Nested Hierarchies (Tree of life)

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Do you want to be my cousin?
Sure. If not me, then who?

  1. “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution. This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates. The three basic assumptions of cladistics models are: a) Any group of organisms are related by descent from a common ancestor (UCD – universal common descent); b) There is a bifurcating pattern of cladogenesis; c) Change in characteristics occurs in lineages over time. Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism” and not by a process generated by a designer that also happens to make use of biologic reproduction.
  2. No assumption can be tested by the model that uses them. That is why they’re called ‘assumptions’ and not ‘conclusions’. Instead, assumptions have to be tested independently through an entirely separated method or be accepted as axioms. An UCD “mechanism” has never been observed or proved elsewhere and is not “self-evidently true”, therefore not a valid axiom. Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis. Furthermore the conclusions of any “cladistic analysis” will always and trivially be compatible with the UCD assumption in that model.
  3. Hypothesis testing requires an alternative (null) hypothesis and a procedure that demonstrates how the data available is compatible with the successful hypothesis and at the same time is statistically incompatible with the alternative hypothesis. In the “cladistic analysis” case, the alternative hypothesis to UCD is “common design”, and of course UCD cannot be an assumption of such an analysis. However this rule is violated twice, first by the use of an assumption also presented as conclusion, and second by the prejudiced rejection of the alternative “common design” hypothesis before analysis. This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD. What “cladistic analysis” is instead is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points.
  4. The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility. This is not surprising as designers are free to incorporate whatever mechanism they want, including intelligent “selection” (human breeders do!) and “common descent” (human breeders do!) if they so desire.
  5. The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false. On one hand, we do know the history of the automobile, so a proper classification must be able to reconstruct their unique “evolution”. Yes, vehicle share parts, so to get to the actual development tree, we must group them differently than organisms since mass production works differently than biologic reproduction. On the other hand, organisms may not be uniquely classified as demonstrated by the numerous revisions and exceptions to the “tree of life”, and in any case, “uniquely classified” is an absolute claim that can never be proven since it is impossible to compare the infinity of possible organism classifications.
  6. The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails. Anatomy is not independent of biochemistry. Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited. This is not to say that the fossil record is complete, or that fossils can be positively linked to one another and the living without – once again – presupposing UCD. The claim that “there is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry” is false as the ‘designer’ hypothesis produces the same result when one designer creates all morphologies, and furthermore “I cannot think of an alternative reason why…” is not a valid argument.
  7. A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure. To decide the position of a certain organism, the human creators of the “tree” have to decide which morphologic/biochemical/genetic characteristics to include and what weight to attach to each of those measures. This further supports the claim that “cladistic analysis” is ‘curve fitting’ rather than ‘hypothesis testing’ – if a tree must be built, a tree will be built as in this example: “The close relationship between animals and fungi was suggested by Thomas Cavalier-Smith in 1987, […] and was supported by later genetic studies. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants […].”

 

1,009 thoughts on “Nested Hierarchies (Tree of life)

  1. Joe Felsenstein,

    I believe you have previously suggested that anyone interested in how this actually works might consider reading Inferring Phylogenies. It’s not a bad idea, except that despite its clarity and accessibility, I don’t think it would be either for Bill or nonlin. Maybe Mung could get something out of it.

  2. Joe Felsenstein,

    A discussion of how the rain runs off the roof can go forward without any discussion of what caused it to rain.

    Thank you for the analogy. When John discusses the tree and the nested hierarchy that is fine. His claim that this discussion is separate from mechanism is also fine.

    What becomes problematic is when he leaps to the claim that the only explanation of the nested hierarchy is common descent. He must have made this assertion without support 200 times in the famous 5000 thread op.

  3. John Harshman,

    If this means anything, and I’m not sure it does, it refers to your main confusion, the one between an explanation of nested hierarchy and an explanation of the various differences in features that happen within the hierarchy. Have you in fact learned absolutely nothing during all our conversations over a period of years?

    I think we agree that the nested hierarchy does not explain the origin of the spliceosome it only explains the pattern the spliceosome is a part of.

    Design does explain the origin of the spliceosome. It is a differentiating feature of the hypothesis.

    Both design and common descent explain similar genes being observed in different organisms.

    Design explains the same gene set being observed in two organisms that do not share a common ancestor that is not observed in the organisms that do share a common ancestor.

    The example is genes shared by chimps and rats that don’t exist in humans and mice.

  4. colewd:
    John Harshman,

    I think we agree that the nested hierarchy does not explain the origin of the spliceosome it only explains the pattern the spliceosome is a part of.

    Design does explain the origin of the spliceosome.It is a differentiating feature of the hypothesis.

    I’m afraid you are still hopelessly confused about what we’re talking about. That’s because you don’t actually have a design hypothesis. You only have the word “design”, which to you just means anything God might do anywhere at any time. If the spliceosome is designed, that’s fully compatible with common descent. That particular design is irrelevant to what we’re discussing here. We could argue about whether anything other than design could produce the spliceosome, but it’s still irrelevant.

    Both design and common descent explain similar genes being observed in different organisms.

    True, but only because design is just a word that could in principle apply to anything. If you try to set forth a real theory of common design, it fails instantly. Design doesn’t explain nested hierarchy, and it doesn’t explain why those supposedly re-used parts are different in different species.

    Design explains the same gene set being observed in two organisms that do not share a common ancestor that is not observed in the organisms that do share a common ancestor.

    The example is genes shared by chimps and rats that don’t exist in humans and mice.

    Genes shared by chimps and rats are also compatible with common descent; they just require two losses. But I don’t see how they’re compatible with design unless you just choose to interpret anything whatsoever as compatible with design. What design requirements could chimps and rats possibly share that they wouldn’t also share with humans and mice? And why, if this is re-use of parts, aren’t the genes identical in the two species? (One might also check to see if the genes in question are found in other species and if remnants of those genes are found in other species, including humans and/or mice.)

  5. colewd: What becomes problematic is when he leaps to the claim that the only explanation of the nested hierarchy is common descent. He must have made this assertion without support 200 times in the famous 5000 thread op.

    No, you just ignore the support. The support is simple: a nested hierarchy is exactly what we would expect from common descent (with branching). It’s not what we expect from separate creation of species, which is what you mean by “common design”. It’s not to be expected from your buzzphrase “re-use of parts”. It’s not to be expected from anything you have ever mentioned. There being no alternative that would produce such a pattern — if there were you would have come up with one by now — common descent is sole remaining hypothesis.

  6. John Harshman:
    Joe Felsenstein,

    I believe you have previously suggested that anyone interested in how this actually works might consider reading Inferring Phylogenies. It’s not a bad idea, except that despite its clarity and accessibility, I don’t think it would be either for Bill or nonlin. Maybe Mung could get something out of it.

    I plead innocent. I think I have referred people there for abstruse technical details, but I wouldn’t recommend it to people less interested in the minutiae. David Baum and Stacy Smith’s Tree Thinking: An Introduction to Phylogenetic Biology would be much more accessible. (Of course neither book is aimed at people who have difficulty with evolution, so they shouldn’t be surprised if their favorite criticisms are not covered).

  7. John Harshman,

    No, you just ignore the support. The support is simple: a nested hierarchy is exactly what we would expect from common descent (with branching). It’s not what we expect from separate creation of species, which is what you mean by “common design”.

    This is again just an assertion. Do you understand what supporting an argument means? It does not mean repeating this is what we expect and this is what we don’t expect it explains why and supports the argument with data.

    How do you know that we would not expect a nested hierarchy from special creation?

    Why do you expect a hierarchy from common ancestry?

    Thats what I would expect from special creation due to re-used genes base on basic design principals. I would not expect common ancestry to necessarily to create a hierarchy. Where we know common descent is likely there is very little hierarchical structure.

  8. colewd:
    John Harshman,
    How do you know that we would not expect a nested hierarchy from special creation?

    Because I can’t think of a model of special creation that implies a hierarchy. Can you?

    Why do you expect a hierarchy from common ancestry?

    I would have thought this was obvious. If events happen at particular times in particular evolving lineages, and those lineages split, the descendants will inherity the results of that event. If a fair number of such events happen at various points on a tree, the data will reflect that tree and will thus form a nested hierarchy. I would draw you a picture if I could, but hey, there’s a fine picture in the croc paper. Do you see Fig. 2? That actually shows all the changes in the sequence, mapped onto the tree, showing where each of them happens. See how that makes a nested hierarchy?

    Thats what I would expect from special creation due to re-used genes base on basic design principals.I would not expect common ancestry to necessarily to create a hierarchy.

    Why would re-used genes create a nested hierarchy? Why would re-used genes have different sequences in different species rather than the same sequence, and why would those different sequences themselves form a nested hierarchy? Why would different genes form the same nested hierarchy? Why would junk DNA form the same nested hierarchy?

    And why would you not expect common ancestry to create a hierarchy?

    Where we know common descent is likely there is very littlehierarchical structure.

    What do you mean by that?

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