The Bacterial Flagellum

DeRosier, David J.  “The Turn of the Screw: The Bacterial Flagellar Motor.”  Cell 93(1):17–20.  Apr 3, 1998.  Read in the Wayback copy of the publisher's PDF.  DeRosier is a structural biologist at Brandeis University and not a design advocate.  Mirror:  Archive.org

1. 1a.

   Page 17, section Flagellar Architecture:  “More so than other motors, the flagellum resembles a machine designed by a human (Figure 1a).”  The sentence opens the section and introduces a diagram. ↩

2. 1b.

   Page 17:  “they also deliver constant torque of 4500 pN nm (Berry and Berg, 1997) at speeds over 6000 rpm”. ↩

3. 1c.

   Page 17:  “About 50 genes are particular to the flagellum and its chemosensory machinery.”  The passage continues with about 40 fla genes, two mot genes, six che genes and about as many receptor genes.  Mot mutants have a flagellum that is completed and does not rotate.  The PDF's text layer prints the "about" sign before 40 as the letter z. ↩ ↩

Pallen, Mark J., and Nicholas J. Matzke.  “From The Origin of Species to the origin of bacterial flagella.”  Nature Reviews Microbiology 4(10):784–790.  Oct 2006.  Read in the publisher's PDF as served by Gale Academic OneFile.  The first PDF page is page 784.  Mirror:  Link.gale.com

1. 2a.

   Page 784:  “there is no such thing as ‘the’ bacterial flagellum.”  “either there were thousands or even millions of individual creation events, which strains Occam’s razor to breaking point, or one has to accept that all the highly diverse contemporary flagellar systems have evolved from a common ancestor.” ↩

2. 2b.

   Page 785:  “only about half seem to be universally necessary”.  “This reduced flagellum is still a challenge to explain”. ↩

3. 2c.

   Page 786:  “However, the scientific community is divided on the nature of their common ancestor.”  “We, and others, have argued that the two systems are sister groups”. ↩

4. 2d.

   Page 787, table 1:  “Homologies of flagellar proteins”.  The column headed "Indispensable?" reads "Mutant retains full motility" for FlhE and FliL, "Mutant retains some motility" for FliH, and "Absent from Gram-positive bacteria" for FlgA, FlgH and FlgI. ↩ ↩ ↩ ↩

5. 2e.

   Page 788:  “one can envisage the ur-flagellum arising from mergers between several modular subsystems”.  Four are named:  a secretion system, a filament, a motor and a chemotaxis apparatus. ↩

6. 2f.

   Page 788:  “However, one could still question how, from such bricolage, natural selection could lock on to an evolutionary trajectory leading to an organelle of motility in the first place, when none of the components alone confer the organism with a selective advantage relevant to motility. The key missing concept here is that of exaptation”. ↩

7. 2g.

   Page 788:  “However, the flagellar research community has scarcely begun to consider how these systems have evolved.” ↩

Berg, Howard C.  “The Rotary Motor of Bacterial Flagella.”  Annual Review of Biochemistry 72:19–54.  2003.  Read in a Wayback copy of a Cambridge teaching copy.  The printed page is the PDF page plus 18, anchored on the running heads of pages 20 and 40.

1. 3a.

   Page 19, section abstract:  “A motor is about 45 nm in diameter and is assembled from about 20 different kinds of parts.” ↩ ↩

2. 3b.

   Page 20:  “the flagellar motor is the output organelle of a remarkable sensory system, the components of which have been honed to perfection by billions of years of evolution.” ↩ ↩

3. 3c.

   Page 24, table 1:  “Proteins of E. coli involved in flagellar motor assembly and function”.  Page 25:  “Including proteins involved in gene regulation but not in signal processing.”  The table runs over pages 24 and 25 and has 40 rows:  FlgA to FlgN, FlhA to FlhE, FliA, FliC to FliT, MotA and MotB. ↩

4. 3d.

   Page 25:  “Later it was found that both the M- and S-rings (now called the MS-ring) comprise different domains of the same protein, FliF (25, 26).” ↩

5. 3e.

   Page 25:  “Other mutations are nonmotile, and the null phenotypes are nonflagellate.”  Said of fliG, fliM and fliN. ↩

6. 3f.

   Page 33:  “This number is about 1200 (175).” ↩

7. 3g.

   Page 34:  “their rotation speeds can be remarkably high, up to 1700 Hz (180, 181).” ↩ ↩

8. 3h.

   Page 37:  “crossing the 0-torque line at about 300 Hz.” ↩

9. 3i.

   Page 39, foot of the page, running on to page 40:  “Therefore, by this crude estimate, the efficiency of the motor, power output divided by power input, is about 90%.”  Page 40:  “the efficiency could be 1, the value expected for a tightly coupled engine running slowly close to stall (175).”  The estimate uses a torque of 4600 pN nm at 10 Hz.  Page 40 also gives the proton motive force as about −170 mV. ↩ ↩ ↩

Chevance, Fabienne F. V., and Kelly T. Hughes.  “Coordinating assembly of a bacterial macromolecular machine.”  Nature Reviews Microbiology 6:455–465.  2008.  Read in the PMC author manuscript, whose pages are not the journal's.  Mirror:  PMC

1. 4a.

   Section introduction:  “a long, helical filament that is composed of up to 20,000 subunits of a single protein”. ↩

2. 4b.

   Section introduction:  “After the export of FlgM, the production of filament substrates can begin.” ↩

3. 4c.

   Section Flagellar gene hierarchy:  “The flagellar regulon of S. typhimurium includes more than 60 genes”. ↩

Macnab, Robert M.  “How Bacteria Assemble Flagella.”  Annual Review of Microbiology 57:77–100.  2003.  Read on archive.org in the microfilm of the volume, by paragraph search, and not stored.  The printed page is the leaf minus 15, anchored at leaves 92 and 115 from the site's page map.  Read in part.  Mirror:  Archive.org

1. 5a.

   Page 77, section abstract:  “Six of the components of the export apparatus are integral membrane proteins and are believed to be located within the flagellar basal body. Three others are soluble: the ATPase that drives export, a regulator of the ATPase, and a general chaperone. Exported substrates diffuse down a narrow channel in the growing structure and assemble at the distal end”. ↩ ↩

2. 5b.

   Page 88:  “The hook develops to a rather precise length of 55 nm (24a).”  The same paragraph reports that fliK mutants produce long polyhooks with no filaments. ↩ ↩

3. 5c.

   Page 95, section Concluding remarks:  “How they evolved is another matter, although it has been proposed (53) that the flagellum is the more ancient device, since it exists in bacterial genera that diverged long before eukaryotic hosts existed as virulence targets.” ↩

Johnson, Steven et al.  “Molecular structure of the intact bacterial flagellar basal body.”  Nature Microbiology 6:712–721.  2021.  Read in the PMC author manuscript.  Mirror:  PMC

1. 6a.

   Section abstract:  “The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall.” ↩

Tan, Jiaxing et al.  “Structural basis of assembly and torque transmission of the bacterial flagellar motor.”  Cell 184(10):2665–2679.  May 13, 2021.  Read in the Wayback copy of the publisher's PDF.  The first PDF page is a cover sheet, so the printed page is the PDF page plus 2663.  Mirror:  Archive.org

1. 7a.

   Page 2665, section summary:  “consisting of 175 subunits with a molecular mass of approximately 6.3 MDa.”  Page 2677 of the same paper says that the flagellum has been proposed to be the evolutionary ancestor of the secretion systems. ↩

Deme, Justin C. et al.  “Structures of the stator complex that drives rotation of the bacterial flagellum.”  Nature Microbiology 5:1553–1564.  2020.  Read in the PMC author manuscript.  Santiveri and colleagues reported the same five-to-two form in Cell in the same year.  Mirror:  PMC

1. 8a.

   Section abstract:  “The structures reveal an unexpected asymmetric A5B2 subunit assembly in which the five A subunits enclose the two B subunits.” ↩

2. 8b.

   Section Common architecture across multiple bacterial ion-driven machines:  “The MotAB system is related at the sequence level to the ExbBD complex found in Gram-negative bacteria”.  “Both displayed a 5:2 ExbB:ExbD stoichiometry”. ↩

Beeby, Morgan et al.  “Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold.”  Proceedings of the National Academy of Sciences 113(13):E1917–E1926.  2016.  Mirror:  PMC

1. 9a.

   Page E1918:  “flagellar motors incorporate 13 and 17 stator complexes, respectively, compared with the ∼11 in enteric bacteria.”  The motors are those of Vibrio and Campylobacter.  Page E1924 adds spirochaetes with 16. ↩ ↩

Nakamura, Shuichi, and Tohru Minamino.  “Flagella-Driven Motility of Bacteria.”  Biomolecules 9(7):279.  2019.  Mirror:  PMC

1. 10a.

   Page 2:  “The maximum motor speed reaches 300 revolutions per second in E. coli and Salmonella [11] and 1700 revolutions per second in a marine bacterium Vibrio alginolyticus [12].” ↩

2. 10b.

   Page 4:  “The hook length is controlled by the molecular ruler protein FliK, which is secreted via a type III protein export apparatus during hook assembly”. ↩

3. 10c.

   Page 1:  “the flagella of spirochetes reside within the periplasmic space”. ↩

Berg's 2003 review was searched for "universe" and for "most efficient" and returns neither.  The phrase appears in design literature without a citation to anything Berg wrote.  His review gives the efficiency estimate quoted here³ and credits the system to evolution.³ ↩

Aizawa, Shin-Ichi.  “What is Essential for Flagellar Assembly?”  Pili and Flagella: Current Research and Future Trends, 91–98.  Caister Academic Press.  Edited by Ken F. Jarrell.  2009.  Read on archive.org by paragraph search.  The item cannot be borrowed and was not stored.  The printed page is the leaf minus 14, anchored at leaves 30 and 200 from the site's own page map.  Only page 91 was read.  The chapter title is from the publisher's listing.

1. 12a.

   Page 91:  “In Salmonella enterica, flagellar assembly and function requires about 50 genes, among which 21 gene products are incorporated in the complete flagellar structure as component proteins.” ↩

2. 12b.

   Page 91:  “Since the flagellum is so well designed and beautifully constructed by an ordered assembly pathway, even I, who am not a creationist, get an awe-inspiring feeling from its ‘divine’ beauty (Pallen and Matzke, 2006). However, if the flagellum has evolved from a primitive form, where are the remnants of its ancestor? Why don’t we see any intermediate or simpler forms of flagella than what they are today?”  The rest of the chapter was not read, so Aizawa's own answer is not reported. ↩

Dembski, William A.  No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence.  Rowman and Littlefield.  2002.  Read on archive.org by paragraph search.  The item cannot be borrowed and was not stored.  The printed page is the leaf minus 32, anchored at leaves 60 and 400 from the site's page map.

1. 13a.

   Page 268:  “The issue is not whether fewer parts can be used for some other function, but whether they can accomplish the same function as the original system.” ↩

2. 13b.

   Page 282:  “For a part to be indispensable to a system, not only must knocking it out destroy the system’s function, but also knocking it out in combination with other parts must destroy the system’s function.” ↩

3. 13c.

   Page 287:  “By requiring around thirty distinct proteins in even its simplest known forms, the bacterial flagellum clearly possesses numerous and distinct parts.” ↩

United States District Court for the Middle District of Pennsylvania.  Kitzmiller v. Dover Area School District, trial transcript, Day 20, afternoon session, testimony of Scott A. Minnich.  Nov 3, 2005.  The page number is printed at the head of each page.  The numbers in the left margin are question numbers.

1. 14a.

   Page 107, line 22:  “One mutation, one part knock out, it can't swim. Put that single gene back in we restore motility.”  Page 108, line 1:  “By definition the system is irreducibly complex. We've done that with all 35 components of the flagellum, and we get the same effect.”  The organism is Yersinia enterocolitica. ↩ ↩

Counted from Table 1 of Pallen and Matzke,² taking the row "FlgBCFG" as four proteins and "FlhDC" as two, which gives 42.  The column "Indispensable?" reads "Yes" for 23:  FlgB, FlgC, FlgD, FlgE, FlgF, FlgG, FlgK, FlgL, FlhA, FlhB, FliC, FliE, FliF, FliG, FliI, FliK, FliM, FliN, FliP, FliQ, FliR, MotA and MotB.  The column "Homologies" is blank or reads "None" or "None yet known" for 15.  In the table as printed, 9 proteins have a relative outside both the flagellum and the secretion system:  FlgA, FlhD, FlhC, FliA, FliG, FliH, FliI, MotA and MotB.  FliJ is listed there with a secretion-system relative only, and moves to the first class on the structural evidence of 2011,⁵⁰ which gives 10, 8, 9 and 15.  Two later results move proteins out of the last class:  FliL to the first, on its 2019 structure,⁵² and FliO to the third, on the 2025 survey,²⁷ which gives 11, 8, 10 and 13.  Doolittle and Zhaxybayeva, as quoted by Matzke, give Matzke's own summary as 20 universal, 15 without relatives and 2 with both properties.⁶⁷  The printed table has 23 universal, and New Scientist reported 23.⁶⁶  The table's text lists FlgJ with no relative, although the article's text says its second domain is shared with many proteins. ↩ ↩

Behe, Michael J.  Darwin's Black Box: The Biochemical Challenge to Evolution.  Free Press.  10th anniversary edition.  2006.

1. 16a.

   Page 70:  “The rotor has been identified as the M ring in Figure 3-3, and the stator as the S ring.” ↩

2. 16b.

   Page 72:  “Because the bacterial flagellum is necessarily composed of at least three parts—a paddle, a rotor, and a motor—it is irreducibly complex.” ↩

3. 16c.

   Page 72:  “no scientist has ever published a model to account for the gradual evolution of this extraordinary molecular machine.” ↩

4. 16d.

   Page 72, last lines:  “The bacterial flagellum, in addition to the proteins already discussed, requires about forty other proteins for function.” ↩

5. 16e.

   Page 73:  “As the number of required parts increases, the difficulty of gradually putting the system together skyrockets, and the likelihood of indirect scenarios plummets.” ↩

6. 16f.

   Page 268, section afterword:  “there's no reason that parts or subassemblies of irreducibly complex systems can't have one or more other functions”. ↩

7. 16g.

   Page 269, section afterword:  “even in principle sequence comparisons can't show whether a structure arose by random mutation and natural selection.” ↩

Minnich, Scott A., and Stephen C. Meyer.  “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria.”  Design and Nature II, 295–304.  WIT Press.  Edited by M. W. Collins and C. A. Brebbia.  2004.  Conference paper.  The printed page is the PDF page plus 294, anchored on the running heads of pages 296 and 303.

1. 17a.

   Page 295, section abstract:  “Y. pestis has lost the ability to assemble flagella (the genes are present on the chromosome)”. ↩

2. 17b.

   Page 302:  “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.” ↩

3. 17c.

   Page 302:  “In other words, if anything, the pump evolved from the motor, not the motor from the pump.” ↩

Dembski, William A.  “Still Spinning Just Fine: A Response to Ken Miller.”  Discovery Institute.  Feb 17, 2003.

1. 18a.

   Section Connecting the Type III Secretory System to Bacterial Flagellum:  “One might just as well say that because the motor of a motorcycle can be used as a blender, therefore the motor evolved into the motorcycle.” ↩

2. 18b.

   Section Connecting the Type III Secretory System to Bacterial Flagellum:  “The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique.” ↩

Behe, Michael J.  Darwin Devolves: The New Science About DNA That Challenges Evolution.  HarperOne.  2019.  Read in the EPUB.  Pages are from its printed-page anchors.

1. 19a.

   Page 287, last lines, running on to page 288:  “a grand total of zero serious attempts to show how the elegant molecular machine might have been produced by random processes and natural selection.” ↩

2. 19b.

   Page 288:  “The first serious try at coming to terms with the flagellum wasn’t published until 2006, a decade after Darwin’s Black Box.” ↩

3. 19c.

   Page 294:  “It turns out that the system was switched back on by loss-of-FCT mutations.” ↩

4. 19d.

   Page 294:  “says nothing about the mechanism of evolution.” ↩

DeVowe, Steven.  “The amazing motorized germ.”  Creation 27(1):24–25.  Dec 2004.  Creation Ministries International.

1. 20a.

   Paragraph last:  “But this secretory apparatus, as well as the plague bacterium’s drilling apparatus, are a degeneration from the flagellum.” ↩

2. 20b.

   Paragraph second from last:  “only about 10 of the 40 components can possibly be explained by co-option, but the other 30 are brand new.”  Page fetched on 29 September 2026. ↩

Gillen, Alan L.  “A New Spin on the Bacterial Flagellum: Its Normal Niche and Displacement.”  Answers in Depth 17.  Aug 3, 2022.  Answers in Genesis.

1. 21a.

   Section abstract:  “The bacterial flagellum is a perfect example of irreducible complexity because all its parts must be present from the start for it to function at all.” ↩

Sherwin, Frank.  “Debating Design: The Bacterial Flagellum.”  Acts & Facts 36(9):15.  2007.  Institute for Creation Research.

1. 22a.

   Paragraph 2:  “Creation scientists state that these subunits do not have the same evolutionary descent, but rather the same Designer.” ↩

Minamino, Tohru, and Keiichi Namba.  “Distinct roles of the FliI ATPase and proton motive force in bacterial flagellar protein export.”  Nature 451:485–488.  Jan 24, 2008.  Read on archive.org in the microfilm of the issue, by paragraph search, and not stored.  Leaf 134 is page 485 and leaf 139 is page 490 on the site's page map.  The first page was read.  The scan prints FliI as "Flil".  Mirror:  Archive.org

1. 23a.

   Page 485:  “A fliH fliI double null mutant was weakly motile.”  “A fliH null mutant was weakly motile whereas a fliI null mutant was non-motile”. ↩ ↩

Erhardt, Marc et al.  “ATPase-Independent Type-III Protein Secretion in Salmonella enterica.”  PLoS Genetics 10(11):e1004800.  2014.  Mirror:  PMC

1. 24a.

   Page 2, section Author Summary:  “suggesting that a proto ATPase was added to a primordial proton-powered type-III export system with the evolutionary benefit of facilitating the export process.” ↩

2. 24b.

   Page 5:  “of a fliHIJ deletion mutant to about 11% of the wildtype”.  The helper mutation removed the ATP synthase gene atpA, which raises the proton motive force.  The same page gives about 25% for a strain lacking FliH and FliI, and 41% to 54% when a second helper mutation was added to strains lacking parts of the complex.  The abstract on page 1 reports functional flagella without the ATPase. ↩

Barker, Clive S. et al.  “FliO Regulation of FliP in the Formation of the Salmonella enterica Flagellum.”  PLoS Genetics 6(9):e1001143.  2010.  Mirror:  PMC

1. 25a.

   Page 1, section abstract:  “gave rise to pseudorevertants containing extragenic bypass mutations in FliP at positions R143H or F190L.”  Page 2 says that FliO shows a sporadic distribution in bacteria. ↩

McLatchie, Jonathan.  “Two of the World’s Leading Experts on Bacterial Flagellar Assembly Take on Michael Behe.”  Evolution News.  Mar 8, 2013.  Discovery Institute.  A review of a book chapter by Kelly Hughes and David Blair that was not obtained.

1. 26a.

   Paragraph third from last:  “I would concede that the chaperone protein FliJ, the ATPase FliI, and its regulator FliH are dispensable for flagellar export.” ↩

Andrianova, Ekaterina P. et al.  “FliO is an evolutionarily conserved yet diversified core component of the bacterial flagellar type III secretion system.”  Proceedings of the National Academy of Sciences 122(34):e2512476122.  Aug 21, 2025.  A genome survey with laboratory tests.  It searched 30,238 representative genomes from 131 bacterial phyla for FliO with low-threshold profile searches, gene-neighbourhood evidence and predicted structures, then deleted FliO in Campylobacter jejuni.  It overturns the earlier view, based on BLAST, that FliO is sporadic, and shows how sequence searches undercount fast-changing flagellar proteins.  Mirror:  PMC

1. 27a.

   Section Abstract:  “we found that approximately 40% of bacterial genomes contain flagellar genes—significantly fewer than previously reported.”  “we demonstrate that FliO is present in ~95% of genomes encoding the core flagellar components FliP, FliQ, and FliR. This suggests that FliO is a nearly ubiquitous and ancestral core component of the flagellar type III secretion system (fT3SS).”  “We identify FliO homologs not only in canonical flagellar systems but also in some virulence-associated T3SS and even some nonflagellated organisms”. ↩ ↩ ↩ ↩ ↩

2. 27b.

   Section Results, A Computational Strategy for Identifying FliO Homologs:  “FliO sequences from B. subtilis (RefSeq accession NP_389516.1 ) and E. coli ( NP_416457.4 ) share less than 30% identity over 76 aligned residues, yielding a BLAST E-value of 0.093”. ↩

3. 27c.

   Section Results, FliO and the AMIN Domain Modestly Impact In Vitro Motility:  “the ΔfliO mutant exhibited a 35% reduction in swimming motility compared to wild-type (WT) C. jejuni”.  Measured as spreading in soft agar. ↩

Taylor, Tiffany B. et al.  “Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system.”  Science 347(6225):1014–1017.  Feb 27, 2015.  The published abstract was read from Europe PMC.  The body was read in the authors' last submitted version, whose wording may differ from the version of record.  Mirror:  Centaur.reading.ac.uk

1. 28a.

   Page 1014, section abstract:  “Under strong selection for motility, these bacteria consistently regained flagella within 96 hours via a two-step evolutionary pathway.”  “Step 1 mutations increase intracellular levels of phosphorylated NtrC, a distant homolog of FleQ”.  “Step 2 is a switch-of-function mutation that redirects NtrC away from nitrogen uptake and toward its novel function as a flagellar regulator.” ↩ ↩

2. 28b.

   Section submitted manuscript, line 92:  “NtrC is a distant homologue of FleQ, sharing 30% amino acid identity and the same three structural domains”. ↩

3. 28c.

   Section submitted manuscript, line 117:  “While de novo origination of new functions in nature is likely to take longer and involve more mutational steps, this system enables us to understand the adaptive process in detail at the genetic and phenotypic level.” ↩

Ridone, Pietro et al.  “The rapid evolution of flagellar ion selectivity in experimental populations of E. coli.”  Science Advances 8(47):eabq2492.  2022.  Mirror:  PMC

1. 29a.

   Page 1, section abstract:  “we used CRISPR engineering to replace the native Escherichia coli H+-powered stator with Na+-powered stator genes and report the spontaneous reversion of our edit in a low-sodium environment.” ↩

Miller, Kenneth R.  “The Flagellum Unspun: The Collapse of "Irreducible Complexity".”  Debating Design: From Darwin to DNA, 81–97.  Cambridge University Press.  Edited by William A. Dembski and Michael Ruse.  2004.  Read in the author's pre-publication copy on his own website.  The printed book was not read, so the wording is the web copy's and the locators are its section headings.

1. 30a.

   Section The Type-III Secretory Apparatus:  “Yet the TTSS is indeed fully-functional, even though it is missing most of the parts of the flagellum.” ↩

2. 30b.

   Section Counterattack:  “the objection that the TTSS does not tell us how either it or the flagellum evolved. This is certainly true, although Aizawa has suggested that the TTSS may indeed be an evolutionary precursor of the flagellum (Aizawa 2001).” ↩

United States District Court for the Middle District of Pennsylvania.  Kitzmiller v. Dover Area School District, trial transcript, Day 1, afternoon session, testimony of Kenneth R. Miller.  Sep 26, 2005.  The page number is printed at the head of each page.  The word "pre-cursor" or "precursor" occurs on page 11 at lines 15 and 17, on page 18 at line 8 and on page 39 at line 11, each time in a quotation from Behe.  The morning session of the same day does not contain it.

1. 31a.

   Page 16, line 5:  “Behe's prediction is that the parts of any irreducibly complex system should have no useful function.” ↩

2. 31b.

   Page 19, line 9:  “So it's very clear that a subset of those proteins has an entirely different function, a beneficial function, not for us, but for the bacterium”. ↩

United States District Court for the Middle District of Pennsylvania.  Kitzmiller v. Dover Area School District, Memorandum Opinion.  Dec 20, 2005.

1. 32a.

   Page 76:  “identified a possible precursor to the bacterial flagellum, a subsystem that was fully functional, namely the Type-III Secretory System.”  Slip opinion page.  The same page records Minnich's testimony that all three orderings were under study. ↩

Luskin, Casey.  “Study Challenges Evolutionary Relationship Between Flagellum and Type III Secretory System.”  Evolution News.  May 14, 2021.  Discovery Institute.

1. 33a.

   Paragraph 3:  “and thereby could be a “precursor” to the flagellum.” ↩

Gophna, Uri et al.  “Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events.”  Gene 312:151–163.  2003.  Abstract only, from Europe PMC.  The body is behind payment and was not obtained.

1. 34a.

   Section abstract:  “Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another.” ↩

Saier, Milton H.  “Evolution of bacterial type III protein secretion systems.”  Trends in Microbiology 12(3):113–115.  Mar 2004.  Read on archive.org in the microfilm of the issue, by paragraph search, and not stored.  The printed page is the leaf plus 99, anchored at leaves 10 and 30 from the site's page map.  Mirror:  Archive.org

1. 35a.

   Page 114:  “First, the TTSS came first; second, the Fla system came first; or third, both systems evolved from a common precursor. At present, too little information is available to distinguish between these possibilities with certainty.”  Saier leaned to the flagellum being older. ↩

Abby, Sophie S., and Eduardo P. C. Rocha.  “The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems.”  PLoS Genetics 8(9):e1002983.  2012.  Mirror:  PMC

1. 36a.

   Section abstract:  “Phylogenomic and comparative analyses of these systems argue that the NF-T3SS arose from an exaptation of the flagellum”.  “by successive deletions, innovations, and recruitment from other molecular systems.” ↩

2. 36b.

   Section Discussion:  “In this work we provide independent lines of evidence showing that the flagellum was primordial and that the NF-T3SS arose via exaptation. Firstly, the ATPase tree robustly roots the T3SS tree within flagella (Figure 3). Secondly, confirming prior results [93], the phylogenetic distribution of the flagellum is much broader than that of the NF-T3SS. Thirdly, our data suggests that the last common ancestor of the NF-T3SSs lacked a secretin.” ↩ ↩

3. 36c.

   Section Multiple recruitments of secretins to NF-T3SSs:  “Our analysis shows that the secretin was recruited three times: in Chlamy (from T2SS), in the other systems (possibly from T4P) and then again in Rhizo (from Tad systems).” ↩

Denise, Rémi et al.  “The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries.”  Trends in Microbiology 28(5):372–386.  2020.  Abstract only, from Europe PMC.

1. 37a.

   Section abstract:  “occurred by the co-option of machineries for motility, conjugation, injection, or adhesion.” ↩

Matzke, N. J.  “Evolution in (Brownian) space: a model for the origin of the bacterial flagellum.”  TalkDesign.  2003.  Version 1.0, last updated 10 November 2003.  A web essay of about 29,000 words.  Not peer reviewed.  Locators are its section numbers.

1. 38a.

   Section abstract:  “The model consists of six major stages: export apparatus, secretion system, adhesion system, pilus, undirected motility, and taxis-enabled motility.”  “this involves five subsystem-level cooption events.” ↩

2. 38b.

   Section abstract:  “The selectability of each stage is documented using analogies with present-day systems.” ↩

3. 38c.

   Section abstract:  “First, analysis of dispersal at low Reynolds numbers indicates that even very crude motility can be beneficial for large bacteria.” ↩

4. 38d.

   Section 3.2.2:  “For the purposes of the current discussion it will be assumed that type III virulence systems are derived”. ↩

5. 38e.

   Section 4:  “duplication events within the core system were invoked 11 times for origin of 12 axial proteins from one, and an additional time for the divergence of FliN and FliM.” ↩

6. 38f.

   Section 4.1:  “Of the remaining 18 components, four (FliI, MotA, MotB, and FliM) have well-accepted nonflagellar homologs based on significant sequence similarity.”  This count is of 30 structural components and includes FliM, which the 2006 table links only to FliN and a secretion-system protein. ↩

Liu, Renyi, and Howard Ochman.  “Stepwise formation of the bacterial flagellar system.”  Proceedings of the National Academy of Sciences 104(17):7116–7121.  2007.  Mirror:  PMC

1. 39a.

   Section abstract:  “we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria.” ↩

2. 39b.

   Section abstract:  “These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.” ↩ ↩

3. 39c.

   Section Core Flagellar Proteins Arose Through the Duplication …:  “Pair-wise comparisons among these core proteins revealed that ten are homologous to other core proteins when applying an e-value cutoff of 10−4 (Fig. 3).” ↩

4. 39d.

   Section legend of Figure 3:  “Aside from these matches to other core proteins, pairwise comparisons of these flagellar proteins to the >4,000 nonflagellar proteins encoded by the entire E. coli genome recovered cumulatively a total of only 24 hits that reached the same level of significance.” ↩

5. 39e.

   Section Core Flagellar Proteins Arose Through the Duplication …:  “paralogous pairs are between 18% and 32% identical”. ↩

Chaban, Bonnie et al.  “Evolution of higher torque in Campylobacter-type bacterial flagellar motors.”  Scientific Reports 8:97.  2018.  Mirror:  PMC

1. 40a.

   Page 1, section abstract:  “Observation of ~12 stator complexes in many proteobacteria, yet ~17 in ε-proteobacteria suggest a “quantum leap” evolutionary event.” ↩ ↩

2. 40b.

   Page 1:  “at the molecular level, we are limited to inferring ancestral states by observation of contemporary diversity.” ↩

3. 40c.

   Page 2:  “During our previous work, we discovered that each accessory protein is essential, posing a conundrum: how could proteins have been added stepwise to form this (naively “irreducibly complex”) motor?” ↩

Matzke, Nick.  “Flagellum evolution paper exhibits canine qualities.”  The Panda's Thumb.  Apr 2007.  A blog post by the co-author of the 2006 review.

1. 41a.

   Paragraph 2:  “But much of it ranges from dubious to just irremediably wrong.”  Paragraph near the end:  “There is just no way that the flagellum evolved by diversification of a single gene.” ↩

Doolittle, W. Ford, and Olga Zhaxybayeva.  “Evolution: Reducible Complexity — The Case for Bacterial Flagella.”  Current Biology 17(13):R510–R512.  Jul 3, 2007.  Not obtained in full.  The standfirst was read from Europe PMC, and longer passages only as quoted by Matzke.

1. 42a.

   Page R510, section standfirst:  “proposes a (perhaps too simple) scheme for the evolution of bacterial flagella.” ↩

Liu, Renyi, and Howard Ochman.  “Correction for Liu and Ochman, Stepwise formation of the bacterial flagellar system.”  Proceedings of the National Academy of Sciences 104(27):11507.  Jul 3, 2007.  The authors' published correction to their April 2007 paper.  It changes the search settings and cutoff behind Figure 3 and the count of matches to proteins outside the flagellum, and states that the conclusions are unaffected.  Mirror:  PMC

1. 43a.

   Page 11507, right column:  “the phrase ‘‘by using the Bl2seq program (with default options)’’ should instead read: ‘‘by using the Bl2seq program (with the ‘-F F’ option).’’ Additionally, in the Fig. 3 legend, line 3, the cutoff value 10⁻⁴ should instead appear as 9 × 10⁻⁴. Applying this cutoff yields a total of 70, not 24, hits of flagellar core proteins to nonflagellar proteins in the entire E. coli K-12 genome. These errors do not affect the conclusions of the article.”  The option -F F switches off the program's filter for low-complexity sequence. ↩

Matzke reported that the authors "forthrightly volunteered the filters correction to correspondents."⁶⁷  On the usual reading of an E-value as the number of chance matches expected in one comparison, the corrected figures can be checked roughly.  About 24 core proteins against more than 4,000 other E. coli proteins make some 96,000 comparisons, and a cutoff of 9 × 10^-4 should let through about 86 by chance.  So the 70 matches to other proteins are near what chance alone gives, and they were never a strong contrast.  The 276 comparisons among the 24 core proteins should let through about 0.25 by chance, so the matches among core proteins are well above chance.  With the filter off, stretches of simple, repetitive sequence can inflate both figures.  Neither figure shows that all 24 proteins descend from one gene. ↩

Behe, Michael J.  “Darwinism Gone Wild: Neither sequence similarity nor common descent address a claim of Intelligent Design.”  Evolution News.  Apr 19, 2007.  Discovery Institute.

1. 45a.

   Paragraph 6:  “Evidence for common descent is NOT evidence for RM/NS.”  RM/NS is random mutation and natural selection.  The next paragraph says of Matzke's criticism that his point is well taken. ↩

Selçuk, Berkay et al.  “The last bacterial common ancestor encoded a complex flagellum.”  bioRxiv.  Jun 12, 2026.  A preprint, not yet peer reviewed.  It combines sensitive profile searches across the bacterial tree with co-occurrence of genes, gene-tree clustering and gene neighbourhoods to ask which flagellar genes were present before the main bacterial lineages split.  It finds 52, more than twice the 24 of Liu and Ochman, and argues that the ancestral flagellum was complex rather than minimal.  The authors include three leading flagellar laboratories, those of Zhulin, Beeby and Erhardt.

1. 46a.

   Page 2, section Abstract:  “did the last bacterial common ancestor encode a simpler, partial flagellum that was elaborated later in a lineage-specific manner, or does the apparent absence of conserved components reflect limitations in detecting highly diverged homologs?”  “We identify 28 additional flagellar gene families whose distributions and evolutionary histories support an origin before major bacterial diversification, yielding a 52-gene ancestral flagellum. The ancestral flagellum included all proteins of the secretion/export apparatus, basal body, axial components, motor-force generators and regulatory checkpoints required to build and operate a functional, contemporary flagellum.” ↩ ↩ ↩

2. 46b.

   Page 10:  “Across genomes encoding at least 25 core components, most retained between 41 and 44 ancestral proteins”. ↩

3. 46c.

   Page 13, section Discussion:  “Previous reconstructions proposed that the last bacterial common ancestor encoded 24 ancestral flagellar genes 14, implying that modern flagella might have been assembled gradually through sequential addition of new components. Our results support a different scenario.”  Reference 14 is Liu and Ochman 2007. ↩

4. 46d.

   Page 14:  “This reconstruction supports a “complexity-first” model of flagellar evolution from the LBCA onward.”  Page 15:  “Subsequent evolution was driven primarily by selective retention, repeated loss, and lineage-specific remodeling of an already complex ancestral machine, whereas the evolutionary steps that gave rise to this system remain to be resolved.” ↩

Cascales, Eric et al.  “The TolQ-TolR proteins energize TolA and share homologies with the flagellar motor proteins MotA-MotB.”  Molecular Microbiology 42(3):795–807.  2001.  Abstract only, from Europe PMC.

1. 47a.

   Section abstract:  “present structural and functional homologies not only to ExbB and ExbD of the TonB system but also with MotA and MotB of the flagellar motor.” ↩

Imada, Katsumi et al.  “Structural similarity between the flagellar type III ATPase FliI and F1-ATPase subunits.”  Proceedings of the National Academy of Sciences 104(2):485–490.  2007.  Mirror:  PMC

1. 48a.

   Page 485:  “A high sequence similarity (29% identity as shown in Fig. 1) has been identified between the ATPase domain of FliI”.  “These results imply an evolutionary relation between the flagellum and F0F1-ATPsynthase”. ↩

Pallen, Mark J. et al.  “Evolutionary links between FliH/YscL-like proteins from bacterial type III secretion systems and second-stalk components of the FoF1 and vacuolar ATPases.”  Protein Science 15(4):935–941.  2006.  Mirror:  PMC

1. 49a.

   Page 935, section abstract:  “Here we use PSI-BLAST searches to show that some noncalatytic components are also conserved between type III secretion systems and proton-translocating ATPases.”  The misspelling is the journal's. ↩

Ibuki, Tatsuya et al.  “Common architecture of the flagellar type III protein export apparatus and F- and V-type ATPases.”  Nature Structural & Molecular Biology 18:277–282.  2011.  Abstract only, from Europe PMC.

1. 50a.

   Section abstract:  “the structure of FliJ derived from Salmonella enterica serovar Typhimurium is remarkably similar to that of the two-stranded α-helical coiled-coil part of the γ subunit”. ↩ ↩

Snyder, Lori A. S. et al.  “Bacterial flagellar diversity and evolution: seek simplicity and distrust it?”  Trends in Microbiology 17(1):1–5.  2009.  Abstract only, from Europe PMC.

1. 51a.

   Section abstract:  “structural evidence for homology between FliG (a component of the flagellar motor) and MgtE (a magnesium transporter).”  Pallen and Matzke's table of 2006 marks this match as failing to reach significance by sequence. ↩

Takekawa, Norihiro et al.  “Structure of Vibrio FliL, a New Stomatin-like Protein That Assists the Bacterial Flagellar Motor Function.”  mBio 10(2):e00292-19.  2019.  A crystal structure of the part of FliL that lies outside the inner membrane, from the polar flagellum of Vibrio alginolyticus, with mutations testing its role.  A structure database search matched it to the SPFH domain found in stomatin, prohibitin, flotillin and HflK/C, membrane proteins of bacteria, archaea and animals.  The match is by shape, not by sequence.  Mirror:  PMC

1. 52a.

   Section Results, The FliL C structure resembles the SPFH domain of stomatin:  “The Dali database search revealed that FliL C shows remarkable structural similarity (Z-score of 9.5) to the stomatin/prohibitin/flotillin/HflK/C (SPFH) domain of stomatin from Mus musculus (Mm-stomatin)”.  “although the amino acid sequence identity is only 17%”. ↩ ↩

Chen, Songye et al.  “Structural diversity of bacterial flagellar motors.”  The EMBO Journal 30:2972–2981.  2011.  Mirror:  PMC

1. 53a.

   Page 2972, section abstract:  “allowing the occasional misrepresentation of the motor as an invariant, ideal machine.” ↩

2. 53b.

   Page 2972, section abstract:  “While a conserved structural core was observed in all 11 bacteria imaged, surprisingly novel and divergent structures as well as different symmetries were observed surrounding the core.” ↩

3. 53c.

   Page 2977:  “16 copies of the stator complexes are clearly seen in the averaged tomograms of the spirochaetes”. ↩

Albers, Sonja-Verena, and Ken F. Jarrell.  “The archaellum: how Archaea swim.”  Frontiers in Microbiology 6:23.  2015.  Mirror:  PMC

1. 54a.

   Page 5:  “archaeal flagella were in fact a rotating variant of type IV pili with no evolutionary relationship to bacterial flagella”. ↩

Beeby, Morgan et al.  “Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia.”  FEMS Microbiology Reviews 44(3):253–304.  2020.  Abstract only, from Europe PMC.

1. 55a.

   Page 253, section abstract:  “flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force.” ↩

2. 55b.

   Page 253, section abstract:  “Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure.” ↩

Maezawa, Kazuki et al.  “Hundreds of Flagellar Basal Bodies Cover the Cell Surface of the Endosymbiotic Bacterium Buchnera aphidicola sp. Strain APS.”  Journal of Bacteriology 188(18):6539–6543.  2006.  Mirror:  PMC

1. 56a.

   Page 6539, section abstract:  “the Buchnera cell surface is covered with hundreds of hook–basal-body (HBB) complexes.” ↩

2. 56b.

   Page 6543:  “Buchnera is nonmotile, and the flagella lack the essential components of motility such as a filament (the propeller) and the Mot complex (the stator of the motor).”  Page 6540 lists nine missing genes, fliA, fliC, fliD, fliL, fliO, fliS, fliT, flgM and flgL, and adds that the master genes flhDC and the stator genes motAB are missing too.  FliC is the filament protein. ↩

3. 56c.

   Page 6543:  “we suggest that the Buchnera HBB is a plausible candidate for an export apparatus”. ↩

Toft, Christina, and Mario A. Fares.  “The Evolution of the Flagellar Assembly Pathway in Endosymbiotic Bacterial Genomes.”  Molecular Biology and Evolution 25(9):2069–2076.  Sep 2008.  Abstract read on archive.org in the microfilm of the issue, by paragraph search, and not stored.  Leaf 282 is page 2069 and leaf 289 is page 2076 on the site's page map.  The scan prints "type II]" for "type III".  Mirror:  Archive.org

1. 57a.

   Page 2069, section abstract:  “genes responsible for flagellar assembly have been partially or totally lost in most intracellular symbionts of gamma-Proteobacteria.” ↩

Zhu, Siqi et al.  “The common origin and degenerative evolution of flagella in Actinobacteria.”  mBio 14(6):e02526-23.  2023.  Mirror:  PMC

1. 58a.

   Page 1, section Importance:  “Later lineages underwent massive flagellar losses”.  “leading to the simplest rod known so far.” ↩

Koskiniemi, Sanna et al.  “Selection-Driven Gene Loss in Bacteria.”  PLoS Genetics 8(6):e1002787.  2012.  Mirror:  PMC

1. 59a.

   Page 4:  “It is notable that the calculated expected cost of running flagella is 4.5% of the cells total energy expenditure”. ↩

2. 59b.

   Page 5:  “they remove all or parts of the fli operon and inactivate flagellum function.”  Page 1, section abstract:  “after serial passage of wild-type bacteria in rich medium for 1,000 generations we observed fixation of deletions that substantially increased bacterial fitness”. ↩

Poggio, Sebastian et al.  “A Complete Set of Flagellar Genes Acquired by Horizontal Transfer Coexists with the Endogenous Flagellar System in Rhodobacter sphaeroides.”  Journal of Bacteriology 189(8):3208–3216.  2007.  Mirror:  PMC

1. 60a.

   Page 3208, section abstract:  “Phylogenic analysis suggests that the flagellar system that was initially characterized was in fact acquired by horizontal transfer”. ↩

Philip, Jamiema Sara et al.  “Mapping the loss of flagellar motility across the tree of life.”  The ISME Journal 19(1):wraf111.  Jun 13, 2025.  A genome survey.  It searched 11,365 bacterial genomes for 54 flagellar proteins by sequence and by predicted structure, then mapped motility onto a tree of 4,125 species.  It reconstructs a motile last common ancestor and measures how often each part is lost and gained.  Nicholas Matzke, co-author of the main evolutionary model of the flagellum, is one of the authors.  Mirror:  PMC

1. 61a.

   Section Discussion, Common bacterial ancestor was motile:  “We confirmed, as reported elsewhere [ 12 ], that the last bacterial common ancestor (LBCA) likely contained a flagellar motor (posterior probability of 0.99).”  Section Abstract:  “We confirmed that the last common bacterial ancestor had flagellar motility and that the rate of loss of this motility was four-fold higher than the rate of gain.”  The Results give a mean rate of 0.8058 from motile to non-motile against 0.21987 the other way.  Reference 12 is Coleman and colleagues' rooted tree of bacteria, Science, 2021. ↩ ↩

2. 61b.

   Section Discussion, What use is half a motor?:  “Our model, and experimental experience [ 41 , 42 ], asserts that an incomplete flagellar system cannot confer motility, and we validate this, but the question remains how did a half motor come to be?”  The authors introduce the question as a paraphrase of St George Mivart, an early critic of Darwin. ↩

3. 61c.

   Section Discussion, What use is half a motor?:  “Conversely, we saw that 11% of non-motile species had at least one rotor protein (FliG, FliM, FliN) but no filament proteins.”  “the presence of rotor proteins without a filament raises the possibility that rotor components could have an alternative function.”  “Incomplete modules of the motor may also represent remnants of a motor following gene loss.” ↩

Behe, Michael J.  The Edge of Evolution: The Search for the Limits of Darwinism.  Free Press.  2007.  Behe's second book.  It takes the observed rarity of chloroquine resistance in malaria, which needs two specific mutations, as a yardstick for what random mutation and selection can do, and argues from it that a protein complex needing two new binding sites is beyond their reach.  It is the one place the design side puts a number on the kind of step the flagellum would need, which is why it matters here.

1. 62a.

   Page 142, chapter 7:  “The number of cellular protein-protein binding sites developed by random mutation and natural selection for each (one for human—due to sickle cell hemoglobin—and zero for the other species) is plotted against the species’ population size.”  The four species are humans, E. coli, HIV and the malaria parasite. ↩

2. 62b.

   Page 146, chapter 7:  “the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10²⁰ times 10²⁰, which is 10⁴⁰. There have likely been fewer than 10⁴⁰ cells in the world in the past four billion years, so the odds are against a single event of this variety in the history of life.”  A "CCC" is Behe's name for a cluster of mutations as hard to get as chloroquine resistance. ↩

3. 62c.

   Page 146, chapter 7:  “With the criterion of two protein-protein binding sites, we can quickly see why stupendously complex structures such as the cilium, the flagellum, and the machinery that builds them are beyond Darwinian evolution. The flagellum has dozens of protein parts that specifically bind to each other; the cilium has hundreds.” ↩

Matzke, Nick.  “Full text of 'The Edge of Creationism'.”  The Panda's Thumb.  Oct 30, 2007.  The text of Matzke's review of The Edge of Evolution, published in Trends in Ecology and Evolution 22 (2007), 566–567, doi 10.1016/j.tree.2007.09.004, as he submitted it.  Matzke is co-author of the main evolutionary model of the flagellum, so his is the critic's reply most directly aimed at Behe's use of the flagellum.

1. 63a.

   Paragraph 4 of the review:  “Behe obtains the crucial 10²⁰ number from an offhand estimate in the literature that considered only the few CQR alleles that have been detected because they have taken over regional populations.”  “Behe’s decision to square the probability for two binding sites depends on the assumption that two binding sites would have to evolve at once, but the assumption is false for the same reasons that Behe’s “irreducible complexity” argument failed in the first place”.  CQR is chloroquine resistance. ↩

Behe, Michael J., and David W. Snoke.  “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues.”  Protein Science 13(10):2651–2664.  2004.  A population-genetics model of a duplicated gene that must gain two or more specific residues, with no selectable benefit until all are in place, before it acquires a new feature.  It found that a two-change feature needs populations of about a billion over a hundred million generations.  It prices the duplication step that Matzke's flagellum model uses twelve times.  Mirror:  PMC

1. 64a.

   Page 2661:  “seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.” ↩

Schulz, Waldean A.  “An Engineering Perspective on the Bacterial Flagellum: Part 2—Analytic View.”  BIO-Complexity 2021(2):1–16.  2021.  A design-side journal.  The paper was searched for Matzke, Pallen, Ochman and Abby and cites none of them.  It does cite Chaban 2018 and Beeby 2020.

1. 65a.

   Page 15, section Conclusions:  “Meanwhile, the evolutionary biological community has yet to hypothesize a likely, detailed, step-by-step scenario to explain how the flagellum and its control system could have been blindly engineered naturalistically.” ↩

Jones, Dan.  “Uncovering the evolution of the bacterial flagellum.”  New Scientist 197(2643):40–43.  Feb 16, 2008.  Journalism, cited only for the quoted words of named scientists.  Read on archive.org in the microfilm of the issue, by paragraph search, and not stored.  Leaf 45 is page 40 and leaf 48 is page 43 on the site's page map.  Mirror:  Archive.org

1. 66a.

   Page 42:  “When Pallen and Matzke looked for homology among their 23 modern core- proteins”.  The stray hyphen is the scan's. ↩

Matzke, Nick.  “Current Biology on flagellum evolution.”  The Panda's Thumb.  Jul 2007.  Quotes Doolittle and Zhaxybayeva at length.

1. 67a.

   Section quotation from Doolittle and Zhaxybayeva:  “only 20 are universally required/detectable in all flagella, only 15 have no known homologs, and only two are both universally required and have no homologs.”  Section Matzke's closing note:  “Liu & Ochman forthrightly volunteered the filters correction to correspondents.” ↩ ↩