Re: Peer reviewed ID publications

From: Michael Roberts <michael.andrea.r@ukonline.co.uk>
Date: Thu Nov 03 2005 - 13:48:06 EST

Frankly three peer reviewed papers by so many IDer s is in fact very few and
is nearer what each researcher should be producing each year.

I am unable to challenge Pim's comments

Michael
----- Original Message -----
From: "Pim van Meurs" <pimvanmeurs@yahoo.com>
To: "Hofmann, Jim" <jhofmann@exchange.fullerton.edu>
Cc: <jcannon@washjeff.edu>; <asa@calvin.edu>
Sent: Thursday, November 03, 2005 4:58 PM
Subject: Re: Peer reviewed ID publications

None of these seem to be very relevant to ID. Over time the DI and ID
proponents have been touting various other papers and/or books as being
peer reviewed. Behe's testimony and the followup revelations show how
limited peer review of academic books can be.

Stephen Meyer, “The Origin of Biological Information and the Higher
Taxonomic Categories” Proceedings of the Biological Society of
Washington 117(2004):213-239.

This paper is a very poor overview of the Cambrian period and provides
no relevant hypotheses, pathways or mechanisms relevant to ID. This
paper was reviewed in depth at pandasthumb
http://www.pandasthumb.org/pt-archives/000484.html and was repudiated by
the Biological Society of Washington
(http://www.ncseweb.org/resources/news/2004/ZZ/608_bsw_repudiates_meyer_9_7_2004.asp)

Jonathan Wells, “Do Centrioles Generate a Polar Ejection Force? /Rivista
di Biologia/Biology Forum/ 98 (2005): 37-62. Again, this paper
formulates an "it looks like a turbine, perhaps it is one" hypothesis
which has little relevant to ID.

Scott Minnich and Stephen C. Meyer, “Genetic Analysis of Coordinate
Flagellar and Type III Regulatory Circuits,” /Proceedings of the Second
International Conference on Design & Nature/, Rhodes Greece, edited by
M.W. Collins and C.A. Brebbia (WIT Press, 2004

This paper again provides no relevant hypotheses pathways or mechanism,
and is 'peer reviewed' only at the level of a conference paper. PT has
documented various flaws in the arguments
(http://www.pandasthumb.org/pt-archives/000503.html)

Unfortunately, Meyer’s arguments did not improve (or change appreciably)
in the intervening months. All of Meyer’s points have obvious problems.
Taking them point-by-point:

   1.

      Regulation is a fairly trivial thing to change. All that would be
      required to solve Minnich and Meyer’s problem of differential
      regulation would be a simple change in the temperature sensitivity
      of the regulation of one of the secretion systems. Numerous
      bacteria, including disease-causing bacteria, have multiple
      secretion systems. The number of secretion systems can vary even
      between closely related bacteria, and furthermore the secretion
      systems are often found on plasmids that can be duplicated and
      transferred to other bacteria. Besides, if differential regulation
      is really so hard to evolve, then on Minnich and Meyer’s analysis,
      bubonic plague was intelligently designed. This resonates rather
      well with medieval notions about the cause of the Black Death
      (demons, curses, etc.), but is not likely to have much of a future
      in 21st century medicine.

   2.

      Meyer says, “the other thirty proteins in the flagellar motor
      (that are not present in the TTSS) are unique to the motor and are
      not found in any other living system.” This is flat-out mistaken,
      as Meyer would have known if he had read my survey of the
      peer-reviewed literature
      <http://www.talkdesign.org/faqs/flagellum.html> on the
      evolutionary origin of the flagellum. Off the top of my head,
      nonflagellar homologies have been documented — in the scientific
      literature, not by me — for the 2 motor proteins (MotAB) (see here
      <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11669642>),
      the 10 or so chemotaxis and MCP proteins, FlgA, FliA, the FlgJ
      C-terminal domain, the two master regulator genes FlhDC mentioned
      by Minnich in the paper, and FliK. Furthermore, FliM is
      essentially a fusion of another flagellum protein (FliN) and a
      chemotaxis protein (CheC), and all of the 11 or so flagellar axial
      proteins (rood, hook, flagellar filament, linkers, caps) are
      probably homologous to each other (the references for most of the
      proteins discussed can be found here
      <http://www.talkdesign.org/faqs/flagellum.html>, although I
      discovered a few of these homologies after that article was
      written). Altogether, there are very few flagellar proteins
      “unique to the motor” in Meyer’s sense, particularly if we throw
      in a few more that are probably homologous to each other (4
      chaperones), those probably homologous to Type II secretion (FlgH,
      FlgI), and those that can be deleted with little or no obvious ill
      effect (FliL, FliE, FlgM).

   3.

      Meyer writes, “present-day bacteria need an elaborate system of
      genetic instructions as well as many other protein machines to
      time the expression of those assembly instructions. Arguably, this
      system is itself irreducibly complex.” This is, first of all,
      moving the goalposts to a different system — protein assembly and
      gene expression systems, which probably date back almost to
      pre-cellular replicators. You can’t ask someone to explain the
      origin of the bacterial flagellum, and when they do, turn around
      and say “no, I actually meant you have to explain the origin of
      life.” Second, irreducibly complex protein systems have evolved in
      recent history, mostly by the kinds of regulational changes Meyer
      and Minnich say can’t happen (see references here
      <http://www.evowiki.org/index.php/Toxin_degradation_pathways>).

   4.

      Meyer concludes, “Finally, phylogenetic analyses of the gene
      sequences [20] suggest that flagellar motor proteins arose first
      and those of the pump came later.” Reference 20 is Nguyen /et al./
      <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10939240>,
      and it is a popular bit of ID folklore that this paper showed that
      TTSS genes were phylogenetically derived from flagellar genes. The
      paper was indeed about “Phylogenetic analyses of the constituents
      of Type III protein secretion systems,” but the actual
      phylogenetic trees of flagellar proteins produced by Nguyen /et
      al./ showed TTSS proteins as sister to, not nested within,
      flagellar proteins. Meyer therefore gets this point exactly
      backwards. Despite the gene sequences, it is still possible to
      argue that flagella came before (known) Type III secretion systems
      based on other evidence (this is the approach Nguyen /et al./
      take), but this is quite different than Meyer’s statement [2].

A peer-reviewer who knew the relevant literature well would have missed
none of these points, and thus I conclude that the Minnich and Meyer
paper was not seriously peer-reviewed.
Received on Thu Nov 3 13:51:59 2005

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