Bacterial Flagellum:  Assembly vs. Evolution

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September 9, 2010 Tags: Design

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

Bacterial Flagellum:  Assembly vs. Evolution

Last time, I described how the bacterial flagellum spontaneously assembles in an orderly way, without the help of a conscious agent. I didn’t intend to suggest that ID advocates argue otherwise, but I did say that they often write about assembly in unclear and misleading ways. Today I want to justify this assertion with some examples.

ID advocates commonly point to the self-assembly of complex structures like the flagellum to argue that they couldn’t have been produced by evolutionary mechanisms. In his 2007 book The Edge of Evolution, Michael Behe includes an entire appendix on how the bacterial flagellum assembles to make this connection. In the first paragraph, he writes:

The need to spontaneously assemble intricate machinery enormously complicates any putative Darwinian explanation for the foundation of life, which has to select from tiny, random steps…In a cellular nanobot, where machines run the show without the help of conscious agents, everything has to be assembled automatically (p261).

How the flagellum originated and how it assembles are of course two different (though not completely unrelated) questions, but the distinction is lost in much of the ID literature. According to ID, assembly supposedly presents a significant hurdle for the evolutionary origin of the flagellum because evolution has to account not only for the production of all the parts, but for the manufacturing process as well. Following Behe, Jonathan Witt, Senior Fellow at the Discovery Institute, assumes that the basic forces of nature can’t produce complex structures that self-assemble:

[E]ven if nature had on hand all the right protein parts to make a bacterial flagellum, something would still need to assemble them in precise temporal order, the way cars are assembled in factories. He goes on to describe how the genetic instructions for the particular protein components are interpreted sequentially, in the order that the parts are needed. This added layer of complexity, on top of an already irreducibly complex structure (the flagellum itself), supposedly points to an even more sophisticated level of engineering than was previously appreciated.

Manmade vs. molecular machines: same or different?

The rhetorical effectiveness of this line of reasoning rests on the comparison between manmade machines or buildings and molecular ones. The argument seems especially compelling because the process of designing and assembling a car or building is shot through with design language: planning, foresight, blueprints, etc. For instance, in a chapter called What Darwinism Can’t Do, Behe regales us with detailed descriptions of how cilia1 and bacterial flagella are built. He likens the process to the construction of an observation tower at his university called Iacocca Hall:

Like all such buildings, it was built in what could be called a “bottom up-top down” fashion. By bottom up I mean that of course the foundation of the building had to be poured first, the ground floor next, and so on…By top down I mean that the building was planned. Blueprints were followed, supplies ordered, ground purchased, equipment moved in, and so on—all with the final structure of the observation tower in mind (p85).

It turns out that the construction of big structures in the cell requires the same degree of planning—the same foresight, the same laying in of supplies, the same sophisticated tools—as did the building of the observation tower at Iacocca Hall. Actually, it requires much more sophistication, because the whole process is carried out by unseeing molecular robots rather than the conscious construction workers who assemble everyday buildings in our everyday world (p87).

The construction of complex structures in the cell, Behe says, requires even more planning and sophistication than the construction of a manmade building. Who, we may ask, does all this planning? Behe certainly doesn’t mean there’s a miniature foreman in the cell directing the assembly (he refers to unseeing molecular robots, after all) but it’s hard not to imagine a “man behind the curtain,” to borrow an image from The Wizard of Oz. He is speaking of an Intelligent Designer, who must have pre-loaded the bacterium with all the instructions it would need to construct the flagellum.

In our everyday experience, the more intelligence and design that goes into the manufacturing process, the less conscious intervention is needed to assemble a complex machine. Cars can be made on an assembly line almost entirely by unthinking robots, but only because the robots themselves are intelligently designed. Cellular machines like the flagellum assemble spontaneously with no conscious intervention. Thus, by this logic, the control processes that guide assembly must be the work of a truly superior Designer.

But are we justified in applying this kind of planning/foresight language to what goes on inside the cell? Just how far can we take the parallel of molecular machines with manmade ones? I would argue that the differences are real and substantial. How often have you seen a manmade machine assemble and even repair itself, as the flagellum does? Or a whole factory reproduce itself, as the cell does? Perhaps these amazing features of life point not to a specific design event but to the fact that God’s laws that govern biology are even more powerful and creative than we previously recognized.

Confusing conflation of assembly and evolution in the ID literature

While scientists frequently liken the cell to a factory that produces complicated machines, they rightly recognize the limits of the comparison: the cell is decidedly unlike a factory when it comes to how assembly actually happens. As biophysicist Sarah Woodson put it in a 2005 Nature commentary,

The cell’s macromolecular machines contain dozens or even hundreds of components. But unlike man made machines, which are built on assembly lines, these cellular machines assemble spontaneously from their protein and nucleic-acid components. It is as though cars could be manufactured by merely tumbling their parts onto the factory floor.

Woodson’s statement is powerful because it points out how unintuitive it is that molecular machines assemble from random collisions between molecules. But Behe uses this quote in a peculiar way to brush aside one “unintelligent” alternative to evolution by natural selection, called self-organization theory:

Some very simple rush hour traffic patterns are self-organizing, but self-organization does not explain where very complex carburetors, steering wheels, and all the other physical parts come from, let alone how “cars could be manufactured by merely tumbling their parts onto the factory floor” (p159).

I say this is peculiar because neither evolution nor self-organization theory claims to explain how all the protein parts physically come together to assemble a functioning machine like the flagellum. (They do aim to explain where the parts come from in the first place.) Perhaps unwittingly, Behe attacks a straw man when he says these theories cannot answer a question they don’t claim to address in the first place.

At the end of his appendix on how the bacterial flagellum assembles, Behe again conflates evolution and assembly in a misleading way. First he describes a real debate in the scientific literature about how the bacterial flagellum is related to a similar structure in the cell, called the type III secretory system (TTSS). He then proclaims that “none of the papers seriously addresses how either structure could be assembled by random mutation and natural selection.” As evidence he writes of a 2003 review article entitled, How Bacteria Assemble Flagella:

How did such a pathway [of flagellum assembly] evolve by random mutation? In the approximately seven-thousand-word review, the phrase “natural selection” does not appear. The word “evolution” or any of its derivatives occurs just once, in the very last sentence of the article. Speaking of the flagellum and the TTSS, Macnab writes: “Clearly, nature has found two good uses for this sophisticated type of apparatus. How [the TTSS and the flagellum] evolved is another matter…” Darwinism has little more of substance to say.

Behe pulls the quote grossly out of context. Macnab was not aiming to describe what is known about the evolution of the flagellum. It is “another matter”, not because nothing is known about it, but because it is a different subject entirely from how assembly works. It is therefore not surprising that the words “evolution” and “natural selection” appear so infrequently! Thus the flagellum is another example—like the antibody generation system—in which Behe fails to seriously engage with the scientific literature, giving the impression that there isn’t any on the topic.

Next time we’ll begin to look at the irreducible complexity argument in detail and discuss whether it in fact does pose a problem for the gradual development of the bacterial flagellum.

Notes:

1. Cilia are molecular machines every bit as marvelous and complex as bacterial flagella. While the two get about equal time in Michael Behe’s books, cilia aren’t nearly as famous as flagella. Why? Perhaps because cilia do several different jobs in the body and are thus harder to explain in a sound bite. Flagella, on the other hand, do one job—help bacterial swim—and, in the words of ID advocate Jonathan Witt, “images of the flagellum practically scream design.” Cilia might also be less famous because they’re less “family friendly:” the wriggling tails of sperm are actually long cilia! Making sperm the icon for the ID movement would not exactly have been a good marketing strategy.


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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beaglelady - #31401

September 22nd 2010

beaglelady, are you deaf?  How many times have I told you that ID doesn’t employ supernatural explanations?

So an explanation can be neither natural nor supernatural?


beaglelady - #31403

September 22nd 2010

Evolution doesn’t proceed by “chance alone,”

You are so right.


Rich - #31407

September 23rd 2010

beaglelady (31403)::

Actually, I never said that evolution—real evolution—proceeds by chance alone.  I was referring to the neo-Darwinian account of evolution championed by the people I mentioned.  But you’ve steadily been unable or unwilling to digest such distinctions in this discussion.

In classic Darwinian and neo-Darwinian evolution, despite the claims made for the “creative” power of natural selection, in fact natural selection does not create a blessed thing.  As I’ve explained here numerous times, all the creative work in Darwinian evolution is done by the random mutations.  Darwin warned his readers of the metaphorical way of speaking involved in “natural selection”; and anti-ID biologist Allen MacNeill, praised by the Darwinists here, also makes very clear that “natural selection” is neither power nor an agent of any kind, but a *result*.  It doesn’t “do” anything.  What survives, survives.  Natural selection explains zero about “the arrival of the fittest.”  So “chance plus natural selection” boils down to chance, *as far as the explanation of biological novelty is concerned*.

Your “researcher” ally “John” strikes out again.  I suggest relying on more informed sources.


Rich - #31409

September 23rd 2010

beaglelady (31403):

Rich:  How many times have I told you that ID doesn’t employ supernatural explanations?

beaglelady:  So an explanation can be neither natural nor supernatural?

I have no idea what you are talking about.  Why do you answer a question with a question?  Why don’t you make an *extended statement*, responding to the explanation I gave (about “detecting design” versus “detecting supernatural interventions”), in which you expose your own reasoning for all of us to see?  It’s easy to fire off one-line questions and one-line statements that are shrouded in ambiguity; it’s much harder to *articulate a position*.  Or do you have a position, beyond, “I agree with whatever the majority of scientists says”?


Johan - #31455

September 23rd 2010

@Beaglelady

//So an explanation can be neither natural nor supernatural?//

It depends on what you mean by “natural” and ‘supernatural”, if by “natural” you mean “material” explanation, and by “supernatural” you mean “magical” explanation, then I would say yes, an explanation can easily be both non-material and non-magical at the same time. For example, consider the information on a printed page, now there is nothing in the chemistry of the ink or the paper itself that would explain the arrangement of the letters on the printed page. However, this doesn’t mean there is a magical explanation necessary to explain the origin of the information on the printed page. It’s simply means there is a non-material explanation for the origin of this information.


beaglelady - #31504

September 23rd 2010

Indeed, intelligent design is just the Logos theology of John’s Gospel restated in the idiom of information theory.

Is the Logos theology of St. John’s Gospel supernatural?


beaglelady - #31505

September 23rd 2010

For the third time, what sort of research proposals have the ID guys submitted lately?  (What exactly is it that ID researchers do?) ID research could also be privately funded, as I believe HHMI is.  And look at Answers in Genesis; they raised a ton of money from believers to build their state-of-the-art creation museum.  So what are the ID research proposals being denied funding?


John - #31508

September 23rd 2010

beaglelady asked a perfectly reasonable question:
“For the third time, what sort of research proposals have the ID guys submitted lately?”

You won’t get a straight answer. That sort of question just makes their eyes roll back into their heads and causes a random venomous response to spew out. In their minds, you’re a bad person just for asking it.

Rich wrote:
“Actually, I never said that evolution—real evolution—proceeds by chance alone.  I was referring to the neo-Darwinian account of evolution championed by the people I mentioned.”

That’s not the way they account for it at all. You are deliberately misrepresenting their views. Moreover, modern evolutionary theory, unlike Intelligent Design Creationism, is clearly defined independently of any one person’s account of it.


Johan - #31513

September 23rd 2010

//For the third time, what sort of research proposals have the ID guys submitted lately?//

ID theorists ask the question, what exactly can Darwinian processes do? How small should the steps be in cofiguration space so that they can lead from point a to point b?, and are these steps available that are small enough as to be reasonable probable?

On a similar note, ID theorists ask, how rare are functional proteins? as compared to all the possible ways there are of arranging the amino acids of a protein that is the same lenght? What is the ratio of meaningless sequences versus functional sequences when we look at a protein as small as 150 amino acids in lenght (to be generous)? These are quantitive scientific questions that ID asks.


beaglelady - #31517

September 23rd 2010

Evidently three is not the charm! This is getting to be like “100 bottles of beer on the wall”

For the fourth time, What sort of research proposals have the ID guys submitted lately?  (You know, applications for funding)


Arthur Hunt - #31546

September 23rd 2010

I’m wondering - just how does one find out what research proposals the ID vanguard has submitted?  If it were me, I would gladly point people to funded projects (this is public info anyways), but I’m not going to divulge information about unfunded proposals.  You never know who will steal your ideas, and even titles and abstracts are enough to lead to one’s getting scooped.


Johan - #31549

September 23rd 2010

What sort of research proposals have the ID guys submitted lately?//

ID proposes that we grow bacteria, we nuke em, we mutate em until the cows come home in order to see what Darwinian processes can do.

ID proposes that we test the sensitivity of proteins, we take a functional protein we knock a few amino acids out and we test to see if this enzyme can still serve it’s purpose.

ID proposes that we test to see how many sequences are functional, when we look at all the possible ways there are of arranging the 20 different amino acids if we take a small 150 amino acid long protein. ID wants to know if it’s easy to jump from the one functional protein to the next in sequence space. This is science.


beaglelady - #31583

September 23rd 2010

John said,

You won’t get a straight answer. That sort of question just makes their eyes roll back into their heads and causes a random venomous response to spew out. In their minds, you’re a bad person just for asking it.

So I see.  They complain about lack of funding, and I’m just wondering exactly what they’d like funding for.  It’s like nailing jello to the wall.


Rich - #31590

September 23rd 2010

beaglelady (31517):

If I were you, I would let the biochemists and probability theorists and information theorists discuss whether or not ID people have reasonable research proposals on the table, and concentrate instead on obtaining a basic understanding of ID.

The way to get an understanding of ID is not to take trips to museums and attend book signings by Ken Miller and sermons by John Polkinghorne, or to listen to distortions and half-truths spread by people like Pennock and Scott.  It’s to read entire theoretical works by ID proponents, and to read entire works by Darwin and substantive discussions of neo-Darwinian theory, trying to discern what the debate is about.  I recommend you do this before offering further opinions.

For months now I have been challenging you on your false charge that ID appeals to supernatural causes.  You have not offered one extended discussion of your own to substantiate this view.  I’m challenging you again: find me texts in theoretical works by ID proponents where the argument for design depends upon positing a supernatural intervention into natural processes.  (This will be particularly hard if you have read few or none of those works, which I strongly suspect to be the case.)


beaglelady - #31594

September 23rd 2010

Johan,

Are the things you mention in comment 31549 actually part of specific requests?  To which organizations were the requests made?

I am interested in this one experiment you mention:

ID proposes that we grow bacteria, we nuke em, we mutate em until the cows come home in order to see what Darwinian processes can do.

How do you propose that ID theorists control for the designer in said experiment?  Is it assumed that he is currently inactivated, having worked his wonders in the remote past only?  Or could you simply post a picture of God with a red bar through it?  Inquiring minds want to know!


beaglelady - #31597

September 23rd 2010

If I were you, I would let the biochemists and probability theorists and information theorists discuss whether or not ID people have reasonable research proposals on the table, and concentrate instead on obtaining a basic understanding of ID.

You are the one who mentioned lack of funding for ID research, so it seemed reasonable to ask you what research you were referring to.


beaglelady - #31598

September 23rd 2010

re 31590:

“Intelligent design is just the Logos theology of John’s Gospel restated in the idiom of information theory”

-Wm Dembski


Rich - #31600

September 23rd 2010

beaglelady:

No, “nailing jello to the wall” is trying to get any biologist here or anywhere in the world to propose a mathematically testable hypothetical evolutionary pathway for any major organ, system, or body plan.  If you ask that question, you’ll get one of three answers:

1.  Evasiveness and sputtering defensiveness (That’s not a fair question!  It’s unreasonable to expect evolutionary biologists to do what theorists in every other science are routinely expected to do—provide quantifiable, testable, working models to explain how and why a natural process happens!);

2.  An I.O.U., promising the answer with “further research” (150 years, including nearly 60 since the unravelling of the DNA mystery, isn’t enough), but strangely not coupled with the withdrawal, until the I.O.U. is made good, of the claim that Darwinian evolution ‘is a scientific accomplishment on the level of the theory of gravitation’;

3.  If all else fails, the “killer argument”:  “You don’t have a Ph.D. in biology and therefore are not qualified to speak about evolution.”  (Except of course if you are on the Darwinist side, in which case an M.A. in geography or a Ph.D. in physics or a B.A. in music qualifies you eminently.)


beaglelady - #31602

September 23rd 2010

For crying out loud, you either know of research funding requests or you don’t! Stop tap-dancing.  Why complain about the lack of funding if you don’t even know if funding has been requested?


Rich - #31604

September 23rd 2010

beaglelady (31598):

Nope, your’e not getting away with a one-liner again.

First, I doubt you could tell me what work of Dembski that quotation comes from—*without looking it up on the internet*; I doubt you’ve read the work at all.  The quotation itself is easily obtainable from anti-ID sources.  And unless you’ve read the work, you’re quoting out of context, which is standard practice for TEs and atheist Darwinists, but academically dishonest.

Second, if you *have* read the work, prove by a detailed argument (passages plus your personal analysis, please!) that “the Logos theology of John’s Gospel” implies, for Dembski, supernatural interventions in the evolutionary process.

Third, I specified *theoretical* works, not Christian writings (where ID proponents express personal theological views which are not essential to ID as such), and just to be clear, I mean: Design Inference, No Free Lunch, Design of LIfe, Darwin’s Black Box, Edge of Evolution, Signature in the Cell.  I doubt you’ve managed to get all the way through even one of those, but anyhow, that’s your task, to document your claim from those works.  Until you’ve done it, you are intellectually obligated to withdraw all claims that ID demands miracles.


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