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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 - #27295

August 27th 2010

Jim M. & Ronnie,

If you believe the Bible, then you must accept that nature IS the Word of God, “

And God said, Let there be light: and there was light…. And God said , Let there be a firmament in the midst of the waters, and let it divide the waters from the waters… And God said, Let the waters under the heaven be gathered together unto one place, and let the dry land appear: and it was so ... And God said, Let the earth bring forth grass, the herb yielding seed, and the fruit tree yielding fruit after his kind, whose seed is in itself, upon the earth: and it was so.

So when we use reason to study nature we are made aware of General Revelation. Together with Special Revelation, the two truths become the unified Truth embodied in Christ.

Unfortunately Protestants came to rejection half of God’s revelation after the Reformers which reached its zenith with Karl Barth. I’m willing to bet you are not aware of this.


Johan - #27336

August 28th 2010

Applegate’s logic is flawed because this basically means, if I had to design a machine capable of self-assembly, this according to Applegate’s logic would mean that the machine is therefore not designed, and this is false.

Applegate is basically knocking down her own straw man because I know of no ID theorist that argues intelligence is actively guiding the assembly of these molecular machines.

People should try to understand intelligent design reasoning first before trying to refute it.


Johan - #27338

August 28th 2010

And I disagree with Applegate, natural forces don’t work like “magic”, if it did, sand storms and erosion would be able to carve out faces on mount rushmore. If natural forces worked like magic, we would never be able to tell when certain patterns are best explained by intelligence. It’s precisely because natural forces don’t work like magic that leads us to the conclusion that patterns such as the patterns found on Mount rushmore are best explained by intelligence.


Ronnie - #27359

August 28th 2010

R Hampton:

The bible names Jesus Christ as the Word of God in John 1:1. If nature were the Word of God, it would be equal to Jesus, or the created thing equal to its Creator which is contrary to scripture. We humans are created also, and it would be a terrible sin to even try to put ourselves as equal to Jesus.

As for the assembly of the flagellum, it appears to perform like magic because of the amazing and wondrous system of intelligence (in its DNA) placed there by its Creator, Jesus Christ,  that causes it to form. Its growth follows an extremely precise set of instructions that ‘builds’ an incredibly complex ‘propulsion mechanism’ in the space of only about 20 minutes! If we see a beautiful painting, what a slap in the face it would be to the painter if it were said to be a result of numerous accidental paint spills! The flagellum is but one (very) small example of Gods paintings. Biologos and others who wish to harmonize evolution (slow, gradual, natural processes) with the bible are taking the brush out of Gods hands!


Roger A. Sawtelle - #27374

August 28th 2010

I think that we must back up a little bit.  As far as I can tell, the debate between ID and Darwin is not about evolution, but how evolution takes place.  As is well known that Darwin & Co. maintain that evolution takes place on a kind of trial and error process.  ID maintains that evolution has been designed, which indicates that it is the product of an Intelligent Designer.   

Our author maintains that the cleverly engineered complex flagelleum does not require special intervention by God to produce but can be explained naturally.  “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”

The question that arises for me is “From where do natural laws come, if not from intelligence?”  Nature itself is not able to think.  Water does not think itself into rain, but still the water cycle is a carefully designed system based on natural laws.


Roger A. Sawtelle - #27379

August 28th 2010

Part 2

Christians & Jews believe that nature & its laws are created by God & are intelligent & good.  Science maintains that the universe is comprehensible and thus intelligent in that sense, however Darwin based on his atheology wanted evolution to be based on random chance, rather than rational process.  He based his theory on the ideas of T. Malthus, and this is the heart of the conflict between believers & D.   

I do not support ID, because it is not a science.  At best it is a philosophy of S.  If it says that E is a process which has been designed by God, like other natural processes, I agree.  If it says there was divine intervention to make E work, I disagree.

In defending E as a natural system people say that it is a cleverly designed system governed by natural laws. This is counter to the stupid trial & error system of D.  In explaining E they use ecological concepts like symbiots, lateral gene transfer, & niche theory.

The defenders of Darwinist selection use ecology, which contradict the system they are trying to defend.  Ecology is much more compatible with Christianity than D.  This is where the problem is and the the sooner we understand this, the better it will be for all who love the Truth.


Johan - #27384

August 28th 2010

I do not support ID, because it is not a science.//

ID asks the scientific question “could patterns exhibited by finite arrangement of matter signify intelligence? and if it could, how could we tell?”

These questions are scientific, regardless how we answer them.

Same goes for scientific projects like SETI, SETI asks the simple question, “are there aliens in the universe?” or “is there evidence for aliens in the universe?” these questions are scientific, regardless of the answers to these questions.

ID is a scientific research program that asks the important question “could patterns exhibited by finite arrangements of matter signify intelligence?”


Rich - #27418

August 28th 2010

Johan (27336 etc.):

Thanks for your posts.  And reinforcing your claim that Dr. Applegate has misrepresented Behe’s argument, we have two articles by John West, who certainly ought to know what ID actually claims about the bacterial flagellum:

http://www.evolutionnews.org/2010/08/behe_critic_on_bacterial_flage037561.html#more

http://www.evolutionnews.org/2010/08/a_biologist_misunderstands_int037571.html#more


Jim M. - #27439

August 29th 2010

R. Hampton said: “If you believe the Bible, then you must accept that nature IS the Word of God, “

No, you are mistaken.  God gave a command using words &  nature came into existence in response to those words.  Nature is separate from His words. 

The concept of general revelation has been around for a long time.  General revelation can tell us that God exists and that He is all powerful and very wise, but beyond that, it can’t say much.  We need special revelation to know God and learn about history, the future, and spiritual things we know not of.  Special revelation trumps general revelation every time.  The flood is a good example of that. Without out special revelation, we would think the rocks were formed over billions of years, but we know that is not the case because the Bible tells us of the worldwide flood.

Don’t quite see how general & special revelation unite to form the unified truth embodied in Christ.  The Bible does not say this. 

“Protestants came to rejection half of God’s revelation after the Reformers…”

What in the world does that mean?  What Protestants?  I"m Protestant and I don’t reject half of God’s revelation unless you are talking about the Apocrypha, etc.


John VanZwieten - #27509

August 29th 2010

Is there someone who could provide a larger quotation from The Edge of Evolution pp. 125-126?


Jim M. - #27526

August 30th 2010

Roger said:

“I think that we must back up a little bit.  As far as I can tell, the debate between ID and Darwin is not about evolution, but how evolution takes place. “

Not necessarily.  Not all ID scientists believe in common descent.  For instance Behe does and if I’m not mistaken, Casey Luskin questions that.

Plus, you have to define evolution if you want to make a statement like that.  Even creationists believe in what some would call evolution - change within species.  For instance, natural selection, mutations, etc working on the dog kind could easily have produced the large diversity of dogs we see today starting with a single pair of dogs with a rich genetic make-up in a relatively short amount of time.  But in the end, you still have dogs, dingos, maybe wolves, etc - all descended from the original pair of dogs created by God.  But that is only macro-evolution.  Hardly anyone disputes this type of evolution.  It is macro-evolution where the rift occurs.  You need to define your term.


Roger A. Sawtelle - #27579

August 30th 2010

Jim M.;

You confirm what I said.  The question is not about whether evolution in some form takes place or not for most folk, just how it takes place.  We need to confine our discussion to that issue, which is what I am trying to do.


Roger A. Sawtelle - #27582

August 30th 2010

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?

Response:  Clearly humans cannot have a spirit without a mind.  If the mind was created by natural processes, which seems to be the case, then human spirit could also be.

Now if God directly created an eternal soul which lives for eternity, then that soul would have to be good by nature.  In which case salvation is unnecessary.  God’s people live forever with God because they are saved by grace and justified by faith, not because they have an eternal spirit.


Roger A. Sawtelle - #27584

August 30th 2010

Part 2

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

What evidence do you have for your interpretation?  .... Certainly creation has meaning and purpose, but is that what the word “good” really mean (here)? .... 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”?

R:  John 1 names Jesus Christ as the Word or Logos of God.  Logos is a deep concept with more than one level of meaning, but a clear one is that Jesus Christ is the Meaning & Purpose of the Universe.  Yes, the universe does have a very profound meaning and purpose.

You also bring up the problem of death & suffering in the universe.  We know that evil is caused by sin.  This is the message of Gen 2-3.  But God must have created death because God told the first humans that if they ate the fruit of the tree, they would die. 

Suffering & death are not evil per se because Jesus Christ suffered & died.  He said Christians must also suffer & die.  God is not evil because God created a universe that contains suffering & death, because God gives us the Answer to sin, evil, suffering and death, Jesus Christ.


R Hampton - #27588

August 30th 2010

Jim M.
General & Special are part of the same truth, so neither is superior to the other. Each has authority for its given area whereas Special Revelation can tells us about the moral issues involved in the Flood, General Revelation tells us about the mechanical issues. Thus it’s wrong to use General Revelation to learn morality and Special Revelation to learn mechanics.

But Protestants like yourself believe that if General & Special Revelation are in conflict, then the General must give way to Special. That is how you have come to reject half of God’s word by misapplying the authority of Scripture upon Science and Nature.


Roger A. Sawtelle - #27621

August 31st 2010

Johan wrote:

ID asks the scientific question “could patterns exhibited by finite arrangement of matter signify intelligence? and if it could, how could we tell?”

I said that ID is an aspect of the philosophy of science.  The issue is seen clearly in your statement.  What is intelligence?  How is it defined?  Philosophy, the love of wisdom, is the discipline that is most directly concerned with how people know and intelligence.  Intelligence per se does not lend itself to scientific definition, but it does to philosophical understanding.

If Einstein was right, that the universe is comprehensible by the human mind, then it follows that it based on intelligible or intelligent design.  This is not a pure science issue. 

SETI is something quite different, even though I am not in agreement with it.  Any intelligent life form would be thousands of light years distant from us so real communication would be impossible.  If they are there, I expect they will find us or we will stumble on them.

A question would be the interpretation of finding intelligent alien life forms.  Have you seen the article by Paul Davies where he makes the absurd statement that finding of aliens would be a serious challenge to Christianity?


Rich - #34125

October 10th 2010

For those interested, a substantive scientific reply to Kathryn’s May posts on randomness and immunity, written by someone with a Ph.D. is immunology, is now up at:

http://www.uncommondescent.com/intelligent-design/comments-on-kathryn-applegate’s-may-posts-on-biologos/


glsi - #64303

August 27th 2011

Dr. Applegate,


You write wonderfully on the intricacies of the flagellum.  Thank-you!
However, your conclusion that it’s own self-assembly “isn’t tricky at all” leaves me speechless.  Even if you somehow imagine that this is a product of random chemical evolution surely the self-assembly is jaw dropping each time it occurs.  Or not?  What would the cell have to do to really impress a Darwinist?  And you had just stated that you were “awed” by the process and praising God.  Quite confusing.  Are you awed or are you yawning?

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