Nested Hierarchies (Tree of life)

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

Do you want to be my cousin?
Sure. If not me, then who?

  1. “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution. This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates. The three basic assumptions of cladistics models are: a) Any group of organisms are related by descent from a common ancestor (UCD – universal common descent); b) There is a bifurcating pattern of cladogenesis; c) Change in characteristics occurs in lineages over time. Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism” and not by a process generated by a designer that also happens to make use of biologic reproduction.
  2. No assumption can be tested by the model that uses them. That is why they’re called ‘assumptions’ and not ‘conclusions’. Instead, assumptions have to be tested independently through an entirely separated method or be accepted as axioms. An UCD “mechanism” has never been observed or proved elsewhere and is not “self-evidently true”, therefore not a valid axiom. Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis. Furthermore the conclusions of any “cladistic analysis” will always and trivially be compatible with the UCD assumption in that model.
  3. Hypothesis testing requires an alternative (null) hypothesis and a procedure that demonstrates how the data available is compatible with the successful hypothesis and at the same time is statistically incompatible with the alternative hypothesis. In the “cladistic analysis” case, the alternative hypothesis to UCD is “common design”, and of course UCD cannot be an assumption of such an analysis. However this rule is violated twice, first by the use of an assumption also presented as conclusion, and second by the prejudiced rejection of the alternative “common design” hypothesis before analysis. This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD. What “cladistic analysis” is instead is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points.
  4. The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility. This is not surprising as designers are free to incorporate whatever mechanism they want, including intelligent “selection” (human breeders do!) and “common descent” (human breeders do!) if they so desire.
  5. The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false. On one hand, we do know the history of the automobile, so a proper classification must be able to reconstruct their unique “evolution”. Yes, vehicle share parts, so to get to the actual development tree, we must group them differently than organisms since mass production works differently than biologic reproduction. On the other hand, organisms may not be uniquely classified as demonstrated by the numerous revisions and exceptions to the “tree of life”, and in any case, “uniquely classified” is an absolute claim that can never be proven since it is impossible to compare the infinity of possible organism classifications.
  6. The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails. Anatomy is not independent of biochemistry. Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited. This is not to say that the fossil record is complete, or that fossils can be positively linked to one another and the living without – once again – presupposing UCD. The claim that “there is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry” is false as the ‘designer’ hypothesis produces the same result when one designer creates all morphologies, and furthermore “I cannot think of an alternative reason why…” is not a valid argument.
  7. A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure. To decide the position of a certain organism, the human creators of the “tree” have to decide which morphologic/biochemical/genetic characteristics to include and what weight to attach to each of those measures. This further supports the claim that “cladistic analysis” is ‘curve fitting’ rather than ‘hypothesis testing’ – if a tree must be built, a tree will be built as in this example: “The close relationship between animals and fungi was suggested by Thomas Cavalier-Smith in 1987, […] and was supported by later genetic studies. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants […].”

 

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

  1. colewd:
    Yes, I remember.This is a piece of evidence for common descent if the gene turns out to truly be without function. How is it verified that the identified gene is without function?

    1. You’re missing the point. Here it goes again: John mentioned that genes can be broken and then accumulate mutations. You called that speculation. I clarified that such thing was no speculation and offered that gene as example that there’s documented cases.

    2. Whether a pseudogene has acquired another function after losing the encoded protein, or not, that it’s broken in the same way across different species is still evidence of common ancestry. The evidence is in how the gene is broken, not in whether the gene has some function unrelated to its prior coding capacity. The probability of breaking coding sequences by exactly the same mutation(s) in separate lineages is very small. Thus, it’s reasonable to infer that these lineages inherited the broken version from a common ancestor.

    colewd:
    There is also evidence against common descent

    No, there isn’t.

    colewd:
    and Johns comments are full of assumptions.

    Not as far as I have seen, and as I explained above.

    colewd:
    One of those being that common descent is true.

    That’s not an assumption, but a conclusion from years of experience and actual exposition to the data. Bill.

    colewd:
    Another one that is almost certainly false is that there are lots of gene turnover as we see lots of gene preservation over time.

    But we also see a lot of turnover over time. That functioning genes are preserved, while no longer useful ones would be eroded shouldn’t come too much as a surprise.

    colewd:
    He may make a reasonable point if he can quantify “lots”.

    I do not understand why. If we know examples, we know examples. I suspect, though, that this is yet another case where you are being unreasonably skeptical of evolution, while being excessively naïve about some creationist “article” even though you don’t seem to understand it. Thus, I doubt that we will get anywhere. I think I’ll stop here.

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  2. John Harshman,

    I will admit that I don’t remember any. Remind me.

    One I can remember is you misquoted the genetic variation of dogs in a paper we were discussing. A small issue and you apologized for it.

    it’s that you don’t understand the simplest things, as shown by your inability to read Figure 9.

    I mis read figure 9 so I don’t understand the simplest things.

    This is both a logic failure and a TSZ rule violation. Keiths would be proud.
    Maybe you’re not trying to argue from authority however this lack of self awareness you are showing with your logic failure maybe why you’re projecting something you don’t intend to.

    Stop being so defensive and admit it to yourself.

    I already agreed that I did not understand how modules related to gene families in figure 9. I suggest you stop trying to make a mountain out of a mole hill.

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  3. colewd: I mis read figure 9 so I don’t understand the simplest things.

    You misread it 6 times, the last two after having it explained to you twice. I really don’t think that drawing a generalization from that is problematic.

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  4. Entropy,

    1. You’re missing the point. Here it goes again: John mentioned that genes can be broken and then accumulate mutations. You called that speculation.

    What is speculation is assuming this conclusion from an observed strand of DNA. No one doubts this could happen.

    2. Whether a pseudogene has acquired another function after losing the encoded protein, or not, that it’s broken in the same way across different species is still evidence of common ancestry.

    First if it has function it may never have been an encoded protein. Your hypothesis that it was previously an encoded protein is speculation. Yes, it is positive evidence for ancestry, positive evidence for design and evidence agains the null hypothesis.

    No, there isn’t.

    Sure there is, convergent evolutionary is an example.

    But we also see a lot of turnover over time. That functioning genes are preserved, while no longer useful ones would be eroded shouldn’t come too much as a surprise.

    What we count today is 20000 functioning genes of which the genes that were “lost” in both mice and humans were also functional. Johns argument was not grounded in reality.

    though you don’t seem to understand it. Thus, I doubt that we will get anywhere. I think I’ll stop here.

    I did not understand a single issue of the figures in the paper. This mountain out of a mole hill stuff is not very credible. I think a break is warranted at this point unless you want to read the paper.

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  5. John Harshman,

    You misread it 6 times, the last two after having it explained to you twice. I really don’t think that drawing a generalization from that is problematic.

    Sure it is John. Its one issue and there was more to it than reading a single sentence. As it turns out you don’t really understand it either by your comment this morning. The issue is also not critical to understanding the basic theme of the paper.

    But keep trying to make mountains out of mole hills. This is a theme of unsuccessful people.

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  6. colewd:

    I mis read figure 9 so I don’t understand the simplest things.

    John:

    You misread it 6 times, the last two after having it explained to you twice. I really don’t think that drawing a generalization from that is problematic.

    Bill,

    Reread the account of the events at Dum Bol-der.

    I will be sending John more robes to rend and more ashes for his forehead.

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  7. This is both a logic failure and a TSZ rule violation. Keiths would be proud.

    As predicted simple keiths took the bait 🙂

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  8. What bait? I’m mocking you, and the mockery is hitting home.

    And far from it being a logic failure, what John said is right:

    If you think I’m making an argument from authority, you don’t understand either what my argument is or what an argument from authority is. The problem isn’t that you don’t understand complex things; it’s that you don’t understand the simplest things, as shown by your inability to read Figure 9. Stop being so defensive and admit it to yourself.

    John has shown admirable patience in correcting you, day after day, despite your defensiveness and resistance to learning. Let go of your ego. You are here to learn from people who are brighter and better educated than you. John is doing you a favor. Stop being such a petulant ass. Adopt a more productive attitude and try to learn instead of constantly derailing the conversation with your inane objections.

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  9. colewd:
    What is speculation is assuming this conclusion from an observed strand of DNA.No one doubts this could happen.

    I don;t know what you’re referring to here, but I corrected you specifically about calling the breaking of genes and their accumulation of mutations a load of speculations. They’re no such thing.

    colewd:
    First if it has function it may never have been an encoded protein. Your hypothesis that it was previously and encoded protein is speculation.

    If the regions looks similar to regions encoding a working protein involved in the biosynthesis of vitamin C, well beyond what would be expected by chance, only containing a mutation that alters the gene in a way that a working protein can no longer be produced, then it’s rational to infer that there was an encoded protein. That’s not speculation.

    colewd:
    Yes, it is positive evidence for ancestry, positive evidence for design and evidence agains the null hypothesis.

    No, it’s not evidence for design. Come on Bill, we’ve been through this. We are the only designers you can point to, and we have the broken vitamin C gene.

    colewd:
    Sure there is, convergent evolutionary is an example.

    That’s not evidence against common ancestry. That’s evidence that there’s more than one solution to some problems.

    colewd:
    What we count today is 20000 functioning genes of which the genes that were “lost” in both mice and humans were also functional.

    That they did not make it into the figure doesn’t mean they were not there. It just means that they didn’t make it into the figure. John explained this to you. So did I. Then, if any of them is really absent in both humans and mice, it just means they were lost. If they’re pseudogenes or not, you cannot know from that figure either. You’s have to go check the original data to verify if there’s pseudogenes there, if the regions were simply not sequenced, if the regions were sequenced, ut the automatic annotations missed those genes, etc, etc, etc.

    colewd:
    Johns argument was not grounded in reality.

    As far as I read, John explained quite a few reasons why some genes could be missed in a figure. I don’t see how if we point to potential problems with a figure, we should ignore our experience dealing with genomic sequences and just say, surely those genes were missing, therefore god-did-it.

    More importantly because there’s such things as copy number variations (mjst be the third time I say this, did you even read that?)

    colewd:
    I did not understand a single issue of the figures in the paper.

    From where I sit, it looks like that’s but a symptom of a larger issue.

    colewd:
    This mountain out of a mole hill stuff is not very credible.

    Credible to whom? All I said was that you’re irrationally skeptical of evolution, which you are, and exceptionally naïve about a creationist “paper” that you don’t seem to understand. This is true beyond reasonable doubt. I’ve never seen you been skeptical about creationist literature despite creationists being famous for their dishonesty. Yet, with evolution, man!

    colewd:
    I think a break is warranted at this point unless you want to read the paper.

    So be it, because I’m not in the mood to read that kind of crap.

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  10. Entropy,

    Ok. I understand your reluctance to read the paper but without this the discussion is too far out of context.

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  11. keiths:

    What bait?

    colewd:

    Clueless.

    Bill, people don’t have to be baited into laughing at your incompetence. It comes naturally.

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  12. colewd: What is speculation is assuming this conclusion [deletion mutations, for example] from an observed strand of DNA. No one doubts this could happen.

    Why is that speculation? You have admitted that crocodiles are descended from a common ancestor. Given that, isn’t it more than speculation to claim that differences, such as deletions, in crocodile DNA arose by mutation in particular lineages?

    But apes have considerably less genetic distance than crocs, so by your reasoning shouldn’t that also be true of apes, including humans? Thus we should be able to infer that differences among apes are also the result of mutation in particular lineages. In both cases, crododiles and apes, we have good evidence for gene loss. Would you not agree?

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  13. Bill,

    I would just like to point out that I am not trying to make fun of you. I’m trying to convince you of a few simple points, one of which is that you don’t understand Ewert’s paper, not even the easiest parts of it, e.g. what the circles in Fig. 9 represent. Given your confusion on the most basic of basics, how can you possibly understand anything else in it?

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  14. John Harshman,

    Why is that speculation? You have admitted that crocodiles are descended from a common ancestor.

    I have said based on the limited data that I have looked at that common descent cannot be ruled out as reasonable inference among crocs.

    But apes have considerably less genetic distance than crocs, so by your reasoning shouldn’t that also be true of apes, including humans?

    What do you mean by less genetic distance? The inference is based on less then 1% DNA variation between crocs from the limited data. Also I have no data that suggests different splicing codes among crocs.

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  15. John Harshman,

    Given your confusion on the most basic of basics, how can you possibly understand anything else in it?

    Because this is a small issue based on all the relevant issues in the paper as a result this is not where I initially focused my time. The real issue is the relationship with gene groups whether they are modules or gene families and how they form a dependency pattern.

    John I have learned a lot from you over the years and if I don’t understand something and it is important I will drive to understand it. Instead of trying to make a point with me just correct me and explain it.

    I was wrong in this case and admitted it but you were not able to let it go. As a leader people will follow your example. If you make it impossible for people to admit error they won’t.

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  16. colewd: Instead of trying to make a point with me just correct me and explain it.

    I was wrong in this case and admitted it but you were not able to let it go. As a leader people will follow your example. If you make it impossible for people to admit error they won’t.

    Explaining it is exactly what I did. You failed to notice. How do I make it impossible for you to admit error?

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  17. colewd:
    John Harshman,

    I have said based on the limited data that I have looked at that common descent cannot be ruled out as reasonable inference among crocs.

    Can’t you see how hyper-skeptical you are of real science and how comparatively credulous you are of any creationist claim?

    What do you mean by less genetic distance? The inference is based on less then 1% DNA variation between crocs from the limited data. Also I have no data that suggests different splicing codes among crocs.

    This claim has always puzzled me, though I’ve never made an issue of it before. Where do you get this “less than 1% DNA variation? From the paper: “Other uncorrected divergences within Crocodylia range from 1.2% (Caiman–Paleosuchus) to 6.4% (Gavialis–Melanosuchus). Divergences vary by region, with intron distances 1.2–9.4%, the coding region distances of 0.6–3.9%, and 3′ UTR distances of 1.1–10.5%.”
    Now, if you wanted to compare the results from whole genomes, the intron distances are the best comparison, i.e. 9.4% across crocs. By contrast, the whole-genome distance between humans and chimps is 1.3%.

    The splicing code thing is just a straw you’re grasping at.

    So, why do you accept the evidence of crocs (to the limited, weaselly extent you do) but not the evidence of apes?

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  18. John Harshman,

    John Harshman
    July 31, 2018 at 1:56 am
    Ignored
    colewd: Figure 9: Subset of the dependency graph inferred from the HomoloGene database The graph only shows modules with at least 100 GENES,
    John:
    You have misunderstood again. But I will agree that what you quote is confusing, so you can’t really be blamed. It isn’t the families that have at least 100 genes, it’s the modules.

    So back to the earlier conversation I quoted that the modules had 100 genes and you said I misunderstood again. Then you went on to say that the module had 100 genes.

    You said I didn’t understand and then repeated what I quoted. Do you think it is reasonable that you lost a little credibility at this point as a good resource to understand this detail of figure 9?

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  19. John Harshman,

    So, why do you accept the evidence of crocs (to the limited, weaselly extent you do) but not the evidence of apes?

    Lost genes, and splicing differences among others.

    The splicing code thing is just a straw you’re grasping at.

    No, it appears to be a large driver of species diversity.

    Can’t you see how hyper-skeptical you are of real science

    Real science?

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  20. colewd: The mechanism being functionally observed and it accounting for the pattern are two very different things.

    No not really. That’s the whole point. The mechanisms being observed inexorably lead to such patterns.

    How long does it take for two mutations accounting for an adaption to get fixed in a population? Michael Lynch attempted to answer this.

    Please tell me what you believe Michael Lynch has shown and where he showed it.

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  21. colewd: Rumraket: No, there isn’t any evidence against common descent. There are genetic loci that can’t be used to infer common descent, and therefore aren’t evidence for common descent. But there are none which are evidence against common descent.

    colewd: This shows a lack of objectivity. Convergent evolution among other things is evidence against all organisms being linked together only by reproduction.

    No what I wrote is still absolutely correct and this again demonstrates how poor your reasoning is. Homoplasies can make it difficult to determine relationships, and at least in principle if they are extenstive enough can make it impossible to infer common descent from the locus in question. But that doesn’t make them evidence against common descent.

    Not having evidence FOR a hypothesis does not automatically make it evidence AGAINST the hypothesis. That can only be the case if the hypothesis predicts that the particular evidence should be a certain way. In such a case then finding that the evidence is not the way the hypothesis predicts it should be, can be evidence against the hypothesis. But common descent does not predict that homoplasies should not exist, so they can’t be evidence against common descent.

    I suspect what we’re seeing here is that your own lack of objectivity is leading you to make these simple errors in reasoning over and over and over again.

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  22. colewd: Those two are not mutually contradictory. The fact that SOME fraction of genes are preserved doesn’t mean THE REST has to be

    This is a straw-man.

    I’m getting tired of your vacuous one-liner responses. How is it a straw man? It’s basically what you said.

    “Another one that is almost certainly false is that there are lots of gene turnover as we see lots of gene preservation over time.” – Bill Cole

    So you say there can’t be “lots” of gene-loss implied by the tree, because we see “lots” of preservation. I then correctly point out these two facts are not in contradiction, and you just declare this is a straw man.

    How have I straw manned your statement? I pointed out the logical error it implied. If you did not intend to convey the message that there can’t be lots of gene loss because there’s been lots of conservation of genes too, then what message did you intend to convey and why didn’t you write that instead of the nonsense you wrote?

    Bill, wake the fuck up please.

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  23. colewd:
    John Harshman,

    Lost genes, and splicing differences among others.

    What makes you think crocs don’t have lost genes and splicing differences? And why have you ignored the question of genetic differences within crocs? Need I point out that this is another case of you being unable to read a paper?

    No, it appears to be a large driver of species diversity.

    Where is your support for this claim? Why do you believe that particular bit of science, if it is indeed science, but not other science, like the relationship between humans and chimps?

    Real science?

    Yes.

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  24. Rumraket,

    Not having evidence FOR a hypothesis does not automatically make it evidence AGAINST the hypothesis. That can only be the case if the hypothesis predicts that the particular evidence should be a certain way. In such a case then finding that the evidence is not the way the hypothesis predicts it should be, can be evidence against the hypothesis. But common descent does not predict that homoplasies should not exist, so they can’t be evidence against common descent.

    But common descent does not predict that homoplasies should not exist, so they can’t be evidence against common descent.

    Did it predict that features could pop up and re emerge all the time? So something occurred that the theory did not predict.
    Do you not see how silly this is?

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  25. Rumraket,

    I’m getting tired of your vacuous one-liner responses. How is it a straw man? It’s basically what you said.

    No, it is not what I said. Not even close.

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  26. John Harshman,

    Need I point out that this is another case of you being unable to read a paper?

    I really have no interest continuing at this point. I read this paper a while ago which you wrote. I showed how this rule breaking claim was faulty the last time and you continue to move forward with this narrative.

    I don’t think you have any objective standard for determining common descent other then assuming it is true. I tried to suggest one for discussion purposes which is less then 1% variation. You just showed greater then that in crocs so I guess this rules out the common descent hypothesis in crocs based on that standard.

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  27. colewd: So back to the earlier conversation I quoted that the modules had 100 genes and you said I misunderstood again. Then you went on to say that the module had 100 genes.

    We’ve established that you can cut and paste quotes. What we haven’t established, and in fact have seen contradicted on many occasions, is that you understand what you quote. I see that you have reconfigured this entire encounter in your memory in order to make you the hero; that’s a common human failing that you should try to guard against.

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  28. colewd: I don’t think you have any objective standard for determining common descent other then assuming it is true. I tried to suggest one for discussion purposes which is less then 1% variation. You just showed greater then that in crocs so I guess the rules out the common descent hypothesis in crocs based on that standard.

    Are you denying that you were unable to read for comprehension when you mistakenly claimed that crocs showed less than 1% variation? Where does this 1% standard come from and why have you chosen it? And are you flouncing for real this time?

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  29. John Harshman,

    I see that you have reconfigured this entire encounter in your memory in order to make you the hero;

    John I am not a hero and you understand evolution to a much greater extent then I do. I am simply trying to show you that you were painting a false narrative which is rule breaking. This issue was never a big deal.

    Argue your case not what you think your opponents weaknesses are. When try to argue the failings of your opponent you are simply being manipulative.

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  30. John Harshman,

    Are you denying that you were unable to read for comprehension when you mistakenly claimed that crocs showed less than 1% variation? Where does this 1% standard come from and why have you chosen it? And are you flouncing for real this time?

    John, I read the paper once. You were the author of this paper. I assumed that you would help me understand it. I saw a limited data set that showed less than one percent variation. I tried to say that might imply common descent. Now you want to shove that claim up my ass.

    Whats your strategy here?

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  31. Corneel:
    1. You are acting a bit paranoid here, don’t you agree? No, I was not going to mention hybrids. If you must know: I just want to make sure that at the end of the day, you are not going to change lions into domestic cats because, hey, “it’s just like tanning”. Can we now please agree that the variations within Felidae are true breeding? No strings attached.

    2. Ahhhh, you named the M-word. Was it necessary that the modificationswere introduced at once, or could they have been added piecemeal?

    3. And … you … dodged the question … again. Are all Felidae related OR were the variations created de novo, using some generic cat as a template? Can you even tell the difference between these two scenarios?

    4. I did read that, but – let me repeat my answer because you seem to have trouble getting this: “Just because you have a hard time answering my questions doesn’t make them senseless.”

    And you DO have a hard time answering them, don’t you, mister I-don’t-pretend-to-know-how-biologic-creation-happened?

    5. It is a senseless question because it is getting us nowhere. Yes, I am sure cats won’t be born from dogs, because that doesn’t comport with what we know about reproduction. Yes, I trust science (no need for capitalization, you can stop kneeling too). Now, what were you trying to accomplish with that question?

    1. If a wolf can become chihuahua, I don’t see why a lion cannot become a cat with sufficient effort from an intelligent breeder.
    2. Don’t know. Could be piecemeal, why not? Ask the Designer, not me.
    3. Don’t know. Designers generally do not create de novo when it’s easier to modify.
    4. You’re asking questions that should not be addressed to me – I am NOT God or a prophet.
    5. Wrong again. Venter claims to have done that (more or less): http://science.sciencemag.org/content/351/6280/aad6253 . Trying to determine how we would know if one hypothesis or the other is true. A must per the scientific method. Are you not part of the “Praise Science!” crowd? Now stop being a chicken and answer to the best of your knowledge.

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  32. Corneel: Nobody is doing that. It is possible that the LUCA never existed. Fact is: if you ask why there can’t be multiple LUCA’s you make yourself look silly. just sayin’

    You see what I see.What I see is variations around a fixed theme. ONE theme. All life is one.

    No, I make YOU and all others claiming LUCA look silly. How does “evolution” work if no LUCA? Are you saying the wonderful trees your buddies build are fake?

    Yes, we do see one theme, but LUCA claims more than that.

    I am fine with the definition highlighted below. ARE YOU?
    an·ces·tor
    [ˈanˌsestər]
    NOUN
    a person, typically one more remote than a grandparent, from whom one is descended.
    “my ancestor Admiral Anson circumnavigated the globe 250 years ago”
    synonyms: forebear · forefather · predecessor · progenitor · antecedent · primogenitor
    an early type of animal or plant from which others have evolved.
    synonyms: forebear · forefather · predecessor · progenitor · antecedent · primogenitor
    an early version of a machine, system, etc..
    “this instrument is an ancestor of the lute”

    synonyms: forerunner · precursor · predecessor · prototype

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  33. Joe Felsenstein: 1. John Harshman wondered aloud whether there was anything that Design would not predict.
    2. I said, in reply to John, maybe junk DNA, because the Design people get upset at the thought that it was there.

    Note that I wasn’t answering anything by nonlin.org. Nor was I, in that comment, arguing for the existence of junk DNA. Just commenting on what Design advocates get upset by.

    “Junk DNA” would not disprove Design in any way and I am most definitely not upset. Just pointing out that it’s a typical unsubstantiated claim in the most traditional Darwinist spirit. More importantly, No word on the explanation provided? Did it make sense to you?

    On another note, Mr. Gardner of bushes, trees and circles, can you comment on whether this OP is misrepresenting your “trade” or not? Perhaps people or bots (to be PC) like Entropy are not really qualified to defend you despite their best efforts? Much appreciated.

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  34. Nonlin.org: can you comment on whether this OP is misrepresenting your “trade” or not?

    It is misrepresenting it. While it is true that phylogeny programs will always come up with a tree (or trees), the fact that they come up with a tree does not validate the tree — the trees are validated if multiple different parts of the genome come up with more-or-less the same tree. (More-or-less because the inference is always somewhat noisy). That is what Doug Theobald was addressing in his papers and at Talk.Origins.

    In addition points 5 and 7 make no sense, and point 6 is wrong.

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  35. colewd:
    John Harshman,

    John, I read the paper once.You were the author of this paper.I assumed that you would help me understand it.I saw a limited data set that showed less than one percent variation.I tried to say that might imply common descent.Now you want to shove that claim up my ass.

    Whats your strategy here?

    My strategy has three parts:

    1. To get you to make clear claims about what you believe and to support those claims with what you think is evidence.

    2. By asking questions, to get you to turn the nonsense you generally post into the clear claims/evidence mentioned above.

    3. Once you have made those claims, to present arguments and evidence that your claims are untrue, assuming that they are (which has so far been a safe assumption).

    I have been unsuccessful in this strategy because you almost never give straight answers to questions, or any answers for that matter; for example, in the very comment I’m responding to here, you failed to answer any of the three questions I asked you.

    Now, if you want my help understanding anything, you should try asking me questions. I do actually attempt to answer.

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  36. Joe Felsenstein: Nonlin.org: can you comment on whether this OP is misrepresenting your “trade” or not?

    It is misrepresenting it.

    I would just like to point out that it’s my trade too, and I’ve told nonlin many times that he(?) is misrepresenting it. But it has no effect.

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  37. John Harshman: I would just like to point out that it’s my trade too, and I’ve told nonlin many times that he(?) is misrepresenting it. But it has no effect.

    I’m grateful that we have you here as a voice of experience, wisdom, and sanity in discussions, particularly in the “tree trade”. You’ve made a great contribution to this blog (and others). I wish I had your patience.

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  38. John Harshman,

    1. To get you to make clear claims about what you believe and to support those claims with what you think is evidence.

    Fair enough.

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  39. colewd:
    John Harshman,

    Fair enough.

    4. And to stop you giving pointless, two-word answers to small parts of entire comments while ignoring the rest.

    At this also I have failed.

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  40. John Harshman: 4. And to stop you giving pointless, two-word answers to small parts of entire comments while ignoring the rest.

    That one resonates with me. I write almost whole treatises for Bill, and then get an “answer” that shows that there was no reading involved.

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  41. colewd: Not having evidence FOR a hypothesis does not automatically make it evidence AGAINST the hypothesis. That can only be the case if the hypothesis predicts that the particular evidence should be a certain way. In such a case then finding that the evidence is not the way the hypothesis predicts it should be, can be evidence against the hypothesis. But common descent does not predict that homoplasies should not exist, so they can’t be evidence against common descent.

    But common descent does not predict that homoplasies should not exist, so they can’t be evidence against common descent.

    Did it predict that features could pop up and re emerge all the time?

    What features? What is “pop up and re emerge” supposed to mean? How frequent is “all the time”?

    So something occurred that the theory did not predict.

    At the level of sequence, we actually expect occasional homoplasies for simple statistical reasons. As in we expect that it will some times happen that the same mutation happen in two independent lineages just by chance.

    Do you not see how silly this is?

    I’m not at all sure what it is you’re having difficulty with.

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  42. colewd: I’m getting tired of your vacuous one-liner responses. How is it a straw man? It’s basically what you said.

    No, it is not what I said. Not even close.

    Then what did you intend to convey when you wrote:
    “Another one that is almost certainly false is that there are lots of gene turnover as we see lots of gene preservation over time.” ?

    I took this to mean that you think there can’t be large amounts of gene loss over some period of time, because other genes are simultaneously conserved.

    If that is not what you meant by your rather straightforward statement, then what did you mean to say? Clarify!

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  43. Nonlin.org: 1. If a wolf can become chihuahua, I don’t see why a lion cannot become a cat with sufficient effort from an intelligent breeder.

    You are way too quarrelsome to even acknowledge a simple and evident claim. Never mind, we’ll see how it goes.

    Nonlin.org: 2. Don’t know. Could be piecemeal, why not? Ask the Designer, not me.
    3. Don’t know. Designers generally do not create de novo when it’s easier to modify.

    At face value, you seem to be be OK with the premises of descent with modification then. If you have no opinion on these matters, then why do you oppose (universal) common descent so strongly? Why can all felids be related, but not all life?

    Nonlin.org: 4. You’re asking questions that should not be addressed to me – I am NOT God or a prophet.

    Sssssst! Didn’t you get the memo? You are not allowed to speculate on the identity of the Designer.

    Nonlin.org: 5. Wrong again. Venter claims to have done that (more or less): http://science.sciencemag.org/content/351/6280/aad6253 .

    Craig Venter claims to have dogs give birth to cats? Really? Well, I think that is nonsense. BTW, you appear to have linked to the wrong site, no mention of cats and dogs there.

    Nonlin.org: Trying to determine how we would know if one hypothesis or the other is true. A must per the scientific method. Are you not part of the “Praise Science!” crowd? Now stop being a chicken and answer to the best of your knowledge.

    I already answered your do-dogs-give-birth-to-cats question. Not sure which other question you want answered.

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  44. Nonlin.org: How does “evolution” work if no LUCA? Are you saying the wonderful trees your buddies build are fake?

    Why wouldn’t evolution “work” if eukaryotes, bacteria and archaea do not share an ancestor? Why would that fact disprove phylogenetic trees within those groups?

    Nonlin.org: I am fine with the definition highlighted below. ARE YOU?

    Fine, I guess, as long as we are talking about machines. For humans and other organisms I would stick with the non-bolded part.

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  45. John Harshman: 4. And to stop you giving pointless, two-word answers to small parts of entire comments while ignoring the rest.

    … amongst my strategy…. amongst my strategy…are such elements as…. I’ll come in again.

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  46. Corneel:
    You are way too quarrelsome to even acknowledge a simple and evident claim. Never mind, we’ll see how it goes.

    If it goes at all, which I doubt. Nonlin doesn’t seem to be able to use some basic mental abilities.

    Corneel:
    Why wouldn’t evolution “work” if eukaryotes, bacteria and archaea do not share an ancestor? Why would that fact disprove phylogenetic trees within those groups?

    Nonlin doesn’t seem to understand the difference between universal and non-universal. I explained this three or four times, and poor Nonlin didn’t get it. For example, all the times Nonlin insists on thinking that UCD is assumed, when it’s enough if common ancestry can be established for a group before starting a phylogenetic analysis. Somehow she thinks that if it’s not universal it’s not common ancestry either.

    I doubt you’ll get anywhere. Not once has Nonlin actually dealt with the points I raise, which is why I try not to direct my explanations to her.

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  47. Entropy: I doubt you’ll get anywhere. Not once has Nonlin actually dealt with the points I raise, which is why I try not to direct my explanations to her.

    Yeah, I know. The only thing I was hoping to get out of this exchange is a little insight into the reasons for Nonlin’s utter rejection of anything faintly smelling of evolution, which is what interests me (hey, and that is what TSZ is for, right?).
    Common descent of felids seems to go down well (most creationists accept that they are a related group), but I sure am curious where the dividing line is drawn this time. 😉

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  48. Corneel: The only thing I was hoping to get out of this exchange is a little insight into the reasons for Nonlin’s utter rejection of anything faintly smelling of evolution

    Oh, that’s somewhat easy. Nonlin googled some words, looking for things that would look bad (in Nonlin’s opinion), or good (for Nonlin’s position). Then she composed some incoherent piece of crap, thinking that she’s a genius, of course, and that the universe will follow her commands. That’s it. She has thus proven that evolution is bullshit. You don’t agree? Then take your problem to google, or wikipedia, or whatever other dictionary she misused. She becomes deaf to anything you say or explain. The most she’ll do is repeat the same shit you already showed to be plainly wrong, and call you a moron or something to that effect.

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