Background

Introduction

The article "Evolution in (Brownian) space: a model for the origin of the bacterial flagellum" is an attempt to put forward a reasonably detailed model for the evolutionary origin of the bacterial flagellum. The flagellum is a complex structure that some bacteria use for swimming, and it has featured prominently in the arguments of the "Intelligent Design" movement. The article is long and somewhat technical, and may not be readily accessible to many readers. This page attempts to give readers some background, and recommend some introductory material that will (hopefully) make the full article much more digestible. Suggestions for further improvements along these lines are welcome.

Background

For some time, advocates of "Intelligent Design" (ID) have been promoting Mike Behe's "irreducible complexity" argument. Behe argues that biological systems with multiple required components could not have evolved gradually, because intermediates lacking components would be nonfunctional. The argument has been answered in general terms numerous times (see http://www.talkorigins.org/faqs/behe.html for a survey), and detailed treatments of the evolution of specific "irreducibly complex" biochemical systems are now available in the case of blood clotting (see Ken Miller's article on the Evolution of Vertebrate Blood Clotting) and the immune system (see Matt Inlay's very detailed article Evolving Immunity).

However, the ID movement's favorite example of irreducible complexity, the bacterial flagellum, has not received similar treatment. The bacterial flagellum was only discussed briefly in Behe's Darwin's Black Box, but perhaps because of the counterarguments and literature available on the evolution of other systems, the bacterial flagellum soon became the favorite example of irreducible complexity, and has ascended to near-iconic status for the ID movement. Part of the problem with discerning the evolutionary origin of the bacterial flagellum is that the flagellum is billions of years older than Behe's other example IC systems. With blood-clotting and the immune system, homologs of many of the proteins have been well-known for decades. As the phylogeny of multicellular animals is reasonably well understood, the identification of ancestral systems is not too difficult. In bacteria, on the other hand, phylogeny is confused, and for a long time not many homologs of flagellar proteins were known. Only recently have enough homologs of flagellar proteins been identified to make it possible to piece together a reasonable scenario.

The question of the origin of the bacterial flagellum has intrigued me for some time, and it always struck me as a topic that "someone" should examine in more detail. It seemed clear that more could be said on the topic than "flagella don't fossilize." For awhile I followed debates on the topic, and slowly accumulated relevant literature. With the publication of thorough, up-to-date reviews of flagellum function and assembly by Berg (2003) and Macnab (2003), I realized that I probably had enough information to give it a try, and made it my extracurricular summer project. It took rather longer than I planned to synthesize the data into an article, but a version is finally done and I think that several of the findings advance our understanding of flagellar origins significantly.

Like any scientific model, this one will have some inadequacies. Some of them are due to our basic lack of knowledge: the functions of many flagellar proteins are uncharacterized, the molecular mechanisms of motor function and protein export are vague, and large-scale bacterial phylogeny is unresolved. There may also be some errors attributable to the inexpert nature of the author; formally I have nothing more than an undergraduate background in biochemistry, although I daresay that I've read enough of the relevant literature to at least avoid major errors, and even to correct a few errors in the peer-reviewed literature. As no one has ever really given the topic of flagellar origins the serious treatment it deserves, there is currently no such thing as an expert. If the article is deemed sufficiently provocative, some of this material may eventually find its way into a journal; however, the article is a bit long and unconventional compared to most journal articles, so releasing it first on the web seemed appropriate. Comments, corrections, suggestions for improvement, and suggestions about more formal publication venues are welcome and should be directed to my email (above). Alternatively, you may post comments at the EvoWiki page for Comments on "Evolution in (Brownian) space".

Introductory resources

As not every reader will be very familiar with the relevant molecular systems and proteins, I have included some background links that should help bring readers up to speed. To have any hope of following the article, readers should read and understand the below material first. Berg's popular article is particularly recommended as a starting point.

Flagellum

• A good short introduction to the three unrelated kinds of "flagella" can be found at Wikipedia: flagellum
• A detailed popular article on the bacterial flagellum by Howard Berg
• Chapter 15 of Alberts et al. (1994), Molecular Biology of the Cell, 3rd edn.
• Section 34.4 of Berg, Tymoczko, and Stryer (2002), Biochemistry

F₁F₀ ATP synthetase (also known as ATP synthase or ATPase)

• Hongyun Wang's webpage on his ATP synthase research
• Chapter 14 of Alberts et al. (1994), Molecular Biology of the Cell, 3rd edn.
• Section 18.4 of Berg, Tymoczko, and Stryer (2002), Biochemistry

Life in the viscous microscopic world of bacteria

• Life at Low Reynolds Number by Purcell (1976)

Intelligent Design arguments about the flagellum

The article is an attempt at a "straight" science piece, with no attempt made to address the various tenditious arguments and equivocating definitions of ID proponents. For articles discussing ID arguments about the flagellum specifically, see the articles below by Miller and Musgrave. At some point I may attempt to write an article comparing ID proponents' wild misconceptions about evolutionary models of flagellar origins (e.g., Bill Dembski's use of cake-baking as an analogy for the evolutionary origin of the flagellum) to an actual serious evolutionary model of flagellar origins. For the moment, however, I encourage readers to look up some of the ID proponents' articles on the topic, and to compare them to the proposed model. Relevant links are given below.

• Behe on the flagellum in Darwin's Black Box (1996)
• Molecular Machines and Irreducible Complexity at the Access Research Network
• Dembski on the flagellum: Chapter 5, No Free Lunch (2002)
• Bracht, The Bacterial Flagellum: A Response to Ursula Goodenough (2002)
• Mike Gene, Evolving the Bacterial Flagellum Through Mutation and Cooption (2001-2)

Rebuttals to ID flagellum arguments

Miller, Kenneth (2003) "Answering the biochemical argument from design." In: Manson, N. (Ed.), God and design: the teleological argument and modern science, Routledge, London, pp. 292-307.

Miller, Kenneth (2004) The Flagellum Unspun: The Collapse of Irreducible Complexity." In: Dembski, W., and Ruse, M. (Eds.), Debating Design: from Darwin to DNA, Cambridge University Press, New York, pp. 81–97.

• See also Ken Miller's website. Dembski responded to Miller in an online essay Still Spinning Just Fine on his Design Inference website

Musgrave, Ian (2004). "Evolution of the Bacterial Flagellum." In: Young, M., and Edis, T. (Eds.), Why Intelligent Design Fails: A Scientific Critique of the Neocreationism, Rutgers University Press, Piscataway, N.J., pp. 72-84.

Matzke, Nicholas J. (2004). "Behe's Blunder: Irreducible Complexity and Change of Function." Bay Area Skeptics Information Sheet, pp. 7-9. April-June 2004.

Pallen MJ, Matzke NJ. (2006). “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology, 4(10), 784-790. October 2006. (Published online ahead of print on September 5, 2006.) [PubMed] [Journal] [DOI] [Google Scholar]

• Nick Matzke's post on the Panda's Thumb blog, "Flagellum evolution in Nature Reviews Microbiology" summarizes a key point in the article for readers and contains further discussion in the comments. See also the PT flagellum evolution section.