Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.

Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.

That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.

The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”

So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.

So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.

5,145 thoughts on “Common Design vs. Common Descent

  1. I pointed out Cox1 gave a very nice Linnaen looking hierarchy here:

    http://theskepticalzone.com/wp/common-design-vs-common-descent/comment-page-81/#comment-203116

    In contrast, here is a different hierarchy based on BMP2 which I performed professional grade cherry picking and fudging to make birds and other tetrapods “neighbor” with lungfish. I’m accused of not understanding, but when I demonstrate that I understand how to fudge the data like professional phylogenticists, I don’t get any credit! Here is proof I know how do it and make a tree that conforms to the prevailing narrative that giraffes are fish.

    So what was that about all the congruence of data? It congrues if you cherry pick and fudge till it congrues.

    Click to enlarge:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/bmp_fudge.png

  2. stcordova: The problem is with the method, not the data that says the species are dis-similar with respect to that gene. Not accounting for the fact a gene is missing in one species and present in another is cherry picking.

    You’re still missing the point, so I cannot start on your other issue until you understand why you’re mistaken on this one. If a gene is missing on one species then there’s no point in putting that species in the tree done with the gene that such species is missing. It doesn’t make sense because the measuring stick is lost.

    It’s not cherry picking. It’s obvious that without the gene we cannot measure the relative separation of the organisms missing the gene with respect to those that have the gene, unless we can find an appropriate measuring stick.

    Do you understand that part now?

    stcordova: This is analogous to ignoring the fact placental mammals have placentas and fish don’t. You ignore all the features that aren’t shared by a creature, and you can aggregate them in not very proper ways — such as claiming giraffes are fish.

    Not really, because when we compare the aligned sequences we take into account, both their similarities and their differences. Their differences are analogous to some organisms having placentas, while the others lie eggs.

  3. Entropy: Not really, because when we compare the aligned sequences we take into account, both their similarities and their differences.

    I would also like to point out that you could indeed build a tree based on presence or absence of particular genes. You would just have to code the characters differently from coding for a DNA or protein sequence analysis, i.e. as two-state binary characters, one per gene. You could even do neighbor-joining with the resulting matrix, if you cared to, though I suspect that parsimony or maximum likelihood would work better. I predict that you would get the same tree of vertebrates as other nuclear gene data would give you.

    And in fact similar trees have been produced for some taxa, based on presence or absence of particular indels or particular SINE or LINE insertions.

    See, for example, Yuri et al. 2013 or Suh et al. 2011.

  4. John Harshman:

    I would also like to point out that you could indeed build a tree based on presence or absence of particular genes.

    You mean a tree that is built on the presence and absence of genes as reflected in the Pan-Genome diagram (below) that you hate so much?

    Genes present in Mice and Men, but absent in Zebra Fish: 16002+892 = 2949
    Genes present in Men but and Zebra Fish but absent in Mice: 73 + 105 = 178
    Genes present in Mice and Zebra Fish but absent in Men: 57+89 = 146

    Conclusion: Mice and Men are better Neighbors than Fish and Men. Ergo, it is reasonable to say a mammal isn’t a fish! Exactly my point.

  5. Rumraket: Now you’re describing a theory of evolutionary change…

    Yes. Darwin’s theory. I don’t know what other theory we could be talking about.

  6. Mung: Yes. Darwin’s theory. I don’t know what other theory we could be talking about.

    I see your confusion. Darwin had lots of theories, not just one. In the Origin, he put forth two of them: natural selection and common descent or the principle of divergence. Not the same thing. Natural selection operating on random variation was his proposed mechanism of change. Common descent/divergence was his explanation for the branching pattern into which differences were organized.

  7. Entropy:

    You’re still missing the point, so I cannot start on your other issue until you understand why you’re mistaken on this one.

    You got it backward. You’re the one mistaken and you won’t fix your mistake until you understand you’re the one who doesn’t understand.

    I cannot start on your other issu

    Sure you can, and then you’ll see how mistaken you are.

  8. Sal:

    Conclusion: Mice and Men are better Neighbors than Fish and Men. Ergo, it is reasonable to say a mammal isn’t a fish! Exactly my point.

    Could he possibly be this stupid?

    Yes. Yes, he could.

  9. stcordova: You got it backward.You’re the one mistaken and you won’t fix your mistake until you understand you’re the one who doesn’t understand.

    What’s my supposed mistake Sal? That I understand why when a gene is missing we have no measure of divergence to work with? If not what? be very precise please. It doesn’t look as if you read my comment in full.

    stcordova: Sure you can, and then you’ll see how mistaken you are.

    No. You keep saying that’s cherry-picking. All your issues seem to go around that idea fixed in your brain, and you still don’t seem to understand why we use genes present in all organisms. To you it’s cherry-picking, but you don’t explain why we should use genes not present in all organisms under analysis, or how. For example, how would you align a non-present gene with present genes? How would you use the missing information to infer relative divergence distances? How would you know if that distance reflects anything other than the absence of the gene?

    P.S. Thanks for the link to the Zebrafish genome paper.

  10. stcordova:
    Entropy,
    I’m sorry it’s not worth my time until you admit I’m right.

    That you’re right about what? You seem to jump all over the place. Right about the cherry-picking? Sorry, you’re too obviously wrong. Painfully obviously wrong.

    But you don’t seem to read the comments in full, so it’s not worth my time to continue only to get most of each comment ignored.

  11. stcordova: Common Design doesn’t predict the nested hierarchy will be there, but it doesn’t predict it will not be there either! The same could be said for the theory of celestial mechanics. Celestial mechanics doesn’t predict a nested hierarchy of life will be there but it does not predict it will not be there either.

    Just a point, no one claims celestial mechanics is responsible for the variety of life, some claim design is. Your argument is specious.

  12. Knowledge of the genome has placed a crushing burden on the claims of intelligent design. It can no longer just shrug at the details of living organisms and invoke a designer to account for them. It now has to explain why our genome everywhere proclaims “descent with modification,” to use Darwin’s favorite phrase for evolution.

    – Only a Theory. Kenneth R. Miller. p. 109

    Made me laugh.

    It’s the “descent with modification” crowd who want to avoid details, as seen in this very thread. They’d much rather not to need to invoke anything or give any account at all.

    And ID now has to explain why our genome everywhere proclaims “descent with modification” but the “descent with modification” crowd here doesn’t?

    At least Darwin tried to give an explanation.

  13. Mung: It’s the “descent with modification” crowd who want to avoid details, as seen in this very thread. They’d much rather not to need to invoke anything or give any account at all.

    Any chance you might give some details or give any account at all to show the descent with modification crowd how it is done?

  14. John Harshman: Darwin had lots of theories, not just one. In the Origin, he put forth two of them: natural selection and common descent or the principle of divergence. Not the same thing. Natural selection operating on random variation was his proposed mechanism of change. Common descent/divergence was his explanation for the branching pattern into which differences were organized.

    But you seem to be agreeing with what I say, which is that his theory of common descent with it’s “principle of divergence” at least attempts to explain the differences. Others are claiming it doesn’t explain the differences and doesn’t need to.

    Any thoughts on an evolutionary author who best explains Darwin’s theory of descent with modification? Mayr perhaps?

  15. Mung:
    It’s the “descent with modification” crowd who want to avoid details, as seen in this very thread. They’d much rather not to need to invoke anything or give any account at all.

    That’s just plain bullshit. In every way it can be bullshit. It’s bullshit in that the truth is the direct opposite. No design proponent ever offers any details, other than just typing in the word “design”. That’s it, that’s the totality of detail anyone ever gets from a design proponent.

    Everything you just wrote screams hypocrisy. If you’re fine with just saying design, then you can’t complain without being a hypocrite, if someone says “evolution by mutation, natural selection, genetic drift and so on”.

    And it’s bullshit because I have posted.multiple.times to explain how we know how differences arise, and with explanations and references to research where ancestral states were reconstructed in the laboratory, based on phylogenetic methods, and then actually tested for their functions.

    What have we been offered in comparison? Oh yeah, this:

  16. Mung: But you seem to be agreeing with what I say, which is that his theory of common descent with it’s “principle of divergence” at least attempts to explain the differences. Others are claiming it doesn’t explain the differences and doesn’t need to.

    No, I’m not agreeing at all. The theory of common descent doesn’t explain the differences. It explains the nested hierarchical pattern in which those differences are arranged. These are not at all the same thing.

  17. Mung: But you seem to be agreeing with what I say, which is that his theory of common descent with it’s “principle of divergence” at least attempts to explain the differences.

    No, he wrote “the branching pattern into which differences were organized”.

    Common descent explains the branching pattern in the organization of differences. It does not explain how the differences arise.

    Depending on the phenomenon in question, a theory of evolutionary change at the molecular, and/or cellular, and/or developmental biological level, does explain how differences arise. But then you need a theory of common descent to explain the branching pattern of those differences.

    How did there come to be gene X in this clade? Common descent doesn’t actually say. It just says that, the reason that gene displays the branching pattern that it does inside that clade, is because of common descent.
    To explain how gene X arose in the first place requires a theory of mutations, and to explain why it persists and proliferated (maybe even rapidly?) into many species, requires a theory of evolution by natural selection, drift, and so on.

    Going a level down, we can even look at individual mutations. Common descent does not explain why two arbitrarily picked protein coding genes which are similar, from chimp and human, are actually different at some number of positions that they are different. It could be as little as one or two nucleotides that are different, for example.

    Why are those two genes different by two nucleotides? How did those differences arise?
    It’s pretty obvious that if we merely answered: “Because they descend from a common ancestor”, that doesn’t explain that.

    But “because they each, or one of them, suffered mutations” does. The implication being that they used to be completely identical, but mutations happened which created the differences.

  18. Rumraket: What have we been offered in comparison?

    The Zinc Finger.

    John thinks I’m confused and I think you are confused.

    Evolution, that is, descent with modification from a common ancestor, gave a straightforward earthly explanation of this hierarchy.

    – Doubting Darwin? Sahotra Sarkar. p. 8

    So it is evolution that explains the hierarchy. It is descent with modification from a common ancestor that explains the hierarchy. If you haven’t explained the modifications you haven’t explained the hierarchy.

  19. Rumraket: Okay, but I agree with John.

    Which means you disagree with Sarkar.

    But on the bright side, we’re finally, after over 4000 posts, discussing whether we are even talking about the same theory.

  20. Rumraket,

    I too commenced a response in which the word ‘bullshit’ played a significant role. Good job I read ahead first! ‘4000 comments in’, Mung thinks we’re finally getting to what the thread is about. But telegraphs the opposite quite clearly.

    It does seem to boil down to a weird insistence, on that side of the divide, that you can’t infer that motion occurred without detailed knowledge of the mode of transport.

  21. Mung: The Zinc Finger.

    John thinks I’m confused and I think you are confused.

    So it is evolution that explains the hierarchy. It is descent with modification from a common ancestor that explains the hierarchy. If you haven’t explained the modifications you haven’t explained the hierarchy.

    Yeah, you’re still confused. “Evolution” is a catchall term for many different things; in this case the reference is to common descent. You’re fixated on the reasons for modification, which are not relevant. It’s the distribution of modifications across species that count.

  22. (A haggard figure appears)

    “SINE data … croak! … look to SINE data!”

    (shuffles on)

    Any given SINE insert is a useful proxy for all the concepts being squirted around like squid ink. It appears at its site out of the blue, much as an orfan gene (although in this instance we can trace it – using sequence analysis and phylogenetics, yet! – to other such sequences).

    Once inserted, it stops being a ‘difference’ and becomes a ‘similarity’. The Creationist response? “Until you have a detailed account of when it arose and how, you have no theory”. Wha? So, if a SINE is shared at a given position by an entire clade, we are disbarred from considering that they all got it from a common ancestor if we don’t know how that ancestor got it? That makes no sense.

    At this point, I guess Sal will favour us with something unrelated he’s found out about SINEs, Mung will offer a snippet from a book of unexplained relevance and Bill will talk about protein space.

  23. Rumraket,

    You forgot to explain how information poofed into existence before your nonsense theory can even start making any sense at all…
    I guess it’s not important …all one needs is faith….lol

  24. Virtually all the proofs for evolution listed by Darwin in the Origin actually consist of evidence for common descent.

    – One Long Argument. Ernst Mayr. p. 24

    Apparently Darwin was too stupid to know the difference.

  25. J-Mac:
    Rumraket,
    You forgot to explain how information poofed into existence

    I wonder if it’s worth trying to get you to understand how this works. I’ll give it a small try: What the hell are you talking about?

    J-Mac:
    before your nonsense theory can even start making any sense at all…

    I don’t know what Rumraket’s theory might be, but, do you think you can offer a good theory instead? What would that be?

    J-Mac:
    I guess it’s not important …all one needs is faith….lol

    If you find your religious inclinations so laughable, why do you hold to them?

  26. Mung: Apparently Darwin was too stupid to know the difference.

    It’s this sort of unexplained one-liner that led me to “ignore” you in the first place. If you want to talk about anything, stop that.

  27. Allan Miller:
    stcordova,

    Hey, do you have a more taxonomically rich version of that endlessly reposted diagram? Or is that kind of it?

    Note that it isn’t even a diagram of orphan genes, just of orthologs.

  28. There is an equivocation going on when Darwinists say common descent predicts a nested phylogenetic hierarchy. Common descent predicts one kind of nested phylogenetic hierarchy, but not another kind of nested phylogenetic hierarchy.

    If we are talking gene trees, where a gene starts out in a species and then as time goes on, the gene in the descendants mutates — this can create a nested phylogenetic hierarchy. Rumraket showed the principle, and I confirmed it with phylogeny software. It was a PREDICTABLE outcome. Sooooooo…I agreed. In principle that the sort of nested phylogenetic hierarchy evolution can generate. No problem in principle, maybe a problem in practice, but let’s grant it is no problem for the sake of argument…

    But that’s not the only nested phylogenetic hierarchy in play. There is the problem of highly unpreditable novel complex features that also create nested phylogenetic hierarchies. One might call them synampomorphies, but I don’t, I called them orphan systems. That didn’t go over well, so how about another term: POOF-omorphy. POOF-omorphy is maybe descriptive because, well, it shows up unpredictably — kind of like a poof. An example is the placenta or mammary gland or insulin regulated metabolism, etc.

    So even John Harshman admitted common descent does not account for these new features. And to be meticulous, even the origin of those genes from which gene trees are built, in many cases they must have POOFed onto the scene sometime in the past too.

    Common descent doesn’t predict those kinds of POOFs which define taxonomic nested hierarchies built on highly discrete characters (like the placenta). So evolutionists should stop pretending common descent predicts hierarchies defined by complex features with no traceable ancestor or a mechanistically predictable route to these new features.

    To point to the gene trees as confirmation of the prediction of nested hierarchy is an equivocation, because predicting the gene tree structure is only a necessary but not sufficient condition for proving common descent. Another necessary condition that must be met is common descent must predict the part of the nested hierarchy defined by these complex features with no ancestor or no feasible route from a known ancestor to a descendant state. By John’s own admission common descent does not predict such features.

    So John has failed to prove his point, and now he and Rumraket and Keiths and Theobald get called out on their equivocation of what nested hierarchy really means. They pretend the gene tree nested hierarchy is the same as the nested hierarchy defined by suddenly emerged complex novel features.

    I realized this as I was pondering the issue of neighbor joining of species when missing genes were in play as well as morphological features like the placenta. Then it dawned on me, many of these genes just poofed onto the scene in one lineage and not another, and thus making them missing in one lineage. And not just genes, but also a variety of complex features like the placenta.

    To paraphrase Kluge, these POOFs are singularities that don’t obey Neyman-Pearson statistics for the simple fact statistical models don’t predict the evolution of placentas and elephants from fish. Unlike the prediction of gene trees, these POOF-omorphies don’t follow any sort of statistical prediction.

    So common descent doesn’t explain the real hierarchy in question. Common descent maybe explains the nested hierarchy in gene trees, not the nested hierarchy created by suddenly emerged complex novel features. Evolutionists only pretend the nested hierarchy that might get created in gene trees is the same as the nested hierarchy created by sudden emergence of complex novel features. It’s not. To represent both nested hierarchies as the same thing is an equivocation, and equivocations are logical fallacies that leverage rhetorical gimmickry, it’s not science, it’s not truth.

  29. stcordova: So John has failed to prove his point, and now he and Rumraket and Keiths and Theobald get called out on their equivocation of what nested hierarchy really means. They pretend the gene tree nested hierarchy is the same as the nested hierarchy defined by suddenly emerged complex novel features.

    Why does the standard phylogenetic tree of life inferred from morphology (and therefore by presense/absense of “biosystems”, or what you would call an Orfan-system, or POOF-omorphy), still so significantly corroborate the gene trees?

    With a good taxon sample and multiple independent data sets (several different genes for example), you can get a conensus tree and compare it your morphological tree. And what do you get? They corroborate each other to an exceptional degree of statistical significance.

    What good, quantifiably predictive design explanation is there for that fact? Well there is none.

    It is only possible to account for this fact with an ad-hoc rationalization that doesn’t make logical sense:
    It’s what the designer wanted to design because he wanted to make it look like the taxa emerged by common descent through a branching genealogical process.

    In other words: The designer is lying to us.

  30. John Harshman,

    I dug out the original paper; there’s an interesting figure immediately below the Venn diagram showing the residual teleost WGD gene duplicates, giving a pretty strong signal mapping chromosomes in pairs, but with a minor pattern of apparent ‘chunk migration’ of subchromosomal fragments to other chromosomes. All reasonably inferred as common descent of true paralogs: gross duplication followed by migration.

    Not sure what ‘common design’ would have to say on this – yet another thing that makes sense on an evolutionary basis, with design’s best guess a feeble ‘maybe the gene order’s functional’. Well, maybe, probably not on that scale though, and I bet closer relatives have a closer gene order mapping than more distant, in any taxon of one’s choosing. Karyotype evolution’s something else to ignore, I guess.

  31. stcordova,

    The problem you have is that while you are busy ogling the genes you might call TRGs, the genes to left and right are all busily following that ‘gene tree’ pattern. Thousands of ’em. At a higher taxonomic level they too might once have popped up as a TRG in the more distant past. All coalescing different clades: subsets, sets, supersets. That’s why it’s a tree.

    What you are pushing for might be a kind of Intelligent Tinkering, but it ain’t really YEC.

  32. stcordova,

    Sal,

    It looks a lot like your problem is a mismixture of problematic conceptual frameworks, and your revolt at the idea that you might be related to chimpanzees and fish. I think we can clarify things a bit, unless you prefer to hide behind conceptual problems and misapplied semantics.

    Common descent is a relationship. To make you happy, let’s call it an inferred relationship. This can be made into a hypothesis suggested by some data. For example, Carlitos Linnaeus’ taxonomic classification, which he made on the basis of morphological traits (shared and unshared, otherwise we would get all organisms into a single taxonomic species, rather than the hierarchy that Carlitos came up with). Then there comes the other Carlitos, Darwin, who put together lots of evidence showing that species can arise from prior species, thus, maybe the relationships that Carlitos L described, are true relationships, since the process of evolution would explain how that hierarchy might be produced by natural processes.

    Now, given the data, the traits in common and not in common, suggesting a nested hierarchy, by Carlitos L, and the process of evolution, maybe there’s common descent. Then somebody discovers that proteins are polymers, and that they vary from organism to organism. Some genes are present, some genes are not. So, the prediction would be that if we examine genes in common, if common descent, as suggested by both Carlitos’ data, is real, here we have a way to check if it holds to the variation in gene sequences. We align proteins in common, check their similarities and differences, and find a very similar hierarchy. Even better, the patterns of similarity show, say, 30% identical positions defining the common core, then one lineage has a few more common positions, a sub-lineage a few more, etc, thus forming a nested hierarchy like the traits in Carlitos L’s hierarchy.

    OK, then comes the idea of using, rather than protein sequences, or DNA sequences, to use each gene as a trait, and do this again. So, we get a few genes in common defining the core, a few more in common for lineage A, a few more in common with lineage B that are not in lineage A, sub-lineages with more shared genes, etc. Like Calitos L’s hierarchy, at a different level.

    So far so good. Nested hierarchies agree with each other at different levels of analysis. Thus common descent is confirmed, since it predicted that we would get very similar nested hierarchies, and that’s that.

    Now, what about explaining those differences? Those traits defining one lineage, those mutations defining one lineage, those genes defining one lineage? That’s not the task of common descent. Common descent only explains-then-predicts-then-explains the patterns. Common descent, again, is a relationship, not a process. If you ask about where those traits come from, then you have to look for the processes, and the processes are the evolutionary processes. Evolution as a set of processes explains how new traits arise, and predicts the relationship: common descent.

    I know the concepts have been mixed and remixed in the conversation and in the literature, that common descent is used when people mean evolution, that evolution is used when people mean common descent, etc. But the main point here is that if we agree to our terms, if we try and understand each other, and then keep consistency in the conversation, we might get somewhere.

    It’s possible that you don’t care one bit about this explanation, which would mean that this is it.

    Have a nice day.

  33. Rumraket:

    Why does the standard phylogenetic tree of life inferred from morphology (and therefore by presense/absense of “biosystems”, or what you would call an Orfan-system, or POOF-omorphy), still so significantly corroborate the gene trees?

    With a good taxon sample and multiple independent data sets (several different genes for example), you can get a conensus tree and compare it your morphological tree. And what do you get? They corroborate each other to an exceptional degree of statistical significance.

    What good, quantifiably predictive design explanation is there for that fact? Well there is none.

    As much as we disagree, now you’re talking! The pomts you raise can be explored in a bit more methodical detail.

    The first issue is whether in general individual gene trees in general show this tree (quasi Linnaean, giraffes are NOT fish):
    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/nj_differnces_circled2-11.png

    or this tree (Axel Meyer-ian, giraffes ARE fish):
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/bmp_fudge.png

    The first issue is how to treat about Pan-Genomic anomalies — that is to say a gene appears in Coelecanths and in Humans but a really really weakly in Lungfish and tuna so as to practically be non existent! I saw that right away with BMP2 homologs. A typical researchers might say “this gene is too noisy, lets not use it for analysis.” But hang on! If that pattern isn’t due to sequencing and assembly errors, it can’t legitimately be discarded as a data point. When I tried to assemble the tree with BMP2 it was a mess. I had to keep fudging by deleting and outgrouping to make it look “right”. The gene missing in species is still a data point, in fact it is the issue I raised regarding what is legitimate and illegitimate neighbor joining.

    Going back to your phylogenetic example. One can build that tree based on the distance matrix which then is used to approximate a least squares fit using the Neighbor Joining algorithm. Conceptually what is going on is attempt to aggregate the most similar species together in to ever larger groups.

    My point? First I really don’t know how things will actually aggregate if hypothetically we somehow incorporate total genomic data and phenotypic data. My best guess is giraffes will neighbor join better with a kangaroo than a lungfish, etc. I would bet lungfish neighbor join better with other fish than giraffes. If so, the prevailing tree which is described by Axel Meyer’s statement that “we’re all Sarcopterygiian fish” is false. Proper Neighbor Joining of extant taxa without any ad hoc rationalizations or imposition of presumed evolutionary trajectories I predict will conflict with Axel Meyer’s claim. It will look more like this tree from Cox1 which look quasi-Linnaean where mammals are no where near the fishes (Pices, to use Linnaeuses terms).

    So the bottom line, if we start from scratch, is to work out a policy for what is the proper way to lay out similarities and differences and then do neighbor joining or whatever unprejudiced phylogenetic technique should be used. Throwing Tiktaalik and fossils into the question is throwing a narrative in and prejudicing the interpretation of the data.

    If you insist on throwing Tiktaalik in, ok, let’s have at least a picture of what the raw data say, then we can argue later. Why? If we allow any ad hoc rationalization, we can just as easily argue fish evolved from giraffes since as Maztke rightly pointed out, we can’t rigorously demonstrate ancestral relationships, only sister relationships. So I would insist we first just show the sister relationships as best we can. That is done nicely with distance matrix methods and approximations thereof like the Neighbor Joining algorithm.

    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/nj_differnces_circled2-11.png

  34. Rumraket:

    With a good taxon sample and multiple independent data sets (several different genes for example), you can get a conensus tree

    Ideally you compare entire chromosomes, the synteny patterns, the non-coding regions. I hear when the few times this is done, it’s clearer what the hierarchies can and cannot be. Supposedly that’s why Chimps are put with Humans after there had been a very very long debate as to which primate is more genetically similar. The full blown large scale comparison rather than individual genes were supposedly more informative.

    So, with respect to missing genes, to the extent comparisons can be made on genome wide level, then that might be a more legitimate comparison in as much as the issue of presence and absence of genes between species is automatically accounted for by such large scale comparisons. How such genomes would be “aligned” is an interesting question given the lungfish genome is on the order of 100 giga base pairs! For that reason, morphological comparisons are much more accessible, as Linnaues was able to show.

  35. Technical question (which I don’t know the answer to).

    Dispersed repeats like transposons have a mechanism to explain them. Short micro satellite repeat (a few nucleotides) seem to have a good biochemical explanation. But what about long tandem repeats like D4Z4 in the dystrophin gene? That repeat is over 3 kilobases. It don’t believe it is a transposon. 100 such tandem repeats are normal for a healthy human, less than 11 D4Z4 repeats creates muscular dystrophy. How are the boundaries of the repeats so exquisitely defined through replication? I actually don’t know what the prevailing mechanistic explanation is.

    This obviously has some relevance to the question of random mutations.

  36. stcordova: But what about long tandem repeats like D4Z4 in the dystrophin gene?

    When there’s duplicates of a gene in somewhat close proximity, it is very easy for them to recombine with each other (in sister chromosomes), and thus make more copies in one chromosome, while reducing the number of copies in the other. This can make repeats grow quite a bit.

    For simplicity, imagine that D is your gene, and we have two chromosomes:

    –D1a-D2a–
    –D1b-D2b–

    Since each of the “D” genes is identical, then they can recombine either way, so if D1a recombined with D2b we’d get:

    –(D1a/2b)–
    –D1b-(D2b/1a)-D2a–

    We’d have only one copy in one chromosome, the “hybrid” (D1a/2b), and three on the other: D1b, hybrid (D2b/1a), and D2a.

    As the copies increase, so does the opportunity to further mis-recombinations and further increase of the copies. You end up with several versions of the “locus” with different numbers of copies of the gene.

    Also, if the gene is in a region with lots of other copies, then the other copies might act in a similar fashion. The story for D4Z4 might be out there somewhere, but I don’t have time to look for it, or check for places where recombinations can occur besides the obvious.

  37. stcordova: But what about long tandem repeats like D4Z4 in the dystrophin gene?

    Interesting change of topic. I’m curious to see where this leads.

    According to the OMIM catalogue the D4Z4 tandem repeat does not occur in dystrophin, but in the gene for facioscapulohumeral muscular dystrophy (FSHD1). It has its own page, so you can knock yourself out. I don’t believe the page explains how the expansion of copy numbers occurred, but if I were to guess I’d go for unequal crossing over.

    So why did you ask?

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