Self-Assembly of the Bacterial Flagellum: No Intelligence Required

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August 19, 2010 Tags: Design

Today's entry was written by Kathryn Applegate. You can read more about what we believe here.

Self-Assembly of the Bacterial Flagellum: No Intelligence Required

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. Next time I’ll review some other examples from the ID literature where assembly is discussed in confusing or misleading ways.

Notes:

1. Some would say this kind of statement violates the sovereignty of God. Not so! I fully believe God is sovereign, but I don’t take that to mean he himself carries out everything that happens inside each cell.

References

Macnab, Robert M. “How Bacteria Assemble Flagella.” Annu. Rev. Microbiol. 57:77-100. 2003.


Kathryn Applegate is Program Director at The BioLogos Foundation. She received her PhD in computational cell biology at The Scripps Research Institute in La Jolla, Calif. At Scripps, she developed computer vision software tools for analyzing the cell's infrastructure, the cytoskeleton.

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nedbrek - #26207

August 19th 2010

How does observing “self-assembly” lead to the conclusion “no designer”?  A computer boots itself just fine without intelligence, should we conclude they are not designed?


Charlie - #26213

August 19th 2010

nedbrek,

Research the similarities between the flagellum and a molecular syringe in some bacteria.  They share many of those same proteins.  This shows how it’s possible the flagellum could have evolved from the syringe.  As far as the assembly goes, I think she’s just making the point that no intelligence is needed for assembly.


Bill Pratt - #26216

August 19th 2010

I’m afraid the author of this post doesn’t understand what ID advocates are saying.  They are not saying that some kind of mind has to assemble each and every bacteria flagellum.  They are saying that an intelligent agent is behind the original complex specified information necessary for a bacteria flagellum to assemble.  Once information is put into a system, and that system can successfully communicate that information on its own, the agent is no longer needed to superintend the process. 

Nedbrek’s comment about a computer booting up is a perfect example.  The original designer of the computer doesn’t have to supervise the booting up of every computer after the first one was designed.


nedbrek - #26217

August 19th 2010

Charlie, the words “red” and “reed” are very similar.  It’s easy to imagine circumstance where one might be typed (or written) instead of the other.

However, given documents with one word or the other, how do we know which is the original?

Evolutionists assume the simple comes first.  How can we know this?


Ben - #26220

August 19th 2010

Nedbrek and Bill,

“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.”

Kathryn’s getting into the evidence for gradual development of the flagellum in future posts.  She’s choosing to use the synthesis of the flagellum as an introduction for that evidence.  Some arguments take a while to unpack for an audience outside of a specialized field (I’m no molecular biologist, either).


Bill Pratt - #26226

August 19th 2010

Ben,
I appreciate that these arguments take time to unpack.  I am looking forward to the future posts.  But I think a fair reading of this particular post leads one to believe that ID theorists are arguing for some kind of intelligent agent who is actively designing or guiding the assembly of each and every bacteria flagella.  That is not what ID theorists are saying at all.  Am I misunderstanding the thrust of the post? 

How should I interpret this sentence by Dr. Applegate?

“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.”


nedbrek - #26227

August 19th 2010

Ben, I understand arguments take time to unpack.  However, my argument is orthogonal to any possible argument an evolutionist can make.


CM - #26228

August 19th 2010

It seems to me that the example of the computer being switched on here doesn’t quite work. For a computer to boot, it needs to be switched on every time by someone who knows how, and further, each one requires its own assembly. There’s an energy and intentional input required at several levels (i.e. to turn it on and put it together). As Bill points out, even ID proponents don’t think a creator or designer is involved every time a flagellum is assembled. And as Dr. Applegate points out, even cells that don’t naturally contain these structures can produce them faithfully if provided only the genes for the necessary components (i.e. no hypothetical sophisticated assembly apparatuses, comparable to the person/machine assembling a computer). Rather than hypothesizing a designer which interacted on MANY occasions with nature to create natural order and function (as ID seems to), it makes far more sense to me (and is supported by things we can observe) to put the creator or “designer” at the head of these processes, as having ordained the natural forces (laws and principles of protein assembly, folding, function for example – the universal movement toward increased entropy).


CM - #26229

August 19th 2010

(cont.)
THESE are ther fruits of the Creator that allow, guide, and sustain these events. Everything biology needs to exist and function appears – to the best of our God-given educated eyes and minds – to have been provided in a rational and elegant universe. No further assembly required. Thanks for this article Dr. Applegate! Looking forward to more.


nedbrek - #26231

August 19th 2010

CM, I am no supporter of ID.  I believe God directly created creatures in sets of kinds, and that the creatures we find today are descended from those creatures.

It’s interesting that you mention entropy.  Entropy and information theory indicate that the amount of information can only be reduced by noise.  Evolution proposes the exact opposite, that information comes from the noise of the environment.


Roger A. Sawtelle - #26232

August 19th 2010

Dawkins and friends talk about genetic mutation as the source of evolution.  This example seems to show that evolution takes place when organisms interact with each other.  Are they the same or are they like American football and soccer also called football?  They are both sports played on a field with a ball and have some other superficial resemblances, but are fundamentally different. 

As I understand it ID is flawed because it maintains that God must intervene to produce the complexity found in the flagellum, et al.  I would maintain that ecological symbiosis has been shown to be the source of the development of complexity in life forms.  This is important because it maintains the integrity of both points of view it seems to me.


Roger A. Sawtelle - #26233

August 19th 2010

Part 2:

Evolution in the broad sense is true in that ecological evolution maintains that it is a real, natural process.  Intelligent design in the broad sense is true that evolution is based on interaction between organism, rather than gene mutation, ala Richard Dawkins.  Still God must be able to create complexity through natural processes that God created and God called good.  God does not lose sovereignty by delegating responsibilities to the processe divinely created and to humans God also created. 

“All things work together for good for those who love God.”  (Romans 8:28 NRSV)  If Darwin’s understanding of life as conflict were true, this does not make sense.  If ecology’s understanding of life as mutualism is true, it make lots of sense.


Michael Fugate - #26237

August 19th 2010

A good place to learn about idea that no designer is needed is to view Daniel Dennett’s talk from the Chicago Darwin Fest available at:
http://darwin-chicago.uchicago.edu/List of Video Talks.html


Scott Mapes - #26238

August 19th 2010

This whole debate has been quite enlightening and has reminded me of a parallel in theology.  There are times in some theological discussions in which I have engaged where it is clearly evident that the two opposing sides (for example, Calvinism vs. Arminianism, Western vs. Eastern, modern vs. postmodern) are far closer to one another than they would care to admit.  With Bill Pratt’s clarification in mind regarding ID, I wonder if this matter of “design” (however one may define it) may be an area where our disagreements might simply be a matter of definitions.  Just a thought from a guy whose only “scientific” achievement was winning the Bausch and Lomb High Schol Science Award in 1978!


Mike Gene - #26239

August 19th 2010

Front-loading and self-organization are two phenomena that can co-exist in a synergistic fashion. Self-organization may be part of front-loading and front-loading can build on or exploit self-organization.


Bill Pratt - #26243

August 19th 2010

Scott,
I have been wondering the same thing.  ID theorists make no claims about when or how intelligent agents have input complex specified information (CSI) into biological organisms.  They are merely arguing that there is CSI present in biological organisms and that the only known source for CSI is intelligent agency.  Somewhere in history, a mind had to be involved.

When I see theistic evolutionists (TE’s) saying that God implanted the capability for bacterial flagella to develop at creation, are they not making the same general claim?  Both groups are claiming a mind had to be involved, that completely materialistic explanations for the origin of bacteria flagella are incomplete.

The main difference I can see is that the ID folks have developed some scientific theories to test whether there is CSI present in specific biological systems.  I assume that TE’s would deny that this is possible to do.


RBH - #26247

August 19th 2010

Roger A. Sawtelle wrote

Dawkins and friends talk about genetic mutation as the source of evolution.

No, in fact they don’t.  Genetic mutation, according to Dawkins, et al., and essentially every other evolutionary biologist, is the root source of variation, and natural selection operates on that variation to produce adaptations.  Both components together, variation and selection, are the “source” of evolution.  Either alone is not.


RBH - #26248

August 19th 2010

Bill Pratt wrote

ID theorists make no claims about when or how intelligent agents have input complex specified information (CSI) into biological organisms.

Which is why it is ludicrous to treat ID as an “explanation.”  An “explanation” that doesn’t address the “when” and “how” questions is vacuous.

Incidentally, can anyone refer me to an ID source where the actual CSI of any biological structure is calculated?  I’ve read a whole lot of ID literature and have never seen that done.  Not even Dembski did it in No Free Lunch.  A core metric like that must have an operational definition somewhere, but so far I’ve not found one.


Mike Gene - #26252

August 19th 2010

Hi RBH,

“Incidentally, can anyone refer me to an ID source where the actual CSI of any biological structure is calculated?  I’ve read a whole lot of ID literature and have never seen that done.  Not even Dembski did it in No Free Lunch.  A core metric like that must have an operational definition somewhere, but so far I’ve not found one.”

Good question.  You’ve not seen such a calculation because it probably cannot be done.  Specification is something that requires insight into the designer’s mind (either direct insight or indirect insight through experience with the designer’s previous work).  How are we supposed to know that a particular pattern was actually a specification that originated from a mind?  Without independent evidence of the designer (our controls), we cannot escape the subjective dimension of a design inference.


Roger A. Sawtelle - #26264

August 19th 2010

RBH,

Thank you for your clarification.  My point was that mutation comes first and natural selection accepts or vetos the change.  Whether this process is based on adaptation is not clear.  Dawkins claims that it is not and Dennett rails against those who are “adaptionists.” 

This example of flagelleum indicates that change does not take place by mutation, which is spontaneous changes in the DNA caused by such things as radiation and mistakes in the division and uniting process of the DNA.  This is the basis of the “random” and gradual nature of evolution. 

Symbiosis points to changes in life forms by the uniting of either two life forms to form a new life form like the lichens, or sharing of DNA to form new structures as in the flagelleum (or maybe using borrowed DNA for a new purpose)  or having symbiots living within another organism as humans do in many forms or of course two life forms coevolving to help one another.  None of these changes involve mutation, but they are all a part of evolution, demonstrating the weakness, if not the failure, of Darwinian thought to explain how evolution really functions.


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