Is Macroevolution True? A Response To Tim D.

When Frank recently informed me that he planned to publish a guest article by atheist Tim Duck on the scientific evidence for neo-Darwinian evolution, I was immediately intrigued. As someone with some background and academic training in biology (I hold a degree in the field), I looked forward to reading what Tim had to say. When Frank forwarded me Tim’s final draft of his essay, however, the result was a tremendous anti-climax. The first half of the essay (which you can view here) was essentially wasted in laying out elementary concepts of biology known by every freshman undergraduate. When he finally did get around to presenting his case, the result was disappointing.

We were treated to a lengthy discussion of Michigan State University biologist Rick Lenski’s now-famous experimental work on E. coli (about which we are not ignorant). The only other identifiable positive argument for the claim in question was the assertion – without justification – that an indefinite extrapolation from micro- to macro- evolution is warranted. But since this is what Tim – allegedly – set out to prove, this constitutes a remarkable instance of begging the question.

But before getting into the specifics, allow me to highlight a few areas on which Tim and I are agreed. We agree that evolution possesses explicative power (we disagree over the extent). We agree that evolution does not entail atheism (one can accept evolution and remain a Christian theist). We agree that evolution, strictly speaking, has nothing to say on the origin of life. And we agree that argumentum ad consequentiam is a logical fallacy.

So, at which point does Tim err?

Tim’s first significant error relates to the false misconception – as prevalent as it may be – that the totality of traits possessed by an organism is ultimately determined at the gene level. This is somewhat of a simplistic view of development, and one can see quite clearly why one might naively come to think that the kind of evolutionary change required for the origin of novel body plans can simply be accomplished by the workings of microevolution on a grander scale.

In reality, however, the difference is not quantitative but qualitative. While DNA is responsible for the specification of protein structure (via an RNA intermediate), it does not alone determine the kind of spatial specificity required for proper cell-type differentiation, nor does it determine how these respective cell types are arranged into different tissues and organ systems, and ultimately the formation of an organism’s body plan. I have addressed this subject before, and readers are invited to read my previous writing on the subject for some explanation as to the immense problems with the DNA-centric understanding of development.

If, indeed, it is the case that DNA (and its interaction with the environment) is not the whole story as far as the morphogenesis of organismal form is concerned, then there is no reason to think that the extrapolation from ‘micro-evolution’ (which results from mutations affecting DNA) is at all justified. Indeed, we are only now learning that the 3D structure of the zygote itself plays a foundational role in producing an animal’s body plan. At any rate, given that an organism’s body plan is established right at the start of development, the situation looks bleak anyway because mutations affecting early development are the least likely kinds of mutations to be tolerated by animals (I explain why here and, in more detail, here).

After a full commentary on the process of natural selection and all that it entails, we are subsequently treated to a discussion of Richard Lenski’s famous laboratory work with E. coli. What we are not given, however, is a rebuttal to the numerous pertinent comments which have been given by ID proponents with regards to Lenski’s work. Michael Behe, for example, discusses Lenski’s work on pages 140-142 of his book, The Edge of Evolution, and — more recently — in a peer-reviewed article in the Quarterly Review of Biology. Behe has also been keeping tabs on Lenski’s work over on his Uncommon Descent blog.

As to the specific example of adaptive evolution given to us by Tim D., this same example — as I recall — was given by Richard Dawkins in his most recent popular book, The Greatest Show on Earth. The case of the citrate transporter seems, to me, to be a weak one because it has been documented that wild-type E. coli can already use citrate under low-oxygen conditions. Under these conditions, citrate is transported into the cell (Pos et al. 1998). The gene in E. coli specifies a citrate transporter. In the presence of high levels of oxygen, it is thought that the citrate transporter doesn’t function or is not produced. Thus, wild-type E. coli already possesses the genes necessary for the transportation of citrate into the cell and its subsequent utilisation. Indeed, Lenski et al. (2008) note that “A more likely possibility, in our view, is that an existing transporter has been co-opted for citrate transport under oxic [high oxygen level] conditions.” Such a scenario could take place by a loss of gene regulation (meaning that the gene is no longer expressed exclusively under low oxygen conditions) or a loss of transporter specificity.

Tim gives us one or two other uncontested examples of the occurrence of natural selection in the wild, reminding us that “[Evolution] is about divergence, not progression. To ‘evolve’ does not mean ‘to get stronger’ or ‘to get better,’ or to ‘improve’. It simply means to ‘change.'” Well, no one is going to dispute that living species change over time, or even that this change is, in part, facilitated by natural selection. But if one is to justify the stupendous extrapolation from natural selection and random mutation as an explanatory framework for microevolution within existing species, to be an all encompassing explanation for all of biodiversity, one has to demonstrate something just a tad more impressive than “species change over time.”

At the end of his essay, Tim states that “I know I haven’t addressed *all* of the criticisms that are out there.” I don’t think that Tim has really addressed any of them. Tim’s entire argument rests on the unjustified assumption that minor changes within existing species can be extrapolated to account for the origin of species. But this premise is merely asserted, and not justified. He has not given us an explanatory framework — within the paradigm of neo-Darwinism — which adequately accounts for structures which possess the quality of irreducible complexity, or for that matter even attempts to (see, for example, my discussion of flagellar assembly here), nor have we been given an explanation which would adequately account for the successful evolutionary search for sparse functional protein folds (which are extremely rare with respect to combinatorial sequence space), e.g. see Axe (2004) and Axe (2010a).

Moreover, as documented by Axe and Gauger (2011), even a seemingly trivial switch from Kbl to BioF function requires at least seven co-ordinated mutations, putting the transition well beyond the reach of a Darwinian process within the time allowed by the age of the earth. Their paper studies the PLP-dependent transferases superfamily. They identified a pair within the superfamily with close structural similarity but no overlapping function. The enzymes chosen were Kbl (which is involved in threonine metabolism) and BioF (which is part of the biotin synthesis pathway). And they used a three-stage process to identify which sequences were most likely to confer a change in function.

This three stage process involved:
1. Using structural and sequence comaprisons of the two enzymes to identify candidate amino acids most likely to be functionally significant.

2. Mutating these amino acids in BioF, making them like Kbl, and checking for loss of BioF activity.

3. Testing whether changing these groups in Kbl to look like BioF would enable the Kbl to substitute for the function of BioF.

And thus they estimated that seven or more mutations would be required to convert Kbl to BioF function.

Axe and Gauger’s paper is not an isolated result. One recent review in Nature reported that changing an enzyme’s chemistry may require multiple neutral or deleterious mutations.

Another review stated,

“Interchanging reactions catalyzed by members of mechanistically diverse superfamilies might be envisioned as ‘easy’ exercises in (re)design: if Nature did it, why can’t we?…Anecdotally, many attempts at interchanging activities in mechanistically diverse superfamilies have since been attempted, but few successes have been realized.”

When these results are taken into account in the context of the predictions of population genetics with regards the waiting time for multiple co-ordinated non-adaptive mutations which are required to facilitate a given transition (e.g. see Axe 2010b), the situation for neo-Darwinism appears to be bleak.

I could continue on in a similar vein for some time. Suffice it to say for the time being that Tim has not given us any credible reason to think that these profound conundrums can be overcome. Should Tim desire to respond with some more substantive arguments, he will of course be most welcome to do so.

In summary then,

1) Richard Lenski’s work on E. coli, as fascinating as it is, does not demonstrate anything remotely like what Tim’s thesis requires.

2) There is not just an absence of evidence for the micro- to macro- extrapolation. There is also an evidence of absence — That is to say, there is positive evidence which militates against the claim that the extrapolation is justified (what I outline above is only the tip of the iceberg).

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8 replies
  1. Tim D. says:

    Just some brief forewords here:

    The first half of the essay (which you can view here) was essentially wasted in laying out elementary concepts of biology known by every freshman undergraduate.

    I’ll have to go ahead and accept that criticism, except to offer one reason for it in my defense: I wasn’t exactly sure what my target audience would be. I don’t really know the average age of readers here (I’ve spoken to people my age, as well as people much younger and older), and so I didn’t know if I would be talking to college-educated professionals or younger people or somewhere in between. So for what it’s worth, I wasn’t trying to deliberately insult anyone’s intelligence, I was trying to be concise.

    The only other identifiable positive argument for the claim in question was the assertion – without justification – that an indefinite extrapolation from micro- to macro- evolution is warranted.

    I also partially accept this criticism, but I also must tell you right off the bat, that the article I submitted was not anywhere NEAR as complete as I would have preferred given more space….with that in mind, I basically ran out of space. But I still feel I did what I set out to do, which was demonstrate the common ground between “macro-” and “micro-“evolution; the driving point I aimed to make was, the unit used to measure the two (the gene), and the method by which this unit is altered, is the same. So to differentiate between the two (at least for the reasons I’ve heard here and elsewhere by prominent religious scholars — such as the “body types” argument) seems odd to me. I didn’t want to say so in the original posting because I thought it sounded rude, but I wanted to say that I think that, if we have reason to believe that small changes happen, and we have a solid idea of how they happen, then it follows rationally that, so long as they can happen, they will happen, at least if we base them both on the same original evidence.

    If it makes things any clearer (which it may or may not), to mediate the fact that I had so little space, I decided to try and focus on how it is possible (and how it happens), rather than providing a long list of evidences (which didn’t seem to suit the format). I didn’t want to just list a bunch of fossils and say, “poof, there ya go,” in the event that the reason why those things constitute proof to me is not clear. I’ve done that a million times on blogs and forums and it never gets anywhere — we (and by “we” I mean “people I talk to, and myself”) just get in shouting matches and break everything down until we end up discussing something completely unrelated.

    And yes, that last example was taken from The Greatest Show On Earth by Richard Dawkins. It was meant as a mild demonstration of the fact that small evolutionary changes can result in the alteration of body parts in ways that are “stackable” (i.e. that can be passed on to future generations successfully). It was also meant as a side-note response to a common question I hear (one that someone here asked me awhile back, as it were) — “if we’ve been evolving for billions of years, then how come we’re not super beings right now?” I know that may seem like a silly question, but like I said, I had no clue who I would be addressing, so I tried to consider all possible options.

    I hope to give a more proper response soon; sorry for being so short right now.

    Reply
  2. Jonathan McLatchie says:

    Tim: If you want to respond with a second guest post rather than a comment, we can accommodate that (just email it to Frank). But please throw in some evidence next time.

    Josiah: Yes, you’re right. Thanks for catching that.

    J

    Reply
  3. Tim D. says:

    Tim: If you want to respond with a second guest post rather than a comment, we can accommodate that (just email it to Frank). But please throw in some evidence next time.

    OH SNAP!

    But seriously….yeah, this is a topic that interests me a lot (I’m kind of knee-deep in a sea of neurobiology texts at the moment), and I’d love to keep going one way or another. There might be pauses here and there between my responses, though, as I’ll be starting school again in a couple weeks, and in the meantime I’m (A) speeding through a bunch of follow-up/refresher courses, (B) trying to get a record label off the ground (money issues), and (C) pulling OT. So if I don’t answer *right* away, it’s not because I’m not interested!

    I also like this:

    As someone with some background and academic training in biology (I hold a degree in the field)

    That means I don’t need to hold back at all 😀

    Just as an aside note (not relevant to this immediate discussion), though….may I ask which field, exactly? It’s not really my business or anything, I was just wondering — truth is, I’ve been looking into some O-chem-related jobs and I’m kind of lost at the moment….

    Reply
  4. Tim D. says:

    Hey hey CE crowd! Sorry for the 4-month delay. I got busy with life and other irrelevant crap. But I finally finished it. If anyone still cares, I wrote a response piece and posted it on my blog. You can find it if you google-search “The AlabamAtheist another defense of Darwinian evolution.”

    And now I’m on my merry way~ Although I will say, it’s a tad disappointing that both of these topics only got like 2 comments, and only 1 between the two of them that wasn’t from either myself or Mr. McLatchie. Ah, well. Ya live ‘n ya learn, I guess!

    Reply
  5. Roger says:

    “If, indeed, it is the case that DNA (and its interaction with the environment) is not the whole story as far as the morphogenesis of organismal form is concerned, then there is no reason to think that the extrapolation from ‘micro-evolution’ (which results from mutations affecting DNA) is at all justified.”

    From the above it’s obvious to me you have a simplistic and incorrect view of evolution. The working definition that biologist use for evolution is this “The change in genetic composition of a population over successive generations” (allele frequency). Lenski’s experiment falls neatly within this definition. You deny macro without giving the working definition that biologist use which is simply changes in the gene pool over time; which is basically the same as micro the main difference being the time-span. To deny macro could be an outcome of micro is akin to denying seconds give rise to minutes.

    Your accusation of Tim committing the informal fallacy of begging the question is mistaken since you focused on his *motives* and not whether his conclusion was implicit in the premises of his argument. You thereby committed the fallacy of appeal to motive.

    If you respond to my comment do so but only if you’re willing to use the correct definition of the subject at hand.

    Reply

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