proteins

Losing the Forest by Fixating on the Trees — A Response to Venema’s Critique of Undeniable

I was asked recently to take part in an online symposium. The journal Sapientia, published by the Carl F.H. Henry Center, invited four theistic evolutionists to review my book, Undeniable: How Biology Confirms Our Intuition That Life Is Designed, after which I was to provide a single response. Anticipating that the reviews would all be negative, I saw this not as an opportunity to convert my critics but rather as an opportunity to demonstrate to open-minded people the power of common-sense reasoning. This is, after all, the main theme of Undeniable: that ordinary curious people are well equipped to see through all the technical huff and bluff used by people with PhDs to defend the evolutionary explanation of life.

I agreed to participate, even though the deck was stacked against me in several respects. First, considering the critical view I take not just of Darwinism but also of the academic echo chamber that, with iron-lung-like artificiality, allows this otherwise dead theory to persist, it should be clear that I wrote primarily for people outside the echo chamber. The exclusion of anyone who fits that description from providing even one of the reviews of my book therefore raises questions about the true intent of the exercise. Second, although I was offered the advantage of having the last word, my response was restricted to about a third the total length of the four critiques (though I did get this adjusted upward a bit). And third, I only realized after my response was submitted that it would be published a full month after the first of the critiques became public.

I hereby unstack the deck.

My official symposium response, to be published March 5, doesn’t give much space to my first critic, Dennis Venema. This is mostly because, not knowing the order in which the critiques would be published, I had already dealt with the problems that Venema’s piece shares with the others — his complete lack of engagement with the actual argument of Undeniable, his misconstrual of this as an argument from intuition, and his accompanying charge of anti-intellectualism. The second reason I chose not to spend many words on Venema is that he relied heavily on technical criticisms, whereas the whole point of Undeniable is to give people a better option than trying to follow the technical toing and froing. My claim is that you don’t need to be able to follow technical arguments about genes and proteins and mutations in order to understand why Darwin’s explanation of life can’t possibly be correct.

That said, I don’t want to give the impression that Venema’s technical criticisms can’t be answered. They can. My point is that people can have a perfectly solid basis for knowing that Venema’s position is wrong even if they can’t fully follow his technical points or my responses to those points (below). If I’m right about this, then Venema’s “Trust me — I’m a scientist” approach isn’t going to work. He’s going to have to enable intelligent non-scientists to make sense in their own minds of the claim that things like humming birds and cheetahs and humans just happen in a universe like ours.

I’m pretty sure he can’t do so (though I would welcome an attempt). Perhaps he has his own doubts about this, which would explain why he chose to ignore the main argument of Undeniable.

My forthcoming official response makes that point. Here I’d like to show why you should be cautious about trusting Venema’s take on this simply because he’s a scientist.

First, the fact that Venema looks to a non-scientist — Vincent Torley, an English teacher with a PhD in the philosophy of mind — as though he were an authority on my protein work serves as a strong indicator that Venema isn’t an authority either in this area. With that in mind, let’s consider Venema’s dual claims in order: 1) “we now know that proteins do not need to be stably folded in order to function,” and 2) “we also know that functional proteins are not rare within sequence space.”

Conditional Folding Is Still Folding

On the first point, Venema surely knows he’s misleading his readers. With respect to proteins, foldingrefers to the process by which initially floppy protein chains lock into well-defined three-dimensional structures that perform specific functions within cells. Venema cites a good review paper on so-called “intrinsically disordered proteins,” claiming the existence of this class of proteins shows that protein function doesn’t actually require folding. However, if Venema read the paper, he knows it has a section titled “Coupled folding and binding,” referring to the “mechanism by which disordered interaction motifs associate with and fold upon binding to their targets” (emphasis added). In other words, the term “intrinsically disordered proteins” is a misnomer (whoever coined the term evidently didn’t know what the word intrinsic means). A better term would be conditionally folded proteins.

Moreover, anyone who reads this review paper with open eyes will see that conditional folding is in fact a remarkable design feature. As the authors say, “An exciting recent finding is that many proteins containing low-complexity or prion-like sequences can promote phase separation to form membrane-less organelles within the cytoplasm or nucleoplasm, thus contributing to their compartmentalization in a regulated manner.” Speaking of conditionally folded proteins in general, the authors note that the levels of these proteins within cells are “tightly regulated to ensure precise signaling in time and space, and mutations in [them] or changes in their cellular abundance are associated with disease.”

So, if Venema pictures these conditional folders as being easy evolutionary onramps for mutation and selection to make unconditionally folded proteins, he’s badly mistaken. Both kinds of proteins are at work in cells in a highly orchestrated way, both requiring just the right amino-acid sequences to perform their component functions, each of which serves the high-level function of the whole organism. The point of Undeniable is that we don’t need to know the exact improbabilities of each of these component functions to know that the whole thing can’t happen by chance. We merely need to see that a great many things have to come together in the right way for systems like this to be made. The obvious fact that every one of these things is improbable if left to chance makes getting the whole thing utterly impossible.

Storytelling Isn’t Science

On the second point (the rarity of functional sequences) Venema appeals to two lines of evidence. First, he sees “strong evidence” that “new genes that code for novel, functional proteins can pop into existence from sequences that did not previously encode a protein.” The authors of the paper he cites in support of this are more cautious. Like all authors, they want to think the evidence they provide is strong, but considering the number of assumption involved, they are compelled to be more tentative: “These results suggest that BSC4 may be a newly evolved gene” (emphasis added).

The observable facts are what they are: brewers’ yeast has a gene that isn’t found intact in similar yeast species and appears to play a back-up role of some kind. The question is how to interpret these facts. And this is where Venema and I take different approaches. Like most biologists, Venema starts with the assumption that evolution works as claimed (or maybe he would say openness to the possibility that it does) and then he looks at genomes as if they were the record of evolutionary accomplishments — evolution’s CV, as it were. But once you go down this road of thinking you can divine the past by “reading” it from genomes, you tend to get sucked in. The distinction between stories and facts becomes blurred to the point where every new story is seen as confirmation of that initial assumption that evolution works. Then, having become hooked on this way of thinking, you have no inclination to step back and take a critical view of the whole thing.

A more critical approach is necessary for getting the science right. Stories about how things happened can’t become scientifically compelling until we show: 1) that things could have happened that way, and 2) that no other way they could have happened is comparably likely. Having taken this critical approach for decades, I’ve become convinced that all naturalistic explanations of life fail at step 1. That’s the point of Undeniable, and while Venema may dislike this point, his aversion to it is not an answer to it.

To ignore is not to refute.

If we retain an appropriate degree of skepticism about the grand evolutionary story, other interpretations of the facts surrounding BSC4 present themselves, one being that similar yeast species used to carry a similar gene which has now been lost. The fact that the version of this gene in brewers’ yeast is interrupted by a stop codon that reduces full-length expression to about 9 percent of what it would otherwise be seems to fit better with a gene on its way out than a gene on its way in. I admit that’s just another story, the point being that there’s usually more than one possible story.

The motives for telling these stories can be as interesting as the stories themselves, as this paper in Nature Reviews Genetics reveals. The abstract starts by presenting a problem:

Gene evolution has long been thought to be primarily driven by duplication and rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood.

Translation: Genomic sequencing has revealed something that contradicted evolutionary thinking — namely, an abundance of genes that don’t appear to have any evolutionary history (hence the name orphan genes).

Now, if biologists were as cautious about stories as they ought to be, this discovery would have been a huge wakeup call. Instead it was merely an occasion to recraft the story, keeping it true to the grand theme of life being the product of natural causes. By this constrained way of thinking, orphan genes must be able to pop into existence naturally because, well — here they are! Accordingly, the authors of the above paper “solve” the problem they posed by positing that “de novo evolution out of non-coding genomic regions is emerging as an important additional mechanism” for the origin of existing genes.

Don’t Forget: The Point in Dispute Is the Sufficiency of Chance

The focus should indeed be on mechanisms — detailed, self-critical, scientifically tested accounts of just how new functional genes would “pop into existence.” More specifically, with respect to the present debate, the key question is not what happened when and where. As interesting as that question is, the crucial question for our purposes is this: Could these things have happened by chance?

Venema and I both believe the universe popped (banged) into existence long ago, and we both recognize the implausibility of the claim that this just happened. Likewise, we both understand the profound significance of this distinction between an intended universe and an accidental one. Given all this agreement, Venema should be equally concerned to make the same distinction for life, all the way down to individual genes. The crucial question isn’t whether genes popped into existence but whether they popped into existence by chance. If he recognized this, he would be less distracted by the stories and more genuinely interested in the probabilities. After all, the only adjudicator on questions of chance is probability.

Rhetoric Isn’t Science

To his credit, Venema at least gives a nod in this direction by citing a piece of experimental work by Neme and coworkers that claims to show functional DNA sequences are highly probable — abundant within the space of possibilities. These scientists inserted synthetic pieces of DNA with random sequences into an existing genetic element that, when placed in bacterial cells, forces these cells to churn out loads of RNA from the inserts and also to churn out any protein chain they might happen to encode (by chance). After experimenting with these encumbered bacterial strains, they claim that “the majority of randomly generated sequences have reproducible biochemical activity.”

Though the shortcomings of this study wouldn’t be evident to every reader, they were evident to me when I read the paper last spring, just after it appeared. I was therefore pleased to see a polite explanation of some of the problems published in Current Biology last July. The authors of this critique left no doubt as to the magnitude of the flaws: “we have reservations about the correctness of the conclusion of Neme et al. that 25% of their random sequences have beneficial effects…”

Indeed, it’s hard to escape the conclusion that Neme and coworkers deliberately overstated their case. They concluded that most randomly generated sequences have “biochemical activity,” but what they showed is far less impressive. They merely showed that if you burden bacteria by forcing them to churn out RNA and protein from random inserts, it’s fairly easy to find sequence-dependent effects on growth — not because anything clever has been invented, but because the burden of making so much junk varies slightly with the kind of junk. That means any junk that slows the process of making more junk by gumming up the works a bit would provide a selective benefit. Such sequences are “good” only in this highly artificial context, much as shoving a stick into an electric fan is “good” if you need to stop the blades in a hurry.

Yes, junk sequences can have a measurable effect in situations like this, but the word function implies something considerably more than mere effect, and the term “biochemical activity” used by Neme et al.is so clearly incorrect that it’s hard to believe the reasons for choosing it weren’t more rhetorical than scientific.

In the end, then, Venema’s technical complaints come to nothing. In his position, I would probably be inclined to respond with more technical complaints. He is, of course, free to do so, but he would do himself a favor to hit pause and consider whether there really may be a clear logical reason that the natural causes he wants to credit with inventing life can’t actually deserve that credit.

Source: Evolution News