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. Hi John,

    I am thinking of creating an OP on one or both of your papers, but I don’t want to start an OP and misrepresent your work in it.

    Are you saying that your papers support, or provide evidence for, the hypothesis of universal common ancestry, using the methods of cladistics?

    Or do they perhaps make a much more modest claim, such as shared common ancestry within a specific taxon.

    Thanks

  2. Mung:
    Hi John,

    I am thinking of creating an OP on one or both of your papers, but I don’t want to start an OP and misrepresent your work in it.

    Are you saying that your papers support, or provide evidence for, the hypothesis of universal common ancestry, using the methods of cladistics?

    Or do they perhaps make a much more modest claim, such as shared common ancestry within a specific taxon.

    Thanks

    What you should ask John is how many people, other than him, speculated about it . You should never ask John Harshman about the experimental evidence…Him and his buddy Joke F somethingare afraid of the outdoors…

  3. Joe Felsenstein: Loud ill-explained declarations on a website don’t count.

    But once pronounced by Nonlin, and combined with “ill-informed,” they become laws that the universe has to follow.

  4. Joe Felsenstein,

    Is there any set of data that we could not explain as the result of “common design”? It predicts anything and everything (and therefore predicts nothing).

    I don’t think we need “common design” to explain the origin of Mungs DNA. We could eliminate design as a primary cause in that case. 🙂

    All that being said if it is the ultimate cause of the universe then it explains everything and I am not sure what it predicts.

    For science sake when we can get to more specific causes we should. Part of getting there is eliminating design and random as causes.

  5. John Harshman: Every model contains assumptions, and the fit of the model to data can be used to test whether the assumptions are valid for the data. A chi square test is a simple example. And an inference made in one study can then be used as an assumption in another

    False. They’re called ‘assumptions’ and not ‘conclusions’ because they have to be tested independently through an entirely separated method or be accepted as axioms.

    as·sump·tion
    [əˈsəm(p)SH(ə)n]
    NOUN
    a thing that is accepted as true or as certain to happen, without proof.

    “they made certain assumptions about the market” · [more]
    synonyms: supposition · presupposition · presumption · premise · belief · [more]

  6. colewd: Thanks for the conversation this am it was very helpful

    Thanks. Let me just offer two suggestions.

    1.) Don’t extend Ewart’s paper beyond what it actually says and can support.

    2.) Any “hypothesis of common design” needs to be fleshed out with additional detail before it can qualify as a hypothesis.

  7. colewd: I don’t think we need “common design” to explain the origin of Mungs DNA.

    I could share that information with you, but then I would have to kill you. Then, that would explain your failure to evolve.

  8. Neil Rickert: 2. No assumption can be tested by the model that uses them.

    This seems absurd.

    Why do I have to explain common sense. Do a search next time:
    as·sump·tion
    [əˈsəm(p)SH(ə)n]
    NOUN
    a thing that is accepted as true or as certain to happen, without proof.

    “they made certain assumptions about the market” · [more]
    synonyms: supposition · presupposition · presumption · premise · belief · [more]

  9. Mung: I am not of the opinion that over time God has “poofed” new species into existence from nothing, either recently, or over long ages.

    I am interested in understanding better why I accept common descent. Beyond accepting it as current science. If I came across someone who did not accept common descent, how would I convince them of my position.

    Opinions are not proof.

    You accept “common descent” because you have been indoctrinated. It’s not about “accept” or “reject” but about sufficient proof or not. Unless guided as in ID, “common descent” makes zero sense.

  10. Mung,

    Thanks. Let me just offer two suggestions.

    1.) Don’t extend Ewart’s paper beyond what it actually says and can support.

    2.) Any “hypothesis of common design” needs to be fleshed out with additional detail before it can qualify as a hypothesis.

    I agree.

  11. Mung,

    I could share that information with you, but then I would have to kill you. Then, that would explain your failure to evolve.

    Priceless 🙂

  12. Joe Felsenstein: For example, with 10 species, there are over 282 million possible trees (trees with labeled tips and unlabeled interior nodes). When we run a phylogeny program we will come up with one of those 282 million. Now we take another region of the genome (say another gene) and consider its sequences for the same set of 10 species.

    Does nonlin.org really think that, for that second set of sequences, it is not surprising if it comes up with the same tree, or with a tree that is closely similar?

    I do think that it is not surprising, but that is because the pattern of differences between sequences reflects evolution on the same underlying genealogy, the same phylogeny. But nonlin.org thinks that the similarity of these two trees is not evidence of there being a common underlying genealogy. Because, implicitly, what nonlin.org is saying is that there is some reason other than shared genealogy that those two trees would be the same, or nearly the same.

    What is that reason?

    Your samples are not IID. “The annotation IID is particularly common in statistics, where observations in a sample are often assumed to be effectively IID for the purposes of statistical inference.”

    Furthermore, you “think that it is not surprising” is not proof of anything. UCD and “evolution” are assumptions hence cannot be proven by the curve-fitted tree. How many time do I have to repeat?

  13. John Harshman: But it now seems apparent that nonlin accepts common descent; he just insists that random mutation and natural selection just have nothing to do with differences among species. As long as Jesus directly causes mutation and fixation, he’s cool. When he said otherwise, he was just being incoherent.

    Whatever you’re smoking, put it down cause it’s not good for your brain.

  14. Erik: Granted for microevolution. Anything specific to macroevolution?

    1. Some (including the ID crowd) accept microevolution defined as observable adaptations in populations, while rejecting macroevolution defined as the never observed and very much doubtful Darwinist “common descent”. The problem is that micro and macro are just generic qualifiers that come in pairs, while evolution – the word retained – is in fact the concept in question.
    2. Accepting microevolution creates confusion and is self defeating for those that reject Darwinist macroevolution. A better choice than microevolution is adaptation – an ancient concept (predates evolution), and an observed feature of all living organisms.

  15. John Harshman: But of course that isn’t even what you’re talking about. You’re actually trying to insinuate that mutation, selection, and drift can’t accumulate to result in big changes within populations. Do you have any evidence to support that claim?

    You have it backwards. The burden is on you. And is unmet.

  16. Joe Felsenstein: Of course we need other identifiers. Why is this news to you?

    Because it’s wrong news. I know people who work on this.

    The main issue is with phylogenies. Why do you think we can’t reconstruct them if we only have DNA from living species? I work on this, have written and distributed computer programs to do it, and have carried out computer simulations to check how well it works.

    You “can’t reconstruct” what?

    I gotta believe that some of the books and papers written are wrong (yours included). For proof, all you need to do is read some of the older books and you will find that a majority are full of errors including conceptual ones.

    I have created and run countless computer simulations, so I know exactly what I am talking about. And if you indeed have the experience you claim, you should know that this OP reflects the reality of computer modeling 100%.

    Now, do you have any valid arguments?

  17. Mung:
    I am thinking of creating an OP on one or both of your papers, but I don’t want to start an OP and misrepresent your work in it.

    There has already been an OP on one of those papers. It came to nothing because none of the creationists managed to read or understand the paper.

    Are you saying that your papers support, or provide evidence for, the hypothesis of universal common ancestry, using the methods of cladistics?

    No. They support common descent within particular groups, not universal common descent. For universal common descent, you should check out the often-cited-here Theobald 2010. I used the methods of cladistics if you define “cladistics” loosely enough to refer to any phylogenetic methods.

    Or do they perhaps make a much more modest claim, such as shared common ancestry within a specific taxon.

    Bingo. It seems that you could figure that out from the titles.

  18. Joe Felsenstein: Because it’s wrong news. I know people who work on this.

    The main issue is with phylogenies. Why do you think we can’t reconstruct them if we only have DNA from living species? I work on this, have written and distributed computer programs to do it, and have carried out computer simulations to check how well it works.

    You “can’t reconstruct” what? Your sentence is incoherent.

    I gotta believe that some of the books and papers written are wrong (yours included). For proof, all you need to do is read some of the older books and you will find that a majority are full of errors including conceptual ones.

    I have created and run countless computer simulations, so I know exactly what I am talking about. And if you indeed have the experience you claim, you should know that this OP reflects the reality of computer modeling 100%.

    Now, do you have any valid arguments?

  19. J-Mac:
    I think the time has finally come to end this very productive discussion (I get the sense that TSZ was set up to have discussions only. I hope I’m wrong)and test experimentally whether nested hierarchies are actually valid…

    Why do you think experiment is the only valid way to do science?

    How do we test them?

    That’s easy: by analyzing multiple independent data sets. If different data support the same tree, that demonstrates nested hierarchy.

    I don’t mean to put Harshman on the spot, but he is the one who objected to one of the experiments I was performing… Maybe he can propose some clear-cut experiment that could test these speculations and end them forever…

    Your “experiments” were not seriously intended and I doubt they ever actually happened. Nobody has any interest in testing your speculations.

    I have been particularly intrigued by the evolution of flightless birds as some of you my know… Surprisingly, one of myfavorite experimental scientists who have performed mutagenesis experiments for over 30 years, WE Loennig, seems to disagree with me on this issue…

    Who is WE Loennig and how do you know he disagrees with you?

    So, I’d propose an experiment that would put the some flightless birds underselective pressure to regain the bone they apparently had lost while adapting to the environment…

    I don’t understand how this is supposed to test the evolution of flightlessness. Shouldn’t you, if anything, be putting flying birds under selective pressure not to fly and see if their keels go away? Incidentally, there are two more big problems with your notion: 1) there is no lost bone; the keel is part of the sternum, and loss of the keel is just a change in the shape of the sternum; 2) this has nothing at all to do with testing nested hierarchy.
    I think that Harashman and his supporters could communicate with Dr. Loennig and come up with some kind of a solution…This is one of the time opportunity for evolutionists and “creationists” to cooperate to kill a rebel… lol

    Who is this “Dr. Loennig”?

  20. Erik: To return to reproductive isolation, it is importantly different in microevolution and macroevolution. In microevolution, it means that the separated populations of the originally same species ceased to have contact – they could still yield offspring, but don’t. In macroevolution, it means that the different species cannot yield offspring even if they wanted.

    You should realize that you know nothing about evolutionary biology. What you say above just isn’t true. Geographic separation of populations is not referred to as reproductive isolation. That’s reserved for reduced interbreeding that has a genetic component. I should also point out that we see all intermediate stages of reproductive isolation from none to absolute, as we would expect if speciation is a gradual process.

    In the context of macroevolution, my question is: Were those species (say, ancestors of apes and humans) ever able to yield offspring? How do you demonstrate that? What is the evidence?

    The evidence is the evidence that they were once a single species. There is also genetic evidence that the chimp and human lineages occasionally exchanged genes for up to a million years after their separation. But what were you looking for?

    You are the biologist here. I assume that the evidence for accumulating mutation, selection, and drift has already been collected and you can readily show how it results in macroevolutionary changes.

    I can as well as you can show that accumulated microlinguistic changes result in macrolinguistic changes.

    Please don’t play the fool. Just place the different editions of Shakespeare over the centuries side by side and take a look.

    Hmmm. As far as I can see those editions generally reproduce the 17th Century language.

    Or Beowulf.

    Again, Beowulf over the centuries has generally been reproduced in Old English. How many Middle English translations of Beowulf are you aware of? Sounds fascinating. However, there are two obvious responses: 1) That’s all just microlinguistics, change within a single language; you can’t extrapolate it to macrolinguistics, change from one language to a different language; 2) Those translations are just isolated entities, and you can’t show that they reflect continuous change within a language lineage.

    Or Caesar in Latin and Italian. Or Plato in Ancient, Medieval, and Modern Greek.

    Same objections apply there too.

    This should be a striking illustration of language change, even though the more correct way is to observe the gradual changes in phonology, morphology, vocabulary, etc. over the centuries – paradigmatic changes, not syntagmatic.

    You can’t observe that; you haven’t been observing for long enough. All you can see is various historical snapshots that you can’t prove are connected. And anyway, you can’t extrapolate from those small changes to the big changes that separate different languages.

    What does it matter how knowledge of the evolution of specifically Indo-European came about?

    Because it contradicts your claim about how that knowledge came about. Anyway, it was the first attempt to consider the descent of two languages from a common ancestor.

    That words change was always known by e.g. manuscript copyists. It is arguably already noted in the Bible itself.

    Just microlinguistics. You can’t use that to prove that macrolinguistics happened or is even possible.

  21. John Harshman: Who is this “Dr. Loennig”?

    Wolf-Ekkehard Lönnig, a retired plant mutational breeder and expert on systematics of bladderworts. An ID advocate who is made much of by the Discovery Institute.

    The usual you-can’t-get-there-from-here-as-far-as-I-can-see argument.

  22. John Harshman: The evidence is the evidence that they were once a single species. There is also genetic evidence that the chimp and human lineages occasionally exchanged genes for up to a million years after their separation. But what were you looking for?

    I was looking for the evidence. Are you saying that your statement “there is evidence” is in itself evidence?

    “There is also genetic evidence that the chimp and human lineages occasionally exchanged genes for up to a million years after their separation.” I’d like to take a look, thank you very much.

    John Harshman: Again, Beowulf over the centuries has generally been reproduced in Old English. How many Middle English translations of Beowulf are you aware of? Sounds fascinating. However, there are two obvious responses: 1) That’s all just microlinguistics, change within a single language; you can’t extrapolate it to macrolinguistics, change from one language to a different language; 2) Those translations are just isolated entities, and you can’t show that they reflect continuous change within a language lineage.

    The objections don’t apply at all, because if it were microlinguistics (whatever that is), a translation would not be needed in the first place. Translation is far beyond updating of spelling.

    If the analogy (comparing linguistic change and biological change) is true, then macroevolution is the point where reproductive isolation has become an irreversible genetic fact. And if the analogy is true, it should be possible to demonstrate how it gradually arises.

    But okay, I get it. You scoff at every field of science, including your own.

  23. Nonlin.org: You “can’t reconstruct” what?

    Phylogenies, and ancestors, from extant sequences. It can be done using the methods of phylogenetics.

    Scientists can take sequences from extant species (or individuals from a population) and reconstruct their evolutionary history, including reconstructing the sequences of the ancestors. They can then biochemically synthesize those reconstructed ancestors in the laboratory, put them into a living organism and test them for their functions.

    And such methods have been tested on real, known phylogenies to assess their general accuracy. See for example:
    Randall, R. N. et al. An experimental phylogeny to benchmark ancestral sequence reconstruction. Nat. Commun. 7:12847 doi: 10.1038/ncomms12847 (2016).

  24. Erik:. And if the analogy is true, it should be possible to demonstrate how it gradually arises.

    Erik: Why wouldn’t issues arising assuming the analogy is true be taken as evidence that the analogy is false. Especially for scientific theories which are part of the scientific consensus.

    I have no general issues with philosophical arguments being used to demonstrate conceptual problems in a science, but I think such arguments must be informed by an understanding the scientific theories in question and how terms and concepts are used in those theories.

    Analogies on their own my be helpful for an initial understanding, but they should not be cornerstones of a rigorous argument against a well-defined and supported scientific theory. If you are arguing that the purported evidence does not support the theory, I think you need to have a detailed understanding of how the science uses that evidence.

  25. Erik: But okay, I get it. You scoff at every field of science, including your own.

    Nah. He just played your role in “objecting” to the language evolution analogy, and, as a result, you made his point.

  26. Erik: I was looking for the evidence. Are you saying that your statement “there is evidence” is in itself evidence?

    No, I was just mentioning that there is evidence. Here’s some for human-chimp introgression. You can just google “primate philogeny” if you want some evidence for the tree.

    The objections don’t apply at all, because if it were microlinguistics (whatever that is), a translation would not be needed in the first place. Translation is far beyond updating of spelling.

    “Microlinguistics” is a word I invented just now in order to make the analogy clear. Since Old English and Middle English are the same language, English, any changes are just microlinguistics and so irrelevant to your argument that one language can change into another. I see that you have not attempted to provide evidence that Beowulf has changed from the original. Or Shakespeare either.

    If the analogy (comparing linguistic change and biological change) is true, then macroevolution is the point where reproductive isolation has become an irreversible genetic fact. And if the analogy is true, it should be possible to demonstrate how it gradually arises.

    I recommend Speciation by Jerry Coyne and H. Allen Orr, if you’re interested int he details.

    But okay, I get it. You scoff at every field of science, including your own.

    No, you don’t get it. I scoff at your understanding of evolutionary biology and of the justification for your own beliefs about languages. You appear to have no idea how science works, even your own. Or logic. Hey, remember your claim that notB implies notA means the same as B implies A?

  27. John Harshman: No, I was just mentioning that there is evidence. [—>] Here’s some for human-chimp introgression.

    Your attempted link at the indicated point is either yet another bad joke or an honest mistake. Either way, too many of them by now.

    John Harshman: You can just google “primate philogeny” if you want some evidence for the tree.

    You mean “phylogeny”, right? Another joke?

    The search results are either pics, whose value as evidence is precisely in question, or they are paywalled articles. Your answers amount to “yes, there is evidence, just nothing to show”.

  28. BruceS: Analogies on their own my be helpful for an initial understanding, but they should not be cornerstones of a rigorous argument against a well-defined and supported scientific theory.

    The thing is, I know what linguistic evidence consists of and how it backs up the linguistic theories. You may scoff at the level of rigorousness in the science, but then please show me that the rigorousness in your own preferred science is at least as good. Thus far no such luck.

    Therefore, my generous assumption is that the analogy is false and biological facts, methodology, and the overall nature of the science are importantly different from linguistics. Because the assumption that they are the same to the level that Darwin and Theobald believed is not furthering any understanding of either biology or of linguistics.

  29. Entropy: He just played your role in “objecting” to the language evolution analogy, and, as a result, you made his point.

    Yes, he played. If linguistics and biology worked the same way to the relevant degree, it would have been an awesome joke. But as it is, it’s a sad joke.

  30. Erik: The thing is, I know what linguistic evidence consists of and how it backs up the linguistic theories. You may scoff at the level of rigorousness in the science, but then please show me that the rigorousness in your own preferred science is at least as good. Thus far no such luck.

    Therefore, my generous assumption is that the analogy is false and biological facts, methodology, and the overall nature of the science are importantly different from linguistics. Because the assumption that they are the same to the level that Darwin and Theobald believed is not furthering any understanding of either biology or of linguistics.

    I was not making any comment on linguistics, only on the usefulness of analogy of nested hierarchies and other concepts in both sciences

    If the analogy breaks down as you say in your second paragraph, then the way forward to criticize of some theory in biology would be, I think, to obtain a similar knowledge to what you have in the details of linguists, namely “an advanced level of understanding of how the evidence is used in [ biology ] and how it backs up the [biological theories]. This would take sustained study of biology and is not something I can see one getting from online forums.

    This respect for having the needed expertise to make detailed criticism seems another example of comments made about Keith’s concerns with KN’s ideas that were made in another thread. (ETA: KN having the philosophical expertise in that case).

  31. BruceS: This would take sustained study of biology and is not something I can see one getting from online forums.

    You’d be surprised how much one can learn from discussions such as these if you’re just reading for comprehension, because you want to learn and understand, rather than to deny or nitpick.

  32. Rumraket,

    Yep. Sometimes I see very good explanations, only to see the creationists jump over the interesting and informative parts, and “answer” some small sentence in ways that make the jumping over all too obvious.

  33. Erik: Your attempted link at the indicated point is either yet another bad joke or an honest mistake. Either way, too many of them by now.

    No idea why that didn’t work. Try this:
    https://www.nature.com/articles/nature04789

    Now of course it’s paywalled, but that’s the problem with a lot of the scientific literature. You can often find a non-paywalled version, but I couldn’t with that one. Still, you might accept that the abstract doesn’t lie about the content.

    You mean “phylogeny”, right? Another joke?

    Your inability to distinguish a joke from a typo does your skills as a linguist no credit.

    The search results are either pics, whose value as evidence is precisely in question, or they are paywalled articles. Your answers amount to “yes, there is evidence, just nothing to show”.

    The paywall issue is a problem, but should you use it as an excuse to claim that there is no evidence? Again, you would have to assume that the abstracts are consistently lying. Further, you don’t seem that good at search. When I did it, this was the very top of my results:
    http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1001342

    And I also get

    https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-9-259

    As for the paywalled articles, you can often find them in unpaywalled form by searching on the titles, but I haven’t done any of that for you. Shouldn’t those two do for now?

  34. Nonlin.org: You accept “common descent” because you have been indoctrinated.

    Thank you. I did not know that.

    Did it perhaps happen in the baptist churches I grew up attending every sunday and wednesday? Because they also appeared to have wiped my memory of it as well.

  35. Erik: Yes, he played. If linguistics and biology worked the same way to the relevant degree, it would have been an awesome joke. But as it is, it’s a sad joke.

    You would have to demonstrate the truth of this claim by presenting some kind of argument, preferably a valid one. Try responding directly to the post.

  36. Joe Felsenstein: I asked you whether you could explain why phylogenies from different sets of genes come out so similarly. So you first, please.

    This is what I said and you missed:
    “Your samples are not IID. “The annotation IID is particularly common in statistics, where observations in a sample are often assumed to be effectively IID for the purposes of statistical inference.”

    Furthermore, you “think that it is not surprising” is not proof of anything. UCD and “evolution” are assumptions hence cannot be proven by the curve-fitted tree. How many time do I have to repeat?”

  37. Joe Felsenstein: I have a whole web page listing not only typos in the various printings of my book, but erroneous statements as well.

    Do you really think I was referring to typos and what you consider “erroneous”? Very funny.

  38. Rumraket: Nonlin.org: You “can’t reconstruct” what?

    Phylogenies, and ancestors, from extant sequences. It can be done using the methods of phylogenetics.

    Scientists can take sequences from extant species (or individuals from a population) and reconstruct their evolutionary history, including reconstructing the sequences of the ancestors. They can then biochemically synthesize those reconstructed ancestors in the laboratory, put them into a living organism and test them for their functions.

    So this is more of the same modeling and curve fitting based on the same old UCD assumption that cannot be verified by the very same model using it – as explained like a million times.

    How can I verify independently the validity of “reconstructing the sequences of the ancestors”? And what does “put them into a living organism and test them for their functions” prove?

    This is the whole discussion:

    “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.

    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.

    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.

    Joe Felsenstein: 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.

    Nonlin.org: Last I checked, genealogies go back several generations to specific ancestors. Say grandma was cremated and grandpa’s DNA was also lost during a war. Then your family tree will be very stunted if you rely only on DNA…or you get some vague and meaningless maps of origins: https://www.ancestry.com/ And on a practical basis, the DNA of long lost relatives from “the old country” are nowhere to be found since no one will go check the DNA of whole populations to trace one’s ancestry.
    Of course we need other identifiers. Why is this news to you?

    Joe Felsenstein: The main issue is with phylogenies. Why do you think we can’t reconstruct them if we only have DNA from living species? I work on this, have written and distributed computer programs to do it, and have carried out computer simulations to check how well it works.

    What Joe Felsenstein is saying is that you can “reconstruct” great-great-great-…-great-grandmother from the DNA of a few living descendants. This is preposterous and not how ancestry.com operates – GO CHECK IT OUT.

  39. Entropy: Yep. Sometimes I see very good explanations, only to see the creationists jump over the interesting and informative parts, and “answer” some small sentence in ways that make the jumping over all too obvious.

    Swap “creationists” with “Darwinists” and it’s exactly my experience. And then they repeat their “argument” at infinitum as if nothing was ever said… See, we do have something in common 😊

  40. Mung: Thank you. I did not know that.

    Did it perhaps happen in the baptist churches I grew up attending every sunday and wednesday? Because they also appeared to have wiped my memory of it as well.

    You’re welcome.

    Sunday and Wednesday for a few hours? Your church was fighting a loosing battle against the government indoctrination machine (to not mention all other propaganda machines of the modern society). And they were not even dedicating all the time to it.

    Either way, it helps the think for yourself. I do.

  41. Nonlin.org: What Joe Felsenstein is saying is that you can “reconstruct” great-great-great-…-great-grandmother from the DNA of a few living descendants. This is preposterous and not how ancestry.com operates – GO CHECK IT OUT.

    What do you mean by “reconstruct”, and do you mean the same thing as Joe Felsenstein? If I can say with fair certainty that two (or more) people had the same great…..great grandmother, while two (or more) other people had a different one, does that count?

    I think what Joe is saying is that we can construct a table (or graph) of relationships based on similarity of DNA among a very large number of DNA samples of different critters. And if we discover that the graph that best fits this collection of similarities takes the form of a tree, this is at least suggestive.

  42. 1. Although one can make estimates of the DNA sequences of ancestors, this is not what we do in inferring phylogenies. Surely nonlin.org knows that.

    2. Yes, I have heard of the “independent and identically distributed” (i.i.d.) condition, but it is not strictly required for inferring phylogenies. nonlin.org, being apparently well-acquainted with all these methods, will know all about “mixing conditions” as they affect the Law of Large Numbers, and also such methods as the “block bootstrap” (Künsch, 1989).

    3. Nonindependence of changes in different characters (such as the sequences of different genes) can occur, but has to be very strong to invalidate the statistical consistency of the estimate of the phylogeny.

    4. May I assume that nonlin.org has some substantial evidence, or some convincing argument, that changes in different genes are very strongly nonindependent? Strongly enough that nonlin.org is not surprised when trees made from two different genes, genes that are in different parts of the genome and function in different biochemical pathways, lead us to infer closely similar trees?

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