Intelligent Design and Nylon-Eating Bacteria

| By on Letters to the Duchess

During World War II, nylon stockings were recycled into parachutes for U.S. pilots and paratroopers. Photo c. 1942. Source: Wikipedia

Intelligent Design and Nylon-Eating Bacteria

Like many of our readers, I watched the recent debate between Intelligent Design advocate Stephen Meyer, atheist Lawrence Krauss, and evolutionary creationist Denis Lamoureux. Meyer struggled (admirably) through an intense migraine to make his case – one I am quite familiar with, since I have read Meyer carefully over the years. Recently, I have been working through portions of Meyer’s book Darwin’s Doubt – specifically, the sections where he makes his case for the claim that evolution cannot produce enough information to make a new protein fold. Meyer also used this argument during the debate, and has reiterated it in a post-debate follow-up post. Given the importance of this argument for Meyer, and its recent use in a public forum, it seems worthwhile to me to discuss what I see as the problems with this claim. Put simply, I think there is good evidence that evolution is not hindered in the way Meyer thinks it is – but it will take some effort to understand why.

Understanding proteins

Many of the functions of cells are performed by proteins, which are sequences of amino acids that fold up into stable three-dimensional shapes. The sequence of amino acids for a given protein is what determines its shape, and the correct sequence of amino acids is determined, in turn, by the DNA sequence that makes up the gene that codes for it. This “code” is read off in sets of three DNA “letters” at a time. For example, the DNA sequence “ATG” specifies the amino acid methionine, the sequence “CCC” specifies the amino acid proline, and the the sequence “GGA” specifies the amino acid glycine (these groupings of three DNA letters that code for amino acids are called “codons”). The DNA sequence “ATG CCC GGA CCC ATG ATG” thus would specify the following short sequence of amino acids: Methionine-Proline-Glycine-Proline-Methionine-Methionine. This sequence would be constructed by the ribosome, the enzyme that uses a single-stranded RNA copy of the gene as a template for adding amino acids in the correct order to the growing protein as it is being made.

In order for ribosomes to do their job correctly, they need to operate in what is called the correct “reading frame”. For the above sequence, this means starting with the first “ATG” codon, and then proceeding to read “CCC”, and so on. If an insertion mutation of one DNA letter were to occur, this would shift the ribosome into an incorrect reading frame. For example, let's consider what would happen if an “A” were inserted as follows:

ATG A CCC GGA CCC ATG ATG   →   ATG ACC CGG ACC CAT GAT G   

In this case, the ribosome would not “know” that a DNA letter had been added, and would still attempt to construct the protein by reading off codons in sets of three letters each. The protein would still start with methionine, but thereafter all the codons are different (and so too are the amino acids). The new reading frame has produced a protein that bears no resemblance to the original one – it’s a new amino acid sequence.

The relevance of this type of mutation will soon become obvious – but let’s return to Meyer’s argument to better understand the claim he is making.

The rarity of protein folds

Meyer’s claim is relatively straightforward. In order for proteins to function, they need to fold up into stable shapes – “protein folds”. Meyer claims, based on the work of his colleague Douglas Axe, that stable protein folds are vanishingly rare – on the order of only one in 10 to the 77th power. As such, Meyer argues, evolution cannot find the needle (a functional protein) in the haystack (the vast number of functionless possibilities). So, the argument goes, when we see information for correctly folded proteins, we can infer that information was designed (in the sense that it did not arise through what we would perceive as a “natural” process):

In any case, the need for random mutations to generate novel base or amino-acid sequences before natural selection can play a role means that precise quantitative measures of the rarity of genes and proteins within the sequence space of possibilities are highly relevant to assessing the alleged power of mutation-selection mechanism. Indeed, such empirically derived measures of rarity are highly relevant to assessing the alleged plausibility of the mutation-selection mechanism as a means of producing the genetic information necessary to generating a novel protein fold. Moreover, given the empirically based estimates of the rarity (conservatively estimated by Axe at 1 in 1077 and within a similar range by others) the analysis that I presented in Toronto does pose a formidable challenge to those who claim the mutation-natural selection mechanism provides an adequate means for the generation of novel genetic information -- at least, again, in amounts sufficient to generate novel protein folds…

It follows that the 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.

All of this hinges, of course, on just how accurate Axe’s estimate is: are functional proteins really that rare? There are good reasons not to think so. Axe only tested one type of protein in his experiment, so his estimate only applies to the frequency of sequences that can do one particular function. There are other reasons to doubt his estimate as the one true estimate of the prevalence of all functional proteins, and I have commented (PDF) on these caveats elsewhere (as have others). Yet even more convincing, however,  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.

Enter Nylonase

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.

And here’s the kicker: this brand-new protein folded into a stable shape, and acted as a weak nylonase. Later duplications, mutations and selection would make a very efficient nylonase from this starting point. Additionally, 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.

Put another way, if only one in 10 to the 77th proteins are functional, there should be no way that this sort of thing could happen in billions and billions of years, let alone 40. Either this was a stupendous fluke (and stupendous isn’t nearly strong enough of a word), or evolution is in fact capable of generating the information required to form new protein folds.

And if this can happen in 40 years, what might millions of years of evolution produce?

Notes

Citations

MLA

Venema, Dennis. "Intelligent Design and Nylon-Eating Bacteria"
http://biologos.org/. N.p., 7 Apr. 2016. Web. 25 June 2017.

APA

Venema, D. (2016, April 7). Intelligent Design and Nylon-Eating Bacteria
Retrieved June 25, 2017, from http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/intelligent-design-and-nylon-eating-bacteria

References & Credits

For further reading

Ohno, S. (1984).  Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence. Proc Natl Acad Sci USA 81(8): 2421–2425.

Negoro, S., Ohki, T.  Shibata, N.,  Mizuno, N., Wakitan, Y., Tsurukame, J., Matsumoto, K., Takeo, M., and Higuchi, Y. (2005). X-ray Crystallographic Analysis of 6-Aminohexanoate-Dimer Hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme. Journal of Biological Chemistry 47; 39644-39652.

McKnight, S. and Venema, D. Adam and the Genome: Reading Scripture After Genetic Science. Brazos (forthcoming January 2017). In one of my chapters (“What about Intelligent Design?”) I examine ID arguments in depth in light of evolutionary evidence.

About the Author

Dennis Venema

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia and Fellow of Biology for BioLogos. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. 

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