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. Allan Miller:
    We can build phylogenetic trees because the data permits organisation in that way. We can gain confidence in those trees by wider sampling and discovering that this too converges on the same relationships.

    That’s an important point that the creationists here continue to ignore. The convergence as new data are added strongly supports the theory of common descent and disconfirms the orchard model.

  2. Patrick: That’s an important point that the creationists here continue to ignore. The convergence as new data are added strongly supports the theory of common descent and disconfirms the orchard model.

    He who worships the god of the gaps worships an incredibly shrinking god.

    But perhaps they are mollified by the creation of two new gaps for every one filled.

    It’s a bit like polishing a telescope mirror. The more you refine the surface, the greater the number of pits.

  3. Sal is now sulking in his tent. Who will be his Patroclus?

    LOL! I’m not trifling. You have not made a case fish can evolve in to birds except by your circularly reasoned phylogenetic reconstructions.

    In your Baramin thread, I discussed how Baramin are determined, I posted at length how inferences are made and either confirmed or falsified or left as an open question via rings and hybridizations. I boycotted your Baramin thread since you invited creationists to respond and when I responded to your question but didn’t give you the answers you wanted you accused me of not responding to respond to your questions. I won’t trifle with that sort of mischaracterization. You lost that discussion pretty quickly didn’t you?

    But this thread isn’t the baramin thread, this is the evolutionary theory by circular reasoning thread.

    You reassured me you don’t have any arguments except your circular reasoning. You don’t address the mechanical difficulties except by more circular reasoning like saying snakes evolved from lizzards.

    Thanks for the conversation as it confirms the some of the themes in my manuscript that you guys have little more than circular reasoning to account for the patterns of similarity and diversity in varieties of biological forms. All you had were a few quibbles and word mincing with cryptic remarks which you won’t have in the future when my book comes out since I know your playbook now. Thank you very much.

  4. stcordova: LOL! I’m not trifling.You have not made a case fish can evolve in to birds except by your circularly reasoned phylogenetic reconstructions.

    In your Baramin thread, I discussed how Baramin are determined, I posted at length how inferences are made and either confirmed or falsifiedor left as an open question via rings and hybridizations. I boycotted your Baramin thread since you invited creationists to respond and when I responded to your question but didn’t give you the answers you wanted you accused me of not responding to respond to your questions.I won’t trifle with that sort of mischaracterization. You lost that discussion pretty quickly didn’t you?

    But this thread isn’t the baramin thread, this is the evolutionary theory by circular reasoning thread.

    You reassured me you don’t have any arguments except your circular reasoning.You don’t address the mechanical difficulties except by more circular reasoning like saying snakes evolved from lizzards.

    Thanks for the conversation as it confirms the some of the themes in my manuscript that you guys have little more than circular reasoning to account for the patterns of similarity and diversity in varieties of biological forms.All you had were a few quibbles and word mincing with cryptic remarks which you won’t have in the future when my book comes out since I know your playbook now.Thank you very much.

    Oh, your prejudices were reaffirmed by your prejudicial take on the exchange.

    How gratifying it must be for you. And it’s inevitable, no less, since it’s predicated on nothing but your own circular thinking.

    Glen Davidson

  5. stcordova:
    . . .
    Thanks for the conversation as it confirms the some of the themes in my manuscript that you guys have little more than circular reasoning to account for the patterns of similarity and diversity in varieties of biological forms.All you had were a few quibbles and word mincing with cryptic remarks which you won’t have in the future when my book comes out since I know your playbook now.Thank you very much.

    Confirms your themes because there was never any chance that you’d change your mind based on the evidence. I guess the chance to fleece the rubes with a new book now that Dembski has given up the ID con is too much for a good Christian like yourself to resist.

  6. Entertainingly for someone who is so proud of their mad poker skillz, Sal has a ‘tell’.

  7. dazz: stcordova: You don’t address the mechanical difficulties

    I will ask Sal the same question I’ve asked other ID supporters.

    What event in the history of life — be specific — violates entropy or any other physical law or theory?

    I’m not interested in crockaduck stories. Just point to a specific gap in the fossil record or in the molecular phylogeny and say, this violates the following physical law.

    That could start an interesting conversation.

    I would like to know when the violation occurred, and what really happened.

  8. stcordova:

    But this thread isn’t the baramin thread, this is the evolutionary theory by circular reasoning thread.

    You reassured me you don’t have any arguments except your circular reasoning.You don’t address the mechanical difficulties except by more circular reasoning like saying snakes evolved from lizzards.

    Sal, you and Cole keep insisting that the arguments for phylogenetics and evolution are based on circular reasoning, but neither of you have substantiated the claim. I don’t even think that Cole knows what circular reasoning actually means, but you’ve at least demonstrated you get the gist. So here try this – define the “A” and “B” in the phylogenetic/evolution arguments and place them in the equation:

    A is true because B; B is true because A

    I already showed you were providing a strawman argument earlier to disprove your claim of circularity. To wit:

    Sal: Here is an editorially improved version of the circular reasoning argument used by Allan Miller and John and the TSZ evolutionists :“it’s physically possible to evolve a fish into a bird because we can build phylogenetic trees, we can build phylogenetic trees because it is physically possible to evolve a fish into a bird.”

    Except no one who understands evolution makes the latter claim at all. We don’t think we can build phylogenetic trees because it is physically possible to evolve a fish into a bird; that’s a conclusion derived from phylogenetic relationships.

    From: http://theskepticalzone.com/wp/phylogeny-the-bigger-picture/comment-page-8/#comment-131599

    So really…where’s the circularity?

  9. stcordova:In your Baramin thread, I discussed how Baramin are determined, I posted at length how inferences are made and either confirmed or falsifiedor left as an open question via rings and hybridizations.

    No, in fact you did not. You mentioned that if hybridization happens between two species, that means to you that they’re in the same kind. Now that does answer one of my questions, whether a kind can encompass more than one species, but it does little for any of the others. I had already said that in the original post. Same for “mechanical infeasibility”. Already mentioned, doesn’t answer any of the questions, for the reasons outlined in my original post. Then you talked about ANOPA, for no discernible reason, since you made no claims for it. And you mentioned that hybridization, if it happened, would show that foxes were in the dog kind. That again answers none of my questions. Let me boil it down to a single request/question, which you may answer here or in that thread:

    Please name one kind (holobaramin) that you are sure of, and explain your reasons for its delimitation. I can work with that.

  10. Another huge problem with Sal’s criteria to determine kinds is that hybridization doesn’t even help explain hierarchies within kinds: you have wolves, coyotes, and you can have hybrid coywolves, therefore, all belong to the same kind and can potentially descend from one another. Cute, but which came first? Which one was specially created? Doesn’t even matter, right?

    You might be inclined to invoke phylogenetic analysis within kinds, but wouldn’t that be in fact circular? phylogenetics only work within kinds because their members can hybridize, but hybridization is how you defined kinds and how you delimited mechanical feasability. Therefore in your mind, phylogenetics only work where you arbitrarily defined it to apply.

    What if I was to invoke “hybridization unfeasability” and claim that it requires the intervention of the FSM everytime one tries to cross two different animals?

  11. Also Sal, if you think that posting a picture of the heart of a reptile and claiming “look! I can’t imagine how that could have possibly evolved!” is evidence of any kind of mechanical barrier of evolution, well, it’s not, and won’t cut it to shift the burden of proof when you say we should show exactly how that happened to falsify your “principle” (prototypical argument from ignorance plus burden of proof shift).

    But more importantly, even if we were to concede for the sake of argument that you might be right on that one (and you are not) that would in no way mean that “mechanical unfeasability” is the null hypothesis and applies to any transition other than that particular reptile heart.

    You need evidence for mechanical unfeasability for each instance of special creation!

  12. stcordova,

    You don’t address the mechanical difficulties except by more circular reasoning like saying snakes evolved from lizzards.

    “If you are struggling in a debate, just say ‘circular reasoning’. A lot. If your interlocutors challenge you to demonstrate the circularity using propositional calculus, just say it again. Then append it to every statement, even those that only contain one part. As another tack, try writing a sentence down and then writing it in reverse and saying ‘that’s circular reasoning that is’. If you say it often enough, it becomes true. Works with Natural Selection too.”

    How to debate with evolutionists, 1st Ed.

  13. dazz,

    Yep, a point I have made repeatedly. If phylogenetics is circular, it is circular in all instances, not merely those deemed mechanically infeasible.

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