Intelligent Design and Nylon-Eating Bacteria


(system) #1
Stephen Meyer claims that evolution can't produce new protein folds. However, in the last century, evolution did exactly that.
This is a companion discussion topic for the original entry at https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/intelligent-design-and-nylon-eating-bacteria

(Dcscccc) #2

several important points about this interensting topic: first- the nylonase activity doesnt need a lot of amino acid. in other words: its a simple function. we cant compare that with a complex functions like blood clothing or a vision system. the enzyme of axe experiment was about 150 aa long. how many aa need to diggest a nylon? not very much. actually- a lot of proteins already do other side functions.

more then this- we can even see a new functions “evolving” in non- living object. for example: a motorcycle can evolve a new function by adding a used gum in its front side. now we can stick things like papers and so on. by extrapolation of milion years can we say that this motorcycle will evolve a gps system because we see a small changes in it? not at all. so why in living things it will be any different?


(Dennis Venema) #3

Hi dsc - the de novo nylonase protein that arose from the frameshift mutation was 392 amino acids long - over twice as long as the 150 aa length in the Axe experiment. How can you say that it “doesn’t need a lot of amino acids”?

Also, no one thinks that blood clotting or vision arose all at once. The point here is that what ID claims should be impossible happened readily.


(Dcscccc) #4

hi denis.

true. but how many of them required to this function? the fact that even other genes can evolve this trait in a blink prove that not very much:

http://aem.asm.org/content/61/5/2020.long

another possibility (but less likely) is that this trait need a lot of amino acid, but its very common in the sequence space. its important to remember that some function can be very rare and some are less. even axe paper mantion other several experiment that showed a variation between 10^24 and 10^59 for the same size protein!.

true. if so- we are both agree that there is a limit for the size of the jump in the sequence space that evolution can take. so the real question is if evolution cant do it step wise. and my gps example show its impossible.


(Jon) #5

Because he does not understand what he is talking about.


(Dennis Venema) #6

Hi dcs - maybe read the quotes from Meyer in the original post again - and then decide if his argument is still valid. :slight_smile:


(Dcscccc) #7

its valid when we add the correct assumptions. and this is what i did in my comment above. actually, even one amino acid can be functional. but its doesnt mean that we can go from one amino acid into a 100 amino acid cytochrome c:

http://www.uniprot.org/uniprot/P99999


#8

While aware of nylonase, I hadn’t heard the details of the story and I found it very interesting that the protein was, in effect, largely de novo due to the frameshift. I had originally assumed that this function came about through the modification of an already extant active site. I appreciate DCs efforts to offer a critique, but from what I can see, nearly everything he has said is either largely speculative or beside the point, making it a bit of a wasted exercise (seems to be attempting a “murder by a thousand qualifications”, leaving the main point actually fairly healthy).

Putting aside Meyer’s questionable claim about protein folding, I find that this nylonase story has a far more useful function in the larger debate. It serves as an incredibly simple counterpoint to all of the bluster about the impossibility of “creating new information”. Not that this claim was actually compelling or even particularly meaningful in the first place, but it is definitely one of the most parroted claims; it shows up all over the place and is repeated with impressive levels of confidence by anyone and everyone who probably shouldn’t be showing impressive levels of confidence on such matters. It is so universal, that it needs a simple argument, not involving esoteric powerpoint presentations about Claude Shannon and entropy, in order to make it obvious that it is deeply wrongheaded conviction. A simple example of a function arising from scratch and improving through selection is handy, making any claims about what is or isn’t possible sound a little vapid. This could be called a “proof is in the pudding” argument …probably needs to be in Latin to catch on.


(Dennis Venema) #9

Exactly. Nothing like a clear-cut example to show up the argument as specious.


#10

Not surprisingly, I can see that AiG has addressed this issue, and according to Georgia Purdom, the ability to “eat” nylon is based on nothing more than a single base pair in the active site of the enzyme EII, which breaks down a substance very similar to nylon.

This is obviously completely different from what you are saying. From what I can see, she seems to have made an error involving an unintentional (hopefully) mix-up with a second instance (Prijambada et al 1995) where the ability to breakdown nylon was induced in a laboratory by providing no other sources of carbon and nitrogen. In this second case, there was no effort to identify the changes involved or the mode of action at the active site from what I can see (maybe there was x-ray crystallography or protein modeling in a separate study, but I cant find it), so Im not sure that this was where Purdom was getting the information involved in the mix-up, but it`s my best guess. It might explain why the response to this new function is so often “Oh but that’s was just a tiny change in an enzyme active site involving loss of specificity” instead of “wow, did you just say frameshift mutation?!”.

That said, Wikipedia points to an article in 2007 (Negoro et al) that suggests that no frameshift mutation was actually involved in this first case either. I scanned the article fairly quickly, but I couldn’t see where it made this suggestion.

Basically, my survey is fairly incomplete, so let me know if I’m off track on any of these points, especially since I don’t want to run with the frameshift mutation point if it is debatable.


(Dennis Venema) #11

As I understand it, confusion arises that there are duplications of the enzyme after the initial frameshift mutation that creates the first nylonase. These duplications undergo mutations that improve their specificity (recall that the first nylonase is a pretty poor nylonase). If you look at the second reference I list in the “further reading” section you can get more info about the ancestral vs modified nylonases.


(John T Mullen) #12

The only Latin we should need for this is “A Fortiori.” The argument is from a claim about what is actual to a weaker claim about what is possible. And the weaker is implicit in the stronger. So… p, therefore (a fortiori) possibly p.

Or more to the point: New protein folds formed within 40 years, therefore it is possible for new protein folds to form within 40 years.

The situation is a little trickier though, because we are dealing with probabilities. The conclusion is that Meyer’s probability estimate is mistaken. So it’s more like… New protein folds formed within 40 years, therefore it is extremely unlikely that new protein folds are as unlikely to form as Meyer says they are.

Okay, maybe we do need some more Latin for that.


#13

I checked the reference and I see that they review these points briefly. I’ll go through more of it when I get the chance. Thanks for the clarification!


#14

"Put another way, if only one in 10 to the 77th proteins are functional, there should be no way that this sort of thing could happen in billions and billions of years, let alone 40. Either this was a stupendous fluke (and stupendous isn’t nearly strong enough of a word), or evolution is in fact capable of generating the information required to form new protein folds.

And if this can happen in 40 years, what might millions of years of evolution produce?

An ID response should be–God engineered the new protein. ID does not (to my knowledge) assert that God no longer interacts with his Creation.

So, some 45 years ago, God decided to add a new protein into his Creation and (somehow) made that happen.

Or something.


(Benjamin Kirk) #15

Hello fmiddel,

This is why the ID movement doesn’t do science. If they wanted to study something that they hypothesize is designed, the questions who, how, and when are highly relevant–and pursued zealously by real scientists who study intelligently designed objects, for example anthropologists.


#16

That is so very true. For example, scientists don’t simply look at stone tools and proclaim that they were designed. They are keenly interested in who made them, how they were made, and when they were made. Scientists sometimes learn how to do flint knapping as part of their studies.


(Steve Schaffner) #17

I have to confess that, when I read Ohno’s paper proposing the frameshift origin for the enzyme, I found it really opaque. I ended up quite confused.


(Chris Falter) #18

Actually, a two-word phrase in English will do the trick:

Bayes Theorem


#19

I’ve come to understand this. It’s nice to have a “historical hypothesis” but it doesn’t lead to or answer the “how” questions.


(Martin Mayberry) #20

according to Answers in genesis and creation .org this bacteria has NOT evolved any new abilities,they said it had never been tried on nylon before! so that it evolved is Nonsense! just like the antibiotic resistant bacteria,they still remain just bacteria and turn into nothing more so they say is this evolution? No they say! And knowing what i know about antibiotic resistant bacteria not turning into anything else but bacteria i must agree. the issue with Bio-logos readers is that other opinions also exist like Answers in genesis and creation. org and the Bio logos readers do not turn to them for information or what could be a differing opinion. that is the issue the steven C meyers says happens all the time.