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 - #31605

September 23rd 2010

For months now I have been challenging you on your false charge that ID appeals to supernatural causes.

Here’s another quote:

If we take seriously the word-flesh Christology of Chalcedon (i.e. the doctrine that Christ is fully human and fully divine) and view Christ as the telos toward which God is drawing the whole of creation, then any view of the sciences that leaves Christ out of the picture must be seen as fundamentally deficient.

(William Dembski, Intelligent Design: The Bridge Between Science and Theology, Downers Grove, InterVarsity Press, 1999.)

Look up the book on amazon.com or use my link above.  amazon lets you “Look inside the book”

In the preface (p 13) Dr. Dembski says “Intelligent Design is three things:....”

Look what his number three is:  “A way of understanding divine action”


Rich - #31607

September 23rd 2010

beaglelady (31602):

“For crying out loud,” either you can document the theoretical connection between design detection and miracles or you can’t.  “Stop tap-dancing” around the real issue, which is that you’ve been talking about ID for months now, by all indications based 90% on rumor and hearsay.  Demonstrate your knowledge in coherent, paragraph-style prose, or retract your statements.

It’s a bit rich for you to complain about one unanswered question, beaglelady, when over the past six months, you’ve left dozens of my rebuttals and questions unanswered, or answered them with ambiguous one-liners almost devoid of content.  The mote and the beam—you may have heard that story in church.


John - #31608

September 23rd 2010

Johan wrote:
“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.”

1) People propose things. ID doesn’t propose anything.
2) It’s already been done.
3) It isn’t a test of an ID hypothesis. No one has sufficient faith to empirically test an ID hypothesis.


John - #31609

September 23rd 2010

Johan wrote:

“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.”

1) People propose things. ID doesn’t propose anything.
2) It’s already been done.  You’re also misrepresenting it. We make amino-acid substitutions. I’ve even done this myself, and my data aren’t consistent with Axe’s data. That’s why Axe hasn’t published any new data for MORE THAN TEN YEARS.
3) It isn’t a test of an ID hypothesis. No one has sufficient faith to empirically test an ID hypothesis.


John - #31610

September 23rd 2010

Johan wrote:

“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.”

But It’s already been done, and you don’t have a clue as to the existing data.  It’s very easy to jump from one functional protein to another (not “the next”) in sequence space.

This is science, no one in the ID movement is doing it, and It isn’t a test of an ID hypothesis. No one has sufficient faith to empirically test an ID hypothesis. That’s intellectual and theological cowardice.


Rich - #31611

September 23rd 2010

beaglelady:

I specify *theoretical works* and you quote *again* from a *religious* work, published by Inter-Varsity Press.  Do you need the distinction explained to you?  Or do you keep referring solely to Dembski’s religious works because you haven’t read the theoretical ones?  That would explain much.

It is also interesting that your source is from *1999*, a long time ago (like most of your other sources).  Do you have any knowledge whatsoever of Dembski’s *current* views?  In particular, do you know any *recent* passage where Dembski has addressed the question *whether intelligent design, as a theory, requires miraculous intervention*?  Not whether he personally inclines toward divine intervention, but *whether ID theory requires it*?  If you have knowledge, trot it out.  But it may require (gasp!) reading *a whole book* by an ID proponent, as opposed to scrounging up snippets on the internet to support a position you’ve already decided on, and by gosh, we can’t let our positions be decided by *research*, can we?


Rich - #31615

September 23rd 2010

Johan:

You might ask “John” where he has published his alleged “data” which is inconsistent with Axe’s data.  It’s amusing to hear “John” rail against ID people for lack of “faith” in their hypothesis, when they put their names and careers on the line, while he has so little lack of “faith” in his research that he hides his identity and won’t link to any of his publications, so that the world can weigh his claims against those of the ID people.  But of course, the scientific qualifications of “John” are very much in question; months ago I disproved a claim of his about the use of a very basic biological term—“genome”—in evolutionary literature.  I find it hard to believe that anyone so unfamiliar with the basic jargon in his alleged field could produce any scientific research worth mentioning.


John - #31618

September 23rd 2010

Rich wrote:
“You might ask “John” where he has published his alleged “data” which is inconsistent with Axe’s data.”

Our data *are* inconsistent with Axe’s data. They were published in JBC, Cell, PNAS, and BMC Cell Biology.

“…so that the world can weigh his claims against those of the ID people.”

Science is about data, not claims. The ID people can’t be bothered to produce any data themselves.

“But of course, the scientific qualifications of “John” are very much in question; months ago I disproved a claim of his about the use of a very basic biological term—“genome”—in evolutionary literature.  I find it hard to believe that anyone so unfamiliar with the basic jargon in his alleged field could produce any scientific research worth mentioning.”

If you’re so sure, Rich, how much are you willing to bet?


John - #31619

September 23rd 2010

Whoops! Forgot one: in Neuron.


Rich - #31628

September 23rd 2010

Johan:

Well, I tried, but “John” is still concealing both his name and the titles of his articles, making them impossible to locate.  He appears to think it is sporting to sneer at Doug Axe, whose name and published papers are available to all, while he himself hides beyond anonymity and unnamed research which allegedly shows Axe wrong.  That certainly is not the standard behavior of one scientist who challenges another.  “John” thus ranks below even an insulting loudmouth like Myers in my books.  At least Myers identifies himself, thus making himself equally vulnerable to criticism as the ID people he attacks.  But I’m so far from expecting anything like intellectual and professional integrity from most ID critics, that I just take the behavior of “John” as the new normal.  We live in dark times, and apparently we must lower our expectations for public discourse.  It’s very sad, though, to think of the classy, gentlemanly behavior my generation expected from scientists, in comparison with the vulgar displays of temper and partisanship that this generation of Ph.D.s is willing to stoop to, in order to enforce evolutionary orthodoxy upon an unwilling and unpersuaded population.


John - #31629

September 23rd 2010

Rich wrote:
“Well, I tried, but “John” is still concealing both his name and the titles of his articles, making them impossible to locate.”

I’m perfectly willing to reveal all when you reveal how much you are willing to bet that I haven’t published them—and put that money up.

We all know you won’t.

“He appears to think it is sporting to sneer at Doug Axe, whose name and published papers are available to all, while he himself hides beyond anonymity…”

No, Rich, I’m hiding behind a pseudonym. I authorize the webmaster to reveal the IPs from which I post to you, if that helps.

“...and unnamed research which allegedly shows Axe wrong.”

Try reading what I actually wrote, Rich. You won’t, because deception is all you’ve got in your tiny bag of tricks.

“That certainly is not the standard behavior of one scientist who challenges another.”

What a preposterous falsehood!

It’s SOP in real science to challenge someone else’s conclusions and proposals without revealing one’s name. We call it “anonymous peer review” because the reviewers don’t use pseudonyms, unless you’d call “Reviewer #2” a pseudonym.


John - #31632

September 23rd 2010

Rich whined to beaglelady:
“I specify *theoretical works* and you quote *again* from a *religious* work, published by Inter-Varsity Press.”

Why aren’t there any empirical works?

“It is also interesting that your source is from *1999*, a long time ago (like most of your other sources).”

You’ve presented no evidence that Dembski’s view has changed.

“Do you have any knowledge whatsoever of Dembski’s *current* views?”

The question is, do YOU, Rich?

“In particular, do you know any *recent* passage where Dembski has addressed the question *whether intelligent design, as a theory, requires miraculous intervention*?”

That was a thoroughly dishonest move of the goalposts. Your claim is simply, “ID doesn’t employ supernatural explanations,” Rich. Thanks for implicitly admitting that your claim is objectively false.


John - #31634

September 23rd 2010

Rich:
“Not whether he personally inclines toward divine intervention, but *whether ID theory requires it*?”

There is no ID theory:
“Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a real problem.”
Paul Nelson, interviewed in Touchstone 17 (6): 60–65.

“If you have knowledge, trot it out.”

Your hypocrisy is staggering. Trot out your knowledge, Rich. I’m especially interested in your implicit claim that you are a better spokesman for ID than either Dembski or Nelson.


beaglelady - #31641

September 23rd 2010

I specify *theoretical works* and you quote *again* from a *religious* work, published by Inter-Varsity Press.

Well, first you said the following before moving the goalposts:

For months now I have been challenging you on your false charge that ID appeals to supernatural causes.

And I provided an answer to your challenge.  Besides, Dr. Dembski made a statement; why not take it at face value?  Perhaps you should specify that the answer must come from a book published between 2009 and 2010 that has a red dust jacket and has between 398 and 403 pages.

In particular, do you know any *recent* passage where Dembski has addressed the question *whether intelligent design, as a theory, requires miraculous intervention*?

Now why would he say anything like that,  after losing a court case?  There are wealthy people out there who don’t (officially or legally) have any money in the bank, you know.


beaglelady - #31642

September 23rd 2010

Do you have any knowledge whatsoever of Dembski’s *current* views?

Does he change his views often?


John - #31652

September 23rd 2010

beaglelady: “Does he change his views often?”

That one’s gotta hurt. So, Rich, does he?


Rich - #31658

September 24th 2010

beaglelady:

First of all, I didn’t say Dembski has changed his mind; he may or may not have.  Yet intelligent people, unlike dogmatists, change their minds now and then when thinking about difficult theoretical issues.  That’s why anyone with proper university training seeks statements of authors that are as recent as possible.  Apparently this habit wasn’t encouraged in your educational program.

Second, the statements of Dembski which you quoted, in themselves, without further contextual information, do not imply that Dembski was arguing for intervention in the creation or evolution of life.  And because you were quote-mining (was that approved practice in your music essays?), you had no interest in providing the necessary context.

Finally, it’s clear from your evasions that you don’t know the ID theoretical works well enough to even discuss them, let alone debate them; it’s also clear that you refuse to consult the explicit definitions of ID which separate it from supernatural causes, such as can be found in numerous places on Discovery and elsewhere.  You’ve simply planted your feet in a massive display of stubbornness, so I leave you comfortable with your invented facts and your invented universe.


Johan - #31673

September 24th 2010

@Beaglelady

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

What Dembski is saying here is this; “to say in the beginning was the Word [Logos] “is the same as saying in the beginning was information. Now, Dembski is free to interpret this verse as such, but Dembski understands well that ID even if true in every respect it wouldn’t prove Christianity over any other theistic religion. Dembski clearly understands that ID doesn’t prove Christianity over any other religion. Now here is a quote you would never see an evolutionist cherry pick:

“ID’s metaphysical openness about the nature of nature entails a parallel openness about the nature of the designer. Is the designer an intelligent alien, a computional simulator (a la THE MATRIX), a Platonic demiurge, a Stoic seminal reason, an impersonal telic process, …, or the infinite personal transcendent creator God of Christianity? The empirical data of nature simply can’t decide.”


Johan - #31674

September 24th 2010

Does he change his views often?//

Well said Rich, and I agree, many great scientists of the past have changed their minds. For example, Mivart started out as a staunch proponent of natural selection, but eventually became one of Darwin’s fiercest critics. Karl Ernst von Baer[ father of developmental biology] started out as a moderate evolutionist who accepted Darwin’s ideas, although later he grew skeptical and became a fierce critic and published a book long critique on Darwin’s Origin of species. Jacob von Uexkull [father of biocybernetics, biosemiotics] use to be a moderate Darwinist, however he later became one it’s fiercest critics. To name a few.


beaglelady - #31700

September 24th 2010

First of all, I didn’t say Dembski has changed his mind; he may or may not have.  Yet intelligent people, unlike dogmatists, change their minds now and then when thinking about difficult theoretical issues.  That’s why anyone with proper university training seeks statements of authors that are as recent as possible.  Apparently this habit wasn’t encouraged in your educational program.

You don’t know Dembski’s latest views?  Even you don’t keep up with his latest views, you who study ID theoretical works day and night?  How can I keep up with the latest views of ID guys if even you can’t? We are doomed!

Here’s a suggestion:  Create a site just like Yahoo Finance.  You enter the name of the ID guy and you get his views for the day.


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