Uncommon Descent Serving The Intelligent Design Community

John Sanford on claims about brand new nylonase genes


Recently, we noted that John Sanford was speaking at NIH on human health and mutations. Philip Cunningham writes to mention a 2017 paper by Sanford and S. T. Cordova, Nylonase Genes and Proteins – Distribution, Conservation, and Possible Origins on whether the ba cteria that digest nylon evolved new genes:

We began this work hoping to better understanding the various claims regarding the de novo origin of certain nylonase genes. The idea that nylonases would have arisen very recently, de novo, was based upon the widely-held assumption that nylonases would have been essentially non-existent prior to the artificial manufacture of nylon. This basic assumption would not be justified if there were any nylonlike polymers in nature, or if nylonase activity required very low specificity, such that enzymes with other functions might also possess or acquire nylonase activity.

Our analyses indicate that nylonase genes are abundant, come in many diverse forms, are found in a great number of organisms, and these organisms are found within a great number of natural environments. We also show that nylonase activity is easily acquired through mutation of other enzymes, which strongly suggests that nylonase activity has very low specificity of the active site. These findings refute the widely held assumption that nylonases were essentially non-existent before 1935. In this light, there is no reason to believe that any nylonase emerged since 1935, and so there is no solid basis for invoking any de novo nylonase genes. Therefore, it seems only reasonable to reexamine the earlier claims of de novo genes. More.

More from the Biologic Institute about nylon-eating bacteria.

Hat tip: Philip Cunningham

Follow UD News at Twitter!

See also: John Sanford gives lecture at NIH on mutations and human health

John Sanford: Darwin a figurehead, not a scientist


John Sanford: Accepting Darwinism’s collapse is a matter of scientific integrity

Call it whatever you like. I consider it a 'glass half full' situation since you gave me an opportunity to once again expose, for unbiased readers, how atheistic Darwinists support their theory, not by any compelling empirical evidence, but by systematic censorship, intimidation and even expulsion of anyone who dares challenge what is, in reality, the pseudoscientic religion of Darwinian evolution. Of related note, Dr. Behe deserves kudos for standing up for the truth in the face of the Darwinian schoolyard bullies:
So, Michael Behe Was Right After All; What Will the Critics Say Now? - Casey Luskin July 16, 2014 Excerpt: Will Ken Miller, Jerry Coyne, Paul Gross, Nick Matzke, Sean Carroll, Richard Dawkins, and PZ Myers now Apologize to Michael Behe? (for their ad hominem attacks),,, Is an apology from Behe's critics then forthcoming? In a world where debates were conducted with the goal of discovering truth rather (than) scoring points, it sure ought to be. Unfortunately, I'm not sure we live in that world. What we'll probably get is nothing more than PZ Myers's concession, offered in the context of the rant quoted above,,, http://www.evolutionnews.org/2014/07/so_michael_behe087901.html
You can pre-order Dr. Behe's forthcoming book now:
Michael Behe Is Returning With His Latest Book, Darwin Devolves https://www.youtube.com/watch?v=kaHKqOCT3IM Darwin Devolves — Preorder Behe’s New Book; Plus Video Course on Intelligent Design! November 14, 2018 https://evolutionnews.org/2018/11/darwin-devolves-preorder-behes-new-book-plus-video-course-on-intelligent-design/
OK, so even you admit that your argumentum ad gannitum doesn't hold water. Bob O'H
You really do need to read what I wrote before you respond to me Bob (and weave), I already addressed that point in post 4. And I did not even touch upon the many careers that have been ruined by the "Darwinian Gestapo" But since you brought it up:
“In the last few years I have seen a saddening progression at several institutions. I have witnessed unfair treatment upon scientists that do not accept macroevolutionary arguments and for their having signed the above-referenced statement regarding the examination of Darwinism. (Dissent from Darwinism list)(I will comment no further regarding the specifics of the actions taken upon the skeptics; I love and honor my colleagues too much for that.) I never thought that science would have evolved like this. I deeply value the academy; teaching, professing and research in the university are my privileges and joys… ” Professor James M. Tour – one of the ten most cited chemists in the world https://uncommondesc.wpengine.com/intelligent-design/a-world-famous-chemist-tells-the-truth-theres-no-scientist-alive-today-who-understands-macroevolution/
At the beginning of the following video Dr. Behe tells of how the president of the National Academy of Sciences sought to ostracize him for supporting Intelligent Design:
TEDxLehighU - Michael Behe - Intelligent Design - video http://www.youtube.com/watch?v=FCP9UDFNHlo
In the following article, Casey Luskin points out that the following anti-ID philosopher even goes so far as to publish a paper saying that the bullying tactics of neo-Darwinists are justified since many ID proponents are Christian:
Anti-ID Philosopher: "Ad hominem" Arguments "Justified" When Attacking Intelligent Design Proponents - Casey Luskin - June 4, 2012 http://www.evolutionnews.org/2012/06/anti-id_philoso060381.html While Ranting about "Quote Mining" in "Creationists Texts," Paper in Scientific Journal Misquotes and Misrepresents Pro-ID Article - Casey Luskin - March 31, 2015 Excerpt: These following two articles, (published by people with backgrounds in the field of rhetoric, writing in journals dedicated to studying science communication), discuss how evolutionists seek to marginalize dissenters with ridicule and incendiary rhetoric, rather than meeting us head-on with arguments and evidence. http://www.evolutionnews.org/2015/03/while_ranting_a094851.html
If silencing by intimidation, and/or censorship, does not work, often Darwinists simply 'EXPEL' anyone who disagrees with them:
Expelled: No Intelligence Allowed (full movie) http://www.youtube.com/watch?v=V5EPymcWp-g Slaughter of Dissidents - Book "If folks liked Ben Stein's movie "Expelled: No Intelligence Allowed," they will be blown away by "Slaughter of the Dissidents." - Russ Miller http://www.amazon.com/Slaughter-Dissidents-Dr-Jerry-Bergman/dp/0981873405 Origins - Slaughter of the Dissidents with Dr. Jerry Bergman – - video https://www.youtube.com/watch?v=2v5nAYU2GD0&t=10s Discrimination is a pervasive reality in the scientific world. It’s also a hidden reality. Scott Minnich Richard Sternberg Günter Bechly Eric Hedin Don McDonald David Coppedge Caroline Crocker Bryan Leonard Martin Gaskell Dean Kenyon Roger DeHart Granville Sewell https://freescience.today/stories/ Here are many more examples of discrimination against people who dare question Darwinism https://uncommondesc.wpengine.com/intelligent-design/review-of-darwins-doubt-slams-id-theorists-for-not-publishing-in-darwinist-run-journals/
ba77 - there are ID-friendly journals out there too (e.g. Bio-Complexity), so I'm afraid the "nasty evilutionists are censoring our work" excuse doesn't work. Bob O'H
Of related note: In spite of the rampant systematic bias against ID, here are some of the peer reviewed papers supporting ID that have been published anyway:
Peer-Reviewed Scientific Literature Building a Compelling Case for ID - podcast - February 2012 http://intelligentdesign.podomatic.com/entry/2012-02-06T17_08_55-08_00 BIBLIOGRAPHIC AND ANNOTATED LIST OF PEER-­REVIEWED PUBLICATIONS SUPPORTING INTELLIGENT DESIGN - UPDATED – July 2017 http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=10141 Bio-Complexity Publication Archive http://bio-complexity.org/ojs/index.php/main/issue/archive Biological Information - New Perspectives - Proceedings of the Symposium - published online May 2013 http://www.worldscientific.com/worldscibooks/10.1142/8818#t=toc Dr. John Sanford - Links to Selected Papers http://www.logosresearchassociates.org/john-sanford Evolutionary Informatics Lab - Main Publications http://evoinfo.org/publications/
And let's not forget the many distinguished scientists at "The Third Way" who, despite shunning ID, have none-the-less found Darwinian explanations to be grossly inadequate for explaining how all life came to be on earth:
The Third Way - List of Scientists who think Darwinism is inadequate http://www.thethirdwayofevolution.com/people
One final note, it is interesting to note that Darwinian evolution, since Darwinists refuse to accept a rigid falsification criteria for their theory, fails to even qualify as a rigorous science in the first place but is instead best classified, (since again Darwinists refuse to accept a rigid falsification criteria for their theory), as a unfalsifiable pseudoscience:
Darwin’s Theory vs Falsification – video https://www.youtube.com/watch?v=8rzw0JkuKuQ
The following further highlights the fact that Evolution simply fails to qualify as a science by any reasonable measure of science one might wish to invoke and thus, once again. Darwinian evolution is more properly classified as a pseudoscience than a real science.
“There are five standard tests for a scientific hypothesis. Has anyone observed the phenomenon — in this case, Evolution — as it occurred and recorded it? Could other scientists replicate it? Could any of them come up with a set of facts that, if true, would contradict the theory (Karl Popper’s “falsifiability” tests)? Could scientists make predictions based on it? Did it illuminate hitherto unknown or baffling areas of science? In the case of Evolution… well… no… no… no… no… and no.” – Tom Wolfe – The Kingdom of Speech – page 17 Darwinian Evolution Fails the Five Standard Tests of a Scientific Hypothesis – video https://www.youtube.com/watch?v=L7f_fyoPybw
Regardless of the rampant censorship against ID, unless you are a Darwinist, there is nothing surprising about these findings for "preexistent" and widespread Nylonase since they match previous research in this area and also match what was found for antibiotic bacteria: i.e. Though Darwinists love to claim Nylonase as 'new', the simple fact is that it is only a minor variation on previous enzymatic activity:
Debate Debrief: The Two-Prong Canard Demonstrated Within 24 Hours - The Curious Case of Nylonase – March 20, 2016 - Cornelius Hunter Excerpt: Such adaptation to nylon manufacture byproducts has been repeated in laboratory experiments. In a matter of months bacteria acquire the ability to digest the unforeseen chemical. Researchers speculate that mechanisms responding to environmental stress are involved in inducing adaptive mutations. That is not evolution. In fact it refutes evolution. http://darwins-god.blogspot.com/2016/03/debate-debrief-two-prong-canard.html Character and Theology Aside, What About Denis Lamoureux's Science? - David Klinghoffer - March 21, 2016 Excerpt: Lamoureux mentioned the discovery of Nylon-eating bacteria as empirical proof that evolution can create new complex specified information and new proteins (nylonase enzyme) within only 40 years of time.,, Newer research by Negoro et al. (2007) has shown that the nylonase enzyme did not evolve by gene duplication and frameshift mutation as originally assumed, but arose from a pre-existing carboxyesterase enzyme, which already had some capacity to degrade nylon oligomers. In other words: Nylonase is NOT new information (also see here)! http://www.evolutionnews.org/2016/03/character_and_t102708.html The Nylonase Story: When Imagination and Facts Collide - Ann Gauger - May 4, 2017 Excerpt: Thus, EII? and EII did not have frameshifted new folds. They had pre-existing folds with activity characteristic of their fold type. There was no brand-new protein. No novel protein fold had emerged. And no frameshift mutation was required to produce nylonase.,,, Tests revealed that both the EII and EII? enzymes have carboxylesterase and nylonase activity. They can hydrolyze both substrates. In fact it is possible both had carboxylesterase activity and a low level of nylonase activity from the beginning, even before the appearance of nylon. https://www.evolutionnews.org/2017/05/the-nylonase-story-when-imagination-and-facts-collide/ The Nylonase Story: The Information Enigma - Ann Gauger - May 8, 2017 https://www.evolutionnews.org/2017/05/the-nylonase-story-the-information-enigma/ Relationship between nylon oligomer hydrolytic and esterolytic activities” Excerpt: “Based upon the following findings, we propose that the nylon oligomer hydrolase has newly evolved through amino acid substitutions in the catalytic cleft of a pre-existing esterase with the b-lactamase-fold”. Taku Ohkia, Yoshiaki Wakitania, Masahiro Takeoa, Kengo Yasuhiraa, Naoki Shibatab, Yoshiki Higuchib, Seiji Negoroa FEBS Letters 580 (2006) 5054–5058 https://uncommondesc.wpengine.com/intelligent-design/intelligent-design-and-the-demarcation-problem/comment-page-12/#comment-362219
Even Wikipedia, which is notorious for its bias against Intelligent Design, admits that nylonase 'most probably developed as a single-step mutation', thus the adaptation is well within what Dr. Behe has set for the 'Edge of Evolution':
Nylon-eating bacteria - Mar. 2016 Excerpt: There is scientific consensus that the capacity to synthesize nylonase most probably developed as a single-step mutation that survived because it improved the fitness of the bacteria possessing the mutation. http://en.wikipedia.org/wiki/Nylon-eating_bacteria#Role_in_evolution_teaching
As stated previously, this research on “preexistent” and widespread Nylonase also matches what was found for supposedly 'new' antibiotic resistant genes:
(Ancient) Cave bacteria resistant to antibiotics - April 2012 Excerpt: Antibiotic-resistant bacteria cut off from the outside world for more than four million years have been found in a deep cave. The discovery is surprising because drug resistance is widely believed to be the result of too much treatment.,,, “Our study shows that antibiotic resistance is hard-wired into bacteria. It could be billions of years old, but we have only been trying to understand it for the last 70 years,” said Dr Gerry Wright, from McMaster University in Canada, who has analysed the microbes. http://www.scotsman.com/news/health/cave-bacteria-resistant-to-antibiotics-1-2229183# Antibiotic resistance genes are essentially everywhere - May 8, 2014 Excerpt: The largest metagenomic search for antibiotic resistance genes in the DNA sequences of microbial communities from around the globe has found that bacteria carrying those vexing genes turn up everywhere in nature that scientists look for them,, http://www.sciencedaily.com/releases/2014/05/140508121347.htm
Bob O'H asks,
"Has this been published yet? I can find a pre-print from August 2018, but no published version."
Due to the fact that peer-reviewed journals are thoroughly dominated by Darwinists, it is notoriously difficult for IDists to have anything published in peer-reviewed journals. In fact, many times, Darwinists have tried to outright censor ID related research.
How the Scientific Consensus is Maintained (censorship) – Granville Sewell (Professor of Mathematics University of Texas – El Paso) – video http://www.youtube.com/watch?v=vRLSwVRdNes Censorship Loses: Never Forget the Story of Biological Information: New Perspectives Casey Luskin - August 20, 2013 http://www.evolutionnews.org/2013/08/censorship_lose075541.html ID theorist Mike Behe was refused a response in Microbe - September 22, 2013 https://uncommondesc.wpengine.com/irreducible-complexity/id-theorist-mike-behe-was-refused-a-response-in-microbe/ The Letter that Science Refused to Publish - November 8, 2013 Excerpt: Stephen Meyer sought the opportunity to reply, in the pages of Science, to UC Berkeley paleontologist Charles Marshall, who reviewed Darwin's Doubt in the same publication. Without explanation, the editors refused to publish the letter. We offer it for your interest. See more at: http://www.evolutionnews.org/2013/11/the_letter_that078871.html Censor of the Year: Who Will It Be? - David Klinghoffer January 17, 2014 Excerpt: Charles Darwin himself, whose birthday is commemorated on the day bearing his name, insisted that getting at the truth, sorting true from false, requires an unimpeded airing of views: "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question." Ironically, it is his latter-day advocates and defenders who are the most eager to muffle dissenting opinions, and the most unashamed about doing so. And again, not just unashamed, but proud. A victory in shutting down a college class, punishing a teacher, thwarting a law intended to protect educators from administrative reprisals, intimidating a publisher into a canceling a book contract, erasing words from the wall of a public museum -- such things are not merely done, they are candidly, brazenly bragged about. - per Evolution News and Views It’s Darwin Day, and the “Censor of the Year” Poster Has Landed – February 12, 2014 http://www.evolutionnews.org/2014/02/its_darwin_day_082121.html Casey Luskin - Examining the Evidence for Evolution, podcast - pt. 1 (March 2015) (Censorship and Ad Hominem) http://www.discovery.org/multimedia/audio/2015/03/examining-the-evidence-for-evolution-pt-1/
As well, in regards to censorship, many times Darwinists will try to cite Wikipedia as a reliable source for information, yet the fact is that Wikipedia is not reliable as a source for information especially when it comes to the Intelligent Design/Evolution debate because of the problem of censorship within Wikipedia:
Wikipedia's Tyranny of the Unemployed - David Klinghoffer - June 24, 2012 Excerpt: PLoS One has a highly technical study out of editing patterns on Wikipedia. This is of special interest to us because Wikipedia's articles on anything to do with intelligent design are replete with errors and lies, which the online encyclopedia's volunteer editors are vigilant about maintaining against all efforts to set the record straight. You simply can never outlast these folks. They have nothing better to do with their time and will always erase your attempted correction and reinstate the bogus claim, with lightning speed over and over again. ,,, on Wikipedia, "fact" is established by the party with the free time that's required to wear down everyone else and exhaust them into submission. The search for truth (on Wikipedia) yields to a tyranny of the unemployed. http://www.evolutionnews.org/2012/06/wikipedias_tyra061281.html Wikipedia: where truth dies online - April 2014 Excerpt: Wikipedia has been a massive success but has always had immense flaws, the greatest one being that nothing it publishes can be trusted. This, you might think, is a pretty big flaw. There are over 21 million editors with varying degrees of competence and honesty. Rogue editors abound and do not restrict themselves to supposedly controversial topics,,, Sock puppets are a big problem for Wikipedia because so many of its editors are anonymous. This makes it almost impossible to verify bona fide users. Wikipedia literally has no idea who many of its editors are. ,,, One columnist for The Times has likened Wikipedia’s reliance on consensus ahead of accuracy to an interminable political meeting with the end result dominated by the loudest and most persistent voices. Jaron Lanier, a computer scientist writing for an online publication, Edge, described Wikipedia as a ‘hive mind’ that is ‘for the most part stupid and boring’. http://www.spiked-online.com/newsite/article/wikipedia-where-truth-dies-online/14963#.U2KB0Vc9iSq Wikipedia Erases Paleontologist Günter Bechly - David Klinghoffer - October 10, 2017 Excerpt: Günter Bechly is a distinguished paleontologist, specializing in fossil dragonflies, exquisitely preserved in amber for tens of millions of years. After revealing his support for the theory of intelligent design, he was pushed out as a curator at the State Museum of Natural History in Stuttgart, Germany. He subsequently joined Discovery Institute’s Center for Science & Culture as a Senior Fellow. Now we learn that our colleague has suffered another act of censorship: he has been erased from Wikipedia, ostensibly for not being “notable” enough.,,, ,,, It’s a mad world, a funhouse world, where the notability of a paleontologist of Günter Bechly’s stature is uncontested one day but, following his admission of finding ID persuasive, suddenly and furiously contested, to be ruled upon by a 23-year-old “boy” and 500-year-old wizard called “Jo-Jo.” Such is the alternative reality of Wikipedia. https://evolutionnews.org/2017/10/wikipedia-erases-paleontologist-gunter-bechly/
Has this been published yet? I can find a pre-print from August 2018, but no published version. Bob O'H

Leave a Reply