Tuesday, November 03, 2015

Going ape over Adam

i) Dennis Venema seems to be the big gun at BioLogos these days. This year he's done a running series attacking Vern Poythress, before he turned his guns on W. L. Craig. 

I don't know where Venema gets the theistic component of theistic evolution. Perhaps that's from the fine-tuning argument.  However, Venema is a biologist by training, whereas the fine-tuning argument would seem to be the provenance of an astronomer. If so, then for the branch of science he's least qualified to assess, he thinks the evidence points to  supernatural origins, and in the branch of science he's best qualified to assess, he thinks the evidence is indistinguishable from naturalistic origins. That doesn't inspire confidence in his synthesis. 

ii) I think creationists are sometimes guilty of special pleading. That's hardly a fatal admission, for from my reading, Darwinians are often guilty of special pleading. From the standpoint of somebody like William Provine, Venema's theistic evolution is a makeshift position. 

To be on the defensive posture tends to be a position of weakness. Instead of giving positive reasons for his position, or reasons for why he thinks the alternative is wrong, someone on the defensive is simply attempting to deflect criticism. That puts him at a disadvantage. May look like special pleading. Because creationism is under constant attack, it can foster that impression, but that's because the critics, the person on the offensive, enjoys a tactical advantage. 

Yet every side in this debate (young-earth creationist, old-earth creationist, Intelligent design theorist, theistic evolutionist, deistic evolutionist, naturalistic evolutionist) plays offense and defense at one time or another. 

Every side begins with set of facts. What they take to be a core of well-established facts. And that functions as their standard of comparison when they evaluate the evidence or prima facie counterevidence. 

Every position must contend with obstreperous data that don't easily assimilate into their paradigm. Yet, in principle, you could flip that around. You could make the recalcitrant data your starting point, and use that as the standard of comparison. There's nothing that automatically selects for or privileges what subset of evidence will constitute the benchmark in relation to which "anomalous" data must be reinterpreted and harmonized. 

I'm not saying the choice is purely arbitrary. But everyone is in the same boat in that regard, even if they occupy different decks. 

iii) Venema strikes me as a good student. Someone who believes what he's taught, learns the rules, and follows the rules. Unquestioning. Submissive. Dutiful. 

Following the rules can produce good science. Following the rules can make small, incremental contributions to scientific knowledge. 

But that can also inhibit scientific progress. Venema doesn't seem to have the kind of mind that moves science forward in dramatic new directions. That opens new vistas in the frontiers of science. That requires a more creative and iconoclastic turn of mind. 

iv) With those preliminaries out of the way, I will venture a few comments on this post:

On the face of it, this is one of the more impressive arguments for common descent. I'll just mention some of the questions and considerations that come to mind when I read something like this:

v) One point of contention is how much DNA humans generally share with the great apes, or chimps in particular. 98% is a popular figure. but that doesn't strike me as very significant one way or the other. 

a) To begin with, the higher the figure, the harder it is to account for drastic differences between humans and great apes. It threatens a paradox. 

b) More to the point, I doubt this is relevant to the creation/evolution debate. Even before the advent of comparative genomics, it was obvious that humans have more in common with some animals than others. We have more in common with mammals than reptiles. We have more in common with some mammals than other mammals. By process of elimination, we will have more in common with one particular species than other species. 

That's inevitable given biological diversity, which can be arranged along a spectrum of similarity and dissimilarity. Given that continuum, there's bound to be degrees of increasing similarity and dissimilarity. Bound to be species that range along our section of the continuum. Bound to be a species most like us. You can arrange them in ascending or descending orders of similarity, with many borderline cases. 

c) Apropos (b), suppose we view DNA as a blueprint. That's a popular, if simplistic, metaphor. Why would two species have similar blueprints? From a theological standpoint, the answer is that if God wants to make two similar species, he will give them similar blueprints. 

So in that respect, genetics doesn't furnish independent evidence for common descent. That's a circular appeal. 

The deeper question is why God would want to create two kinds of animals that are alike. And the answer, or at least one answer, is that God wanted to create a world full of variety. Variations illustrate divine ingenuity. In that event, some animals will be more alike while other animals will be more unalike. 

So I don't think that provides even prima facie evidence for common descent. It's entirely consistent with creationism. 

vi) However, Venema is appealing to a more specific kind of evidence for common descent. Not designed commonalities, but acquired characteristics. Historical accidents (e.g. deletion of the same DNA letter in three primate species).

For humans and great apes to share that in common implies common derivation. Can't be coincidental. 

Well, what about that inference? 

a) Let's take a comparison: how did lactase persistence develop? Would it be possible for humans to adapt to adult milk consumption if enough adult humans sampled milk or dairy products on a regular basis? Even if that was initially nauseating, when food is scarce, humans will eat anything. 

b) Assuming that adaptive mutation is possible, then lactase persistence could develop repeatedly and independently in isolated populations by the same process of adaptation. 

c) Finally, in terms of DNA sequences, is it just happenstance where these "letters" occur, or must their placement be in a certain order for the code to be functional? 

If so, then even if you had independent genetic developments, you'd expect the pattern to be the same in case the pattern must be the same. If certain "letters" are out of place, then it's selected out. The code won't work. The organism won't be viable. 

Mind you, I believe the code has enough redundancy that it can survive some errors. 

So those are some doubts I have about the validity of his inference. 


  1. It's important to realize that Venema's argument here is from so-called pseudogenes. Given the major questions that have been raised about so-called junk DNA, I think that pseudogene arguments should be viewed with a lot of suspicion. And if these DNA variants are in fact doing something functional, at that point the idea that they were designed that way *in order to* do functional things (that are slightly more similar between humans and chimps than between humans and orangutans, for example) becomes a completely live option.

  2. Steve and Lydia have made excellent points. I'd like to offer my meager two cents, even though it'll pale in comparison to their sterling silver.

    A disclaimer: much of what I'll say is simplified, although I hope not oversimplified.

    1. Venema frames the debate between common ancestry and not common ancestry: "If indeed these three species share a common ancestral population, then this pattern is easily explained" vs. "The alternative hypothesis, that humans, chimpanzees, and orangutans do not share a common ancestral population..."

    Why not frame the debate as, say, common design or not common design?

    At the least, there are different angles by which to look at the data.

    2. Of course, Venema is ultimately comparing and contrasting a single tree of life (monophyletic) model with an orchard of trees (polyphyletic) model, and arguing the data supports the tree of life model.

    However, even if Venema's argument is correct, it does not necessarily support the tree of life model. For one thing, it's possible neither the tree of life nor orchard of trees models are correct. It could be we just don't know and currently have no model by which to accommodate the data. Agnosticism could be a viable option here.

    3. Venema argues common ancestry is preferable to not common ancestry because common ancestry is ultimately more parsimonious. But why should parsimony be such a decisive factor in the case at hand?

    And even if it is, why this type of parsimony rather than other types of parsimony?

    Related, since Venema argues for the parsimony of common descent as an explanation over and against not common descent (e.g. common design), then why couldn't one argue deistic evolution would be a more parsimonious explanation than theistic evolution?

    4. Genes may be one piece of the puzzle. But what about other pieces of the puzzle?

    What about epigenetics which according to one study "show significant epigenetic differences between these two species [i.e. humans and great apes including chimps and orangutans]" (source)?

    What about other aspects at the molecular and cellular levels?

    What about tissues, organs, systems?

    What about micro and macro (gross) anatomy, physiology, pathophysiology?

    What about cognitive faculties?

    What about behavior?

    And so on and so forth.

    1. 5. As Lydia points out, this is about pseudogenes.

      a. Pseudogenes ("false genes") are sequences of DNA which resemble functional genes yet appear to be non-functional. Evolutionists commonly cite one reason why pseudogenes are non-functional is because they've acquired mutations over thousands and millions of years which have rendered them non-functional (or they've always been non-functional).

      Venema's argument in this particular post focuses on olfactory receptor (OR) genes and pseudogenes. OR genes are responsible for encoding olfactory receptors, which in turn are how we (and chimps and orangutans and many other animals) detect smells. Not only do we have OR genes, but we have OR pseudogenes as well. As above with pseudogenes in general, OR pseudogenes resemble functional genes but are thought to be non-functional because they've acquired mutations over millennia which have rendered them non-functional.

      b. However, such contentions about pseudogenes are highly debatable - i.e. that pseudogenes are non-functional and that pseudogenes have acquired mutations which render them non-functional.

      For instance, pseudogenes may be functional, or at least not non-functional. Evgeniy Balakirev and Francis Ayala have argued the following for example:

      "The human olfactory receptor (OR) pseudogenes may be important for the generation and maintenance of receptor diversity. Intensive intergenic gene conversion has been revealed for this multigene family that leads to segment shuffling in the odorant binding site, and evolutionary process reminiscent of somatic combinatorial diversification in the immune system. Although OR pseudogenes have lost full coding function, they are apparently under new evolutionary constraints: OR pseudogenes adopt noncoding functions as CpG islands, enhancers, and matrix attachment regions" (source).

      c. Also, check out Jonathan Wells' book The Myth of Junk DNA. It's a bit dated, and evolutionists have responded to it, though Wells and others have replied, but it's a decent starting point. At the very least to get the lay of the land if nothing else.

      d. Dr. Sean Pitman's post on pseudogenes is worth reading as well, but it may prove too detailed for some.

      6. I'd add Venema's argument about pseudogenes is an argument from vestigial genes to (universal) common descent. In this respect, one could deploy or re-deploy similar arguments against "vestigial organs, therefore evolution" against vestigial genes. For starters, perhaps take a look at both Jonathan Wells' review of Why Evolution Is True by Jerry Coyne as well as Jonathan McLatchie's review of the same.

      7. Indeed, human olfaction is a highly complex system. Perhaps as complex as our immune system. See this post for a sample. Or peruse through the lectures of the 2004 Nobel Prize laureates who won their prize for their discoveries about the olfactory system. There's still much we don't understand.

      8. Finally, at least for now, the point about "nested hierarchy" is a bit circular, for it assumes these gene mutations originate from a common ancestor in order to argue for the common ancestry of humans, chimps, and orangutans.

      Besides, different evolutionary trees can be created using different criteria and different data.