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Self-Assembly of the Bacterial Flagellum: No Intelligence Required

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August 19, 2010 Tags: Design
Self-Assembly of the Bacterial Flagellum: No Intelligence Required

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

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.


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.


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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Roger A. Sawtelle - #26714

August 23rd 2010

R Hampton

If you think that ecological evolution is what evolutionists have been talking about for 150 years, then you need to explain this to Darwin, H. Spencer, E.O. Wilson, Dawkins, Dennett, and everyone else.  When will people realize that Malthusism was a mistake that evolutionists want to inflict on the rest of the world? 

Stop dreaming and wake up and smell the coffee.

Trevor K. - #26852

August 25th 2010

For those who haven’t considered it, please go and read here:


This is another point of view to consider.
Flame it if you want. Your choice.

Ronnie - #26887

August 25th 2010

Self Assembly? No Intelligence needed? On the contrary, there is a tremendous amount of intelligence needed for the assembly of a miniscule, yet highly complex and ordered “machine”  such as the flagellum. Information may be a better term, which can only come from intelligence!

God created the bacteria with its flagellum fully formed right from the start, and programmed into it the ability to reproduce as well as form its flagellum so that it appears to be an unguided self-assembly process, but in reality it follows a very precise set of instructions, which Ms. Applegate describes in the article, yet states her belief that the flagellum developed gradually (as in, evolved).

This is the slippery slope Biologos is on: to say the Bible is the inspired Word of God, yet turn their back on the account of creation in Genesis, exchanging the truth of Gods creation for the lie of evolution (Romans 1:25).

She states correct answer in the first paragraph: “its perfectly logical to infer a Designer”! Let’s praise our Designer, as well as our Savior, Jesus Christ, for the wonders of His creation!

Jon Garvey - #26897

August 25th 2010

@Ronnie - #26887

Romans 1.25: Perhaps I’m slow, but I didn’t get the impression from the article that Kathryn Applegate worships and serves the bacterial flagellum instead of the Creator, which would seem the only valid application of your citation. Neither does that verse mention evolution, as a lie or not.

Do we treat the interpretation of the word of God seriously, or do we wrest verses from it to beat other believers over the head? Paul did, after all, also write chapter 14 of Romans.

Ronnie - #26949

August 25th 2010


I cited Romans 1:25 in reference to Biologos mission statement of attempting to harmonize science (evolution) and faith. Evolutionary science is contrary to the creation account of Genesis and therefore cannot be in harmony with the Word of God. Evolution is the lie that Biologos is trying to say is true.

Ms. Applegate did an excellent job of describing the wondrous, “like magic”  formation of the flagellum, which indeed is amazing! However, she states that it requires no intelligence and was a result of gradual development (i.e., product of evolution). The answer is in her words, yet she can’t see it because it doesn’t fit the evolutuionary model of origins.

R Hampton - #26953

August 25th 2010

The Roman Catholic Church, which represents over a billion people, accepts Evolutionary theory and has proclaimed (many times) that all of Science (General Revelation) and Scripture (Special Revelation) are harmonious because both are the Word of God.

ken - #26956

August 25th 2010

I, too, am skeptical about the “majic”.  I don’t think this is “self-assembly” either, rather, this is assembly under program control.  The manifestation of this organelle is the expression of an intstruction set contained in the organism’s DNA.  The whole thing absolutely reeks intellingence.  There’s even a language convention in the coding.  For goodness sakes….

Jonathan Bartlett - #26969

August 26th 2010


I don’t calculate CSI, but I do calculate Active Information here (abstract C1).  You can also see my poster and slides.

I agree that Active Information is difficult to put into use biologically, but Active Information is at least estimable in some circumstances.

Jim M. - #26978

August 26th 2010

I find the reasoning in this article severely lacking. 

She admits the flagellum looks & functions like an outboard motor, but says that since it assembles itself spontaneously, without the help of any conscious agent, we can rule out intelligence.  What?? 

She thinks that this motor because it can assemble itself, rules out intelligence?  What??

Personally, if someone could develop an outboard motor that could assemble itself without the help of any conscious agent, I think that would take more design and intelligence than it took to develop the outboard motor that we have now!  But that’s just me.  I’m not a scientist, so what do I know.  I should just keep my mouth quiet & bow down to what the scientific experts tell me.

She wants us to praise God while she steals all His glory by claiming He had nothing to do with the emergence of this amazing motor.  He didn’t design it.  She thinks that just happened by accident.  Nor did He write the software for the self-assembly process.  That too just magically appeared.  She would rather have us believe in magic than an omnipotent, omniscient loving Creator.

This is what happens when we start with science and let science interpret Scripture.  We end up denying God’s truth!

Jim M. - #26979

August 26th 2010

“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 & functions automatically according to known natural laws. No intelligence required.”

Come on now.  It has to be guided by something!.  She doesn’t expect us to believe that each and every flagellum that comes into existence is an accident and yet that accident is repeated trillions of times each day does she?  No way.  It is guided by the genes.  But the question then is, who wrote the software that controls this self-assembly process?  Surely she doesn’t expect us to believe that the software wrote itself does she?  The engines self assembles thanks to a software program that wrote itself?  So that is the extent Biologos is willing to go in order to make the Bible fit with science! 

Perhaps the Creator is not guiding the assembly of each flagellum motor that comes into existence, but common sense would tell us that intelligence is necessary to explain the origin of the software that guides this self assembly.  Again, I don’t follow her reasoning.

Biologos rather than ID is creating confusion.

Jim M. - #26991

August 26th 2010

Roger says “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.”

Roger, how do you think natural processes created our spirit?  Don’t you think God created our spirit - the part of us that lives on for all of eternity?

Roger: “God looked at the universe and called it good, meaning it had meaning and purpose.”

What evidence do you have for your interpretation?  You can’t just put your own meaning into God’s Word to make if fit your views.  Certainly creation has meaning and purpose, but is that what the word “good” really means in this passage?  That is the question.  What did the author mean - or rather what did God mean when He gave those words to Moses?  In fact God called it “very good”.  Does that mean the universe has “lots of meaning and purpose”?

I will continue this in the next post.



Jim M. - #26993

August 26th 2010

Roger, I think the word “good” means just what it says.  It was very good in every way.  There was nothing evil, unwelcome, or unwanted in creation.  The world was created just as He had planned and envisioned it.  When we read Gen. 1 & 2, we see some clues as to what that means.  There was no bloodshed because the animals were all vegetarians.  There were 2 perfect humans created in God’s own image who were living in a special garden designed and prepared just for them.  It was peaceful.  Food was plentiful.  It was beautiful.

Do you think God would call a world filled with struggle, pain, disease, death, extinction, catastrophes, mutations, weeds, etc as “very good”? 

Personally, that doesn’t fit w/the God of the Bible.

The Bible tells us that God is going to restore everything.  Acts 3:21 What’s He going to restore it to?  A world filled with killing, death, suffering, disease, etc?  No.  Read Rev. 21:3,4.  He is going to restore it to a time when these “bad” things didn’t exist.  He is going to restore it to the way the world used to be, the very good world He originally created before sin entered the world and creation was put in bondage and suffered decay. Rom. 8:21,22.  This broken world was not God’s plan!

Dolly Sheriff - #27012

August 26th 2010

Enough with the straw men.  I do not know anyone in the ID movement that believes that every component in the bacterial flagellum was made by special creation?  So what is the dear lady on about?  The flagellum didn’t appear by magic .. neither do ID proponents believe that God waved a magic wand. We are “skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life”. The truth, we believe is way more marvelous

I don’t think Prof Behe makes or intends to make it sound like each interaction of the flagellum is the product of special design. If the author had taken the time to read his books she would know that Prof Behe favors common descent, which would be a little contradictory, no?

Did God make the system that made the Flagellum and in doing that did He have the Flagellum in mind?  Probably. Did God make the system and not care about the detail. Unlikely. Did God create each component separately and assemble them just-in-time like in a factory. ID Straw men believe this. Did God speak the universe into existence through his everlasting word. Absolutely!

Ronnie - #27014

August 26th 2010

R Hampton:

I’m not catholic and I don’t know much about the catholic faith, but I do know they are wrong to accept evolution. Compare the theory of evolution and the creation account in Genesis, they are diametrically opposed to one another. The catholic church has capitulated to secular science and just like Biologos is deceiving their flock of over a billion.

The devil gets a foot in the door whenever a person is convinced that Gods Word may not mean what it says, and will not stop until the entire Bible is made to be of no significance. Thats the devils goal: to turn the truth of God into a lie.

I was accused in an earlier post of using a verse to beat someone over the head, and I certainly don’t want you to think I’m beating you over the head but the following verse came to mind. I am very concerned about the damage evolution (actually the forces behind it) is doing to our country, the church and to believers and non believers alike, so it is out of Gods love that I share this scripture with you:

“Enter through the narrow gate. For wide is the gate and broad is the road that leads to destruction, and many enter through it.” Matthew 7:13.

Jeff Snipes - #27114

August 26th 2010

“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.”

Fully functioning nanobots would also be capable of self-assembly too, so that must mean no directive intelligence was involved in the production of those either, right?

R Hampton - #27132

August 26th 2010


The devil gets a foot in the door whenever a person is convinced that Gods Word may not mean what it says, and will not stop until the entire Bible is made to be of no significance. Thats the devils goal: to turn the truth of God into a lie.

And when Conservative Protestants deny Natural Revelation, they are guilty of the aforementioned crime.

I won’t beat you over the head the Catholic doctrine, but please do understand that happy, healthy, traditional Christians who attest to the Creeds and Evolutionary theory exist in tens - if not hundreds - of millions. Yes, they really do exist. Yes they defend the Truth. No, their faith is not weak.

Jim M. - #27149

August 27th 2010

“And when Conservative Protestants deny Natural Revelation, they’re guilty of the aforementioned crime.”

R. Hampton, let’s forget about the Prot/Cath thing.  Rome has been wrong in the past.  The big issue I see here is how do natural & supernatural revelation interact?

You seem to put them on equal terms.  You forget that much interpretation goes into reading “natural revelation.”  We can look at the rocks and see many layers in them, but that doesn’t tell us how they got there.  One can take the position that they were formed by the nat. processes we see at work today.  But that is a guess that finds support simply because it fits w/evolutionary theory. Evolution needs an old earth.

One could also start w/the Bible & accept a global flood.  Here is where supernatural revelation must trump natural revelation.  A fllood explains the rock layers w/out resorting to an old earth and the anti-biblical view that death, suffering, disease, bloodshed, etc. were a part of God’s original creation.

Whichever view you take, depends on your view of natural revelation vs supernatural revelation.  God’s Word must take precedence over the biased naturalistic views of modern day fallible men who were not there to see what happened..

Ronnie - #27180

August 27th 2010


The fact that the flagellum and syringe share some of the same proteins still begs the question: where did the proteins come from? Its perfectly reasonable to conclude that God made the proteins so efficient and useful they can be used for both the flagellum and syringe.

Its possible Ms. Applegate could have meant there is no intelligence from an outside source needed for the assembly, and she would be right, but she doesn’t mention it anywhere in the article. The intelligence (information, program, set of instructions) is already there in its genetic makeup, and it can only come from a source greater than itself, which is God Himself.

R Hampton:

I agree with Jim H. you are putting natural revelation above supernatural revelation. Nature got here supernaturally, during the creation week, and was affected by other supernatural events such as the flood. Allow me to quote the entire verse of Romans 1:25:

        For they exchanged the truth of God for a lie, and worshiped and served
        the creature rather than the Creator, who is blessed forever. Amen.

Evolution theory does exactly that, puts nature above its Creator, even worse, denies its Creator.

Ronnie - #27181

August 27th 2010

Forgive me, in my above post I meant to say Jim M.

R Hampton - #27289

August 27th 2010

You forget that just as much interpretation goes into reading Scripture.

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