutionary theory. The TOL concept “should not be an essential element in our struggle against those who doubt the validity of evolutionary theory, who can take comfort from this challenge to the TOL only by a wilful misunderstanding of its import.” If this is a broadside against ID, it is an unfortunate choice of words. ID advocates are fond of the phrase “follow the evidence wherever it leads” and we applaud the authors for their analysis of the TOL concept. However, we want to encourage discussion of the import of this research and reserve the right to come to a different judgment. To describe this as “wilful misunderstanding” is actually opting out of scientific discourse.

    Pattern pluralism and the Tree of Life hypothesis
    W. Ford Doolittle and Eric Bapteste
    Proc. Natl. Acad. Sci. USA, Early Edition 29 Jan 2007 | doi 10.1073/pnas.0610699104

  205. JoeG: The discussion is not about what we observe but what we would expect given the mechanism(s) involved.

    It’s always about what we observe.

    JoeG: And therefore that the pattern is observed in other taxa that allegedly evolved from cellular domains means it was not expected.

    That’s correct. Though Darwin was careful to suggest that the trunk of the tree of life may have more than one ancestral population, most scientists have long believed that the Theory of Common Descent applied to the origin of cellular life. That means the nested hierarchy was expected, and the further back they could look, the more it seemed this was true. However, recent evidence (last couple of decades) has indicated otherwise, and the domain of the Theory of Common Descent has been modified to exclude that aspect of cellular evolution which appears now to be due to some sort of endosymbiosis — still an evolutionary process, but not naive common descent. There are a number of other important exceptions, but the exceptions to the rule can’t be understood without understanding the rule.

    That’s the way science works. Observations inform theory.

    JoeG: Here is a pattern (that no one expected) formed by a tree:

    Most of those trees look artificial, but certainly some trees do not naturally form a nested hierarchy. And this shows that you have at least an intuitive understanding of the pattern. Good. Please, quit pretending otherwise.

    JoeG: Seeing that trees CAN and DO form many different patterns, what does that do to Zachriel’s argument?

    JoeG, I really wish you would read for content instead of for the oppportunity to handwave.

    Zachriel: So, for instance, a paternal family tree is a nested hierarchy, as are the twigs of a typical tree grouped by branch, though it may not be readily discernable by merely examining the sons or twigs… The nested hierarchy is the inevitable outcome of heredity along uncrossed lines, such as the twigs and branches of a typical tree… The tree is such an archetypical image of a nested hierarchy that I have trouble believing that you retain your position.

  206. One more time for the learning deficient:

    Just because a nested hierarchy is always an ordered set such that each subset is strictly contained within its superset, does NOT mean that everything that can be placed in an ordered set such that each subset is strictly contained within its superset forms a nested hierarchy.

    To form a nested hierarchy the pattern must also conform to the principles of hierarchy theory.

    JoeG: And therefore that the pattern is observed in other taxa that allegedly evolved from cellular domains means it was not expected.

    Zachriel:
    That’s correct.

    Thank you. That means the discussion is over. My premise has been confirmed.

    The discussion is not about what we observe but what we would expect given the mechanism(s) involved.

    Zachriel:
    It’s always about what we observe.

    As always you live and argue in your own little world.

    Good luck with that.

  207. JoeG: Just because a nested hierarchy is always an ordered set such that each subset is strictly contained within its superset, does NOT mean that everything that can be placed in an ordered set such that each subset is strictly contained within its superset forms a nested hierarchy.

    I think what you mean here is whether or not they naturally arrange into a nested hierarchy based on some independent rule or criteria. That is certainly true. So the twigs on a typical tree associated by branch, decendents of an uncrossed lineage, legionaries in a cohort, do form a nested hierarchy. On the other hand, a typical spider’s web does not form a nested hierarchy.

    JoeG: Thank you. That means the discussion is over. My premise has been confirmed.

    As I had posted this on your own blog nearly a year ago, and repeatedly since then, including on this very thread, I’m glad you finally read it. Common Descent is now believed not to properly apply to the origin of the cellular domains. However, it does largely apply within each of the domains.

    What is amazing is that scientific investigation, such as that by Doolittle and Bapteste, can reveal anything at all about such early events in cellular evolution.

  208. Just because a nested hierarchy is always an ordered set such that each subset is strictly contained within its superset, does NOT mean that everything that can be placed in an ordered set such that each subset is strictly contained within its superset forms a nested hierarchy.

    Zachriel:
    I think what you mean here is whether or not they naturally arrange into a nested hierarchy based on some independent rule or criteria.

    Don’t think. You aren’t even close. Do not interpret what I say. What I said is as clear as difference between black and white.

    JoeG: Thank you. That means the discussion is over. My premise has been confirmed.

    Zachriel:
    As I had posted this on your own blog nearly a year ago, and repeatedly since then, including on this very thread, I’m glad you finally read it.

    LoL!! I not only had read it but also responded the same way! What I find amazing is that you continue to babble-on after the matter has been settled.

    And again if we did NOT observe a nested hierarchy Common Descent could explain that also. THAT has been the point all along.

    FYI- Darwin did not use Common Descent to explain NH. He was forced to invoke several well-placed extinction events in order to explain the distinct categories.

  209. Sorry, but your last post made very little sense and added even less content. Darwin only included a single diagram in Origin of Species, a phylogenetic tree, that is, an ordered set such that each subset is strictly contained within its superset.

    This is how I would have presented a case for Common Descent:

    1. Define a specific set relationship.
    2. Provide explicit rules for grouping objects.
    3. Examine what we would expect to observe from various descendent patterns.
    4. Show how nearly all taxa fit the specified set relationship.
    5. Document successful empirical predictions.

    I’m sorry, JoeG, but you are still stuck on #1. I believe the evidence is overwhelming that you really don’t want to engage in a discussion of the relevant issues. If you change your mind, let me know.

  210. Zachriel:
    Sorry, but your last post made very little sense and added even less content.

    Relativity. IOW it may have not made sense to you but what does that mean to me? And it may have “added even less content” to you but again, what does that mean to me?

    Zachriel:
    This is how I would have presented a case for Common Descent:

    Unless you include how to account for the differences observed, your methodology is very faulty.

    Zachriel:
    I believe the evidence is overwhelming that you really don’t want to engage in a discussion of the relevant issues.

    True projection at its finest.

    Thanks again for the entertainment.

    BTW not all patterns that are an ordered set such that each subset is strictly contained within its superset can be classified as being a nested hierarchy. Only an ordered set such that each subset is strictly contained within its superset which conforms to the principles of hierarchy theory can be considered a nested hierarchy.

    The fact you can’t accept that basic fact demonstrates your dishonesty.

  211. JoeG: BTW not all patterns that are an ordered set such that each subset is strictly contained within its superset can be classified as being a nested hierarchy. Only an ordered set such that each subset is strictly contained within its superset which conforms to the principles of hierarchy theory can be considered a nested hierarchy.

    By definition, a superset is higher in the hierarchy. By definition, a subset is lower in the hierarchy. Hence, they are ordered.

    But that’s immaterial. As in any such argument, we can define terms as long as they are unambiguous.

    Let A be the set of even numbers.
    Let D be the set of sets of the numbers 1 to 10 taken two at a time.
    Let X be an ordered set such that each subset is strictly contained within its superset.

    Because you won’t acknowledge a simple definition for the purpose of discussion, it clearly demonstrates that you refuse to engage the argument. That is your choice.

  212. Joe

    And MORE support for my position:
    Dr. N Wells:

    IOW just as I had mentioned earlier the pattern formed by descent with modification can resemble that of a star network.

    Cool. Then you can devise a diagram illustrating this supposed “star network”, and we can see if a nested hierarchy is there or not. As far as I can see you are taking a reasonable statement by N.Wells, and using it to support a fantasy. If you can give us the “star network” diagram, I might believe you.

    By the way, you never answered my question in post 165. This would seem to be fundamental to our disagreement. Here it is again:

    The ordering of levels: there are several criteria whereby other levels reside above lower levels

    So how many criteria do you need? What is the minimum number, below which it does not count as a hierarch?
    And why?

  213. the Pixie:
    Then you can devise a diagram illustrating this supposed “star network” , and we can see if a nested hierarchy is there or not.

    First YOU have to demonstrate you understand nested hierarchy. And neither you nor Zachriel has demonstrated that.

    the Pixie:
    As far as I can see you are taking a reasonable statement by N.Wells, and using it to support a fantasy.

    Seeing that is your inference I can see we don’t have anything left to discuss.

    Ya see the Pixie taxonomy relies on characteristic traits. N Wells has confirmed the premise that those characteristic traits can be lost or gained- just as Dentin depicted in comment 77.

    Therefore any arrangement that depends on characteristic traits can only be indicative of Common Descent if said traits are immutable.

    To Zachriel,

    My argument is over. You have already conceded the point.

    Zachriel:
    As in any such argument, we can define terms as long as they are unambiguous.

    That is false. But I understand why you would want it to be so.

  214. Joe

    First YOU have to demonstrate you understand nested hierarchy. And neither you nor Zachriel has demonstrated that.

    Good dodge! Because we all know you will never be able to admit that we understand, whether we do or not, which neatly avoids you having to answer the chalenge.

    Perhaps worth reminding everyone that I first made this challenge (to Inunison) way back on the 23rd January (post 16), just so we are all clear this is the latest in a string of avoiding tactics.

    Seeing that is your inference I can see we don’t have anything left to discuss.

    You did not discuss it anyway. You quoted, and asserted it supported your position, with no explanation as to why. Hmm, perhaps you do not know why? Or realised you were wrong?

    Ya see the Pixie taxonomy relies on characteristic traits. N Wells has confirmed the premise that those characteristic traits can be lost or gained- just as Dentin depicted in comment 77.

    Ah, so you will discuss it. Right, so it is entirely possible that (hypothetically) the underlying nested hierarchy cannot be reconstructed, which is what taxonomy attempts to do. That does not lead one to believe there is no underlying nested hierarchy though. And as the taxonomy was around before Darwin proposed common descent, it is a bit moot really.

  215. JoeG: Seeing that is your inference I can see we don’t have anything left to discuss.

    JoeG. I have tried everything to move the discussion forward. I have even abandoned the term “nested hierarchy” to avoid conflation, and proposed a specific definition for that very purpose of making my argument. But you have simply waved your hands and reposted the same material you posted a year ago.

    I’m sorry JoeG. It’s not that we disagree. I’m more than happy to justify my position, or even change that position. Rather, it is clear that you don’t want a discussion and that you have nothing to offer that would cause one to change their mind. If you decide you want an actual discussion, let me know. Good luck to you.

    And thank you, teleologist, for hosting this thread.

  216. Zachriel,

    The ONLY “challenge” you have proposed is to follow you down a one-way, dead-end street.

    My ONLY position is and ALWAYS HAS BEEN that Common Descent, although some may think it can “explain” the observed nested hierarchy using select populations, Common Descent would not expect such a pattern. And as a matter of fact Common Descent would remain unphased if nested hierarchy wasn’t observed.

    I have supported that position by citing scientists who tell us that traits can be gained or lost. And that matters because it is via traits that we catergorize populations. Comment 77 has a relevant diagram along with an explanation. (hint it has to do with derived traits and determining ancestry)

    That you keep avoiding that tells me you never wanted a discussion. You wanted to play railroad. Good luck with that.

    As for what predictions can be made from the observed pattern-> Seeing the observed pattern is wobbling stability, the prediction would be against Common Descent as having any influence on any pattern.

    And finally:

    Bear in mind, cladograms do not directly convey “who came from whom.” Groups closer together on the cladogram simply share a more recent common ancestor.–page 286 Biology: Concepts and Applications Starr fifth edition

    Common Descent is all about “who came from whom”.

  217. I’ve created a new thread, Nested Hieararchy, for Zachriel to post in. Although I doubt he will like the way I’ve structured the post. It would be nice if we all can direct any NH related issue to that thread.

  218. I have just noticed Tel is using this thread to rationalise his accusations that I am an atheist fascist, dishonest, insincere, etc. on a certain thread that I cannot respond to. How very honest of the brave Christian. From that thread:

    teleologist : How about you, do you know of a way to falsify common descent?
    Pixie : Very similar genetic sequences in distantly related organisms, but absent in closely related organisms.
    When I pointed out to him that the purple sea urchin is exactly that type of organism does he admit this falsified his common descent according to his criterion? Of course not, because he is not a sincere debater.

    Here is what Tel posted on this thread as a response, for reference:

    Duh. Isn’t this circular reasoning? How do Darwinians classify phylogeny? You stack the deck and classify organisms as close or distant relative by your perceived sequences and then you want people to disprove it by finding outgroups? But even if I find evidence that this is indeed case would that change you mind? I don’t think so. You know like the purple sea urchin, which has more homology to us than flies or worms.

    Okay, I missed the bit about the sea urchin. Big deal. I was responding to the other point in that paragraph. It is not like Tel ever brought it up again on this thread to prompt me (though looking back, inunison mentioned once, twenty posts later). Oh, no. I might respond.

    After some digging I found this article:

    http://news.ucf.edu/UCFnews/index?page=article&id=0024004105bd60439010c0c76ce2f004299

    Sea urchins are echinoderms, marine animals that originated more than 540 million years ago. The reason for the great interest in sequencing the sea urchin genome is because it shares a common ancestor with humans. Sea urchins are closer to human and vertebrates from an evolutionary perspective than other more widely studied animal models, such as fruit fly or worms. The purple sea urchin, in fact, has 7,000 genes in common with humans, including genes associated with Parkinson’s, Alzheimer’s and Huntington’s diseases and muscular dystrophy.

    So it turns out the purple sea urchin has more homology to us than flies or worms because it is more closely related to us. Which actually supports my prediction. So much for my dishonesty.

    It will be interesting to see if he has the honesty to edits his character assassination page to note that now I have responded.

  219. I have just noticed Tel is using this thread to rationalise his accusations that I am an atheist fascist, dishonest, insincere, etc. on a certain thread that I cannot respond to. How very honest of the brave Christian.

    I AM OUTRAGED! How dare you! How dare you to question my integrity on how I run my blog. Posting on this blog is a privilege and not a right. I have afforded this atheist bigot and internet-troll every opportunity to rant without ever moderating his comments. I challenge him to find another blog that have been so lenient. Do I hear a peep from this hypocrite, criticizing his fellow atheist blogs on how they won’t even let me trackback to their posts?

    Let us not forget, this is coming from an atheist bigot who would persecute an ID proponent and deny him of tenure for no other reason other than the fact that he is a senior fellow of the Discovery Institute. Atheist bigots like Pixie will deny freedom of speech to IDists and Creationist without blinking an eyelash, but have the audacity to insult me for having one post that he cannot inject his usual deceitful trolling? This is the epitome of despicable arrogance and hypocrisy.

    I am more tolerant, lenient and afforded more freedom than any blogs that I know on the internet. This is an OUTRAGE!

  220. On the page Tel has set up specifically to smear me (and I cannot defend myself on), he has responded:

    He had said if similar genetic sequences in distantly related organism (e.g. the purple sea urchin — Phylum: Echinodermata) are found but it is absent in closely related organisms (e.g. flies and worm — Phylum: Chordata) — this would falsify common descent. When confronted with such evidence, what does this troglodyte do? He now claims that this “actually supports my prediction” .

    Tel is confused. Flies and worms are definitely not in phylum chordata.

    Vertebrate animals (and a few others) are in the chordata phylum. Together with the hemichordates and the echinoderms, these make up the deuterostomes, a superphylum. Sea urchins are echinoderms, so people and sea urchins both fall in the deuterostomes superphylum.

    Insects are in the arthropoda phylum, which is in the ecdysozoa superphylum. See here.

    I found a relevant web page here:

    There was great interest in the sea urchin as a target for genome sequencing because these animals share a common ancestor with humans. That ancestor lived over 540 million years ago and gave rise to the Deuterostomes, the superphylum of animals that includes phyla such as echinoderms and chordates, the phylum to which humans and other vertebrates belong. All Deuterostomes are more closely correlation to each other than they are to any other animals not included in the Deuterostome superphylum. For example, among sequenced genomes, the genomes of fruit flies and worms are more distant from the sea urchin genome than is the human genome.

    “Each genome that we sequence brings new surprises. This analysis shows that sea urchins share substantially more genes and biological pathways with humans than previously suspected,” said Dr. Francis S. Collins, director of the National Human Genome Research Institute at the National Institutes of Health. “Comparing the genome of the sea urchin with that of the human and other model organisms will provide researchers with novel insights into the structure and function of our own genome, deepening our understanding of the human body in health and disease”.

    To discover how sea urchins and humans can be so different yet be related by descent from an ancient relative, their genomes were compared. The sea urchin is an invertebrate and the first example of a Deuterostome genome outside the chordates. Most prior invertebrate genomes that were sequenced, such as insects and nematodes, were animals outside the Deuterostome superphylum, eventhough one genome of a chordate invertebrate, the sea squirt, has been sequenced. The sea urchin lies evolutionarily in a large niche between the chordate branch of the Deuterostomes and the non-Deuterostome superphyla.

    “The sea urchin fills a large evolutionary gap in sequenced genomes,” said Dr. George Weinstock, co-director of the BCM-HGSC. “It allows us to see what went on in evolution after the split between the ancestors that gave rise to humans and insects. The sea urchin genome provided plenty of unexpected rewards and was a great choice for sequencing”.

    The comparison of the genes of the sea urchin to the human gene list shows which human genes are likely to be recent innovations in human evolution and which are ancient. It also shows which human genes have changed slowly in the lineage from the ancestral Deuterostome animal and which genes are evolving rapidly in response to natural selection. This will make it possible one day to know the history of every human gene and build a picture of what the extinct ancestors that gave rise to animal life from worms to humans looked like.

    Eventhough invertebrate sea urchins have a radically different morphology from humans and other vertebrates, their embryonic development displays basic similarities, an important shared property of Deuterostome animals. This distinguishes them from Protostomes, which have a different pattern of embryonic development.

  221. My mistake and Pixie is right the fruit fly and worm are taxonomically more distant from human (phylum: Chordata)

    This actually falsifies common descent according to Pixie’s criterion.
    Pixie; Very similar genetic sequences in distantly related organisms, but absent in closely related organisms.

    The fruit fly and nematode actually have more genes in common with us than does the purple sea urchin.

    UCF Professor Cristina Calestani was part of the Sea Urchin Genome Sequencing Group, which recently completed sequencing of the sea urchin genome and published its findings in the November issue of Science. ” The purple sea urchin, in fact, has 7,000 genes in common with humans

    Now consider the number of genetic similarity we have with the fruit fly.

    For example, a comparison of the fruit fly genome with the human genome discovered that about 60 percent of genes are conserved between fly and human.

    What does 60% of the fruit fly genes translates to? The fruit fly has about 14,000 genes, therefore 60% would translate to 8400 genes.

    The fruit fly (Superphylum: Ecdysozoa) has 1400 more homologous genes with humans (Superphylum: Deuterostomia) than the purple sea urchin (Superphylum: Deuterostomia).

    Common Descent has been falsified, will Pixie have the intellectual integrity to admit that Darwinian evolution has been debunked?

  222. Interesting. I have started a thread at ARN to see what people there think. I do not know enough about genetics to be able to comment, but I found links giving figures from 40% to 70% for how many genes we share with the fruit fly.

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