Nested Hierarchies (Tree of life)

Moderator’s remark: this post is long enough to need a “more” tag.  But the wordpress editor will only allow me to add that at the very beginning or the very end.  So here it is at the very beginning.

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 […].”

 

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1,059 thoughts on “Nested Hierarchies (Tree of life)

  1. Neil Rickert: I see both of those as being true.

    That’s odd, since they’re mutually exclusive.

    We could have come up with an entirely different scheme — maybe one where bats were classified with birds and whales were classified with fish.But I doubt that any such scheme would be as useful as the one that we currently use.

    Why not? I would argue that a phylogenetic classification scheme is useful because it’s true. It actually does represent the real phylogeny of the organisms included in it. But bats + birds or whales + fish reflects nothing than a superficial similarity in a couple of features. That would be exactly the caricature that nonlin and his defenders are drawing.

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  2. Mung: Overlooked, neglected, ignored. What’s the difference?

    This is why nobody can take you seriously. You had a previous post vehemently insisting that there was a big difference. Do you enjoy being taken for a troll?

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  3. Sorry Nonlin, I’m not interested in your misconceptions one bit. So I’m not even reading your crap. I answered out of fun, but for onlookers benefit. You’re unreachable. It’s not as if you’re about to change your ways and learn to read.

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  4. Erik:
    Theobald’s example includes cars as a “subjective” nested hierarchy and languages as an “objective” nested hierarchy.

    Do you mean to say that Theobald didn’t say that each and every kind of nested hierarchy works? Fine, then you agree with me that you spoke too soon about whether I agree or disagree with him. I’d have to know how well he explained himself, which I still don’t know, but, of course, I expected that he wouldn’t say each and any.

    Erik:
    In reality, both are objective, depending on the purpose of selecting the specific characteristics to form the hierarchy. Theobald’s example fails.

    Are you sure he wrote “objective” nested hierarchy, rather than a nested hierarchy with an objective basis? Either way, while the second would work better, of course that’s not enough of an explanation. That still doesn’t explain what kinds of nested hierarchies are expected from evolutionary processes, but, again, if you mistake “objective basis” for “objective,” then I understand your confusion. That still doesn’t mean that Theobald said “each and any nested hierarchies,” and thus, when I say that not all nested hierarchies are evolutionary trees, I’m not actually disagreeing with Theobald, right?

    Erik:
    In any case, nested hierarchies cannot serve as evidence for evolution. You seem to vaguely comprehend the main reason: Only a certain very specific nested hierarchy, produced by an evolutionary process, could serve as such.

    There’s nothing vague in my understanding. I’ve been insisting that you have to understand first what kind of nested hierarchies would help. Very clearly.

    Erik:
    However, more is required:

    No kidding! Of course more is required. More is also available.

    Erik:
    Either the very specific nested hierarchy should not be produced by any other process except evolutionary, or the evolutionary process should first be directly observed on independent grounds.

    Now you lost me. Of course the kind of nested hierarchies we see should look as if produced by evolutionary processes. But making it the one and only way is like trying to prove an universal negative, which is philosophically problematic. How could that escape you after you mentioning philosophical problems with whatever you read from Theobald?

    Either way, we’re very fortunate, because there’s other sources of evidence for evolution.

    Erik:
    Let’s take Theobald’s example: Languages … The nested hierarchy is an illustration of observed facts obtained on independent grounds. The observed facts serve as the justification to drawing the nested hierarchy, not the other way around.

    And the same is true for evolution. We find evidence for common ancestry independent of nested hierarchies before attempting to put that into a tree. The tree then serves as further evidence because they produce a kind of nested hierarchy that looks awfully like an evolutionary process, and because different sets of data produce similar trees.

    Erik:
    If Theobald’s examples are true or at least adequate, then it cannot be the case that nested hierarchies are evidence for evolution, because they are certainly not evidence for language families.

    Of course they’re evidence in both cases. It’s about coherence Erik. If the attempts at producing nested hierarchies failed to reproduce what we’ve learned about languages, then that would justify taking a better look. Check for problematic sources, for historical happenstances, like wars between England and France that would cross-contaminate both languages, etc. If even that didn’t work, then we’d still learn that something might be deeply wrong about what’s been said about languages, the testimonials, the writings, the examples of ancient English, etc.

    Erik:
    … and also fails to clarify the kind of nested hierarchy specifically brought about by evolutionary processes, so that it could serve as evidence for evolution specifically.

    This might be the case (again, I don’t know, I didn’t read the whole thing, only a couple sentences).

    Erik:
    It all boils down to: Whatis an evolutionary process? On what grounds does one call a biological process evolutionary. Is it distinguished from a non-evolutionary process or are all biological processes assumed to be evolutionary?

    Oh! Some actual insight. Tempts me to give you a very nice and thorough answer. But I suspect you’d take it the wrong way, I’d be very disappointed, and then angry at myself for giving you the benefit of the doubt.

    OK, let’s see. The way I see it, life and evolution are irremediably linked. Evolution is a natural consequence of there being life. However, I’m still not sure that we could call any life processes evolutionary processes. This is very arguable, so I have to think more deeply about it. Maybe for a few years.

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  5. John Harshman: I would argue that a phylogenetic classification scheme is useful because it’s true.

    I’m inclined to see that the other way around. It is because we find it very useful, that we consider it to be true.

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  6. Neil Rickert: I’m inclined to see that the other way around.It is because we find it very useful, that we consider it to be true.

    But that isn’t what “true” means. A phylogenetic classification is true because it reflects the actual history of the species involved. Whales really are mammals rather than fish. Not because considering them mammals is more useful to us but because they are really, truly more closely related to hippos than to flounders.

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  7. John Harshman: But that isn’t what “true” means.

    My own take on truth, is that a classification system is neither true nor false. We adopt such a system on entirely pragmatic grounds. But, once we have adopted it, there is a tendency to say that it is true.

    A phylogenetic classification is true because it reflects the actual history of the species involved.

    We cannot use a time machine to go back and verify. We can only depend on inference from the present.

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  8. John Harshman,

    Must I remind you that you don’t know what you’re talking about? “Mammals” isn’t a category defined by humans, for which you need only to have certain chosen characteristics to be a member. It’s a taxon, and you’re a member if you are descended from the common ancestor of all mammals.

    This is circular reasoning. Universal common descent is a working assumption just like UC Berkeley stated.

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  9. Neil Rickert: My own take on truth, is that a classification system is neither true nor false.We adopt such a system on entirely pragmatic grounds.But, once we have adopted it, there is a tendency to say that it is true.

    I hae to assume that you aren’t at all familiar with phylogenetics, as this bears no relation to how it’s actually done.

    We cannot use a time machine to go back and verify.We can only depend on inference from the present.

    Sorry, I didn’t realize you were a creationist. That’s “were you there?”, Ken Ham’s favorite line. You should understand that inference from the present is a powerful tool that allows us to arrive at reliable knowledge of the world. It’s how science works.

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  10. colewd: This is circular reasoning. Universal common descent is a working assumption just like UC Berkeley stated.

    None of that had anything to do with universal common descent, just common descent of the species you happen to be dealing with at the moment. And what keeps it from being circular is that analysis tests the assumption. We’ve been over this before, and I wish you would start paying attention.

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  11. The ID fans here seem to be raising the same old disagreements with our inference of common descent, the arguments that led to a 5,000-comment thread. They are taking the view that that was what nonlin.org meant by the rather odd statement that the species “do not come labeled with their position in a cladistics hierarchical structure”.

    I am not going to argue about common descent as we did have that argument. My own view is that the argument showed major failures of the ID/creationist arguments, and that although they of course did not concede, most lurkers will not have been impressed by their approach. Your opinion of that thread’s net effect may be different.

    So what about one of the other points?

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  12. John Harshman,

    And what keeps it from being circular is that analysis tests the assumption. We’ve been over this before, and I wish you would start paying attention.

    Your statement assumes common descent of all mammals. You’re reasoning is circular. and…did you really call Neil Rickert a creationist?

    You haven’t tested anything. You have assumed your conclusion.

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  13. Nonlin.org: You’re very wrong. For any family, you won’t be able to build a genealogy without the labels: vital records, family records, interviews, etc. Yes, every person has a genealogy, but would you ever be able to build the family tree without the labels? And yes, the tree is an artificial human construct – lines and circles/squares of ink on paper or digital.

    That is very odd. Given people’s DNA sequences, yes, we can infer their genealogy without any “labels” to help us. All we have to know is which DNA sequence came from which person.

    Similarly for present-day organisms. Without any further label other than a specimen identifier (or a species name) we can infer their phylogeny. No, we don’t need anyone to tell us what class, or order, or family they are in. nonlin.org’s odd wording implies that nonlin.org thinks that we do need those identifiers.

    Why do we need them?

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  14. Joe Felsenstein,

    Your opinion of that thread’s net effect may be different.

    Common descent is based on an assumption. The inference made by Darwin. The scientific consensus still strongly supports that assumption. Every piece of contrary evidence like convergent evolution and genes not following the tree pattern is swept under the carpet. I for one who has only observed it for a short period of time think you are on a very slippery slope. Every evolutionary paper I have read assumes it is true. The fall here could be epic.

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  15. colewd:
    John Harshman,

    Your statement assumes common descent of all mammals.You’re reasoning is circular.and…did you really call Neil Rickert a creationist?

    Of course my statement assumes common descent of all mammals. But that “assumption” is based on vast amounts of evidence. Any gene you care to look at, or any collection of characters, will show you that (other than one carefully chosen specifically to claim otherwise). That “assumption” is backed up. Can you say the same for anything you say?

    You haven’t tested anything.You have assumed your conclusion.

    On what basis do you make that claim?

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  16. colewd: Every piece of contrary evidence like convergent evolution and genes not following the tree pattern is swept under the carpet.

    Show me some of that contrary evidence and we’ll talk. If you’re talking about Sal’s flower, the problem is that you don’t understand Sal’s flower and have completely forgotten everything I’ve explained to you about it, as you forget everything. We’re always starting from square one. Tiring.

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  17. John Harshman: I hae to assume that you aren’t at all familiar with phylogenetics, as this bears no relation to how it’s actually done.

    I’m not a biologist. However, the disagreement is about truth, not about phylogenetics.

    Sorry, I didn’t realize you were a creationist.

    I’m not.

    That’s “were you there?”

    Actually, it isn’t.

    I’m a pragmatist. I have no problem accepting pragmatic views of the past. I am disagreeing with your assertion that you are using truth rather than pragmatism.

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  18. Entropy: Are you sure he wrote “objective” nested hierarchy, rather than a nested hierarchy with an objective basis?

    So you don’t even know what you’re talking about, even though I directly linked you there and even though you, being an evolutionist, should already have known it. Rather disappointing, but at least it explains why everything else you say has no explanatory force. You simply don’t know any better.

    Erik: It all boils down to: Whatis an evolutionary process? On what grounds does one call a biological process evolutionary. Is it distinguished from a non-evolutionary process or are all biological processes assumed to be evolutionary?

    Entropy: Oh! Some actual insight. Tempts me to give you a very nice and thorough answer. But I suspect you’d take it the wrong way, I’d be very disappointed, and then angry at myself for giving you the benefit of the doubt.

    OK, let’s see. The way I see it, life and evolution are irremediably linked. Evolution is a natural consequence of there being life. However, I’m still not sure that we could call any life processes evolutionary processes. This is very arguable, so I have to think more deeply about it. Maybe for a few years.

    Hopefully you see for yourself how silly your non-answer is. But I don’t blame you. Undisputed experts have not done much better.

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  19. John Harshman,

    On what basis do you make that claim?

    You have no standard to determine if data confirms common descent or not. It is assumed. I have tried to explore this with you and you have insisted I take a firm position. My firm position is you have no credible standard in which to determine common descent.

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  20. Neil Rickert: I am disagreeing with your assertion that you are using truth rather than pragmatism.

    Whatever he is using, it is the same thing we use when we conclude that, for example, that continental drift has occurred.

    Call it what you will, stuff it into whatever philosophical framework you wish.

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  21. John Harshman: “Mammals” isn’t a category defined by humans, for which you need only to have certain chosen characteristics to be a member. It’s a taxon, and you’re a member if you are descended from the common ancestor of all mammals.

    Humans are mammals because they share common features with other mammals. Whether this entails common descent should be determinable on other grounds, not merely based on the fact that humans can be grouped with other mammals.

    As Theobald acknowledges, it is trivial to classify anything subjectively in a hierarchical manner. If you want it to prove something, it should not be trivial.

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  22. colewd: Every piece of contrary evidence like convergent evolution

    As has been explained to you, convergent evolution isn’t evidence against common descent as common descent does not claim that convergent evolution shouldn’t happen.

    Once again, you don’t understand the difference between:
    1. Having evidence for X.
    2. Having evidence against X.
    3. Evidence being neutral with respect to X.

    Convergent evolution, or homoplasies, can only amount to 3 on that list. It can’t constitute 2.

    and genes not following the tree pattern is swept under the carpet.

    What genes? Where are they swept under the carpet and what do you even mean by that?

    Again, if a particular locus fails to corroborate common descent, that doesn’t make it contradictory to common descent, as common descent does not entail all loci must conform to the pattern.

    Tire tracks on the road is evidence that a car drove there. But the absense of those tracks isn’t evidence against a car having been there. After all, we don’t expect the car to always leave melted rubber on the pavement.

    That’s basically what it is like with consilience of independent phylogenies. When we find them, that is evidence of common descent. If we find that not all genetic loci exhibit the pattern, that doesn’t mean it contradicts common descent, it just means that particular locus cannot be used as evidence FOR it. It is an absense of tire tracks, which is not the same thing as evidence for the nonexistence of cars.

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  23. Nonlin.org: 1. No. I am saying that there’s no problem with Intelligently Guided common descent linking all organisms, but RV+NS (including “genetic drift”, etc) common descent is a fantasy because RV fails http://nonlin.org/random-abuse/ and NS fails http://nonlin.org/natural-selection/. Clear?

    Are you saying that you accept universal common descent, with the footnote that all lineage changes are to be attributed to the Designer? Wow, I hadn’t expected it to be this easy.

    Nonlin.org: 2. Fair enough. Let me rephrase: Say one of these days humans get one organism born (include genetic engineering) from a different one (cat from dog or bacteria 1 from bacteria 2, etc.). Would that be proof of Intelligent Design? Darwinian evolution? Both? Neither? Hopefully your attorney won’t object this time 😊

    If humans ever get a cat born from a dog, by genetic cut-n-paste and IVF, then I am happy to acknowledge that this is not an example of Darwinian evolution. I am not sure whether that is intelligent design, because I don’t see the point of going through all the hassle to produce an animal that already exists, but clearly some design is involved.

    Sorry, I still don’t see the relevance. What does the fact that humans can introduce genetic changes have to do with common ancestry?

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  24. Nonlin.org: Just because you’re avoiding a crushing problem, it won’t go away. You’re speculating left and right about LUCA and UCD, etc, but “Don’t know how many times life got started”? Ridiculous and not fooling anyone. How would you know “LUCA has ancestors as well”? Can you prove? Tell me more about your observations on LUCA.

    Again, this simply follows from what LUCA is: the last universal common ancestor. Suppose that an extraordinarily destructive disaster obliterated all life on earth, except an ocelot and a tiger, then LUCA would be a cat. The fact that that animal traces its ancestry through billions of years of evolution doesn’t matter, because all other lineages have disappeared. See?

    Nonlin.org: Don’t remember where “ancestor” discussion started and really don’t care to learn Dutch or Chinese to continue. But now you want to separate organisms from machines when the whole materialism shtick is based on the premise that organisms are nothing more than meat machines? Can you see the irony? Of course not.

    Oh, but I love irony. Tell me, who were comparing living organisms to a WATCH? Mmmmmmmm, let me think.

    ETA: corrected mistake

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  25. Neil Rickert: I’m a pragmatist. I have no problem accepting pragmatic views of the past. I am disagreeing with your assertion that you are using truth rather than pragmatism.

    That is an intriguing position. Of course, the reason that a phylogenetic tree is useful is because it correctly (one hopes) describes the branching order of the species that are in it. I am not entirely sure how you can separate the usefulness of the tree from its correct correspondence to the historical situation.

    PS: didn’t realise you were a closet creationist. Shame on you, Neil 😉

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  26. Rumraket,

    Once again, you don’t understand the difference between:
    1. Having evidence for X.
    2. Having evidence against X.
    3. Evidence being neutral with respect to X.

    I understand that common descent predicts a nested hierarchy or a branching pattern. A branching pattern predicts genes should flow through from the common ancestor to the descendants. In the case of convergent evolution or gene loss they do not.

    This is evidence against x.

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  27. Corneel,

    PS: didn’t realise you were a closet creationist. Shame on you, Neil

    If you can’t beat em shame em 🙂

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  28. Rumraket,

    Tire tracks on the road is evidence that a car drove there. But the absense of those tracks isn’t evidence against a car having been there.

    Tractor tracks are 🙂
    You expect gene set A and you get gene set B.

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  29. colewd: I understand that common descent predicts a nested hierarchy or a branching pattern.

    In some genes, yes. Not all genes at all times without exception.

    A branching pattern predicts genes should flow through from the common ancestor to the descendants.

    Except when they get lost. Or horizontally transferred. Both of those are observed phenomena.

    In the case of convergent evolution or gene loss they do not.
    This is evidence against x.

    No, wrong. Again.

    You again fail to understand the difference between:
    1. Having evidence AGAINST.
    and
    2. NOT having evidence FOR.

    Common descent does not predict that all genes should always be retained, or that homoplasies should never take place. We know this from direct observation of commonly descended populations of organisms.

    The bacteria in Lenski’s experiment all share common descent, but in all 12 lineages different deletions and losses have happened. So we can simply see with our own eyes that common descent does not result in the absense of gene loss, or absense of homoplasy. Both of those happen simultaneously with common descent taking place.

    So when we observe gene loss, or homoplasy, we are not seeing something that common descent says should not happen. So it can’t be evidence against common descent.

    Again, think about the analogy. Cars some times leave tracks on the road. If you find such tracks, that is evidence a car drove there. But it also happens that the car leaves no tracks (it isn’t braking, or isn’t accelerating hard so the rubber isn’t melting and sticking to the asphalt). We can see cars come by without leaving tracks.
    So while the tracks is evidence that a car was there, the absense of those tracks can’t be evidence that no car was there (as there could of course have been a car there that didn’t leave tracks).

    The hypothesis that cars leave tracks when braking or accelerating hard does not say that cars leave tracks under all circumstances. When you find that the track stops that isn’t evidence that the car went out of existence at that point.

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  30. colewd: Tractor tracks are

    No, tractor tracks is not evidence against a car having been on the road. That’s evidence for a tractor having been there, not he absense of a car.

    I recommend thought.

    You expect gene set A and you get gene set B.

    What are you even talking about here?

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  31. Rumraket,

    Common descent does not predict that all genes should always be retained, or that homoplasies should never take place. We know this from direct observation of commonly descended populations of organisms.

    You’re reasoning is circular.

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  32. Rumraket,

    I recommend thought.

    I recommend a better analogy. I expect a car and I get a tractor. I expect gene set A and I get gene set B. Denial is not a river in Africa.

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  33. colewd: This is circular reasoning. Universal common descent is a working assumption just like UC Berkeley stated.

    Nope.

    1. UCD is a working hypothesis supported by several lines of data. Not a mere I-wish-it-to-be-so assumption.
    2. For analyzing whales there’s no need for UCD, it’s enough for there to be common ancestry among mammals, or perhaps all the way to vertebrates (since we’d like to know if whales could be fish instead). I really don’t understand why you focus on universal, as if you didn’t know what the word universal means.
    3. There’s plenty of unequivocal evidence for common ancestry between vertebrates in general and mammals in particular.
    4. You already understand that the evidence for common ancestry can be non-phylogenetic, so, please, don’t act as if you didn’t understand anything so far. It’s offensive, not just to me, but to yourself. It makes you look characterless.

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  34. colewd:
    I understand that common descent predicts a nested hierarchy or a branching pattern. A branching pattern predicts genes should flow through from the common ancestor to the descendants. In the case of convergent evolution or gene loss they do not.

    In the case of convergent evolution they do. We would not know if there was convergent evolution unless we could follow the patterns of inheritance Bill. Now, careful there, very careful. Think slowly and carefully. Can you explain to me how could some kind of evolution be evidence against evolution?

    I cannot understand the kind of mentality required to think that if organisms have common ancestry they should not lose genes. Sounds extraordinarily dumb. So, please, explain this also very carefully. How do you get from common ancestry to the impossibility of losing genes?

    colewd:
    This is evidence against x.

    More like evidence that logic is not your forte.

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  35. Corneel: That is an intriguing position. Of course, the reason that a phylogenetic tree is useful is because it correctly (one hopes) describes the branching order of the species that are in it.

    I was not commenting on the structure of the tree. Rather, I was commenting on that word “correctly”. Because that’s the core of the disagreement.

    The creationist insists that “correctly” comes from his god.
    The evolutionist insists that “correctly” just is, and has no source.

    I say rubbish to both. I say that “correctly” arises from human pragmatism.

    The problem with pragmatism, however, is that it cannot be pinned down. We judge based on what works. But “what works” really means “what works to satisfy some purpose”. And there is disagreement about purposes.

    PS: didn’t realise you were a closet creationist. Shame on you, Neil

    No, I’m not. I generally disagree with the creationists. But colewd made a correct point, so I agreed with that. The appropriate evolutionist response should have been “so what — even if colewd is correct about that point, his argument still does not show what he claims”.

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  36. colewd: Rumraket,

    Common descent does not predict that all genes should always be retained, or that homoplasies should never take place. We know this from direct observation of commonly descended populations of organisms.

    You’re reasoning is circular.

    Prove it. Spell out the circular chain of reasoning for me.

    What you’re saying is completely nonsensical as a response to what you quote. I derive a prediction (we do not expect the absense of homoplasy or gene loss under common descent) from an observation (because we have direct empirical observation that homoplasy and gene loss takes place in commonly descending population).

    How can that be circular reasoning? Bill it looks like you’re just saying stuff again.

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  37. Erik:
    So you don’t even know what you’re talking about, even though I directly linked you there

    I have no interest to defend someone else’s posts, explanations, and examples. I know why and how nested hierarchies indicate evolution though. But I don’t need Theobald. I can think all by myself.

    Erik:
    and even though you, being an evolutionist, should already have known it.

    1. I’m not an evolutionist. I accept evolution because I have no choice in the matter. I just understand and thus accept regardless of whether I like it or not. But I don’t worship evolution. I don’t adhere to it. I just accept things the way they are. It’s a question of honesty.
    2. I already know why nested hierarchies can be evidence for evolution. What I don’t know, and have no reason to know, is how far, how well, and how accurately, Theobald went into it. I’m not that guy.

    Erik:
    Rather disappointing, but at least it explains why everything else you say has no explanatory force. You simply don’t know any better.

    This looks like you didn’t bother to read for comprehension. It’s obvious that I wasn’t explaining how nested hierarchies are evidence for evolution. I was just pointing out the mistakes in your approach towards it. The mistakes and conceptual messes you make. The need to understand that it’s not any nested hierarchies, etc.

    Erik:
    Hopefully you see for yourself how silly your non-answer is.

    Well, I’m sorry that I gave you the benefit of the doubt. I hereby let you know that I don’t know everything, that I have thought about this inevitability of evolution given life, but didn’t go into details because I was only testing the waters. That I see evolution the way I see planetary orbits. Evolution a consequence of life, orbits the consequence of gravitation. That even so, I haven’t thought if any and every life processes could be therefore called evolutionary processes. I have lived too little time (human life is so ephemeral) and worked on other fields. So, I haven’t gone that far, and I doubt I can take a position about it any time soon.

    So, if honesty is silly, then I see why you don’t understand evolution. You cannot give it a honest look because that would be silly. At least in your view.

    Given your incompetence reading for comprehension, I’ll leave it here.

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  38. colewd: I recommend a better analogy.

    No I still think the issue is with how you think.

    I expect a car

    No, the car is the hypothesis. What you expect is evidence of the car. As in something for which the car is the best, most likely explanation.

    Tire tracks on the road is evidence of the car.

    Tractor tracks is evidence of a tractor.

    But tractor tracks is not evidence of the absense of the car. All you can say is that if you fail to find car tracks, in so far as a car was there it didn’t break or accelerate hard enough to make tracks.

    Whatever the tractor did or didn’t do, is irrelevant to what the car did not didn’t do. After all, both cars and tractors can drive on the same road.

    How is it I even have to spell this out?

    and I get a tractor.

    No. You got tractor tracks, that’s what you said.

    What is tractor tracks evidence of? A tractor.

    What do tractor tracks say about cars? Nothing.

    I expect gene set A and I get gene set B.

    What is gene set A and why do you expect it, what is gene set B?

    Denial is not a river in Africa.

    Amazing.

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  39. Neil Rickert: I’m not a biologist.However, the disagreement is about truth, not about phylogenetics.

    Isn’t it about both? Or are you making a universal argument that there is no such thing as truth in the sense I’m claiming, only usefulness, and phylogenetics only happens to be a current instance?

    I’m a pragmatist.I have no problem accepting pragmatic views of the past.I am disagreeing with your assertion that you are using truth rather than pragmatism.

    OK. I think I have no interest in that question.

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  40. colewd:
    John Harshman,

    You have no standard to determine if data confirms common descent or not. It is assumed. I have tried to explore this with you and you have insisted I take a firm position. My firm position is you have no credible standard in which to determine common descent.

    Why not? The standard is presence of a strong and consistent signal in the data supporting a single tree. Nothing other than common descent would produce such a signal. Why isn’t that credible?

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  41. Erik: Humans are mammals because they share common features with other mammals. Whether this entails common descent should be determinable on other grounds, not merely based on the fact that humans can be grouped with other mammals.

    As Theobald acknowledges, it is trivial to classify anything subjectively in a hierarchical manner. If you want it to prove something, it should not be trivial.

    Ah, but mammals are not classified subjectively. If you take a list of characteristics at random from genomes or morphology, you will consistently arrive at the same conclusion, that mammals go together. This is not the case for subjective classifications. If you take different characters from a set of cars, or even if you consider them in a different order, you will get a different tree of cars. Not so for mammals. The consistent consilience of different data sets demands an explanation, and common descent is the only credible explanation.

    Incidentally, “prove” is not a word you should be using in science. The data provide strong evidence, but there’s no such thing as proof.

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  42. Seems to me that evolution also predicts that, given enough time since lineage splits, they will show no DNA similarity. Kind of like a molecular event horizon?

    If that’s right, do we know how long it will take?
    At that point we’ll we need to rely on literature instead of evidence, to accept common descent between those lineages?

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  43. John Harshman,

    Why isn’t that credible?

    It’s simply an assertion you repeat. I see contradictory evidence which I am being told is not contradictory evidence and I should expect it. It appears the predictions are coming after the data and not before.

    I have no direct evidence that reproduction can create the odd patterns we see.

    We now have evidence that design can create a hierarchical pattern and the data can be arranged to fit a dependency diagram.

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  44. John Harshman: Do you enjoy being taken for a troll?

    Yes.

    John Harshman: This is why nobody can take you seriously. You had a previous post vehemently insisting that there was a big difference.

    But my post was serious, you just failed to understand it. Obviously the words have different meanings. Somewhere in my vast pile of literature I have a book on figures of speech. Perhaps if I find time I will explain why my post to Joe wasn’t meant to be taken literally. It was meant to make a point. Sorry if you don’t get it.

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  45. Officer Doe: “We found shells in the crime scene. Ballistics confirmed they were shot by the suspect’s gun. We also have his fingerprints all over the crime scene”

    Billy: “Wait a minute, there are also shells in the suspect’s backyard where he’s been shooting cans, and fingerprints on his coffee mug. He’s innocent!”

    Officer Doe: “WTF?”

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  46. Neil Rickert: We cannot use a time machine to go back and verify. We can only depend on inference from the present.

    You sound like you are defending Nonlin. 😉

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  47. colewd:
    John Harshman,

    It’s simply an assertion you repeat.I see contradictory evidence which I am being told is not contradictory evidence and I should expect it. It appears the predictions are coming after the data and not before.

    This is just you misunderstanding what you see. You have shown yourself incapable of evaluating evidence, time after time. You have no understanding of the crocodylian paper, for example. You have never even looked at the data.

    I have no direct evidence that reproduction can create the odd patterns we see.

    What would constitute such evidence?

    We now have evidence that design can create a hierarchical pattern and the data can be arranged to fit a dependency diagram.

    You don’t understand that paper either. You just like it because it attacks evolution. But how is whatever evidence you think that paper contains more direct than the evidence that supports phylogeny?

    Let’s go back to basics. Deal with the croc paper. Why doesn’t it support common descent of crocodylians?

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  48. Joe Felsenstein: So what about one of the other points?

    Let’s take point #2.

    No assumption can be tested by the model that uses them.

    I don’t know what this means. Is cladistics a model that was meant to test the assumption of universal common ancestry? If that is the claim Nonlin is making I find it dubious in the extreme.

    I’m pretty sure that Joe is familiar with the use of models, I’m not sure about John. Thoughts from folks who actual do science on the role of models? Are they used to test assumptions?

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