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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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R Hampton - #26272

August 19th 2010

RBH,
You might find this interesting (you can download the paper in full at the link):

An Algorithmic Information Theory Critique of Statistical Arguments for Intelligent Design
Sean D Devine, September 15 2009 (rev 4)

... Dembski’s decision process first asks whether a structure as an outcome can be explained by the regularity of natural laws ... The Dembski decision template, which eliminates natural processes in the first decision step, is flawed, forcing a design outcome when none is warranted. Dembski also introduces a 4th law of thermodynamics, the law of conservation of information to argue information cannot emerge from random processes. However if a more robust measure of information based on algorithmic entropy is used, the so called 4th law is seen to contain no more than the second law of thermodynamics. In conclusion, despite the good intentions, the approach fails to offer any new insights into the adequacy of evolutionary theory and should not be regarded as demonstrable science.


R Hampton - #26274

August 19th 2010

In modern “Darwinan” terms, “symbiosis” can occur by lateral gene transfer (LGT), for example:

Congruence of Flagellar Genes with Organismal Phylogeny of Bacteria
Renyi Liu & Howard Ochman, PNAS, March 8, 2007

The distribution of the 24 core genes among divergent bacterial phyla is most consistent with an ancient origin, predating the shared ancestor of Bacteria. However, the distribution could have been achieved through later horizontal transfer. We tested these alternatives by comparing the phylogeny of the flagellar core proteins with the phylogeny of the corresponding bacterial phyla based on 25 universally distributed genes. The phylogenies are largely congruent on branches that have >75% bootstrap support; however, there are two inconsistencies between the core-gene and the organismal phylogenies; in the placement of both the alphaproteobacterial Zymomonas mobilis and a clade of three Betaproteobacteria within the Gammaproteobacteria. Because individual flagellar genes within the core set show the same evolutionary history, these incongruities have likely resulted from the transfer of the entire flagellar gene complexes between proteobacterial lineages after their separation from other major bacteria groups.


Scott F - #26305

August 20th 2010

Even if Dembski et al are right that information cannot be created, there is a far better candidate source for CSI than a designer: the environment.  Each phenotypically significant mutation will have some affect on the organism’s interaction with its environment.  If the interaction improves the chances that the mutation will be successfully replicated in descendant organisms, then new information has been added to the organism (do maladaptive mutations add information, too?)

Notice that the CSI of the organism may have increased but NOT via designerly tweakage.  The information has been copied, if you will, from the environment within which the organism operates. 

Problem solved - pending peer review and Nobel application, of course


defensedefumer - #26316

August 20th 2010

Great article!

I would like to point out a technical mistake in the article—there are many types of bacterial flagella, and the type spoken about in the article is a eubacterial flagellum. Other than that, I have no qualms with the article.

(I hope I’m not mistaken!)


Mark - #26373

August 20th 2010

“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.” This is also true of a conveyor belt or any automated bread maker. It demonstrates that the author has not used her intelligence to see that ID proponents see ID in components and in assembly processes. This post does not demonstrate anything. It is simply describing the assembly of a flagellum and then claiming that this process proves natural law can produce amazing complex motors. This has not been demonstrated anywhere by anyone. What the flagellum does is assemble itself according to a specific and detailed plan which no one yet fully understands, and who’s origin certainly has not been found. It may be natural, or it may be ID. This post does not add anything to the discussion.


Scanman - #26380

August 20th 2010

Charlie - #26213

“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.”

The Flagellum is still ‘Irreducibly Complex’...remove any one component and it cannot function as a means of propulsion. The same holds true for the molecular injector…as far as injection goes.

The flagellum and the molecular injector do not share any ‘function’, other then the penetration through the cellular wall. This is a similar argument used by the ‘anti’ ID crowd, when they wear a mousetrap as a tieclip.

What processes brought the proteins together to form the molecular injector?

I am a Theistic Evolutionist, so I hold that God manipulates environmental pressures to bring about design/selection.

Peace


Bill Pratt - #26392

August 20th 2010

RBH said:
“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.”

Then I guess neo-Darwinian theory is likewise vacuous because it cannot pinpoint precisely when any specific mutations occurred in the distant past that gave rise to new anatomical body plans and it cannot explain precisely how those specific mutations were selected by the environment (hand-waving, high level accounts don’t count).  Given the lack of precise details, neo-Darwinists nevertheless ask us to believe that evolution through random mutations and natural selection occurred.

Historical sciences can never pinpoint when’s or how’s with regard to isolated events that occurred once or only a few times in the distant past.  You can get to an imprecise and wide range of when’s and you may be able to posit how’s, but never with any great confidence.

ID, as a historical science, is positing that information from a mind was put into biological organisms in the distant past once or a few times.  I think anyone can see that according to the methods of historical science, that is an explanation because it explains the origins of biological information.


Dunemeister - #26396

August 20th 2010

Design is not an inference; it’s a presupposition, one which I share. Evolution is a miracle. So are the other laws of nature. I just don’t understand why we are so intent on driving a large wedge between the natural and the supernatural (a modernist distinction that has had its day). The self assembly of the flagellum inspires awe in the author of this article because she rightly sees it as redounding to the glory of the Creator? Same might be said of any of the other things which take our breath away in nature. So I find the whole tenor of the article (not to say its substance) as objectionable. “No intelligence required”! Gimme a break!


nedbrek - #26397

August 20th 2010

“Evolution is a miracle” A miracle always has a message behind it.  And God (almost?) always tells us what the meaning of that message is…

(I’m trying to think of a miracle without the message given, but I’m coming up blank)


CM - #26411

August 20th 2010

Nedbrek - looks like we had a little bit of a misunderstanding.
I was referring to thermodynamic entropy, which is a measure of disorder in a chemical system (inversely related to its energy), specifically as it relates to the “arrow of time” and molecular events. My point was that it is directly related to things like protein folding, molecular assembly, and function. We can understand what drives nearly any molecular system by examining the energies involved and how they change with function and movement using the second law of thermodynamics. Every system wants to get to the lowest energy state, resulting in increased entropy (somewhat more complicated, but to the best of my understanding this is what it distills down to.)

We might still disagree (or not? I’m not sure), but I hope this at least clarifies what I meant.


nedbrek - #26416

August 20th 2010

CM, ok.  “Entropy” is also used to measure information content in Information Theory.

Yes, the formation of ice crystals (snowflakes) is another good example of self-assembly.  But there is no “information” (formally defined) in these structures.


Bilbo - #26419

August 20th 2010

Kathryn,

First you write:

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.

cont.


Bilbo - #26420

August 20th 2010

Then you write:

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).

What you fail to mention is that Behe was referring to the “master sequence” that you just described, not to the process of self-assembly.  A little misleading.


Bilbo - #26422

August 20th 2010

Correction.  The part Kathryn quotes from Behe is from his argument for the two binding-sites binding rule, where he is explaining how much specification between proteins is needed for self-assembly to work.  Kathryn is being very misleading (or should I say dishonest?) in implying that self-assembly is what Behe says the problem is.  Now he also devotes an appendix to the need for order in activating the various flagellar genes, which is a whole new level of design.  Thanks for confirming that, Kathryn.


Chip - #26423

August 20th 2010

No intelligence required…  and I want to praise our great God.

If no intelligence at all is required, then the Dawkins faction is certainly right:  The process—as impressive as it is— got started arbitrarily, gets periodically updated, and consequently chugs along quite nicely through completely undirected and non-intelligent mechanisms.  God and any intelligence he might have are either non-existent or superfluous.  Why praise a person for an accidental process he has nothing to do with? 

If, on the other hand, praise is warranted, it can only be because God had something intentional  to do with the creation and/or sustenance of the BF’s assembly process (the context in which Applegate made her statement)—even if that something was frontloading the programming that allows the process to function “without the help of any conscious agent.”


Chip - #26424

August 20th 2010

—2—

For the record, I compeltely agree with Applegate’s “awe and wonder well up inside me” sentiments—the process is extraordinary.  I further agree that I want to praise our great God.  But praise can’t happen in a fully-naturalistic vaccuum.  And this is the continuing challenge for BioLogos:  instead of (yet another…) polemic against Behe, or ID, or YEC, how about a positive argument explaining why God is great (as opposed to why unintelligent natural processes are great) from a scientific perspective.


Alan Fox - #26481

August 21st 2010

OT @ Bilbo


Hi Bilbo

Someone has been trying to contact you via your blog. See comments.


Roger A. Sawtelle - #26670

August 23rd 2010

In modern “Darwinan” terms, “symbiosis” can occur by lateral gene transfer (LGT), for example.

R Hampton #26274

Thank you for pointing out the importance of symbiosis in evolution.  This is much confusion between evolution and Darwin.  Many people confuse the PROCESS of natural change with the THEORY of a human being.  That is not good scientific thinking, because D’s theory describes how he understood how evolution takes place, not that evolution takes place.

The article that you quoted states that evolutionary change can and does take place laterally, that is, symbiotically by interaction between life forms to produce a new life form.  Nothing like this was foreseen by Darwin.  As we know he said that claimed that life changed by conflict between life forms for survival, not sharing and interacting together. 

His theory saw evolution linearly by mutation, while symbiosis sees evolutionary change as non linear as lateral gene transfer indicates.  Further symbiosis takes many forms and has been developed by ecology into a comprehensive description on how organisms interact necessary for understanding of how evolution takes place.  Thus evolution is ripe for scientific revolution as a new model takes over.


Roger A. Sawtelle - #26672

August 23rd 2010

Part 2

In terms of ID I do not agree with it except in the broadest general terms.  I agree that God, an intelligent Being is the Source of the universe, but that does not preclude, but indeed makes possible the development of intellectual and spiritual beings, humanity, by “natural” processes.  Intellect and design are found in the basic structures of nature, that is in the laws of nature.  God looked at the universe and called it good, meaning it had meaning and purpose.  We can say now that the universe was designed in such as way that human life is possible, and since this has happened we can say that it has purpose.

Darwin and his followers say that life developed linearly by random trial and error.  Ecology and LGT indicates that life developed non linearly and symbiotically based on the interplay of organisms.  LGT may indicate that life is like a set of Legos that organisms put together creatively and synergetically. 

Darwinian evolution is not consistent with the God of the Bible in my opinion.  Ecological evolution is and is much better grounded in science as this article indicates.


R Hampton - #26698

August 23rd 2010

Roger A. Sawtelle,

The point is that modern “Darwinian” evolutionary theory includes lateral gene transfer, as well as epigenetics, sexual selection, et. al.—contrary to your arguments. The “revolution” the you insist has yet to come has, in fact, an evolution (no pun intended) of science in the last 150 years. So what you refer to as “ecological evolution” is really just plain ‘ol evolution, and thus consistent with a biblical God.


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