Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 122 (8781 total)
Current session began: 
Page Loaded: 08-19-2017 2:49 PM
354 online now:
Chatting now:  Chat room empty
Newest Member: evilsorcerer1
Post Volume:
Total: 816,490 Year: 21,096/21,208 Month: 1,529/2,326 Week: 865/345 Day: 103/124 Hour: 4/11

Announcements: Reporting debate problems OR discussing moderation actions/inactions


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Prev1234
5
67Next
Author Topic:   The Death Knell for ID?
Genomicus
Member
Posts: 846
Joined: 02-15-2012
Member Rating: 3.3


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 acknowledged this reply

  
PaulK
Member
Posts: 12969
Joined: 01-10-2003
Member Rating: 3.2


Message 62 of 102 (652774)
02-16-2012 1:41 AM
Reply to: Message 56 by Genomicus
02-15-2012 6:41 PM


quote:

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.

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

quote:

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.

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.


This message is a reply to:
 Message 56 by Genomicus, posted 02-15-2012 6:41 PM Genomicus has responded

Replies to this message:
 Message 64 by Genomicus, posted 02-16-2012 4:06 AM PaulK has responded

    
Dr Adequate
Member
Posts: 15948
Joined: 07-20-2006
Member Rating: 4.8


Message 63 of 102 (652779)
02-16-2012 3:10 AM
Reply to: Message 51 by Genomicus
02-15-2012 5:51 PM


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.

However, it is true that removing one part of the system destroys its function (using OmpF). 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.

The fact that each mutation was adaptive is just what shows that they were wrong. The evolutionist case against Behe is not that such combinations of mutations can with reasonable probability arise all at once by chance, but that the series of changes leading to the final system can be produced by a series of steps each of which is adaptive even though it does not produce the final system having the final function. This experiment shows a case of that happening.

So this part of your post seems completely ass-backwards:

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.

No, that would have been a problem for the evolutionists. They would be left with no known mechanism to explain why this pathway is followed, and followed repeatedly, in reruns of the experiment, since this could not be explained by chance (too many long shots coming up) or by the cumulative effect of natural selection (which would not, by hypothesis, act).

Meanwhile Behe could have gone around saying that this was the first observed instance of his invisible designer magically tampering with genomes to produce an IC system.

The actual observation is therefore a blow against ID precisely because the system evolved by completely normal Darwinian processes, as evolutionists claim that such systems evolve.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 51 by Genomicus, posted 02-15-2012 5:51 PM Genomicus has responded

Replies to this message:
 Message 67 by Genomicus, posted 02-16-2012 4:50 AM Dr Adequate has responded

  
Genomicus
Member
Posts: 846
Joined: 02-15-2012
Member Rating: 3.3


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 responded

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

  
PaulK
Member
Posts: 12969
Joined: 01-10-2003
Member Rating: 3.2


Message 65 of 102 (652784)
02-16-2012 4:23 AM
Reply to: Message 64 by Genomicus
02-16-2012 4:06 AM


quote:

Behe considers the evolution of a function that requires two individually non-adaptive mutations to be implausible for primates

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 ?

quote:

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.

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

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.


This message is a reply to:
 Message 64 by Genomicus, posted 02-16-2012 4:06 AM Genomicus has responded

Replies to this message:
 Message 66 by Genomicus, posted 02-16-2012 4:41 AM PaulK has responded

    
Genomicus
Member
Posts: 846
Joined: 02-15-2012
Member Rating: 3.3


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 responded

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

  
Genomicus
Member
Posts: 846
Joined: 02-15-2012
Member Rating: 3.3


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 responded

Replies to this message:
 Message 71 by Trixie, posted 02-16-2012 6:04 AM Genomicus has responded
 Message 83 by Dr Adequate, posted 02-17-2012 4:13 AM Genomicus has not yet responded
 Message 84 by Trixie, posted 02-17-2012 5:02 AM Genomicus has responded

  
PaulK
Member
Posts: 12969
Joined: 01-10-2003
Member Rating: 3.2


Message 68 of 102 (652789)
02-16-2012 5:04 AM
Reply to: Message 66 by Genomicus
02-16-2012 4:41 AM


quote:

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.

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?

quote:

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

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

quote:

It would seem to be completely irrelevant to what?

To the assertion that I was explicitly addressing. Reading in context is often helpful. But just to remind you of what you said, here it is again:


it seems that it's less probable for an IC system to evolve than for a non-IC system to evolve.

This message is a reply to:
 Message 66 by Genomicus, posted 02-16-2012 4:41 AM Genomicus has responded

Replies to this message:
 Message 69 by Genomicus, posted 02-16-2012 5:12 AM PaulK has responded

    
Genomicus
Member
Posts: 846
Joined: 02-15-2012
Member Rating: 3.3


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 responded

Replies to this message:
 Message 73 by Wounded King, posted 02-16-2012 6:32 AM Genomicus has not yet responded
 Message 76 by PaulK, posted 02-16-2012 2:28 PM Genomicus has responded

  
Wounded King
Member (Idle past 1591 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 70 of 102 (652791)
02-16-2012 5:49 AM
Reply to: Message 60 by Trixie
02-15-2012 8:53 PM


Re: Deja Vu
As far as I could tell, the fourth mutation never occurred without the others, but the others occurred without the fourth.

If you mean that the A3034G mutations never arose without the 3 other mutation classes having already occurred then this is incorrect as can be seen from strains F2 and H4 in fig 3. You seem to be basing your whole analysis on fig 2 covering the initial experiment and ignoring fig 3 which shows the wider range of mutations in both the 'ancestral range' and OmpF utilising strains from their larger scale replay experiments.

Looking back at the paper I wonder if their claim ...

Meyer et al., 2012 writes:

In the λ population that evolved to use OmpF in the initial experiment, the A3034G mutation was the fourth and final step

... is really substantiated by the results. After all, these strains were all evolving in parallel and the data don't provide any sort of time course, beyond the initial ancestral strain as a t0, the evolved strains assayed were collected on the same day. So what they are really saying is that for the EvoA strain to become OmpF competent A3034G would be the last required mutation. There isn't actually any evidence presented as to the order the mutations actually occurred in the EvoC strain or in any of the replay strains. This is a shame since from the way they describe their protocol this is data they could have collected.

TTFN,

WK


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

Replies to this message:
 Message 74 by Trixie, posted 02-16-2012 6:39 AM Wounded King has responded

    
Trixie
Member (Idle past 1202 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


Message 71 of 102 (652792)
02-16-2012 6:04 AM
Reply to: Message 67 by Genomicus
02-16-2012 4:50 AM


Eh?
Genomicus writes:

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.

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.

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?

In EofE Behe claimed that the "edge" of evolution was two non-selective mutations in the malarial parasite, conferring chloroquine resistance and calculated erroneous probailites. What he failed to take into account was that each individual mutation could confer increased resistance and so could be selected for. Time and again Behe has done calculations based on no selective advantage for a given mutation. What the Lenski paper does and the chloroquine resistance does is show that his basic assumption on which rests his statistics is wrong so his statistiocs are wrong. Thus his conclusions based on his statistics are wrong.


This message is a reply to:
 Message 67 by Genomicus, posted 02-16-2012 4:50 AM Genomicus has responded

Replies to this message:
 Message 72 by Genomicus, posted 02-16-2012 6:20 AM Trixie has not yet responded

  
Genomicus
Member
Posts: 846
Joined: 02-15-2012
Member Rating: 3.3


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:
 Message 71 by Trixie, posted 02-16-2012 6:04 AM Trixie has not yet responded

  
Wounded King
Member (Idle past 1591 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 73 of 102 (652794)
02-16-2012 6:32 AM
Reply to: Message 69 by Genomicus
02-16-2012 5:12 AM


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.

This is in fact what the paper suggests, they note several features of the 'prior' mutations in the strains that cannot use OmpF that would indicate that they are subject to positive selection.

Possibly, we're not communicating very well, though.

This seems to be the case, and it is certainly not helped by the fact the Irreducible Complexity has had more than one definition. I think part of the problem is that people are mixing up the figure for the evolution of the Chloroquine complex of mutations, which as you say came from someone else's previous work, with Behe's subsequent use of this as a basis for predicting the likely frequency of more complex compound mutations.

TTFN,

WK


This message is a reply to:
 Message 69 by Genomicus, posted 02-16-2012 5:12 AM Genomicus has not yet responded

    
Trixie
Member (Idle past 1202 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


Message 74 of 102 (652795)
02-16-2012 6:39 AM
Reply to: Message 70 by Wounded King
02-16-2012 5:49 AM


Re: Deja Vu
Near the bottom of page 429 the authors state

We performed two additional assays to confirm that only phage with all four mutations can infect lamB mutants. The assays were performed using isolates EvoA, F2 and H4 that each had three of the four canonical mutations and D7 that had all four and no others. Only D7 exhibited a measurable adsorption rate on lamB mutants in the medium used in the evolution experiments. These findings indicate an "all or none" form of epistasis among the four mutations responsible for the novel receptor phenotype

From that I take that F2 and H4 did not have the mutation enabling them to use OmpF, but did have the other three. You seem to be suggesting that F2 and H4 had the mutation necessary for OmpF utilisation and no others. I think it means the opposite, but I could be wrong.

Or are we just talking past each other here?


This message is a reply to:
 Message 70 by Wounded King, posted 02-16-2012 5:49 AM Wounded King has responded

Replies to this message:
 Message 75 by Wounded King, posted 02-16-2012 8:03 AM Trixie has responded

  
Wounded King
Member (Idle past 1591 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 75 of 102 (652800)
02-16-2012 8:03 AM
Reply to: Message 74 by Trixie
02-16-2012 6:39 AM


Re: Deja Vu
Or are we just talking past each other here?

This is why I keep asking you to be more specific. There is no 'the mutation necessary for OmpF utilisation' what is needed is all four mutations.

The way you describe it is that there are three intermediary mutations which then potentiate a final specific fourth mutation which actually confers the ability to utilise OmpF. But the evidence suggests that this is not what happens, there are a spectrum of mutations which occur and all four mutations of particular types are required for OmpF utilisation. But these are arising independently, there is nothing to suggest that they need to occur in any specific order.

What H4 and F2 both have is the A3034G mutation which is what I assumed you meant when you said 'the fourth mutation never occurred without the others', since it is the difference between the EvoA and EvoC strains in fig.2. If you actually told me what mutation you meant it would make things a lot simpler, but as far as I can tell none of the mutations would fit your description of requiring the other three before it could occur.

So what mutation, specifically, were you talking about?

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 74 by Trixie, posted 02-16-2012 6:39 AM Trixie has responded

Replies to this message:
 Message 77 by Trixie, posted 02-16-2012 5:04 PM Wounded King has acknowledged this reply

    
Prev1234
5
67Next
Newer Topic | Older Topic
Jump to:


Copyright 2001-2015 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2017