Question about nylonase issue and Meyer's response in Four Views book


(Dave Hudson) #1

Just finished reading this book, and I am new to posting in the Biologos forum. I appreciated the format, and (somewhat) equal time given to each perspective. I wish that Deborah Haarsma could have been able to respond to Stephen Meyer’s rejoinder, though, regarding the Nylonase issue. The question was left open, and I would love to see it resolved.


Four Views On Creation, Evolution, And Intelligent Design (New Book)
(Christy Hemphill) #2

Welcome to the forum, Dave! I’m going to move your post to a new topic so people see your question.


(Christy Hemphill) #3

Maybe you could reiterate a little what the question/issue was, for everyone who hasn’t read the book or doesn’t remember the part you are referring to.


(Dave Hudson) #4

I no longer have access to the book, but the issue had to do with a significant difference between the two authors in the probability level of a functional protein developing from a mutation. A nylon-dissolving bacteria that developed within 40 years of the invention of nylon was used as an example by Haarsma, and Meyer refuted this by saying that it was not a new functional protein, or something like that. I am not a scientist, but I have read a lot of books on both EC and ID. So my question is, what would Haarsma’s response to Meyer’s rejoinder be?


(Christy Hemphill) #5

@DennisVenema has written a response to Meyer’s arguments about nylon eating bacteria. Have you seen that one? https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/intelligent-design-and-nylon-eating-bacteria


(Dave Hudson) #6

Wow… no I have not. I will take a look at this see if it resolves the issue. Thanks!


(Dave Hudson) #7

I see. So it has to do mainly with the frame-shifting creating a completely new protein, which was not addressed by Meyer in his rejoinder. It makes more sense to me now.


(Daniel Fisher) #8

Sir, if interesting, Ann Gauger has engaged on nylonase and Dr. Venema’s position recently as well (https://evolutionnews.org/2017/05/the-nylonase-story-when-imagination-and-facts-collide/) and (https://evolutionnews.org/2017/07/nylonase-move-on-nothing-to-see-here-says-theistic-evolutionist/)

This topic has been fascinating to me, as it really is one (in fact the only one I have ever found) that, if true, would seem to clearly refute the claims of ID. A frameshift mutation, wherein the information to create a fully functional, brand-new function arose completely de novo with no precursors from a completely random string of codons would suggest that these functions could simply arise by chance. When I first read about such a frameshift, my reaction was that, if true, my confidence in ID would have been seriously shaken.

I dug into the literature referenced by Dr. Venema, and admittedly much is well above my level. But I noticed at the time even in my own reading of the literature what Dr. Gauger seems to be getting at, that being that the Nylonase arose from a preexisting esterase.

I concur that a fully functioning enzyme arising by frameshift would constitute major counterevidence to the ID position. An adaptation of an already functioning enzyme, however, would simply be yet another example of the micro-evolution that Meyer et al already believe and defend. If Gauger’s reading of the literature is correct (and I have not found Dr. Venema to have refuted her reading), then Nylonase is in fact an example of the latter.


#9

If evolution can produce new proteins with new function from pre-existing proteins that didn’t have that function, why isn’t that a challenge to the claims of ID? Don’t ID folks like Ann Gauger argue that you can’t get novel functions by changing the sequence of already existing genes?


(Daniel Fisher) #10

I don’t know the specific details of this protein well enough to comment. But the general principle is that most folks sympathetic to ID or even creationism in its various forms have no issue with all manner of microevolution, whether at the protein/molecular level or the larger organism level.

For instance, i could imagine birds in general reproducing and making all manner of variations, some which make their legs even stronger and more adaptive to running over flying (like a sandpiper, roadrunner or ostrich), and others’ wings adapt for different purposes and use them like rudders or diving planes rather than wings (like penguins). This is a far cry from suggesting, though, that these structures arose entirely complete and functional with no precursor through a fortuitous conglomeration of random mutations, which is what was being claimed about nylonase.

To my understanding, that is the analogy to these enzymes. You already have a functioning enzyme, with the chemical properties and physical structure, folds, and active sites that already function to break down certain chemicals… a few relatively minor adjustments (the paper Gauger addresses notes a grand total of 2 point mutations that led to the nylonase activity, if I read correctly?) and they are able now to break down a new material. This is a small adaptation, that made use of lots of already existing function and structure, a rather minor modification allowed it to do something it couldn’t before.

Dr. venema’s interpretation, if I understood it, and which if correct would constitute a major counter-evidence to the ID claim, was that this fully functioning, properly folded, perfectly structured and chemically active protein simply arose entirely de novo due to a frame shift mutation. This would indeed be remarkable, and would indeed be evidence that all sorts of functional proteins could arise in relatively short order just by inserting random sequences into the system; that is, functional sequences are really not that rare.

But even when I first heard of nylonase years ago, I found the idea that such perfectly suited functional proteins could just poof into existence very difficult to believe.

So to your question, my understanding is that ID proponents like Gauger do in fact believe that all sorts of novel functions and abilities can arise, provided we are talking about small modifications of already complex functioning systems that benefit an organism and which “new” functions, in essence, are really just the result of small modifications. “Tampering”, if you will.


#11

“Two conceivable ways for this not to pose an insurmountable barrier to Darwinian searches exist. One is that protein function might generally be largely indifferent to protein sequence. The other is that relatively simple manipulations of existing genes, such as shuffling of genetic modules, might be able to produce the necessary new folds. I argue that these ideas now stand at odds both with known principles of protein structure and with direct experimental evidence.”–Douglas Axe
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1

Here is a paper by Gauger and Axe arguing against microevolution of an existing protein:
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1

Then you should have no problem with the evolution of tetrapod limbs from pre-existing fish fins, which is what scientists have proposed. Is that “microevolution”?[quote=“Daniel_Fisher, post:10, topic:37525”]
To my understanding, that is the analogy to these enzymes. You already have a functioning enzyme, with the chemical properties and physical structure, folds, and active sites that already function to break down certain chemicals… a few relatively minor adjustments (the paper Gauger addresses notes a grand total of 2 point mutations that led to the nylonase activity, if I read correctly?) and they are able now to break down a new material. This is a small adaptation, that made use of lots of already existing function and structure, a rather minor modification allowed it to do something it couldn’t before.
[/quote]

Keep repeating this process and you can walk a mile with many steps. This is why ID/creationists argue against even microevolution because they know that there is nothing stopping small changes from adding up to large changes.[quote=“Daniel_Fisher, post:10, topic:37525”]
So to your question, my understanding is that ID proponents like Gauger do in fact believe that all sorts of novel functions and abilities can arise, provided we are talking about small modifications of already complex functioning systems that benefit an organism and which “new” functions, in essence, are really just the result of small modifications. “Tampering”, if you will.
[/quote]

Then it is interesting that there are many instances of Gauger and Axe arguing just the opposite.


(Daniel Fisher) #12

Sure, but what is being discussed regarding nylonase is a protein that, if I understand properly, does not in fact have any new folds. To my very limited understanding, a replacement of only two amino acids (all that was necessary to effect nylonase activity in this enzyme) was sufficient to produce different chemical sensitivities at the active site that is already extant due to pre-existing folds. This isn’t unlike various antibiotic resistance, to my limited understanding that Behe, Gauger, Axe et al I believe are quite familiar with…

In principle, no. I’m not convinced that it did or could, but no, in principle, I don’t object to the basic idea that a functional limb with bones, muscles, etc., could undergo a series of small modifications one after another to take on a different general function.

But there are simply some things that I don’t see small gradual changes as being able to accomplish, especially when we are talking about brand new functional body systems or organs with very specific functions integrated into larger systems that appear with no precursor. I can swim 2 miles easily, keep repeating that process and I can swim from California to Hawaii? Not exactly how it works in all cases.


#13

Then new protein folds aren’t even needed for evolution of new genetic information. This also shoots a hole in the ID argument.[quote=“Daniel_Fisher, post:12, topic:37525”]
But there are simply some things that I don’t see small gradual changes as being able to accomplish, especially when we are talking about brand new functional body systems or organs with very specific functions integrated into larger systems that appear with no precursor. I can swim 2 miles easily, keep repeating that process and I can swim from California to Hawaii? Not exactly how it works in all cases.
[/quote]

The problem is that you claim it has to be an all new system, but all too often it is an alteration of an existing system as is the case with tetrapod limbs being modified fish fins.


(Bill Wald) #14

OK, say the odds are 1 out of 10 to the 77th power and one considers every cc of the earth’s surface down to the ocean flood as an independent experiment . . . what are the odds of all those experiments being successful?


(Lynn Munter) #15

Huh? Who said all life experiments were successful? Where did you even get your ‘odds,’ and what exactly are they the odds of?


(system) #16

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