Susumo Ohno (who coined the term “junkDNA”) published a paper in 1984 through the National Academy of Sciences that was used by the NCSE, Ken Miller and Dennis Venema to claim “proteins can evolve without God’s help”. At the request of John Sanford, a courtesy associate research professor at Cornell, I was recruited to write a paper to refute Ohno’s evolutionary hypothesis on nylonases. I wrote it under John’s guidance based on his intuitions about genetics, his life-long specialty of 40 years and for which he became famous as attested by the fact he is one of the few geneticists who had their work featured in the Smithsonian National Museum of American History.
The actual paper is now in review, but it is not intended to be published in any journal, but will be released in a variety of channels shortly. It is hoped the material can be used by others to actually create papers that enter peer review. The motivation for releasing the paper in this way is to counter Venema’s book while it is still hot off the press.
The paper is being also published in this way so as to invite discussion since it isn’t intended to be considered a completely vetted product but one that welcomes improvement. That said, the sentiment among IDists and creationists who’ve seen the drafts is that paper has utterly discredited Ohno’s claims and thus the claims of the NCSE, Ken Miller and Dennis Venema connected to Ohno’s hypothesis of nylonase evolution.
Because the draft paper is a massive VJTorley-sized paper (15 pages in the main section and almost 80 pages of supplemental material) I’m establishing this thread at TSZ to invite review of the some of the themes from the paper that I’m releasing on the nylonase.XYZ website piece by piece in a format adapted for a website.
As I release each webpage, I’ll post in the comment section at TSZ a link to the newly constructed page so as to invite commentary on that page. Thank you in advance to all those willing to participate in this public review of my research on nylonase evolution.
NOTES:
1. “proteins can evolve without God’s help” is a paraphrase of the title of an NCSE article New Proteins Without God’s Help. Thwaites at the NCSE basically framed the debate over nylonase evolution in this way:
We’ve been trying to explain all this to the protein “experts” at ICR for the last seven years. We have told them that new proteins could indeed form from the random ordering of amino acids. We have warned them that their calculations were based on faulty assumptions and soon someone would document the natural formation of a new protein from the random association of amino acids.
Now it has happened! Not one, but two, new proteins have been discovered. In all probability new proteins are forming by this process all the time, but this seems to be the first documentation of this phenomenon. The newly discovered proteins are enzymes that break down some of the byproducts produced during nylon manufacture. Since nylon first came into commercial production in 1940, we know that the new enzymes have formed since that time.
2. The nylonase.XYZ website is under construction, so don’t click around the website too much yet. In the comment section at TSZ I will link to individual pages of the website that can be reviewed individually.
3. The first comments by me at TSZ will be more technical, not for the beginners regarding Ohno’s work. The beginner and introductory stuff will be added later to the website.
He’s certainly an IDist when it comes to assuming that “God” can make new proteins sans any evidence at all.
One can’t really publish a paper that assumes an imaginary cause to be the default explanation. Just part of Darwinist “persecution,” this demand for evidence of ID claims.
Glen Davidson
OMagain,
Sal likes free handouts, for himself.
I like it even more when other people are forced to pay for it.
Speaking of the Kansas hearings, this is how I first learned of John Sanford, his awesome testimony at the Kansas hearings in 2005, 12 years ago!
A highlight of the corresponding co-author, John Sanford, of my paper (Dr. Sanford listed me as principal author):
So that was 12 years ago, and now you’ll get to see a paper by me and John Sanford in not too long. 🙂
On which he listed you as principle author.
That is a nice personal testimony without any actual arguments or evidence. Fits nicely into the creationist worldview, so it makes creationists feel good to read it. And that’s what matters of course, not evidence and facts.
Q: How do you tell if a scientist is a creationist?
A: When Sal mentions his name, he puts “Doctor” in front of it. And maybe “eminent” or words to that effect too.
Nice story, but I don’t believe a word of it. Sanford is fooling himself. By the way, what sort of creationist is he? Is he YEC? Does he believe in a flood? What does he think a “kind” is?
Those clever evolutionists. They avoided scrutiny by not being allowed to testify.
Sal,
I genuinely can’t wait to see scientific evidence of an alternative to evolution.
It appears so
I made a post showing Sanford is actually a YEC, they had a couple of links. The post does not seem to be here? In any case, Sanford seems to be a proper hard core YEC basically because he thinks that purifying selection could not have removed mutations from humans in such a long time period as evolution requires.
perhaps I can edit the link in: http://blog.drwile.com/junk-dna-and-evolution/
As such, perfect lab partner for Sal. Did you get near a lab Sal, out of interest? ;P
It seems any post I make with a link in is marked as spam. go here: blog.drwile.com/junk-dna-and-evolution/
It seems any post I make with a link in is marked as spam. go here: blog.drwile.com and search for junk-dna-and-evolution
There will invariably be a nice history about his looong career with lots of papers and patents and hard-working “cutting edge” research at some prestigious, well-respected, (or “highly reputable”), well-funded, institution with lots and lots of employees.
And yes, all of those are various phrases Sal have used to describe institutions and journals when he can fit them into his arguments.
Let’s see some examples. I found these simply by searching for the words “professor”, “harvard”, “prestigious”, and “Cold spring”. With those as your search terms, you OVERWHELMINGLY find Sal posts.
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Seriously, this one almost makes me vomit. It’s one long argument from authority. The authority of the soo prestigious institution NIH with all it’s money and projects and esteemed researchers bla bla blearugh!
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Yes, here he’s responding to me calling him out on the constant silly namedropping of institutions.
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Aaand then I got tired copy-pasting. The list is basically endless. This is one of Sal’s chief methods of argumentation, the appeal to a cherry-picked authority fallacy. It seems he literally cannot even mention a publication in so far as it is published in nature, without saying that and making sure to emphasize that it is a prestigious journal.
How disgustingly pretentious.
I think it’s ok that Salvador makes sure we know he only reads prestigious journals. None of that AiG crap for him.
And if it’s in the peer-reviewed prestigious scientific journal nature, well gee I guess it must be true.
Like associate professor and PhD biochemist Douglas Theobald’s (who’s peer-reviewed publications were cited over 260 times in 2016 alone) A formal test of Universal Common Descent.
Or highly respected PhD biochemist and Nobel Laureate, Dr. Jack Szostak’s (from Harvard Medical School and who’s work was cited over three thousand times in 2013 alone) papers on the origin of life.
And now I’ll go and vomit.
Would you prefer I cite “Kairos Focus at UncommonDescent”?
stcordova,
We would prefer that when you cite something you don’t accompany it with puffery. We would prefer that when you mention a creationist you don’t accompany his name with puffery. You should listen to me because I have a PhD from the prestigious University of Chicago and have published in the prestigious journals Science and PNAS. And I drive a shiny car.
If John had ever been listed as principal author he would have mentioned it. Sorry John, but you’re no Salvador Cordova. But don’t give up.
Rumraket,
Pardon my lack of manners here, I should have thanked you earlier for finding the explanation for “sp”. I actually got hung up on what it meant when writing the paper last month and eventually gave up trying to figure it out. I actually thought it might mean “spherical”! So, profuse thanks.
Also thank you for taking the time to explain plasmids and chromosomes. Having taken biochemistry (but not organic chemistry), I was in a lecture where they described the rolling circle replication, and I would have sworn the professor said the chromosome was a plasmid, but well, I didn’t pursue it further since that really wasn’t the main data points of the lecture. It was all this stuff about initiation complexes etc. So that was very interesting what you said.
I was aware of BAC amplification and all, but I was curious how the bacteria process all these circular forms floating around. Perhaps a more fundamental question is how does the bacteria know it’s chromosome is a chromosome and not a plasmid? Is it just the sheer size? When they do gene sequencing how do they distinguish the plasmid DNA form chromosomal DNA? That doesn’t seem like an easy thing to do unless one can actually pull a chromosome out of the bacteria or a plasmid out of the bacteria in isolation. Do bacteria have more than one chromosome? I really want to take a microbiology class, a cellular biology class, an anatomy and physiology class, etc. So much to learn. Thank you again for taking the time to explain this basic stuff to me.
I hope there is something of value you are getting in exchange from me in these interactions. Thank you again.
John Harshman,
Not just Sal. It is a distinctive habit of VJ Torley’s too.
Allan (BSc (Hons), partial-PhD, 25 Yard Swimming Certificate).
Yeah pretty much.
Some pretty basic low-tech things like centrifugation, differences in solubility determined by size or charge, or gel electrophoresis can separate molecules by size quite easily.
You can get commercial plasmid purification kits where you go through a few steps with a couple of different methods and end up with only plasmids extracted from cell culture.
https://www.jove.com/science-education/5062/plasmid-purification
Allan (BSc (Hons), partial-PhD, 25 Yard Swimming Certificate),
So nice to see our resident biochemist! How ya doin’?
I (Sal the trouble maker) have a picture here of a peptide bond which I’ll explain it’s relevance to nylon, in the next comment.
Here is a nylon-6 dimer composed of two 6-aminohexanoic acids (with the one on the left de-hydrated). You’ll notice the peptide bond joining the two 6-amino hexanoic acids. Do you agree that it makes sense that a protease like trypsin can cleave such a nylon dimer in light of the similarity of peptide bonds in proteins with peptide bonds in nylon-6 dimers?
Proteases are generally more specific than that. They don’t cleave just any peptide bond. Trypsin, for example, cuts the bond between lysine or arginine and anything except proline. (Proline is odd, because it isn’t actually an amino acid.)
In at least some bacteria, the chromosome is attached to the cell membrane, but plasmids are not.
stcordova,
I confess I have stumbled in somewhat underprepared (just grasped the opportunity for a smartass joke, as one does), but surely this could be established empirically?
I was alluding to an actual experiment in 1959 that established trypsin to be a nylonase. Even mammals express trypsin genes….
I actually found the experiment tracking back Ohno’s paper and the references;
Ohno 1984 referenced Okada 1983 which referenced Kinoshita 1977 which referenced Kinoshita 1975 which referenced Fukumura 1966 which referenced Ebata 1959. Ebata showed trypsin cleaved nylon.
When I learned of this, I was motivated to actually look at the molecular structure of nylon. The nylon monomers are dehydrated 6-aminohexanoic acids, and 6-aminohexanoic acids are Lysine analogs.
6-aminohexanoic acid is also known as aminocaproic acid. You can see the similarity below between the nylon-6 monomer (aka aminocaproic acid) and lysine. The peptide bond in nylon is in proximity to the epsilon carbon not the alpha carbon (such as in proteins) , but I’m told (and I don’t have organic chemistry under my belt) the peptide/amide bond is structurally similar that connects nylon monomers to each other in a nylon polymer as peptide/amide bonds that connect amino acids in a protein.
I suspect these similarities are why bacteria are able to cleave a man-made substance because the man-made substance has passing resemblance to a biological substance.
That said, mammals can’t actually live off of nylon, it takes more than a nylonase enzyme to make a nylon metabolism workable.
Note that trypsin is not very good at digesting nylon dimers. I think that’s a more important point than what you’re trying to make.
Rumraket,
Thanks for the information about plasmids. Reviewing the list of organisms with nylB, it would be interesting to see which of the organisms had the nylb on the plasmid or the chromosome. UNIPROT lists proteins based on the organism it was found in, and perhaps in many cases it’s actually on a plasmid rather than a chromosome.
Thanks again.
Rumraket,
Thanks for the link on the plasmid extraction. Also on that page was an advertisement about genetic engineering through biolistic bombardment with gold particles which was the technique John Sanford pioneered. It actually shows the modern Gene gun.
https://www.jove.com/video/2090/generation-of-transgenic-c-elegans-by-biolistic-transformation
Interesting discussion, anyway. But, seeing a protein as ‘not-all-that-novel’ doesn’t particularly help the anti-evolution cause, as far as I can see. They have to come from somewhere, to state the obvious. But we get this heads-I-win-tails-you lose thing. If they were lacking above-threshold homology, they’d be ORFan genes, another ID favourite.
What would be cool is a set of frozen samples going back to 1935, filling in history a bit.
Agreed, and I’ve gone on record as taking a little bit more on the Darwinist side of the issue of protein capabilities of function.
The fact that trypsin can cleave nylon is an example of an enzyme that can undertake multiple functions.
The classic example, quite well confirmed, is Rubisco whose active site works as either a carboxylase or an oxygenase.
The other issue shown is that there are multiple architectures that can break down nylons: proteases, lipases, beta lactamases, 6-aminohexanote hydrolases, amidases , peptidases, etc.
That said, I going to list Doug Axe’s work on beta lactamases, not because I’m 100% convinced it’s correct, but because I think the issue is not completely settled. There may be an infinite number of ways to be lock and key systems, and in fact, there may be numerous different keys that can fit in a lock, it doesn’t make the lock highly probable. If we look at the active enzyme site as a lock and the substrates that can be inserted in the active site as the variety of keys, then the question is open, imho.
I also do think a single or double residue change can enable a nylonase homolog (“nylonase” is a misnomer) to actually adapt and cleave nylon. But that also means a single or double residue change can break the adaptation. Something about nylon makes it a low hanging fruit. I haven’t looked at the activation energy profiles of the amide bonds in nylon. Should they be the same as for the amide bonds in biological organisms? That’s not my specialty.
stcordova,
Axe? Meh. Extensively discussed. Basically, if you donit know the density of function, you can’t really come to any conclusion about it. I threw a rock and failed to hit a buffalo. There are no buffaloes.
The Axe reference constitutes 1 or 2 sentences in an 80 page paper.
Most of the discussion is an ad nauseam listing of the widespread distribution *(geographically and organismally and proteomically) of nylonase capabilities. Thus it refutes the notion that nylonase NylB was a 400-residue instant evolutionary response via frameshift to the arrival of nylon after 1935 as Ohno and Venema and Ken Miller claimed.
Instead of Ohno, Dr. Sanford and I argue the nylonase homologs pre-existed and were adapted (if at all) to nylon via mechanism akin to those observed in evolution of antibiotic resistance.
stcordova,
So what does this reduce the known number of frameshifted homologies down to? Probably not zero. It seems to me that one has taken on the task of trying to prove the negative.
Certainly, scientists have doubted Ohno’s suggestion in this case. But the very fact that a couple of bases could give rise to this ability refutes the Creationist notion about ‘no new information’. Of course the back mutation and many others will break it – but that is where selection comes in. If A – B removes information, there is clearly a logical case to be made that B – A would add it.
Perhaps you suck at rock throwing.
This is hardly an earthshaking discovery. Are you quite sure it isn’t well-known in the literature already? It seems in fact to be an obvious conclusion from data that had been known before Ohno wrote the paper, which required him to jump through some implausible hoops.
Why was there any point to the Axe reference, no matter how brief?
And when you say “those observed in evolution of antibiotic resistance”, what mechanisms specifically are you talking about, and why not just name them instead of this vague allusion?
Yes. It’s not well known by the Darwin promoters like Ken Miller (expert witness at Dover vs. Kitzmiller) and Dennis Venema of Biologos.
“Well known” may mean many things. Maybe to the specialists, but not the average scientist. Our paper is intended to help ensure people know the truth!
Venema in 2016, who fancy’s himself as some sort of expert on the creation evolution controversy and who wrote an anti-creationist book in 2016 wrote:
http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/intelligent-design-and-nylon-eating-bacteria/
If Venema doesn’t know he’s mistaken, then in my opinion it isn’t well known enough in the literature. So in answer to your question, “Yes”!!!!!!
Venema is proof.
stcordova,
Of course I was referring to the specialists. It’s ordinary scientific courtesy if you’re going to publish a paper to check whether your idea has already been published by someone else. Have you done that? Are there any published scenarios for the evolution of NylB other than Ohno’s? Do you cite them? Are there any published papers in which Ohno’s scenario is critiqued? Do you cite them? This is the sort of thing a literature search, part of the ordinary scientific process before writing and publishing a paper, is supposed to deal with. You shouldn’t take credit for work already done by someone else.
There are in fact papers that argue against Ohno’s frameshift hypothesis. Sal himself have brought them up in previous discussions.
Yeah, I know there are such papers. So in fact Sal’s paper is actually just a literature review. Nothing wrong with that, as long as he actually reviews and cites the relevant literature. Might I suggest a search of BIOSIS for papers that cite Ohno 1983?
Thanks, and btw, it’s Ohno 1984.
I tried your suggestion just now, and Dr. Sanford and I should have tried it earlier. So thanks for pointing out our oversight.
That said, BIOSIS is outside my personal institutional access from a remote location. I don’t feel like driving out there right this moment.
That said, I found something even better just now at the NIH!
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC345072/citedby/
Which are mostly favorable citings of Ohno.
This whole argument about what specialists know seems a bit moot given the state of affairs of journals still citing Ohno 1984 as a credible source. YIKES! Goes to show how gullible the industry is. 🙂 And why our paper needs to be written and put on the table.
stcordova,
Have you actually looked at those references? Almost nothing you found is relevant to the origin of NylB. I looked at the most promising one, and the reference to Ohno is nothing more than a statement that he had an idea of how one particular gene had originated, with no assessment of his credibility. Didn’t even mention the gene, and said nothing about whether the theory was true. How many of the rest are like that? No, you have to find discussions of NylB evolution that cite Ohno, not irrelevant papers. I notice that the relevant ones I know about are not on that list, for whatever reason.
24 papers are citing Ohno according to pubmed. Only some of them are about de novo gene emergence by frameshift mutation.
“The industry” is gullible. Riight.
Besides, there are actually papers citing Ohno not listed as citing him on pubmed, at least one of which argues against the frameshift hypothesis. One example is
Negoro S, Ohki T, Shibata N, Mizuno N, Wakitani Y, Tsurukame J, Matsumoto K, Kawamoto I, Takeo M, Higuchi Y. X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme.
PMID: 16162506 DOI: 10.1074/jbc.M505946200
BIOSIS indexes many, many more journals than PubMed does. But I’m surprised not to see a JMB paper on the PubMed list.
Rumraket,
Thanks for the 2005 article. But for the record, I’ve cited the earlier 1991 paper by Kato (that has at least one of the same authors as the 2005) many times here at TSZ and in our paper. The 1991 Kato paper says:
compare this with the great discovery in 2005!
I could have mentioned the 2005 paper in our paper, but I felt the 1991 paper by Kato should have been sufficient. Strangely Kato 1991 however didn’t mention Ohno. Ohno passed away in 2000. I could be totally wrong, but that seems like a decent thing to spare the old man from having to try to defend himself in his old age. Just a speculation.
Our paper however criticize a post-1935 gene duplication scenario that Negoro and Okada and company have been promoting instead of Ohno’s hypothesis. It’s simply non-parsimonious given nylB and nylB’ pairs are spread throughout the bioshphere. The are often non-sequence similar between organisms even though UNIPROT calls them nylB and nylB’ genes.
John Harshman,
Do you use the BIOSYS system a lot in your work? I think you gave an excellent suggestion. I’ll pass the suggestion on.
Part of the reasoning for Dr. Sanford and I writing the paper is to clarify and codify our own thoughts on the matter. The writing process is an extension of our own thought process.
The paper is a monstrosity, and Dr. Sanford said he wanted feedback on it’s accuracy before trying to go to something more formal like a journal paper. I doubt it can be digested whole by any journal in present form since it is so enormous. I suggested to him we solicit feedback in the public sphere for the minutia of the paper.
We both felt, minutia aside, we had effectively falsified the claims of Veneman and Ken Miller and so publishing the paper outside typical channels served the purpose of inviting critical review of our work but falsifying the claims of Venema and Ken Miller in their respective books.
So in many respects, it’s somewhat satisfying that Dr. Sanford and I were able to arrive at the conclusions we did on our own by synthesizing the data available to us.
If what we wrote duplicates the work of someone else, then we will take it as confirmation we were on the right track. Of course, we would want very much to acknowledge if someone else has said what we have said. So to that end, I take your suggestion seriously, and if you do find such evidence of someone saying what is essentially said in our paper, we would gladly give proper attribution to him.
Thanks again for your time.
I’m saying that it’s your responsibility to discover if there are such people. I also find it odd that you say your paper is so long, because so far it doesn’t seem to be saying much that requires great length.
BIOSIS is the standard database of journal citations. Used to be printed, but I don’t know if that happens any more. Sanford didn’t know about it?