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

    Christianity is refuted.

    The basis for Christianity is supposed to be evident to those who are born again. But that would constitute testing them by the model that uses them.

  3. Nonlin:

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

    Scientists routinely test their assumptions (and their models) by asking “What would I expect to observe if these assumptions (or this model) were true?”, and then comparing that to what they actually observe.

    This has been done for both common descent and creationism. Common descent fits the evidence literally trillions of times better. So rational people accept common descent and reject creationism.

    To accept creationism over common descent is a massive intellectual failure. It’s right up your alley.

  4. Wow. That OP could really be eight separate OPs. Mashing all that together in a single OP will just confuse people here.

  5. keiths: Common descent fits the evidence literally trillions of times better [than creationism]. So rational people accept common descent and reject creationism.

    How do you define creationism, the creation ex nihilo of all past and current species?

    I don’t know anyone who believes that anyways, so you’re not saying much

  6. “This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates.”

    Except that its basis started long before the advent of zealous “evolution” advocates.

  7. “This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD.”

    Since nobody has claimed that this is proof of UCD, I guess we are OK.

    “The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility.”

    The design hypothesis can never fail because ID refuses to postulate any mechanism or the nature of the designer. ‘God-Dig-it’ is not falsifiable.

  8. keiths, to Nonlin:

    Scientists routinely test their assumptions (and their models) by asking “What would I expect to observe if these assumptions (or this model) were true?”, and then comparing that to what they actually observe.

    This has been done for both common descent and creationism. Common descent fits the evidence literally trillions of times better. So rational people accept common descent and reject creationism.

    To accept creationism over common descent is a massive intellectual failure. It’s right up your alley.

    Mung:

    How do you define creationism, the creation ex nihilo of all past and current species?

    It doesn’t matter, because the evidence is just as damning of ID — including its “guided evolution” variants — as it is of creationism.

    ID, like creationism, is a massive intellectual failure.

  9. Mung: How do you define creationism.

    keiths: It doesn’t matter.

    Mung: Of course it matters.

  11. Almost everything in the OP is wrong and incredibly ignorant. But it isn’t worth it to argue with the person who made the OP, because this individual denies there’s a correlation between phenotype (the physical characteristics of an organism, like it having camouflage, or eyes, or wings) and it’s ability to survive and reproduce. I’m not kidding. The person who wrote the OP has explicitly claimed that there is no correlation between the physical characteristics of an organism and it’s ability to persist in nature.

    How does one have an argument with such a person? How would one even begin? If a person cannot see the survival value in being able to hide from predators, or sneak up on prey, or take flight to escape a ground-bound predator, then how does one explain that to them? Children get it at the age of 5 or even younger.

    Besides this post I’m not going to engage with such a level of complete and inane lunacy. The person who wrote the OP isn’t here to actually discuss the concepts listed. S/he’s here to make lists using words and terms s/he’s head here without understanding them, and then using the same style act out defiance and denial when challenged: making lists of declarations that are barely mostly wrong, barely coherent, and incredibly ignorant.

  12. Rumraket: How does one have an argument with such a person?

    By showing how his arguments lack substance. Like I do with keiths.

  13. Mung’s fantasy:

    Mung: How do you define creationism.

    keiths: It doesn’t matter.

    Mung: Of course it matters.

    The reality:

    keiths: Common descent fits the evidence trillions of times better than creationism.

    Mung: How do you define creationism?

    keiths: It doesn’t matter, because ID — including its ‘guided evolution’ variants — fits the evidence just as poorly.

    Mung, like Trump, will never let defeat prevent him from declaring victory.

  15. keiths: It doesn’t matter, because the evidence is just as damning of ID — including its “guided evolution” variants — as it is of creationism.

    Well, we can examine the evidence for each, in turn, but first you’d have to define what you’re talking about. And since you can’t even be bothered to say what you mean when you use the word “creationism”, we really don’t know whether your claim about it is true or false.

    keiths: Scientists routinely test their assumptions (and their models) by asking “What would I expect to observe if these assumptions (or this model) were true?”, and then comparing that to what they actually observe.

    This has been done for both common descent and creationism.

    How many different models for creationism are there in science, who developed those models, where were they published, and how were they tested?

    If you want o be taken seriously you need to support your claims with something more substantive than “it doesn’t matter.”

  16. This was welkl done approaching excellent. i thought at first it might be too wordy but naw.
    AMEN. the prejudice/rejection of the option for a creator using common design principals DOES nullify the nested tree thing. this is a intellectual failure of evolutionists. its clumsy thinking especially when they use the nested tree to fight creationists.
    A common design. with common desugn mechanisms within, to allow diversity in body plans DEMANDS that common descent conclusions based on body plan likeness ARE just unsupported assumptions.
    Everyone having eyeballs would be a creators idea TO. Its not proof to thoughtful people of a critter with a original eyeballs from whence all eyeballs came!

    indeed nested treeism is just a old school idea of grouping traits.
    likeness means like origin. OKAY thats a option for minor things but not major things.
    Its just extrapolation from a line of reasoning.
    Creationism has a good point here for the public at large. i think it will become a common jab in the future.

    Evolutionists not only flunk the logic of a option for common design that then nullifies common descent as the only option AND THAT option is what persuades them ,BUT ALSO FLUNKS that biological mechanisms also would have a common design allowing response to needs.
    Seeing likeness equals common descent was a superficial shallow jump to a conclusion.
    Once again creationists are the Sherlock Holmes to Scotland yards inspectors.
    A imagination curve is with us even if prompted by already a hunch.

  17. Creationists could use Nonlin to claim that no amount of “sequence space resources” could produce someone that astoundingly idiotic. That the amount of idiocy can not be attained randomly. That you could fill the universe with random people, and you would be nowhere closer to finding someone that stupid. Therefore Nonlin was designed by an intelligent being with a sadistic sense of humor.

  18. 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.

    Every multi-paragraph post needs a “more” tag. And if the poster doesn’t stick it after the first paragraph at the latest, there should be a bot to stick it at the very beginning.

  19. Entropy:

    Creationists could use Nonlin to claim that no amount of “sequence space resources” could produce someone that astoundingly idiotic. That the amount of idiocy can not be attained randomly. That you could fill the universe with random people, and you would be nowhere closer to finding someone that stupid. Therefore Nonlin was designed by an intelligent being with a sadistic sense of humor.

    CSS, or Complex Specified Stupidity.

  20. Erik: Every multi-paragraph post needs a “more” tag. And if the poster doesn’t stick it after the first paragraph at the latest, there should be a bot to stick it at the very beginning.

    When I see a problem, I’ll normally add a “more” tag after a paragraph or two. But this particular post is structured (as a list structure) in such a way that the “more” has to be at the top or the bottom. So I put it at the top.

    Authors — please don’t structure your posts that way.

  21. So keiths got caught telling a story and can’t defend it. Bluff called. But can you really blame him for trying?

  22. Mung: So keiths got caught telling a story and can’t defend it. Bluff called. But can you really blame him for trying?

    Said the quote miner.

  23. keiths:

    It doesn’t matter, because the evidence is just as damning of ID — including its “guided evolution” variants — as it is of creationism.

    Mung:

    Well, we can examine the evidence for each, in turn, but first you’d have to define what you’re talking about.

    I’ve already presented the evidence and the argument many times, going all the way back to 2012.

    You couldn’t refute it then, and I confidently predict that you still can’t.

  24. keiths: You couldn’t refute it then, and I confidently predict that you still can’t.

    I don’t need to refute it. All I need to do is ask a few pointed questions and watch you dance around in obvious discomfort. Same old same old with you.

    For example, why won’t you point us to the scientific models of guided evolution? You as much as claimed that they exist, so where have they been published and ? Of course, if you’re just making things up, well, we certainly don’t expect you to produce any actually evidence to support your claims in that case.

    Scientists routinely test their assumptions (and their models) by asking “What would I expect to observe if these assumptions (or this model) were true?”, and then comparing that to what they actually observe.

    And they publish in respected peer-reviewed journals.

    Which models do you claim have been tested?

  25. Mung:

    I don’t need to refute it.

    You can’t refute it.

    It’s the usual story: the evolutionists succeed, and the IDers — including you and Bill — fail.

  26. keiths: You can’t refute it.

    Why should I refute something that allegedly refutes something that no one believes anyways?

  27. Mung,

    Why should I refute something that allegedly refutes something that no one believes anyways?

    No one believes in creationism and guided evolution? Um, that’s an interesting claim.

  28. keiths: No one believes in creationism and guided evolution? Um, that’s an interesting claim.

    You’re dancing. If you’re claiming that people believe in creationism then you’ll need to define what that term means. But you’ve declined to do that. So we don’t know which ‘model’ of creation you’re referring to. We also don’t know what you mean by guided evolution, or which ‘model’ of it you’re referring to.

    My guess is you don’t have a model for either one and your original claim was just vacuous nonsense.

    Scientists routinely test their assumptions (and their models) by asking “What would I expect to observe if these assumptions (or this model) were true?”, and then comparing that to what they actually observe.

    What are these “creationist” models and where were they published and tested by scientists?

  29. Mung,

    You’re dancing.

    No, I’m pointing out the obvious: There are people who accept creationism, and there are people who accept guided evolution.

    I’ve shown that those people are wrong, and that unguided evolution fits the evidence literally trillions of times better.

    You have no refutation, and neither does Bill. You’ve failed again.

  30. keiths:
    Mung,

    No, I’m pointing out the obvious:There are people who accept creationism, and there are people who accept guided evolution.

    I’ve shown that those people are wrong, and that unguided evolution fits the evidence literally trillions of times better.

    You have no refutation, and neither does Bill.You’ve failed again.

    Is anything in the universe LITERALLY TRILLIONS OF TIMES BETTER!
    How was this demonstrated beyond the hundreds of billions examples?!
    Unguided evolution is LITERALLY, trillionisticly, impossible to have created complexity and diversity of biology within/without self contained organisms.
    Unless i’m missing something. NAW.

  32. keiths: No, I’m pointing out the obvious: There are people who accept creationism, and there are people who accept guided evolution.

    So what. Your claim was much more specific than that. The claim that you continue to fail to back up. Instead we’re treated to yet another keiths shuffle.

  33. Mung,

    Here’s my claim:

    No, I’m pointing out the obvious: There are people who accept creationism, and there are people who accept guided evolution.

    I’ve shown that those people are wrong, and that unguided evolution fits the evidence literally trillions of times better.

    You have no refutation, and neither does Bill. You’ve failed again.

    Failure is a bitter pill, and you and Bill have overdosed on it. Them’s the breaks.

  36. So this post isn’t your claim?

    Because in Mung World, every person has one and only one claim.

    Dipshit.

  37. This should be fun.

    Okay, Mung. In your own words, tell us why my argument fails. You can borrow ideas from Winston Ewert, since you won’t be able to come up with them on your own, but express them in your own words.

    I’ve already made my argument. The ball’s in your court.

  38. From the Ewert paper:

    Defenders of common design argue that the products of design tend to fit hierarchical patterns because, “Common design predicts re-usage of parts in a non-random manner that fulfills design constraints required by the system.” However, no hypothesis has been put forth to explain why this “non-random” re-usage of parts would exhibit the appearance of a nested hierarchy pattern.

    Even if the defenders of common design had an explanation for the approximate hierarchical pattern, this would not be sufficient. Such an explanation would almost certainly be less parsimonious than common descent in accounting for the hierarchy and just as unparsimonious as common descent in accounting for the exceptions to the hierarchy. The only way a new explanation can claim to be a better explanation than common descent is if life exhibits another pattern, and has only been interpreted as an approximate hierarchy because of the similarity of the two patterns.

  39. keiths: Because in Mung World, every person has one and only one claim.

    And you are unable to figure out which of your claims I am referring to. Why not just ask?

  40. keiths: Okay, Mung. In your own words, tell us why my argument fails.

    Easy. Your argument fails because it is false.

    ETA: And I don’t even have to refer to the Ewert paper

  43. oh God. You think that the Ewert quote was a response to something you wrote?

    LoL

  44. Ewert:

    Since no explanation has been put forward that demonstrates such an extended pattern, no explanation so far can claim to be a better explanation for the approximate hierarchy than common descent.

    Not that I’ll get any credit for sticking with common descent because it is the best explanation we have, lol. I feel like I am right on the edge of becoming a creationist. I feel a book coming on. The Edge of Creationism.

  45. Mung,

    Do you understand Ewert’s argument? If so, present it in your own words.

    If you can’t do that, then we can safely conclude that you glommed onto it based not on understanding, but out of sheer desperation. You couldn’t refute my argument, so you went around looking for someone or something you hoped would be able to.

    Hail Mary.

  46. Mung:

    oh God. You think that the Ewert quote was a response to something you wrote?

    Where did you get that idea? Damn, Mung.

  47. Mung:

    Not that I’ll get any credit for sticking with common descent because it is the best explanation we have, lol.

    Judging by the “Common design vs. common descent” thread, you don’t even understand why common descent is the best explanation we have. Why should you get credit for not understanding something important?

  48. Mung:
    From the Ewert paper:

    LOL, well at least they’re now finally acknowledging some of the evidence for common descent.

    Ewert makes a number of startling admissions in that paper that won’t sit well with many IDcreationists, for example that the much used “common design” rationalization doesn’t actually explain the hiearchical pattern of life. But since it comes packaged with a claim that a superior explanation to common descent is being developed, I guess they’ll let it slide.

  49. Specifically, programmers do not usually write new programs entirely from scratch. Instead they reuse standard modules.

    *snigger*

    NOT from scratch!?! No increase in FI then. Pity

  50. I note that Ewert suggests that genes are re-used in other species. Ewert considers a gene (what he calls a “part” or “module”) re-used in a species, if he can find a similar one in another. He explicitly ignores the actual sequence except to note that in so far as they are similar enough (to be classified as belonging to the same family), he considers it the same “module” reused. Funny thing is I was reading through the paper thinking he was going to do exactly that(ignore sequences). And there we go.

    PREDICTIONS
    As mentioned, the dependency graph predicts a pattern similar to but distinct from common descent. Is this prediction actually borne out by the data? For this paper, we will focus on the distribution of genes amongst various species. There are a number of different techniques to represent this data. The simplest is to record the presence or absence of each gene family in each species [32–34]. Some models extend this idea by taking into account the number of members of a gene family, not simply their presence or absence [35–39]. Quantitative evaluations of common descent often consider exact DNA sequences [10, 13, 15]. For this study, we adopt the simplest representation: the presence/absence of gene families, leaving other representations and data to future research.

    I guess we just have to wait then.

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