References for Evolution of flagella
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: CS1 maint: multiple names: authors list (link)Some references to the work of Cavalier-Smith and others on the origin of the cilium, cytoskeleton, and components thereof (and a few on related aspects of Cavalier-Smith's work on the origin of the cell)
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ignored (help)CS1 maint: multiple names: authors list (link)[W]hen criticizing existing evolutionary explanations, Behe uses intellectually dishonest double standards. He dismisses my first treatment of the origin of cilia2 [footnote 2: the 1978 paper] as non-quantitative and therefore 'utterly useless', and ignores my later work on the topic3,4 [these are the 1982 and 1987b papers, respectively]. But it does not worry him that his empty, religious notion of 'intelligent design' is equally non-quantitative; worse still, lacking in even qualitative detail of what did the designing, and how the hypothetical design was executed, it explains nothing. He states that 'if a theory claims to be able to explain some phenomenon but does not even generate an attempt at an explanation is should be banished' and 'without details, discussion is doomed to be unscientific and fruitless'. If he had applied these strictures to his panacea of 'intelligent design' we would have been spared this worthless book.
Behe, ignorant of much of the literature, claims that no scientist has ever discussed the origin of vesicle targeting (actually discussed in Ref. 3 [Cavalier-Smith, 1987b], not cited by Behe, though the most detailed one on the origin of eukaryotic biochemical properties) or protein translocation (see Refs 6 [Blobel, 1980, PNAS, v.77, 1496-1500] and 7 [Cavalier-Smith, 1987a]), the most detailed discussion of the origin of the most basic complex cellular biochemical properties, which he deceitfully ignored despite citing the volume containing it as 'evidence' that no paper has ever been published on the subject!). Maybe he did not want his readers to find the papers (Refs 3 and 7) that most clearly show how one can explain (in outline at least -- obviously they are not the final answer) the origins of complex biochemical and cellular structures in logical steps using mutation, selection and detailed phylogenetic arguments. His ignorant assumption that the origin of a protoSRP would have killed the cell is refuted by the absence of the translation arrest domain in the eubacterial signal recognition partical (SRP) RNA8 [Poritz, 1989, Cell, 4-6], which provides a simpler ancestor to the more complex archaebacterial/eukaryotic particle. The problem he raises [p. 112] for the origin of secreted eukaryotic glycoproteins is spurious, because the sugar must have been added to the protein on the non-cytosolic side of the membrane in the common ancestor of eukaryotes and archaebacteria, even before the ER (endoplasmic reticulum) evolved, since it is added thus at the archaebacterial cell surface, as any good biochemist should have known, even without reading my discussion of the origin of the ER (Ref. 3).
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: CS1 maint: multiple names: authors list (link)Not to pile things on, but upon discovering the foregoing I was inspired to double-check Behe's claims about how often the cilium papers Cavalier-Smith (1978) and Szathmary (1987) were cited in other papers. On page 69, Behe says "The scientific community at large has ignored both contributions; neither paper has been cited by other scientists more than a handful of times in the years since publication.7" Note 7 on page 280 reads, "A search of Science Citation Index shows that each paper receives an average of less than one citation per year."
Well, I don't know if Behe made a mistake or if the Science Citation Index was in 1995 just not adequate on these papers for some reason, but my search of the Science Citation Index Expanded (SCI-EXPANDED)--1945-present on the Web of Science, while it lists only six citations of Szathmary (1987), lists 53 citations of Cavalier-Smith (1978). Seven citations are from 1996-present (four of those being in other papers by Cavalier-Smith). For 1995 and before, this leaves 47 citations. Ten of these are in other papers Cavalier-Smith authored or co-authored, leaving 37 citations of Cavalier-Smith (1978) by papers not written by Cavalier-Smith. For those who are counting, that is 2.056 citations per year for the years 1978-1995 inclusive (and including 1978 is being generous to Behe), and while not an overwhelming number, (a) it is higher than "less than one citation per year" and (b) 37 citations (40 to present, and not counting several references in books that I know of) is frankly significantly more attention than the average scientific paper receives.
Out of curiosity, I performed the same search on Cavalier-Smith (1982) and got a result of zero citations. This is clearly a mistake, as not only does Cavalier-Smith reference his 1982 paper in several other papers, but a cursory manual search on Web of Science of the reference lists of other papers reveals that it is cited in (at least) Bermudes et al. (1994), Rizzotti (1995), and Thornhill and Ussery (2000). Obviously there is an error in the Science Citation Index record for the 1982 paper, a good demonstration of the potential risks of relying completely on computer searches.
Cavalier-Smith's 1975, 1987(a), 1987(b), and 1987(c) papers are listed as having 98, 41, 94, and 133 citations respectively, although it appears that self-citation occurs in proportions similar to the 1978 case (self-citation is common in scientific papers).
Finally, Cavalier-Smith recently (November 2001) published in the Journal of Molecular Evolution a long (40 pages, huge for a journal) comprehensive article on the origin of the first cells, a major update of his 1987(a) paper:
I attempt to sketch a unified picture of the origin of living organisms in their genetic, bioenergetic, and structural aspects. Only selection at a higher level than for individual selfish genes could power the cooperative macromolecular coevolution required for evolving the genetic code. The protein synthesis machinery is too complex to have evolved before membranes. Therefore a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level reproductive unit: the proto-organism. I discuss the roles of stereochemistry, gene divergence, codon capture, and selection in the code's origin. I argue that proteins were primarily structural not enzymatic and that the first biological membranes consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids. The peptidyl-tRNAs functioned as genetically-specified lipid analogues with hydrophobic tails (ancestral signal peptides) and hydrophilic polynucleotide heads. Protoribosomes arose from two cooperating RNAs: peptidyl transferase (large subunit) and mRNA-binder (small subunit). Early proteins had a second key role: coupling energy flow to the phosphorylation of gene and peptide precursors, probably by lithophosphorylation by membrane-anchored kinases scavenging geothermal polyphosphate stocks. These key evolutionary steps probably occurred on the outer surface of an 'inside out-cell' or obcell, which evolved an unambiguous hydrophobic code with four prebiotic amino acids and proline, and initiation by isoleucine anticodon CAU; early proteins and nucleozymes were all membrane-attached. To improve replication, translation, and lithophosphorylation, hydrophilic substrate-binding and catalytic domains were later added to signal peptides, yielding a ten-acid doublet code. A primitive proto-ecology of molecular scavenging, parasitism, and predation evolved among obcells. I propose a new theory for the origin of the first cell: fusion of two cup-shaped obcells, or hemicells, to make a protocell with double envelope, internal genome and ribosomes, protocytosol, and periplasm. Only then did water-soluble enzymes, amino acid biosynthesis, and intermediary metabolism evolve in a concentrated autocatalytic internal cytosolic soup, causing 12 new amino acid assignments, termination, and rapid freezing of the 22-acid code. Anticodons were recruited sequentially: GNN, CNN, INN, and *UNN. CO2 fixation, photoreduction, and lipid synthesis probably evolved in the protocell before photophosphorylation. Signal recognition particles, chaperones, compartmented proteases, and peptidoglycan arose prior to the last common ancestor of life, a complex autotrophic, anaerobic green bacterium.
In this paper he repeatedly cites two additional recent papers:
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ignored (help)...both of which came out in the International Journal of Systematic and Evolutionary Microbiology. Together these three papers constitute some 150 pages, and they serve as only the barest introduction to the topic of the origin of the three domains and their various biochemical systems. For more articles by Cavalier-Smith, click over to PubMed and search on "Cavalier-Smith". Be sure to click on "related articles" for topics you are interested in.
If you are looking for a single scientist to serve as the "Darwin of microbiology" as a counter to Mike "the Paley of microbiology" Behe, it would be Thomas Cavalier-Smith.
Some references on the high variability in the construction of the cilium ("the cilium" isn't IC, just a subset of its components), and on the evolution of the cilium in reference to Behe's arguments
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value (help)Some web references on FtsZ-tubulin homology
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Tubulin-like protofilaments in Ca-induced FtsZ sheets by Lowe and Amos
Structure & function of homologous proteins tubulin and FtsZ -- some strong medical applications of this evolutionary deduction
Egelman EH (1998). "Tubulin family: kinship of key proteins across phylogenetic domains". Current Biology. 8 (8): R288–90. doi:10.1016/S0960-9822(98)70175-7. PMID 9550697. ((cite journal))
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Faguy DM, Doolittle WF (1998). "Cytoskeletal proteins: the evolution of cell division". Current Biology. 8 (10): R338–41. doi:10.1016/S0960-9822(98)70216-7. PMID 9601632. ((cite journal))
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Check out this phylogenetic tree of FtsZs.
(Cornelis and Gijsegem, 2000). So if the IDer did after all design the (eu)bacterial flagellum, we also have the IDer to thank for "front-loading" in the potential for some of the nastiest bacterial virulence systems, including those of Salmonella and Yersinia, the latter being better known as the Bubonic Plague or Black Death. Comparing the explanations given for the virulence of Yersinia between the medievals of the 14th century and the ID theorists of the 21st may be a worthwhile research project.
Two pages in the UCSD transport system database note that the flagellar motor proteins (MotA and MotB) are distant homologs of other bacterial membrane proteins (ExbB-ExbD).
For a few months, the Mot-Exb connection was an isolated mention on a webpage. But in October 2001, an article by Kojima and Blair in Biochemistry made it official. The abstract is here. In their conclusion, the authors write (see the article for a comparative graphic),
The occurrence of significant conformational change in the stator has implications not only for the present-day mechanism but also for the evolution of the flagellar motor. A membrane complex that undergoes proton-driven conformational changes could perform useful work in contexts other than (and simpler than) the flagellar motor, and ancestral forms of the MotA/MotB complex might have arisen independently of any part of the rotor. We queried the sequence database using the sequence of the best-conserved part of MotA (the segment containing membrane segments 3 and 4) from Aquifex aeolicus, a species whose lineage is deeply branched from other bacteria. In addition to the expected MotA homologues, the search returned a protein sequence from the archaeal species Methanobacterium thermoautotrophicum (protein MTH1022) that shows significant sequence similarity not only to MotA but also to the protein ExbB (Figure 9). ExbB is a cytoplasmic-membrane protein that functions in conjunction with ExbD, TonB, and outer-membrane receptors to drive active transport of certain essential nutrients across the outer membrane of Gram-negative bacteria. The energy for this transport comes from the proton gradient across the inner membrane. Thus, MotA and ExbB are both components of systems that tap the proton gradient to do work some distance away (at either the rotor-stator interface or the outer membrane; Figure 9).
Other features also point to a connection between the Mot and Exb systems. MotA functions in a complex with MotB, which as noted contains the critical residue Asp32 near the cytoplasmic end of its single membrane segment. ExbB functions in a complex with ExbD, which likewise has a single membrane segment with a critical Asp residue near its cytoplasmic end (Asp25 in ExbD of E. coli; ref 59). Although ExbB has only three membrane segments in contrast to the four in MotA, the membrane segments that show sequence similarity have the same topology. The protein TonB is also present in the complex with ExbB and ExbD (59, 60) and would provide an additional membrane segment to round out the topological correspondence (Figure 9). ExbB contains a well-conserved Pro residue (Pro141 in E. coli ExbB) that is the counterpart of Pro173 of MotA. Although MotB and ExbD do not share close sequence similarity apart from the critical Asp residue, in certain positions in the membrane segment the residues most common in MotB proteins are also common in ExbD proteins. Finally, like the MotA/MotB complex the ExbB/ExbD complex contains multiple copies of each protein (61). Together, these facts make a reasonable case for an evolutionary connection between the Mot proteins of the flagellar motor and the Exb proteins of outer-membrane transport (and by extension the TolQ/TolR proteins, which are related to ExbB/ExbD but whose functions are less understood).
...which appears to improve significantly on the situation as stated in Ian Musgrave's draft flagellum FAQ, "There is no apparent homolog of the motor (MotAB) in type III secretory systems."
For additional information on homologies see:
The UCSD page on The Type III (Virulence-related) Secretory Pathway (IIISP) Family
In addition, the ATPase involved in flagellar construction is thought to be homologous to this family. Rizzotti, in his (2000) book Early Evolution has cited this in his scenario for the origin of the bacterial flagellum from an F1F0 ATPase. In light of the other homologies mentioned here, this is very unlikely, although there may be a connection between the F1F0 ATPase and transport systems at some very remote level.
Discovery Institute fellow Scott Minnich recently (November 2000) spoke at the DI's "Science and Evidence for Design in the Universe" conference. The talk, "Flagella: Tails of Molecular Cooption", is available in audio format online, and includes the muddled reaction from the audience. Minnich raised the issue of Type III virulence systems, speaking of "malevolent design", and suggested "If we're going to use this [flagellum] as a designed system, we're going to have to use this [Type III virulence system] as well", and "In the original design, they [virulence factors] weren't involved. You can almost look at this type III system as a perversion." Compare to Kathryn Brown's introduction to a Yersinia article in Science, "Why, the people wondered? Was the Plague the work of an angry God? A medieval curse? As it happens, the real culprit was a tiny bacterium: Yersinia pestis." And of course its syringe-like, IC, "designed-looking" virulence system. According to ID, apparently the "angry God" and "bacterium" theory for The Plague aren't as mutually exclusive as one might think.
Some online articles on Type III transport virulence systems and flagella
Type III Protein Secretion Systems in Bacterial Pathogens of Animals and Plants by Christoph J. Hueck
Interactions of Salmonella with host cells: Encounters of the closest kind by Jorge Galan
Assembly and Function of Type III Secretory Systems by Cornelis and Gijsegem
Molecular Mechanisms of Bacterial Virulence: Type III Secretion and Pathogenicity Islands by Mecsas and Strauss. On the Center for Disease Control webpage.
Unlocking the Secrets of the Grim Reaper, by Kathryn Brown, introducing an article on Yersinia in Science.
For references and more info on the archaeal flagellum, see almost anything that Ken Jarrell has written, e.g. the articles linked from The Jarrell Laboratory hompage.
Also see this online version of "A twisted tale: the origin and evolution of motility and chemotaxis in prokaryotes", by Faguy and Jarrell
"Recent excitement about the Archaea", by Jarrell, in Bioscience
Finally, in a 1998 article by Bayley and Jarrell, they write,
We feel that the discoveries of archaeal flagella-related putative gene products with similarity to type IV pilus accessory proteins indicate that the archaeal flagella also share this common origin and have evolved it to function as the primary motility apparatus. Although the function of the common origin can only be speculated, this system must predate the last common ancestor of extant life. ("Further Evidence to Suggest That Archaeal Flagella Are Related to Bacterial Type IV Pili", Journal of Molecular Evolution, 46: 370-373, 1998)