It has been widely advertised that nylon eating genes evolved after 1940. I have no problem with that claim in principle since new antibiotic and malaria resistances have evolved since 1940. Even though I can easily accept the possibility of post-1940 nylon-eating evolution in principle, where is the slam dunk evidence that this is actually the case? Did a significant portion of the ability for bacteria to digest nylon take place after 1940 (or 1935 when nylon was first created)?
In an NCSE article New Proteins Without God’s Help we read:
Since nylon first came into commercial production in 1940, we know that the new enzymes have formed since that time.
A similar line of thinking was argued at BioLogos in Biological Information and Intelligent Design, De Novo or Ex Nihilo.
Three nylon eating genes NylA, NylB, NylC were discovered on the Flavobacteria plasmid pOAD2 from 1977-1992, but the researchers concede none of the three have significant sequence homology. Worse, in papers published in 2007, they reported other bacteria contain those same genes in their chromosomes. Unless the researchers have access to pre-1935 bacteria sitting in lab refrigerators, the claim that the genes actually evolved new proteins via mutation is dubious since we have no pre-1935 bacterial samples to actually do a comparison with, especially in the case of NylC. The claim that NylB’s nylon eating ability evolved by gene duplication from a non-functional NylB-prime gene could just as well be interpreted that a functionless NylB-prime gene is a defective copy of a functioning NylB gene!
What’s the proof new nylon eating genes actually evolved after 1940, or is it just speculation? Slam dunk proof would entail having strains of pre-1935 bacteria and then comparing it with the strains after 1935 that supposedly evolved new genes. Is that the case? No. Just speculation which began in 1977 but got less defensible over the next 40 years as more bacteria and non-sequence-homologous genes were discovered to have nylon eating capability.
At least we can credit Richard Lenski who can back up his claims of evolution because he has samples of bacteria in his lab before and after his creatures evolved, whereas the guys promoting the claim the nylon-eaters are new don’t have pre-1935 physical samples of the bacteria. The only pre-1935 samples of the bacteria they have are samples from their imagination.
Incidentally, it is worth pointing out the bacteria that is the centerpiece of the controversy has been mis-classified or misidentified, and thus the name of the bacteria has itself gone through some sort of macro evolution. It was first called Acromobacter gattatus, then renamed as Flavobacterium sp., but then renamed Arthrobacter sp. after it was realized it had been put in the wrong taxonomic category all along.
But anyway, here is the 1977 speculation that became uncritically accepted and exaggerated as fact for the last 40 years:
There are two possible mechanisms for an enzyme to be active towards unnatural synthetic substance such as 6-aminohexanoic acid cyclic dimer; one is that an unnatural compound is hydrolyzed as an analogue of the physiological substrate, and the other is that the compound is hydrolyzed by an evolved enzyme which originally had an activity on a physiological substrate but lost it by the evolutionary mutation. The data obtained in this experiment indicate that this enzyme did not hydrolyze any physiological substrates tested including peptides, cyclic amides, and amides. In addition to the lack of activity on natural compounds, its low turnover number (8 SKcI) compared to other cyclic amide hydrolases (35 – 260 s ~ for penicillinase [12]) supports the possibility that the enzyme has evolved by adaptation to a new synthetic substance which is a waste product of nylon-6 production.
I have no problem if they say “the enzyme has evolved by adaptation to a new synthetic substance which is a waste product of nylon-6 production” when they mean an existing enzyme has changed its pre-existing function to a different one. That is to say, it acquires a new function while also losing its previous one. However, I would have serious issue with the NCSE’s insinuation that this was such a spectacular change that it illustrates how to solve the origin things on the order of the spliceosome or ribosome.
They don’t have strains sitting in a refrigerator from which to compare the “newly evolved” genes with do they? They just guessed, and then 30 years later one of the same team (Negoro) found nylon eating genes on other bacteria, plus reasonable nylon-eating homologues on other bacteria to boot.
Worse, the claim that these are post-1935 genes is weakened by some facts that require a little elaboration. First there is the basic nylon monomer that forms the components of nylon oligomers. NylA, NylB, NylC have different specialties of which nylon oligomer they can degrade. These three enzymes provide what looks like a digestive cascade where N-oligomer substrates are degraded by NylC to dimers which can be further degraded by NylB (and even NylC but to lesser extent). The cascade is described in: Biodegradation of nylon oligomers.
But important to note: NylA, NylB, NylC are not sequence homologous. In A New Nylon Oligomer Degradation Gene (nylC) on Plasmid pOAD2 from a Flavobactenium sp we read:
Sequence alignment by the method of Wirbur and Lipman (21) showed no significant homology among the
nylA, nylB, and nylC genes. These results suggest that the three nylon oligomer-degradative enzymes evolved independently.
There is no pre-1935 bacteria from which to compare with to establish NylC’s true history, much less anything beyond speculation about the nature of NylC’s ancestor. So how can anyone claim it is new (as in post-1935-new)? Just guesses. They’d have to argue these the genes evolved independently since 1935, and in the case of NylC, the ancestor is almost totally without detailed description.
They however argue, a functional NylB arose from a non-functioning NylB-prime gene via gene duplication in a 1991 paper entitled: Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers.
But for all we know NylB’ is a defective copy of a functioning NylB! Where is a Ken-Miller-pseudo-gene-like argument when you need it?
In fairness, another bacteria called Pseudomonas was shown in lab conditions to acquire enzymatic nylon-eating function after a few months. The gene however in Pseudomonas, according to BLASTN, has no sequence homology with Flavobacteria. However, the protein according to BLASTP can align 91% at 37% homology. But even the researchers were astonishingly vague about what actually changed in the bacteria that enabled nylon degredation. The two relevant papers are: Characterization of the 6-aminohexanoate-dimer hydrolase from Pseudomonas sp. NK87 and Emergence of Nylon Oligomer Degradation Enzymes in Pseudomonas aeruginosa PAO through Experimental Evolution.
Unless we have strains sitting in a refrigerator of pre-1935 bacteria, how do we know that the genes actually evolved to digest bacteria? For all we know, it had that capability already or very close to it. And unless we have genes from all existing bacteria in 1935 and can prove all the bacteria on the globe do not have horizontally-transferrable nylon eating genes which could end up on the plasmids of Flavobacteria, we can’t unequivocally argue the three nylon eating genes (NylA, NylB, NylC) in Flavobacteria didn’t already exist pre-1935.
Even if the capability of nylon eating evolved, it is also not necessarily because of a new gene, but new regulation. A mini-example of this possibility had to be raised because even in their lab, they had bacteria with identical nylon eating genes but which could not digest nylon.
it is conceivable that expression of the nylC gene is enhanced in these strains and the elevated enzyme activities made the cells Nom+. However, the following possibilities could not be ignored: (i) KI725R strains may possess an additional nylon oligomer-degrading enzyme which is active
toward a substrate included in Noml, but K1725 has no degradative ability toward the substrate; (ii) nylon oligomer transport proteins are activated in K1725R strains; or (iii) the EIII proteins were altered by mutations in the coding region of the nylC gene by which the specific activities and/or
substrate specificity of the enzyme were changed. The last possibility should be negligible,
So my question is, if we ignore the NCSE hype, does the scientific literature really even prove unequivocally a significant part of nylon eating genes evolved after 1935 and absolutely rule out these genes pre-existed? Maybe yes, maybe no, but the NCSE can’t now brag that any significant evolution (like say compared to evolution of antibiotic resistance) bacteria definitely evolved after 1940 without God’s help. We simply don’t know.
NOTES:
Here are some accession numbers:
NylB (protein) in Flavobacteria: WP_012476894.1
which generates a BLASTP hit on Agromyces accession number: BAE97621.1
NylC (protein) in Flavobacteria: BAA01528
which generates a BLASTP hit also on Agromyces accession number: BAE97629.1
in Pseudomonas, the nylon eating gene accession numbers are : BAA01524 (protein), D10678.1 (DNA)
which generates BLAST hits on a variety of organisms as well
It’s very low, it’s just over 10%. If all we had was sequence my understanding is that a score like that would be too low to infer homology. However with such a good structural alignment I think we can.
It should be noted that there are many, many proteins (apparently 11 pages of them) that fold into similar structures according to the “PDB hits” link given (click on “structure similarity” button) . Many of these deviate quite a lot in sequence from the “best fit” too, so it might be that some of these have higher sequence similarity to Ohno’s ancestral sequence
Is this low homology what suggests that the frame-shift (or is it the duplication?) happened many millions of years ago?
This is a straight up lie. Ohno didn’t delete anything.
Yes yes, now we have to also persuade you personally. I have no hopes that anything could achieve this for someone who thinks a >100 billion light-year across cosmos was created 6000 years ago.
As already explained that would probably be meaningless, since the downstream sequence following Ohno’s typo is so divergent between F-NylB and P-NylB that we have no reason to believe either of them has preserved any information about the ancestral sequence from which they both evolved.
It is only because the upstream region, and the NylB coding regions in both plasmids have been conserved, that we could expect to get something alignable by sequence.
Failure to find either a sequence or a structural alignment for whatever sequence follows Ohno’s typo is therefore irrelevant, since the sequence divergence between the two plasmids is so great, that if we didn’t find any, it might just as well be because the original sequence has been erased by time. So it’s not worth it to do that work, since it logically couldn’t constitute a test of any hypothesis regarding our argument here.
What would probably be more interesting is to take the amino acid sequence of the protein that I found in uniprot, with the 36% similarity, and submit that one to a structure prediction, to see if they look alike.
Neither.
What you need to understand is that there are two versions of the NylB enzyme known from two different species of bacteria. One from Pseudomonas, and one from Agromyces (formerly called Flavobacterium).
These are the enzymes I refer to as P-NylB and F-NylB respectively. They both sit on a plasmid called pOAD2, in both species. Which immediately implies one (or both) of them got that plasmid through HGT.
The two plasmid DNA sequences have been compared in Okata H et al 1983. They’re both 392 amino acids long. The amino acid sequences for these two enzymes is about 88% similar. It is that level of divergence for two 392 residue proteins, that implies they have been diverging for somewhere around 140 million years.
But, there is also evidence that a frameshift mutation happened and created the NylB enzymes. Both of them. The evidence is almost identical in both plasmids. So this suggests two possiblities.
A. Either the exact same frameshift mutation happened independently, twice, in two different species.
B. Or it only happened once, before they diverged by 12%.
The latter hypothesis requires less evolution than the former (one frameshift mutation in one place, rather than two but independently in the same place) and is therefore more likely.
Rumraket,
Thanks
Ohno’s typo resulted in a premature stop codon three codons downstream from his typo. Which means those three amino acids might be off. Not exactly possible to get a “fold” out of that.
We’re talking a 427 amino acid protein used to predict a structure, and you think three amino acids is going to somehow magically make the entire rest of the protein adopt a fold matching an existant protein with that degree of structural similarity?
You couldn’t possibly make a more desperate argument than this. Hahaha.
Just to satisfy your whine, I’ll just correct for Ohno’s typo and re-submit the amino acid sequence with the remaining part of the reading frame reported in correct form by Okata H et al 1983 instead.
That way, if it comes up with the same structural match again, what’s your excuse going to be then?
Rumraket,
Your number 1 alignment (which I showed was pathetic) refers to a human protein.
Not to mention splcesomal introns have to get inserted into a bacterial gene to make it somewhat eukaryotic (YIKES), but do you really want to claim Ohno’s NYLONASE frame shift happened in the common ancestor of Eukaryotes and Prokaryotes?
That’s a billion years of anticipating the emergence of man-made nylon to have a frame shift even before the Eukaryote/Prokaryote split. What an amazing hypothesis for the emergence of nylonases!
I do salute you for the spectacular investigation you are carrying out. It’s spectacular that is, if you’re trying to make us laugh. 🙂
“pathetic” he said 🙂
Explain it Sal. Explain the result. Why does the amino acid sequence Ohno inferred just so happen to adopt that structure? What is your explanation?
Just chance? It just happened by chance?
Then why do you have a problem with evolution, if you believe this can happen just by chance?
Sal, you need to understand the theory you are criticising. There’s no anticipation. There’s just the niche and differential survival.
ETA survival in the sense of reproductive success in the niche.
LOL, why the hell is that scenario suddenly required?
No. These proteins split off from a common ancestor long ago (the frameshift mutation didn’t happen yet), and diverged a lot in sequence over that time, until a frameshift mutation happened still about 140 million years ago and spawned the NylB ancestor.
It just shows that the ancestral protein Ohno inferred, itself has a veeeery long evolutionary history before the frameshift mutation eventually rendered it nonfunctional in Agromyces (or whatever bacterium carried the PR.C gene those approximately 140 mya).
This is all entirely consistent with everything else we know from evolutionary biology.
I get that because of pride and religious doctrine, you have to act out your denial and rejection. I had expected as much. You get to play the guy who never is convinced, and I get to be the guy who has to constantly correct the strawmen, caricatures, and misrepresentations you come up with to try to make your denialism appear somehow reasonable.
Same old story.
A plane crashes into the Rocky Mountains… that’s a 70 million years of anticipating the emergence of man-made planes!
May I ask another question please?
Are these figures based on similar molecular clocks to those which put the last common ancestor of humans and chimps some 5 million years ago, described by Larry here at Sandwalk?
http://sandwalk.blogspot.com.es/2014/02/why-are-human-and-chimpanzeebonobo.html
A simple rule of 3 suggests that if mutations accumulated at the same rate, if a 12% divergence takes 140My, a 1% (human-chimp divergence) would take some 12My, which is in the ballpark of some studies cited in Wikipedia
The 1% (or 1.3%) divergence between humans and chimps is in the average DNA sequence of the entire genome. DNA sequence divergence in protein-coding regions is much less, about 0.5%. And protein sequence divergence is much less than that, though I don’t know of an average number. I do recall an estimate that 30% of protein sequences are identical between humans and chimps, and most of the rest differ by only one or two sites. Don’t confuse protein sequence with DNA sequence.
Also, if a protein-coding sequence (with its protein) is evolving under positive selection, it may change, for a while, much faster than predicted by a protein clock. And if it evolves neutrally for a while, say after a duplication, it may evolve almost as fast. There are many things that might cause a protein clock to run irregularly.
Yes.
Here are the predicted residues using Ohno’s PR.C which he created by a frame shift caused by a Thymine deletion toward the start and Guanine deletion caused by Ohno’s typo at end which caused the remainder of the actual sequence to be shifted out to oblivion.
But here is your number-1-ranked most “similar” protein (where even had to add DAHSED lines to create a gap because the alignment was so crappy):
To argue PR.C actually existed, you might try hoping for a protein sequence that looks like this:
NOT this:
In contrast, let look at Okada’s competing gene duplication hypothesis for nylonase. The original ancestor he said looked like this (NylB’):
and the descendant looked like this (NylB):
One can see the Okada’s hypothetical ancestor (NylB’) and descendant (NylB) are similar (88.65%), which is more than I can say for your supposed similar sequences (with dashes having to be inserted to boot!).
By the way, it was the NylB’ that Kato in 1991 changed by a mere 2-residues to make it as catalytic toward nylon as NylB. If those results were available at the time of Ohno’s 1984 hypothesis, Ohno might not have had any reason to claim a frameshift that changes around 400 residues vs. point mutations that change just 2.
Since the protein folding problem hasn’t been solved, those graphs show how easy it is to force shapes onto sequences without actually solving the protein folding problem, even for proteins generated by typos.
stcordova,
I don’t think you understand protein alignment. Because there are 20 amino acids, 29% similarity, though it may look ridiculous to you, is actually pretty good evidence of homology. Even with that single long gap.
And I don’t think you understand that the evidence for Ohta’s hypothesized frame shift is not dependent on it happening recently.
Finally, I don’t think you understand that the gene duplication and frame shift hypotheses are neither competing nor explanations for the evolution of nylonase activity.
A protein clock? There is a clock?
Is this part of the “its convenient to use language we don’t really mean in evolution-speak,” when we want to talk about things as if they are planned when we mean there is no plan?
Because when you say something evolves “faster” that really isn’t true is it? The mutations happen the same speed no matter what right? Mutations don’t happen faster or slower depending on a “concept” of selection pressure. Selection pressure doesn’t actually exist, there is no pressure right? That’s more convenient evolution-speak.
I think we need a whole thread to talk about evolution-speak, to talk about concepts you make up, which don’t really exist but which you use to make it easier to talk about the unplanned things that look planned so you talk about them as if they are planned. Pressure. Clocks. Increased evolution, decreased evolution, neutral evolution, beneficial evolution, adaptation, all these are just made up, none of them are real.
How would evolution sound if you stopped using words you don’t really mean? We need an OP on this one.
Why?
Notice how Sal avoids trying to give an account for why Ohno’s inferred ancestral amino acid sequence scores hundredsof hits with ~36% similarity for >370 amino acid stretches in database searches.
Why the beginning 33 amino acids of Ohno’s ancestral sequence scores a 97% match to existing proteins.
Why the whole 427 amino acid sequence just so happens to adopt, with a very significant degree of accuracy, a part of a larger protein fold known to exist, despite their low overall sequence similarity (10.3%).
Instead of trying to answer any of these questions, any single one of which by itself is a piece of evidence that Ohno was right and there really used to exist an ancestral reading frame (and that an ancestor of NylB was created by the much dreaded … CHANCE), he now is forced to try to dismiss it all by pointing to things which are complete irrelevancies such as Ohno’s premature stop codon.
Sal is now engaged in a campaign of misdirection (such as the low sequence similarity between the two structures that align) and obfuscation. But the evidence isn’t going to go away.
This seems simple enough, so I’ll give this a try
Take two random sequences of 300 AA’s of length
On average, 1 out of 20 AA’s (5%) will match, because at each position any of the 30 AA’s is equally probable. Any alignment of 2 random sequences will also subsequently produce the same 5% match on average.
by the law of large numbers, the match % will converge to 5% the longer the sequences are
Conversely, even if you “only” have a 25% match over long enough sequences, you can rule out with great confidence that the match is random, and therefore conclude homology.
Not sure if this is too rigorous, but seems to me the random sequence alignment follows a binomial distribution with p=0.05
So using a binomial calculator like this one http://stattrek.com/online-calculator/binomial.aspx
…with the following input
Probability of success on a single trial = 0.05 (5%)
Number of trials = 300 (alignment length)
Number of successes (x) = 87 (a 29% match means 87 out of 300 AA match)
the probability of having at least a 29% match at random (87 or more AA’s match out of 300) is exceedingly low
P(X >= 87) = 0.0000000000000012 = 0.00000000000012%
…and therefore the 29% match is pretty good evidence of homology
John Harshman,
Makes sense, thanks John
phoodoo,
It’s not surprising you are unaware of this, as it’s only been known about for half a century. Given you are still at ~200AD levels of knowledge this is understandable.
I can understand your confusion. “Clocks” are built by humans to tell the time and as such it is confusing to you that there is also a concept of “clocks” beyond this. However that is indeed the case.
This may help: As time goes by: A simple fool’s guide to molecular clock approaches in invertebrates
I picked that paper especially for you. Can you guess why?
Haha, you didn’t read the paper did you fool?
Let me help you out:
So not a clock, a technique And controversial. And perhaps not accurate. And an imbalance between the software and data. And unreliable. And not a clock!
You are spastically funny.
That’s exactly how far phoodoo read. He read a summary wherein it is stated there is controversy, and then that’s it, phoodoo now thinks this means it has been proven that everything about the molecular clock is absolutely and complete bullshit. This is how their brains work. There is no such things as nuances, grey zones, approximations or areas of limited applicatbility. There is just black and white. It is either absolutel certainty, or complete ignorance. If we don’t know everything, then we don’t know anything. That’s their world-view.
There couldn’t possibly be things for which the molecular clock works well and others where it doesn’t. There couldn’t be areas where it is precise, and areas where it is isn’t. Phoodoo doesn’t want to have to read a long document and understand the different possible applications about it. There is controversy surrounding it, so it must all, all of it without any middle ground or confounding factors or limited areas of applicability, be complete bullshit.
It is impossible to have a consersation about a complicated scientific topic with a person who thinks like that. And phoodoo thinks like that. The author of that document made a grave mistake. There is no such thing as a guide for a simple fool.
Darwin,
See phoodoo! Even Darwin said his own theory was absurd! I guess you win.
Oh by the way, I discovered that I have misremembered the degree of homology between F-NylB and P-NylB. It is 37%, not 88% as I mistakenly wrote. I went back to check our conservsation we had on the first page on this thread where we went over these numbers first.
The 88% similarity is between NylB and NylB’ (both of which come from the pOAD2 plasmid in Agromyces), which must therefore have happened more recently (though their divergence must still be millions of years, but perhaps not hundreds).
The 37% similarity between F-NylB and P-NylB is what is estimated to yield a divergence of at least 140 million years according to, in Yomo et al 1992:
This 37% similarity for the two proteins with he same enzymatic function is good enough to infer homology. At least, I presume Sal agrees F-NylB and P-NylB are related, but evolved from a common ancestor by gene-duplication and gradual divergence.
Yet a 36% similarity to lots (hundreds) of other proteins isn’t (according to Sal). And a very significant structural alignment? Well gee I guess there’s either no explanation for it, or it could just be chance that a previous and overlapping reading frame to the F-NylB sequence happens to produce a sequence that can be aligned to other proteins with 36%-ish similarity scores, and it’s just chance that it happens to adopt the fold it does. Sal, the worshipper of chance. What is it Mung says all the time? It just happened, s’all.
If ID was true, I would not expect molecular clocks to ‘tick’ at all. And yet they do, even if as phoodoo himself admits, inaccurately.
Did you? All the way to the end? Or did you just stop at the point they were setting up the scene?
If you are happy to quote and agree with part of the paper then presumably you have no objection to that same papers conclusion? Hence you have hoisted yourself on your own petard.
The problem creationists never want to address is consilience. If we have multiple independent sources of information all pointing to the same conclusion creationists either ignore that fact or attempt to discredit the science.
What approach will your denial take phoodoo?
If two largely independent molecular clock strategies yield concurrent results do you conclude coincidence?
Or is that, somehow, evidence for design?
As we say from your exposure to the law of large numbers and % similarity earlier, it seems you are getting your education for free once again.
Where there is controversy there is opportunity. Perhaps phoodoo will step into the fray with his own paper explaining why everybody else just must be wrong.
The P-NylB enzyme sits on an entirely different plasmid from pOAD2. It will be interesting to find out whether this enzyme also sits inside an overlapping reading frame. I guess I will have to do this work myself sometime in the upcoming week.
Why not?
Rumraket,
Just to be clear, do you really believe that ancestral sequence that Ohno concocted along with the typo really existed millions or billions of years ago?
Do you believe that ancestral sequence that Ohno concocted along with the typo existed just before 1935 when nylon’s debut was made, and then that frame shift happened?
Seriously, if you don’t believe these things, what’s the point of this discussion?
Which pretty much falsifies Ohno’s claim of a post-1935 frame shift. Thank you very much. As you yourself said:
Pretty much falsifies everything you believe about the age of the world ,as well.
Yes I do believe, based on the evidence gathered so far, that there really was once a larger reading frame bracketing the NylB ancestral gene, and that the NylB gene family originated by a frameshift mutation. But that frameshift mutation would have happened
But Ohno didn’t “concoct” it. The sequence really is there on the pOAD2 plasmid. And they apparently yield significant amino acid sequence alignments to other known proteins. And the sequence both before and after the middle T in the ATG NylB start codons, when put together, are predicted by the I-TASSER protein structure prediction server, to match with a high significance, the structure of an existing family of proteins from the eukaryotic nuclear pore complex.
You are right about the typo though. He incorrectly inferred a stop-codon where the DNA sequence doesn’t actually show one. It seems that the reading frame extends beyond where he thought it stopped, but from DNA sequence comparisons the downstream DNA regions of NylB and NylB’ on pOAD2, it appears they highly diverge and as such, I don’t believe that region yields an amino-acid sequence we can trust to be representative of any putative ancestral state.
No, I don’t believe there was an expressed protein there just before 1935. It would have to be much, much older.
Yes and I still think that. I haven’t changed my mind.
But Sal it seems to me you’re stuck between a rock and a hard place here.
If you deny that a frameshift mutation can just so happen to create a new functional protein fold, then how do you explain the fact that Ohno’s inferred ancestral sequence produces such a significant structural alignment, not to mention the sequence-similarities I found?
Either you think a frameshift mutation happened by chance. Or you think the other reading frame that you reject ever coded for a functional protein, nevertheless just so happens to yield this, by chance:
It seems to me none of these options bode well for the ID-creationist case against the evolution of new protein folds and functions.
Heck, the unshifted sequence is on POAD2!!!! You haven’t proven your point.
At issue is PR.C not the unshifted sequence on POAD2.
You want to argue the PR.C sequence was there millions of years ago, including Ohno’s typo? Not believable.
The frame shift isn’t confirmed by amino-acid sequences but by nucleotide sequences. Not to mention some of your hits were in EUKARYOTES!
FWIW, I’m conferencing with some other creationists on this and what you say is being reviewed. So far your amino acid sequences are not deemed persuasive to us, and I’m not so sure your evolutionist peers would find your arguments convincing either.
That said, I do value what you’re saying and I want to give it a fair hearing BECAUSE……..
If I publish an essay on this, we’ll be having to go over the same ground.
Better we settle the issue now. I’m not trying to be combative, we do agree on the major point of interest to creationists:
If by “expressed protein” the protein coded by PR.C then we’ve come to a difficult agreement, but I doubt it existed at all because that would entail believing Ohno’s typo was there too millions of years ago.
It says nothing about the ID argument.
The assumption that because something happened it must have been likely to happen and thus likely to happen all the time is just ludicrous.
Earth calling all Skeptics!
I like this line from Venema:
I see what the distracting tree is in this analogy. I wonder if he ever gets around to explaining what the forest is.
phoodoo,
This is what Venema always pointed to as experimental support for macro evolution. This is a big setback for Bio Logos for those who pay attention. His claim was the sudden evolution of a nylon enzyme through a frame shift. The fact the enzyme previous existed prior to nylon voids his claim.
You posted an “abstract” earlier. Abstracts generally are associated with papers. Will this “essay” be peer reviewed by experts in the field? Why not? You are happy to have your work “reviewed” here. Are you just getting it to a standard where the obvious errors are removed, leaving the rubes in awe?
And of course there are only 6000 years to play with, right?
I don’t know this Venema person, yet it’s absolutely ridiculous to say that he’s used an example of frameshift mutation as “experimental support for macro evolution”.
Obviously he’s never done any such thing.
Oh look, another total non-sequitur. Mutations happened millions and billions of years ago too.
I’ve read Venema’s articles on nylon-eating bacteria and I’ve seen no claims about macroevolution. What he said is that this is experimental evidence of a novel protein, that debunks Axe’s 10^77 nonsense
Uhh yes, where the hell else would it be?
At this stage I have to ask if you’re even aware of what my point is.
Yes, PR.C is the putative ancestral coding frame, and what you here call the “unshifted sequence” is the coding region for NylB. Right?
The PR.C sequence was there millions of years ago, yes. Not including Ohno’s typo though. I don’t know how far the original reading frame extended, but the data we have now also doesn’t allow us (in my estimation) to infer when it stopped. Again, because the downstream DNA region after the NylB and NylB’ stop-codons on pOAD2 diverge a lot in sequence.
They even write this in Okata H et al 1983:
“The Homology of 88% between the nucleotide sequences of the nylB and nylB’ genes decrease remarkably downstream of the termination codon. Tis might indicate a high frequency of nucleotide substitution in plasmids in the absence of a selective force.”
I have attached a picture to show you what I mean.
The upper line in Okata H et al 1983 is the NylB sequence, the line below it is NylB’. The differences are noted with nucleotides in the bottom line, the identities aren’t shown (blank spaces). So where there is a letter in the upper line, but nothing in the line below, the two sequences are identical.
So we can pretty clearly see what they mean. The two downstream regions after the stop codon substantially diverge. This is why I would say that, even if the original reading frame extended into this region, it would be pointless to try to work out how far it extended, because the ancestral state of this region is not preserved, so nothing meaningful can be inferred from it:
So my point is that we have evidence that strongly indicates that there was once another intact reading frame on pOAD2. This is the PR.C reading frame. The one that has been split into two by a single nucleotide (a T-insertion).
A bit inside this PR.C read frame, a single T-insertion created a new start-codon downstream from the PR.C start codon. This is what spawned the NylB/NylB’ ancestor.
We can still see this original reading frame on the plasmid. And it is split in two by that T insertion. It begins upstream from the NylB start codon. And we can still see it overlapping the NylB reading frame on the NylB start codons.
When we put these two sequences together (in effect, we ignore the T that purportedly created the NylB reading frame), we get a larger reading frame. This larger sequence of bases codes for a series of amino acids which, when I sent it to the I-TASSER server for protein structure prediction, I got that very significant structural match to a large portion of an existing protein.
This larger sequence of bases codes for a series of amino acids which, when we do searches for homologous sequences in uniprot, we get hundreds of hits with 30%-ish similarity and significant E-values for stretches of over hundreds of amino acids. One of the best is a hit with 36% similarity for a >350 aa stretch. This is a signficant indication of homology.
Also, the upstream (to the NylB coding region) portion of the PR.C coding region, codes for 32 amino acids before it starts overlapping the NylB reading frame. That 33 amino acid portion of the PR.C region codes for a fragment of a protein that gets a 97% match to an existing protein.
These are all things the frameshift hypothesis explains. Otherwise, why the hell would we even detect these similarities? Why would there be that upstream coding region to NylB if there was never an actual protein there? Why would it be 97% identical to a similar fragment in an existing protein? Why would the rest of the protein produce 30-35% indentical hits to other proteins in uniprot? Why would that whole reading frame get such a significant structural alignment to an existing protein? Why would there even be such a long, larger reading frame in the first place, only really interrupted by that single T nucleotide that Ohno infers was the one that came from an insertion and resulted in a frameshift? For this collection of facts, Ohno’s frameshift hypothesis has remarkable explanatory power. What is your explanation? You don’t even have one. You just sit there and declare that you don’t find it convincing.
You ask why we find matches to proteins in eukaryotes? There are several possible reasons (which we can’t determine which one of is correct with the limited work we’ve done so far). One of which is because the PR.C has a
common evolutionary history that goes that far back.
Or it got into eukaryotes by HGT. Or it got into bacteria from eukaryotes by HGT. This is a complete non-issue for evolution. Heck, it could just as well be another small piece of evidence that testifies to the common evolutionary relationship to eukaryotes and bacteria.