In a podcast on the show, ID the Future (March 14, 2017), Dr. Ann Gauger criticized a popular argument that purports to show how easy it is to get new proteins: namely, the evolution, over a relatively short 40-year period, of nylonase. (Nylonase is an enzyme that utilizes waste chemicals derived from the manufacture of nylon, a man-made substance that was not invented until 1935.) While Dr. Gauger made some factual observations that were mostly correct, her interpretation of these observations fails to support the claim made by Intelligent Design proponents, that the odds of getting a new functional protein fold are astronomically low, and that it’s actually very, very hard for new proteins to evolve. Let’s call this claim the “Hard-to-Get-a-Protein” hypothesis (HGP for short).
To help readers see what’s wrong with Dr. Gauger’s argument, I would like to begin by pointing out that for HGP to be true, two underlying claims also need to be correct:
1. Functional sequences are RARE.
2. New functions are ISOLATED in sequence space.
In her podcast, Dr. Gauger cites the work of Dr. Douglas Axe to support claim #1, when she declares that the odds of getting a new functional protein fold are on the order of 1 in 10^77 (an assertion debunked here). Dr. Gauger says little about claim #2; nevertheless, it is vital to her argument. For even if functional sequences are rare, they may be clustered together – in which case, getting from one functional protein to the next won’t be so hard, after all.
If claims #1 and #2 are both correct, then getting new functions should not be possible by step-wise changes. Remarkably, however, this is precisely what Dr. Gauger concedes, in her podcast, as we’ll see below.
Scientific explanations for the origin of nylonase: a short history
Let me begin by providing my readers with a little background information, from a 2009 article in New Scientist magazine by Michael Le Page:
Nylon was first made in 1935. Just 40 years later, in 1975, a bacterium was discovered that is able to digest and live off not nylon itself, but waste chemicals from its manufacture – chemicals that had not existed before nylon production began.
It was later shown this bacterium, now known as Arthrobacter KI72, has evolved several types of enzymes capable of utilising these waste products. One type, 6-aminohexanoic acid hydrolase, encoded by genes called nylBs, has become known popularly as “nylonase”.
So, how did nylonase evolve? Back in 1983, a team of Japanese scientists proposed that nylonase evolved through a gene duplication and frame shift, caused by the insertion of a single base. Shortly afterwards, Dr. Susumu Ohno defended the “frame shift” hypothesis for the origin of nylonase in PNAS, in a now-famous 1984 paper.
However, a team led by Seiji Negoro of the University of Hyogo, Japan, came up with a different explanation in 2005: they claimed that nylonase actually resulted from from two point mutations in the active site of an existing carboxyl esterase enzyme. It turned out that nylonase is very similar to a common type of enzyme which breaks down natural antibiotics (known as beta-lactamases) that are produced by many different kinds of organisms. Two amino-acid changes – two mutations, in other words – were sufficient to change the beta-lactamase binding-site to a site which was capable of binding a by-product of nylon.
That makes sense. As David Wynick of the University of Bristol points out, it is generally easier to adapt an existing protein to a new function than to wait for a de novo mutation that will generate a completely new reading frame.
However, even if the frame shift hypothesis isn’t required to explain the evolution of nylonase, scientists have other well-established examples of de novo genes from alternate open reading frames. Here are two recent papers on the subject: Evolution: Dynamics of De Novo Gene Emergence (Current Biology, Volume 24, Issue 6, pR238–R240, 17 March 2014) and Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic (Proceedings of the National Academy of Sciences U.S.A., 2016 Oct 11; 113(41): 11537–11542). I wonder what Dr. Gauger would have to say about these cases.
Dr. Gauger’s puzzling admission – and the problems it generates
And now, here’s how Dr. Gauger responded to interviewer Sarah Chaffee’s question, “So, does nylonase shown that purely natural processes can create a new protein?”, in her podcast:
No. I would say, ‘Of course not,’ because we have an explanation for how it came about, through just natural modifications and selection from a starting protein – a starting enzyme, carboxyl esterase. Step-wise path, there you go. But not a frame shift. A frame shift would create a completely novel sequence, a completely novel fold, if it folded at all. And so we have no need of that hypothesis.
I note in passing that Dr. Gauger rejects an explanation for the origin of nylonase that was formerly accepted by Dr. William Dembski back in 2005, when he wrote: “Nylonase appears to have arisen from a frame-shift in another protein.” I also note that Dr. Gauger refers to “a kind of bacterium capable of digesting nylon” (2:35) and to “a whole new enzyme capable of degrading nylon” (2:44), when in fact, what the bacteria digest and live off is not nylon itself, but waste chemicals derived from its manufacture. But let us continue.
In the passage above, Dr. Gauger makes the damaging admission that natural processes can generate a new protein by a step-wise process from a starting protein, carboxyl esterase (also known as nylB-prime). That tells against claim #2 above, that new functions are ISOLATED in sequence space. For if functions really are isolated in sequence space (as Gauger, Axe and Meyers have argued previously), then how is it possible that the researchers easily found two mutations to switch nylB-prime to nylonase? That should be impossible.
In her podcast, Dr. Gauger makes much of the fact that nylonase has two open reading frames (ORFs) going in a forward direction, plus a third open reading frame going in the reverse direction. But if functional proteins are so rare, as she alleges, then how is it even possible to have overlapping ORFS? This type of bi-directional reading of information is ubiquitous in DNA, but it is much more difficult in English text. What this bi-directional reading indicates is that proteins are not so rare, after all – which undermines claim #1 above.
It should also be pointed out that the proteins described by Dr. Gauger in her podcast actually contain a high number of repeats – a point acknowledged by Dr. William Dembski back in 2005, when he described the DNA sequence of nylonase as “a very repetitive sequence.” In other words, the DNA from which this protein is generated is low-information DNA. Again: how is it possible that repetitive, low-information DNA can give rise to a new protein? Shouldn’t this be impossible? Aren’t proteins supposed to be rich in information?
Here’s another awkward question: why does nylB-prime (the protein from which nylonase evolved) appear to have no similar-looking homologs? Dr. Gauger thinks it’s because this protein is ancient. If that were the case, then we should expect to see evidence of its history in a large number of sequence-similar proteins, but we do not see this. Where did all those proteins go? What happened to them?
Finally, how is it that two genes with no homology can sometimes possess nearly the same structure and function? This shows that there are multiple sequence families that are capable of producing the same function, in the same way – which surely counts against the claim that functional sequences are RARE.
Some brief comments on Sal Cordova’s post
I mentioned above that several different kinds of enzymes have evolved in recent decades, which are capable of utilizing nylon waste products. These enzymes are known as NylA, NylB and NylC. However, none of them appear to have significant sequence homology. In a recent post, Sal Cordova puts forward a two-fold argument:
1. NylA, B, C have no homology, so they had to have had different evolutionary origins.
2. We do not know for sure if nylonase existed in nature before, because we aren’t able to go back in time.
Point #1 simply shows that evolving new proteins is easy. The fact that it has happened multiple times is not evidence against evolution, but rather, evidence that evolving new functions is a relatively straightforward matter.
Regarding #2: we know that nylon is a man-made material which does not exist in nature. It would be exceedingly strange if nylonase existed before nylon. That’s why most scientists think that these are new genes.
Finally, I’m not sure I understand the alternative model that Sal is proposing. Does he really believe that these three enzymes were hanging around for thousands of years with no function? Or does he believe that they had a hitherto-unknown function, which science will uncover?
In fact, scientists have frozen bacteria samples from before 1935 – and it isn’t even hard to obtain them. Thus it should be possible to check for the presence of nylonase in those samples. If Sal managed to identify a naturally produced nylon, then that would certainly explain why nylonase had to exist before synthetic nylon, and would suggest that these three enzymes (NylA, NylB and NylC) are not newly functional proteins, but ancient ones. However, he needs to go out and find that evidence. At the present time, scientists are not aware of any natural source of nylon.
Conclusion
Neither Dr. Gauger’s podcast nor Sal Cordova’s substantiates the HGP hypothesis. (NOTE: As Sal correctly notes below [here and here], his post was never intended as an argument for the HGP hypothesis.) For now, it appears that the evolution of new proteins in Nature is – at least sometimes – fairly easy, after all.
What do readers think?
UPDATE: John Harshman has kindly posted a plausible sequence of events for the evolution of nylonase, here, from an earlier comment on Sal Cordova’s thread. As he correctly points out, “the frame shift hypothesis, gene duplication hypothesis, and the two-mutation hypothesis are not mutually exclusive.” Harshman considers it most likely that “all three of these occurred some time in the evolution of NylB.”
You would have done well to read and/or participate in the previous thread on nylonase before posting this, as it covers much of the same ground. For one thing, the frame shift hypothesis, gene duplication hypothesis, and the two-mutation hypothesis are not mutually exclusive. In fact the most likely explanation is that all three of these occurred some time in the evolution of NylB. It’s just that the last one is what turned it into nylonase. The others happened millions of years ago, at different times. Let me repeat the scenario, from the thread you ignore:
1. Ancestral repetitive-sequenced gene, function unknown.
2. Frame shift to produce a new ORF, function unknown.
3. Spread of new ORF to various plasmids in various strains, including what the referenced paper calls P and F.
4. Millions of years pass.
5. Duplication of new ORF in F plasmid to produce precursors to F-NylB and F-NylB’.
6. Millions of years pass.
7. Nylon appears in the environment.
8. Fixation of two new mutations in in the F-NylB precursor that make it a highly effective digester of nylon waste. And changes, so far uncharacterized, in the P-NylB precursor for a similar reason.
F refers to Flavobacter=Agrobacter. P refers to Pseudomonas, which has a nylon-digesting gene homologous to NylB, though the ability is convergent.
I should also note that NylA and NylC do not digest nylon waste, exactly. What they do is turn cyclic oligomers into linear oligomers that NylB can digest. Thus they are of limited function except in the presence of NylB.
Still, good points about the lessons we can get from related genes and multiple ORFs.
Not just any frozen samples will do. What you need is samples of Agrobacter containing the relevant plasmid from the same area in which the nylonase genes were found.
John,
In fairness, Vincent does discuss the earlier thread. See the last section of his OP.
A link to the earlier thread:
No, he discusses the OP, not the thread. It’s the comments in the thread that he should have checked out, but apparently did not. I think he’s also misreading some bits of the OP, but that’s a comparatively minor point.
vjtorley, Why don’t we repeat this experiment in your lab, so that we have no misunderstandings later on…? I have a few lab techs that can travel to your lab within 72 hours or a bit more due to where you are, and try to replicate A. Gauger’s findings. We would appreciate any input from other experimental scientists; J Harshan, L. Moran, D, Graur, PZ.Myers and other insignificant scientists who have contributed to this very important issue by experimenting on the issue rather than making stupid, and unfounded comments…
J-Mac,
Sensible, J-Mac, but why not arrange to have it done it in your own “medical facility”?
It is my impression that rareness of “function” in sequence space depends on defining function as rather efficient function. If we allow in weak function, a lot of randomly generated proteins show weak binding and weak catalysis. That would make “function” much more common.
Or am I wrong about that?
Joe Felsenstein,
I completely agree with you. The requirement to bind weakly ATP and a nuclear proteins requirement to bind to 6 other proteins and perform transcription are two completely different functional requirements. Can an organism sustain life with weak function across its proteins? Can an organism sustain life without a precise DNA repair mechanism?
I’ve gone on record saying one can evolve nyloase ability from something that didn’t have it. Pseudomonas is a good example where nylon eating ability evolved in the lab in 3 months!
It’s semantics if this is a “new” protein. At issue is how tremendous the required change was.
John Harshman was referring to this discussion:
I didn’t argue that nylonase was hard to get from a pre-existing protein. I said so several times and even used the pseudomonas example.
It may be unintentional, but that suggests that I was actually trying to argue that position when I wasn’t.
I’d ask that misrepresentation of my position not be used, because it is not my position!
For completeness, Pseudomonas is not nucleotide homologous to F-NylB, only some portions are remotely (like 37%) amino acid homologous. The pseudomonas example is the most important because in vitro evolution demonstrated nyloanse ability will evolve in 3 months from strains that didn’t have it. Unfortunately, unlike Lenski’s LTEE, the researchers doing the evolving didn’t publish what the genetic changes were and said the cause was unknown!
I don’t see the relevance. All that means is that their common ancestor was very long ago, long enough that the DNA sequences are hard to align. But 37% AA similarity is much easier to align and is good evidence of homology. (The definition of “homology” is of course “similarity due to common descent.)
Hi Sal,
I’ve updated my conclusion in the light of your comments above. Sorry for the misunderstanding: I wasn’t sure where you stood vis-a-vis the claims made in Ann’s podcast, which your post did not mention. My apologies.
Hi John Harshman,
I did actually read some of the comments on Sal’s thread, but not all of them. Yours was down at number 41. I must have missed it. Anyway, I’ve attached an update to my OP, referencing your scenario fro the evolution of nylonase. Cheers.
Hi Sal,
It’s semantics if this is a “new” protein. At issue is how tremendous the required change was.
What concerns me is: is there a new function? For me, the point of the nylonase example is that the bacteria are able to do something new that their ancestors couldn’t do, and what’s more, this new ability doesn’t interfere with any existing ability they possess. I’d say that’s a new function.
John, to SaL:
Just to rub it in. 🙂
Vincent:
A relevant comment from another thread:
vjtorley,
The real issue is if this evidence makes it more likely that standard evolutionary mechanisms can create a new morphological feature that creates an advantage and allow multicellular diversity. I would argue that bacterial adaption provides little evidence to support this because there are only a few proteins involved, and their function is not changed it is simply modified.
Here’s their paper:
Hi everyone,
Re the question of whether or not we are talking about a new protein, I should mention that nylB and nylB-prime differ by 47 amino acids.
By the way, this article looks interesting:
https://reflectionsofayoungcontrarian.com/2013/05/01/addressing-creationist-fallacies-part-1-of-2/
Hi keiths,
Thanks very much for the quote from Andreas Wagner’s book, and for the abstract of the paper he co-authored with Evandro Ferrada. Fascinating!
Still irrelevant, since only two of them have to do with the evolution of nylonase. The other 45 apparently happened since the gene duplication but before NylB gained its new function. Might even be completely neutral evolution. Of course there’s no data that I know of on what the NylB precursor did, if indeed it did anything.
1. An organism with a small enough genome needs less precise repair mechanisms (thus RNA viruses have small genomes). This was discussed by Manfred Eigen and Peter Schuster in their famous paper of 1971.
2. Early in the origin of life there should have been less of a need to have highly efficient metabolism to compete with other efficient organisms.
3. Even in the evolution of a new pathway in an organism which is generally efficient, there may be a selective advantage to having even a modest ability to synthesize the new compound. If you don’t have any synthesis of vitamin C, even a slow synthesis of a small amount may help.
Self-servingly I’ll just note that I was correct in reasoning that NylB’ (aka EII’, or nylB-prime) was probably the ancestral state, since NylB has 200 times higher activity on nylon oligomers compared to NylB’. 🙂
It is interesting that no homologous proteins could be found in any databases, and it took X-ray crystallography to elucidate the structure of the enzyme to discover that it was a derived beta-lactamase.
J-Mac,
J-Mac reminds me of someone …
Anyone else noticed the fantastic irony in the fact that nylB is an evolved beta-lactamase, the very type of enzyme that Douglas Axe did his now infamous work on back in 2004? The very type of enzyme he used in his experiments, to argue that novel functions exist at a rate of 1 in 10^77 in protein sequence space?
Literally that is fantastically ironic.
Regardless, it’s still apparently completely unknown how/from what NylA and NylC evolved.
Rumraket,
Good catch. But I bet if you start chiselling away at it, it too stops working!
VJT
This is an excellent point that I’ve never seen before on this topic.
I would add the antibodies also provide evidence that function isn’t so rare. It doesnt matter whether one thinks that the mechanism for producing antibodies evolved or was designed, the fact that randomly generating a sequence of amino acids (in the bone marrow in 2 weeks) will produce a surface capable of binding just about any other surface in the universe suggests that function isnt rare. Most of the functions in a cell, after all, arise from the specific binding of components.
I think Gauger was just very unclear in making her points ( which is why I’m surprised shes a spokesperson for the DI) Shes saying nylonase preesxisted as a related enzyme and a few point mutations merely changed the substrate specificity. Thats a small change IDers can live with.
Thanks VJ. God bless you.
I wouldn’t have noticed it if you hadn’t said something.
VJT:
Not just that, how is alternative splicing even a thing? (A particular difficulty for the IDist who simultaneously proposes both that AS is overwhelmingly the rule and that function is vanishingly isolated. One might get away with it by saying modular function is rare, and so indeed it may be. But this makes evolution largely a matter of shuffling modules, and hence ‘Hoyle-o-matic’ calculations redundant).
More food for thought: it is possible to introduce a break in a peptide and have that become the site of new C and N terminals, while generating a peptide bond between the original C and N. Essentially, turning the linear peptide into a loop and snipping elsewhere to create a new protein from the same sequence of residues. I was unable to locate a link on a brief search, but it would be a pointless exercise if the product were either nonfunctional, or identical in function to the original. The technique was chemical – acting directly on the peptide – but an identical result could be obtained biologically through DNA.
Rumraket,
Can you imagine being Ann Gauger or Douglas Axe? Dragging yourself to the Biologic Institute every day to fight biology? It must be incredibly depressing.
There’s a Japanese game called Biologic Institute Escape. A shame that it isn’t available in real life.
You were right, in turn, that it had a totally unrelated catalytic function in the same way that Rubisco has, using the same active site.
Thanks.
“She received her Bachelor’s degree from MIT and her Ph.D. from the University of Washington Department of Zoology. She held a postdoctoral fellowship at Harvard University, where her work was on the molecular motor kinesin.
Her research at Biologic Institute has focused on two areas: the limits of neo-Darwinism as a mechanism for change at the protein level, and evidence for the uniqueness of human origins. As Director of Science Communication, she is responsible for communicating the evidence for intelligent design to the wider public.
She serves as an editor of the journal BIO-Complexity, and her scientific work has been published in Nature, Development, Journal of Biological Chemistry, Genetic Regulation of Development, In Vitro, In Vitro Cell and Developmental Biology, BIO-Complexity, and Biological Information: New Perspectives. She has coauthored the book Science and Human Origins and appeared in the documentaries, Metamorphosis, Flight, and The War on Humans. Her web posts appear regularly on Evolution News and Views, and she writes for other on-line and print publications as well.’
Yea, poor Ann.
Not doing a very good job is she?
phoodoo,
Yeah. She and Axe used to be scientists. Now they’re propagandists for a DI-funded “Institute”.
She is being paid to communicate the contents of the empty set?
Easiest job on earth?
Or hardest, if she’s really expected to come up with something plausible (if only to certain folk)?
Glen Davidson
The empty set is full of virtual content, and there are always articles popping into existence for a moment before being annihilated.
I thought about this post quite a bit. The dialog seems to be like this:
IDer (Axe): Finding new genes is realistically outside of chance.
Evo: But new genes happen all the time.
IDer: Statistics say that they shouldn’t, finding them is like finding the tool marks of the designer.
Evo: But they happen all the time.
I don’t think that the Evo can make a case without a clear statistical analysis. I am quite sure that Axe is vastly overstating his case, but the only valid response seems to be statistical, rather than finding evidence that it happens.
It’s the bumblebee argument.
Statistics and the tools of mathematics are best used to describe what happens, and not to argue that what happens cannot happen.
Somebody’s head just ain’t on right.
brucefast,
I may be wrong but I think that Axe’s numbers for function are so low because of the requirement for function. He modified a protein segment that then biologically had to bind to another protein and then break down penicillin.
If this is right then the probability problem gets worse when instead of bacteria you are estimating the probability of proteins forming in multicellular organisms where many proteins have to bind with multiple proteins to perform their function.
This is too simplistic, which is why you go on to say the “Evo” needs to respond with a clear statistical analysis. You have to look into what Axe is actually claiming.
The actual exchange is this:
Axe: Finding new genes is realisticically outside of chance, because functions are exceedingly rare and spread out in protein sequence space.
Evo: But new genes with new functions happen all the time with as little as 1 or 2 mutations, so functions are manifestly NOT rare OR spread out in protein sequence space.
Okay, then you are wrong.
Axe’s numbers for function are so low because he only considers a single function for a single fold and deliberately and artifically sets up his experimental conditions so that, even for that single particular function he tests for that single particular fold, that fold has been constructed to be unrealistically sensitive to mutation.
Yep.
Axe’s is an empirical claim, based on an experiment. He attempts to derive some statistical rule from observations in his experiment, but his experiment is not actually set up so it can inform the statistical rule he wishes to derive.
As such, the only thing we need to do is point out the flaw with the experiment and point him to better ones.
Rumraket,
So do you not get Axe/Gauger’s position, or are you just misrepresenting them. Behe’s entire “edge of evolution” thesis is that any single mutation that produces benefit is within the bounds of reasonable evolutionary possibility. He contends, if I understand correctly, that if two mutations are called for, neither on their own being beneficial nor harmful, then there is a rare outside chance of the mutations occurring (and especially in rapidly breeding organisms like bacteria.)
Now, as far as “genes with new functions happen all the time with as little as 1 or 2 mutations” I think you exaggerate your point. While genes with new abilities happen with 1 or 2 mutations, but the abilities are what you might call neighbor abilities. In the example of nylonase being discussed in this post, an enzyme that digested other stuff now could digest nylon. You don’t get a gene that produces a protein that is a muscle (retracts under electrical signal) to suddenly digest something.
Put it into more human terms, if you have a screw that doesn’t work for a certain situation because it is too large, it is quite within evolutionary capacity to mutate a smaller screw that does work. However, try to mutate, oh, a soap, a surfactant, from the same screw and, well, you’re screwed.
brucefast,
Here is Doug’s explanation of why he started with a sensitive configuration;
brucefast,
Read these two comments: Link, link.
You should also read Wagner’s book Arrival of the Fittest if you haven’t already. It’s full of bad news for IDers.
Better according to Rumraket. Someone has repeated Axe’s work with even more lenient conditions?