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. keiths,

    How many times has the following passage from Theobald been quoted to you?

    So your argument is to continue to cut and paste Theobald.

    On what basis are mammals organized? Is this any less subjective then organizing around an operating system. If you think it is then make an argument.

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  2. Mung: Yes, it probably really does deserve its own OP here. Maybe someone will create one.

    I am stockpiling popcorn, hoping for the day when someone experienced in phylogenetic inference, perhaps Joe Felsenstein , has the time and inclination to analyze the Ewert paper and do an OP on it.

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  3. Corneel,

    Can you really not see that, if dogs and birds do not share a common ancestor, this also rules out common descent of ALL eukaryotes? How can you possibly maintain a single independent origin for the spliceosome if it had to be created multiple times for different eukaryotic lineages?

    The code can have a single origin and be reused or modified and reused depending how the evidence shakes out. Do you think the origin of the code that built flight feathers was consistent with the origin of birds?

    If you want to claim that the beta chain of ATP synthase was preserved by purifying selection for 400 million years, then you MUST accept common descent of all tetrapods, including birds and mammals. You cannot just collect the arguments that you happen to like as if you are doing your groceries.

    If a shark was created 400 million years ago using the code for the ATP beta chain as a component of ATP synthase and a human was created 2 million years ago using the same code used for sharks and the code is 90% preserved would this not be preservation over deep time without common descent of humans and sharks as long as sharks were descended from a common ancestor?

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  4. colewd: The original Mac laptop and desktop in one group with the Lisa as the common ancestor and the objective c Mac os in the second group with the Next computer as the common ancestor.

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  5. colewd:

    So your argument is to continue to cut and paste Theobald.

    No, and that excerpt from Theobald doesn’t contain the argument. Instead, it explains the concept of an objective nested hierarchy, which you, amazingly, still cannot grasp.

    Since you cannot even grasp the concept, you are in no position to challenge the argument.

    You’re simply not bright enough for this discussion, Bill.

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  6. keiths,

    Since you cannot even grasp the concept, you are in no position to challenge the argument.

    If you grasp the concept why can you not explain it in your own words?

    Why is Rumraket not able to explain it in his own words?

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  7. colewd: If a shark was created 400 million years ago using the code for the ATP beta chain as a component of ATP synthase and a human was created 2 million years ago using the same code used for sharks and the code is 90% preserved would this not be preservation over deep time without common descent of humans and sharks as long as sharks were descended from a common ancestor?

    If my aunt had a moustache, would she not be my uncle?

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  8. colewd:

    If you grasp the concept why can you not explain it in your own words?

    I can, and I’ve done so again and again.

    Why is Rumraket not able to explain it in his own words?

    He can, and he’s done so again and again.

    You’re too dumb to get it, Bill. Since you believe in God, have you ever asked him why? Why does he refuse to grant you even the modicum of intelligence that would permit you to participate in these discussions without humiliating yourself? Does he hate you?

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  9. Mung: That one wasn’t a joke. 🙂

    Ha, but mine was 😀

    Mung: The dependency graph model was a better fit, by far.

    Yes, and it put a lancelet (a chordate), together with a sea star (an echinoderm), because they were using the same unique “modules”. If I were you, I’d stick with common descent for a while, Mung.

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  10. Corneel: If I were you, I’d stick with common descent for a while, Mung.

    Sure. 🙂

    The Ewert paper does not propose an alternative to common descent. Don’t let Swamidass confuse you.

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  11. Corneel: Yes, and it put a lancelet (a chordate), together with a sea star (an echinoderm), because they were using the same unique “modules”.

    So?

    Further, did he put them together for the common descent model, the “modules” model, or both?

    ETA: The fact that I didn’t just give you a bare “So?” should be taken as a sign of respect. 🙂

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  12. keiths,

    I can, and I’ve done so again and again.

    Since you understand this so well you can explain why a ‘placenta” or “mammary glans” are less subjective then an “operating system” as an organizing principle.

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  13. Mung: Again? You’re just going to let Bill win?

    “Against stupidity the very gods Themselves contend in vain.” – Friedrich Schiller

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  14. keiths,

    You’re too dumb to get it, Bill. Since you believe in God, have you ever asked him why?

    He was just wondering why one on his brightest processor designers could not defend a simple claim yet continues to be indoctrinated in scientific dogma 🙂

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  15. colewd: Since you understand this so well you can explain why a “placenta” is less subjective then an “operating system” as an organizing principle.

    Bill, both are objective sorting criteria. The problem is that sorting by operating system doesn’t yield nesting clades. You haven’t actually done the sorting based on operating system.

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  16. Mung: The Ewert paper does not propose an alternative to common descent. Don’t let Swamidass confuse you.

    Have you told Bill?

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  17. Rumraket: Have you told Bill?

    Do I need to tell Bill? ok, jsut in case:

    Bill, the Ewert paper does not propose an alternative to common descent. Don’t let Swamidass confuse you.

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  18. Mung,

    Bill, the Ewert paper does not propose an alternative to common descent. Don’t let Swamidass confuse you.

    Joshua’s straw-man does. Is it fair game to argue both ways 🙂

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  19. colewd: Joshua’s straw-man does. Is it fair game to argue both ways

    See Mung? Bill gets so easily confused.

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  20. Rumraket,

    Bill, both are objective sorting criteria. The problem is that sorting by operating system doesn’t yield nesting clades

    In both cases I identified a common ancestor and follow on computers with that operating system.

    Are you claiming that the Lisa as a common ancestor to the original mac and the first mac laptop is not a nested clad?

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  21. Mung: So?

    Further, did he put them together for the common descent model, the “modules” model, or both?

    Here is the paragraph:

    We will now consider a few small examples of cases which our model-fitting method inferred to be explained by modules. A striking example can be found in Nematostella vectensis (scarlet sea anemone) and Branchiostoma floridae (Florida lancelet). These are distantly related organisms with the anemone being in the phylum Cnidaria and the lancelet being in the phylum Chordata. Nevertheless, they contain between 25 and 564 (depending on the database consulted) gene families found in both species but in no other metazoan species in the database. In all datasets where both species are present, a module is inferred to exist to explain the genes found in both species.

    First: I see that I managed to mix up sea stars and sea anemones (oopsie). Sorry.

    Even with common design, you would expect some correlation between similarity at the genetic and at the phenotype level. It could of course be correct that disparate organisms require similar modules to perform some obscure shared function, but my experience with large scale databases tells me that the more parsimonious explanation is that something is wrong with the data.

    ETA: The fact that I didn’t just give you a bare “So?” should be taken as a sign of respect. 🙂

    Damn right. I work hard at this!

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  22. Corneel,

    Even with common design, you would expect some correlation between similarity at the genetic and at the phenotype level.

    What percentage of the genome are you comparing?

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  23. colewd: Are you claiming that the Lisa as a common ancestor to the original mac and the first mac laptop is not a nested clad?

    Lisa was just one of a pool of computer parts and accessories and operating systems that nowadays we call the LUCA (Last Universal Computing Ancestor).

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  24. Corneel: Even with common design, you would expect some correlation between similarity at the genetic and at the phenotype level.

    ok, but he isn’t looking at that. So I don’t see the relevance.

    And to the original point, he’s not lumping them together under the evolutionary model, only under the dependency graph model. So I don’t understand the objection.

    You would have to admit that under the two models the dependency graph has the better fit.

    Perhaps I misunderstood you. It seems like you were saying “but under evolutionary assumptions we would not group them like that!” To which I reply, so what? It seems utterly irrelevant. He’s comparing models to see how well they fit the data.

    The dependency graph model is by far the better fit given the data he used. Perhaps biologists start using dependency graphs. 🙂

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  25. colewd:

    nested clad

    Whereas Bill, fifth, Mung, and J-Mac fall into a hierarchy of nested clods.

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  26. keiths: Whereas Bill, fifth, Mung, and J-Mac fall into a hierarchy of nested clods.

    neologism: clodogram

    🙂

    ETA: But would it be “objective.”

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  27. colewd:
    keiths,

    So your argument is to continue to cut and paste Theobald.

    On what basis are mammals organized?Is this any less subjective then organizing around an operating system.If you think it is then make an argument.

    I love this quote about Theobald’s theory:

    “The “best competing multiple ancestry hypothesis” has one species giving rise to bacteria and one giving rise to Archaea and eukaryotes, said Theobald, a biochemist at Brandeis University in Waltham, Massachusetts.

    But, based on the new analysis, the odds of that are “just astronomically enormous,” he said. “The number’s so big, it’s kind of silly to say it” — 1 in 10 to the 2,680th power, or 1 followed by 2,680 zeros.

    […]

    Biologists call the independent development of similar traits in different lineages “convergent evolution.” The wings of bats, birds, and insects are prime examples: They perform similar functions but evolved independently of one another.

    But it’s highly unlikely that the protein groups would have independently evolved into such similar DNA sequences, according to the new study, to be published tomorrow in the journal Nature.

    “I asked, What’s the probability that I would see a human DNA polymerase [protein] sequence and another protein with an E. coli DNA polymerase sequence?” he explained.

    “It turns out that probability is much higher if you use the hypothesis that [humans and E. coli] are actually related.”The National Geographic

    Since humans and E. Coli appear to be related, and I’m more convinced of that when I read most comments at TSZ, especially keiths’ , story like Theobald’s has gotta be true….

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  28. keiths:
    colewd:

    Looks like keiths got a refund for his 3 neurons…
    You didn’t have to brag… we all knew…

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  29. keiths:
    colewd:

    Dr. Swamidass,
    This and the previous comment by keiths must be what you have been talking about keiths how he “… advocated on behalf of a reasonable Christian.” How it reminded you “…of some of the best of selfless Christian faith…”

    We have a name for it. It’s called narcissism….

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  30. Mung: Perhaps I misunderstood you. It seems like you were saying “but under evolutionary assumptions we would not group them like that!” To which I reply, so what? It seems utterly irrelevant. He’s comparing models to see how well they fit the data.

    What I am saying is: “what the hell are those genes in that module? I need to know”. Because without that knowledge neither of us can tell whether the better fit is grounded in a real biological pattern, or is an artefact from certain quirks of sequencing depth, quality of assembly and/or annotation. Dependency graphs are only useful descriptions in the former case.

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  31. colewd:
    If a shark was created 400 million years ago using the code for the ATP beta chain as a component of ATP synthase and a human was created 2 million years ago using the same code used for sharks and the code is 90% preserved would this not be preservation over deep time without common descent of humans and sharks as long as sharks were descended from a common ancestor?

    How would you know that the human ATP-whatever had the very same sequence as the original one in the shark?

    Now, before reading what’s next (if you read it, which I doubt), keep in mind that the divergence in sequence between sharks and humans is the sum of divergence between each lineage. In other words, the total divergence is what accumulates in both lineages since the separation from the common ancestor. Thus, if you assume separate design, then the total divergence between humans and sharks, starting with sharks 400 million years ago, and humans 2 million years ago, would go to sharks by a factor of 400/2 or 200/1. Rather than fifty-fifty.

    By assuming separate design, you’re adding problems to your already flawed inference of FI. You now assume that the sequences were identical at the moment of design. You’re assuming that the sequences can diverge anyway (so, why start with the very same sequence? why not have some fun in a way that disallowed those evil scientists from inferring evolution?), and that sharks have twice the mutation rate that they have (well, actually much more than twice if you want mutations to cover the whole genome to leave no sequence untouched, which was already a problem with common ancestry, now multiplied by the assumption of separate design with identical sequences at each beginning).

    You really don’t get it Bill. To cover everything under common ancestry you’d have quite a bit of sequence exploration, thus FI would not be a problem at all. If, on top of that, you want sharks to be separated creations, then the rates of divergence would have to be multiplied to fit the data to the observations and to your assumption of complete coverage of all the sequences by mutations. Thus even more dramatic sequence space exploration. It’s a monstrous mess. Of course, that’s because there’s no such thing as ID. That’s because ID has deeply flawed philosophical and scientific grounds. So you end up making excuses over excuses that add nonsense to the already nonsensical ID.

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  32. Corneel: What I am saying is: “what the hell are those genes in that module? I need to know”.

    Perhaps you can elucidate further.

    The way I see it, the entire gene family would have to be invalid before it would make a difference. You would have to dissolve the entire family.

    You seem to be saying the following:

    For this gene family, I need to know all the genes within that family that are in species A. Because perhaps none of those genes actually belong in that gene family.

    Also, for that same gene family, I need to know all the genes within that family that are in species B. Because perhaps none of those genes actually belong in that gene family.

    Do I understand you correctly?

    That seems pretty far fetched. But I suppose if it was some very small number of genes it could be possible. But as the number of genes in the gene family increases it seems to become ever more unlikely.

    Unless such analysis revealed that the gene family doesn’t really exist after all in one of those two species, I don’t see how it would changed Ewert’s results.

    Thoughts?

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  33. Entropy: Of course, that’s because there’s no such thing as ID. That’s because ID has deeply flawed philosophical and scientific grounds. So you end up making excuses over excuses that add nonsense to the already nonsensical ID.

    First you say there is no such thing as ID, then you say that there is. You have just posted self-contradictory nonsense. Go make a clodogram of the eukaryotes as punishment.

    I think it is far more likely that you simply do not understand ID.

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  34. Entropy,

    By assuming separate design, you’re adding problems to your already flawed inference of FI. You now assume that the sequences were identical at the moment of design. You’re assuming that the sequences can diverge anyway (so, why start with the very same sequence? why not have some fun in a way that disallowed those evil scientists from inferring evolution?), and that sharks have twice the mutation rate that they have (well, actually much more than twice if you want mutations to cover the whole genome to leave no sequence untouched, which was already a problem with common ancestry, now multiplied by the assumption of separate design with identical sequences at each beginning).

    I was simply showing Corneel that he could not eliminate some common design from gpuccio’s analysis.

    You really don’t get it Bill. To cover everything under common ancestry you’d have quite a bit of sequence exploration, thus FI would not be a problem at all.

    This is an assumption and it does not seem to be evident from the data and underestimates finding function inside a sequence.

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  35. colewd:
    This is an assumption and it does not seem to be evident from the data and underestimates finding function inside a sequence.

    It’s gpuccio’s assumption Bill. Not mine. I just showed the kinds of numbers that would be necessary to cover every position in a protein, remember? When gpuccio dishonestly showed ordered mutations going on a sequence 14 letters long to show that I was wrong, when what was needed to understand the problem was random mutations? Remember that? He went on to admit that it was more than 14, mentioned 40 from a random model. Leaving aside that he made an ass-hole out of himself, that was but for a sequence 14 letters long. The numbers get exceedingly large when dealing with a sequence immersed in a genome (since to touch every position in the protein you’d have to cover every position in the genome). Thus, quite a bit of sequence space would be explored.

    That’s not my doing Bill. I just noticed that gpuccio’s position about the whole sequence being covered by mutations was contradictory to his claim that very little sequence space can be explored by evolutionary processes. None of what gpuccio claims are my assumptions. They’re all his.

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  36. Mung: For this gene family, I need to know all the genes within that family that are in species A. Because perhaps none of those genes actually belong in that gene family.

    Also, for that same gene family, I need to know all the genes within that family that are in species B. Because perhaps none of those genes actually belong in that gene family.

    Do I understand you correctly?

    I am not quite sure yet I fully understand Ewert’s analysis, but here is how I see it; A genome that has been poorly sequenced and annotated will score a large number of absent gene families. Hence, if there is variation in the quality and completeness among genome sequences this will generate a bias in favor of the dependency graph, as that model will not be as heavily penalised for having to accommodate the apparent repeated gains and losses.
    This will permeate the complete analysis, since it relies on the quality of the database, but I would expect that the oddballs like the anemone-lancelet pair will be most informative (is the anomalous module enriched for singletons, non-coding genes, pseudogenes, etc, etc).
    That’s why I want to take a peek into that unique lancelet-anemone module.

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  37. dazz: Nonlin.org: Now enlighten me

    I can’t, no one can, you’re far too stupid and lacking in reasoning skills to even figure out what LUCA means and entails, let alone evaluate the evidence for it’s existence

    So you got no answer. Of course. Another brain dead jihadist for the Darwinist religion. So what’s new?

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  38. Corneel: No independently created individual species then, that’s good.

    Could you give an example of such a “theme” (= baramin, I guess)? Where does the variation within the themes come from?

    As you might notice, I don’t like to make unsupported claims. But once again, you’re trying to put words in people’s mouths. This tactic is a looser.

    I did not say ‘yes’ or ‘no’ to “independently created individual species”.
    Why don’t you give an example of theme? I am sure you know a lot.
    The variation within themes seems built in by design. I see exactly what you see. The difference is that I would not venture a foolish “just so” story like your buddy Darwin.

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  39. J-Mac: Since humans and E. Coli appear to be related, and I’m more convinced of that when I read most comments at TSZ, especially keiths’ , story like Theobald’s has gotta be true….

    No, that’s just a “convergent evolution” …to brain dead.

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  40. Meanwhile, no one attempts to dispute the claims in this OP. Am I that good? I am flattered…

    Now, for your convenience, here they are again if you want to think:
    1. “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution.
    2. No assumption can be tested by the model that uses them.
    3. Hypothesis testing requires an alternative (null) hypothesis and a procedure.
    4. The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative
    5. The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false.
    6. The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails.
    7. A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure.

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