De novo evolution of Nylonase?

Faith & Science Conversation
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When I first started examining in earnest the evidence back and forth for intelligent design vs unguided evolution, someone brought up to me the nylonase case. Upon first reading it, I recognized it, if true, as very significant contrary evidence that undermined the basic ID theory… that novel, de novo, “specified” complexity and functionality could arise easily and quickly, without any intelligent agency or purpose.

At the time I was skeptical in general - not so much due to my sympathy for ID - but it simply seemed intuitively more likely to me that a digestive enzyme capable of breaking down a polymer would arise from tinkering or “honing” a pre-existing digestive function. But I tried to keep an open mind and explore. If I confirmed this was a de novo enzyme popping out of nowhere, fully formed, fully functioning, created complete and fully functioning out of the more or less random assembly of amino acids that would happen from a frameshift mutation, this would seriously discredit the basic assumptions of ID.

Some sites (manynaimed at refuting creationism) argued it was the result of a frameshift, but I recall later going to wikipedia (that unerring source of all objective and reliable truth,) and reading about nylonase later being confirmed in 2007 as the result of a few point mutations, though the page seemed a bit of a mess, some parts still arguing for frameshift, but still referring to the original study or articles from 1984.

So recently, I noticed this topic was brought up both on this site and in the “Adam and the Genome” book, arguing again that nylonase is the de novo result of a frameshift mutation. But then Ann Gauger from discovery institute recently argued against that, seeming to point to other research that determined nylonase as the result of some point mutations.

I think the discussion fascinating, and the consequences certainly have great import for or against the assumptions of ID. But I’m not familiar enough with the particular research or methods to make a judgment one way or the other.

Can anyone who is more knowledgeable confirm for me one way or another… do we know if Nylonase is the result of a frameshift mutation, point mutations, or as yet undetermined?

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I will let more learned members answer that question, but am curious as to why you feel a framwshift mutation would support ID more so than a series of point mutations? Or duplications? All seem to be common mechanisms of evolutionary theory, and I do not see how any support ID more than the other. Now perhaps if a new gene for nylonace arose unrelated to a prior gene, that would certainly lead to speculation as to how it got there.
As I recall, an enzyme with some limited nylonase activity was found, and it became more active with later mutation, which is what you might expect, but I could be wrong about that.

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This has been discussed before here on the forum:

For a technical discussion of the origins of the brand-new nylonase gene, see the Discussion section of this somewhat recent paper:
http://www.jbc.org/content/280/47/39644.long
I think I understand why there is some confusion about whether the gene is an example of de novo evolution (a frameshift can create a not-previously-used protein sequence, to answer @jpm question above) versus “merely” a repurposing of an existing sequence via “minor” mutational change. The nylon-degrading enzymes that we’re considering form a little family of enzymes, some of which seem to be derivatives of previously existing enzymes. (Side note: that’s a great example of evolution and by itself makes all the talk about “information” look silly.) But there’s an enzyme in the family that seems to have no physical relationship to the others. That’s the new one that we’re talking about, and the topic of the JBC paper I mention above. BTW, the JBC paper is about a further derivative of that new enzyme, so don’t be confused by the abstract which could be misinterpreted to be about minor mutational changes to an existing nylonase.

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If I misspoke, I meant to claim the opposite - a frameshift mutation of this kind would speak against the ID claim that the information in such enzymes cannot simply arise randomly.

If this were in fact a frameshift mutation, this would give me serious pause about the basic claims of ID, or the idea that functional proteins that can accomplish specific functions are particularly rare.

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It’s good to hear that you are considering ID claims in the context of actual data. I don’t know whether it’s true that ID makes a foundational claim of impossibility of de novo gene birth from previously non-coding sequences, but if it does, it’s vulnerable to refutation by ongoing research into the topic. It’s easy to find the papers in this area.

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Thanks for the links… I had read through that study previously, but recognize I’m not adept enough to understand all the details.

I did a quick glance, and wont have time to study in detail for a bit… but the only discussion of “frameshift” that I could find was their acknowledgement of the original 1984 frameshift “hypothesis” of Ohno. (As referenced in footnote 45).

If you have time and inclination, could you point me to the specific paragraph or sentence that affirms the frameshift mutation and/or de novo appearance of the entire enzyme family being discussed? I’m not qualified enough on reading biological items of this detail to fully know what I’m reading.

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Dr. Gauger stated as much in her article on this topic…

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.

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From the discussion in the JBC paper linked in my previous post:

We have previously proposed that the nylon oligomer hydrolase (EII) evolved by gene duplication from the common antecedent of EII and cryptic EII′ proteins located on the same plasmid (8). However, the following two hypotheses have been proposed. (i) The EII enzyme is specified by an alternative open reading frame from a preexisting coding sequence that originally specified a 472-residue-long Arg-rich protein and a frameshift mutation in the ancestral gene, creating a gene responsible for nylon oligomer hydrolysis (45). (ii) There is a special mechanism for protecting a nonstop frame, namely a long stretch of sequence without chain-terminating base triplets, from mutations that generate the stop codons on the antisense strand, and such a mechanism enables the nonstop frame to evolve into a new functional gene (46).

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So, I can’t spend a lot more time on this today but I am rediscovering the nylonase story and I think it’s pretty complicated. The JBC paper I have been discussing, linked above, argues persuasively, as near as I can tell, that the new enzyme arose by conventional modes of duplication and mutation. The authors of that paper describe the sequences that explain (for the most part) the new activity (breakdown of nylon). And they note that the new enzyme has the same overall structure (fold) as the ancestral enzyme. A straightforward frameshift, to a new protein sequence, is not the likely explanation. If that’s what Ann Gauger wrote, then she’s right.

In my post last year, I noted that the original idea by Ohno was not really a frameshift at all, but a very interesting phenomenon called overprinting. Linked in post above.

However, if ID needs de novo gene birth to be a fiction, then ID is dead. Nylonase may not be a good example (or a valid example at all), but new protein sequences are known to be birthed from non-coding sequence, and de novo gene birth is probably more common and likely than we once thought. I’ve written semi-recently about a new gene (protein) coming about by a frameshift, and there are whole excellent review articles on de novo gene birth. Links below.

https://royalsocietypublishing.org/doi/full/10.1098/rstb.2014.0332

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When I tried digging into the nylonase story I found it highly confusing and eventually gave up.

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I also have tried a few times, and I hit the same morass. I agree that it’s probably not a frameshift, but it gets muddled pretty quickly. When I wrote Adam and the Genome I was relying on the usual interpretation, which is now shown to be probably wrong. It’s almost a guarantee that a book on science will have something in it that is later shown to have a better alternate explanation, and it looks like nylonase is my example. Look for a “VENEMA ADMITS HE IS WRONG” headline coming soon to your favourite source of ID news. Though the irony here is of course that it’s just the usual new functional information arising through duplication and mutation, nothing to see here, folks…

If Adam and the Genome ever goes to a second edition I will replace the now-dubious nylonase example with another example where we have better evidence. There are many to choose from, but I’d probably use the yeast BSC4 example at present. The evidence there is very good, and not easily dismissed. Any de novo protein is a problem for Axe and ID.

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Yeah but it’s still odd; the overprinting thing seems right (and interesting) and the weird conserved no-stop sequence on the antisense strand is also odd. Not a frameshift, but something strange going on.

Ask and ye shall receive. Here’s a nice quote from the end of the Intro:

Gadid AFGP presumably evolved very recently, in response to the cyclic northern hemisphere glaciation that commenced in the late Pliocene about 3 Mya. We reason it is unlikely that mutational processes could completely obscure even noncoding sequences within such a short evolutionary time such that the extant form of the AFGP nongenic ancestor should remain identifiable. We, therefore, decided to track the AFGP genotype and its homologs within the gadid phylogeny to pinpoint the ancestral DNA site of origin and reconstruct the gadid AFGP evolutionary path. Here, we report the identification of the noncoding founder sequence and the mechanism by which it gave rise to a new functional gadid AFGP gene. Our results also show that the gadid AFGP evolutionary process likely represents a rare example of the proto-ORF model of de novo gene birth (6, 17) where the noncoding founder ORF existed well before the novel gene arose.

https://www.pnas.org/content/116/10/4400.long

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Sir,

Firstly, thank you for the link to your blog. Now I have more to enjoy reading.

Secondly, you are an extraordinarily talented writer. I laughed out loud at the broccoli GAG and the Dilbert GAA…! And helped explain some relatively complicated items.

Thirdly, I very much appreciate you indulging my insatiable curiosity, but I realize we’re all busy. (I’m already spending far more time researching this than I should, amateur that I am.). Please don’t feel compelled to answer my inquiries right away, if you could indulge a few more points of interest, I’d be most appreciative, but I’m ot in a rush. If it is after the 3 day limit I can post again if the discussion board gods permit, or continue in a private discussion. Please take your time… I love learning and being corrected where I’m misunderstanding, but I’m in no rush

Fourthly, I’ll have to beg your patience… I began my Biology/chemistry majors some 25 years ago before I dropped them for my Religious Philosophy concentration, so it is taking me some time to work through much of the specifics, even if the general concepts are pretty familiar to me.

Fifthly, I’m going to work through some of the various papers I found that argue for de novo gene formation, and would be interested in any others you can send my way… my willingness to learn is insatiable, so you can’t give me too much.

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Sir,

As an ID sympathizer, one clarification if I may be so bold…

Any de novo protein confirmed as arising from essentially random sequences is a problem for ID. That is why I found the nylonase case so interesting… the source of the code for that protein would have indisputably been the gobbledygook coming out of a frameshift, yet even an essentially random sequence like that could give rise to a very functional protein.

de novo proteins, in and of themselves, are essentially predicted by ID theory… the idea being that small tinkering is insufficient to produce certain radical new functions for an organism, thus the designer would have to insert entirely new code in order to produce the new function.

It is assumed by ID, if I understand it rightly, that the intelligent designer has the capacity to design de novo proteins and insert the code for them into the genome.

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Also, in hopes I’m not coming across too fastidious…

But I’m not following what the the irony is to which you are referring here?

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Interesting take, and not quite accurate (if I’m understanding you correctly). ID would be threatened by any de novo protein arising through natural means, whether or not the sequence was “essentially random”. So, nonrandom, noncoding sequences giving rise to de novo coding sequences that produce folded, functional proteins = problem for Axe et al. We have much evidence to support that this does indeed happen, and reasonably frequently, even if nylonase isn’t an example after all.

ID folks like Meyer say that new functional information can only arise by the action of an intelligent agent, and here they have to shoot down the nylonase story by showing evidence that the information used to provide this new function (degrading nylon) came about through natural processes (duplication and mutation of an existing gene).

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Hi Daniel,

I greatly appreciate that you’re asking a lot of good questions and carefully weighing evidence. Well done, friend!

I think it’s important to be careful as we discuss and think about hypotheses, predictions and confirmations. To give an example: Suppose my scientific theory is that every human infant comes into existence through the union of a sperm and an ovum followed by implantation in a woman’s uterus, etc.

Now suppose I find a 3 month old infant crying alongside a street. There is no sign of parents, and passersby do not know how the child got there. Is that evidence against the scientific theory, in favor of a miraculous birth?

If this occurred in village that had recently been attacked by terrorists, then retaken an hour ago by government forces after pitched battle, you would probably think that the child was not born miraculously. Instead, the child had been put in the care of a relative who died, or the parents had died, or some other such tragedy.

In fact, you would probably expect many such orphans to be found in such a village. The carnage of history would have erased the specific origin of many orphans, although you might hope with careful investigation to learn more about the history of at least some of them.

The same may apply to de novo genes. The fact that scientists cannot necessarily identify the evolutionary path for all of them need not indicate that the ID hypothesis is to be preferred; it could simply be that scientists do not have enough information for that particular case to make a reasonable statement about the maximum likelihood estimation.

Note: I am not a biologist! I am speaking here from general knowledge about data and scientific procedures. If any biologists like @sfmatheson, @glipsnort, or @DennisVenema would like to correct or augment what I have written, please step in!

Thanks,
Chris Falter

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Sir,

I can’t speak for Axe et al, or their particular methods, but if interesting, this ID sympathizer wouldn’t be particularly troubled by the non random sequences you mention. The particular complex information in that case is already extant, simply untranscribed.

If I understand the scenario properly, the protein may have arisen “de novo,” but the information to produce said protein was already in the database, if this is what you mean by nonrandom. This is categorically different to me than a protein and its genetic formula literally arising from nowhere or from a truly random sequence in the gene.

In other words, they would be troubled I imagine if it could be demonstrated that the information in the genome that gave rise to the de novo protein had arisen “through natural (I.e., unguided) means. If _that_could be demonstrated, that would indeed prove detrimental.

I’ve done enough work in computer programming to consider an analogy… I’ve played computer games that have “secret hidden areas” that you cannot generally access by playing the game as finished, as the main program will never call upon those subroutines. You need to beak some cheat code or find some glitch to access them, but they were there standing by, sometimes in anticipation of a future addition to the game. If some small bug or fluke lets me access those areas, I don’t ascribe the newly arising but previously unexecuted code as having arisen “de novo” I’m the sense being used here, as theynsprang literally from nowhere. This may or may not be exactly analogous to our newly coding gene, but I mention it simply to demonstrate the basic principle, that simply because the “end product” is new, it does not necessarily follow that the information to construct the said end product must also be “new.”

In short, though, I concur that if we could demonstrate that the information in the code arose randomly, or by unguided natural causes, then yes, that would seriously undermine the basic ID assumptions.

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I completely agree with you here… and apologies if I made it sound otherwise. this particular data point gives no preference to the ID hypothesis. But my only point being that their existence does not somehow rule out or otherwise disprove ID hypothesis.

I simply observe that the idea of a designer designing de novo, novel genes and subsequent proteins is most certainly consistent with and predicted by, the ID hypothesis. In and of itself, it cannot proof against ID. I agree though it is also entirely consistent with the larger Evolutionary theory as you describe.

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Unlike computer code, however, genetic information doesn’t stick around long (in evolutionary terms) if it isn’t used – it starts accumulating random changes. Front-loading doesn’t work in biology.

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