Arthur Hunt posted Entry 2824 on January 14, 2007 09:36 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2814

Douglas Axe recently (well, sort of) published an article in the Journal of Molecular Biology entitled “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” (Axe, J Mol Biol 341, 1295-1315, 2004). In his discussion of the experimental observations, Dr. Axe mentions some numbers that are likely to generate much discussion amongst Intelligent Design advocates and critics. For example, Stephen Meyer (2004) cites Axe at a key point in the argument in his recent article advocating Intelligent Design, “The Origin of Biological Information and the Higher Taxonomic Categories,” much discussed in previous Panda’s Thumb threads (here).

“Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 10^77. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.”

More recently, Dembski cited Axe in his Expert Witness Report for the Dover trial (see this).

“Recent research by Douglas Axe (see Appendix 3) provides such evidence in the form of a rigorous experimental assessment of the rarity of function-bearing protein sequences. By addressing this problem at the level of single protein molecules, this work provides an empirical basis for deeming functional proteins and systems of functional proteins to be unequivocally beyond Darwinian explanation.”

Given that this subject is often raised by ID proponents (such as this), and that the Biologic Institute (where Axe works) has made some news accounts, it seems appropriate to review Axe’s work. The purpose of this PT blog entry is to try and lay out the study cited above (Axe DD, J Mol Biol 341, 1295-1315, 2004) in a form that is accessible to most interested parties, and to discuss a larger context into which this work might be placed. Needless to say, the grand pronouncements being made by the ID camp are not warranted.

Section 1. What Axe did

First, a brief overview of the experiment and results. The object of interest was the so-called large domain of the TEM-1 penicillinase, an enzyme that breaks down antibiotics related to penicillin. (Antibiotics such as penicillin are called, collectively, beta-lactams, and enzymes that break down these antibiotics and confer drug resistance are called beta-lactamases, which is why the term beta-lactamase may pop up in this blog entry from time to time.) Axe was interested in using a mutational approach to explore the constraints for forming a functional large TEM-1 domain, and applying these results to estimate of the density of functional sequences in the space of all possible amino acid sequences

The approach taken was to generate collections of randomized mutant sequence variants in a functional TEM-1 variant and “count” the numbers of mutants that retained some measure of activity. Activity was measured by growth of bacteria containing the variants on relatively low levels of ampicillin, a target (or substrate) of TEM-1. (Cells with active TEM-1 can break down the ampicillin and thus survive, whereas cells with mutant TEM-1 variants that can no longer maintain a stably-folded enzyme cannot break down the antibiotic, and this will not grow.)

Axe anticipated that the native TEM-1 would be rather “resistant” to random mutagenesis, owing to a “buffering effect” contributed by what is probably a robust structural fold. This would preclude a proper assessment of the constraints governing low-level function, which in turn are the constraints relevant to the question of the emergence of functional sequences. Accordingly, he first isolated, by targeted mutagenesis, a so-called “reference sequence”, a TEM-1 variant that was expected to be much more susceptible to the effects of mutational change. (This is a crucial aspect of the experiment, the ramifications of which are discussed in Section 2.) The variant was identified as a temperature-sensitive enzyme that permitted growth of bacteria on selective (ampicillin-containing) media at a permissive temperature (25 °C), and differs from the wild-type at 22% of the 153 positions. (”Temperature-sensitive” enzymes lose function after a small change in temperature. Here, the enzyme had some modicum of activity at a lower temperature – 25 °C – but was inactive at elevated temperatures – e.g., 37°C, the temperature at which E. coli is usually grown.)

Having generated a mutation-sensitive TEM-1 variant, Axe then set about to do the mutagenesis. For this, four ten amino-acid clusters (each of which is spatially separate from the others in the 3-dimensional structure) were partially randomized. The variations that were introduced in each cluster were designed so as to retain the general hydropathic profile (see [1]) at the positions being varied. Populations of randomized pools were plated on selective media (at the permissive temperature) and the numbers of colonies counted. From this (and from other measurements that established the total numbers of screened mutants), the relative frequency of functional mutants was determined. For two of the four clusters, a recovery rate of about 0.03% (e.g., 3x10^-4) was found. For one of the clusters, a rate of 1 in 10^5 was seen. No functional variants for one of the clusters were isolated; based on the total numbers of clones analyzed, this sets a limit of 2x10^-5 as the frequency of functional mutant for the large domain of TEM-1.

These are the experiments and “raw data”. Axe averaged these four values and derived a mean per-residue tolerance to change; this value is 0.38 (roughly speaking, this is the fraction of variants at a given position that will yield a functional enzyme, and thus a functional fold). From this, he calculated that the fraction of all possible variants in the 153 amino-acid TEM-1 fold that will be functional is about 1 in 10^64 (e.g., 0.38 raised to the 153rd power).

This number represents the number of functional variants that are related to the specific reference sequence that was randomized. Axe also compared a great many naturally-occurring “relatives” of the TEM-1 fold and derived a general hydropathic “signature”. From this work, Axe estimated that about 1 in 10^33 of all sequences will possess the TEM-1 hydropathy signature, and hence a fold related structurally to the TEM-1 domain. Since each of the properly-folded (1 in 10^33) variants might be expected to possess a similar range of individual functionality (e.g., 1 in 10^64 or the family of sequences related to each variant is expected to be functional), we can estimate that 1 in 10^97 of all possible 153-mers will possess a functional TEM-1 fold.

Section 2. Going from Axe’s work to “functional proteins are isolated in sequence space”

A claim that is being made by ID proponents (as in Meyer’s paper) is that work such as this shows that functional proteins are so rare in sequence space that the natural origin of new proteins is so improbable as to be effectively impossible. Briefly, the argument is (or will be) that, if function occurs only once every 10^77 sequences (to use one of the numbers from Axe’s work), then it is rather unlikely that new functions can arise in the biosphere. However, Axe’s approach does not permit such a conclusion. The following hopefully conveys this.

Put pictorially, the issue that ID proponents are arguing about is the relative structure, or shape, of the topography of functional sequences in all of sequence space. To illustrate, the issue becomes one of the parameters of the hill shown in this figure (we’ll call it Figure 1):

newerAxeF1b.png

In this illustration, the base formed by the X and Y axes represents the sequence “space”, each hypothetical point or patch would depict a different sequence, and the Z-axis depicts some measure of activity. The “accessibility” of function, using this illustration, is a matter of the area of the base of the hill shown – the broader the base, the greater the number of related and functional sequences, and the greater the number of ways that function may be “found”. The idea that ID proponents push is that, if such a hill has a narrow enough base, then it is not likely that random processes can “find” even the base of the hill, let alone the peak. The experimental approach used by Axe is predicated on the assumption that the shape of this hill can be determined by assessing its susceptibility to mutation. Thus, the greater the sensitivity, the narrower the base, and the less likely is it that function can arise. ID proponents argue that Axe’s work shows that, indeed, the base is very narrow. This follows a. from the numbers given in the preceding; and b. from the nature of Axe’s experimental design.

There is, however, a fly in the ointment. (Actually, there are many.) Recall that Axe did not work with the native TEM-1 penicillinase, but rather with a variant that had a lower activity. The assay system made this necessary. (Scoring bacteria on antibiotic-containing media isn’t particularly discriminating, and it’s hard to tell is, say, if a wild-type detoxifying enzyme has lost 90% of its activity.) In other words, Axe decided to select a particular part of the “hill” such as that shaded in black in the following illustration (Figure 2):

newerAxeF2b.png

(Look carefully - the black patch isn’t very big, because Axe has limited his scope in an analogous fashion.)

In addition, Axe deliberately identified and chose for study a temperature sensitive variant. In altering the enzyme in this way, he molded a variant that would be exquisitely sensitive to mutation. In terms of our illustrations, Axe’s TEM-1 variant is a tiny “hill” with very steep sides, as shown in the following (Figure 3):

newerAxeF3b.png

Obviously, from these considerations, we can see that assertions that the tiny base of the “hill” in Figure 3 in any way reflects that of a normal enzyme are not appropriate. On this basis alone, we may conclude that the claims of ID proponents vis-à-vis Axe 2004 are exaggerated and wrong. Axe’s numbers tell us about the apparent isolation of the low-activity variant, but reveal little (nor can it be expected to) about the “isolation” or evolution of TEM-1 penicillinase. (Or any other enzyme, for that matter.)

Of course, there is more. Most naturally-occurring enzymes are not isolated activities as Figure 1 would imply. Something like the next illustration (Figure 4) is a better depiction – distinct activities and enzymes are often derived from common structural and sequence themes. This expands the base of the “hill” to include those of the neighboring activities; this may be considerable indeed. (In the example of TEM-1 penicillinases, the neighbors would include DD-peptidases; Knox et al, 1996; Adediran et al., 2005.)

newerAxeF4.png

But there is even more. Since the “goal” of the evolutionary exercise is a catalytic activity, and not a particular structure, the possible existence of totally unrelated structures and sequences that possess a similar activity complicates matter even more. This is pertinent for penicillinases, that are beta-lactamases. We know of a number of other families of structures that include beta-lactamases (Helfand and Bonomo, 2003). One of these, the metallo-beta-lactamases (Daiyasu et al., 2001), is quite unrelated to the TEM-1 enzymes. Axe’s study does not “count” these families of enzymes (or their neighbors), nor does it acknowledge that many more such structures are at least hypothetically possible.

Section 3. So how broad is the base of the hill?

That is the real question that Axe, ID proponents, and other who follow this sort of discussion would ask. To get some idea, we can turn to Axe’s paper. Axe mentions two other studies – one deals with experiments done with the lambda repressor, and the other with chorismate mutase. Work with the lambda repressor (Reidhaar-Olson and Sauer, 1990) yielded a “value” for the frequency of functional variants of 1 in 10^63 (roughly) for the 92-mer. Work with chorismate mutase (Taylor et al., PNAS 98, 10596-10601, 2001) gave a value of 1 in 10^24 for the 93 amino acid enzyme. Scaled for a similar size protein, Axe’s work gives a value of 1 in 10^59, which falls within the range established by previous work. (The literature in this area is rather large, far beyond the scope of this article to review. Suffice to say that the range of “probability” stated here is representative of the numerous studies in this area.)

Studies such as these involve what Axe calls a “reverse” approach – one starts with known, functional sequences, introduces semi-random mutants, and estimates the size of the functional sequence space from the numbers of “surviving” mutants. Studies involving the “forward” approach can and have been done as well. Briefly, this approach involves the synthesis of collections of random sequences and isolation of functional polymers (e.g., polypeptides or RNAs) from these collections. Historically, these studies have involved rather small oligomers (7-12 or so), owing to technical reasons (this is the size range that can be safely accommodated by the “tools” used). However, a relatively recent development, the so-called “mRNA display” technique, allows one to screen random sequences that are much larger (approaching 100 amino acids in length). What is interesting is that the forward approach typically yields a “success rate” in the 10^-10 to 10^-15 range – one usually need screen between 10^10 -> 10^15 random sequences to identify a functional polymer. This is true even for mRNA display. These numbers are a direct measurement of the proportion of functional sequences in a population of random polymers, and are estimates of the same parameter – density of sequences of minimal function in sequence space – that Axe is after.

10^-10 -> 10^-63 (or thereabout): this is the range of estimates of the density of functional sequences in sequence space that can be found in the scientific literature. The caveats given in Section 2 notwithstanding, Axe’s work does not extend or narrow the range. To give the reader a sense of the higher end (10^-10) of this range, it helps to keep in mind that 1000 liters of a typical pond will likely contain some 10^12 bacterial cells of various sorts. If each cell gives rise to just one new protein-coding region or variant (by any of a number of processes) in the course of several thousands of generations, then the probability of occurrence of a function that occurs once in every 10^10 random sequences is going to be pretty nearly 1. In other words, 1 in 10^-10 is a pretty large number when it comes to “probabilities” in the biosphere.

The uncertainties in estimating the densities of functional sequences are very high. Obviously, we all would like to home in on a narrower range. This is complicated by the technical and theoretical shortcomings of the various approaches. The “reverse” approach is tied to a single family of sequences and functions and makes assumptions that may not be warranted (Section 2 here is an example). The “forward” approach may find too many things, some (many?) of which may have no biological relevance. Sorting these things out is a tough nut to crack experimentally.

Summary

To summarize, the claims that have been and will be made by ID proponents regarding protein evolution are not supported by Axe’s work. As I show, it is not appropriate to use the numbers Axe obtains to make inferences about the evolution of proteins and enzymes. Thus, this study does not support the conclusion that functional sequences are extremely isolated in sequence space, or that the evolution of new protein function is an impossibility that is beyond the capacity of random mutation and natural selection.

Endnote

1. the hydropathic signature is technical-ese for a particular pattern of polar and apolar amino acid residues in a structure or sequence. In the case of this study, the signature was the guide in determining the extent of variation that was introduced in the ten amino-acid clusters. Also, an aside to help readers with terminology – when we speak of sequence space, we are talking about nothing more than some collection of possible sequences. Thus, for example, the total “sequence space” of polypeptides of 153 amino acids in length is the number of possible polypeptides - 20^153, or 10^199.

Acknowledgements:

Thanks to the efforts of the PT crew, and particularly Ian Musgrave, who helped me keep this on topic. Also, many thanks are due to Douglas Axe, who graciously helped me with early drafts of this essay. Please note that all of these ideas are mine, and I make no claim that any of these thoughts represent Axe’s views.

References:

Axe DD, J Mol Biol 341, 1295-1315, 2004

Meyer SC, Proc Biol Soc Washington 117, 219-239, 2004

Knox JR, Moews PC, Frere JM. Chem Biol. 3, 937-47, 1996

Adediran SA, Zhang Z, Nukaga M, Palzkill T, Pratt RF, Biochemistry 44, 7543-52, 2005

Helfand MS, Bonomo RA., Curr Drug Targets Infect Disord 3, 9-23, 2003. (A review of different types of known beta-lactamases.)

Daiyasu H et al., FEBS Lett 503, 1-6, 2001. (A short review that describes the “connectedness” of metallo-beta-lactamases with other activities.)

Reidhaar-Olson and Sauer, Proteins: Struct Funct Genet 7, 306-316, 1990

Taylor et al., Proc Natl Acad Sci USA 98, 10596-10601, 2001

Cho et al., J Mol Biol 297, 309-319, 2000 (this describes one of the first successes in using mRNA display; Pubmed searches for “mRNA display” will yield many other papers)

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Comment #155230

Posted by Pigwidgeon on January 14, 2007 9:03 PM (e)

‘Ah, a refutation of ID. Hmm… numbers and funny words… lots of them… these are long paragraphs… WHEE! PICTURES! It’s like that scene from Terminator 2! Hey, that one’s got cool colours. More paragraphs… hang on, that’s the end? I missed the ending… ah, so ID is wrong again! Go science!’

Comment #155231

Posted by Pigwidgeon on January 14, 2007 9:05 PM (e)

Perhaps I should add that the above is supposed to reflect on my inability to comprehend the above, rather than any deficiency in the argument. :)

Comment #155233

Posted by Katarina on January 14, 2007 10:11 PM (e)

Oh good, a biologically enlightening post. That’s what I should be doing here:)

Most naturally-occurring enzymes are not isolated activities as Figure 1 would imply. Something like the next illustration (Figure 4) is a better depiction – distinct activities and enzymes are often derived from common structural and sequence themes. This expands the base of the “hill” to include those of the neighboring activities; this may be considerable indeed

Does this mean that if the media included antibiotics besides penicillin, a structure associated with one of those peaks may have chanced to work on them?

Seems there is a parallel with the trouble with “evolving” something in a lab, as noted when we were talking about flagella; That investigators can only test one or two environmental factors at a time, whereas out there in the “real world,” huge populations of bacteria multiply and divide in mixed environments with many selective pressures. Am I off base?

Comment #155235

Posted by Gary Hurd on January 15, 2007 12:13 AM (e)

Very nice. There is a further point that realitic selection space is much larger than the 3D commonly employed for illustrations, and that in realitically high dimensions there are many low curvature, even flat pathways.

Comment #155236

Posted by Ian Musgrave on January 15, 2007 12:40 AM (e)

Katerina wrote:

Does this mean that if the media included antibiotics besides penicillin, a structure associated with one of those peaks may have chanced to work on them?

Yes. Axe only looked at ampicillin resistance (a relative of penicillin). It is entirely possible that other functional beta lactamases activities were conserved, or new ones generated. Mutations can indeed generate novel functions, and if you only look at one function, you may miss the big picture.

If you look at the data of Peimbert M, Segovia L. Evolutionary engineering of a beta-Lactamase activity on a D-Ala D-Ala transpeptidase fold. Protein Eng. 2003 Jan;16(1):27-35, where they mutated the D-Ala D-Ala transpeptidase (one of the family of enzymes from which the beta-lactamases first evolved from) and looked only at ampicilin, you would conclude that those mutations had no effect, while missing out on enormous changes in cefotaxamine resistance (and changes in quite a few other natibiotics as well). Even with related substrates, some showed big changes others little, so without a good panel of beta-lactams to check the function of the crippled enzyme, the functional space represented is under sampled.

Speaking of undersampling, it would have been good to look at the breakdown of common substrates of DD-peptidyl ligases and beta lactamases, such as m-[[(phenylacetyl)-glycyl]oxy]benzoic acid and see what the muations did to these activities. Beta lactamases have kept these activities, despite structural changes which have resulted in losing DD-peptidyl ligase activity, if these activities are kept, then the enzyme is more robust than Axe contends (but to be fair this is harder to monitor in the kinds of experiments Axe did)..

Comment #155242

Posted by gutbag on January 15, 2007 4:27 AM (e)

Arthur Hunt wrote:

…many thanks are due to Douglas Axe, who graciously helped me with early drafts of this essay

Does he accept the criticism of his work?

Comment #155248

Posted by Richard Wein on January 15, 2007 5:23 AM (e)

Correct me if I’m being too simplistic, as I don’t fully understand the biology, but isn’t there a more fundamental problem with this ID argument? Studies like Axe’s only show (at best) that functional proteins are rare in sequence space, not that they are isolated in sequence space. They could well be rare but still connected by paths of functional sequences along which they could evolve. When Meyer infers that the probability of “finding” a functional protein is only 1 in 10^77, he is effectively invoking the old creationist tornado-in-a-junkyard strawman, considering only single-step selection and ignoring cumulative selection.

Moreover, it wouldn’t necessarily matter if areas of functional proteins in a flat sequence space were disconnected. Mutations are not limited to single codons, but can move longer sequences around, possibly bridging gaps between such areas.

Comment #155265

Posted by Katarina on January 15, 2007 8:46 AM (e)

Did Axe just blast the gene with radiation, or selectively knock out base pairs?

Comment #155267

Posted by KC on January 15, 2007 9:25 AM (e)

The argument that Axe’s work supports ID is backward, and reminiscent of Behe’s argument for IC. Behe takes a fully-functional flagellum, and says that because it doesn’t function if you suddenly begin removing a part, it couldn’t have come about (read: evolved) in a Darwinian manner. In a similar way, Axe is taking a sequence that is already susceptible to mutation, and saying that, because it’s difficult to improve function via mutagenesis for that sequence, then RM&NS cannot bring about improved function in general. Neither argument addresses how such a structure or sequence came about, only what happens when one dinks with it once it’s already there.

Comment #155269

Posted by Kim on January 15, 2007 9:28 AM (e)

Ok, we are all falling in one of the basic traps that the ID movement sets, and that is using the unlikeliness of a specific sequence to occur out of the blue as an argument. However, natural selection alters these numbers dramatically.

Comment #155270

Posted by Flint on January 15, 2007 9:59 AM (e)

This presentation still probably requires more knowledge than an interested layman can extract. It sounds to me very much like Axe used an approach used by many researchers (though his specific target may have been different), and that he produced results that fit comfortably within the ranges other researchers have found. Surely all these researchers weren’t constructing their experiments with an eye to showing that natural mechanisms are too improbable to be likely! It doesn’t sound like Axe has constructed his experiments for that purpose either. If Axe’s results are pretty typical, why single him out for ID misrepresentations? Did I misunderstand? It doesn’t sound like Axe himself is misconstruing anything.

If the point here is that ID proponents are carefully drawing invalid conclusions from normal good science, OK. Dog bites man.

Comment #155273

Posted by Katarina on January 15, 2007 11:16 AM (e)

because it’s difficult to improve function via mutagenesis for that sequence, then RM&NS cannot bring about improved function in general. Neither argument addresses how such a structure or sequence came about, only what happens when one dinks with it once it’s already there.

You are right, but the thing is that I don’t even see how an experimental design could provide the NS part in this scenario, and I’m not sure if it can even provide the full range of RMs.

Axe is providing an example with too many restrictions to be meaningful.

Comment #155275

Posted by Russell on January 15, 2007 12:24 PM (e)

If the point here is that ID proponents are carefully drawing invalid conclusions from normal good science, OK. Dog bites man.

True.
But what’s different here is that Axe is claiming that this research supports ID.

Comment #155276

Posted by Katarina on January 15, 2007 12:49 PM (e)

Does he say that? Never mind, who cares what Axe says? It’s what his research supports. And since there’s nothing to support (there’s no positive theory of ID), only something to oppose, does it oppose RM+NS ==> novel function? I don’t know, since Axe is using a microscope to study a whole elephant.

Comment #155279

Posted by Daniel Morgan on January 15, 2007 12:54 PM (e)

Q: How many ID advocates are going to:
i) take the time to read this
ii) understand it if they did (i)
iii) believe it if they did (i) and (ii)
?

A: Zero.

Comment #155280

Posted by Flint on January 15, 2007 1:01 PM (e)

I don’t know, since Axe is using a microscope to study a whole elephant.

But it sounds like every other researcher in this field is doing something essentially similar, and getting essentially similar results. From a layman’s perspective, this seems to be how experimental science learns about elephants anyway - an army of scientists armed with microscopes examine every part of the elephant, and the Big Picture emerges gradually.

Comment #155282

Posted by Katarina on January 15, 2007 1:08 PM (e)

OK, but in the case of Axe’s research, it is being used (whether by him or others) to address a bigger question than it can hope to answer. The other researchers are asking more narrow questions (i.e. how robust is this particular enzyme), as is appropriate for their results. At least I hope so!

Comment #155289

Posted by Flint on January 15, 2007 1:48 PM (e)

Let me ask the question just a little differently. Is Axe doing his research to determine how robust an enzyme is (forget what the ID PR machine does)? Or is Axe attempting to formulate his research methodology in such a way as to obfuscate rather than discover?

It really does sound to me like Axe has done legitimate research, produced useful results entirely in keeping with other research, and presented those results properly in context. Or if he has not, this is not clear to me as a layman from struggling through Arthur Hunt’s essay.

Comment #155290

Posted by Russell on January 15, 2007 2:43 PM (e)

Flint wrote:

It really does sound to me like Axe has done legitimate research, produced useful results entirely in keeping with other research, and presented those results properly in context.

I may not have been paying close enough attention to know; has someone suggested otherwise?

The issue is: does it support ID?
Axe apparently thinks so.
I don’t think so. Art Hunt doesn’t think so.
The Disco Inst doesn’t think.

Comment #155307

Posted by Katarina on January 15, 2007 4:07 PM (e)

From the abstract to the paper cited,

Axe wrote:

Proteins employ a wide variety of folds to perform their biological functions. How are these folds first acquired? An important step toward answering this is to obtain an estimate of the overall prevalence of sequences adopting functional folds.

The broader question he seeks to answer has to do with evolution. The related narrower question he proposes, is whether a wide range of sequences will perform the required function. In Dembki-talk, how specified must the information on the enzyme’s genome be?

His conclusion

Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.

is in line with the findings, but that doesn’t change the fact that he is only looking at one “specific function.”

Comment #155337

Posted by Pete Dunkelberg on January 15, 2007 7:41 PM (e)

Flint, yes Axe is working with the DI although he hasn’t always been in perfect step. See Ed Brayton’s post a couple days back. Also note that Axe is in the Wedge.

Wedge wrote:

Molecular Biology Research Program (Dr. Douglas Axe et al.)

ACTVITIES

(1) Research Fellowship Program (for writing and publishing)

(2) Front line research funding at the “pressure points” (e.g., Daul Chien’s Chengjiang Cambrian Fossil Find in paleontology, and Doug Axe’s research laboratory in molecular biology)

(3) Teacher training

Comment #155412

Posted by Katarina on January 16, 2007 3:41 AM (e)

Wow, I didn’t know he actually supported ID. That gives me pause, but let’s not shy away from getting what his paper is supposed to say, and what it actually says. Is it really left to me to put this in Laymen terms? I’ll try, but someone please smack me if when I get it wrong.

The selective media, as mentioned earlier, could only correspond with one of the multiple peaks from the illustration with multiple peaks.

The other “fly in the ointment” described by A. Hunt is that Axe used a low-function variant to play with, which takes away from the significance of the finding, as illustrated by the hill that is narrow but also very low.

So neither the selective media nor the low-functioning enzyme variant Axe used justify broad conclusions, certainly not that “functional folds require highly extraordinary sequences” in general. What the results do justify is that a low-functioning fold requires extraordinary sequences in order to perform the identical function it performed in the past (i.e. prior to mutation).

An analogy would be changing the shape of a key, which was barely a fit in the first place, and then observing that it doesn’t work very well in the same lock. This observation can be interesting in some contexts, since some enzymes fit really tightly with their substrates and some don’t, and some enzymes’ shapes are more sensitive to mutation than others, (though the poor fit reduces the significance even of these considerations). In the broader context of evolution, it isn’t relevant.

Comment #155766

Posted by RBH on January 17, 2007 2:39 PM (e)

Gary Hurd wrote

Very nice. There is a further point that realitic selection space is much larger than the 3D commonly employed for illustrations, and that in realitically high dimensions there are many low curvature, even flat pathways.

As Sergey Gavrilets has argued with some force. See John Wilkins’ summary.

RBH

Comment #156838

Posted by Arthur Hunt on January 21, 2007 12:14 PM (e)

I thought I should stop by and thank commenters for their ideas. I’ve not much to add to what has been said.

But that’s not to say I’ve nothing to say. Answering a couple of questions/suggestions:

Flint said:

…It doesn’t sound like Axe has constructed his experiments for that purpose either. If Axe’s results are pretty typical, why single him out for ID misrepresentations? Did I misunderstand? It doesn’t sound like Axe himself is misconstruing anything.
If the point here is that ID proponents are carefully drawing invalid conclusions from normal good science, OK. Dog bites man.

I hope my entry doesn’t come across as singling Axe out. I think ID proponents have already singled him out, in a manner of speaking. What I hope I conveyed was that any conclusions to the effect that protein evolution cannot occur that are based on Axe (2004) are not warranted. (Yeah, yeah – dog bites man.)

Later:

Let me ask the question just a little differently. Is Axe doing his research to determine how robust an enzyme is (forget what the ID PR machine does)? Or is Axe attempting to formulate his research methodology in such a way as to obfuscate rather than discover?
It really does sound to me like Axe has done legitimate research, produced useful results entirely in keeping with other research, and presented those results properly in context. Or if he has not, this is not clear to me as a layman from struggling through Arthur Hunt’s essay.

I think you have gotten the gist of my essay. Others might argue (with some justification) that Axe may be angling towards the larger issue; if so, the essay and some of the comments may be viewed as a critical assessment of the broader utility of this approach. In an ideal world, an ID proponent would review the discussion and incorporate the criticisms into a revised and improved theoretical and experimental program.

As far as the complication (raised by several here – thanks to all who have helped articulate the issue) added by the realization that “functional space” is both multidimensional and interconnected beyond the simple illustrations I gave, I can only say I agree.

Once again, thanks to all commenters.

Comment #157380

Posted by sparc on January 24, 2007 9:11 AM (e)

I am not an expert in this field but I think this paper from the latest issue of Current Biology sufficient to convince everybody that Axe’s claims are wrong:
Meier S, Jensen PR, David CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007) Continuous molecular evolution of protein-domain structures by single amino Acid changes. Curr Biol. 17(2):173-178

As stated in an editorial by Todd O. Yeates in the same issue:

Meier et al. [4] weigh in on this question by illuminating an evolutionary transition or ‘‘bridge state’’ between two small protein domains whose folds are Structurally dissimilar. (…) Working with a CRD called NW1 from a different protein (NOWA) of Hydra, they show that their CRD can be converted by single amino acid changes from a structure that resembles the amino-terminal CRD of minicollagen-1 to a structure that resembles the alternative conformation seen in the carboxyterminal CRD of minicollagen-1.

Comment #186475

Posted by carrie on July 7, 2007 2:51 PM (e)

;)Great spirits have always encountered violent opposition from mediocre minds.