The problem of homology

We don’t get to see our granddaughter this morning — she’s getting her pediatric checkup today — so while sitting on my thumbs in my hotel room this morning, I threw together a video on the problem of homology, as misrepresented by Jonathan Wells and Paul Nelson. Seriously, they get it all wrong with tendentious misrepresentations.

There is a real problem of homology, because homology is rendered difficult to see by standard, naturalistic evolutionary processess. Wells and Nelson get it all exactly backwards. That homologies are obscured by the nature of evolutionary change is what we’d expect from evolutionary theory. It’s like how bioinformaticians will talk about the problem of long branch attraction; it’s a real problem, but it doesn’t imply that evolution is wrong, because it’s an expected effect of evolutionary change.

Likewise, evo-devo people will write long papers about the problem of homology, because the action of evolution obscures homologies and we have to struggle to see beyond it. Only a pair of buffoons would argue that it means evolution is false.

I don’t have a script for this one, because it’s just me talking extemporaneously in a dull hotel room, sorry. But I do have a good quote from Mary Jane West-Eberhard, and that’ll have to do if you don’t have the patience to listen to some geezer talking at a camera.

Changing characters do not march ever outward along the branches of a phylogenetic tree. While homology, parallelism, and convergence remain useful conceptual guides, they need to be seen against a background of continual reshuffling with a particulate, mosaic phenotype that renders linear terms like parallelism and convergence only approximate, and potentially misleading, descriptions of evolution.

Does a concept of mixed or partial homology just make a mess of homology? In fact, evolution makes a mess of homology.

Mary Jane West-Eberhard


  1. rpjohnston says

    Alright, so going into this as an “interested layperson – some college”, I’m going to start with…I don’t know what homology is, nor what problems might be with it. I try to read a lot of the lectures you post on this blog but I don’t get all of them.


    4:30 So they know enough to know they’re lying. Utterly and irredeemably contemptible, got it.
    5:24 Sounds like the main point of the first sentence is to name-drop their hobby horse. Whatever philosophy existed at the time bears little resemblance to modern “Intelligent Design” (and even THAT is really no more than a trollish “nuh-uh!” to evolution). But word definitions allow them to equivocate the two as a bait-and-switch.
    6:21 An unnecessary, tautological sentence, meant to sow doubt by proposing a fail for evolution, and then leaving the audience to presume that such a fail exists (why bring it up if it didn’t?), without actually providing that fail.
    7:07 Yeah your reaction there pretty well sums it up. My scientific knowledge isn’t deep but it’s juuuuuust broad enough to know that those are empty buzzwords – not meaningless IN THE RIGHT CONTEXT, with the rightlinguistic handlers – but in this context, meaningless tripe. The purpose: Most people won’t be able to tease out the meaning because there is none, but will assume that it’s because it went over their heads, and thus think the authors must know what they are talking about.
    8:38 They’re squatting on the default, which is also a callback to the first sentence at 4:30. Fun fact: By squatting on the default you can make just about any proposition sound reasonable. My neighbor’s dog disappeared, and while there’s a hole in the fence it doesn’t explain how he got out of the house, so JW breaking in and devouring it remains a possibility that can only be excluded on the basis of questionable assumptions about his morality.

    Squatting on the default is a particularly insidious bad-faith tactic because most people will attempt to prove an alternative, since rejecting the squat means basically saying that the squatter is fulla shit and that’s rude. But of course you can’t prove ANYTHING even in good faith. While your simple explanation of “But we DO have mechanisms” is true, I’d say the main point – and which should be addressed first – is simply saying that they don’t get to squat there.

    For the sake of length, since I hit 10:00, I’m going to post this now, and if there’s any other crapola in that paper that jumps out at me I’ll followup

  2. flange says

    My limited understanding of homology is from an article written, I think, by Stephen Jay Gould years ago. It involved a surgeon transplanting a baboon’s heart into an infant (“Baby Fae”) with a congenital heart defect. The baby of course died a few weeks afterward.
    “… a biologist asked the surgeon why he had chosen a baboon donor, which is a much more distant relative of ours (in evolutionary terms) than a chimpanzee, which is our closest relative (DNA ~99% identical). Wouldn’t there have been less danger of rejection with a heart from a closer relative? The surgeon’s answer: he hadn’t even taken that into consideration, because he didn’t believe in evolution!”
    I guess the doctor confused homology with something else.

  3. rpjohnston says

    10:56 Hahah, “citing little tiny bits” is what I did when I had essays due that needed x number of citations and I didn’t gave a crap about whatever I was writing about. It’s a nice tactic when what you wrote is designed to be read by checklist rather than comprehension.
    11:30 And this brings it all to the head of the bad-faith strain of thought. The way I think of gaps in knowledge is that it’s an opportunity to learn more, to advance. On the occasion I get into arguments on the internet and they smugly point out “oh you can’t explain that”, I put on the “excited schoolchild” hat and say, yeah, we don’t know yet, isn’t it exciting?! We still have so much to learn! We’re doing investigations, and we have some ideas about where to explore, but we don’t really know for sure yet what we’ll find. Man, I love science!

    And that tends to stymie them because the only thing they can really comprehend is chest-beating and pissing matches, dominance displays, winners and losers, not sincerity or growth. Fucken trogs.

  4. Nerd of Redhead, Dances OM Trolls says

    I figured out years ago, from reading the lay literature (Scientific American and American Scientist), is that any question where the creobots/IDiots pretend that it is either their bullshit or evolution, that when asked about the various mechanisms of evolution, and which is right, the answer is likely all of them depending on the species. I have no problem with that. If they even think that there are a limited number of ways evolution works, they are simply stating a pile of bovine feces to protect their ignorance.

  5. wajim says

    Excellent takedown/analysis, as usual. Hope your g-babies (both) are well. But how are you doing PZ? That is, your heart issue(s) under control? Just listening.

  6. says

    The ‘problem’ of homology is not the biology or existence but rather semantic; biologists don’t have sufficient words to accurately symbolize homology in all its complexity.

  7. John Morales says

    Skeptical Partisan, heh.

    You’re bullshitting, and I know you can’t sustain your claim.

    Semantics does not rely on symbology, but rather upon concepts.

    (Or: circumlocution overcomes your objection)

  8. says

    John Morales:

    Alas, I am merely one among the great unwashed languishing at your feet for the unwonted pearls of wisdom that you deign to dribble.

    And while you have condescended to look in my direction, might I implore your learned opinion on the topic of our last communication: chiefly, how would you proceed to communicate complex concepts verbally with simple language, particularly in light of the limits you have placed on semantics, symbolic language and metaphorical language? Won’t you also, for the sake of relieving the ignorance of your loyal supplicant, please clarify how it can be that language and semantics are not symbolic?

  9. John Morales says

    Skeptical Partisan, to the first, I’ve already stated how: circumlocution.

    To the second, you are confused as to what I wrote.

  10. says

    Found the video really interesting. My understanding of homology was pretty basic. This tied together a lot of other things I already knew and gave them better context A couple of things. You mention convergence which Conway Morris makes a big issue of. I’ve read a couple of his books and like the idea at there are natural constraints on evolution which means different organisms doing the same or similar things converge on the same basic form. It offers a nice explanation for the appearance of design. He goes further and suggests that features such as the evolution of intelligence is inevitable. What is your view of this? Also you touched on one deceptive technique used by creationists, that of quote mining. Is there good list of their methods available so people can know what to look for when presented with their offal? Another video perhaps?