Behe: “Design of Life” and the limits of Neo-Darwinism

@article{namba1997molecular,
    author = "NAMBA, KEIICHI and VONDERVISZT, FERENC",
    title = "Molecular architecture of bacterial flagellum",
    year = "1997",
    journal = "Quarterly Reviews of Biophysics",
    abstract = "1. INTRODUCTION 2 2. OVERALL STRUCTURE AND SUBSTRUCTURES 5 2.1 Overall structure and components 5 2.2 Bidirectional rotary motor 5 2.3 Drive shaft 8 2.4 Bushing 8 2.5 Universal joint 9 2.6 Helical propeller 9 2.7 Axial junction 10 2.8 Capping structure 11 3. ASSEMBLY PROCESS OF THE FLAGELLUM 11 3.1 Step by step assembly 11 3.2 Flagellum-specific export apparatus and the channel 12 4. UNIQUE CHARACTERISTICS OF THE FLAGELLAR MOTOR DYNAMICS 13 5. STRUCTURAL DESIGN OF FLAGELLIN FOR ASSEMBLY REGULATION AND POLYMORPHISM 14 5.1 Domain organization and terminal disorder of flagellin 15 5.2 The role of terminal disorder in filament formation and polymorphism 17 5.3 Common structural motif for regulation of self-assembly 21 6. STRUCTURAL DESIGN OF FLAGELLAR FILAMENTS FOR POLYMORPHISM 22 6.1 Polymorphic mechanism 23 6.2 Structures of the filaments deduced by electron microscopy 25 6.2.1 Overview of the electron microscopic studies 25 6.2.2 Helical image reconstruction procedure 27 6.2.3 Structural details of the filament 28 6.3 X-ray fibre diffraction studies 32 6.3.1 Overview of the X-ray studies 32 6.3.2 Orientation of liquid crystalline sols and diffraction patterns 33 6.3.3 Equatorial analysis 35 6.3.4 A preliminary map refined at 11 Åresolution 37 6.4 Overall chain folding of the subunit in the filament 38 6.4.1 Mapping out the terminal and central regions 38 6.4.2 The chain folding and role of each domain 42 6.5 Polymorphic nature of flagellar filament 43 6.5.1 Comparison of the L- and R-type 43 6.5.2 New helical symmetry ‘Lt-type’ 46 6.5.3 Direct comparison of the Lt-type lattice to the other two 48 6.5.4 Plausible conformational changes involved in polymorphism 51 7. PERSPECTIVE 55 8. ACKNOWLEDGEMENTS 55 9. REFERENCES 55",
    url = "https://doi.org/10.1017/s0033583596003319",
    doi = "10.1017/s0033583596003319",
    number = "1",
    pages = "1-65",
    volume = "30"
}

Creationism, the rejection of evolution in favor of supernatural design, comes in many varieties besides the common young-earth Genesis version. Creationist attacks on science education have been evolving in the last few years through the alliance of different varieties. Instead of calls to teach "creation science," one now finds lobbying for "intelligent design" (ID). Guided by the Discovery Institute's "Wedge strategy," the ID movement aims to overturn evolution and what it sees as a pernicious materialist worldview and to renew a theistic foundation to Western culture, in which human beings are recognized as being created in the image of God. Common ID arguments involving scientific naturalism, "irreducible complexity," "complex specified information," and "icons of evolution," have been thoroughly examined and refuted. Nevertheless, from Kansas to Ohio to the U.S. Congress, ID continues lobbying to teach the controversy, and scientists need to be ready to defend good evolution education.

@article{doi101146annurevgenom4070802110400,
    author = "Pennock, Robert T.",
    title = "Creationism and Intelligent Design",
    year = "2003",
    journal = "Annual Review of Genomics and Human Genetics",
    abstract = {Creationism, the rejection of evolution in favor of supernatural design, comes in many varieties besides the common young-earth Genesis version. Creationist attacks on science education have been evolving in the last few years through the alliance of different varieties. Instead of calls to teach "creation science," one now finds lobbying for "intelligent design" (ID). Guided by the Discovery Institute's "Wedge strategy," the ID movement aims to overturn evolution and what it sees as a pernicious materialist worldview and to renew a theistic foundation to Western culture, in which human beings are recognized as being created in the image of God. Common ID arguments involving scientific naturalism, "irreducible complexity," "complex specified information," and "icons of evolution," have been thoroughly examined and refuted. Nevertheless, from Kansas to Ohio to the U.S. Congress, ID continues lobbying to teach the controversy, and scientists need to be ready to defend good evolution education.},
    url = "https://doi.org/10.1146/annurev.genom.4.070802.110400",
    doi = "10.1146/annurev.genom.4.070802.110400",
    openalex = "W2127931101"
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@article{axe2004folds,
    author = "Axe, Douglas D.",
    title = "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds",
    year = "2004",
    journal = "Journal of Molecular Biology",
    url = "https://doi.org/10.1016/j.jmb.2004.06.058",
    doi = "10.1016/j.jmb.2004.06.058",
    number = "5",
    pages = "1295-1315",
    volume = "341",
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Gene duplication is thought to be a major source of evolutionary innovation because it allows one copy of a gene to mutate and explore genetic space while the other copy continues to fulfill the original function. Models of the process often implicitly assume that a single mutation to the duplicated gene can confer a new selectable property. Yet some protein features, such as disulfide bonds or ligand binding sites, require the participation of two or more amino acid residues, which could require several mutations. Here we model the evolution of such protein features by what we consider to be the conceptually simplest route—point mutation in duplicated genes. We show that for very large population sizes N, where at steady state in the absence of selection the population would be expected to contain one or more duplicated alleles coding for the feature, the time to fixation in the population hovers near the inverse of the point mutation rate, and varies sluggishly with the λ th root of 1/ N, where λ is the number of nucleotide positions that must be mutated to produce the feature. At smaller population sizes, the time to fixation varies linearly with 1/ N and exceeds the inverse of the point mutation rate. We conclude that, in general, to be fixed in 10 8 generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 10 9.

@article{behesnoke2004,
    author = "Behe, Michael J. and Snoke, David W.",
    title = "Simulating evolution by gene duplication of protein features that require multiple amino acid residues",
    year = "2004",
    journal = "Protein Science",
    abstract = "Gene duplication is thought to be a major source of evolutionary innovation because it allows one copy of a gene to mutate and explore genetic space while the other copy continues to fulfill the original function. Models of the process often implicitly assume that a single mutation to the duplicated gene can confer a new selectable property. Yet some protein features, such as disulfide bonds or ligand binding sites, require the participation of two or more amino acid residues, which could require several mutations. Here we model the evolution of such protein features by what we consider to be the conceptually simplest route—point mutation in duplicated genes. We show that for very large population sizes N, where at steady state in the absence of selection the population would be expected to contain one or more duplicated alleles coding for the feature, the time to fixation in the population hovers near the inverse of the point mutation rate, and varies sluggishly with the λ th root of 1/ N, where λ is the number of nucleotide positions that must be mutated to produce the feature. At smaller population sizes, the time to fixation varies linearly with 1/ N and exceeds the inverse of the point mutation rate. We conclude that, in general, to be fixed in 10 8 generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 10 9.",
    url = "https://doi.org/10.1110/ps.04802904",
    doi = "10.1110/ps.04802904",
    number = "10",
    pages = "2651-2664",
    volume = "13",
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    x_query = "10.1110/ps.04802904 Simulating evolution by gene duplication of protein features that require multiple amino acid residues Behe, Michael J. and Snoke, David W. 2004",
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@article{pallenmatzke2006,
    author = "Pallen, Mark J. and Matzke, Nicholas J.",
    title = "From The Origin of Species to the origin of bacterial flagella",
    year = "2006",
    journal = "Nature Reviews Microbiology",
    url = "https://doi.org/10.1038/nrmicro1493",
    doi = "10.1038/nrmicro1493",
    number = "10",
    pages = "784-790",
    volume = "4",
    x_citegeist_key = "pallen2006from",
    x_confidence = "1.00",
    x_context = "Michael Behe irreducible complexity bacterial flagellum protein evolution",
    x_input_key = "pallenmatzke2006",
    x_match_score = "1.00",
    x_query = "10.1038/nrmicro1493 From The Origin of Species to the origin of bacterial flagella Pallen, Mark J. and Matzke, Nicholas J. 2006",
    x_source = "crossref:doi:10.1038/nrmicro1493",
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Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. 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.

@article{liu2007flagellum,
    author = "Liu, Renyi and Ochman, Howard",
    title = "Stepwise formation of the bacterial flagellar system",
    year = "2007",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. 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.",
    url = "https://doi.org/10.1073/pnas.0700266104",
    doi = "10.1073/pnas.0700266104",
    number = "17",
    pages = "7116-7121",
    volume = "104",
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    x_query = "10.1073/pnas.0700266104 Stepwise formation of the bacterial flagellar system Liu, Renyi and Ochman, Howard 2007",
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The debate between evolution and intelligent design is usually presented by evolutionary biologists as a clash between science and non-science (creationism and religion) and therefore as a sterile argument which science wins by default. Countering this is intelligent design (ID) and irreducible complexity (IC) which posit that the diversity and complexity of life on earth indicates the hand of a designer, although the nature of that designer is not speculated on. In doing so, proponents of ID and IC bring the argument squarely into the scientific camp and fulfil the requirements of being science, although this is difficult to define. Here, we discuss the claims of ID and IC to provide an alternative to evolution and propose that science can adequately deal with and refute these claims. At the same time, ID and IC fulfil an important role as foils to ‘scientism’ – the belief that science is the best way of answering all questions. In the final analysis, however, despite their value in the debate, ID and IC are not found to be robust or reliable enough to replace evolution as the best way of explaining the diversity of life on earth.

@article{doi104102vev28i194,
    author = "Bateman, Philip W. and Mellis, Josephine",
    title = "Is intelligent design science, and does it matter?",
    year = "2007",
    journal = "Verbum et Ecclesia",
    abstract = "The debate between evolution and intelligent design is usually presented by evolutionary biologists as a clash between science and non-science (creationism and religion) and therefore as a sterile argument which science wins by default. Countering this is intelligent design (ID) and irreducible complexity (IC) which posit that the diversity and complexity of life on earth indicates the hand of a designer, although the nature of that designer is not speculated on. In doing so, proponents of ID and IC bring the argument squarely into the scientific camp and fulfil the requirements of being science, although this is difficult to define. Here, we discuss the claims of ID and IC to provide an alternative to evolution and propose that science can adequately deal with and refute these claims. At the same time, ID and IC fulfil an important role as foils to ‘scientism’ – the belief that science is the best way of answering all questions. In the final analysis, however, despite their value in the debate, ID and IC are not found to be robust or reliable enough to replace evolution as the best way of explaining the diversity of life on earth.",
    url = "https://doi.org/10.4102/ve.v28i1.94",
    doi = "10.4102/ve.v28i1.94",
    openalex = "W2132715969"
}

@article{trotter2014ic,
    author = "Trotter, Meredith V. and Weissman, Daniel B. and Peterson, Grant I. and Peck, Kayla M. and Masel, Joanna",
    title = "Cryptic genetic variation can make “irreducible complexity” a common mode of adaptation in sexual populations",
    year = "2014",
    journal = "Evolution",
    url = "https://doi.org/10.1111/evo.12517",
    doi = "10.1111/evo.12517",
    number = "12",
    pages = "3357-3367",
    volume = "68",
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    x_query = "10.1111/evo.12517 Cryptic genetic variation can make “irreducible complexity” a common mode of adaptation in sexual populations Trotter, Meredith V. and Weissman, Daniel B. and Peterson, Grant I. and Peck, Kayla M. and Masel, Joanna 2014",
    x_source = "crossref:doi:10.1111/evo.12517",
    x_status = "exact"
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Despite its legal and scientific failings, the "intelligent design" (ID) movement has been a public relations success story in the United States. By first creating doubts about the adequacy of evolution to account for the complexity of life, the ID movement has invoked the values of "fairness" and "openness" to argue for inclusion in the classroom and curriculum. In this way, it has attempted to lay claim to the very principles of critical analysis and open discussion at the heart of the scientific enterprise, leaving many researchers in doubt as to how to respond to these challenges. Specific case studies, including the blood-clotting cascade and data from the human genome, show how scientists can have a leading role in deconstructing the arguments advanced in favor of ID. The key to this strategy is remarkably simple and was at the heart of the landmark 2005 Kitzmiller v. Dover trial on ID. It is for researchers to take the claims made by ID proponents seriously, and then to follow them to their logical scientific conclusions. When this is done effectively, the hypothesis of "design" can be publicly falsified in ways that are understandable to laypeople and decision makers in education.

@article{doi101101sqb200974012,
    author = "Miller, Kenneth R.",
    title = "Deconstructing Design: A Strategy for Defending Science",
    year = "2009",
    journal = "Cold Spring Harbor Symposia on Quantitative Biology",
    abstract = {Despite its legal and scientific failings, the "intelligent design" (ID) movement has been a public relations success story in the United States. By first creating doubts about the adequacy of evolution to account for the complexity of life, the ID movement has invoked the values of "fairness" and "openness" to argue for inclusion in the classroom and curriculum. In this way, it has attempted to lay claim to the very principles of critical analysis and open discussion at the heart of the scientific enterprise, leaving many researchers in doubt as to how to respond to these challenges. Specific case studies, including the blood-clotting cascade and data from the human genome, show how scientists can have a leading role in deconstructing the arguments advanced in favor of ID. The key to this strategy is remarkably simple and was at the heart of the landmark 2005 Kitzmiller v. Dover trial on ID. It is for researchers to take the claims made by ID proponents seriously, and then to follow them to their logical scientific conclusions. When this is done effectively, the hypothesis of "design" can be publicly falsified in ways that are understandable to laypeople and decision makers in education.},
    url = "https://doi.org/10.1101/sqb.2009.74.012",
    doi = "10.1101/sqb.2009.74.012",
    openalex = "W2098483115"
}

@article{harms2013biochem,
    author = "Harms, Michael J. and Thornton, Joseph W.",
    title = "Evolutionary biochemistry: revealing the historical and physical causes of protein properties",
    year = "2013",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3540",
    doi = "10.1038/nrg3540",
    number = "8",
    pages = "559-571",
    volume = "14",
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    x_query = "10.1038/nrg3540 Evolutionary biochemistry: revealing the historical and physical causes of protein properties Harms, Michael J. and Thornton, Joseph W. 2013",
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@article{altegoer2014from,
    author = "Altegoer, Florian and Schuhmacher, Jan and Pausch, Patrick and Bange, Gert",
    title = "From molecular evolution to biobricks and synthetic modules: a lesson by the bacterial flagellum",
    year = "2014",
    journal = "Biotechnology and Genetic Engineering Reviews",
    url = "https://doi.org/10.1080/02648725.2014.921500",
    doi = "10.1080/02648725.2014.921500",
    number = "1",
    pages = "49-64",
    volume = "30"
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A longstanding question in science and religion is whether standard evolutionary models are compatible with the claim that the world was designed. In The Compatibility of Evolution and Design, theologian E. V. Rope Kojonen constructs a powerful argument that not only are evolution and design compatible, but that evolutionary processes (and biological data) strongly point to design. Yet Kojonen’s model faces several difficulties, each of which raise hurdles for his understanding of how evolution and design can be harmonized. First, his argument for design (and its compatibility with evolution) relies upon a particular view of nature in which fitness landscapes are “fine-tuned” to allow proteins to evolve from one form to another by mutation and selection. But biological data run contrary to this claim, which poses a problem for Kojonen’s design argument (and, as such, his attempt to harmonize design with evolution). Second, Kojonen appeals to the bacterial flagellum to strengthen his case for design, yet the type of design in the flagellum is incompatible with mainstream evolutionary theory, which (again) damages his reconciliation of design with evolution. Third, Kojonen regards convergent evolution as notable positive evidence in favor of his model (including his version of design), yet convergent evolution actually harms the justification of common ancestry, which Kojonen also accepts. This, too, mars his reconciliation of design and evolution. Finally, Kojonen’s model damages the epistemology that undergirds his own design argument as well as the design intuitions of everyday “theists on the street”, whom he seeks to defend. Thus, despite the remarkable depth, nuance, and erudition of Kojonen’s account, it does not offer a convincing reconciliation of ‘design’ and ‘evolution’.

@article{doi103390rel14070850,
    author = "Dilley, Stephen and Luskin, Casey and Miller, Brian and Reeves, Emily",
    title = "On the Relationship between Design and Evolution",
    year = "2023",
    journal = "Religions",
    abstract = "A longstanding question in science and religion is whether standard evolutionary models are compatible with the claim that the world was designed. In The Compatibility of Evolution and Design, theologian E. V. Rope Kojonen constructs a powerful argument that not only are evolution and design compatible, but that evolutionary processes (and biological data) strongly point to design. Yet Kojonen’s model faces several difficulties, each of which raise hurdles for his understanding of how evolution and design can be harmonized. First, his argument for design (and its compatibility with evolution) relies upon a particular view of nature in which fitness landscapes are “fine-tuned” to allow proteins to evolve from one form to another by mutation and selection. But biological data run contrary to this claim, which poses a problem for Kojonen’s design argument (and, as such, his attempt to harmonize design with evolution). Second, Kojonen appeals to the bacterial flagellum to strengthen his case for design, yet the type of design in the flagellum is incompatible with mainstream evolutionary theory, which (again) damages his reconciliation of design with evolution. Third, Kojonen regards convergent evolution as notable positive evidence in favor of his model (including his version of design), yet convergent evolution actually harms the justification of common ancestry, which Kojonen also accepts. This, too, mars his reconciliation of design and evolution. Finally, Kojonen’s model damages the epistemology that undergirds his own design argument as well as the design intuitions of everyday “theists on the street”, whom he seeks to defend. Thus, despite the remarkable depth, nuance, and erudition of Kojonen’s account, it does not offer a convincing reconciliation of ‘design’ and ‘evolution’.",
    url = "https://doi.org/10.3390/rel14070850",
    doi = "10.3390/rel14070850",
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The rotation of the bacterial flagellum is powered by the MotAB stator complex, which converts ion flux into torque. Despite its central role in flagellar function, the evolutionary origin and structural diversity of this system remain poorly understood. Here, we present the first comprehensive phylogenetic and structural characterization of MotAB and its closest non-flagellar homologs. We gathered homologs from 205 genomes across 27 bacterial phyla, estimated phylogenies, inferred ancestral sequences, and predicted structures for both extant and inferred ancestral proteins using AlphaFold. Our analyses characterized two structurally distinct groups: flagellar ion transporters (FIT) and generic ion transporters (GIT). FIT proteins are structurally conserved, including a characteristic square fold domain and a torque-generating interface (TGI). We further delineate FIT proteins into two subgroups, TGI4 and TGI5s, based on the presence of 4 or 5 short helices within the TGI region. TGI5 motors, such as those found in the Escherichia coli K12 system, are primarily restricted to Pseudomonadota, whereas TGI4 motors, such as the Na + -powered polar motors of Vibrio (PomAB), are distributed across a broader range of bacterial lineages. In contrast, GIT proteins exhibit substantial structural and functional heterogeneity and lack features associated with flagellar motility. Nevertheless, a conserved interaction between the A and B subunits is retained across FIT and GIT proteins, with their corresponding genes typically adjacent to operons. Functional assays in E. coli show that FIT-specific structural elements are indispensable for flagellar motility. Our results suggest that the flagellar stator motor complex evolved once from a common ancestral ion transporter, acquiring unique structural traits to support motility. This work provides a robust framework for understanding the evolutionary diversification of stator complexes and their mechanistic specialization. IMPORTANCE Flagellar motility allows bacteria to propel themselves and direct movement according to environmental conditions. It plays a key role in bacterial pathogenicity and survival. We investigated the molecular and structural diversity of the stator motor proteins that provide the ion motive force to power flagellar rotation. This study uses a comparative approach that integrates phylogenetics, 3D protein structure, motility assays, and ancestral state reconstruction (ASR) to provide insights into the structural mechanisms that first powered the flagellar motor. We provide the first phylogenetic and structural characterization and classification of MotAB and relatives.

@article{puente2025motab,
    author = "Puente-Lelievre, Caroline and Ridone, Pietro and Douglas, Jordan and Amritkar, Kaustubh and Kaçar, Betül and Baker, Matthew A. B. and Matzke, Nicholas J.",
    title = "Evolution and structural diversity of the MotAB stator: insights into the origins of bacterial flagellar motility",
    year = "2025",
    journal = "mBio",
    abstract = "The rotation of the bacterial flagellum is powered by the MotAB stator complex, which converts ion flux into torque. Despite its central role in flagellar function, the evolutionary origin and structural diversity of this system remain poorly understood. Here, we present the first comprehensive phylogenetic and structural characterization of MotAB and its closest non-flagellar homologs. We gathered homologs from 205 genomes across 27 bacterial phyla, estimated phylogenies, inferred ancestral sequences, and predicted structures for both extant and inferred ancestral proteins using AlphaFold. Our analyses characterized two structurally distinct groups: flagellar ion transporters (FIT) and generic ion transporters (GIT). FIT proteins are structurally conserved, including a characteristic square fold domain and a torque-generating interface (TGI). We further delineate FIT proteins into two subgroups, TGI4 and TGI5s, based on the presence of 4 or 5 short helices within the TGI region. TGI5 motors, such as those found in the Escherichia coli K12 system, are primarily restricted to Pseudomonadota, whereas TGI4 motors, such as the Na + -powered polar motors of Vibrio (PomAB), are distributed across a broader range of bacterial lineages. In contrast, GIT proteins exhibit substantial structural and functional heterogeneity and lack features associated with flagellar motility. Nevertheless, a conserved interaction between the A and B subunits is retained across FIT and GIT proteins, with their corresponding genes typically adjacent to operons. Functional assays in E. coli show that FIT-specific structural elements are indispensable for flagellar motility. Our results suggest that the flagellar stator motor complex evolved once from a common ancestral ion transporter, acquiring unique structural traits to support motility. This work provides a robust framework for understanding the evolutionary diversification of stator complexes and their mechanistic specialization. IMPORTANCE Flagellar motility allows bacteria to propel themselves and direct movement according to environmental conditions. It plays a key role in bacterial pathogenicity and survival. We investigated the molecular and structural diversity of the stator motor proteins that provide the ion motive force to power flagellar rotation. This study uses a comparative approach that integrates phylogenetics, 3D protein structure, motility assays, and ancestral state reconstruction (ASR) to provide insights into the structural mechanisms that first powered the flagellar motor. We provide the first phylogenetic and structural characterization and classification of MotAB and relatives.",
    url = "https://doi.org/10.1128/mbio.03824-24",
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Bacterial flagella are rotary nanomachines that enable motility in diverse environments. Although more than 40 genes are required to assemble, operate, and regulate a functional flagellum in model organisms, only 24 flagellar genes have previously been inferred to be conserved across bacteria. This discrepancy raises a fundamental question: 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? Here we combine large-scale profile- and sequence-based searches across a comprehensive bacterial genome set with conserved sequence signatures, gene-tree clustering and flagellar gene-neighborhood evidence to reconstruct the ancestral complexity of bacterial flagellar systems. 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. These findings revise models of early bacterial evolution and overturn the notion that the ancestral flagellum was genetically minimal. Instead, they suggest that the last bacterial common ancestor possessed a highly complex flagellar system comprising more components than are typically found in extant bacteria, many of whose flagella appear to have been shaped by lineage-specific gene loss.

@misc{selcuk2026flagellum,
    author = "Selcuk, Berkay and Andrianova, Ekaterina P. and Beeby, Morgan and Kearns, Daniel B and Erhardt, Marc and Zhulin, Igor B.",
    title = "The last bacterial common ancestor encoded a complex flagellum",
    year = "2026",
    abstract = "Bacterial flagella are rotary nanomachines that enable motility in diverse environments. Although more than 40 genes are required to assemble, operate, and regulate a functional flagellum in model organisms, only 24 flagellar genes have previously been inferred to be conserved across bacteria. This discrepancy raises a fundamental question: 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? Here we combine large-scale profile- and sequence-based searches across a comprehensive bacterial genome set with conserved sequence signatures, gene-tree clustering and flagellar gene-neighborhood evidence to reconstruct the ancestral complexity of bacterial flagellar systems. 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. These findings revise models of early bacterial evolution and overturn the notion that the ancestral flagellum was genetically minimal. Instead, they suggest that the last bacterial common ancestor possessed a highly complex flagellar system comprising more components than are typically found in extant bacteria, many of whose flagella appear to have been shaped by lineage-specific gene loss.",
    url = "https://doi.org/10.64898/2026.06.11.731707",
    doi = "10.64898/2026.06.11.731707",
    x_citegeist_key = "selcuk2026the",
    x_confidence = "1.00",
    x_context = "Michael Behe irreducible complexity bacterial flagellum protein evolution",
    x_input_key = "selcuk2026flagellum",
    x_match_score = "1.00",
    x_query = "10.64898/2026.06.11.731707 The last bacterial common ancestor encoded a complex flagellum Selcuk, Berkay and Andrianova, Ekaterina P. and Beeby, Morgan and Kearns, Daniel B and Erhardt, Marc and Zhulin, Igor B. 2026",
    x_source = "crossref:doi:10.64898/2026.06.11.731707",
    x_status = "exact"
}