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Author Topic:   Meyer's Hopeless Monster
Nic Tamzek
Inactive Member


Message 1 of 207 (136876)
08-25-2004 9:56 PM


You guys might appreciate:

Meyer's Hopeless Monster
http://www.pandasthumb.org/pt-archives/000430.html

Review of Meyer, Stephen C. 2004. The origin of biological information and the higher taxonomic categories. Proceedings of the Biological Society of Washington 117(2):213-239.

by Alan Gishlick, Nick Matzke, and Wesley R. Elsberry

quote:

[The views and statements expressed here are our own and not necessarily those of NCSE or its supporters.]

“Intelligent design” (ID) advocate Stephen C. Meyer has produced a “review article” that folds the various lines of “intelligent design” antievolutionary argumentation into one lump. The article is published in the journal Proceedings of the Biological Society of Washington. We congratulate ID on finally getting an article in a peer-reviewed biology journal, a mere fifteen years after the publication of the 1989 ID textbook Of Pandas and People, a textbook aimed at inserting ID into public schools. It is gratifying to see the ID movement finally attempt to make their case to the only scientifically relevant group, professional biologists. This is therefore the beginning (not the end) of the review process for ID. Perhaps one day the scientific community will be convinced that ID is worthwhile. Only through this route — convincing the scientific community, a route already taken by plate tectonics, endosymbiosis, and other revolutionary scientific ideas — can ID earn a legitimate place in textbooks.

Unfortunately, the ID movement will likely ignore the above considerations about how scientific review actually works, and instead trumpet the paper from coast to coast as proving the scientific legitimacy of ID. Therefore, we would like to do our part in the review process by providing a preliminary evaluation of the claims made in Meyer’s paper. Given the scientific stakes, we may assume that Meyer, Program Director of the Discovery Institute’s Center for Science and Culture, the major organization promoting ID, has put forward the best case that ID has to offer. Discouragingly, it appears that ID’s best case is not very good. We cannot review every problem with Meyer’s article in this initial post, but we would like to highlight some of the most serious mistakes. These include errors in facts and reasoning. Even more seriously, Meyer’s paper omits discussion or even citation of vast amounts of directly relevant work available in the scientific literature.

[...]


Online discussions:

IDist Stephen Meyer in peer-reviewed journal

A Lovely Dissection

ID paper in peer-reviewed journal! Film at 11!


Replies to this message:
 Message 3 by RAZD, posted 08-26-2004 12:18 AM Nic Tamzek has taken no action
 Message 8 by Brad McFall, posted 09-02-2004 12:56 PM Nic Tamzek has taken no action
 Message 11 by Ooook!, posted 09-03-2004 11:10 AM Nic Tamzek has taken no action
 Message 35 by ID man, posted 09-11-2004 10:48 AM Nic Tamzek has taken no action
 Message 84 by ID man, posted 09-16-2004 11:07 AM Nic Tamzek has taken no action
 Message 166 by ID man, posted 09-30-2004 7:52 PM Nic Tamzek has taken no action
 Message 203 by trisha, posted 09-01-2011 6:49 AM Nic Tamzek has taken no action

  
Nic Tamzek
Inactive Member


Message 4 of 207 (137085)
08-26-2004 2:22 PM


Article up at the DI
About 24 hours after the critique came out the DI posted a scan of Meyer's article on their website:

The Origin of Biological Information and the Higher Taxonomic Categories
By: Stephen C. Meyer
Proceedings of the Biological Society of Washington
August 25, 2004
http://www.discovery.org/scripts/viewDB/index.php?command=view&id=2174&program=CSC


Replies to this message:
 Message 5 by RAZD, posted 08-26-2004 2:28 PM Nic Tamzek has taken no action
 Message 6 by Silent H, posted 08-29-2004 5:35 PM Nic Tamzek has taken no action
 Message 7 by RAZD, posted 09-01-2004 12:11 PM Nic Tamzek has taken no action

  
Nic Tamzek
Inactive Member


Message 124 of 207 (144782)
09-25-2004 11:22 PM
Reply to: Message 107 by ID man
09-18-2004 11:16 AM


Re: a response to Meyer's critics
Wow, this thread has really expanded since the last time I checked. Since I'm Nick Matzke (if you hadn't guessed), I might as well answer ID man's question:

ID Man wrote:

quote:
Is talk design a peer-reviewed journal? Is N.J. Matzke a biologist?
What detail is offered on how the bac flag arose?

Biology in the Subjunctive Mood:A Response to Nicholas Matzke

The double-standards are obvious. Reality shows they exist.


In order:

quote:
Is talk design a peer-reviewed journal?

Nope. It's a website put together by a combination of highly interested amateurs and professionals. If you want, you can ignore it. But the people who put together the website do know more about the relevant topics than pretty much anyone else. But no one there argues that their arguments should be accepted on their authority, only because they make sense and take into account the actual peer-reviewed literature on technical topics.

quote:
Is N.J. Matzke a biologist?

Depends what you mean. I have a double B.S. in biology and chemistry from Valparaiso University. I've spent several years doing ecology field work. Since you seem interested, I graduated summa cum laude. This gives me two more relevant degrees than Dembski (the author of "Biology in the Subjunctive Mood:A Response to Nicholas Matzke", which you cite) has when it comes to things like biology.

I also have an M.A. in geography, with an interest in biogeography and statistical modelling of spatial processes, both of which are relevant in various ways to evolution. (As random examples, the process of dispersal is crucial to understanding anything about how the bacterial flagellum arose, and punctuated equilibrium is actually derived from the biogeographic phenomenon of allopatric speciation)

But, I will freely admit that I'm still essentially just at the grad-student level, since I have no biology Ph.D. Disregard me if you like on that score (to be consistent, you'd have to cross out pretty much everyone in the ID movement except maybe Behe). But the articles I cite, for example in the flagellum article, won't go away, no matter what you think of little ol' me.

(In the article, I took pains to look up essentially all of the relevant literature on the origin of the flagellum. Since 2003 I've discovered some stuff I missed, and some new stuff has been published; regardless, the 2003 article proved that there was way more out there than even the ID critics realized.)

quote:
Biology in the Subjunctive Mood:A Response to Nicholas Matzke

Heh. First, Dembski conceded that my science was accurate (even though there are a few weaknesses in my article, he didn't catch them). Second, page-counting, rambling about my qualifications, who told him about the article, whether or not I'm a mathematical child genius, and the like, are just off-topic dissembling.

Third, Dembski's Big Counterpoint is this:

quote:
As for Matzke's claim that his model is step-by-step, that's trivially true -- after all, he defined the model as a series of steps. But are those steps reasonably small so that they constitute what Darwin called "successive, slight modifications." My sense is no -- getting from a type III secretion system to a bacterial flagellum in six steps seems on its face to require at least one big leap somewhere. But intuitions aside, given that Matzke's model is not detailed, there's no way to decide whether the steps are small enough to be accommodated by the Darwinian mechanism.

Intuition? Intuition? He couldn't actually find a big gap in my scenario, so he relies on intuition to tell him there is one?

As for detail, I was quite up front about what the right standard for detail was: breaking down the origin of the flagellum into a linear series of protein-protein-binding-site-evolution events. The evolution of a binding site is itself a rather trival "microevolutionary" event that can be approached gradually -- see for example here, here and here for documentation -- so treating these as the "steps" for the unit of analysis is well justified. Dembski of course grapples with none of this.

quote:

The double-standards are obvious. Reality shows they exist.

Yep, and you've got them all, ID man...


This message is a reply to:
 Message 107 by ID man, posted 09-18-2004 11:16 AM ID man has replied

Replies to this message:
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Nic Tamzek
Inactive Member


Message 184 of 207 (154501)
10-30-2004 9:56 PM


Howdy,

quote:
There's a passage in Meyer's paper that I have a question about:

quote:
---------------------------------------------------------------------
Cassette mutagenesis experiments performed during the early 1990s suggest that the probability of attaining (at random) the correct sequencing for a short protein 100 amino acids long is about 1 in 1065 (Reidhaar-Olson & Sauer 1990, Behe 1992:65-69). This result agreed closely with earlier calculations that Yockey (1978) had performed based upon the known sequence variability of cytochrome c in different species and other theoretical considerations. More recent mutagenesis research has provided additional support for the conclusion that functional proteins are exceedingly rare among possible amino acid sequences (Axe 2000, 2004). Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 1077. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 1077.
---------------------------------------------------------------------

I did read Elsberry's response in regards to Axe's citation here - interesting to say the least.

But I still have a couple of questions:

1. What is cassette mutagenesis, and how does it differ from other mutagenesis techniques?


Mutating a group of amino acids at once. E.g., in a 150 amino acid protein, you might mutated aas 1-10, then 11-20, then 21-30, etc. You might discover that positions 1-10 can be just about anything without destroying whatever function you are testing for, but that 11-20 are very important.

This is useful for certain purposes (figuring out how the protein works) but is not very close to any evolutionary process. In evolution, the main process, point mutation, is 1 mutation at a time, and with this kind of small change you can end up changing many more amino acids than if you blast whole chunks of the protein with cassette mutagenesis. IDists of course prefer the cassette mutagenesis studies and ignore the others.

quote:

2. I seem to have come across an abstract or two that seems to show that cassette mutagenesis certainly has its limitations:

quote:
---------------------------------------------------------------------
To achieve a non-biased random replacement on the amino acid level, oligonucleotide-directed mutagenesis (5) and cassette mutagenesis (6,7) have been carried out. These methods are limited to a defined region of the gene and can not introduce mutations at random positions
http://www.humanapress.com/ChapterDetail...
{Shortened display form of URL, to restore page width to normal - Adminnemooseus}
---------------------------------------------------------------------

Am I incorrect on my assessment? If I am correct, wouldn't Meyer's analysis also be on a limited scope here?


Yes, although the fact that experimental mutation techniques can be biased is not the biggest problem with Meyer's usage of these kinds of studies. The biggest problems are:

(1) Evolution usually doesn't mutate a whole bunch of aas at once (like cassette mutagenesis), typically it's one aa at a time. Selection eliminates the failures and keeps/allows the successes/neutrals.

(2) The studies that Meyer cites take the "reverse" approach to estimating the density of "functional sequences" -- they take a functional protein, mess it up, and see how many mutants retain function. "Forward" studies, which take random sequences and test for function, get much higher numbers, as Axe (2004) explicitly concedes.

(3) Axe (2004), at least, tests for one function, and a fairly specific mechanism for that function. This is a small target. Evolution, OTOH, "tests" for many functions at once, and cares not about mechanism, as long as it works. This is a much bigger target.

(4) The origin of new genes is well understood and there are many papers on the topic, all of which Meyer ignored.

(5) Lastly, cases of new functional proteins are known to have evolved from non-protein-coding sequences in recent history in the wild and in the lab (google on "nylonase evolution"). Therefore such things clearly are possible, and anyone who denies this just doesn't know what they're talking about. Unfortunately this conclusion must apply to Meyer, the editor Sternberg, and the reviewers Sternberg picked.

quote:

3. Anything else in this passage that might be a bit off or misleading?

Axe (2004) actually concluded that the range of density of functional sequences was between 1 in 10^53 (from a similar study) and 1 in 10^77 (from Axe's study). Meyer only cites the 1 in 10^77 figure, ignoring the uncertainty of about 1 million billion billion billion in the figure.

There are numerous other points, e.g. Axe's actual opinion on protein evolution based on his study (he thinks it's quite possible), and the fact that according to Dembski something is supposed to have odds of 1 in 10^150 in order to actually have "CSI." Like the critique says, the mistakes are many and layered. But that's probably enough for now...

This message has been edited by Adminnemooseus, 02-03-2005 17:15 AM


  
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