An Extrapolation revisited II

The Nylonase Story: How Unusual Is That?
Ann Gauger

Editor’s note: Nylon is a modern synthetic product used in the manufacturing, most familiarly, of ladies’ stockings but also a range of other goods, from rope to parachutes to auto tires. Nylonase is a popular evolutionary icon, brandished by theistic evolutionist Dennis Venema among others. In a series of three posts, of which this is the second, Discovery Institute biologist Ann Gauger takes a closer look.

In an article yesterday, “The Nylonase Story: When Imagination and Facts Collide,” I described how some biologists claim that the enzyme nylonase demonstrates that it is easy to get new functional proteins. It has been proposed that nylonase is the result of a frameshift mutation that produced an entirely new coding sequence from an alternate reading frame. I showed why such a claim is false. Now I will explain what that means and something about the unusual properties of the nylB gene that caught molecular geneticist and evolutionary biologist Susumu Ohno’s attention.

What are alternate reading frames? To answer that question, I first need to provide some background information. I will begin by defining some terms I used in yesterday’s post. DNA is composed of two anti-parallel strands of nucleotides. The order of the nucleotides in each strand is what specifies the information the DNA carries. The two strands, called the sense and antisense strands, run in opposite directions. Even though their sequences are complementary, with A always paired with T, and C with G, each strand carries different potential information.

ATG GCA TGC ACC GGC ATT AG → sense
TAC CGT ACG TGG CCG TAA TC ← antisense

Before the information in DNA can be used, it must be copied into what we call messenger RNA. The sequence of one strand of DNA, usually the sense strand, is copied using the same base complementarity: G pairs with C, and A with U (U is used in place of T in RNA). We call that copying transcription. The message that has been transcribed from the DNA into that sequence of RNA is now ready to be translated into protein.


Notice the language of information shot throughout these processes. The names for these processes were given by men fully committed to a naturalistic worldview, men such as Francis Crick and Sydney Brenner. Indeed, they were materialists one and all. Yet they saw the parallels between these processes and the human manipulation of text (language) or code (another form of language). The genetic code is the framework that determines the relationship between groups of nucleotides (codons), and the amino acids they specify. The code specifies how to translate the messenger RNA that has been copied or transcribed from the DNA, so that it can be translated into a new language, the language of proteins. Below is an illustration of the standard genetic code (source here, used with permission):




Notice that the information in DNA is read in groups of three nucleotides (each group is called a codon), and each codon specifies a particular amino acid. Sometimes more than one codon can specify the same amino acid. For example in the top left corner, the table shows that UUU and UUC both specify the amino acid phenylalanine.

The nature of the code is such that it matters where the first codon begins — the first codon to be read establishes the codon groupings going forward. In the table above the “start” codon is AUG (it also specifies the amino acid methionine). The sequence of codons is “read” by a cellular machine called the ribosome, which starts reading the RNA message at AUG, and then proceeds three nucleotides at a time to translate the message into amino acids. In the sequence below, for example, the first codon to be read would be AUG and that codon determines the frame in which of all the other codons are read.

AUG GCA UGC ACC GGC AUU AGU

Now here’s where it gets interesting. Potentially, DNA can be grouped into different codons, or frames, depending on where the ribosome starts reading. See below for an illustration. For example, the sequence could potentially be read with the groupings shown in frame one (ATG GCA etc.) or frame two (TGG CAT etc., if a proper ATG exists somewhere upstream), leading ultimately to a different amino acid sequences for each. In fact there are six possible ways to group the DNA into codons — three frames on the sense strand going left to right (labeled 1-3), and three frames on the antisense strand (labeled 4-6), going right to left. Below I have laid out the six possible frames for the sequence we began with, but with the alternate frames staggered, and the alternate codons separated by spaces. Notice the sequence stays the same — the only thing that changes from frame to frame is how the nucleotides are grouped. It’s the same sequence, but it could be read and translated differently in each frame. This is because each codon specifies a particular amino acid. Thus, each frame results in a completely different string of amino acids.

frame 1  ATG GCA TGC ACC GGC ATT AG
frame 2   TGG CAT GCA CCG GCA TTA G
frame 3    GGC ATG CAC CGG CAT TAG

frame 4  TAC CGT ACG TGG CCG TAA TC
frame 5   ACC GTA CGT GGC CGT AAT C
frame 6    CCG TAC GTG GCC GTA ATC

The codons TAA, TAG, and TGA are stop codons — they specify where the gene ends and protein translation stops. (For extra credit, can you find any ATG or stop codons in the above frames? They are there in both the forward and reverse direction. For more extra credit, can you use the code table to translate different frames, and demonstrate that each frame encodes a different protein?)

So when Venema and others say that nylonase arose by a frameshift mutation that produced a novel protein 392 amino acids long, they are claiming that a completely new coding sequence with frame-shifted codons could generate a functional protein. How likely is that? Not very, given the rarity of functional proteins in sequence space (see my first post). And, as I have already shown in my first post, such an unlikely hypothesis is unnecessary. The nylB gene appears to be the product of a simple gene duplication followed by two stepwise mutations to increase nylonase activity.

There is something special about the nylonase gene’s sequence though, something very odd. nylB has multiple large, overlapping (alternate) open frames that lack stop codons.

How hard is it to get a gene with multiple reading frames?

Let me explain. Roughly one in twenty codons are stop codons. A random DNA sequence will have stop codons about every sixty bases, and may or may not have a start codon. Usually the alternate frames of DNA sequences are interrupted by stop codons. Only the frame that actually specifies the correct gene will have no stop codons at all over a significant length. This system is actually very ingenious. The one frame that needs to be read and translated is identified by an ATG. The other frames will usually lack an ATG and/or will have several stop codons that interrupt their translation, thus preventing the cell from wasting energy on nonsense transcripts.

According to the nylonase story, as told by Ohno and Venema and numerous others, a new ATG start codon was formed by the insertion of a T between an A and G, thus creating a new start codon after the original ATG, which shifted the reading frame for that sequence to that specified by the new ATG, and creating a completely different coding sequence and thus a new protein. Let us grant that scenario for the sake of argument. Normally such a shift would produce a new coding sequence that would be interrupted by stop codons, so the newly frameshifted protein would be truncated. Thus the only reason this frameshift hypothesis for nylonase is even remotely possible is because the sequence coding for nylonase is most unusual, and contains not one, not two, but three open frames Although frameshift mutations are ordinarily considered to be quite disruptive, at least in this case the putative brand new protein sequence would not terminate early due to stop codons.

My point? The first step to getting a new functional protein of any length from a frameshift is to avoid stop codons. The odds of a random coding sequence having an open alternate frame, without stops, are poor. As a consequence, if a protein does have an open frame in addition to its coding sequence, it’s worth paying attention to. And it so happens that nylonase does have more than one open frame. The DNA sequence above illustrates the six frames, numbering them frames 1 through 6. Using that convention, frames 1 and 3 are read from the sense strand. Both have no stop codons over the length of the gene in the sense direction. Frame 4 on the antisense direction has no stop codons either. Frame 1 is the coding frame that specifies the nylonase protein, otherwise known as the open reading frame (ORF). It is defined by the presence of both a start and stop codon. The other two frames have no start codons or stop codons, so I’ll call them non-stop frames (NSFs). They are frames 3 and 4.

The probability of a DNA sequence with an ORF on the sense strand and 2 NSFs is very small. Just exactly how small are the chances of avoiding a stop codon in three out of six frames? We set out to determine that by performing a numerical simulation using pseudorandom numbers to generate sequences at various levels of GC content. (By we I mean that my husband, Patrick Achey, who is an actuary, did the programming work, while I determined the parameters.) We chose to vary the GC content because sequences with a higher GC content have fewer stop codons. Remember, a stop codon always has an A and a T (TAA, TAG, and TGA are the stop codons) so having a sequence with a lower percentage of AT content will reduce the frequency of stop codons. Conversely, higher GC content makes the chances of avoiding stop codons and getting longer ORFs much greater, thus also increasing the chances of NSFs. The genomes of bacteria vary in their GC content, from less than 20 percent to as much as 75 percent, though the reason why is not known. One species of Flavobacterium has a genome with about 32 percent GC and 2400 genes — the precise values varies with the strain. The plasmid on which nylB resides is very different. It has 65 percent GC content. The gene encoding nylonase has an even higher 70 percent GC content, which is near the observed bacterial maximum of 75 percent.

We chose to use a target ORF size of 900 nucleotides (or 300 amino acids) because it is an average size for a functional protein. Nylonase is 392 amino acids long; the small domain of beta lactamase, the enzyme my colleague Doug Axe studied, is about 150 amino acids long. The median length for an E. coli protein is 278 amino acids; for humans, the median length is 375.

As expected, the simulation showed that the higher the GC content, the greater the likelihood that ORFs that are 900+ nucleotides long exist. At 50 percent GC, the average ORF length we obtained was about 60 nucleotides; most ORFs terminate well before 900 nucleotides. Indeed, in our simulation only two out of a million random sequences made it to 900 nucleotides before encountering a stop codon. As a result, we could not determine the rarity of NSFs at 50 percent GC — we would probably have to run the simulation for more than a billion trials to get any significant number of NSFs at all.

Sequences at 60 percent GC gave 57 ORFs at least 900 nucleotides long out of a million trials, while sequences at 65 percent GC produced 404 out of a million, one of which also had an NSF.

NSFs were much more probable for sequences that were 70 percent GC, like nylB. In our simulation 3,021 out of a million trials were ORFs at least 900 nucleotides long. That’s a frequency of .3 percent. Of those 3,021 ORFs, 86 had 1 NSF, and none had 2 NSFs. We had to run 10 million trials at 70 percent GC to see any ORFs with 2 NSFs. From those 10 million randomly generated sequences, we obtained 28,603 ORFs; 903 had 1 NSF and only 9 had 2 NSFs.

Interestingly, at 80 percent GC we got a few sequences with 4 NSFs; but I don’t know of any bacterium with a GC content that high.

Our simulation shows that multiple NSFs are very rare. The probability that an ORF 900 nucleotides long with 70 percent GC content will have two NSFs is 9 out of 28,603, or 0.0003. If these figures are recast to include the total number of trials required to get an ORF of that length and GC content and with 2 NSFs, the probability would be 9 out of 10,000,000 trials.

A sequence like nylB is very rare. In fact, I suspect that for all cases where overlapping genes exist, in other words where alternate frames from the same sequence have the potential to code for different proteins, unusual sequence will necessarily be found. Likely it will be high in GC content. Could such rare sequences be accidental? I think that if we compare the expected number of alternate or overlapping NSFs per ORF, with the actual number we will find that there are more of these alternate open reading frames than would be predicted by chance.

From another study of overlapping genes:

Thus, bacterial genomes contain a larger number of long shadow ORFs [ORFs on alternate frames] than expected based on statistical analysis. Random mutational drift would have eliminated the signal long ago, if no selection pressures were stabilizing shadow ORFs. Deviations between the statistical model and bacterial genomes directly call for a functional explanation, since selection is the only force known to stabilize the depletion of stop codons. Most shadow genes have escaped discovery, as they are dismissed as false positives in most genome annotation programs. This is in sharp contrast to many embedded overlapping genes that have been discovered in bacteriophages. Since phages reside in a long term evolutionary equilibrium with the bacterial host genome, we suggest that overlooked shadow genes also exist in bacterial genomes.
Indeed, a study of the pOAD2 plasmid from which nylB came indicates that there are potentially many overlapping genes on that plasmid. nylB′, for example, a homologous gene on the same plasmid that differs by 47 amino acids from nylB, also has 2 NSFs. These unusual and unexpected features of DNA have consequences for how we think about the origin of information in DNA sequences, as I shall discuss in the next post.

An extrapolation revisited.

The Nylonase Story: When Imagination and Facts Collide
Ann Gauger

Editor’s note: Nylon is a modern synthetic product used in the manufacturing, most familiarly, of ladies’ stockings but also a range of other goods, from rope to parachutes to auto tires. Nylonase is a popular evolutionary icon, brandished by theistic evolutionist Dennis Venema among others. In a series of three posts, Discovery Institute biologist Ann Gauger takes a closer look.

A significant problem for the neo-Darwinian story is the origin of new biological information. Clearly, information has increased over the course of life’s history — new life forms appeared, requiring new genes, proteins, and other functional information. The question is — how did it happen? This is the central question concerning the origin of living things.

Stephen Meyer and Douglas Axe have made this strong claim:

[T]he neo-Darwinian mechanism — with its reliance on a random mutational search to generate novel gene sequences — is not an adequate mechanism to produce the information necessary for even a single new protein fold, let alone a novel animal form, in available evolutionary deep time.
Their claim is based on the experimental finding  by Doug Axe that functional protein folds are exceedingly rare, on the order on 1 in 10 to the 77th power, meaning that all the creatures of the Earth searching for the age of the Earth by random mutation could not find even one medium-size protein fold.

In contrast, Dennis Venema, professor of biology at Trinity Western University, claims in his book Adam and the Genome and in posts at the BioLogos website that getting new information is not hard. In his book, he presents several examples he thinks demonstrate the appearance of new information — the apparent evolution of new protein binding sites, for example. But the best way to reveal Axe and Meyer’s folly, he thinks, (and says so in his book and  a post at BioLogos) would be to show that a genuinely “new” protein can evolve.

…[E]ven more convincing… would be an actual example of a functional protein coming into existence from scratch — catching a novel protein forming “in the act” as it were. We know of such an example — the formation of an enzyme that breaks down a man-made chemical.

In the 1970s, scientists made a surprising discovery: a bacterium that can digest nylon, a synthetic chemical not found in nature. These bacteria were living in the wastewater ponds of chemical factories, and they were able to use nylon as their only source of food. Nylon, however, was only about 40 years old at the time — how had these bacteria adapted to this novel chemical in their environment so quickly? Intrigued, the scientists investigated. What they discovered was that the bacteria had an enzyme (which they called “nylonase”) that effectively digested the chemical. This enzyme, interestingly, arose from scratch as an insertion mutation into the coding sequence of another gene. This insertion simultaneously formed a “stop” codon early in the original gene (a codon that tells the ribosome to stop adding amino acids to a protein) and formed a brand new “start” codon in a different reading frame. The new reading frame ran for 392 amino acids before the first “stop” codon, producing a large, novel protein. As in our example above, this new protein was based on different codons due to the frameshift. It was truly “de novo” — a new sequence.
Venema is right. If the nylonase enzyme did evolve from a frameshifted protein, it would genuinely be a demonstration that new proteins are easy to evolve. It would be proof positive that intelligent design advocates are wrong, that it’s not hard to get a new protein from random sequence. But the story bears reexamining. Is the new protein really the product of a frameshift, or did it pre-exist the introduction of nylon into the environment? What exactly do we know about this enzyme? Does the evidence substantiate the claims of Venema and others, or does it lead to other conclusions?

First, some history. In the 1970s Japanese scientists discovered that certain bacteria had developed the ability to degrade the synthetic polymer nylon. Okada et al. identified three enzymes responsible for nylon degradation, and named them EI, EII, and EIII. The genes that encoded them were named nylA, nylB, and nylC. They sequenced the plasmid on which the genes were found, and discovered that there was another gene on the same plasmid that was very similar to nylB; they named it nylB′. (We will focus on the story of nylB and nylB′ because they are the ones relevant to Venema’s story.)

So far all I have given you are the facts. Now here’s the interpretation of these facts. Some claimed that the nylonase enzyme, as it was called, had originated some time after people began making nylon (in the 1930s). That seemed plausible because nylonase was unable to degrade naturally occurring amide bonds — it could degrade only the amide bonds in nylon — and so had not existed previously, it was thought. The popular conclusion was that the nylonase activity evolved in response to the presence of nylon in the environment, and thus was only forty years old. And here’s the big interpretive leap: it must not be hard to get new enzymes if a new one can evolve within a period of forty years.

Okada et al. had sequenced the genes encoding nylB and nylB′. They concluded that the nylonase activity was the result of a gene duplication followed by several mutations to the nylB gene. But at this point Susumu Ohno, an eminent molecular geneticist and evolutionary biologist, noticed something unusual about the nylB gene sequence (Ohno, 1984). Ohno had a theory that DNA with repeats of the right kind had the potential to code for protein in multiple frames, with no interrupting stop codons, and might thus be a source for “new” proteins. (If you are unfamiliar with the terms I just used, I invite you to take a look at my post tomorrow, where I will explain the necessary concepts. For those already familiar, I present some relevant data concerning the rarity of sequences that can be frameshifted.)

Ohno noticed that nylB, the gene for nylonase, might originally have encoded something else if a certain T was removed. The nylonase gene as it exists now has 1179 bases, which encode a 392 amino acid protein. Without a particular T embedded in the ATG start codon, though, the sequence would have specified a hypothetical original gene with a longer open reading frame (ORF) of 427 amino acids, in a different frame. Thus, Ohno proposed a “new” protein with a new function acting on a new substrate was born when a T inserted in between a particular A and G in the DNA, making a new ATG start codon and shifting the frame to code for a new protein, the protein we now call nylonase.

Ingenious. According to Ohno, nylonase could be a new enzyme, appearing suddenly with no known precursors via a sudden frameshift. (Note that all of this assumes that new protein folds are easy to get.) Ohno published this hypothesis in the Proceedings of the National Academy of Sciences. It was a hypothesis only, however, as a careful reading of his paper shows. One heading, for example:

R-IIA Coding Sequence [nylB] for 6-AHA LOH [nylonase] Embodies an Alternative, Longer Open Reading Frame That Might Have Been the Original Coding Sequence [Emphasis added.]
and the text says:

I suggest that the RS-IIA base sequence [nylB] was originally a coding sequence for an arginine-rich polypeptide chain 427 or so residues long in its length and that the coding sequence for one of the two isozymic forms of 6-ALA LOH [nylonase] arose from its alternative open reading frame. [Emphasis added.]
Ohno presented arguments for why his suggestion was plausible, but did not provide evidence that the “original” gene ever existed or was used (in fact he says it was unlikely to be useful based on its amino acid composition), or that the insertion ever happened. Nonetheless, the frame-shift hypothesis for the origin of nylonase has been widely proclaimed as fact (though, notably, not by Okada et al. who have done most of the work).

If the nylonase story as told above were true, namely that a frameshift mutation resulted in the de novo generation of a new protein fold with a new function, it would indeed constitute a substantial refutation to Meyer and Axe’s claim. If a frame-shift mutation can produce a random new open reading frame in real, observable time, and give rise to a new functional enzyme, then it must not be that hard to make new functional protein folds. In other words, functional protein folds must not be rare in sequence space. And therefore Stephen Meyer’s arguments about the difficulty of getting enough new biological information to generate a new fold must be wrong as well. Venema flatly asserts:

If de novo protein-coding genes such as nylonase can come into being from scratch, as it were, then it is demonstrably the case that new protein folds can be formed by evolutionary mechanisms without difficulty….[I]f Meyer had understood de novo gene formation — as we have seen, he mistakenly thought it was an unexplained process — he would have known that new protein folds could indeed be easily developed by evolutionary processes.
Slam dunk, right?

A little caution in accepting this story without hard evidence would be wise. In genetics we are taught that frame-shift mutations are extremely disruptive, completely changing the coding sequence and resulting in truncated nonsense. In fact, one term for a frameshift mutation is “nonsense mutation.” A biologist’s basic intuition should be that frameshifts are highly unlikely to produce something useful. The only reasons for the widespread acceptance of Ohno’s hypothesis that I can come up with are the unusual character of the sequence itself, Ohno reputation as a brilliant scientist (which he was), and wish-fulfillment on the part of some evolutionary biologists.

Fortunately, science marches on, and evidence continues to accumulate. The same group of Japanese scientists continued their study of the nylonase genes. nylB appeared to be the result of a gene duplication of nylB′ that occurred some time ago. EII′ (the enzyme encoded by nylB′) had very little nylonase activity, while EII (the enzyme encoded by nylB) was about 1000 fold higher in activity. The two enzymes differed in amino acid sequence at 47 positions out of 392. With some painstaking work, the Japanese determined that just two mutations were sufficient to convert EII′ to the EII level of activity.

They then obtained the three-dimensional structure of an EII-EII′ hybrid protein. And with those results everything changed — or should have.

Here’s what Venema takes from the paper and interprets the evidence:

…the three-dimensional structure of the protein has been solved using X-ray crystallography, a method that gives us the precise shape of the protein at high resolution. Nylonase is chock full of protein folds— exactly the sort of folds Meyer claims must be the result of design because evolution could not have produced them even with all the time since the origin of life. [Emphasis added.]
Unfortunately, Venema doesn’t have the story straight. Nylonase has a particular fold, a particular three-dimensional, stable shape. Most proteins have a distinct fold — there are several thousand kinds of folds known so far, each with a distinct topology and structure. Folds are typically made up of small secondary structures called alpha helices and beta strands, which help to assemble the tertiary structure — the fold as a whole. Venema seems unclear about what a protein fold is, and the distinction between secondary and tertiary structures. Nylonase is not “chock full of folds.” No structural biologist would describe nylonase as “chock full of protein folds.” Indeed, no protein is “chock full of folds.” Perhaps Venema was referring to the smaller units of secondary structure I mentioned above, the alpha helices or beta strands. But it would appear he doesn’t know what a protein fold is.

Maybe that explains why Venema missed the essential point of the paper describing nylonase’s structure. The crystal structure of EII-EII’ (a nylonase hybrid necessary to be able to crystalize the protein) revealed that it is not a new kind of fold, but a member of the beta-lactamase fold family. More specifically, it resembles carboxylesterases, a subgrouping of that family. In addition, when the scientists checked EII′ and EII, they found that both enzymes had previously undetected carboxylesterase activity. In other words, the EII’ and EII enzymes were carboxylesterases. If it looks like a duck and quacks like a duck, it is a duck.

Thus, EII′ and EII did not have frameshifted new folds. They had pre-existing folds with activity characteristic of their fold type. There was no brand-new protein. No novel protein fold had emerged. And no frameshift mutation was required to produce nylonase.

Where did the nylon-eating ability come from? Carboxylesterases are enzymes with broad substrate specificities; they can carry out a variety of reactions. Their binding pocket is large and can accommodate a lot of different substrates. They are “promiscuous” enzymes, in other words. Furthermore, the carboxylesterase reaction hydrolyzes a chemical bond similar to the one hydrolyzed by nylonase. Tests revealed that both the EII and EII′ enzymes have carboxylesterase and nylonase activity. They can hydrolyze both substrates. In fact it is possible both had carboxylesterase activity and a low level of nylonase activity from the beginning, even before the appearance of nylon.

nylB′ may be the original gene from which nylB came. Apparently there was a gene duplication at some point in the past. The two genes appear to have acquired mutations since then — they differ by 47 amino acids out of 392. The time of that duplication is unknown, but not recent, because it takes time to accumulate that many mutations. However, at least some of those mutations must confer a high level of nylonase activity on EII, the enzyme made by nylB. The enzyme EII’ made by nylB’ has only a low ability to degrade nylon, while EII degrades nylon 1000 fold better. So one or more of those 47 amino acid differences must be the cause of the high level of nylonase activity in EII. Through careful work, the Japanese workers Kato et al. identified which amino acid changes were responsible for the increased nylonase activity. Just two step-wise mutations present in EII, when introduced into EII’, could convert the weak enzyme EII’ to full nylonase activity.

From Kato et al. (1991):

Our studies demonstrated that among the 47 amino acids altered between the EII and EII’ proteins, a single amino acid substitution at position 181 was essential for the activity of 6-aminohexanoate-dimer hydrolase [nylonase] and substitution at position 266 enhanced the effect.
So. This is not the story of a highly improbable frame-shift producing a new functional enzyme. This is the story of a pre-existing enzyme with a low level of promiscuous nylonase activity, which improved its activity toward nylon by first one, then another selectable mutation. In other words this is a completely plausible case of gene duplication, mutation, and selection operating on a pre-existing enzyme to improve a pre-existing low-level activity, exactly the kind of event that Meyer and Axe specifically acknowledge as a possibility, given the time and probabilistic resources available. Indeed, the origin of nylonase actually provides a nice example of the optimization of a pre-existing fold’s function, not the innovation or creation of a novel fold.

As the scientists who carried out the structural determination for nylonase themselves note:

Here, we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the nylon oligomer hydrolase. [Emphasis added.]
Let’s put to bed the fable that the nylon oligomer hydrolase EII, colloquially known as nylonase, arose by a frame-shift mutation, leading to the creation of a new functional protein fold. There is absolutely no need to postulate such a highly improbable event, and no justification for making this extravagant claim. Instead, there is a much more parsimonious explanation — that nylonase arose by a gene duplication event some time in the past, followed by a series of two mutations occurring after the introduction of nylon into the environment, which increased the nylon oligomer hydrolase activity of the nylB gene product to current levels. Could this series of events happen in forty years? Most certainly. Probably in much less time. In fact, it has been reported to happen in the lab under the right selective conditions. And most definitely, the evolution of nylonase does not call for the creation of a novel protein fold, nor did one arise. EII’s fold is part of the carboxylesterase fold family. Carboxylesterases serve many functions and have been around much longer than forty years.


Douglas Axe and Stephen Meyer readily admit that this kind of evolutionary adaptation happens easily. A protein that already has a low level of activity for a particular substrate can be mutated to favor that side reaction over its original one, often in just a few steps. There are many cases of this in the literature. What Axe and Meyer do claim is that generating an entirely new protein fold via mutation and selection is implausible in the extreme. Nothing in the nylonase story that Dennis Venema tells shows otherwise.

Why attempting to design the undesignable remains a fools errand.

Why Evolution Simulations Fail: Author of Evolutionary Informatics Book Explains
Evolution News | @DiscoveryCSC

f you search for the phrase “evolution simulation” in Google, you’ll get many hits. Come to think of it, computer evolution simulations are an evolutionary icon. What of them? Do they falsify the claims of intelligent design theory?On a new episode of ID the Future, Ray Bohlin takes up the issue with Dr. Winston Ewert, co-author with William Dembski and Robert Marks II of a new book,  An Introduction to Evolutionary Informatics.

Ewert argues that Richard Dawkins’s “Methinks It Is Like a Weasel” simulation doesn’t prove biological evolution and isn’t even very interesting. Ewert says there are some interesting computer evolution simulations, but he explains that they fail to model anything biologically realistic.

Instead they set up a straw man version of intelligent design, and simultaneously sneak teleology in, which kind of defeats the purpose.  Download the podcast here, or listen to it here .

Dr. Ewert’s book is getting raves from some impressive scientists, including star mathematician Gregory Chaitin, author of Proving Darwin: Making Biology Mathematical. He calls the book, “An honest attempt to discuss what few people seem to realize is an important problem.”

Speaking of Chaitin, says Dr. Bijan Nemati of the Jet Propulsion Laboratory and Caltech:

With penetrating brilliance, and with a masterful exercise of pedagogy and wit, the authors take on Chaitin’s challenge, that Darwin’s theory should be subjectable to a mathematical assessment and either pass or fail. Surveying over seven decades of development in algorithmics and information theory, they make a compelling case that it fails.
Congratulations, Dr. Ewert, Dr. Marks, and Dr. Dembski! Get your copy now.