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Author Topic:   The Death Knell for ID?
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 51 of 102 (652733)
02-15-2012 5:51 PM
Reply to: Message 1 by Trixie
01-26-2012 3:40 PM


A new paper has not only cast doubts on Michael Behe's assertions, it's run a freight train over the top of the ID arguments against evolution.

IMHO, this really isn't in any way the "death knell" for ID in any way whatsoever. ID proponents don't claim that the occurrence of 4 mutations is extremely improbable. The real issue here is whether all four mutations only offered a selective advantage once all four mutations had occurred. If this was the case, then this would be quite a difficulty for the ID folks. But sequence analysis doesn't show in any way that each mutation was in itself non-adaptive. Which means it's not a problem at all for ID. If each mutation conferred some selective advantage to the viruses, then the evolution of OmpF wouldn't be implausible at all, and wouldn't offer a difficulty to ID.

Thoughts?


This message is a reply to:
 Message 1 by Trixie, posted 01-26-2012 3:40 PM Trixie has replied

Replies to this message:
 Message 52 by Trixie, posted 02-15-2012 6:06 PM Genomicus has replied
 Message 53 by jar, posted 02-15-2012 6:10 PM Genomicus has taken no action
 Message 63 by Dr Adequate, posted 02-16-2012 3:10 AM Genomicus has replied

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 54 of 102 (652742)
02-15-2012 6:21 PM
Reply to: Message 52 by Trixie
02-15-2012 6:06 PM


When Behe witters on about irreducible complexity he specifically states that he rejects the idea of incremental improvements finally resulting in a complex change.

Not to my knowledge. For example, in The Edge of Evolution, he discusses the evolution of chloroquine resistance in Plasmodium. He stated that two specific mutations are required to result in chloroquine resistance (whether or not this is indeed the case is, of course, a different matter - I'm just stating my understanding of Behe's position) - yet he accepts that chloroquine resistance evolved without teleology. It seems to me, then, that he accepts the thesis that incremental improvements can result in a "complex" change.

It's been suggested by him that each step along the path to an "irreducibley complex" end result wouldn't happen because nearly all mutations are deleterious.

That is not my understanding of Behe's position. IMO, Behe suggests that it is implausible for an IC system to evolve because it would have to involve a circuitous, indirect Darwinian pathway which is much more improbable than a "direct" Darwinian pathway consisting of gradual improvements on a basic function.

In short, the evolution of this function in these viruses doesn't seem, to me at least, very impressive. It's really not any different than the evolution of chloroquine resistance or the evolution of nylonase.

I guess what it boils down to is that we don't quite agree on what Behe's position is.

I'll respond in more detail if required tomorrow, I'm just in from the movies and very tired.

Take your time - I myself am quite busy so please don't feel rushed.


This message is a reply to:
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Replies to this message:
 Message 55 by PaulK, posted 02-15-2012 6:35 PM Genomicus has replied

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 56 of 102 (652746)
02-15-2012 6:41 PM
Reply to: Message 55 by PaulK
02-15-2012 6:35 PM


That was his argument, in the days of Darwin's Black Box but I don't think it's his argument now. I think his argument now is that some evolutionary changes require simultaneous mutations (at least two specific mutations)...

Behe acknowledges that if a function requires two specific mutations - each of which are, in themselves, non-adaptive - such a function can evolve. Chloroquine resistance is an example of this, according to him.

The argument you give above has some serious problems...

Umm, I'm not making any argument regarding irreducible complexity. I was merely stating what Behe's position on irreducible complexity is. I wasn't saying that I agree with him.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 55 by PaulK, posted 02-15-2012 6:35 PM PaulK has replied

Replies to this message:
 Message 62 by PaulK, posted 02-16-2012 1:41 AM Genomicus has replied

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 61 of 102 (652760)
02-15-2012 9:06 PM
Reply to: Message 60 by Trixie
02-15-2012 8:53 PM


Re: Deja Vu
Basically he caims that because two different changes are required for chloroquine resistance, this is evidence for intelligent design.

No, he didn't. Behe said in EoE that chloroquine resistance arose through purely Darwinian mechanisms. I'm not defending Behe's thesis, though. He got a lot of stuff wrong in EoE.

But since only two specific mutations (each being individually non-adaptive) seem to be required for this function to evolve in these viruses, this example of the evolution of a novel function isn't terribly impressive: you could just as well argue that the evolution of nylonase was the death knell for ID, could you not?


This message is a reply to:
 Message 60 by Trixie, posted 02-15-2012 8:53 PM Trixie has seen this message

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 64 of 102 (652782)
02-16-2012 4:06 AM
Reply to: Message 62 by PaulK
02-16-2012 1:41 AM


But isn't it true that he considers it extremely unlikely, and that this is the heart of his case?

Behe considers the evolution of a function that requires two individually non-adaptive mutations to be implausible for primates. In EoE, he cited a paper by Whitman et al. (I could dig up the full reference if you wish), who state that about 10^12 malaria parasites are needed for the evolution of chloroquine resistance. Thus, the evolution of a function requiring two simultaneous mutations is very plausible at the level of bacteria, viruses, and fast-replicating eukaryotes like malaria. But it's not that likely for organisms like primates - that's what he said anyway.

Again, I'm not defending Behe's thesis here - I'm clarifying what his position is.

But does Behe still believe it ? Is it still his position ? At one point he had the idea of changing the definition of irreducible complexity completely, and his more recent argument seems a development of that. Certainly that gives me the impression that his thinking on the matter has changed - and he never had a solid argument against indirect routes in the first place.

I really am not quite sure what Behe's current stand on the issue of irreducible complexity is. However, on the surface at least, it seems that it's less probable for an IC system to evolve than for a non-IC system to evolve.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 62 by PaulK, posted 02-16-2012 1:41 AM PaulK has replied

Replies to this message:
 Message 65 by PaulK, posted 02-16-2012 4:23 AM Genomicus has replied

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 66 of 102 (652786)
02-16-2012 4:41 AM
Reply to: Message 65 by PaulK
02-16-2012 4:23 AM


So, in fact, you were doing a rather poor job of clarifying his position by making a blanket claim that he believed that such functions could evolve. Wouldn't it have been better to clarify the population issue at the start ?

Well, Behe does in fact believe that such functions can evolve - and since the topic of this thread involved phages, I was clarifying his position with regards to viruses and bacteria.

If you aren't sure of his position then you can't really clarify what it is, can you?

I can indeed clarify what his position is with regards to the evolution of functions requiring two or more simultaneous mutations.

As for your other assertion, the relative probability of evolving a specific function by a specific direct route versus a specific indirect route would seem to be completely irrelevant - even if we do not consider the fact that evolution has no preference for direct over indirect routes.

It would seem to be completely irrelevant to what?


This message is a reply to:
 Message 65 by PaulK, posted 02-16-2012 4:23 AM PaulK has replied

Replies to this message:
 Message 68 by PaulK, posted 02-16-2012 5:04 AM Genomicus has replied

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 67 of 102 (652787)
02-16-2012 4:50 AM
Reply to: Message 63 by Dr Adequate
02-16-2012 3:10 AM


Now the IDists' arguments about IC rest on the assumption that in such a case each of the parts separately is useless, and so the system cannot have been assembled a bit at a time by natural selection causing the parts to accumulate, because natural selection would not have acted on the parts.

If that's Trixie's central argument and primary reason for bringing up this piece of research, then it's hardly the death knell for ID. Many ID proponents acknowledge that the parts of an IC system can carry out other functions, which means that IC doesn't automatically mean that a given system could not have plausibly evolved. Not really the "death knell" to ID.


This message is a reply to:
 Message 63 by Dr Adequate, posted 02-16-2012 3:10 AM Dr Adequate has replied

Replies to this message:
 Message 71 by Trixie, posted 02-16-2012 6:04 AM Genomicus has replied
 Message 83 by Dr Adequate, posted 02-17-2012 4:13 AM Genomicus has taken no action
 Message 84 by Trixie, posted 02-17-2012 5:02 AM Genomicus has replied

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 69 of 102 (652790)
02-16-2012 5:12 AM
Reply to: Message 68 by PaulK
02-16-2012 5:04 AM


Provided the population is large enough... Is the population in the experiment large enough to account for 4 mutations arising simultaneously ? In 24 out of 96 cases?

Or are you going to argue that all 4 mutations are beneficial, as required by Behe's argument?

Behe would argue that four simultaneous mutations is too implausible - even for viruses and bacteria. This study does not report that all four mutations must arise simultaneously in order to confer a selective advantage. Indeed, it could be that each mutation conferred some selective advantage.

Now that's just a little disingenuous given that the context was Behe's views on the evolution of IC system.

If I understand Trixie's main point correctly, then it is that ID proponents hold that the evolution of OmpF is extremely implausible because several mutations would be required before any selective advantage appears. Possibly, we're not communicating very well, though.


This message is a reply to:
 Message 68 by PaulK, posted 02-16-2012 5:04 AM PaulK has replied

Replies to this message:
 Message 73 by Wounded King, posted 02-16-2012 6:32 AM Genomicus has taken no action
 Message 76 by PaulK, posted 02-16-2012 2:28 PM Genomicus has replied

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 72 of 102 (652793)
02-16-2012 6:20 AM
Reply to: Message 71 by Trixie
02-16-2012 6:04 AM


Re: Eh?
So ID proponents believe that "irreducibly complex" systems aren't really irreducibly complex? Now that makes no sense. They're still touting it all over the internet as evidence against evolution and for ID, using the common definition which we all know and love.

Irreducibly complex systems are still irreducibly complex. Behe's error was not in concluding that IC systems exist in nature; rather, his error was in assuming that IC systems cannot plausibly arise through Darwinian mechanisms. Even some papers in the peer-reviewed literature state that IC systems do exist in the world of life (see, for example, "A Classification of Possible Routes of Darwinian Evolution," JTB); however, it should not be automatically concluded that an IC system cannot evolve. But if a molecular machine is IC - and it carries out a function that requires the interaction of multiple proteins, then the only really feasible evolutionary pathway for its origin is co-option. And co-option involves the random association of proteins - natural selection only kicks in once the associations have taken place, producing a novel function. I would say then that we need to be just a bit cautious when invoking co-option to explain the origin of a molecular machine like the bacterial flagellum. I digress.

If what I quoted above is accurate with regard to Behe's current stance, then he has abandoned his own definition of irreducible complexity and embraced what everyone has been telling him for decades. So where does that leave ID now that it's main supporting assertion is dead in the water?

I really don't know what Behe's current stance on IC is. Intelligent design, however, isn't dead just because some IC systems can evolve. There's a lot more to ID than irreducible complexity. That said, explaining the origin of molecular machines like flagella is still quite a problem for the non-telic side of the discussion (to be fair, the ID folks haven't gone very far in explaining how the flagellum was designed).

In EofE Behe claimed that the "edge" of evolution was two non-selective mutations in the malarial parasite...

Have you read Behe's EofE, if I may ask?

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


This message is a reply to:
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Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 78 of 102 (652930)
02-16-2012 9:59 PM
Reply to: Message 76 by PaulK
02-16-2012 2:28 PM


So why not concentrate on that rather than arguing about the number of simultaneous mutations that Behe allows...

I have absolutely no problem with concentrating on the implications of the study reported by Trixie, except that it'd be a touch superfluous since I don't think I could do better than Wounded King in explaining why multiple simultaneous mutations are not needed for the OmpF function to evolve in these phages.

That's the problem when you ignore the context. You fail to understand the points being made. The point here is that your "clarification" of Behe's views on IC systems, assumed that Behe still held to the views in Darwin's Black Box . But it is far from clear that that is true, given that Edge of Evolution seems to derive from a radical redefinition of IC that Behe suggested...

I suspect that you have not read EofE. In that book, Behe only mentioned irreducible complexity en passant. In EofE, the central argument is that the limits of Darwinian evolution is around four specific simultaneous mutations. For primates, he concluded that the limits of Darwinian evolution are at the level of two simultaneous mutations. From these arguments, he posited that the huge amount of sophisticated biological systems found in the cell could not have plausibly arisen through purely Darwinian mechanisms. Whether his arguments are, in fact, valid is an entirely different matter, of course.


This message is a reply to:
 Message 76 by PaulK, posted 02-16-2012 2:28 PM PaulK has replied

Replies to this message:
 Message 79 by PaulK, posted 02-17-2012 1:44 AM Genomicus has replied

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 80 of 102 (652968)
02-17-2012 2:36 AM
Reply to: Message 79 by PaulK
02-17-2012 1:44 AM


quote:
Unless Behe indicated that he still held to the views expressed in Darwin's Black Box that is irrelevant - since that is the point we are discussing, as I keep pointing out. And you have already admitted that you do not know if Behe still holds to that position or not, so I fail to see why you can't simply agree that you were wrong to try to "clarify" his position on IC and leave it at that.

I was trying to clarify Behe's views on the "simultaneous mutations" issue, not on IC. Trixie's point seems to tie both points together. I'd be more than willing to agree that I was wrong in trying to clarify Behe's position on IC, except I wasn't trying to do that.


This message is a reply to:
 Message 79 by PaulK, posted 02-17-2012 1:44 AM PaulK has replied

Replies to this message:
 Message 81 by PaulK, posted 02-17-2012 3:10 AM Genomicus has replied

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 82 of 102 (652973)
02-17-2012 3:20 AM
Reply to: Message 81 by PaulK
02-17-2012 3:10 AM


PaulK:

You are indeed right, of course, and I apologize for the confusion I caused. I admit that I do not know what Behe's current stand on the issue of IC is - so I was wrong on that one.


This message is a reply to:
 Message 81 by PaulK, posted 02-17-2012 3:10 AM PaulK has taken no action

  
Genomicus
Member (Idle past 1179 days)
Posts: 852
Joined: 02-15-2012


Message 85 of 102 (652979)
02-17-2012 5:04 AM
Reply to: Message 84 by Trixie
02-17-2012 5:02 AM


I am in complete agreement with you that ID should not be taught in any way in school/science class.

This message is a reply to:
 Message 84 by Trixie, posted 02-17-2012 5:02 AM Trixie has taken no action

  
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