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Kathryn Applegate
 on July 29, 2010

Bacterial Flagellum: Irreducibly Complex?

The bacterial flagellum inspires awe and worship—not because it can't be explained by natural processes, but because it can.


If any symbol captures the spirit of the Intelligent Design movement, the bacterial flagellum is it. Beautiful artistic renderings so frequently adorn ID booksblogs, and videos that ID critic Ken Miller has called it the “‘poster-child’ of the modern anti-evolution movement.”

For many decades, the exquisite structure and function of the bacterial flagellum was unappreciated outside the scientific community. We can thank ID leader Michael Behe for changing that. His 1996 book Darwin’s Black Box introduced the world to the flagellum and at the same time exalted it an impassable obstacle to Darwin’s theory of evolution. Behe used the flagellum to illustrate his principle of irreducible complexity—the idea that some features of life are too complex to have developed gradually. These features, Behe argued, are best explained as the product of a Mind.

Today we’ll take a brief look at the flagellum and see why it remains such a powerful icon for the ID movement. In future posts we’ll consider whether the biology of the flagellum makes more sense in light of an evolutionary or a design paradigm.

What is the bacterial flagellum?

Bacteria typically live in aqueous (watery) environments and need to swim to find food and evade enemies. To accomplish this feat, they use a truly marvelous apparatus, the flagellum.

Bacterial flagella are long, whip-like tails protruding from a base tethered in the cell wall. The base contains a rotary motor powered by an electrochemical gradient: a mismatch in the concentration of hydrogen ions across the membrane provides the energy needed to power the motor. The strength of the gradient controls the speed of rotation; typically the propeller tail spins in the range of several hundred to a thousand RPM. As a result, bacteria can travel up to 60 cell lengths per second! The shape of the propeller and the ability of the rotor to change directions allow the bacterium to either swim in a precise direction or randomly tumble to reorient when needed. The number and arrangement of flagella can vary dramatically by species, yielding great diversity in the way bacteria get around, but the basic unit is the same.

While the cartoon above makes the flagellum look simple enough, in reality the machine is quite complicated. Just like an outboard motor, the flagellum has a rotating element (rotor) and a stationary element (stator) embedded in the cell wall and membrane. These elements are connected to the flexible filament by a hook (see cartoon at left). The parts list for these three components includes about 40 different proteins.

A powerful analogy

Why do some argue that the bacterial flagellum is the product of intelligent design rather than evolution? For starters, it looks like something known to be designed—the outboard motor. ID proponents like Behe are not alone in recognizing the parallel. In 1998, structural biologist David DeRosier marveled, “more so than other motors, the flagellum resembles a machine designed by a human.”

The resemblance is so striking, we find it difficult to resist extending the analogy to how the flagellum originated. We know that all outboard motors are designed by intelligent engineers; the parts are carefully crafted to work together for an intended purpose. The bacterial flagellum also has many well-matched components. Together they perform the same job as the outboard motor—swimming. Since the flagellum wasn’t designed by human engineers, it seems only reasonable to infer that it was designed by Someone Else.

But appearances can be deceiving. Look carefully at the photograph below:

It’s beautiful, isn’t it? A light wind blows playfully, rustling the tall grass. The red rocks in the distance radiate heat from the day. I’d love to be there to watch the clouds unfurl in all the majesty of a prairie sunset.

The only problem is, the place doesn’t exist. This piece of art is not a digitally altered photo, or even a realistic-looking painting. It’s a real scene in miniature, created by 26-year-old artist Matthew Albanese out of faux fur (for the grass), cotton wool (clouds) and tile grout (rocks).

Don’t believe me? If you watched Albanese in action, you would immediately understand how he created this amazing image. Check out his studio setup for making realistic cloud images from a suspended tuft of cotton:

What does this have to do with the bacterial flagellum?

The example above illustrates how deceptive appearances can be. The landscape in the photograph appears to be entirely natural, but every detail is meticulously designed. In contrast, the bacterial flagellum looks entirely unnatural. It seems much too complicated to have arisen through random mutation and natural selection. Yet as we will see in future posts, even the most iconic irreducibly complex system, the bacterial flagellum, can be understood in light of these evolutionary processes.

It’s worth pointing out that understanding the creative process magnifies, rather than diminishes, the work of the artist. I don’t imagine many people fly into a rage when they learn how Matthew Albanese creates his beautiful photographs. Rather than feel deceived, they feel amazed! In the same way, when we see how God created all the marvelous forms of life through an extended dance of natural processes—his laws—the appropriate reaction is not dismay, but worship.

In my last post, I explained why the bacterial flagellum remains so powerful an icon for the Intelligent Design (ID) movement: it looks and functions just like the outboard motor, a machine designed by intelligent human engineers. So conspicuous is the resemblance that it seems perfectly logical to infer a Designer for the flagellum.

Yet as we saw, appearances can be deceiving. ID advocates William Dembski and Jonathan Witt agree that “a careful investigator will be on guard against deceiving appearances. The sun looks like it rises in the east and sets in the west, but really the Earth spins on its axis as it revolves around the sun. A healthy skepticism about appearances is vital…To distinguish appearance from reality, the successful investigator must remain open to various possibilities and follow the evidence.”

Despite the strong appearance of special design, most scientists, myself included, believe the evidence points to a gradual development for the bacterial flagellum. We’ll delve into some of that evidence in future posts. First, however, I want to explain how flagella are assembled in bacteria. This amazing process gives me such delight in our Father’s world; I hope it does for you as well.

How does the flagellum assemble?

The bacterial flagellum may look like an outboard motor, but there is at least one profound difference: the flagellum assembles spontaneously, without the help of any conscious agent. The self-assembly of such a complex machine almost defies the imagination. As I showed with an earlier blog on the self-assembly of viruses (much simpler contraptions by comparison), all such phenomena seem astonishing and counterintuitive.

Because the tail of the flagellum extends well beyond the bacterial cell wall, many of its 40 or so components have to be extruded through an export apparatus that assembles first and makes up the base of the final structure. In general, assembly occurs as a linear process, with components in the base coming together first, followed by the formation of the hook, followed by formation of the filament (see figure).

First, the MS-ring (orange) assembles in the inner cell membrane, most likely in conjunction with some of the export proteins (light green; labeled Type III secretion system). The MS-ring serves as housing for the export apparatus and as a mounting plate for the rotor, which will assemble later.

Next, the stator (gray) assembles around the MS-ring, followed by the rotor (light blue; labeled C-ring). The stator remains fixed in the cell’s frame of reference, while the rotor spins; together, these two parts make up the proton-powered motor.

Now that the base of the flagellum is built, most of the remaining parts are assembled from proteins exported through its center. First comes the rod (yellow), made of four different kinds of proteins, guided by a fifth, the “rod cap,” which is believed to help break down the tough bacterial cell wall.

This “rod cap” is then displaced by a “hook cap,” which guides the formation of the hook structure (dark blue). The hook acts as a universal joint to connect the rod and the filament. When the hook reaches its characteristic length, several “junction zones” form, followed by the export of the “filament cap” protein. This cap structure, different than the rod or hook caps, guides the bundling of more than 20,000 copies of a protein called flagellin into a helical tail (dark green; labeled filament).

The helical filament is long and fragile, but breakage is not too serious a concern for the bacterium. Like a lizard, the flagellum can grow a new tail if it breaks, because flagellin proteins continue to move down the central channel from the cell body toward the tip. Other parts of the flagellum are dynamic as well: individual proteins in the rotor and stator, for example, can exchange with freely-diffusing proteins in the membrane. Such activity may be important for the bacterium’s direction-sensing capability.

How do we know all this?

Scientists are pretty clever at teasing out the workings of microscopic machines like the flagellum. The general order of assembly was meticulously worked out by removing individual protein components one at a time and observing what occurred. If you remove the flagellin protein, for instance, you get the base and the hook, but not the tail. This tells us that the tail forms late in the assembly process. If you remove one of the proteins that make up the MS-ring, on the other hand, the motor elements do not assemble and neither does the rest of the flagellum. That’s how we know the MS-ring isn’t just tacked on at the end.

Other scientists have looked at how the timing of the assembly process is controlled at the genetic level. The genes that contain the instructions for making all the protein components of the flagellum are organized in a number of clusters called operons. Each operon is read when its “master sequence” is activated like a light switch. When the switch is flipped, the genes in that particular operon are interpreted by the cell so that the corresponding proteins are made. It turns out that the genes needed to produce proteins in the base of the flagellum are activated first. Once the base is complete, a clever feedback mechanism flips the next switch, activating the next set of genes, which allows later stages of assembly to occur, and so on. (It’s actually more complicated than that, but you get the idea.) So the parts of the flagellum are made “just in time,” shortly before each piece is needed.

Natural forces work “like magic”

Nothing we know from every day life quite prepares us for the beauty and power of self-assembly processes in nature. We’ve all put together toys, furniture, or appliances; even the simplest designs require conscious coordination of materials, tools, and assembly instructions (and even then there’s no guarantee that we get it right!). It is tempting to think the spontaneous formation of so complex a machine is “guided,” whether by a Mind or some “life force,” but we know that the bacterial flagellum, like countless other machines in the cell, assembles and functions automatically according to known natural laws. No intelligence required.1

Video animations like this one by Garland Science beautifully illustrate the elegance of the self-assembly process (see especially the segment from 2:30-5:15). Isn’t it extraordinary? When I consider this process, feelings of awe and wonder well up inside me, and I want to praise our great God.

Several ID advocates, most notably Michael Behe, have written engagingly about the details of flagellar assembly. For that I am grateful—it is wonderful when the lay public gets excited about science! But I worry that in their haste to take down the theory of evolution, they create a lot of confusion about how God’s world actually operates.

When reading their work, I’m left with the sense that the formation of complex structures like the bacterial flagellum is miraculous, rather than the completely normal behavior of biological molecules. For example, Behe writes, “Protein parts in cellular machines not only have to match their partners, they have to go much further and assemble themselves—a very tricky business indeed” (Edge of Evolution, 125-126). This isn’t tricky at all. If the gene that encodes the MS-ring component protein is artificially introduced into bacteria that don’t normally have any flagellum genes, MS-rings spontaneously pop up all over the cell membrane. It’s the very nature of proteins to interact in specific ways to form more complex structures, but Behe makes it sound like each interaction is the product of special design.

Previously, 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.

About the author

Kathryn Applegate

Kathryn Applegate

Kathryn Applegate is a former Program Director at BioLogos. While working on her PhD in computational cell biology at  Scripps Research (La Jolla, CA), she became passionate about building bridges between the church and the scientific community. In 2010, she joined the BioLogos staff where she has the privilege of writing, speaking, and working with a wide variety of scholars and educators to develop new science and faith resources. Kathryn co-edited with Jim Stump How I Changed My Mind About Evolution (InterVarsity Press, 2016). Among many other projects during her time at BioLogos, Kathryn most recently led the development of Integrate, a new science and faith curriculum for home educators and teachers at Christian schools. Kathryn and her family enjoy exploring the beaches and state parks of Michigan and are helping to plant a new PCA church in Grand Rapids.