Intelligent Reasoning

Promoting, advancing and defending Intelligent Design via data, logic and Intelligent Reasoning and exposing the alleged theory of evolution as the nonsense it is. I also educate evotards about ID and the alleged theory of evolution one tard at a time and sometimes in groups

Thursday, March 23, 2006

Those bluffing evolutionitwits

I don't know. Perhaps it is the rising popularity of Texas hold'em. Perhaps it is just the inherent decption and dishonesty that permeates from evolutionism.

Either way it is very entertaining to watch evolutionitwits try to bluff their way through a debate.

The most recent bluff was made by James "Momma's boy" Wynne:

Then why not take one of the many research papers that deal with the evolution of the flagellum, read it (ha!) and then tell us specifically what your problem with it is, and also tell us about an experiment that you might design to test the hypotheses you think are wrong.

Unlike Texas hold'em calling this bluff doesn't take any $$$, just common sense:

Perhaps James Wynne can provide ONE scientific research paper that demonstrates the bac flag "evolved" via some blind watchmaker-type process.

Then perhaps James will tell us why not one evolutionary biologist has conducted the experiment that would demonstrate that such a transformation is even possible (ie from flagella-less bacteria to bacteria with at least one flagellum).

You know James I have asked you several times what would falsify the premise that the bac flag evolved via some blind watchmaker-type process, yet you NEVER answered the question.


perfesser Scotty Page is another who loves to posture, accuse, assert- IOW he is another puffer bluffer. Each time is is called on his bluffs he runs away, only to return with more of the same.

Don't they realize is all they have to do is substantiate their claims with real data? Or is it that they realize they cannot and bluffing (postering, accusing, assertions, etc.) is all they have left in the bag?

I almost forgot the evolutionitwits have a documented history of bluffing:

One Long Bluff:
The Gishlick, Matzke and Elsberry Response to Stephen Meyer's Peer-Reviewed Article


(content edited to fix a typo- It appears that Momma's boy James Wynne has found a purpose in life. You go girl!)

25 Comments:

  • At 10:24 AM, Blogger James Wynne said…

    Joe, I just don't get it. You critcize the alleged paucity of evidence for evolution, yet you remain ignorant of the details of the evidence, and refuse to admit that you're ignorant of them. In an earlier comment you said (with regard to research papers on evolution of supposedly IC biological structures), "I have read a few but not one deals with a mechanism." Which ones have you read, Joe? What are your specific criticisms of the research? Why are you so reluctant to discuss details? Why do you think that biologists are responsible for confirming the spurious claims of cranks?

    I've just been reading an article by Bruce Gordon, IDist and Dembski's erstwhile assistant director at the short-lived Polanyi Center at Baylor. You can read the full article here.
    Some of the interesting things Gordon says:
    ...design-theoretic research has been hijacked as part of a larger cultural and political movement. In particular, the theory has been prematurely drawn into discussions of public science education where it has no business making an appearance without broad recognition from the scientific community that it is making a worthwhile contribution to our understanding of the natural world. And,

    ...inclusion of design theory as part of the standard discourse of the scientific community, if it ever happens, will be the result of a long and difficult process of quality research and publication. And one last one:

    ...it is crucial to note that design theory is at best a supplementary consideration introduced along- side (or perhaps into, by way of modification) neo-Darwinian biology and self- organizational complexity theory. It does not mandate the replacement of these highly fruitful research paradigms, and to suggest that it does is just so much overblown, unwarranted, and ideologically driven rhetoric.

    So at least one guy on your side recognizes that ID has to prove itself before equal time can be expected. Note that "prove itself" doesn't mean handwaving, obfuscation and arguments from incredulity. It means some actual work has to be done.

    So when does the work start, Joe?

     
  • At 11:25 AM, Blogger Joe G said…

    And it just continues.

    James I am more than aware of the alleged evidence for the theory of evolution. I am also more than aware there aren't any details.

    For example I am aware there isn't any data that demontrates bacteria can "evolve" into anything but bacteria.

    Don't ask which articles I have read, present ONE that substantiates your claim or SHUT UP!

    Then and only then will we have something to discuss.

    The data in "Unlocking the Mystery of Life" demonstrates how intellectually bankrupt any attempt at a non-ID approach to the issue is.

    That ID has been "hijacked" is meaningless. Atheists hijacked the theory of evolution. So what?

    And I wonder what "fruit" the theory of evolution has given us? That is one of the main issues- it is worthless.

    As I pointed out several times, "The Privileged Planet" AND "Unlocking..." are based on scientific research. What is about that research that YOU don't understand?

    STOP BLUFFING

     
  • At 1:04 PM, Blogger James Wynne said…

    Joe said,
    ...Scotty Page is another who loves to posteur...

    Joe, you really can't hope to be taken seriously and have people understand you if you keep making up words.

    Prediction: Joe says (in his best Pee Wee Herman voice)"I MEANT to say that!"

     
  • At 1:12 PM, Blogger Joe G said…

    You KNOW someone has lost when they start picking on typos.

    Truly pathetic, even for a Momma's boy.

    Now run along and go play in heavy interstate traffic.


    (I take it there is no chance of you presenting this blog with that scientific research paper that demonstrates a bac flag can "evolve" via some blind watchmaker-type process. Another prediction fulfilled. Thanks.)

     
  • At 1:44 PM, Blogger James Wynne said…

    You might want to also have a look at the double "is" in the same paragraph.

    You're already aware that there are research papers dealing with evolution of "IC" structures, although you haven't read any of them, and wouldn't understand them if you did, so I'm not sure why you keep asking. What's a "blind watchmaker-type process"? Better yet, why don't you describe the alternative?

     
  • At 4:05 PM, Blogger James Wynne said…

    Once again:

    In an earlier comment you said (with regard to research papers on evolution of supposedly IC biological structures), "I have read a few but not one deals with a mechanism." Which ones have you read, Joe? What are your specific criticisms of the research? Why are you so reluctant to discuss details? Why do you think that biologists are responsible for confirming the spurious claims of cranks?

     
  • At 7:37 PM, Blogger Joe G said…

    James,

    What is preventing you from presenting ONE scientific research paper that demonstrates what you are claiming?


    As for "What's a "blind watchmaker-type process"?"- we have been down that road already. No need to feign ignorance or dishonesty. You have already established your propensity for both.


    Present ONE paper James.

    All honest people understand that neither IC nor ID is anti-evolution. I take it that is your problem- you are too dishonest to understand what is being debated and too stupid (or ignorant) to understand what is involved.

    As for specific criticisms-watch the video. It's all there...

     
  • At 7:41 PM, Blogger Joe G said…

    James,

    All I am asking is that you give it your best shot. However it appears even your best shot is a bluff. Typical...

     
  • At 8:15 AM, Blogger James Wynne said…

    Yes Joe, you're right. Arguing against an IDiot is the same as arguing against ID; definitions change with the question, no one knows what the "theory" is, blather and dissembling are characterized as "intelligent reasoning," and no research ever gets done. Of course I was only bluffing and posteuring. How could I ever have been foolish enough to believe that I could prevail against such an obviously superior intellect?
    Mea culpa.

     
  • At 12:30 PM, Blogger Joe G said…

    James Wynne:
    Yes Joe, you're right.

    It usually works out that way.

    James Wynne:
    Arguing against an IDiot is the same as arguing against ID;

    How is arguing against an idiot like you arguing against ID? How was what you are doing determined to be arguing?

    You have yet to present anything to debate. I keep asking for the data and your just keep on keeping on.

    Unless of course you are equating my continued corrections of your stupidity with arguing, but that is rather naive.

    James Wynne:
    definitions change with the question,

    As do your vague accusations and bald assertions.

    What definitions changed?

    And all you do is question- how about some answers?

    James Wynne:
    no one knows what the "theory" is, blather and dissembling are characterized as "intelligent reasoning," and no research ever gets done.

    That's a good summary of the arguments against the "theory" of evolution.

    What research is being done that would demonstrate bacteria can "evolve" into anything but bacteria?

    James Wynne:
    Of course I was only bluffing and posteuring.

    Of course that is what reality has, and continues to, demonstrate.

    Your infatuation with typos just further exposes that fact.

    Is that it? Is your best shot tantamount to a child's tantrum? Thanks.

    Youa dopa ;)

     
  • At 11:16 AM, Blogger jt said…

    Here are a few, joe. Or do you, like Behe, think this is inadequate?
    ------------

    Aizawa, S. I., 2001. Bacterial flagella and type III secretion systems. FEMS Microbiol Lett. 202 (2), 157-164.

    Albertini, A. M., Caramori, T., Crabb, W. D., Scoffone, F. and Galizzi, A., 1991. The flaA locus of Bacillus subtilis is part of a large operon coding for flagellar structures, motility functions, and an ATPase-like polypeptide. J Bacteriol. 173 (11), 3573-3579.

    Anandarajah, K., Kiefer, P. M., Donohoe, B. S. and Copley, S. D., 2000. Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol. Biochemistry. 39 (18), 5303-5311.

    Arora, S. K., Ritchings, B. W., Almira, E. C., Lory, S. and Ramphal, R., 1998. The Pseudomonas aeruginosa flagellar cap protein, FliD, is responsible for mucin adhesion. Infect Immun. 66 (3), 1000-1007.

    Auvray, F., Ozin, A. J., Claret, L. and Hughes, C., 2002. Intrinsic membrane targeting of the flagellar export ATPase FliI: Interaction with acidic phospholipids and FliH. Journal of Molecular Biology. 318 (4), 941-950.

    Bardy, S. L., Ng, S. Y. and Jarrell, K. F., 2003. Prokaryotic motility structures. Microbiology. 149 (Pt 2), 295-304.

    Bayley, D. P. and Jarrell, K. F., 1998. Further evidence to suggest that archaeal flagella are related to bacterial type IV pili. J Mol Evol. 46 (3), 370-373.

    Berg, H. C., 1993. Random Walks in Biology. Princeton University Press, Princeton.

    Berg, H. C., 1998. Keeping up with the F1-ATPase. Nature. 394 (6691), 324-325.

    Berg, H. C., 2003. The rotary motor of bacterial flagella. Annu Rev Biochem. 72, 19-54.

    Berg, H. C. and Anderson, R. A., 1973. Bacteria swim by rotating their flagellar filaments. Nature. 245 (5425), 380-382.

    Berry, R. M., 2000. Theories of rotary motors. Philos Trans R Soc Lond B Biol Sci. 355 (1396), 503-509.

    Birkenhager, R., Greie, J.-C., Altendorf, K. and Deckers-Hebestreit, G., 1999. F0 complex of the Escherichia coli ATP synthase . Not all monomers of the subunit c oligomer are involved in F1 interaction. Eur J Biochem. 264 (2), 385-396.

    Bischoff, D. S. and Ordal, G. W., 1992. Identification and characterization of FliY, a novel component of the Bacillus subtilis flagellar switch complex. Mol Microbiol. 6 (18), 2715-2723.

    Bitter, W., 2003. Secretins of Pseudomonas aeruginosa: large holes in the outer membrane. Arch Microbiology. 179 (5), 307-314.

    Block, S. M., 1997. Real engines of creation. Nature. 386 (6622), 217-219.

    Blocker, A., Komoriya, K. and Aizawa, S. I., 2003. Type III secretion systems and bacterial flagella: Insights into their function from structural similarities. Proc Natl Acad Sci U S A. 100 (6), 3027-3030.

    Boyer, P. D., 1997. The ATP synthase - A splendid molecular machine. Annu Rev Biochem. 66, 717-749.

    Broome-Smith, J. K. and Mitsopoulos, C., 1999. Overview: Transport of molecules across microbial membranes -- a sticky situation to get to grips with, in: Broome-Smith, J. K., Baumberg, S., Stirling, C. J. and Ward, F. B. (Eds.), Transport of molecules across microbial membranes, General Society for Microbiology, Cambridge University Press, Cambridge, UK, pp.1-14.

    Brown, I. I. and Häse, C. C., 2001. Flagellum-independent surface migration of Vibrio cholerae and Escherichia coli. J Bacteriol. 183 (12), 3784-3790.

    Brown, P. N., Hill, C. P. and Blair, D. F., 2002. Crystal structure of the middle and C-terminal domains of the flagellar rotor protein FliG. Embo J. 21 (13), 3225-3234.

    Buchanan, S. K., 2001. Type I secretion and multidrug efflux: transport through the TolC channel-tunnel. Trends in Biochemical Sciences. 26 (1), 3-6.

    Bullitt, E. and Makowski, L., 1998. Bacterial adhesion pili are heterologous assemblies of similar subunits. Biophys J. 74 (1), 623-632.

    Büttner, D. and Bonas, U., 2002. Port of entry – the type III secretion translocon. Trends Microbiol. 10 (4), 186-192.

    Campbell, N. A., 1993. Biology. Benjamin/Cummings, Redwood City, CA.

    Campos-Garcia, J., Najera, R., Camarena, L. and Soberon-Chavez, G., 2000. The Pseudomonas aeruginosa motR gene involved in regulation of bacterial motility. FEMS Microbiol Lett. 184 (1), 57-62.

    Cao, T. B. and Saier, M. H., Jr., 2003. The general protein secretory pathway: phylogenetic analyses leading to evolutionary conclusions. Biochim Biophys Acta. 1609 (1), 115-125.

    Capaldi, R. A. and Aggeler, R., 2002. Mechanism of the F1-F0-type ATP synthase, a biological rotary motor. Trends in the Biochemical Sciences. 27 (3), 154-160.

    Cascales, E., Lloubes, R. and Sturgis, J. N., 2001. The TolQ-TolR proteins energize TolA and share homologies with the flagellar motor proteins MotA-MotB. Mol Microbiol. 42 (3), 795-807.

    Cavalier-Smith, T., 1978. The evolutionary origin and phylogeny of microtubules, mitotic spindles and eukaryote flagella. Biosystems. 10 (1-2), 93-114.

    Cavalier-Smith, T., 1982. The evolutionary origin and phylogeny of eukaryote flagella. Symposia of the Society for Experimental Biology. 35 (5896), 465-493.

    Cavalier-Smith, T., 1987a. The origin of cells: a symbiosis between genes, catalysts, and membranes. Cold Spring Harbor Symposia on Quantitative Biology. 52 (6111), 805-824.

    Cavalier-Smith, T., 1987b. The origin of eukaryotic and archaebacterial cells. Annals of the New York Academy of Sciences. 503, 17-54.

    Cavalier-Smith, T., 2001a. Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. Journal of Molecular Evolution. 53 (4-5), 555-595.

    Cavalier-Smith, T., 2001b. Early evolution: from the appearance of the first cell to the first modern organisms (review). Quarterly Review of Biology. 76 (2), 233.

    Cavalier-Smith, T., 2002a. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol. 52, 7-76.

    Cavalier-Smith, T., 2002b. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol. 52, 297-354.

    Cavalier-Smith, T., 2002c. Origins of the machinery of recombination and sex. Heredity. 88, 125-141.

    Celandroni, F., Ghelardi, E., Pastore, M., Lupetti, A., Kolsto, A. B. and Senesi, S., 2000. Characterization of the chemotaxis fliY and cheA genes in Bacillus cereus. FEMS Microbiol Lett. 190 (2), 247-253.

    Chapman, M. R., Robinson, L. S., Pinkner, J. S., Roth, R., Heuser, J., Hammar, M., Normark, S. and Hultgren, S. J., 2002. Role of Escherichia coli curli operons in directing amyloid fiber formation. Science. 295 (5556), 851-855.

    Chothia, C., Gough, J., Vogel, C. and Teichmann, S. A., 2003. Evolution of the protein repertoire. Science. 300 (5626), 1701-1703.

    Christie, P. J., 2001. Type IV secretion: intercellular transfer of macromolecules by systems ancestrally related to conjugation machines. Mol Microbiol. 40 (2), 294-305.

    Christie, P. J. and Vogel, J. P., 2000. Bacterial type IV secretion: conjugation systems adapted to deliver effector molecules to host cells. Trends Microbiol. 8 (8), 354-360.

    Claret, L., Calder, S. R., Higgins, M. and Hughes, C., 2003. Oligomerization and activation of the FliI ATPase central to bacterial flagellum assembly. Mol Microbiol. 48 (5), 1349-1355.

    Cohen-Krausz, S. and Trachtenberg, S., 2003. The structure of the helically perturbed flagellar filament of Pseudomonas rhodos: implications for the absence of the outer domain in other complex flagellins and for the flexibility of the radial spokes. Mol Microbiol. 48 (5), 1305-1316.

    Copley, S. D., 2000. Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends in Biochemical Sciences. V25 (N6), 261-265.

    Cordes, F. S., Komoriya, K., Larquet, E., Yang, S., Egelman, E. H., Blocker, A. and Lea, S. M., 2003. Helical structure of the needle of the type III secretion system of Shigella flexneri. J Biol Chem. 278 (19), 17103-17107.

    Corliss, J. O., 1980. Objection to "undulipodium" as an inappropriate and unnecessary term. Biosystems. 12 (1-2), 109-110.

    Cornelis, G. R. and Van Gijsegem, F., 2000. Assembly and function of type III secretory systems. Annu Rev Microbiol. 54, 735-774.

    Coutte, L., Alonso, S., Reveneau, N., Willery, E., Quatannens, B., Locht, C. and Jacob-Dubuisson, F., 2003. Role of adhesin release for mucosal colonization by a bacterial pathogen. J Exp Med. 197 (6), 735-742.

    Cox, G. B., Jans, D. A., Fimmel, A. L., Gibson, F. and Hatch, L., 1984. Hypothesis. The mechanism of ATP synthase. Conformational change by rotation of the beta-subunit. Biochim Biophys Acta. 768 (3-4), 201-208.

    Crago, A. M. and Koronakis, V., 1998. Salmonella InvG forms a ring-like multimer that requires the InvH lipoprotein for outer membrane localization. Mol Microbiol. 30 (1), 47-56.

    Dailey, F. E. and Macnab, R. M., 2002. Effects of lipoprotein biogenesis mutations on flagellar assembly in Salmonella. J Bacteriol. 184 (3), 771-776.

    Darwin, C., 1851. A Monograph of the Sub-class Cirripedia, with Figures of all the Species. The Lepadidae; or, Pedunculated Cirripedes. Ray Society, London. Online text.

    Darwin, C., 1854. A Monograph of the Sub-class Cirripedia, with Figures of all the Species. The Balanidae (or Sessile Cirripedes); the Verrucidae, etc. Ray Society, London. Online text.

    Darwin, C., 1862. On the various contrivances by which orchids are fertilised. J. Murray, London. Online text.

    Darwin, C., 1872. The origin of species by means of natural selection. 6th edition. John Murray, London. Online text.

    de Duve, C., 1995. Vital Dust: Life as a cosmic imperative. Basic Books, New York.

    de Souza, M. L., Seffernick, J., Martinez, B., Sadowsky, M. J. and Wackett, L. P., 1998. The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol. 180 (7), 1951-1954.

    DeLong, E. F. and Pace, N. R., 2001. Environmental diversity of bacteria and archaea. Systematic Biology. 50 (4), 470-478.

    DeRosier, D. J., 1998. The turn of the screw: the bacterial flagellar motor. Cell. 93 (1), 17-20.

    Dillon, R., Fauci, L. and Gaver, D., 3rd, 1995. A microscale model of bacterial swimming, chemotaxis and substrate transport. J Theor Biol. 177 (4), 325-340.

    Doolittle, R. F. and Feng, D. F., 1987. Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins. Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function. LII, 869-874.

    Durand, E., Bernadac, A., Ball, G., Lazdunski, A., Sturgis, J. N. and Filloux, A., 2003. Type II protein secretion in Pseudomonas aeruginosa: the pseudopilus is a multifibrillar and adhesive structure. J Bacteriol. 185 (9), 2749-2758.

    Dusenbery, D. B., 1996. Life At Small Scale: The Behavior of Microbes. Scientific American Library, New York.

    Dusenbery, D. B., 1997. Minimum size limit for useful locomotion by free-swimming microbes. Proc Natl Acad Sci U S A. 94 (20), 10949-10954.

    Dusenbery, D. B., 1998. Fitness landscapes for effects of shape on chemotaxis and other behaviors of bacteria. J Bacteriol. 180 (22), 5978-5983.

    Dyer, B. D., 2003. A Field Guide to Bacteria. Cornell University Press, Ithaca.

    Eisenbach, M., 2000. Bacterial chemotaxis, Nature Encyclopedia of Life Sciences, Nature Publishing Group, London.

    Emerson, S. U., Tokuyasu, K. and Simon, M. I., 1970. Bacterial flagella: polarity of elongation. Science. 169 (941), 190-192.

    Faguy, D. M. and Jarrell, K. F., 1999. A twisted tale: the origin and evolution of motility and chemotaxis in prokaryotes. Microbiology. 145 (Pt 2), 279-281.

    Faguy, D. M., Jarrell, K. F., Kuzio, J. and Kalmokoff, M. L., 1994. Molecular analysis of archael flagellins: similarity to the type IV pilin-transport superfamily widespread in bacteria. Can J Microbiol. 40 (1), 67-71.

    Fan, F., Ohnishi, K., Francis, N. R. and Macnab, R. M., 1997. The FliP and FliR proteins of Salmonella typhimurium, putative components of the type III flagellar export apparatus, are located in the flagellar basal body. Mol Microbiol. 26 (5), 1035-1046.

    Fernandez, L. A. and Berenguer, J., 2000. Secretion and assembly of regular surface structures in Gram-negative bacteria. FEMS Microbiol Rev. 24 (1), 21-44.

    Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y. L. and Postlethwait, J., 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics. 151 (4), 1531-1545.

    Francis, N. R., Sosinsky, G. E., Thomas, D. and DeRosier, D. J., 1994. Isolation, characterization and structure of bacterial flagellar motors containing the switch complex. J Mol Biol. 235 (4), 1261-1270.

    Fraser, G. M., Gonzalez-Pedrajo, B., Tame, J. R. and Macnab, R. M., 2003. Interactions of FliJ with the Salmonella Type III Flagellar Export Apparatus. J Bacteriol. 185 (18), 5546-5554.

    Gandon, S. and Roussett, F., 1999. Evolution of stepping-stone dispersal rates. Proc R Soc Lond B Biol Sci. 266 (1437), 2507-2513.

    Ganfornina, M. D. and Sanchez, D., 1999. Generation of evolutionary novelty by functional shift. Bioessays. V21 (N5), 432-439.

    Geer, L. Y., Domrachev, M., Lipman, D. J. and Bryant, S. H., 2002. CDART: protein homology by domain architecture. Genome Res. 12 (10), 1619-1623.

    Giron, J. A., Torres, A. G., Freer, E. and Kaper, J. B., 2002. The flagella of enteropathogenic Escherichia coli mediate adherence to epithelial cells. Mol Microbiol. 44 (2), 361-379.

    Gogarten, J. P. and Kibak, H., 1992. The bioenergetics of the last common ancestor and the origin of the eukaryotic endomembrane system. Biosystems. 28 (1-3), 131-153.

    Gogarten, J. P., Kibak, H., Dittrich, P., Taiz, L., Bowman, E. J., Bowman, B. J., Manolson, M. F., Poole, R. J., Date, T. and Oshima, T., 1989. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci U S A. 86 (17), 6661-6665.

    Gogarten, J. P., Starke, T., Kibak, H., Fishman, J. and Taiz, L., 1992. Evolution and isoforms of V-ATPase subunits. J Exp Biol. 172, 137-147.

    Gonzalez-Pedrajo, B., Fraser, G. M., Minamino, T. and Macnab, R. M., 2002. Molecular dissection of Salmonella FliH, a regulator of the ATPase FliI and the type III flagellar protein export pathway. Mol Microbiol. 45 (4), 967-982.

    Goodenough, U., 1998. The Sacred Depths of Nature. Oxford University Press, New York.

    Goodenough, U., 2002. Of flagella and outboard motors, accessed online. URL: http://www.metanexus.net/archives/printerfriendly.asp?archiveid=7143.

    Gophna, U., Ron, E. Z. and Graur, D., 2003. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene. 312, 151-163.

    Gould, S. J. and Lewontin, R. C., 1979. The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programmme. Proceedings of the Royal Society of London, Series B. 205 (1161), 581-598.

    Guerrero, R., Esteve, I., Pedrós-Alió, C. and Gaju, N., 1987. Predatory bacteria in prokaryotic communities. Annals of the New York Academy of Sciences. 503, 238-250.

    Hanumanthaiah, R., Day, K. and Jagadeeswaran, P., 2002. Comprehensive analysis of blood coagulation pathways in Teleostei: evolution of coagulation factor genes and identification of zebrafish factor VIIi. Blood Cells, Molecules, and Diseases. 29 (1), 57-68.

    Harris, R. J. and Elder, D., 2002. Actin and flagellin may have an N-terminal relationship. J Mol Evol. 54 (2), 283-284.

    Harshey, R. M. and Toguchi, A., 1996. Spinning tails: homologies among bacterial flagellar systems. Trends Microbiol. 4 (6), 226-231.

    Hayward, C. A., 2000. Microorganisms, Nature Encyclopedia of Life Sciences, Nature Publishing Group, London.

    He, S. Y., 1998. Type III protein secretion in plant and animal pathogenic bacteria. Annual Reviews in Phytopathology. 36, 363-392.

    He, S. Y. and Jin, Q., 2003. The Hrp pilus: learning from flagella. Curr Opin Microbiol. 6 (1), 15-19.

    Henderson, I. R., Navarro-Garcia, F. and Nataro, J. P., 1998. The great escape: structure and function of the autotransporter proteins. Trends Microbiol. 6 (9), 370-378.

    Hirano, T., Minamino, T. and Macnab, R. M., 2001. The role in flagellar rod assembly of the N-terminal domain of Salmonella FlgJ, a flagellum-specific muramidase. J Mol Biol. 312 (2), 359-369.

    Homma, M., DeRosier, D. J. and Macnab, R. M., 1990a. Flagellar hook and hook-associated proteins of Salmonella typhimurium and their relationship to other axial components of the flagellum. J Mol Biol. 213 (4), 819-832.

    Homma, M., Kutsukake, K., Hasebe, M., Iino, T. and Macnab, R. M., 1990b. FlgB, FlgC, FlgF and FlgG. A family of structurally related proteins in the flagellar basal body of Salmonella typhimurium. J Mol Biol. 211 (2), 465-477.

    Honma, Y. and Nakasone, N., 1990. Pili of Aeromonas hydrophila: purification, characterization, and biological role. Microbiol Immunol. 34 (2), 83-98.

    Hooper, S. D. and Berg, O. G., 2003. On the nature of gene innovation: duplication patterns in microbial genomes. Mol Biol Evol. 20 (6), 945-954.

    Hueck, C. J., 1998. Type III protein secretion systems in bacterial pathogens of animals and plants. Microbiol Mol Biol Rev. 62 (2), 379-433.

    Jackson, M. W. and Plano, G. V., 2000. Interactions between type III secretion apparatus components from Yersinia pestis detected using the yeast two-hybrid system. FEMS Microbiol Lett. 186 (1), 85-90.

    Jarrell, K. F., Bayley, D. P., Correia, J. D. and Thomas, N. A., 1999. Recent excitement about the archaea. Bioscience. 49 (7), 530-541.

    Jarrell, K. F., Bayley, D. P., Correia, J. D. and Thomas, N. A., 2000. Archaeal flagella, Nature Encyclopedia of Life Sciences, Nature Publishing Group, London.

    Jarrell, K. F., Bayley, D. P. and Kostyukova, A. S., 1996. The archaeal flagellum: a unique motility structure. J Bacteriol. 178 (17), 5057-5064.

    Jiang, Y. and Doolittle, R. F., 2003. The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes. Proc Natl Acad Sci U S A. 100 (13), 7527–7532.

    Johnson, G. R., Jain, R. K. and Spain, J. C., 2002. Origins of the 2,4-dinitrotoluene pathway. Journal of Bacteriology. 184 (15), 4219-4232.

    Jones, W. J., Nagle, D. P., Jr. and Whitman, W. B., 1987. Methanogens and the diversity of archaebacteria. Microbiol Rev. 51 (1), 135-177.

    Josenhans, C., Labigne, A. and Suerbaum, S., 1995. Comparative ultrastructural and functional studies of Helicobacter pylori and Helicobacter mustelae flagellin mutants: both flagellin subunits, FlaA and FlaB, are necessary for full motility in Helicobacter species. J Bacteriol. 177 (11), 3010-3020.

    Kalir, S., McClure, J., Pabbaraju, K., Southward, C., Ronen, M., Leibler, S., Surette, M. G. and Alon, U., 2001. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science. 292 (5524), 2080-2083.

    Karner, M. B., DeLong, E. F. and Karl, D. M., 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature. 409 (6819), 507-510.

    Kennedy, M. J., 1987. Role of motility, chemotaxis, and adhesion in microbial ecology. Annals of the New York Academy of Sciences. 503, 260-273.

    Kerr, B., Riley, M. A., Feldman, M. W. and Bohannan, B. J., 2002. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature. 418 (6894), 171-174.

    Khan, S., 1997. Rotary chemiosmotic machines. Biochim Biophys Acta. 1322 (2-3), 86-105.

    Kim, J. F., 2001. Revisiting the chlamydial type III protein secretion system: clues to the origin of type III protein secretion. Trends Genet. 17 (2), 65-69.

    Kirby, J. R., Kristich, C. J., Saulmon, M. M., Zimmer, M. A., Garrity, L. F., Zhulin, I. B. and Ordal, G. W., 2001. CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis. Mol Microbiol. 42 (3), 573-585.

    Knutton, S., Shaw, R. K., Anantha, R. P., Donnenberg, M. S. and Zorgani, A. A., 1999. The type IV bundle-forming pilus of enteropathogenic Escherichia coli undergoes dramatic alterations in structure associated with bacterial adherence, aggregation and dispersal. Mol Microbiol. 33 (3), 499-509.

    Koch, A. L., 2003. Were Gram-positive rods the first bacteria? Trends Microbiol. 11 (4), 166-170.

    Kojima, S. and Blair, D. F., 2001. Conformational change in the stator of the bacterial flagellar motor. Biochemistry. 40 (43), 13041-13050.

    Koretke, K. K., Lupas, A. N., Warren, P. V., Rosenberg, M. and Brown, J. R., 2000. Evolution of two-component signal transduction. Mol Biol Evol. 17 (12), 1956-1970.

    Kreft, J. U., Picioreanu, C., Wimpenny, J. W. and van Loosdrecht, M. C., 2001. Individual-based modelling of biofilms. Microbiology. 147 (Pt 11), 2897-2912.

    Lebreton, J., Khaladi, M. and Grosbois, V., 2000. An explicit approach to evolutionarily stable dispersal strategies: no cost of dispersal. Math Biosci. 165 (2), 163-176.

    Lenski, R. E., Ofria, C., Pennock, R. T. and Adami, C., 2003. The evolutionary origin of complex features. Nature. 423 (6936), 139-144.

    Long, M., 2001. Evolution of novel genes. Curr Opin Genet Dev. 11 (6), 673-680.

    Lupas, A., Van Dyke, M. and Stock, J., 1991. Predicting coiled coils from protein sequences. Science. 252 (5010), 1162-1164.

    Macnab, R. M., 1978. Bacterial motility and chemotaxis: the molecular biology of a behavioral system. CRC Crit Rev Biochem. 5 (4), 291-341.

    Macnab, R. M., 1999. The bacterial flagellum: reversible rotary propellor and type III export apparatus. J Bacteriol. 181 (23), 7149-7153.

    Macnab, R. M., 2003. How bacteria assemble flagella. Annu Rev Microbiol. 57, 77-100.

    Macnab, R. M. and DeRosier, D. J., 1988. Bacterial flagellar structure and function. Can J Microbiol. 34 (4), 442-451.

    Manson, M. D., Tedesco, P., Berg, H. C., Harold, F. M. and Van der Drift, C., 1977. A protonmotive force drives bacterial flagella. Proc Natl Acad Sci U S A. 74 (7), 3060-3064.

    Margulis, L., 1980. Undulipodia, flagella and cilia. Biosystems. 12 (1-2), 105-108.

    Marie, C., Broughton, W. J. and Deakin, W. J., 2001. Rhizobium type III secretion systems: legume charmers or alarmers? Curr Opin Plant Biol. 4 (4), 336-342.

    Mathews, M. A., Tang, H. L. and Blair, D. F., 1998. Domain analysis of the FliM protein of Escherichia coli. J Bacteriol. 180 (21), 5580-5590.

    Mathias, A., Kisdi, E. and Olivieri, I., 2001. Divergent evolution of dispersal in a heterogeneous landscape. Evolution Int J Org Evolution. 55 (2), 246-259.

    Maynard Smith, J., 1975. The Theory of Evolution. Cambridge University Press.

    Mayr, E., 1976. The emergence of evolutionary novelties, Evolution and the diversity of life, Harvard University Press, Cambridge, pp. 88-113.

    McBride, M. J., 2001. Bacterial gliding motility: multiple mechanisms for cell movement over surfaces. Annu Rev Microbiol. 55, 49-75.

    McCarter, L. L., 2001. Polar flagellar motility of the Vibrionaceae. Microbiol Mol Biol Rev. 65 (3), 445-462, table of contents.

    Mecsas, J. J. and Strauss, E. J., 1996. Molecular mechanisms of bacterial virulence: type III secretion and pathogenicity islands. Emerg Infect Dis. 2 (4), 270-288.

    Melendez-Hevia, E., Waddell, T. G. and Cascante, M., 1996. The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution. J Mol Evol. 43 (3), 293-303.

    Merz, A. J. and Forest, K. T., 2002. Bacterial surface motility: slime trails, grappling hooks and nozzles. Curr Biol. 12 (8), R297-303.

    Miller, K. R., 2003. Answering the biochemical argument from design, in: Manson, N. (Ed.), God and design: the teleological argument and modern science, Routledge. URL: http://www.millerandlevine.com/km/evol/design1/article.html

    Miller, K. R., 2004. The Flagellum Unspun: The Collapse of "Irreducible Complexity", in: Ruse, M. and Dembski, W. (Eds.), Debating Design: from Darwin to DNA, Cambridge University Press, Cambridge, MA. URL: http://www.millerandlevine.com/km/evol/design2/article.html

    Minamino, T., Gonzalez-Pedrajo, B., Kihara, M., Namba, K. and Macnab, R. M., 2003. The ATPase FliI can interact with the type III flagellar protein export apparatus in the absence of its regulator, FliH. J Bacteriol. 185 (13), 3983-3988.

    Minamino, T., Gonzalez-Pedrajo, B., Oosawa, K., Namba, K. and Macnab, R. M., 2002. Structural properties of FliH, an ATPase regulatory component of the Salmonella type III flagellar export apparatus. J Mol Biol. 322 (2), 281-290.

    Minamino, T. and Macnab, R. M., 1999. Components of the Salmonella flagellar export apparatus and classification of export substrates. J Bacteriol. 181 (5), 1388-1394.

    Minamino, T. and Macnab, R. M., 2000. FliH, a soluble component of the type III flagellar export apparatus of Salmonella, forms a complex with FliI and inhibits its ATPase activity. Mol Microbiol. 37 (6), 1494-1503.

    Minamino, T., Tame, J. R., Namba, K. and Macnab, R. M., 2001. Proteolytic analysis of the FliH/FliI complex, the ATPase component of the type III flagellar export apparatus of Salmonella. J Mol Biol. 312 (5), 1027-1036.

    Mitchell, J. G., 2002. The energetics and scaling of search strategies in bacteria. The American Naturalist. 160 (6), 727-740.

    Mitchell, P., 1985. Molecular mechanics of protonmotive F0F1 ATPases. Rolling well and turnstile hypothesis. FEBS Lett. 182 (1), 1-7.

    Mitchison, T. J., 1995. Evolution of a dynamic cytoskeleton. Philos Trans R Soc Lond B Biol Sci. 349 (1329), 299-304.

    Mivart, S. G., 1871. Genesis of Species. Macmillan, London.

    Mocz, G. and Gibbons, I. R., 2001. Model for the motor component of dynein heavy chain based on homology to the AAA family of oligomeric ATPases. Structure (Camb). 9 (2), 93-103.

    Moens, S. and Vanderleyden, J., 1996. Functions of bacterial flagella. Crit Rev Microbiol. 22 (2), 67-100.

    Mortlock, R. P. (Ed.), 1992. The Evolution of Metabolic Function. CRC Press, Boca Raton Fla.

    Muller, W. E., Blumbach, B. and Muller, I. M., 1999. Evolution of the innate and adaptive immune systems: relationships between potential immune molecules in the lowest metazoan phylum (Porifera) and those in vertebrates. Transplantation. 68 (9), 1215-1227.

    Musgrave, I., 2004. Evolution of the Bacterial Flagellum, in: Young, M. and Edis, T. (Eds.), Why Intelligent Design Fails: A Scientific Critique of the Neocreationism, forthcoming from Rutgers University Press, Piscataway, N. J.

    Nguyen, L., Paulsen, I. T., Tchieu, J., Hueck, C. J. and Saier, M. H., Jr., 2000. Phylogenetic analyses of the constituents of Type III protein secretion systems. J Mol Microbiol Biotechnol. 2 (2), 125-144.

    Nilsson, D.-E. and Pelger, S., 1994. A pessimistic estimate of the time required for an eye to evolve. Proceedings of the Royal Society of London Series B: Biological Sciences. 256, 53-58.

    Noji, H., Yasuda, R., Yoshida, M. and Kinosita, K., Jr., 1997. Direct observation of the rotation of F1-ATPase. Nature. 386 (6622), 299-302.

    Nougayrede, J. P., Fernandes, P. J. and Donnenberg, M. S., 2003. Adhesion of enteropathogenic Escherichia coli to host cells. Cell Microbiology. 5 (6), 359-372.

    Novikova, N. A., Levitsky, D. I., Metlina, A. L. and Poglazov, B. F., 2000. Interaction of bacterial flagellum filaments with skeletal muscle myosin. IUBMB Life. 50 (6), 385-390.

    Ohnishi, K., Fan, F., Schoenhals, G. J., Kihara, M. and Macnab, R. M., 1997. The FliO, FliP, FliQ, and FliR proteins of Salmonella typhimurium: putative components for flagellar assembly. J Bacteriol. 179 (19), 6092-6099.

    Oplatka, A., 1998a. Are rotors at the heart of all biological motors? Biochem Biophys Res Commun. 246 (2), 301-306.

    Oplatka, A., 1998b. Do the bacterial flagellar motor and ATP synthase operate as water turbines? Biochem Biophys Res Commun. 249 (3), 573-578.

    Oster, G. and Wang, H., 2003. Rotary protein motors. Trends Cell Biol. 13 (3), 114-121.

    Pasquier, L. D. and Litman, G. W. (Eds.), 2000. Origin and Evolution of the Vertebrate Immune System (Series: Current Topics in Microbiology and Immunology). Springer, Berlin.

    Peabody, C. R., Chung, Y. J., Yen, M. R., Vidal-Ingigliardi, D., Pugsley, A. P. and Saier, M. H., Jr., 2003. Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Microbiology. 149 (Pt 11), 3051-3072.

    Pei, Z., Burucoa, C., Grignon, B., Baqar, S., Huang, X. Z., Kopecko, D. J., Bourgeois, A. L., Fauchere, J. L. and Blaser, M. J., 1998. Mutation in the peb1A locus of Campylobacter jejuni reduces interactions with epithelial cells and intestinal colonization of mice. Infect Immun. 66 (3), 938-943.

    Pellmyr, O. and Krenn, H. W., 2002. Origin of a complex key innovation in an obligate insect-plant mutualism. Proc Natl Acad Sci U S A. 99 (8), 5498-5502.

    Plano, G. V., Day, J. B. and Ferracci, F., 2001. Type III export: new uses for an old pathway. Mol Microbiol. 40 (2), 284-293.

    Poethke, H. J. and Hovestadt, T., 2002. Evolution of density- and patch-size-dependent dispersal rates. Proc R Soc Lond B Biol Sci. 269 (1491), 637-645.

    Prum, R. O. and Brush, A. H., 2002. The evolutionary origin and diversification of feathers. Q Rev Biol. 77 (3), 261-295.

    Pugsley, A. P., 1993. The complete general secretory pathway in gram-negative bacteria. Microbiol Rev. 57 (1), 50-108.

    Purcell, E. M., 1977. Life at low Reynolds number. American Journal of Physics. 45, 3-11.

    Purcell, E. M., 1997. The efficiency of propulsion by a rotating flagellum. Proc Natl Acad Sci U S A. 94, 11307-11311.

    Rizzotti, M., 2000. Early Evolution: From the appearance of the first cell to the first modern organisms. Birkhäuser Verlag, Boston.

    Rosenhouse, J., 2002. Probability, optimization theory, and evolution. Evolution. 56 (8), 1721-1722.

    Sabbert, D. and Junge, W., 1997. Stepped versus continuous rotatory motors at the molecular scale. Proc Natl Acad Sci U S A. 94 (6), 2312-2317.

    Sadowsky, M. J., Tong, Z., de Souza, M. and Wackett, L. P., 1998. AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes. J Bacteriol. 180 (1), 152-158.

    Saier, M. H., Jr., 2003. Tracing pathways of transport protein evolution. Mol Microbiol. 48 (5), 1145-1156.

    Salvini-Plawen, S. V. and Mayr, E., 1977. On the evolution of photoreceptors and eyes. Evolutionary Biology. 10, 207-263.

    Sandkvist, M., 2001. Biology of type II secretion. Mol Microbiol. 40 (2), 271-283.

    Sauer, F. G., Barnhart, M., Choudhury, D., Knight, S. D., Waksman, G. and Hultgren, S. J., 2000. Chaperone-assisted pilus assembly and bacterial attachment. Curr Opin Struct Biol. 10, 548-556.

    Scharfman, A., Arora, S. K., Delmotte, P., Van Brussel, E., Mazurier, J., Ramphal, R. and Roussel, P., 2001. Recognition of Lewis x derivatives present on mucins by flagellar components of Pseudomonas aeruginosa. Infect Immun. 69 (9), 5243-5248.

    Schmitt, R., 2003. Helix rotation model of the flagellar rotary motor. Biophys J. 85 (2), 843-852.

    Seffernick, J. L. and Wackett, L. P., 2001. Rapid evolution of bacterial catabolic enzymes: a case study with atrazine chlorohydrolase. Biochemistry. 40 (43), 12747-12753.

    Shah, D. S., Perehinec, T., Stevens, S. M., Aizawa, S. I. and Sockett, R. E., 2000. The flagellar filament of Rhodobacter sphaeroides: pH-induced polymorphic transitions and analysis of the fliC gene. J Bacteriol. 182 (18), 5218-5224.

    Shah, D. S. and Sockett, R. E., 1995. Analysis of the motA flagellar motor gene from Rhodobacter sphaeroides, a bacterium with a unidirectional, stop-start flagellum. Mol Microbiol. 17 (5), 961-969.

    Silverman, M. and Simon, M., 1974. Flagellar rotation and the mechanism of bacterial motility. Nature. 249 (452), 73-74.

    Smyth, C. J., Marron, M. B., Twohig, J. M. and Smith, S. G., 1996. Fimbrial adhesins: similarities and variations in structure and biogenesis. FEMS Immunol Med Microbiol. 16 (2), 127-139.

    Spormann, A. M., 1999. Gliding motility in bacteria: insights from studies of Myxococcus xanthus. Microbiol Mol Biol Rev. 63 (3), 621-641.

    Stoodley, P., Sauer, K., Davies, D. G. and Costerton, J. W., 2002. Biofilms as complex differentiated communities. Annu Rev Microbiol. 56, 187-209.

    Suerbaum, S., 1995. The complex flagella of gastric Helicobacter species. Trends Microbiol. 3 (5), 168-171.

    Sukhan, A., Kubori, T. and Galán, J. E., 2003. Synthesis and localization of the Salmonella SPI-1 type III secretion needle complex proteins PrgI and PrgJ. J Bacteriol. 185 (11), 3480-3483.

    Szurmant, H., Bunn, M. W., Cannistraro, V. J. and Ordal, G. W., 2003. Bacillus subtilis hydrolyzes CheY-P at the location of its action: the flagellar switch. J Biol Chem. 14, 14.

    Thanassi, D. G., 2002. Ushers and secretins: channels for the secretion of folded proteins across the bacterial outer membrane. J Mol Microbiol Biotechnol. 4 (1), 11-20.

    Thanassi, D. G. and Hultgren, S. J., 2000a. Multiple pathways allow protein secretion across the bacterial outer membrane. Curr Opin Cell Biol. 12 (4), 420-430.

    Thanassi, D. G. and Hultgren, S. J., 2000b. Assembly of complex organelles: pilus biogenesis in gram-negative bacteria as a model system. Methods. 20 (1), 111-126.

    Thanassi, D. G., Saulino, E. T. and Hultgren, S. J., 1998. The chaperone/usher pathway: a major terminal branch of the general secretory pathway. Curr Opin Microbiol. 1 (2), 223-231.

    Thar, R. and Kuhl, M., 2002. Conspicuous veils formed by vibrioid bacteria on sulfidic marine sediment. Appl Environ Microbiol. 68 (12), 6310-6320.

    Thomas, N. A., Bardy, S. L. and Jarrell, K. F., 2001. The archaeal flagellum: a different kind of prokaryotic motility structure. FEMS Microbiol Rev. 25 (2), 147-174.

    Thomas, N. A., Mueller, S., Klein, A. and Jarrell, K. F., 2002. Mutants in flaI and flaJ of the archaeon Methanococcus voltae are deficient in flagellum assembly. Mol Microbiol. 46 (3), 879-887.

    Thornhill, R. H. and Ussery, D. W., 2000. A classification of possible routes of Darwinian evolution. J Theor Biol. 203 (2), 111-116.

    Trachtenberg, S., Gilad, R. and Geffen, N., 2003. The bacterial linear motor of Spiroplasma melliferum BC3: from single molecules to swimming cells. Mol Microbiol. 47 (3), 671-697.

    True, J. R. and Carroll, S. B., 2002. Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol. 18, 53-80.

    van Wely, K. H., Swaving, J., Freudl, R. and Driessen, A. J., 2001. Translocation of proteins across the cell envelope of Gram-positive bacteria. FEMS Microbiol Rev. 25 (4), 437-454.

    Velicer, G. J., Lenski, R. E. and Kroos, L., 2002. Rescue of social motility lost during evolution of Myxococcus xanthus in an asocial environment. J Bacteriol. 184 (10), 2719-2727.

    Vogel, S., 1988. Life's devices: the physical world of animals and plants. Princeton University Press, Princeton, NJ.

    Vogel, S., 1994. Life in Moving Fluids. Princeton University Press, Princeton, NJ.

    Vogler, A. P., Homma, M., Irikura, V. M. and Macnab, R. M., 1991. Salmonella typhimurium mutants defective in flagellar filament regrowth and sequence similarity of FliI to F0F1, vacuolar, and archaebacterial ATPase subunits. J Bacteriol. 173 (11), 3564-3572.

    Walz, D. and Caplan, S. R., 2002. Bacterial flagellar motor and H(+)/ATP synthase: two proton-driven rotary molecular devices with different functions. Bioelectrochemistry. 55 (1-2), 89-92.

    Weber, J., Muharemagic, A., Wilke-Mounts, S. and Senior, A. E., 2003a. F1F0-ATP synthase. Binding of delta subunit to a 22-residue peptide mimicking the N-terminal region of alpha subunit. J Biol Chem. 278 (16), 13623-13626.

    Weber, J. and Senior, A. E., 2003. ATP synthesis driven by proton transport in F1F0-ATP synthase. FEBS Lett. 545 (1), 61-70.

    Weber, J., Wilke-Mounts, S. and Senior, A. E., 2003b. Identification of the F1-binding surface on the delta-subunit of ATP synthase. J Biol Chem. 278 (15), 13409-13416.

    Whitesides, G. M., 2001. The once and future nanomachine. Scientific American. 285 (3), 78-83.

    Whitman, W. B., Coleman, D. C. and Wiebe, W. J., 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci U S A. 95, 6578-6583.

    Wilkens, S. and Capaldi, R. A., 1998. Solution structure of the epsilon subunit of the F1-ATPase from Escherichia coli and interactions of this subunit with beta subunits in the complex. J Biol Chem. 273 (41), 26645-26651.

    Wu, H. and Fives-Taylor, P. M., 2001. Molecular strategies for fimbrial expression and assembly. Crit Rev Oral Biol Med. 12 (2), 101-115.

    Yamashiro, T., Nakasone, N., Honma, Y., Albert, M. J. and Iwanaga, M., 1994. Purification and characterization of Vibrio cholerae O139 fimbriae. FEMS Microbiol Lett. 115 (2-3), 247-252.

    Youderian, P., Burke, N., White, D. J. and Hartzell, P. L., 2003. Identification of genes required for adventurous gliding motility in Myxococcus xanthus with the transposable element mariner. Mol Microbiol. 49 (2), 555-570.

    Young, G. M., Schmiel, D. H. and Miller, V. L., 1999. A new pathway for the secretion of virulence factors by bacteria: the flagellar export apparatus functions as a protein-secretion system. Proc Natl Acad Sci U S A. 96 (11), 6456-6461.

    Young, K. D., 2001. Peptidoglycan, Nature Encyclopedia of Life Sciences, Nature Publishing Group, London.

    Zaar, A., Fuchs, G., Golecki, J. R. and Overmann, J., 2003. A new purple sulfur bacterium isolated from a littoral microbial mat, Thiorhodococcus drewsii sp. nov. Arch Microbiology. 179 (3), 174-183.

    Zhai, Y. F., Heijne, W. and Saier, M. H., 2003. Molecular modeling of the bacterial outer membrane receptor energizer, ExbBD/TonB, based on homology with the flagellar motor, MotAB. Biochim Biophys Acta. 1614 (2), 201-210.

    Zhulin, I. B., Nikolskaya, A. N. and Galperin, M. Y., 2003. Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. J Bacteriol. 185 (1), 285-294.

     
  • At 8:08 AM, Blogger Joe G said…

    JT,

    Which artocledemonstrates that bacteria without a flagellum can evolve into bacteria with a flagellum via some blind watchmaker-type process?

    I noticed your list contains some Ken Miller papers. Miller has been refuted.

    However this is a prime example of the sort of bluffing evolutionists employ. They throw out many papers but upon close inspection not one substantiates their claims.

    Charles Darwin didn't even know what was inside of a cell. Putting his work in the list just screams of desperation.

     
  • At 9:42 AM, Blogger James Wynne said…

    Joe G. said,
    ...this is a prime example of the sort of bluffing evolutionists employ. They throw out many papers but upon close inspection not one substantiates their claims.

    You haven't closely inspected anything on the list, Joe. If you had, you would have accepted my earlier challenge to choose one of them, read it, and offer specific objections, and tell how ID non-theory would approach the problem differently and still augment the body of knowledge.

    A great deal of intelligence may be invested in ignorance when the need for illusion is deep.--Saul Bellow

     
  • At 11:00 AM, Blogger Joe G said…

    Joe G. said,
    ...this is a prime example of the sort of bluffing evolutionists employ. They throw out many papers but upon close inspection not one substantiates their claims.


    James Wynne baldly asserts:
    You haven't closely inspected anything on the list, Joe.

    Yes I have James. That is why I am asking anyone to present ONE that meets my requirements.

    Why is it that neither you nor JT can do that?

    We know Darwin didn't deal with the evolution of the bac flag. Why is he on the list?

    Did JT read what he listed? Check this out-

    Darwin, C., 1872. The origin of species by means of natural selection. 6th edition. John Murray, London. Online text.

    "There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved."


    I am still aware there isn't any data that demontrates bacteria can "evolve" into anything but bacteria. I am also still aware there isn't any data that demonstrates bacteria with a flagellum can evolve into bacteria with via some blind watchmaker-type process.

    James, you have yet to demonstrate that that evo #6 has augmented anything. That is what you should concentrate on- substantiating YOUR claims.

     
  • At 11:06 AM, Blogger Joe G said…

    A great deal of intelligence may be invested in ignorance when the need for illusion is deep.--Saul Bellow

    Again James portrays the evolutionitwits perfectly. THEY need the obvious design to be an illusion. That is their deep conviction. And it is a conviction borne of ignorance...

     
  • At 7:25 PM, Blogger jt said…

    joe g:
    Which artocledemonstrates that bacteria without a flagellum can evolve into bacteria with a flagellum via some blind watchmaker-type process?


    They all, taken together, provide incremental evidence that supports the concept of evolution of the flagellum. With a rudimentary understanding of how natural science research works, you would know that.

    Present me a similar list of articles in peer reviewed, scientific journals supporting the notion that flagellum were designed by any intelligence (aliens, God, Mbombo, Inyan, black helicopters, Zeus, Mangala, the matrix, Coatlique, Enki, etc.). Then we can begin a discussion.

    joe g:
    I noticed your list contains some Ken Miller papers. Miller has been refuted.


    I am sorry but Ken Miller has not been "refuted". If some creationist, feeling their religion threatened, criticizes him, it does not mean he is "refuted".

    joe g:
    However this is a prime example of the sort of bluffing evolutionists employ. They throw out many papers but upon close inspection not one substantiates their claims.


    You may not like it but that is the way it works, by incremental, cumulative knowledge. Go ahead, throw out a similar list of papers with evidence supporting ID.

    joe g:
    Charles Darwin didn't even know what was inside of a cell. Putting his work in the list just screams of desperation.


    Excuse me but this is a reference list. Since the topic is evolution, I think Darwin is appropriate. Sorry, I did not realize your limitations to understand that.

     
  • At 10:50 PM, Blogger FishyFred said…

    Yes I have James. That is why I am asking anyone to present ONE that meets my requirements.

    For crying out loud man, there must be at least 300 articles on that list (I stopped counting at 50 and I wasn't even out of the letter C). If you want to know how an "irreducibly complex" system can evolve without hyperextending your brain, I'd suggest you go read this old post at the old Pharyngula and just look at the pretty pictures.

     
  • At 7:48 AM, Blogger Joe G said…

    JT:
    They all, taken together, provide incremental evidence that supports the concept of evolution of the flagellum.

    Perhaps to you they do. However I noticed a mechanism is missing. This debate is all about the mechanism. So which papers on your list demonstrate, incrementally, that a bac flag can "evolve" via some blind watchmaker-type processes?
    With a rudimentary understanding of how natural science research works, you would know that.

    joe g:
    I noticed your list contains some Ken Miller papers. Miller has been refuted.


    JT:
    I am sorry but Ken Miller has not been "refuted".

    Actually he has:

    Still spinning just fine- Miller refuted

    Anyone with a basic understanding of biology can see Miller is just full of it.

    Add to that fact his "papers" (on your list) never went through peer-review and you get non-scientific diatribe.

    joe g:
    Charles Darwin didn't even know what was inside of a cell. Putting his work in the list just screams of desperation.


    JT:
    Excuse me but this is a reference list. Since the topic is evolution, I think Darwin is appropriate.

    The topic isn't evolution. The following is the topic of this thread:

    Perhaps James Wynne can provide ONE scientific research paper that demonstrates the bac flag "evolved" via some blind watchmaker-type process.

    Then perhaps James will tell us why not one evolutionary biologist has conducted the experiment that would demonstrate that such a transformation is even possible (ie from flagella-less bacteria to bacteria with at least one flagellum).

    You know James I have asked you several times what would falsify the premise that the bac flag evolved via some blind watchmaker-type process, yet you NEVER answered the question.


    Try to follow along. That way you don't appear so dishonest when you are exposed.

    Also I take it you missed the fact that Darwin admitted he is a Creationist. If life didn't arise from non-living matter via some blind watchmaker-type process there would be no reason to infer its subsequent diversity arose solely due to those type of processes.

     
  • At 8:02 AM, Blogger Joe G said…

    To FishyFred,

    The link you provided does NOT discuss a mechanism. Also just about anything can work on paper. Reality is another story.

    One more time for the learning impaired- IC does not mean the structure could not have evolved. The debate is about the mechanism of evolution- design vs. willy-nilly (culled by NS).

    An experiment has been proposed. Why are evolutionitwits so afraid of that experiment?

     
  • At 3:32 PM, Blogger FishyFred said…

    Anyone with a basic understanding of biology can see Miller is just full of it.

    Add to that fact his "papers" (on your list) never went through peer-review and you get non-scientific diatribe.


    Wow, your ad hominem is showing. Miller only co-wrote one of the leading textbooks on the subject. He sounds really "full of it" to me.

    Of course his papers went through peer review, and I'd think twice about accusing someone of bypassing the peer review process while ID proponents did it with Meyers' paper. Why do you think Sternberg was "Sternberged?"

    Regarding the Pharyngula post: The mechanism to get to an IC system in that post is random mutation in a member of the population that reproduced. Nothing more, nothing less. And it does happen in reality, as PZ pointed out. It happens ALL THE TIME.

    You have absolutely no understanding of evolution if you think of it as "willy-nilly."

    An experiment has been proposed. Why are evolutionitwits so afraid of that experiment?

    Before scientists do your dirty work for you, please explain why those at the Discovery Institute, with their insane amount of funding, can't be bothered to do it. They had enough money to hire that huge PR firm. I apologize for not grabbing the name off the NCSE website, but I'm late for class.

     
  • At 5:25 PM, Blogger jt said…

    joe g:
    Perhaps to you they do. However I noticed a mechanism is missing. This debate is all about the mechanism. So which papers on your list demonstrate, incrementally, that a bac flag can "evolve" via some blind watchmaker-type processes?


    They all do - together! Did you read them? Did you, unlike Behe, read any of them?


    joe g:
    Still spinning just fine- Miller refuted


    The actual title is:
    "Still Spinning Just Fine:
    A Response to Ken Miller"

    I feel embarrassed to point this out to you but a "response" is not the same as "refuted".

    Still having trouble with the honesty thing eh? Fact checking you is a full time job.


    joe g:
    The topic isn't evolution.


    OK the topic is "...provide ONE scientific research paper that demonstrates the bac flag "evolved"..." But papers about evolution are off topic? Hard to argue with that logic - or understand it. Is the problem that you just want one and only one? Is the problem that you cannot assimilate more than one?

    Have you been able to scrape together that ONE paper that demonstrates that any biological structure or process was intelligently designed? How about many that show it incrementally?


    joe g:
    Also I take it you missed the fact that Darwin admitted he is a Creationist.


    Now you are resorting to urban myths as arguments. Look it up.

     
  • At 8:06 AM, Blogger Joe G said…

    An experiment has been proposed. Why are evolutionitwits so afraid of that experiment?

    FishyFred:
    Before scientists do your dirty work for you, please explain why those at the Discovery Institute, with their insane amount of funding, can't be bothered to do it.

    I have already explained it, as has Dr. Behe. Simple common sense really. The experiment would validate the claims of evolutionitwits and refute an ID icon. If IDists did the experiment and it failed to produce a flagellum who would believe it?

    Anyone with a basic understanding of biology can see Miller is just full of it.

    Add to that fact his "papers" (on your list) never went through peer-review and you get non-scientific diatribe.


    FF:
    Wow, your ad hominem is showing.

    As is your dishonesty.

    FF:
    Miller only co-wrote one of the leading textbooks on the subject. He sounds really "full of it" to me.

    Miller co-wrote a book on the evolution of the bac flag via some blind watchmaker type process?

    FF:
    Of course his papers went through peer review,

    Not the two listed in this thread. Can you follow the discussion?

    FF:
    and I'd think twice about accusing someone of bypassing the peer review process while ID proponents did it with Meyers' paper. Why do you think Sternberg was "Sternberged?"

    Reality demonstrates Meyer's paper went through peer-review.

    FF:
    Regarding the Pharyngula post: The mechanism to get to an IC system in that post is random mutation in a member of the population that reproduced. Nothing more, nothing less. And it does happen in reality, as PZ pointed out. It happens ALL THE TIME.

    Again perhaps PZ will take his work to the lab and demonstrate his premise works. Until then it is nothing more than a very un-scientific just-so story.

    FF:
    You have absolutely no understanding of evolution if you think of it as "willy-nilly."

    Let's see- the mutations are allegedly random- that fits "willy-nilly". Natural selection is allegedly blind and without purpose. Yup, willy-nilly is correct- that is in your accepted scenario.

     
  • At 8:22 AM, Blogger Joe G said…

    joe g:
    Also I take it you missed the fact that Darwin admitted he is a Creationist.


    JT:
    Now you are resorting to urban myths as arguments. Look it up.

    What's a matter? Can't you read? I provided the quote from YOUR refernce. Here it is again:

    "There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved."

    By the logic of anti-IDists that makes Darwin a Creationist (for the same reason Dr. Behe is labeled a Creationist).

    The response to Miller refutes his claims. That makes it a refutation.

    joe g:
    The topic isn't evolution.


    JT:
    OK the topic is "...provide ONE scientific research paper that demonstrates the bac flag "evolved"..."

    Your dishonesty cut off my sentence before the relevant part. Go figure.

    JT:
    But papers about evolution are off topic?

    As I have stated several times "evolution" isn't being debated. The mechanism is.

    JT:
    Hard to argue with that logic - or understand it.

    I doubt you can understand anything.

    JT:
    Is the problem that you just want one and only one?

    I want one that fits my criteria. And I am still waiting.

    JT:
    Is the problem that you cannot assimilate more than one?

    No. The problem is you can't present one (that fits the criteria)

     
  • At 9:48 AM, Blogger Joe G said…

    JT's list of references comes from the Matzke diatribe:

    Evolution in (Brownian) space:
    a model for the origin of the bacterial flagellum


    Notice that this paper has not been submitted for peer-review. Also it has been responded to and shown to be lame:

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

    "Matzke, throughout his article, invokes gene duplications and mutations at key points where the Darwinian mechanism is supposed to effect transitions that are reasonably probable. But what gene exactly is being duplicated? And what locus on a gene is being mutated? Matzke never says. Indeed, his model is so unspecific that he cannot answer these questions. But unless we know the answer to such questions, there's no way to know whether the transitions Matzke describes are reasonably probable and therefore of the type required by Darwin's theory."

    Gene dupications? How were gene dupications determined to be "random"?:

    Dr. Spetner discussing mutations:
    "The motion of these genetic elements to produce the above mutations has been found to a complex process and we probably haven’t yet discovered all the complexity. But because no one knows why they occur, many geneticists have assumed they occur only by chance. I find it hard to believe that a process as precise and well controlled as the transposition of genetic elements happens only by chance. Some scientists tend to call a mechanism random before we learn what it really does. If the source of the variation for evolution were point mutations, we could say the variation is random. But if the source of the variation is the complex process of transposition, then there is no justification for saying that evolution is based on random events."

     
  • At 11:35 AM, Anonymous Anonymous said…

    Great blog! I live in a community filled with "evolutionitwits" My only refuge is my art.

     

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