Another Bogus Claim of "Novel Function Arising Through Mutation and Selection" - Evolution News & Views

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Another Bogus Claim of "Novel Function Arising Through Mutation and Selection"

Intelligent Design and the Origin of Information: A Response to Dennis Venema

In this article, Part 6, we:
• Understand why Dennis Venema's citation of Joseph Thornton's steroid research does do not demonstrate a "fascinating case of a novel function arising through mutation and selection"
• Review the multiple responses to Thornton's research from leading ID proponents (all ignored by Venema) who found the changes were not information-rich, not necessarily produced by natural selection, entailed diminishment rather than gain of function, and well within the 'edge of evolution'
• See that Venema undercuts his own claims by admitting, "Steroid hormones are a closely related molecules -- it's not too surprising that slightly different molecules fit into a related group of protein receptors"

Other Installments:
Part 1: Intelligent Design and the Origin of Biological Information: A Response to Dennis Venema
Part 2: Why Did One Theistic Evolutionist Part Ways with BioLogos?
Part 3: What Is a Proper Test of Intelligent Design?
Part 4: The False Dichotomy Between Intelligent Design and Natural Causes
Part 5: Richard Lenski's Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information
Part 7: Confusing Evidence for Common Ancestry with Evidence for Random Mutation and Natural Selection
Part 8: Critically Analyzing the Argument from Human / Chimpanzee Genetic Similarity
In the case of Richard Lenski's Long Term Evolution Experiments (LTEE) with E. Coli bacteria, we saw that Dennis Venema of BioLogos cited purported examples of natural selection increasing specified and complex information -- but intelligent design (ID) proponents had long before critiqued these examples. For example, Lenski's LTEE had been critiqued by Michael Behe when they first came out in 2008, and then later in Behe's 2010 paper in Quarterly Review of Biology. Venema, however, discussed none of these critiques.

But Venema has a second empirical example he cites to supposedly show the Darwinian evolution of what he calls "CSI on Steroids." Citing research co-published by University of Oregon biologist Joe Thornton in 2006, Venema calls this "a second fascinating case of a novel function arising through mutation and selection." But here too, ID proponents had extensively critiqued the experiment when it was first published. And again, Venema failed to discuss or respond to any of these prior arguments from ID proponents. It's hard to ignore responses from the ID camp to Thornton's research since there are so many of them. These responses were all published back in 2006 when Thornton's research was first published:

Many of these responses will be discussed below.

Venema claims that Thornton's research shows "a second fascinating case of a novel function arising through mutation and selection." As we will see, if by "novel function" Venema means "diminishment of function," then perhaps he is correct. As a brief and cursory summary of problems with the Thornton et al. research, consider the following points:

  • The Thornton et al. research cited by Venema merely found that an alleged precursor enzyme could potentially perform two functions, and then supposedly lost the ability to perform one of those functions. At worst it shows loss-of-function through two mutations. At best, this is an example of small-scale change, which the research of ID proponents like Michael Behe readily concedes is possible. Because Thornton et al.'s research only supported small-scale evolution, which ID proponents don't question, Behe wrote in response: "This continues the venerable Darwinian tradition of making grandiose claims based on piddling results. There is nothing in the paper that an ID proponent would think was beyond random mutation and natural selection. In other words, it is a straw man."
  • Christoph Adami reviewed Thornton et al.'s research in Science, claiming it refuted ID. The research was also puffed in the New York Times as addressing intelligent design after the authors issued a press release entitled "Evolution of 'Irreducible Complexity' Explained," purporting to be a direct response to "[a]dvocates of Intelligent Design." Whether they are right or wrong, this is amusing since we see ID-critics debating over the scientific controversy that they claim does not exist.
  • The authors' press release gave a retroactive confession of ignorance, admitting that "[h]ow natural selection can drive the evolution of tightly integrated molecular systems ... has been an unsolved issue in evolutionary biology." Yet in the New York Times article, Thornton commented that "There's no scientific controversy over whether this system evolved. The question for scientists is how it evolved." So before this study they didn't know how it evolved, yet somehow they knew it did evolve. It sounds like they are assuming the truth of Darwinian theory rather than testing it.
  • Before the paper was published, Thornton had stated on his website that his "goal is to illustrate how a complex, tightly integrated molecular system -- one which appears to be "irreducibly complex" -- evolved by Darwinian processes." After ID-theorist Paul Nelson pointed out that this implied that Thornton saw irreducible complexity as a legitimate scientific challenge, the words "irreducibly complex" magically disappeared from Thornton's website. The episode demonstrates that ID raises legitimate scientific challenges of interest to Darwinian evolutionary biologists, even as they sometimes deny that fact for political reasons.
  • In sum, this study doesn't show how Darwinian evolution scales Mount Improbable, as Dawkins has put it. It simply shows that neo-Darwinism can get you the last 10 yards up the mountain after you've already spent 10 hours hiking. It's an exercise in what Behe called "making grandiose claims based on piddling results."
But there's much more to say in response to this research. Since much of the work responding to it has already been done, the best thing is simply to quote from some of these responses:

Response 1: Michael Behe's comments:

The bottom line of the study is this: the authors started with a protein which already had the ability to strongly interact with three kinds of steroid hormones (aldosterone, cortisol, and "DOC" [11-deoxycorticosterone]). After introducing several simple mutations the protein interacted much more weakly with all of those steroids. In other words, a pre-existing ability was decreased.

That's it! The fact that this extremely modest and substantially irrelevant study is ballyhooed with press releases, a commentary in Science by Christoph Adami, and forthcoming stories in the mainstream media, demonstrates the great anxiety some folks feel about intelligent design.

In the study the authors wished to see if two related modern proteins called the glucocorticoid (GR) receptor and mineralocorticoid receptor (MR) could be derived from a common ancestral protein. Using clever analysis the authors made a protein that they thought represented the ancestral protein. That protein binds several, structurally-similar hormones, as does modern MR. They then introduced two amino acid changes into the protein which are found in modern GR. The two changes caused the ancestral protein to bind the different kinds of hormones anywhere from ten- to a thousand-fold more weakly. That protein bound aldosterone about three-fold more weakly than cortisol. The authors note that modern GR (in tetrapods) also binds aldosterone more weakly than cortisol. So perhaps, the thinking goes, an ancestral gene that could bind both hormones duplicated in the past, one copy accumulated those two mutations to become the modern GR, and the other copy became modern MR.

[...]

Here are number of comments in response:

1) This continues the venerable Darwinian tradition of making grandiose claims based on piddling results. There is nothing in the paper that an ID proponent would think was beyond random mutation and natural selection. In other words, it is a straw man.

2) The authors (including Christoph Adami in his commentary) are conveniently defining "irreducible complexity" way, way down. I certainly would not classify their system as anywhere near IC. The IC systems I discussed in Darwin's Black Box contain multiple, active protein factors. Their "system", on the other hand, consists of just a single protein and its ligand. Although in nature the receptor and ligand are part of a larger system that does have a biological function, the piece of that larger system they pick out does not do anything by itself. In other words, the isolated components they work on are not irreducibly complex.

3) In the experiment just two amino acid residues were changed! No new components were added, no old components were taken away.

4) Nothing new was produced in the experiment; rather, the pre-existing ability of the protein to bind several molecules was simply weakened. The workers begin their experiments with a protein that can strongly bind several, structurally-very-similar steroids, and they end with a protein that at best binds some of the steroids ten-fold more weakly. (Figure 4C)

5) Such results are not different from the development of antibiotic resistance, where single amino acid changes can cause the binding of a toxin to a particular protein to decrease (for example, warfarin resistance in rats, and resistance to various AIDS drugs). Intelligent design proponents happily agree that such tiny changes can be accomplished by random mutation and natural selection.

6) In the "least promising" intermediate (L111Q) the protein has essentially lost its ability to bind any steroid. In the "most promising" intermediate protein (the one that has just the S106P alteration) the protein has lost about 99% of its ability to bind DOC and cortisol, and lost about 99.9% of its ability to bind aldosterone. (Figure 4C)

7) Although the authors imply (and Adami claims directly) that the mutated protein is specific for cortisol, in fact it also binds aldosterone with about half of the affinity. (Compare the red and green curves in the lower right hand graph of Figure 4C.) What's more, there actually is a much larger difference (about thirty-fold) in binding affinity for aldosterone and cortisol with the beginning, ancestral protein than for the final, mutated protein (about two-fold). So the protein's ability to discriminate between the two ligands has decreased by ten-fold.

8) One would think that the hundred-fold decrease in the ability to bind a steroid would at least initially be a very detrimental change that would be weeded out by natural selection. The authors do not test for that; they simply assume it wouldn't be a problem, or that the problem could somehow be easily overcome. Nor do they test their speculation that DOC could somehow act as an intermediate ligand. In other words, in typical Darwinian fashion the authors pass over with their imaginations what in reality would very likely be serious biological difficulties.

9) The fact that such very modest results are ballyhooed owes more, I strongly suspect, to the antipathy that many scientists feel toward ID than to the intrinsic value of the experiment itself.

10) In conclusion, the results (and even the imagined-but-problematic scenario) are well within what an ID proponent already would think Darwinian processes could do, so they won't affect our evaluation of the science. But it's nice to know that Science magazine is thinking about us!

Behe's point (10) is especially noteworthy since Venema writes about Thornton et al.'s research that "Over and against these lines of evidence, however, the Intelligent Design Movement claims that such novelty is inaccessible to random mutation and natural selection." But Behe has made it clear that these kinds of modest loss-of-function changes are exactly the type of changes we might expect from Darwinian evolution. So Venema is misrepresenting the claims of the ID movement.

In fact, Venema undercuts his own argument that this research represents significant novel CSI by admitting that: "Steroid hormones are a closely related molecules -- it's not too surprising that slightly different molecules fit into a related group of protein receptors." This research does not demonstrate that natural selection and random mutation can produce functional, information-rich genes and proteins because what was produced was not information-rich. If anything, function was diminished or lost rather than gained.

Response 2: Stephen Meyer's Comments:

The Bridgham et al. study published in Science is trivial. ID theorists have long known that a few mutations can slightly alter an existing protein fold. What we question is whether mutation and selection are sufficient to search the enormous combinatorial space of possibilities necessary to finding fundamentally new protein folds and structures. This study does nothing to allay our skepticism on that score.

Contrary to what the authors assume receptor-hormone pairs do not constitute irreducibly complex systems. The receptor-hormone pair is only a small component of a signal transduction circuit that regulates other complex physiological processes. For such pairs to have any selective or functional advantage many other protein components have to be present, including the other components of a signal transduction circuit and the physiological processes that such circuits regulate. If this is the best that Michael Behe's critics can do after ten years of trying to refute him, then neo-Darwinism is in deep trouble.

The really interesting thing about this paper is not the science it contains--its scientific results are trivial--but the sociological dynamics surrounding the publication of these papers. The AAAS has repeatedly insisted there is no scientific controversy about intelligent design. Now Science, the AAAS flagship journal, publishes two articles taking positions on a controversy that the AAAS says doesn't exist. Will Science now allow Michael Behe to respond or will it only publish articles about the controversy which claim that ID is wrong?

Response 3: "How to Explain Irreducible Complexity -- A Lab Manual": Another response to the Thornton et al. research came from various Discovery Institute authors in a fun piece titled How to Explain Irreducible Complexity -- A Lab Manual:
What [Bridgham/Thornton et al.] do say, however, is biologically meaningless.

A Tutorial in Evolutionary Theory

To understand why, we need a brief primer in fundamental evolutionary theory. Natural selection preserves randomly arising variations only if those variations cause functional differences affecting reproductive output. Since Bridgham et al. tell their story by invoking natural selection (see below), the system whose origin they claim to explain must have a selectable function for it to qualify as irreducibly complex. Indeed, given that natural selection favors only functionally advantageous variations, Behe has made clear that "function" in a biological context necessarily means a selectable functional advantage, for an obvious reason: a system of well-matched parts that performs a function can't lose that function unless it possesses one to begin with. Unfortunately, these receptor-ligand pairs do not meet Behe's definition of irreducible complexity for an equally obvious reason: receptor-ligand pairs do not by themselves confer any selective functional advantage.

Indeed, in Bridgham et al.'s scenario, the function undergoing natural selection is not simply MR-aldosterone binding, but electrolyte homeostasis, the complex physiological regulation of essential cellular ions such as potassium or calcium. The novel receptor MR evolved, they write, "because it allowed electrolyte homeostasis to be controlled" (p. 100).

Natural selection is acting, therefore, not on MR-aldosterone binding alone. Indeed, it cannot, because unspecified binding confers no functional advantage.

But that is what Bridgham et al. do not seem to understand. They think they are explaining the origin of a single receptor-ligand pair, the mineralocorticoid receptor (MR) protein and the steroid hormone aldosterone. But that is biological nonsense. It is nonsense, moreover, strictly on the grounds of evolutionary theory itself.

Let's suppose the newly-evolved cellular receptor, MR, interacts with a hormone ligand, aldosterone. This is a novel relationship. Now, will natural selection preserve it?

Who knows? Without more information -- that is, without more details about the cellular or organismal effect of that novel binding -- the bare function "aldosterone binds to MR" is biologically vacuous.

Compare: Pound a nail, we tell you. Where and why? you ask. Never mind that, we say, just go pound a nail. So you hammer a three-penny nail through the power supply of this blog's server.

In any case, the receptor-ligand pair by itself is certainly not irreducibly complex. These pairs represent only small components of complex physiological processes such as metabolism, inflammation, immunity, and electrolyte homeostasis. For such pairs to have any selective advantage as part of the regulation of larger physiological processes, many other protein components have to be present. In particular, all the other components of a complete signal transduction circuit have to be present, as well as the component parts of the physiological process that such circuits regulate. (Even the ligand aldosterone itself doesn't exist apart from a separate enzyme that produces it, and Bridgham et al.'s gene duplication scenario does not account for the origin of this necessary component either.)

Bridgham et al. appear to grasp the need for more details (albeit in a distressingly loose way) because both early and late in their paper they specify the functional role of MR. The receptor "is activated by aldosterone to control electrolyte homeostasis" (p. 97) they note, and evolved "because it allowed electrolyte homeostasis to be controlled" (p. 100).

Thus, in Bridgham et al.'s scenario, the actual system undergoing natural selection is electrolyte homeostasis, not simply MR-aldosterone binding. There's a good reason for that: as noted, the function "aldosterone-MR binding," considered in isolation, cannot be a target for natural selection. Try it, if you think it can. You'll quickly find that you are floating in biological limbo. Aldosterone binds to MR...MR interacts with aldosterone...MR and aldosterone...OK, enough of that. Why does MR interact with aldosterone? Hello? Can we get an organism here?

Back to Biological Reality

So -- is the physiological system of electrolyte homeostasis, of which both MR and aldosterone are small parts, irreducibly complex? Maybe. Take a look at a physiology textbook, or even any review paper on steroid or receptor biochemistry. Bridgham et al. don't say much about the complexity of electrolyte homeostasis, however, because they are unaware that they have completely misunderstood the relevant unit of selection in their scenario. They write (p. 98):

It is not obvious how the tight aldosterone-MR partnership could have evolved. If the hormone is not yet present, how can selection drive the receptor's affinity for it? Conversely, without the receptor, what selection pressure could guide the evolution of the ligand?
By Bridgham et al. 's own account, however -- although they don't realize it -- natural selection is not acting at this level (the MR-aldosterone relationship alone) at all. To have any selectable function, many more components need to brought into the story. Genuine irreducible complexity re-emerges, and will be quite unexplained by the Bridgham et al. scenario.
Response 4: My Own Comments:
[L]ook at the bottom line of what this research really found: Adami highlights that the lock and key fit of the glucocorticoid enzyme with the cortisol substrate is based upon the specificity of merely two amino acids, where the precursor molecule was also functional (lacking those 2 mutations).

In other words, one enzyme might have evolved into another via 2 mutations. This would appear to be a fairly simple system--and, assuming it did evolve in this fashion, an unimpresive example of evolution. Two meager mutations (something which even Behe and Snoke's (2004) simulations found could evolve under mutation and selection) is not an impressive evolutionary leap and there seems no reason to assume that many enzyme-substrate interactions might not require the simultaneous substitution of many more amino acid residues in order to function, vastly decreasing the likelihood of their evolution. (In fact, this research would not address the origin of complex molecular machines requiring many interacting parts, like the bacterial flagellum.) Even if we grant that this present system is "reducibly complex" (with regards to at least 2 meager amino acids, that is), why should we assume that all the other enzyme-substrate interactions in biology follow suit?

The last two commentaries combine to make two important points:

First, the fact that one precursor enzyme could potentially perform two functions, and then lost the ability to perform one of those functions, does not imply that all biologically functional enzymes can evolve in this fashion.

Second, we must keep in mind that the research of Bridgham/Thornton et al. involved intelligently directing mutations in these enzymes. Since they did not identify specific selective advantages, intelligent agents were doing the selection in a goal-directed fashion, hoping to select for future function. This is important when we consider the research of Axe (2010), discussed previously in this series. Axe found that when there is no selective advantage to a given mutation, it has a much smaller chance of becoming fixed in a population. Thus, while a series of intelligently directed mutations might lead back to a functional ancestor, Bridgham/ Thornton et al. have not demonstrated that this pathway is likely to have been followed under natural conditions.

Venema stated that "If any natural mechanism can be shown to produce "functional, information-rich genes and proteins," then intelligent design is no longer the best explanation for the origin of information we observe in DNA." But in this example we have seen that:

  • The change was not information-rich
  • It's not clear that natural selection produced this change
  • Function was diminished or lost rather than gained
In fact, Venema undercuts his own argument that this research represents significant novel CSI by admitting in a comment that: "Steroid hormones are a closely related molecules -- it's not too surprising that slightly different molecules fit into a related group of protein receptors." ID proponents would say the same thing, which is why this research does not demonstrate that a "natural mechanism can be shown to produce 'functional, information-rich genes and proteins.'"