@article{axe2004folds,
  author = {Axe, Douglas D.},
  title = {Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds},
  journal = {Journal of Molecular Biology}, year = {2004}, volume = {341}, number = {5}, pages = {1295--1315},
  doi = {10.1016/j.jmb.2004.06.058}, url = {https://doi.org/10.1016/j.jmb.2004.06.058}
}
@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},
  journal = {Protein Science}, year = {2004}, volume = {13}, number = {10}, pages = {2651--2664},
  doi = {10.1110/ps.04802904}, url = {https://doi.org/10.1110/ps.04802904}
}
@article{pallenmatzke2006,
  author = {Pallen, Mark J. and Matzke, Nicholas J.},
  title = {From The Origin of Species to the origin of bacterial flagella},
  journal = {Nature Reviews Microbiology}, year = {2006}, volume = {4}, number = {10}, pages = {784--790},
  doi = {10.1038/nrmicro1493}, url = {https://doi.org/10.1038/nrmicro1493}
}
@article{liu2007flagellum,
  author = {Liu, Renyi and Ochman, Howard},
  title = {Stepwise formation of the bacterial flagellar system},
  journal = {Proceedings of the National Academy of Sciences}, year = {2007}, volume = {104}, number = {17}, pages = {7116--7121},
  doi = {10.1073/pnas.0700266104}, url = {https://doi.org/10.1073/pnas.0700266104}
}
@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},
  journal = {Evolution}, year = {2014}, volume = {68}, number = {12}, pages = {3357--3367},
  doi = {10.1111/evo.12517}, url = {https://doi.org/10.1111/evo.12517}
}
@article{harms2013biochem,
  author = {Harms, Michael J. and Thornton, Joseph W.},
  title = {Evolutionary biochemistry: revealing the historical and physical causes of protein properties},
  journal = {Nature Reviews Genetics}, year = {2013}, volume = {14}, number = {8}, pages = {559--571},
  doi = {10.1038/nrg3540}, url = {https://doi.org/10.1038/nrg3540}
}
@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},
  journal = {mBio}, year = {2025}, volume = {16}, number = {10},
  doi = {10.1128/mbio.03824-24}, url = {https://doi.org/10.1128/mbio.03824-24}
}
@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}, doi = {10.64898/2026.06.11.731707}, url = {https://doi.org/10.64898/2026.06.11.731707}
}
@article{weber1998biochemical,
  author = {Weber, Bruce H.}, title = {Biochemical Complexity: Emergence or Design?},
  journal = {Rhetoric and Public Affairs}, year = {1998}, doi = {10.1353/rap.2010.0113}, url = {https://doi.org/10.1353/rap.2010.0113}
}
@article{boudry2010irreducible,
  author = {Boudry, Maarten and Blancke, Stefaan and Braeckman, Johan},
  title = {Irreducible Incoherence and Intelligent Design: A Look into the Conceptual Toolbox of a Pseudoscience},
  journal = {The Quarterly Review of Biology}, year = {2010}, volume = {85}, number = {4},
  doi = {10.1086/656904}, url = {https://doi.org/10.1086/656904}
}
@article{pennock2003creationism,
  author = {Pennock, Robert T.}, title = {Creationism and Intelligent Design},
  journal = {Annual Review of Genomics and Human Genetics}, year = {2003}, volume = {4}, pages = {143--163},
  doi = {10.1146/annurev.genom.4.070802.110400}, url = {https://doi.org/10.1146/annurev.genom.4.070802.110400}
}
@article{miller2009deconstructing,
  author = {Miller, Kenneth R.}, title = {Deconstructing Design: A Strategy for Defending Science},
  journal = {Cold Spring Harbor Symposia on Quantitative Biology}, year = {2009},
  doi = {10.1101/sqb.2009.74.012}, url = {https://doi.org/10.1101/sqb.2009.74.012}
}
@article{dilley2023relationship,
  author = {Dilley, Stephen and Luskin, Casey and Miller, Brian and Reeves, Emily},
  title = {On the Relationship between Design and Evolution}, journal = {Religions}, year = {2023}, volume = {14}, number = {7},
  doi = {10.3390/rel14070850}, url = {https://doi.org/10.3390/rel14070850}
}
@article{namba1997molecular,
  author = {Namba, Keiichi and Vonderviszt, Ferenc}, title = {Molecular architecture of bacterial flagellum},
  journal = {Quarterly Reviews of Biophysics}, year = {1997}, volume = {30}, number = {1}, pages = {1--65},
  doi = {10.1017/S0033583596003319}, url = {https://doi.org/10.1017/S0033583596003319}
}
@article{beck2014mutational,
  author = {Summers, Robert L. and Dave, Anurag and Dolstra, Tegan J. and Bellanca, Sebastiano and Marchetti, Rosa V. and Nash, Megan N. and Richards, Sashika N. and Goh, Valerie and Schenk, Robyn L. and Stein, Wilfred D. and Kirk, Kiaran and Sanchez, Cecilia P. and Lanzer, Michael and Martin, Rowena E.},
  title = {Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite's chloroquine resistance transporter},
  journal = {Proceedings of the National Academy of Sciences}, year = {2014}, volume = {111}, number = {17}, pages = {E1759--E1767},
  doi = {10.1073/pnas.1322965111}, url = {https://doi.org/10.1073/pnas.1322965111}
}
