Claim CB200.1:
Bacterial flagella and eukaryotic cilia are irreducibly complex,
Since nonfunctional intermediates cannot be preserved by natural
selection, these systems can only be explained by intelligent design.
Source:
Behe, Michael J. 1996. Darwin's Black Box, New York: The Free Press, pp.
 59-73.
Response:
-  This is an example of argument from incredulity,
 because
   irreducible complexity can evolve naturally. 
 Many of the
   proteins in the bacterial flagellum or eukaryotic cilium are similar to
   each other or to proteins for other functions.  Their origins can
   easily be explained by a series of gene duplication events followed by
   modification and/or co-option, proceeding gradually through
   intermediate systems different from and simpler than the final
   flagellum.
   One plausible path for the evolution of flagella goes through the
   following basic stages (keep in mind that this is a summary, and
   that each major co-option event would be followed by long periods of
   gradual optimization of function):
-  A passive, nonspecific pore evolves into a more specific passive
       pore by addition of gating protein(s).  Passive transport
       converts to active transport by addition of an ATPase that couples
       ATP hydrolysis to improved export capability.  This complex forms
       a primitive type-III export system.
 -  The type-III export system is converted to a type-III secretion
       system (T3SS) by addition of outer membrane pore proteins (secretin
       and secretin chaperone) from the type-II secretion system.  These
       eventually form the P- and L-rings, respectively, of modern
       flagella.  The modern type-III secretory system forms a structure
       strikingly similar to the rod and ring structure of the flagellum
       (Hueck 1998; Blocker et al. 2003).
 -  The T3SS secretes several proteins, one of which is an adhesin (a
       protein that sticks the cell to other cells or to a substrate).
       Polymerization of this adhesin forms a primitive pilus, an
       extension that gives the cell improved adhesive capability.  After
       the evolution of the T3SS pilus, the pilus diversifies for various
       more specialized tasks by duplication and subfunctionalization of
       the pilus proteins (pilins).
 -  An ion pump complex with another function in the cell fortuitously
       becomes associated with the base of the secretion system structure,
       converting the pilus into a primitive protoflagellum.  The initial
       function of the protoflagellum is improved dispersal.  Homologs of
       the motor proteins MotA and MotB are known to function in diverse
       prokaryotes independent of the flagellum.
 -  The binding of a signal transduction protein to the base of the
       secretion system regulates the speed of rotation depending on the
       metabolic health of the cell.  This imposes a drift toward
       favorable regions and away from nutrient-poor regions, such as
       those found in overcrowded habitats.  This is the beginning of
       chemotactic motility.
 -  Numerous improvements follow the origin of the crudely functioning
       flagellum.  Notably, many of the different axial proteins (rod,
       hook, linkers, filament, caps) originate by duplication and
       subfunctionalization of pilins or the primitive flagellar axial
       structure.  These proteins end up forming the axial protein family.
 
   The eukaryotic cilium (also called the eukaryotic flagellum or
   undulipodium) is fundamentally different from the bacterial flagellum.
   It probably originated as an outgrowth of the mitotic spindle in a
   primitive eukaryote (both structures make use of sliding microtubules
   and dyneins).  Cavalier-Smith (1987; 2002) has discussed the origin of
   these systems on several occasions.
 -  The bacterial flagellum is not even irreducible.  Some bacterial
   flagella function without the L- and P-rings.  In experiments with
   various bacteria, some components (e.g. FliH, FliD (cap), and the
   muramidase domain of FlgJ) have been found helpful but not absolutely
   essential (Matzke 2003).  One third of the 497 amino acids of flagellin
   have been cut out without harming its function (Kuwajima 1988).
   Furthermore, many bacteria have additional proteins that are required
   for their own flagella but that are not required in the "standard"
   well-studied flagellum found in E. coli.  Different bacteria have
   different numbers of flagellar proteins (in Helicobacter pylori, for
   example, only thirty-three proteins are necessary to produce a working
   flagellum), so Behe's favorite example of irreducibility seems actually
   to exhibit quite a bit of variability in terms of numbers of required
   parts (Ussery 1999).
   Eukaryotic cilia are made by more than 200 distinct proteins, but even
   here irreducibility is illusive.  Behe (1996) implied and Denton
   (1986, 108) claimed explicitly that the common 9+2 tubulin
   structure of cilia could not be substantially simplified.  Yet
   functional 3+0 cilia, lacking many microtubules as well as some of the
   dynein linkers, are known to exist (Miller 2003, 2004).
 -  Eubacterial flagella, archebacterial flagella, and cilia use entirely
   different designs for the same function.  That is to be expected if
   they evolved separately, but it makes no sense if they were the work of
   the same designer.
 
Links:
Matzke, N. J. 2003.  Evolution in (brownian) space:
 a model for the origin of the bacterial flagellum.
 http://www.talkdesign.org/faqs/flagellum.html
 or
 http://www.talkreason.org/articles/flag.pdf
 (see also 'Background to "Evolution in (Brownian) space"',
 http://www.talkdesign.org/faqs/flagellum_background.html
 or
 http://www.talkreason.org/articles/flagback.cfm)
Dunkelberg, Pete. 2003.  Irreducible complexity demystified
 http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html
Musgrave, Ian. 2000.  Evolution of the bacterial flagella.
 http://www.health.adelaide.edu.au/Pharm/Musgrave/essays/flagella.htm
References:
-  Blocker, Ariel, Kaoru Komoriya, and Shin-Ichi Aizawa. 2003.  Type III
   secretion systems and bacterial flagella: Insights into their function
   from structural similarities.  Proceedings of the National Academy of
 Science USA 100(6): 3027-3030.
   http://www.pnas.org/cgi/content/full/100/6/3027
 -  Cavalier-Smith, T. 1987. The origin of eukaryote and
   archaebacterial cells.  Annals of the New York Academy
   of Sciences 503: 17-54.
 -  Cavalier-Smith, T. 2002. The phagotrophic origin of eukaryotes and
   phylogenetic classification of Protozoa.  International Journal of
   Systematic and Evolutionary Microbiology 52: 297-354.
 -  Denton, M. 1986.  Evolution: A Theory in Crisis.
   Bethesda, MD: Adler & Adler.
 -  Hueck, C. J. 1998.  Type III protein secretion systems in bacterial
   pathogens of animals and plants.  Microbiology and Molecular Biology
   Reviews 62: 379-433.
 -  Kuwajima, G. 1988. Construction of a minimum-size functional
   flagellin of Escherichia coli. Journal of Bacteriology 170:
   3305-3309.
 -  Matzke, N. J. 2003.  (see above)
 -  Miller, K. 2003.  Answering the biochemical argument from design.
   in: Manson, N. (Ed.), God and design: the teleological argument and 
   modern science, Routledge, London, pp. 292-307. 
   http://www.millerandlevine.com/km/evol/design1/article.html
 -  Miller, K. 2004.  The flagellum unspun. In Debating Design: from
   Darwin to DNA, 81-97, eds. Dembski, W., and M. Ruse, New York:
   Cambridge University Press.
   http://www.millerandlevine.com/km/evol/design2/article.html
 -  Ussery, D. 1999. (see below)
 
 
Further Reading:
Ussery, David. 1999.  A biochemist's response to "The biochemical
 challenge to evolution".  Bios 70: 40-45.
 http://www.cbs.dtu.dk/staff/dave/Behe.html
created  2001-2-17, modified  2003-12-15