Comparative Anatomy Viewer

Take the machine apart

Living things are full of systems that work only when all their parts are present and matched. Pull five of them apart in 3D, remove any part and see what fails, and compare how one designer could reuse a single plan in different environments.

Every model is schematic, and every claim is sourced.

In plain English

  1. The question. Can systems like these be built one small, useful step at a time, as unguided evolution requires? Or do they work only when their parts arrive together, as a designed machine does?
  2. Irreducible complexity is the biochemist Michael Behe's term for a system of several matched parts in which removing any one stops it working. Such a system cannot be built directly by gradual steps, because the earlier, incomplete versions would not work.
  3. How to use it. Choose a model, then rotate, pan and zoom it. Pull it apart with the Explode slider. Click any part to highlight it and read what it does, what happens without it and why that matters. Press Simulate removal to take it out and see what fails.
  4. Not every part is equally essential, and the viewer says so. Each part is marked as causing system failure, severe impairment or degraded function when removed, based on real mutants and clinical cases. Each part also gives the mainstream reply, as the rest of this site does.

Drag to rotate · right-drag or shift-drag to pan · scroll to zoom · click a component. Shows protons streaming through the stator channels (the flow that drives the rotor), flagellin subunits fed into the export gate, and new subunits joining the tip.

The argument, the reply and the response

Bacterial flagellum: the design case

The design argument

Michael Behe (1996) defined an irreducibly complex system as one made of several well-matched, interacting parts that all contribute to the basic function, where removing any one of them stops the system working. Such a system cannot be produced directly by slight, successive modifications of a precursor, because a precursor missing a part does not work. The flagellum is his best-known example.

The flagellum also assembles itself in a fixed order, from the inside out, under a genetic program in which each stage switches on the next (Minnich & Meyer 2004). Design proponents argue that both the machine and its assembly instructions would have to arise together.

The mainstream reply

Critics such as Miller (2004) and Pallen & Matzke (2006) accept that Behe's argument rules out a direct route but not indirect ones, in which parts first served other functions and were later co-opted. Many flagellar parts have relatives in other systems: the export gate in the injectisome, the stators in other ion-driven motors, the ATPase in ATP synthase.

The design response

Design proponents reply that homologous parts are not a demonstrated pathway. Each intermediate would need its own selectable function, the parts would need to be co-adapted to each other, and the assembly order would need to evolve alongside them. No such series has been shown experimentally. The finding that the injectisome descends from the flagellum also removes the most-cited candidate precursor.

What the model simplifies

  • Schematic: proportions are approximate and the filament is shortened about 100-fold. The positions of the export gate and ATPase are simplified.
  • Shown is the E. coli / Salmonella type. Flagella vary between species in stator number, scaffolds and sheaths.
  • Removing a part removes one gene product at a time. Real mutations can be partial, and a few phenotypes are leaky, as noted on each part.

Intelligent design and creation literature

  1. Axe D (2016). Undeniable: How Biology Confirms Our Intuition That Life Is Designed. HarperOne. Book Develops the idea of 'functional coherence': parts arranged in a hierarchy that serves one top-level function.
  2. Behe MJ (1996). Darwin's Black Box: The Biochemical Challenge to Evolution. Free Press. Book
  3. Minnich SA, Meyer SC (2004). Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria. In Design and Nature II (Proceedings of the 2nd International Conference on Design and Nature, Rhodes), WIT Press. Not verified in a citation index.

Primary research and mainstream reviews

  1. Abby SS, Rocha EPC (2012). The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems. PLoS Genetics 8:e1002983. doi:10.1371/journal.pgen.1002983
  2. Berg HC (2003). The rotary motor of bacterial flagella. Annual Review of Biochemistry 72:19–54. doi:10.1146/annurev.biochem.72.121801.161737
  3. Chevance FFV, Hughes KT (2008). Coordinating assembly of a bacterial macromolecular machine. Nature Reviews Microbiology 6:455–465. doi:10.1038/nrmicro1887
  4. Deme JC, Johnson S, Vickery O, et al. (2020). Structures of the stator complex that drives rotation of the bacterial flagellum. Nature Microbiology 5:1553–1564. doi:10.1038/s41564-020-0788-8
  5. Imada K, Minamino T, Tahara A, Namba K (2007). Structural similarity between the flagellar type III ATPase FliI and F1-ATPase subunits. PNAS 104:485–490. doi:10.1073/pnas.0608090104
  6. Johnson S, Furlong EJ, Deme JC, et al. (2021). Molecular structure of the intact bacterial flagellar basal body. Nature Microbiology 6:712–721. doi:10.1038/s41564-021-00895-y
  7. Liu R, Ochman H (2007). Stepwise formation of the bacterial flagellar system. PNAS 104:7116–7121. doi:10.1073/pnas.0700266104
  8. Macnab RM (2003). How bacteria assemble flagella. Annual Review of Microbiology 57:77–100. doi:10.1146/annurev.micro.57.030502.090832
  9. Miller KR (2004). The flagellum unspun: the collapse of 'irreducible complexity'. In Dembski WA, Ruse M (eds) Debating Design, pp. 81–97, Cambridge University Press. doi:10.1017/cbo9780511804823.006
  10. Minamino T, Imada K (2015). The bacterial flagellar motor and its structural diversity. Trends in Microbiology 23:267–274. doi:10.1016/j.tim.2014.12.011
  11. Minamino T, Namba K (2008). Distinct roles of the FliI ATPase and proton motive force in bacterial flagellar protein export. Nature 451:485–488. doi:10.1038/nature06449
  12. Pallen MJ, Matzke NJ (2006). From The Origin of Species to the origin of bacterial flagella. Nature Reviews Microbiology 4:784–790. doi:10.1038/nrmicro1493
  13. Paul K, Erhardt M, Hirano T, Blair DF, Hughes KT (2008). Energy source of flagellar type III secretion. Nature 451:489–492. doi:10.1038/nature06497
  14. Reid SW, Leake MC, Chandler JH, et al. (2006). The maximum number of torque-generating units in the flagellar motor of Escherichia coli is at least 11. PNAS 103:8066–8071. doi:10.1073/pnas.0509932103
  15. Santiveri M, Roa-Eguiara A, Kühne C, et al. (2020). Structure and function of stator units of the bacterial flagellar motor. Cell 183:244–257. doi:10.1016/j.cell.2020.08.016
  16. Thornhill RH, Ussery DW (2000). A classification of possible routes of Darwinian evolution. Journal of Theoretical Biology 203:111–116. doi:10.1006/jtbi.2000.1070
  17. Wagner S, Grin I, Malmsheimer S, et al. (2018). Bacterial type III secretion systems: a complex device for the delivery of bacterial effector proteins into eukaryotic host cells. FEMS Microbiology Letters 365:fny201. doi:10.1093/femsle/fny201
How this viewer is built

Reading the plates

  • Schematic models. The shapes are built from simple geometry with the right parts, in the right number and arrangement. They are not to scale, and each plate lists what it simplifies.
  • Honest failure ratings. Removing a part shows system failure only where the real knock-out, mutant or clinical condition stops the system. The ATPase of the flagellum and the vitreous of the eye, for example, are rated lower, because their loss is survivable.
  • Assembly order. In the flagellum, removing a part also removes the parts that cannot be built without it, as happens when the gene for it is knocked out.
  • Two readings of similarity. The limb plate presents shared structure as reuse of a proven plan by a common designer. The homology claim card on Pillar 3 grades both readings.
  • Sources. Each part cites its sources, split into intelligent-design and creation literature and primary research. DOIs were checked against Crossref. Items marked * could not be confirmed in a citation index.
  • More detail. The flagellum and molecular machines studies in the Lab go further into the proteins and the probability arguments.