Phylogeny – the Bigger Picture

During recent discussions on phylogeny, we saw a distinct failure to communicate, probably felt by both sides. The ‘evos’ attempted to consider the role of molecular data in determining relationship. Given that an obvious cause of common sequence is common descent, due to the significant but not perfect fidelity of the DNA replication process, the phylogenetic inference is that sequence similarity is indicative of common descent. This, critics feel, is a circular argument.

In this, they may be following Jonathan Wells in Icons of Evolution. His criticism is that “homology is inferred from common ancestry, then turned around and used as evidence for common ancestry”. Yet in molecular genetics, the term ‘homology’ tends to be used to indicate sequence similarity alone, not a descent relationship. DNA probes and separate-strand annealing rely upon ‘high homology’, meaning only complementary sequence. The similarity is an observation, not an inference. If one had two sequences, XXXXXXXY and XXXXXXXZ, they certainly aren’t inferred to be similar: they really are similar. The retention of similarity (with variations) in a line of descent is also an observation. It is not clear to me where the circularity comes in in putting those two observations together and inferring that sequence similarity is supportive of common descent. Particularly when other sites are brought in to the analysis. Each site verifies the assumption for the other(s); Creationists on the other hand lump the whole into a composite sequence, and expect ‘independence’ to come from something other than sequence identity. You can’t verify genes using genes, or something.

Well, if the argument is circular, we must apply that razor to within-species comparisons as well – paternity testing, forensics, molecular genealogy and ethnic investigations must all be based upon circular reasoning too. Which I suspect no-one would try and argue in court. Broadening this out to between-gene-pool sequence similarity, among species that are even termed ‘closely related’, we presumably don’t have a major problem with sequence being commonly derived from a common ancestor there either. So the question is: as one goes ‘upwards’ in the Linnaean classification system, where does the circularity arise, if it is not there throughout? The differences identified between higher taxa are inevitably greater than those at lower, as one would expect from the same process of descent with modification that explains similarity among relatives, extended in time. As time goes on, the similarities erode and the differences increase. But there is no boundary detectable, no clear transition at which ‘circular reasoning’ comes in, nor where there is an abrupt difference as would be expected from separate origins. Differences remain a matter of degree, albeit confounded by rare events and inevitable statistical artefacts.

The Creationist alternative for sequence similarity is ‘Common Design’. I confess I can never make any sense of this. At what point does Common Descent stop and Common Design take over? In a process whereby a Designer generated in initial version of a sequence, and then allowed nature to take its course, the similarities between subsequent lineages would actually be due to Common Descent, not the initial Design.

OK, we might propose a Designer making separate taxa. The similarities in sequences between any two such taxa could be termed Common Design. But members of Taxon A and Taxon B are still commonly descended from that point on, from the moment of creation. So you can never separate out Common Design completely from Common Descent. In any process where similarities were initiated by Common Design, residual within-taxon similarities still indicate Common Descent from those points. The exact same kind of data has two completely different explanations across that assumed boundary, which is extravagant and inconsistent. The boundary is not a real boundary in the data.

If we follow the differences in Taxons A and B back, attempting to reverse out evolutionary history, we get to a point where the ‘ur-sequences’ exhibit a high degree of sequence similarity. Something which, if we observed it today, would strongly support a genetic relationship. So what would persuade us that, at that point in history, the relationship was not, in fact, genetic?

Common Design is sometimes invoked as ‘like creatures need like DNA’. But if we envisage the Design occurring at a high enough taxonomic level, we are saying that some very unalike ‘creatures’ had like DNA, at the moment they were … created. They only have unalike DNA now, after a few million years of separate change.

Further, none of this helps explain genetic similarities at loci that have little to do with phenotypic difference. One of the principal markers used in paternity testing are SINEs – a kind of transposon. Intergenic examples have no apparent phenotypic effect, and vary in humans (obviously, or they’d be no use). But there are also SINE inserts that are held in common between humans and chimps, others that are diagnostic at still higher taxonomic levels. They can’t all be essential to the form of the members of the clade they are restricted to – can they?

I’ve taken a somewhat circuitous route to my point, and the reason for the title. Consider the following not-very-treelike tree.

i-5feb4cbd88250bf87fba504db8ff9f8c-Eukaryote_tree

It represents the result of extensive phylogenetic analysis of the entire eukaryote clade. Reminiscent of those ‘you are here’ pictures of the Milky Way, ‘animals’ are all stuffed in the red box at bottom right. That’s everything: vertebrates, insects, sponges, nematodes … Fungi are just above, and land plants, seaweeds and Volvocales at about 11 o’clock. That’s pretty much it for multicellular life. The tree overwhelmingly consists of unicellular eukaryotes of bewildering diversity – what used to be called protists, and still are when we aren’t being cladistically rigorous. Never mind beetles, thats what the designer has an inordinate fondness for! If we had no place on this tree, I suspect people would have no problem with it, or the methods used to infer it. Of course we notice the multicellular life more than anything else. They’re bigger. It’s us, it’s our pets, food, materials and enemies. But most of the tree is minute, and does not indulge colonial clumping, amendments of which cause the ‘mechanical impossibility’ arguments ranged against phylogeny.

The discussions involved in resolving and testing these ‘protistan’ branches are surprisingly heated. It’s not just a question of assuming a relationship; the relationships are teased out of the data. If there were no relationship, that too would be apparent from the data. So where, in the progression to the interior of this diagram, and trying not to be bamboozled by the contents of that little red box, does circular reasoning come into it? Likewise, where does Common Design take over from Common Descent as the cause of similarity?

415 thoughts on “Phylogeny – the Bigger Picture

  1. stcordova: Universal Common Ancestry (UCA) descent is challenged by mechanical feasibility.

    Which is something you invented….

  2. stcordova,

    So says the expert who said mtEve is not the MRCA of all female humans.

    She isn’t. She is only the possessor of the ancestor of all mitochondria, plus she’s the matrilineal MRCA of all humans. That is different from being the MRCA of all females, who may easily have lived more recently, the coalescent of a non-mitochondrial locus.

  3. Neil Rickert,

    I’m impressed with Allan’s patience, repeatedly explaining in detail to deaf ears.

    Heh heh. It’s not necessarily a positive character trait I’m exhibiting here!

  4. Alan Fox,

    But I’d never have glanced at some of the fascinating stuff on the web without being prompted. There are some great expositions on evolutionary pathways.

    Oh, I’m not knocking it. I do learn stuff from reading hair-tearing misrepresentations and going to primary sources.

  5. Allan Miller: Oh, I’m not knocking it. I do learn stuff from reading hair-tearing misrepresentations and going to primary sources.

    I do appreciate Sal as the patron saint of lost causes.

    Is he threatened with extradition to Turkey?

  6. stcordova,

    What happens when you bring in more branches to resolve potential anomalies? Does no other node shed any light on this whatsoever? Or is the whole of phylogenetics to be thrown away due to a curious (and not general) pattern in a 3-member data set?

    The problem is acknowledged in the literature, I’m not saying something original here.

    Reference?

  7. stcordova: That means the mother-of-the-clade that includes zebrafish and humans had a large number of genes and presumably uses for those genes such that there is this similarity between humans and zebrafish and for that matter all such anomalous numbers of shared genes

    The problem is acknowledged in the literature, I’m not saying something original here.

    some 13000 shared genes out of 20-30K. Why should the ancestor have so many genes? Why are those “such anomalous numbers of shared genes”? Seems to me you’re begging the question. It’s not an anomalous number if they share a (distant) common ancestor. Care to post a link to the relevant literature?

  8. It would be kind of cool to have a visual explorer for the molecular tree. I suspect there are such tools, but a nice friendly one would be useful. There are projects like this for fossils, but as has been pointed out, fossils are often confused as ancestors to living organisms.

  9. Sal,
    Do you stand by this comment?

    FACT: prokaryotes don’t become eukaryotes in any lab or field observation. That is a scientific fact. Evolutionism claims the opposite. Evolutionism isn’t science.

    Comment
    by from discussion
    inDebateAChristian

    If so, can you provide a citation where some specific notable proponent of evolutionism claims that?

  10. OMagain: If so, can you provide a citation where some specific notable proponent of evolutionism claims that?

    Am I reading this correctly? Is Sal complaining that something that happened maybe one time in a billion years is not repeatable in the lab?

  11. Confusion between history and scientific principle. Substitute ‘owl’. Or ‘trilobite’. Or ‘lichen’.

  12. petrushka: Am I reading this correctly? Is Sal complaining that something that happened maybe one time in a billion years is not repeatable in the lab?

    And they aren’t becoming what already exists.

    Monkeys aren’t turning into humans.

    How many ways are such statements both wrong and miserably ignorant? To even suggest that smart people are saying what Sal claims is appalling.

    I know he’s not interested in learning, in advancing knowledge, or in portraying evolutionary theory correctly. But doesn’t he have any interest in making even plausibly correct attacks on science, rather than showing his ignorance repeatedly, without any improvements?

    Glen Davidson

  13. GlenDavidson: But doesn’t he have any interest in making even plausibly correct attacks on science, rather than showing his ignorance repeatedly, without any improvements?

    Perhaps not, it he is actually trying to destroy ID as a workable concept.

  14. Not accusing Sal of being dishonest, but I sometimes think he is playing devil’s advocate.

    His arguments have the flavor of rhetorical questions. He makes ridiculous arguments just to illustrate how ridiculous ID really is.

  15. petrushka: Is Sal complaining that something that happened maybe one time in a billion years is not repeatable in the lab?

    I read it as evolutionists claim that X becomes Y in the lab, and it does not and that’s a FACT therefore evolutionists are wrong!
    But that’s probably my ahem less then charitable reading of Sal…

  16. petrushka: Not accusing Sal of being dishonest, but I sometimes think he is playing devil’s advocate.

    Allan Miller: Confusion between history and scientific principle. Substitute ‘owl’. Or ‘trilobite’. Or ‘lichen’.

    Hi Allan, Hi Petrushka

    I decided I had better things to do, but alas idle morbid curiosity got the better of me and I returned.

    Every time I read the piffle you patiently respond to I am reminded of Wolfgang Pauli’s:

    “Das ist nicht nur nicht richtig, es ist nicht einmal falsch!” = “That is not only not right, it is not even wrong,”

    For the longest time, I reckoned that Sal epitomized Poe’s Law – but now realize I was far too generous in that assessment and wondered if anybody had even invented a name for Sal’s condition. As it turns out, Sal in fact is the very acme of the Dunning-Kruger Effect – where someone makes a “not even wrong” argument but lacks the meta-cognitive ability to recognize that they don’t know enough even to make a wrong argument, never mind a right one… a Sal-worthy multi-syllabic epithet if ever there was one.

  17. It’s the people who Sal is teaching all this to that I fear for! Hopefully they can google….

  18. OMagain: evolutionists claim that X becomes Y in the lab

    Where would that be? I can’t imagine that even Sal could say something like that.

  19. BTW, I checked (or at least I tried to with my limited knowledge) to BLAST TITIN humans to zebrafish and sharks and found that they all match about a 70%

    Then found this:

    http://www.timetree.org/search/pairwise/homo%20sapiens/selachii
    http://www.timetree.org/search/pairwise/homo%20sapiens/actinopterygii
    http://www.timetree.org/search/pairwise/Selachii/actinopterygii

    according to this zebrafish and humans diverged from sharks about 480M years ago and zebrafish and humans diverged 440M years ago, so all three species have been diverging for almost the same time. That would explain the BLAST results wouldn’t it?

  20. But then again, I run BLAST for both TITIN and CFTR and in both cases humans matched sharks better than zebra fish (73% to 65% TITIN, 71% to 56% CFTR)
    I’m curious as to why would that be

  21. dazz: I’m curious as to why would that be

    Many proteins are not evolving in a clocklike fashion in many taxa. That’s one reason why BLAST ≠ phylogeny.

  22. Thanks gentlemen. That settles it. Interestingly the match between shark and zebra fish is pretty much the same as human vs zebra fish. Perfectly consistent with the explanation as far as I can see provided that human and zebra fish are evolving in a clocklike fashion.

  23. petrushka: I can’t imagine that even Sal could say something like that.

    That’s what I’m saying he said when I quoted him. If not then what are the evolutionists claiming precisely? We should assume they propose it happens in the field but not in the lab? The quote did not offer that option. It deliberately mangles the two concepts , in my opinion.

    Sal: FACT: prokaryotes don’t become eukaryotes in any lab or field observation. That is a scientific fact. Evolutionism claims the opposite.

  24. stcordova: I do understand the difference between a distance matrix and the cost matrix that is used generate the distance matrix.

    Then you should be more careful about what you write, because what you write says otherwise. Whatever did “PHYLIP Dayhoff PAM matrix study” mean to you?

    But in any case, you’ve not provided unequivocal references to fossils that are mothers of the clades in the direct line to humans, neither did anyone here bother to even describe a viable evolutionary trajectory of the heart of the mother of the reptile clade to extant reptile hearts.

    Of course not. I have explained why there are no such references. It’s what we expect.

    As for the hearts, I have suggested that perhaps the cartoon you reference is not the best source of information on the actual natures of the hearts you wonder about. It isn’t my specialty, but there is a literature on the subject, which perhaps you should explore before deciding that transitions are impossible. The fossil record won’t help, as hearts just don’t get preserved. But it will show that there were animals that were in other respects transitional, which gives us reasons to suppose that the heart transitions are possible.

    So says the expert who said mtEve is not the MRCA of all female humans.

    And indeed she is not. She is the MRCA of the mitochondria of all humans. She is the MRCA of all female humans through a strictly female lineage, though in fact the mitochondria may be the only surviving remnant of that descent. What she most certainly is not is the MRCA of all female humans. In fact I see no reason to suppose that there is such a thing. Different linkage groups should have different MRCAs, with no reason to suppose that these MRCAs would ever coalesce.

    BLAST establishes similarity.Claims of common descent are driven by patterns of similarity and diversity. BLAST comparisons on newly sequenced molecular data are potentially falsifying circularly reasoned phylogenies, therefore it is good for phylogenetic analysis as it helps falsify them.

    This is you expressing ignorance again. It’s just a chain of your favorite buzzphrases.

    It doesn’t surprise me at all that despite the claims of the Early Bird project that Rhipidistia is a clade, there have been those that object to Rhipidistias status as a clade, not to mention there isn’t a fossil that would qualify as the mother of Rhipidistians.

    More evidence that you don’t read. Clearly you have never bothered to find out what Early Bird is. (There’s a hint in the name.) Rhipidistia isn’t a clade and I have never said it is; in fact I have never mentioned it here. It’s an old name for a collection of basal sarcopterygians, i.e. a paraphyletic group. We have discussed your obsession with mothers elsewhere.

    Furthermore comparisons between species force phylogenies to invoke epicycles such as with the case of shark DNA looking closer to human DNA than ray-fin fish DNA.The phylogenies have to be ad hoc kludged with the assumption of the mother of the overarching clade having all the genes that are then selectively appearing in some lines and not in others all the while avoiding the problem of the absurdity of the mother-of-the clade having more genes and uses for those genes than she can handle.

    Not sure at all what data you are even referring to here. Is this individual gene sequences, presence/absence of orthologs, presence/absence of any homologs, or what? It’s so confused I can’t tell. Nor can I tell what ad hoc kludges you think are going on. I see no sign that you have ever looked into any phylogenetic analysis or method of analysis at all. You seem stuck on BLAST as your sole resource, though you have mentioned PHYLIP, without showing any comprehension of what it is or what it does.

    Your supposed paradox will need more explanation before it can be dealt with. Are you claiming that genes cannot be gained or lost by any known mechanisms?

    The BLAST comparisons show the absurdity of various phylogenies

    How? Which ones? Be specific and detailed.

  25. John Harshman

    Rhipidistia isn’t a clade

    contrast with Wiki

    https://en.wikipedia.org/wiki/Rhipidistia

    The Rhipidistia, also known as dipnotetrapodomorphs (formally Dipnotetrapodomorpha)[1] are a clade of lobe-finned fishes which include the Tetrapods and lungfishes

    The cladogram presented below is based on studies compiled by Philippe Janvier and others for the Tree of Life Web Project,[3] Mikko’s Phylogeny Archive[4] and Swartz 2012.[5]

    But I mentioned Rhipidisitia to point out, not everyone actually agrees it should be a clade in the first place.

  26. So says the expert who said mtEve is not the MRCA of all female humans.

    And indeed she is not. She is the MRCA of the mitochondria of all humans. She is the MRCA of all female humans through a strictly female lineage, though in fact the mitochondria may be the only surviving remnant of that descent. What she most certainly is not is the MRCA of all female humans. In fact I see no reason to suppose that there is such a thing. Different linkage groups should have different MRCAs, with no reason to suppose that these MRCAs would ever coalesce.

    In one sentence you say mtEve is the MRCA of all female humans in another sentence you say she is not. Now who is not being clear?

    But in any case:

    https://en.wikipedia.org/wiki/Mitochondrial_Eve

    Mitochondrial Eve is the matrilineal most recent common ancestor (MRCA) of all currently living humans. This is the most recent woman from whom all living humans today descend, in an unbroken line, on their mother’s side, and through the mothers of those mothers, and so on, back until all lines converge on one woman,

    But let me remind the readers of what John Harshman said February 3, 2016.

    Still a Theory in Crisis

    mtEve is not the MRCA of all female humans

    So on February 3, 2016 you said, “mtEve is not the MRCA of all female humans”. Is that what you think I should subscribe to and teach? You keep insisting I’m arrogant and I just assume you are wrong. I don’t assume you or anyone is right all the time. I’m posing objections that I think are legitimate. That’s all, no need to get offended.

  27. stcordova: In one sentence you say mtEve is the MRCA of all female humans in another sentence you say she is not. Now who is not being clear?

    She is the MRCA of the mitochondria of all humans.

    That does not mean she is the only female of her era that contributed to the human lineage or even the only contributor to the female lineage.

    Think.

  28. Allan Miller asked for a reference on the idea of a common ancestor with all the genes:

    http://www.evolutionnews.org/2013/10/to_build_new_an077541.html

    Moreover, even if some universal Precambrian genome originally contained all the genes that later became taxonomically restricted, whatever process distributed these genes to some lineages, but not others, necessarily involved the addition of new information into the biosphere….

    (9) Marshall seems to have an idiosyncratic view of animal evolution, depicting the evolution of animals as a reductive process in which pre-existing genetic information from a universal Precambrian gene set is selectively lost to some lineages but not to others. This contrasts markedly with a more standard neo-Darwinian view in which form and information gradually accumulate over time.

    So the idea seems traceable to Marshall as far as a pre-Cambrian critter with all the genes! I didn’t do any calculation, but just pointed out the absurdity of assuming a simple creature had all the genes that were conserved and appeared as taxonomically restricted genes. Are we talking all the TRGs for all extant and extinct species?

  29. stcordova: And indeed she is not. She is the MRCA of the mitochondria of all humans. She is the MRCA of all female humans through a strictly female lineage, though in fact the mitochondria may be the only surviving remnant of that descent. What she most certainly is not is the MRCA of all female humans. In fact I see no reason to suppose that there is such a thing. Different linkage groups should have different MRCAs, with no reason to suppose that these MRCAs would ever coalesce.

    In one sentence you say mtEve is the MRCA of all female humans in another sentence you say she is not. Now who is not being clear?

    But in any case:

    But let me remind the readers of what John Harshman said February 3, 2016.

    So on February 3, 2016 you said, “mtEve is not the MRCA of all female humans”.Is that what you think I should subscribe to and teach?You keep insisting I’m arrogant and I just assume you are wrong.I don’t assume you or anyone is right all the time.I’m posing objections that I think are legitimate.That’s all, no need to get offended.

    What is your objection? All you do above is quote a statement that means exactly what I said. Is it possible that you don’t see the difference between “the MRCA of all female humans” and “the MRCA of all female humans through a strictly female lineage”? Those extra words do indeed mean something. The first statement is false. The second is true. Yes, you should subscribe to that. But no, I don’t think you should be teaching anyone.

  30. stcordova,
    I had no idea that Rhipidistia had been revived. I will note that the first reference to that tree (Janvier) neither mentions Rhipidistia nor resolves the trichotomy. I see you ignored the point about Early Bird.

  31. At least according to David Hillis (who would certainly know), taxonomic information on Wikipedia is pretty unreliable. Caveat emptor.

  32. I never looked at Early Bird, I conflated it with Tree of Life since I heard you use them once in the same paragraph and thought the were the same body of projects. I thought they were both under NSF sponsorship and they spend the taxpayer money just the same way on projects of little medical or technological utility.

    I made a mistake, I admit it, and that’s why I’m here to get things cleaned up. But in contrast, it seems you have some explaining to do:

    What is your objection? All you do above is quote a statement that means exactly what I said. Is it possible that you don’t see the difference between “the MRCA of all female humans” and “the MRCA of all female humans through a strictly female lineage”?

    I see the difference in wording, but mtEve being “the MRCA of all female humans through a strictly female lineage” is still the MRCA of all female humans. As wiki said:

    This is the most recent woman from whom all living humans today descend

    What’s the matter John? You can’t admit you made a mistake because you got called on it by me?

    But I’m just putting this out on display to contrast to everyone how I react to correction (and will admit to a mistake) compared to you who will go to no end to try to give the impression of being an inerrant authority and in the process just make more mistakes.

    Nevertheless, this was an interesting discussionas it highlights one little complication. Whether Rhipidistia is a clade or not (which is no longer at tolweb if it ever was even though a cladogram with Rhipidistia was compiled for tolweb), there remains a complication regarding the rates of evolutionary change.

    There are three descendant lines supposedly proceeding from the ancestor Sarcoptegeryii that resulted in extant species according to evolutionary literature:

    1. lungfish: 1 species or a few highly similar subspecies, few if any novel-then-extinct descendant species

    2. coelecanths: 1 species or a few highly similar subspecies, few if any novel-then-extinct descendant species

    3. tetrapodamorpha: just for tetrapods alone, there are 21,100 extant species, many more extinct and many more in the parent clade of tetrapodamorpha

    So why would one line of lobe-finned fishes remain mostly unchanged for hundreds of millions of years while the other diversified to tens of thousands of forms? That doesn’t look wholesome. We have two lobe-finned fish lines still alive, and that’s two lines of evidence change tends to be rare for lobe finned fishes, and thus the other tetrapodomorpha line is likely just an imaginary construct force fitted on 21,100 species that never descended from a lobe fined fish in the first place. If one wants to invoke UCA, perhaps it would be better to say, “unspecified ancestor” than to insist it was a lobe finned fish (Sarcopterygii). At least if you say “unspecified ancestor” instead of Sarcopterygii, one avoids having to deal with the problem I just highlighted.

  33. stcordova,

    What’s the matter John? You can’t admit you made a mistake because you got called on it by me?

    He didn’t make a mistake. I said exactly the same thing also. You bolded part of a sentence, and omitted, in your haste to puff yourself up against the expert, to recognise that the sentences in full did not contradict each other. You are looking increasingly silly with this ego trip stuff.

  34. Really, Sal?
    “MRCA” stands for Most Recent Common Ancestor.
    Imagine Eve has two daughters.
    John reproduces with both of them.
    Everyone except Eve’s grandchildren die.
    Eve is now the the MRCA of all humans (and of all females) through a strictly matrilineal line. All humans descend, in an unbroken line, on their mother’s side, from Eve.
    BUT, John is the MRCA of all humans.
    Twit.

  35. Y’know, Allan, between this ninja and the reciprocal one on the McLatchie thread, it seems more and more like we’re the same effing person.
    ROFL!

  36. As I said, I accept taxonomic nested hierarchies as real. The sequence comparisons confirm a general nested pattern with some anomalies.

    But a taxonomic nested hierarchy does not imply a unique phylogenetic tree. What’s preventing some unspecified ancestor being the ancestor of all creatures in such a way that tetrapods dosn’t descend from a lobe-finned fish?

    Evolutionists say convergence is rare, but that’s based on the circularly reasoned argument that Universal Common Ancestry is correct. Convergence could be ubiquitous.

    We know convergence happens even under evolutionary assumptions.

    The first known case of convergent molecular evolution in ruminant lysozymes, for example, was shown to lend parsimony support to a dramatically wrong phylogeny that placed cows within the primates, even though only a small number of convergent substitutions took place.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881246/

    there is one case of molecular convergence that seems to me to border on astronomically improbable if random, therefore they invoke natural selection.

    We recently discovered a remarkable case of convergent molecular evolution involving more than 100 parallel amino-acid changes across all 13 mitochondrially-encoded proteins of snakes and agamid lizards. Just a few of these convergent substitutions were sufficient to positively mislead the inference of phylogeny, even with thousands of sites providing latent support for the correct underlying relationships. Since this example demonstrates that molecular convergence can happen en masse in nature, affecting multiple genes, it is important to consider the threat this poses to molecular systematics, and careful genome-wide assays for convergent molecular evolution are warranted. This result implies that the protein adaptive landscape is sometimes highly constrained.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881246/

  37. Really, Sal?
    “MRCA” stands for Most Recent Common Ancestor.
    Imagine Eve has two daughters.
    John reproduces with both of them.
    Everyone except Eve’s grandchildren die.
    Eve is now the the MRCA of all humans (and of all females) through a strictly matrilineal line. All humans descend, in an unbroken line, on their mother’s side, from Eve.
    BUT, John is the MRCA of all humans.
    Twit.

    I was referring to the female MRCA, since mtDNA refers to mtDNA, not the male MRCA since Eve is a female in case you didn’t notice. Also I was referring to the line involving mtDNA, not some some hypothetical scenario where female MRCA has all boys who become father of all humans.

    I assumed it was known I was talking the female MRCA with the mtDNA line since it is well known the male MRCA can have a different date. But I’ll qualify with the word female in the future since it’s appears you guys need to be reminded Eve was a female.

    DNA_Jock:

    Twit.

    Insults, DNA_Jock, having to mince words now. That’s fine. Thanks for the editorial improvements.

  38. DNA_Jock:

    BUT, John is the MRCA of all humans.
    Twit.

    But we were talking mtEve which refers to the MRCA with the mitochondrial DNA that descends through the human females. Not the mtDNA that doesn’t get transmitted from the father to the children, so I obviously was not talking about a possible male MRCA.

    Also I was referring to the line involving mtDNA, not some some hypothetical scenario where female MRCA has all boys who become father of all humans.

    But well, when you don’t have much to criticize, you mince words. That’s fine, you won’t have the opportunity on that point again. Call me twit all you want, the mis-reading was yours if you were willing to see it, I got the editorial improvement I was looking for.

    If you think I’m here to promote ID by what I write at TSZ then your mistaken. Your free-of-charge hostile review is worth the price of admission.

    So you and Allan and John mince words, and strain at typos, it just shows your not willing or able to counter the real arguments summarized here:

    Phylogeny – the Bigger Picture

  39. stcordova: I see the difference in wording, but mtEve being “the MRCA of all female humans through a strictly female lineage” is still the MRCA of all female humans. As wiki said:

    This is the most recent woman from whom all living humans today descend

    What’s the matter John? You can’t admit you made a mistake because you got called on it by me?

    Why can’t you just give up when you’re behind? If that’s what Wikipedia says, it’s wrong. The statement is ambiguous. In one reading (the most recent woman whom everyone alive today has as an ancestor) it’s almost certainly false. That woman is probably much more recent than mtEve, and her mitochondria might not even be present in any living human (if it chances that nobody is in her strictly female lineage). Another reading your favored one that she is one of a male/female pair that are the ancestors of all our genomes, is definitely false. A sense in which it’s true doesn’t immediately come to mind other than that her mitochondria are the ancestors of all our mitochondria, and that would be a weird way to say it. Note, by the way, that this statement no longer refers to the ancestry of women but of the entire population.

    You occasionally admit a small error, but nothing of any real significance. I have admitted errors before too, as in my ignorance that Rhipidistia had been resurrected. But this is no error. Why not admit some of your bigger errors?
    Regarding Rhipidistia, I have no reason to suppose that a cladogram containing it was compiled for TolWeb. What is your reason? More importantly, why should we care whether it’s a clade? How is that relevant to anything we’re discussing? I know you think it is, but I can’t tell why. Does it somehow support your claim that birds aren’t descended from fish? If so, how?

    So why would one line of lobe-finned fishes remain mostly unchanged for hundreds of millions of years while the other diversified to tens of thousands of forms? That doesn’t look wholesome. We have two lobe-finned fish lines still alive, and that’s two lines of evidence change tends to be rare for lobe finned fishes, and thus the other tetrapodomorpha line is likely just an imaginary construct force fitted on 21,100 species that never descended from a lobe fined fish in the first place. If one wants to invoke UCA, perhaps it would be better to say, “unspecified ancestor” than to insist it was a lobe finned fish (Sarcopterygii). At least if you say “unspecified ancestor” instead of Sarcopterygii, one avoids having to deal with the problem I just highlighted.

    There are many possible responses to this. Let’s see how many I can think of.

    1. You are very close to the trope “If we came from monkeys, why are there still monkeys?” Morphological and molecular evolution and speciation all happen at different rates in some taxa than others. You seem to be conflating at least two of these and assuming that a clock is required in each. Not the case.

    2. There are way more extinct species of lungfish and coelacanths than living ones, encompassing much greater disparity than there is now. Don’t constrain their radiation based on what is left today.

    3. Species diversity and morphological change are not strongly coupled. There are lots more species of tetrapods than of other sarcopterygians, but then again there are many more species of teleosts than of tetrapods, and all those teleosts are things you would dismiss as “still fish”.

    4. You have no idea how phylogenetic analysis is done and thus no standing to declare any of its conclusions to be “imaginary constructs”. No force-fitting, no a priori conclusions.

    5. Why have tetrapods been more successful? There seems a simple explanation: they invaded a new environment with no serious competitors for the position of “large animal”. And they ran with it. Literally, some of them.

    6. What, if anything, does “wholesome” mean here?

    7. You didn’t highlight a problem. You imagined one. The ancestor of all those fish was a sarcopterygian. Well, that’s how “sarcopterygian” was defined, so it can’t help being. But more importantly, we can figure out what sort of animal it is by using those trees you seem to think are just made up to fit. Now that is definitely insulting as well as being some kind of conspiracy theory. You’re the one here whose beliefs are conditioned by the need to fit an external story, i.e. Genesis.

    That should do for now. Please read, think, and respond. In that order.

  40. stcordova: But a taxonomic nested hierarchy does not imply a unique phylogenetic tree. What’s preventing some unspecified ancestor being the ancestor of all creatures in such a way that tetrapods dosn’t descend from a lobe-finned fish?

    Depends on the hierarchy and how we interpret it. If we suppose that ranks in the hierarchy are intended to be clades, then every rank is a node. If that rank-hierarchy is fully resolved, it implies a single, fully resolved tree. If it isn’t fully resolved (i.e. there are more than two taxa of the next-lower rank directly subordinate to any taxon), then it implies a polytomy. By the way, these days taxonomic hierarchies are subsequent to trees, not prior to them. None of this has much to do with your question here.

    What’s preventing the conclusion you like is that the tree constrains estimates of the ancestral state. The tree we have (even if some nodes are unresolved) tells us that the ancestor in question was a lobe-finned fish. Notably, the presence of Eusthenopteron, Panderichthys, and Tiktaalik on the “fish” side of the line and of Ichthyostega and various other -stegas and -erpetons on the tetrapod side, all of them fairly similar in characters, should make it easy to see.

    You could say “Yeah, but the tree is just made up”. No, it isn’t. It’s determined by the data. You need to attack the data. Go for it.

  41. stcordova,

    Careful, Sal. You’re starting to whine. You really need to understand the difference between “female ancestor” and “strictly matrilineal ancestor”. They are two quite different things, not quibbles. Same with “the female MRCA of all people”, and “the MRCA of everyone’s mitochondria”.

  42. Oh dear.
    Eve has two daughters.
    Let’s call them Janet and Ann.
    Janet and John Bouvier have a daughter Jacqueline. Ann and George Skakel (unrelated to John) have a daughter Ethel.
    Jacqueline Bouvier and Ethel Skakel marry two half-brothers. Let’s call them Jack and Bobby Kennedy, and pretend they have different fathers, but the same mother, Rose…
    Everybody but JFK & RFK’s children dies.
    Eve is the MRCA of all females, and all humans, through a strictly matrilineal line. All humans descend, in an unbroken line, on their mother’s side, from Eve.
    Rose Kennedy is the MRCA of all females (and all humans). And female.
    Like I said, twit.

  43. stcordova: If you think I’m here to promote ID by what I write at TSZ then your mistaken. Your free-of-charge hostile review is worth the price of admission.

    I’d like to discus this view of your reasons for posting here on Noyau, if you’re willing…

  44. John Harshman: You’re the one here whose beliefs are conditioned by the need to fit an external story, i.e. Genesis.

    Ah, but surely you know that Sal has no problem acknowledging that, now that’s he’s an AiG YEC instead of a DI crypto-creationist.

    Oh, wait… He’s not acknowledging that he’s switched to AiG talking points.

    Anyway, he has his worldview, and you have your worldview. Same data, different interpretations, explainable entirely in terms of differences in worldview.

  45. 2. There are way more extinct species of lungfish and coelacanths than living ones, encompassing much greater disparity than there is now. Don’t constrain their radiation based on what is left today.

    I don’t constrain their radiation, it’s right there in evolutionary literature in the cladograms where lungfish radiate only to other subspecies of lungfish and coelecanths radiate only to other subspecies of coelecanths. That is based on the fossil and extant data. You’re arguing on data we don’t have. That’s fine, but let’s not pretend you have an empirical argument, only one of pure speculation appealing to non-discovered, likely non-existent entities.

    6. What, if anything, does “wholesome” mean here?

    One line of lobe-fined fishes presumably very similar to lungfish and coelecanths (since presumably they are all from the Sarcopterygii ancestor with no ancestor in the fossil record) diversifies to 21,100 extant species and even more extinct species while the other two lines diversify to only a few subspecies.

    There are widely differing rates of change. That means one line got so many lucky mutations that enabled diversification, and the other didn’t. That doesn’t seem right.

    Much of the literature comparing Coelecanths and Lungfish is full of phylogenetic interpretation rather than straight forward sequence comparison. The inferred tick rate of mutations between Coelecanths and Lungfish could be very slow, whereas the Tetrapodamorpha line could be fast by comparison. The substantially differing rates is unwholesome.

    That said, since there is so little sequence data on these, a more fruitful area of looking for unwholesome tick rates is in bacteria. I mentioned aaRS genes before as a candidate. That may be pursued later.

    we can figure out what sort of animal it is by using those trees you seem to think are just made up to fit

    Those trees assumes there is mechanical feasibility in the first place of evolving a fish into a reptile with differing circulatory systems and a host of many other problems.

    I showed you a problem of mechanical feasibility, and then you said it wasn’t your specialty. Well, that just confesses you just assume mechanically feasibility with no basis in actually considering the mechanical problems.

    Years ago, I passed that question on to anatomy and physiology professors and they referred it to evolutionary biologists like you, and you just referred it to somewhere else. The cartoon helps the evolutionary case since it hides away even more daunting details like developmental mechanisms, specific relocation of muscles for valves, etc. So the cartoon would actually generously strengthen the case for evolution not against it.

    When PZ Myers addressed the question of heart evolution in passing he referred to phylogenetic reconstructions, not mechanical arguments.

    So you, like evolutionary biologists, assert mechanical feasibility not by actually making mechanical arguments, but appealing to mostly irrelevant circularly argued phylogenies. The circularity goes like this, “phylogeny proves the animals existed and the transitionals were mechanically feasible, we know the phylogeny is true because the transitionals were mechanically feasible and the animals existed (even though we don’t have fossils of the ancestors).”

    Being able to build phylogenies does not imply the mechanical feasibility of Universal Common Ancestry operating under any semblance of ordinary conditions and plausible changes to the organism.

  46. Careful, Sal. You’re starting to whine. You really need to understand the difference between “female ancestor” and “strictly matrilineal ancestor”. They are two quite different things, not quibbles. Same with “the female MRCA of all people”, and “the MRCA of everyone’s mitochondria”.

    Since I knew you would quibble like that, the comment was already amended, and you’re responding to the unedited version of the comment above. You apparently missed reading the edit.

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