Nylon has only been around for about 40 years. Did the bacteria just happen to evolve their eating habits during that period or is the story more complex? Is design a better explanation? You can comment on the story here at UD (though not at ENV).
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? More.
You may also wish to look at Parts II and III from Gauger:
Part II The Nylonase Story: How Unusual Is That?
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.
Part III The Nylonase Story: The Information Enigma
The problem is that there can be multiple competing causes that explain the observed effects. The only way to strengthen the argument is to rule out all other competing causes. And design is a particularly strong competing hypothesis. We know design is a cause capable of producing the effect in question, namely the generation of new functional proteins by the addition of frame-shifted code. In fact, given what we know about the rarity of functional proteins in sequence space, as demonstrated experimentally here, here, and here, and theoretically here, design is a better explanation than the neo-Darwinian one.
Until someone demonstrates experimentally, in real time, that a frameshift mutation can generate a new functional protein (not just a loss of function) by undirected processes, the inference that it is easy to do so is unjustified. And nylonase is not that demonstration.
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Information drives the development of life. But what is the source of that information? Could it have been produced by an unguided Darwinian process? Or did it require intelligent design? The Information Enigma is a fascinating 21-minute documentary that probes the mystery of biological information, the challenge it poses to orthodox Darwinian theory, and the reason it points to intelligent design. The video features molecular biologist Douglas Axe and Stephen Meyer, author of the books Signature in the Cell and Darwin’s Doubt.