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 […].”

 

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

  1. Erik:
    And that proves evolution?

    I’d like to know how you jumped from an explanation of what a nested hierarchy is to “that proves evolution.” I didn’t see such implication in that quote.

  2. Erik:
    It’s in the very first words of the OP. Has this part been disputed?

    1. The OP was not written by John.
    2. Explaining what a nested hierarchy means doesn’t make it a claim that it proves evolution.
    3. That evolutionary trees can be thought of as nested hierarchies doesn’t mean that any nested hierarchies are evolutionary trees.
    4. Understanding the way in which evolutionary trees can be thought of as nested hierarchies is necessary before offering counter-examples, like those Russians dolls.
    5. The claims in the OP are horribly misinformed and misleading at many levels (they’re not simply true or false, they’re a conceptual mess).
    6. It doesn’t help if you jump to conclusions the way you did.

  3. Entropy: 1. The OP was not written by John.

    You clearly have no clue what the discussion is about. John referred me, once upon a time, to Theobald’s evidence for evolution that happens to cite nested hierarchies among others. John either still supports it or not. So the OP should be undisputed at least on this particular point.

  4. Entropy: 3. That evolutionary trees can be thought of as nested hierarchies doesn’t mean that any nested hierarchies are evolutionary trees.

    So you disagree with Theobald’s evidence too? Great!

    I also think his attempted distinction of objective and subjective nested hierarchies is bollocks.

  5. Erik:
    You clearly have no clue what the discussion is about.

    Clearly?

    Erik:
    John referred me, once upon a time, to Theobald’s evidence for evolution that happens to cite nested hierarchies among others.

    Therefore any kinds of nested hierarchies should be evidence for evolution? Did you read what I wrote at all?

    Erik:
    John either still supports it or not.

    I don’t know what John thinks, but I suspect that he’d be adamant that you should understand what is meant in biological/evolutionary terms, before offering “counter-examples” like those Russian dolls.

    Erik:
    So the OP should be undisputed at least on this particular point.

    I don’t see why a conceptual mess should go undisputed. Let me give you a few clues (from the bullshit OP):

    “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution.

    1. Nested hierarchies are not the same as a cladistic analysis.
    2. Neither is the same as consilience of independent phylogenies.
    3. Evolution is not just Darwinian (let alone “Darwinist”).

    That’s but the first sentence. There’s more problems with the rest. As I said, it’s not simply true/false problems, it’s a messy pice of crap.

  6. John Harshman: Then you shouldn’t complain about people ignoring you.

    You’ve lost me. Are you referring to my comment to Joe? I didn’t say he ignored me. I said he’d overlooked my comment.

    If I had a complaint it would be that his statement is factually inaccurate.

  7. Erik: You clearly have no clue what the discussion is about.

    And yet he’s right and you are wrong.

    John referred me, once upon a time, to Theobald’s evidence for evolution that happens to cite nested hierarchies among others.

    I don’t believe I ever referred you to that. I may have referred you to a paper by Theobald, but that isn’t it.

    John either still supports it or not. So the OP should be undisputed at least on this particular point.

    You are confused about what Theobald says, about what I say, and perhaps even about what the OP says. I could try to explain, but I fear it would be futile.

  8. Mung: You’ve lost me. Are you referring to my comment to Joe? I didn’t say he ignored me. I said he’d overlooked my comment.

    If I had a complaint it would be that his statement is factually inaccurate.

    One reason people ignore you is your constant playing around with wording, such as the meaningless distinction you make above. And let’s face it, your comment is not a serious attempt to defend any points in the OP. It’s just another meaningless bit of wordplay.

  9. Erik:
    So you disagree with Theobald’s evidence too? Great!

    Now I’d like to know how you jump from “not all nested hierarchies are evolutionary trees” to “the way life forms arrange into nested hierarchies is not expected from evolutionary processes.”

    Erik:
    I also think his attempted distinction of objective and subjective nested hierarchies is bollocks.

    I do not understand what you’re trying to say here, which is not too surprising given the conceptual mess that you’ve made so far.

    P.S. No wonder you’d like what Nonlin wrote. Conceptual messes are your thing, aren’t they?

  10. John Harshman: You are confused about what Theobald says, about what I say, and perhaps even about what the OP says. I could try to explain, but I fear it would be futile.

    So you don’t even try to explain, which leaves a rather strong impression that you cannot defend it.

    Theobald’s two entire paragraphs where he tries to illustrate the distinction of objective and subjective nested hierarchies with languages and cars are bollocks, both scientifically and philosophically. I would elaborate on this, but I restrict my word count to roughly your word count, so that everything is fair.

    When you don’t explain, it liberates me from the same task. You can remain as confused as you like without ever getting to know about it.

  11. John Harshman to Erik:
    You are confused about what Theobald says, about what I say, and perhaps even about what the OP says. I could try to explain, but I fear it would be futile.

    Rightly said. Maybe I should also leave it.

  12. Erik:
    So you don’t even try to explain, which leaves a rather strong impression that you cannot defend it.

    After a few exchanges with you, Erik, I think it’s more of an impression that you’d be unable to follow.

  13. Entropy: I do not understand what you’re trying to say here, which is not too surprising given the conceptual mess that you’ve made so far.

    The conceptual mess comes directly from Theobald. “Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between “subjective” and “objective” is crucial and requires some elaboration, and it is best illustrated by example.”

    So, if his example fails (which it does), the fact remains that “it is trivial to classify anything subjectively in a hierarchical manner”. This is why I hope evolutionists would come up with some actual evidence for their theory, not imagined evidence. Or at least explain why nested hierarchies are not imagined evidence.

  14. Erik:
    The conceptual mess comes directly from Theobald.

    Sorry, but no. The conceptual mess came directly and unambiguously from you. I’m referring to our exchange so far, not to anything said by anybody else. It’s you who thinks that nested hierarchy means any nested hierarchy. It’s you who jumps from “not any nested hierarchy” to “evolutionary processes would not produce nested hierarchies.” It’s you who jumps from an explanation of what nested hierarchy means to “any nested hierarchies are evidence for evolution.” You cannot blame Theobald or John for your misconceptions. the mess is all yours, whether Theobald had some misconceptions himself or not.

    Erik:
    the fact remains that “it is trivial to classify anything subjectively in a hierarchical manner”.

    Sure. That doesn’t mean that anybody is claiming that any nested hierarchies are evidence for evolution. Again, you have to understand what kinds of nested hierarchies are meant, in terms of evolutionary processes. Without that understanding, your complains look like you making a semantic and conceptual mess, rather than like some biologist’s fault.

    Erik:
    This is why I hope evolutionists would come up with some actual evidence for their theory, not imagined evidence. Or at least explain why nested hierarchies are not imagined evidence.

    The explanations seem to be all over the place, but, immersed as you are in conceptual and semantic messes, I’m not surprised that you’d reject them. You have to be a tad more willing to understand what’s meant, rather than imagine that your misconceptions and semantic problems are the perfect foundation to judge the merits, or lack thereof, of evidence for evolution.

  15. Entropy: It’s you who jumps from “not any nested hierarchy” to “evolutionary processes would not produce nested hierarchies.”

    Now, where did I jump to that? Clearly, you are the one jumping. I whole-heartedly agree that evolutionary processes would produce nested hierarchies – as do lots of other processes, including artificial.

    The question is not whether the nested hierarchies are there. They clearly are there. The question is whether they came about by evolutionary processes.

    I will later take a look if you managed to correct this misconception of yours about my position and then we may perhaps talk some more.

  16. Entropy: Sometimes I like you Mung. Unfortunately, only sometimes. (That was genius.)

    It wasn’t my first choice of comment, but I’m glad I went with it. 🙂

  17. Erik:
    Now, where did I jump to that?

    Well, you quoted:

    Erik quoting Entropy:
    3. That evolutionary trees can be thought of as nested hierarchies doesn’t mean that any nested hierarchies are evolutionary trees.

    To which you “responded”:

    Erik:
    So you disagree with Theobald’s evidence too? Great!

    That means that you’re mistaking “not all nested hierarchies are evolutionary trees” for “evolutionary processes are not expected to produce nested hierarchies,” since Theobald’s proposal is that evolutionary processes would produce nested hierarchies, and you think that if not all nested hierarchies are evolutionary trees, that means that I disagree with Theobald about whether evolutionary processes would produce nested hierarchies.

    Erik:
    Clearly, you are the one jumping. I whole-heartedly agree that evolutionary processes would produce nested hierarchies – as do lots of other processes, including artificial.

    Then you should not jump from “not every nested hierarchy is an evolutionary tree” to “Theobald is wrong.” Unless Theobald said that any and every nested hierarchy is evidence for evolution, which doesn’t seem to be the case. As I said, you have to understand what Theobald meant before offering those misconceived and conceptually messy “counter-examples” as Russian dolls.

    Erik:
    The question is not whether the nested hierarchies are there. They clearly are there. The question is whether they came about by evolutionary processes.

    And again, before understanding that, you need to understand what kinds of nested hierarchies Theobald is talking about, which, given your “counter-example,” you have no idea about.

    Erik:
    I will later take a look if you managed to correct this misconception of yours about my position and then we may perhaps talk some more.

    Oh, how graceful of you to say that after the mess you made. I’m so grateful! Erik might talk to me! So nice!

    The mess is all yours. I mean the floor is all yours.

  18. Entropy: And again, before understanding that, you need to understand what kinds of nested hierarchies Theobald is talking about, which, given your “counter-example,” you have no idea about.

    Theobald’s example includes cars as a “subjective” nested hierarchy and languages as an “objective” nested hierarchy. In reality, both are objective, depending on the purpose of selecting the specific characteristics to form the hierarchy. Theobald’s example fails.

    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.

    However, more is required: 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.

    Let’s take Theobald’s example: Languages. It’s true that evolution of a language family produces a nested hierarchy. However, a nested hierarchy is never used by any linguist as evidence or proof that such-and-such languages are related by common descent. Rather, it’s known from written records how languages evolve, which characteristics of language evolve in which way. Then this knowledge is organised as a nested hierarchy, a language family tree. 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. (The nested hierarchy is evidence for exactly nothing. It is only what evolution of a language looks like, because that’s what we have observed generation by generation through centuries and millennia.)

    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. The other option is that his examples are false, thus he fails at the attempt of drawing a distinction between objective and subjective nested hierarchies, 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.

    It all boils down to: What is 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?

  19. Joe Felsenstein,

    Sorry for the delay I have been on vacation.

    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.

    I think this is true. There are others but lets start with one.

  20. Mung is right, I neglected the one response I received (from Mung):

    Mung: ok, let’s start with the last one from the OP.

    A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure

    That seems trivially obvious to me. Except for the part about cladistics giving us a hierarchy. Cladistics gives us trees.

    Very non-obvious to me. The genealogy of life could be a perfect tree (it isn’t a perfect one) without there being labels on life forms telling you where they fit into the tree.

    Just as there can be orbits of planets without the planets having labels on them talking about the orbits.

    So that whole point of nonlin.org’s is mysterious. Perhaps Mung can explain it and clear up that mystery.

  21. I see colewd responded too, on the same point, just now. I gave my reaction just now. I will await a clear explanation of what nonlin.org’s point #1 means, from either or both of you.

  22. Joe Felsenstein: I will await a clear explanation of what nonlin.org’s point #1 means, from either or both of you.

    The meaning should be obvious if you read with some generosity.

    It’s asserted that nested hierarchies are evidence for evolution. Questions: How does it work? In what other science does “evidence” work by similar logic? Theobald’s explanations on this point are false. Do you have a better explanation?

  23. Joe Felsenstein,

    A “tree of life” is an artificial human construct

    Lets purge the controversial word- artificial.

    A “tree of life” is a human construct. Does this make sense?

    The hierarchal structure is based on criteria humans select. ie Why is a whale categorized as a mammal?

  24. colewd:
    The hierarchal structure is based on criteria humans select.ie Why is a whale categorized as a mammal?

    Do you know the answer to your own question? I think it’s unlikely you do. A whale is characterized as a mammal, these days, because all the data place it within Mammalia. These days, of course it’s mostly molecular data, but morphological data work fine too. The only way to avoid that conclusion is to pick data specifically for the purpose of forcing a different conclusion, in which case you might use such fine characters as “fish-shaped”. So in fact subjectivity would be employed only in a conclusion that whales are not mammals. Any objective analysis would conclude that they are, even if data were selected purely at random.

  25. colewd: A “tree of life” is a human construct.

    Yes, it is. And, for that matter, Christianity is a human construct.

    The hierarchal structure is based on criteria humans select.

    Agreed. But they selected those criteria for good reason. If you disagree with the criteria, then you need to suggest better criteria and explain why they are better.

    ie Why is a whale categorized as a mammal?

    Perhaps because they have mammary glands.

    Linnaeus is usually considered to be a creationist. Or, at least, many creationists claim him as one of their own. And he already classified the whales as mammals.

  26. John Harshman: Because you have so far been shown incapable of coherently explaining yourself

    Joe Felsenstein: So far in vain, though a couple of ID advocates who comment here have said that they’d take a look at it.

    Come on guys, all you’re offering is opinions and displeasure. Don’t be naïve – we all know your opinions, so there’s no point repeating.

    Come back with some counterarguments when you have any. Yes, even when you claim “incoherence” you must be able to give examples and seek clarifications. I know this goes against the Darwinist dogma, but maybe (could it be?) your communication is at fault.

  27. Neil Rickert,

    Linnaeus is usually considered to be a creationist. Or, at least, many creationists claim him as one of their own. And he already classified the whales as mammals.

    My point was not against this classification as being rational only to show that it was a human construct and perhaps a rational one.

    Again the only argument I was supporting is; is the tree of life as a human construct. So I think Nonlin’s claim is valid if we remove the inciting word, artificial.

  28. Corneel: 1. Ah, you associate common descent with natural selection? Rejoice, for they are distinct concepts. Quoting myself from one of the many times this has come up:

    2. You have accused me multiple times of putting words in your mouth, so now I have learned my lesson. I will not answer your question until you have carefully explained to me what the connection is between making a synthetic bacterial genome and “dogs giving birth to cats”, ’cause I sure as hell don’t see one.

    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?

    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 😊

  29. colewd:
    Neil Rickert,

    My point was not against this classification as being rational only to show that it was a human construct and perhaps a rational one.

    Again the only argument I was supporting is; is the tree of life as a human construct. So I think Nonlin’s claim is valid if we remove the inciting word, artificial.

    Talk about incoherence. Is it an objective fact that whales are mammals, or is it a human construct that could have been decided differently based on what data one chose to consider?

  30. Corneel: Don’t know how many times life got started, sorry.

    Why do you mention abiogenesis? Did you miss the point that LUCA has ancestors as well? You did, didn’t you?

    Nonlin.org: The definition shows that “ancestor” – if you chose to use that word – needs not be tied to biologic reproduction (mitosis, meiosis).

    An argument ad lexicon? That’s a new one.

    Are your ancestors prototypes of you? Did you get an upgrade lately? What nonsense! You cannot use the meaning of prototype for biological organisms. I note that this appears to be a quirk of the English language. In Dutch for example, “voorouder” doesn’t have that additional meaning for machines. Are we discussing linguistics or biology?

    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.

    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.

    Joe Felsenstein:
    Corneel, I agree,nonlin.orgjust hasn’t understood what LUCA is. LUCA is not the first organism but is the Last Universal Common Ancestor, so LUCA could have ancestors, who would be Universal Common Ancestors but just not Last ones.Think of a tree which is Y-shaped.LUCA is at the fork, not at the bottom of the stem.

    How can you prove any of that? Call it LUCA or UCA or Whatever or Whatnot – how does that change your dilemma “Either life started Once and Only Once making abiogenesis a singularity that screams for an explanation, or abiogenesis is trivial under the right condition in which case your tree gardeners are clueless and we’re looking at multiple trees if not independent creation events. The other two “explanations”: Darwin’s “four or five” or “they all died except LUCA that miraculously survived to fill the earth” are downright ridiculous.”?

  31. Entropy: Now, of course there’s ways to establish common ancestry independent of cladistics. I gave an example, of several, in the vitamin-C pseudogene being broken in the very same way in different primate species, like humans, chimps, gorillas. The probability of breaking a gene in the very same way in three independent lineages is so small, that the best explanation is that the gene broke once, in a common ancestor, and we all inherited that version of the broken gene from that ancestor.

    From your whole rant I was able to extract this semi-intelligent claim, so kudos!

    Now, let’s focus on this “proof” – are you saying that before this “proof” there was no UCD assumption whatsoever? Because I didn’t get the impression that Darwin knew about your “proof”, yet him and generations after him were already taking UCD for granted without knowing of your “proof”.

    And who said that UCD is “the best explanation” for this? What other explanations have you guys considered, and how is this “best” compared to the others? Do tell.

    And these being said, the not so subtle point of this OP is not that UCD is true or not, but that cladistics cannot prove UCD when UCD is in fact an assumption of the cladistic analysis – that would be circular logic.

  32. Entropy:
    1. Nonlin here is mistaking phenomena with the history of life. Evolution proceeds regardless of how many ancestors there might have been for current life forms.

    Nonlin.org:
    Either life started Once and Only Once making abiogenesis a singularity that screams for an explanation,

    2. Oooooh How scary! Screaming for an explanation! Must be that fi we didn’t know then god-did-it! Magical-being-in-the-sky for the win!

    Nonlin.org:
    or abiogenesis is trivial under the right condition

    3. Interesting dichotomy, either a “singularity” or trivial, nothing in-between. Isn’t Nonlin clever? She saved us a lot of time figuring things out. If it’s not trivial it must be a “singularity.” So simple and obvious. How come we never thought of that!?

    Nonlin.org:
    4. in which case your tree gardeners are clueless and we’re looking at multiple trees

    If “trivial” were the case, there would be indications of it. So far none.

    Nonlin.org:
    if not independent creation events.

    5. Ah! Right! Let’s not forget to include fantasies as potential explanations!

    Nonlin.org:
    The other two “explanations”: Darwin’s “four or five” or “they all died except LUCA that miraculously survived to fill the earth” are downright retard. Now, which one is it?

    6. It’s interesting that Nonlin would be so fond of absolutist false dichotomies. I’d mention coalescence to Nonlin, or the possibility of life being a mosaic of several ancestral life forms, or ask Nonlin if he understands that Darwin was just speculating about alternatives he could think of at a time when data was much more scarce, etc. etc. But what for? It’s not as if Nonlin would start reading for comprehension, or even cared.

    1. Huh? Proceeds from what? You have a big problem telling the story from Big Bang to today while conveniently skipping a crucial chapter.
    2. This is childish – tries and fails to hide the mega-problem
    3. Soo? Is your answer singularity, trivial or retard?
    4. Agree. Yet Darwinistas are at work trying to prove the trivial scenario – remember Miller Urey that “almost” created life? What a joke!
    5. I don’t see you offering a logical alternative. And to not enter a wormhole now, you have many, many problems with the materialist story – like “how material is matter”? http://nonlin.org/im-materialism/
    6. I mention Darwin because his retard story remains the default dogma. Are you voting for the retard alternative? Let alone any proof of anything…😊

  33. Nonlin.org: I am saying that there’s no problem with Intelligently Guided common descent linking all organisms

    You mean linking all first-cousins, don’t you?

  34. Entropy: 1. Nested hierarchies are not the same as a cladistic analysis.
    2. Neither is the same as consilience of independent phylogenies.
    3. Evolution is not just Darwinian (let alone “Darwinist”).

    That’s but the first sentence. There’s more problems with the rest. As I said, it’s not simply true/false problems, it’s a messy pice of crap.

    Hey, I am just capturing the Darwinist mumbo-jumbo. I don’t actually speak astrology-evolution-phrenology. What other than Darwinist “evolutions” are out there?

  35. John Harshman: Is it an objective fact that whales are mammals, or is it a human construct that could have been decided differently based on what data one chose to consider?

    I see both of those as being true.

    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.

    And that, of course, is part of the argument between science and religion. Science is fundamentally pragmatic. It tries to do things in the most useful way that it can. Religion, by contrast, is bound to tradition and tries to do things in ways that best fit its traditions.

  36. colewd: Again the only argument I was supporting is; is the tree of life as a human construct. So I think Nonlin’s claim is valid if we remove the inciting word, artificial.

    I haven’t been following closely enough to know what Nonlin has been claiming.

  37. Nonlin.org: And these being said, the not so subtle point of this OP is not that UCD is true or not, but that cladistics cannot prove UCD when UCD is in fact an assumption of the cladistic analysis – that would be circular logic.

    I’m not a biologist, so I won’t comment on whether UCD is an assumption of cladistics. I’m inclined to trust John Harshman on that.

    What seems completely clear, is that UCD was never an assumption of the Linnaeus classification. Yet it was from following the Linnaeus scheme that Darwin and others saw the strong evidence for common descent.

  38. Joe Felsenstein: Very non-obvious to me. The genealogy of life could be a perfect tree (it isn’t a perfect one) without there being labels on life forms telling you where they fit into the tree.

    Just as there can be orbits of planets without the planets having labels on them talking about the orbits.

    So that whole point of nonlin.org’s is mysterious. Perhaps Mung can explain it and clear up that mystery.

    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.

  39. Neil Rickert: And that, of course, is part of the argument between science and religion. Science is fundamentally pragmatic. It tries to do things in the most useful way that it can. Religion, by contrast, is bound to tradition and tries to do things in ways that best fit its traditions.

    Nope. The “argument” is artificial and recent created by atheists. In fact there is no science WITHOUT religion: http://nonlin.org/philosophy-religion-and-science/

  40. colewd:
    John Harshman,

    Only after the category mammals are defined by humans and whales pass the check list.

    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. We determine that whales are mammals not because they have a set of arbitrarily chosen characters but because they show evidence of common descent with other mammals.

    If “mammal” wasn’t a natural group not dependent on human definition, we could assign whales to some other group defined by different characters. Let me repeat the statement that whales could be assigned to a “fish” group if we defined that group by having fins, being roughly fish-shaped, and living in water. So, is “fish” as good a home for whales as mammals is, or isn’t it?

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