Bacterial Flagellum: Assembly vs. Evolution

| By on Endless Forms Most Beautiful

Last time, I described how the bacterial flagellum spontaneously assembles in an orderly way, without the help of a conscious agent. I didn’t intend to suggest that ID advocates argue otherwise, but I did say that they often write about assembly in unclear and misleading ways. Today I want to justify this assertion with some examples.

ID advocates commonly point to the self-assembly of complex structures like the flagellum to argue that they couldn’t have been produced by evolutionary mechanisms. In his 2007 book The Edge of Evolution, Michael Behe includes an entire appendix on how the bacterial flagellum assembles to make this connection. In the first paragraph, he writes:

The need to spontaneously assemble intricate machinery enormously complicates any putative Darwinian explanation for the foundation of life, which has to select from tiny, random steps…In a cellular nanobot, where machines run the show without the help of conscious agents, everything has to be assembled automatically (p261).

How the flagellum originated and how it assembles are of course two different (though not completely unrelated) questions, but the distinction is lost in much of the ID literature. According to ID, assembly supposedly presents a significant hurdle for the evolutionary origin of the flagellum because evolution has to account not only for the production of all the parts, but for the manufacturing process as well. Following Behe, Jonathan Witt, Senior Fellow at the Discovery Institute, assumes that the basic forces of nature can’t produce complex structures that self-assemble:

[E]ven if nature had on hand all the right protein parts to make a bacterial flagellum, something would still need to assemble them in precise temporal order, the way cars are assembled in factories. He goes on to describe how the genetic instructions for the particular protein components are interpreted sequentially, in the order that the parts are needed. This added layer of complexity, on top of an already irreducibly complex structure (the flagellum itself), supposedly points to an even more sophisticated level of engineering than was previously appreciated.

Manmade vs. molecular machines: same or different?

The rhetorical effectiveness of this line of reasoning rests on the comparison between manmade machines or buildings and molecular ones. The argument seems especially compelling because the process of designing and assembling a car or building is shot through with design language: planning, foresight, blueprints, etc. For instance, in a chapter called What Darwinism Can’t Do, Behe regales us with detailed descriptions of how cilia1and bacterial flagella are built. He likens the process to the construction of an observation tower at his university called Iacocca Hall:

Like all such buildings, it was built in what could be called a “bottom up-top down” fashion. By bottom up I mean that of course the foundation of the building had to be poured first, the ground floor next, and so on…By top down I mean that the building was planned. Blueprints were followed, supplies ordered, ground purchased, equipment moved in, and so on—all with the final structure of the observation tower in mind (p85).

It turns out that the construction of big structures in the cell requires the same degree of planning—the same foresight, the same laying in of supplies, the same sophisticated tools—as did the building of the observation tower at Iacocca Hall. Actually, it requires much more sophistication, because the whole process is carried out by unseeing molecular robots rather than the conscious construction workers who assemble everyday buildings in our everyday world (p87).

The construction of complex structures in the cell, Behe says, requires even more planning and sophistication than the construction of a manmade building. Who, we may ask, does all this planning? Behe certainly doesn’t mean there’s a miniature foreman in the cell directing the assembly (he refers to unseeing molecular robots, after all) but it’s hard not to imagine a “man behind the curtain,” to borrow an image from The Wizard of Oz. He is speaking of an Intelligent Designer, who must have pre-loaded the bacterium with all the instructions it would need to construct the flagellum.

In our everyday experience, the more intelligence and design that goes into the manufacturing process, the less conscious intervention is needed to assemble a complex machine. Cars can be made on an assembly line almost entirely by unthinking robots, but only because the robots themselves are intelligently designed. Cellular machines like the flagellum assemble spontaneously with no conscious intervention. Thus, by this logic, the control processes that guide assembly must be the work of a truly superior Designer.

But are we justified in applying this kind of planning/foresight language to what goes on inside the cell? Just how far can we take the parallel of molecular machines with manmade ones? I would argue that the differences are real and substantial. How often have you seen a manmade machine assemble and even repair itself, as the flagellum does? Or a whole factory reproduce itself, as the cell does? Perhaps these amazing features of life point not to a specific design event but to the fact that God’s laws that govern biology are even more powerful and creative than we previously recognized.

Confusing conflation of assembly and evolution in the ID literature

While scientists frequently liken the cell to a factory that produces complicated machines, they rightly recognize the limits of the comparison: the cell is decidedly unlike a factory when it comes to how assembly actually happens. As biophysicist Sarah Woodson put it in a 2005 Nature commentary,

The cell’s macromolecular machines contain dozens or even hundreds of components. But unlike man made machines, which are built on assembly lines, these cellular machines assemble spontaneously from their protein and nucleic-acid components. It is as though cars could be manufactured by merely tumbling their parts onto the factory floor.

Woodson’s statement is powerful because it points out how unintuitive it is that molecular machines assemble from random collisions between molecules. But Behe uses this quote in a peculiar way to brush aside one “unintelligent” alternative to evolution by natural selection, called self-organization theory:

Some very simple rush hour traffic patterns are self-organizing, but self-organization does not explain where very complex carburetors, steering wheels, and all the other physical parts come from, let alone how “cars could be manufactured by merely tumbling their parts onto the factory floor” (p159).

I say this is peculiar because neither evolution nor self-organization theory claims to explain how all the protein parts physically come together to assemble a functioning machine like the flagellum. (They do aim to explain where the parts come from in the first place.) Perhaps unwittingly, Behe attacks a straw man when he says these theories cannot answer a question they don’t claim to address in the first place.

At the end of his appendix on how the bacterial flagellum assembles, Behe again conflates evolution and assembly in a misleading way. First he describes a real debate in the scientific literature about how the bacterial flagellum is related to a similar structure in the cell, called the type III secretory system (TTSS). He then proclaims that “none of the papers seriously addresses how either structure could be assembled by random mutation and natural selection.” As evidence he writes of a 2003 review article entitled, How Bacteria Assemble Flagella:

How did such a pathway [of flagellum assembly] evolve by random mutation? In the approximately seven-thousand-word review, the phrase “natural selection” does not appear. The word “evolution” or any of its derivatives occurs just once, in the very last sentence of the article. Speaking of the flagellum and the TTSS, Macnab writes: “Clearly, nature has found two good uses for this sophisticated type of apparatus. How [the TTSS and the flagellum] evolved is another matter…” Darwinism has little more of substance to say.

Behe pulls the quote grossly out of context. Macnab was not aiming to describe what is known about the evolution of the flagellum. It is “another matter”, not because nothing is known about it, but because it is a different subject entirely from how assembly works. It is therefore not surprising that the words “evolution” and “natural selection” appear so infrequently! Thus the flagellum is another example—like the antibody generation system—in which Behe fails to seriously engage with the scientific literature, giving the impression that there isn’t any on the topic.

Next time we’ll begin to look at the irreducible complexity argument in detail and discuss whether it in fact does pose a problem for the gradual development of the bacterial flagellum.


1. Cilia are molecular machines every bit as marvelous and complex as bacterial flagella. While the two get about equal time in Michael Behe’s books, cilia aren’t nearly as famous as flagella. Why? Perhaps because cilia do several different jobs in the body and are thus harder to explain in a sound bite. Flagella, on the other hand, do one job—help bacterial swim—and, in the words of ID advocate Jonathan Witt, “images of the flagellum practically scream design.” Cilia might also be less famous because they’re less “family friendly:” the wriggling tails of sperm are actually long cilia! Making sperm the icon for the ID movement would not exactly have been a good marketing strategy.




Applegate, Kathryn. "Bacterial Flagellum: Assembly vs. Evolution" N.p., 9 Sep. 2010. Web. 11 December 2018.


Applegate, K. (2010, September 9). Bacterial Flagellum: Assembly vs. Evolution
Retrieved December 11, 2018, from /blogs/kathryn-applegate-endless-forms-most-beautiful/bacterial-flagellum-assembly-vs-evolution

About the Author

Kathryn Applegate

Kathryn Applegate is Resources Editor at BioLogos. She received her PhD in computational cell biology at The Scripps Research Institute in La Jolla, Calif. At Scripps, she developed computer vision tools for analyzing the cell's infrastructure, the cytoskeleton. Kathryn joined the BioLogos staff in 2010.

More posts by Kathryn Applegate