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Do nylon-eating bacteria show that new functional information is easy to evolve?


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).

From Ann Gauger of the BioLogic Institute at Evolution News & Views:

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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Dr. Gauger, Here is another link for people associated with Brosius https://campus.uni-muenster.de/en/zmbe/the-institutes/inst-of-exp-pathology/research-group-pd-dr-juergen-schmitz/publications/list-of-publications/ It seems my ideas have been discussed by researchers and thank you for the book section by Nelson and Buggy. So now in the future I can point to this review. The book section by Nelson and Buggy did not mention Brosius or his colleagues in their references. It seems that their work would be relevant in the study of TRG's. But as the book section says their ideas would probably only account for a small number of new proteins. The Nelson and Buggy section will challenge my understanding. Thanks for the reference. jerry
Caleb @9 An excellent informative read. Thank you very much.
Gauger: It boils down to this. Do we say that frameshifted functional proteins are easy to generate, because after all, they exist? Or do we acknowledge that such proteins are not easy to generate and so may be evidence for design?
The last sentence represents the reasonable option. The prior naturalistic option does not make any sense. As you have argued thoughtfully and convincingly, there is no naturalistic explanation for a non-functional sequence with alternate frames that stays open. Given random mutations and neutral evolution, the absence of stop codons is simply unexplainable. Therefore, this absence points to design. I would like to highlight this “…. easy to generate, because after all, they exist”. With this, if I am not mistaken, you exemplify a typical line of thinking of our naturalistic friends. You do something very similar here:
But it’s not outside the realm of possibility that such sequences should exist by pure chance somewhere. After all, nylB does.
“After all, nylB does”. Sigh. That’s how they "argue" right? It must be possible by pure chance because nylB exists ... Another example would be: Can life arise from inanimate matter? Well, we are here, are we not? The mistake is of course the uncritical assumption of the truth of naturalism. Origenes
It would be an enormous amount of work to do what you propose. But the work is already under way. https://www.researchgate.net/profile/Richard_Buggs/publication/304039133_Next-generation_apomorphy_the_ubiquity_of_taxonomically_restricted_genes/links/57643bab08ae421c44830c91.pdf caleb
Dr. Gauger, I read the arguments for the rarity of new proteins and I am not qualified to evaluate the research that calculates the actual level of that rarity. However, after reading Brosius's arguments a few years ago I thought of an approach for testing whether his approach has merit. I assume they don't. His assumptions require that new proteins will have left forensic evidence of the trail leading up to the new protein, not in the species with the new unique protein but in related species from which it separated. Here is a rough description of a research approach that I believe would answer Brosius and put to rest that there is enough resources and time to create many new proteins let alone all the different proteins that we see.
There is a potential research process that could answer once and for all whether coding sequences for proteins arose naturally or not. I assume current technology with a lot of computer time, money and researchers could solve it. Take a family with a large number of species in it and just concentrate on it. For simplicity, I will take bovidae which has 143 living species. First a data base of proteins for this family should be developed and then find out the percentage that is common to all species. Then a list could be made of the remaining proteins and related coding sequences and how they are distributed among each species. A list of proteins and coding sequences that are unique to each species could be made. This is simplistic because protein combinations could be what distinguishes a species from another species and not just one or two unique proteins. My guess that each species should have some unique coding sequence or group of coding sequences or else why is it a separate species. For each of these species, there should be some indication of how each unique coding sequence arose. It should have sequence counterparts in similar species that are close but do not code for a protein. In other words there should be very similar but non-coding sequences in closely related species. (using Brosius' thesis, the sequences have not been exapted into a coding sequence into some species while in others they have) The non-coding sequences could be found by some computer analysis that should be able to identify them as similar to coding sequences in related species. Then one could examine the mutations that would be necessary to have converted the non-coding sequence into a coding sequence. It may also be that the non-coding sequences were once coding sequences but mutations eliminated them as such. One possibility that should be investigated is that the difference between species may be due to loss of coding sequences and their associated proteins. In other words there has been devolution or a narrowing of the gene pool for some species within the family. From this process there should emerge a list of unique coding sequences that either could not have come from a series of mutations of a previous coding sequence or the pathway to the coding sequence should be able to be identified. For those coding sequences that have no evolutionary pathway, the evolutionary biologist would have to explain their origin. I use Brosius' ideas as an accepted way that could explain new proteins. If his approach fails then that is one more nail in the coffin of naturalistic evolution. This is a simple framework for a type of analysis that could isolate unique coding sequences and their associated proteins and then look for how they arose. My guess is that there wouldn’t be too many unique coding sequences in a family and then one would have to look at families from the next level up which in Wikipedia is called an infraorder. Nothing special about bovidae, just that it may be a manageable group. And this process would begin to isolate really unique proteins that have no coding sequences or non-coding sequences anywhere else.
I have offered this up a few times here but no one would respond so I thought you might. I hope it is clear what I am proposing. I am sure there are a lot of issues that have not been considered and wanted to get someone who works in the field to comment. Logically, it should work but I have no idea how practical it would be to gather the required information. Maybe too hard. jerry
I think he gets it, Origenes. What did you think of part 3? caleb
Jerry @7 Jerry
Yes, I read all three articles.
So, how can you say that Gauger says that the enzyme arose by a frameshift?
Jerry: Dr. Gauger responded to my comments and her reply is above.
Indeed. And again, just like in the article, Ann Gauger tells you that she argues against Venema's frameshift hypothesis.
Ann Gauger #4: “By scratch” from Venema means that the frameshift (putative) caused a whole new coding sequence that produced a whole new amino acid chain, never having been subject to selection, presumably. I am arguing precisely against this position. The enzyme already existed, and by just two mutations, developed the ability to hydrolyze nylon byproducts. The enzyme is NOT from scratch.
Did you even read Gauger’s article Jerry?
Yes, I read all three articles. Dr. Gauger responded to my comments and her reply is above. jerry
Jerry @3
Venema: This enzyme, interestingly, arose from scratch ...
Jerry: No it didn’t unless I misunderstand what Ann is saying. It arose from a frame shift which is what the three articles are about.
Did you even read Gauger's article Jerry? If so, how can you make this claim? Ann Gauger explicitly denies that the enzyme arose from a frameshift. First Gauger explains that if the enzyme arose from a frameshift intelligent design advocates would be wrong:
Gauger: 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.
Then after providing and explaining the evidence she writes:
Gauger: 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.
She goes on arguing that instead of by a frameshift
... nylonase arose by a gene duplication event some time in the past, followed by a series of two mutations ...
How could she have been any more clear on this point? Origenes
Dr. Gauger, I assume that caleb and you are the same. First, I have no formal background in micro biology or evolutionary biology but have been reading about it for over 20 years. So my knowledge is restricted in many ways but I have read quite a lot, less so in recent years. I used to comment here frequently and only by chance saw this thread as it is a cold rainy day here in New York. Let me provide a couple of links for Jurgen Brosius. The first time I heard about him was in a 2005 journal edition of Paleobiolgy dedicated to Stephen Gould.
Paleobiology - March 2005; 31 (2 Suppl)
Allan MacNeill who commented here mentioned a book by Vrba and Eldredge titled
Macroevolution: Diversity, Disparity, Contingency: Essays in Honor of Stephen Jay Gould (Laws of Life Symposia Series)
This book is nothing more than a reprint of this journal edition. Brosius was given the honor of writing the initial article for the journal. He had co authored some articles with Gould. His article is entitled
"Disparity, adaptation, exaptation, bookkeeping, and contingency at the genome level"
Given that the journal edition is about Gould, the Brosius article is about the basis for punctuated equilibrium. Or as I remember, non coding sequences mutating away till they are exapted and made into coding sequences. Some links for him at his university in Germany https://campus.uni-muenster.de/en/zmbe/the-institutes/inst-of-exp-pathology/ and https://campus.uni-muenster.de/en/zmbe/the-institutes/inst-of-exp-pathology/publications/ I have a pdf of his Paleobiology article if you cannot access the journal. He is quite a strident atheist. I have some thoughts that I developed over the years on a research process that would solve the problem of protein origin. Given that I am not a biologist but do have a background in science, I would be interested in your feedback if you have time. jerry
Hi Jerry, Thanks for your comments. Let me try to clarify a few points, as I see that a number of people have misread the article (my fault). 1. "This enzyme, interestingly, arose from scratch." That's Venema's position, not mine. "By scratch" from Venema means that the frameshift (putative) caused a whole new coding sequence that produced a whole new amino acid chain, never having been subject to selection, presumably. I am arguing precisely against this position. The enzyme already existed, and by just two mutations, developed the ability to hydrolyze nylon byproducts. The enzyme is NOT from scratch. 2. The expectation among protein scientists and biochemists has been until recently that random sequence is unlikely to make a functional fold. This, despite efforts to create such things by screening libraries of random sequences (This is fodder for another post.) Protein engineers who work at trying to create new activities for existing proteins, or new proteins themselves, know how hard this is, even using all the resources they can bring to bear. In fact, according to Doug Axe it is extremely unlikely to make a functional fold by chance. 1 in 10^77 unlikely. So if an enzyme like nylonase DID arise from frameshift, creating a new functional fold out of random sequence, that would argue that Axe is wrong. Striking it lucky at those odds would seem to disprove the correctness of the odds. But once again, to be clear, the whole point of my article is that it DIDN'T happen by frameshift, no novel functional fold was created etc. 3. Third quibble: see #2. If you could provide the reference for Brosius I would appreciate it. My take is that any novel proteins that can be demonstrated to have arisen "naturally" in the past will either have an origin like nylonase's, or would be better explained as evidence of design. See the third part of the argument. I intend to go into this more in another post. caleb
There are some logical and technical issues that do not have any relevance to the overall argument. This is a very instructive set of articles First Quibble
This enzyme, interestingly, arose from scratch
No it didn't unless I misunderstand what Ann is saying. It arose from a frame shift which is what the three articles are about. Rising from scratch would be a sequence that arose from some Junk DNA for example by a series of mutations over the eons. There are researchers who claim that random mutational processes are the origin of numerous proteins. See Jurgen Brosius and his work. Frameshifting is different. It would be the last step in a long process that produced a non functioning coding sequence and turned it into a functional one. Second Quibble
Venema is right. If the nylonase enzyme did evolve from a frame shifted 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.
There are a couple problems with this. First, Venema is not right if the nylonase enzyme did evolve from a frame shift that new proteins are easy to evolve. All this demonstrates is that on rare occasions something does happen. We have shown the origins of one protein and have about a couple hundred thousand to go. An example of one is not proof that something is easy. I would expect even more such examples and this would still not be proof that proteins are easy to evolve. Second, One protein does not invalidate Intelligent Design. Now if one was able to show how 10,000 proteins arose naturally, then that would be a strong argument but only if one could explain other things. The protein developing process still has to be explained. Third Quibble
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
Again there are a couple problems with this. First, One example of a true de novo protein does not refute Meyer and Axe's basic claim. Maybe the claim would have to refined to say nearly all proteins with a new function are not generated by natural means instead of a single one. The claim is too absolute and it is not necessary to be that absolue. Agan see Jurgen Brosius for examples of proteins arising naturally. But only a few. Second, Again an example of one or even a thousand does not mean the production of a new protein is easy. Too Absolute. The reasoning in these articles is extremely interesting and something I had not seen before. I am still trying to digest it. But essentially what Ann is saying is that the sequence that produced nylonase is so rare that it has to be questioned as to how it could have arisen by natural means. Once it exists, alternative functional proteins are likely but the sequence itself is near impossible to generate by random means. Interested in any constructive feedback as always could be seeing this wrong. jerry
News, thanks for this. Gauger offers a thoughtful deconstruction of Venema’s “nylon-argument”. The bottom line, as I see it, is that Venema in general does not understand the topic and specifically does not understand the research to which he refers in order to “back-up” his wishful speculations. The following part is amusing: at one point Venema's ignorance is showing when he states that: “Nylonase is chock full of protein folds— exactly the sort of folds Meyer claims must be the result of design ….”. Gauger has great difficulty keeping a straight face:
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.
In her article Ann Gauger offers historical background and a step-by-step explanation of the ‘Nylonase story’, and concludes:
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.
I thought they would be all over this over at TSZ. But crickets. Mung

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