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Author Topic:   Musgrave, Reuland, and Cartwright critique Behe and Snokes (2004)
Nic Tamzek
Inactive Member


Message 1 of 8 (149232)
10-11-2004 9:40 PM


This is an epic take-down, recently posted on Panda's Thumb, of the recent paper by Behe (and a physicist collegue, David Snokes) in Protein Science, which didn't argue for ID, but did argue that most protein binding sites couldn't evolve.

Theory is as Theory Does
by Ian F. Musgrave, Steve Reuland, and Reed A. Cartwright
http://www.pandasthumb.org/pt-archives/000480.html

(A critical review of this paper:

Michael J. Behe and David W. Snoke (2004). "Simulating evolution by gene duplication of protein features that require multiple amino acid residues." Protein Science, Published online before print August 31, 2004. DOI: http://dx.doi.org/10.1110/ps.04802904
http://www.proteinscience.org/cgi/content/abstract/ps.04802904v1 )

Musgrave et al.'s conclusion:

quote:
Conclusion
We began this essay with a quotation from Behe complaining that a paper describing an evolutionary simulation (Lenski et al. 2003) had “precious little real biology” in it. What we see here is that Behe and Snoke’s paper is acutely vulnerable to the same criticism. A theoretical model is useful to the extent that it accurately represents or appropriately idealizes the processes that occur in the phenomenon being studied. Although it is worthwhile to investigate the importance of neutral drift, Behe and Snoke have in our opinion over-simplified the process, resulting in questionable conclusions.

Their assumptions bias their results towards more pessimistic numbers. The worst assumption is that only one target sequence can be hit to produce a new function. This is probably false under all circumstances. The notion that a newly arisen duplicate will remain selectively neutral until the modern function is firmly in place is also probably false as a general rule. Their assumption that 70% of all amino acid substitutions will destroy a protein’s function is much too high. And finally, we have shown that their flagship example does not require a large multi-residue change before being selectable.

And ironically, despite these faulty assumptions, Behe and Snoke show that the probability of small multi-residue features evolving is extremely high, given the types of organisms that Behe and Snoke’s model applies to. When we use more realistic assumptions, though many bad ones still remain, we find that the evolution of multi-residue features is quite likely, even when there are smaller populations and larger changes involved. In fact, the times required are within the estimated divergence times gleaned from the fossil record. We can therefore say, with confidence, that the evolution of novel genes via multi-residue changes is not problematic for evolutionary theory as currently understood.


This message has been edited by Nic Tamzek, 10-11-2004 08:42 PM


Replies to this message:
 Message 2 by AdminJar, posted 10-11-2004 10:48 PM Nic Tamzek has not yet responded

  
AdminJar
Inactive Member


Message 2 of 8 (149263)
10-11-2004 10:48 PM
Reply to: Message 1 by Nic Tamzek
10-11-2004 9:40 PM


One problem I see with this is that the full text of the Behe rebuttal is not available without subscription. That means all we have to go on is battling rebuttals.

Is it possible to get links to copies of the full text so that readers can make an informed decision?


This message is a reply to:
 Message 1 by Nic Tamzek, posted 10-11-2004 9:40 PM Nic Tamzek has not yet responded

  
Nic Tamzek
Inactive Member


Message 3 of 8 (149515)
10-12-2004 9:07 PM


The various PT people who've critiqued the paper have access via university subscriptions etc. (and, I think the pre-publication version was free online for awhile). In the interests of scholarly inquiry I can email the pdf to any individuals who are interested, if they email me with an obviously nonspam title at chrysothamnusATyahoo.com.
Replies to this message:
 Message 4 by AdminJar, posted 10-12-2004 9:13 PM Nic Tamzek has not yet responded

  
AdminJar
Inactive Member


Message 4 of 8 (149517)
10-12-2004 9:13 PM
Reply to: Message 3 by Nic Tamzek
10-12-2004 9:07 PM


Given that the detailed information will not be directly available, is there enough here for a discussion or should this just be placed in Links and Information?

I really feel that without equal and unfettered access to the full text for both sides that no debate will really happen.

I'd like for a couple other moderators to take a look at this but as it stands I can't see how it could form a basis for informed debate.


This message is a reply to:
 Message 3 by Nic Tamzek, posted 10-12-2004 9:07 PM Nic Tamzek has not yet responded

Replies to this message:
 Message 5 by AdminNosy, posted 10-12-2004 9:56 PM AdminJar has not yet responded

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 5 of 8 (149536)
10-12-2004 9:56 PM
Reply to: Message 4 by AdminJar
10-12-2004 9:13 PM


Copyright problems
It seems if there is a copyright on the Behe rebuttal we can not allow distribution of it. We would also have to be rather careful about the extent to which it was quoted here.

However, how about this:

Is there anyone who would like to take up the ID side of this and use the Behe rebuttal as source material? They would have to have access to it in a legitimate fashion and then be prepared to paraphrase it a lot in support of their arguments.

Actually just using it as the source of the arguments would work.

I agree with Jar that, though I'd like to watch such a discussion, it is not fair to have the Behe supporters with part of their "amunition" taken from them.

It is completely moot if there is no one interested in taken up the Behe side though. Why don't we wait until someone puts a Suggestion up in "Questions and Suggestions"?


This message is a reply to:
 Message 4 by AdminJar, posted 10-12-2004 9:13 PM AdminJar has not yet responded

  
Nic Tamzek
Inactive Member


Message 6 of 8 (149804)
10-13-2004 11:35 PM


Howdy,

There's some confusion here, by "Behe rebuttal" do you mean the Protein Science article by Behe and Snoke?

It's your call what you wish to do regarding a discussion -- there is nothing huge at stake IMO, I just posted the suggestion because I like to see what people think of the Behe & Snoke paper and the Musgrave et al. rebuttal. However, regarding access, the Behe and Snoke Protein Science article is no different than essentially all other journal articles that regularly get discussed (except the few that are open access journals). If you're going to limit threads based on this you're risking shutting off most of the relevant source material...

Regarding copyright, obviously one needs permission to post an article on a website (usually journals give permission to the article authors if they ask), but it is common practice to send a photocopy or a pdf to another individual with a scholarly interest in the topic. This is classic scholarly "fair use." The point of academic papers is, after all, academic discussion, not profit.


Replies to this message:
 Message 7 by AdminNosy, posted 10-14-2004 1:37 AM Nic Tamzek has not yet responded

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 7 of 8 (149811)
10-14-2004 1:37 AM
Reply to: Message 6 by Nic Tamzek
10-13-2004 11:35 PM


Fair Use
It may be fine to send it to one person but then the debate would be kind of behind closed doors here.

Personally I'd really like to see this thrashed out but there are some issues of fairness I think. In the meantime there has been no clue that anyone wants to discuss it from the Behe side.


This message is a reply to:
 Message 6 by Nic Tamzek, posted 10-13-2004 11:35 PM Nic Tamzek has not yet responded

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 8 of 8 (180357)
01-24-2005 11:25 PM


Thread moved here from the Proposed New Topics forum.
  
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