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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 - #31233

September 21st 2010

If we found a building like the Taj Mahal on Pluto, we would know it was designed, without having the slightest idea how it got there.

So we would say, “how interesting, this was designed!” and the go about our merry way?  Wouldn’t we want to ask who, when, why and how?  Shouldn’t questions like that be allowed?


Rich - #31238

September 21st 2010

beaglelady (31233):

Rich:
If we found a building like the Taj Mahal on Pluto, we would know it was designed, without having the slightest idea how it got there.

bl:  So we would say, “how interesting, this was designed!” and the go about our merry way? 

In asking this question, you seem to have forgotten that Richmond Dorkins, the noted atheist, and Kendreth Pillar, his Christian friend, had argued in best-selling popular books that the structure on Pluto could easily be explained by the random action of earthquakes and cosmic ray bombardments.  The conclusion of design would thus be a refutation of a widely-touted view, and therefore non-trivial.

bl: Wouldn’t we want to ask who, when, why and how?  Shouldn’t questions like that be allowed?

Of course questioning should be allowed.  But the person who answers the other questions won’t be the same as the person who answers the question of design.  A scientist can point out the design, but is not competent to identify the designer.


Rich - #31241

September 21st 2010

Alan:

“I think honest accommodation (“what you say is plain daft but I respect your right to say it”) is the way forward.”

Ah, if only this could be the guiding principle in these debates at all levels. 

But at the academy, it’s:  “I respect your right to say it, but if you do say it, I’ll do everything in my power to make sure that you never get tenure, and if you have tenure, I’ll do everything in my power to make sure you never get any research grants, and I’ll also operate a private blog using university facilites where I smear your name by accusing you of academic incompetence and personal dishonesty.”

And at the door of courts and legislatures, it’s: “I respect your right to say it, as long as you don’t say it on school property; we can’t have religion in the schools, and criticizing neo-Darwinism in the schools, using the tools of science—probability theory and information theory and biochemical theory—is obviously religion and violates the First Amendment.”

Have a good vacation, Alan.


John - #31313

September 22nd 2010

Rich wrote:
“In asking this question, you seem to have forgotten that Richmond Dorkins, the noted atheist, and Kendreth Pillar, his Christian friend, had argued in best-selling popular books that the structure on Pluto could easily be explained by the random action of earthquakes and cosmic ray bombardments.  The conclusion of design would thus be a refutation of a widely-touted view, and therefore non-trivial.”

So what? How would their arguments prevent you from studying anything?

bl: “Wouldn’t we want to ask who, when, why and how?  Shouldn’t questions like that be allowed?”

Rich: “Of course questioning should be allowed.  But the person who answers the other questions won’t be the same as the person who answers the question of design.”

Why not? You’re not making any sense.

“A scientist can point out the design, but is not competent to identify the designer.”

That’s simply insane. Real working scientists who identify designs, such as archaelologists, competently identify designers and builders all the time.

Your handwaving is just clumsily covering up the religious motivations underlying ID creationism.


beaglelady - #31327

September 22nd 2010

Of course questioning should be allowed.  But the person who answers the other questions won’t be the same as the person who answers the question of design

What? Why not?  These important questions are integrated, and it’s part of a scientist’s job to answer them. Talk about a science-stopper!

Imagine an archaeologist saying, 
“Someone built this, we just don’t know or care who built it or when it was built, or how it was built or why it was built, or who lived here or why the site was abandoned.” 

Imagine an anthropologist saying,
“Yeah, someone or something made this out of flint, but it’s not my concern exactly who did it or how they did it or why they did it or when they did it.”


beaglelady - #31330

September 22nd 2010

The philosopher Robert Koons is spot on when he writes:
“How could it be proved that something could not possibly have been formed by a process specified no more fully than as a process of ‘numerous, successive, slight modifications’?And why should the critic [of evolution] have to prove any such thing?”

Well, Robert Koons doesn’t realize that science isn’t about proofs. Science works by inference to the best explanation.


Rich - #31337

September 22nd 2010

beaglelady (31327):

You are missing the point of the illustration.  The debate between ID and Dawkins-Dennett-Coyne is about whether chance alone, without any intelligent plan, could have produced all the marvels of life that we observe.  ID says “No”, the atheists say “Yes.”

The Pluto illustration was meant to point out what everyone grants in the practice of their lives, i.e., that integrated complex structures don’t arise by chance.  No one, not even the stubbornest TE, would argue that a Taj Mahal on Pluto arose out of earthquakes or lightning etc.  No one would argue that “methodological naturalism” constrains scientists to explain a Taj Mahal on Pluto by chance.  Everyone would agree that the design inference was legitimate.

*Of course* in an actual Pluto situation, we would go on and try to identify who built the structure.  I was not recommending otherwise.  You’re misreading the analogy by taking it literally. The analogy points out that *the inference to God* is outside the sphere of science, whereas *the inference to design* is not.  The analogy was a response to your continuing confusion between “design” and “supernatural intervention.”  It’s a confusion endemic among TEs, but not among ID theorists.


Rich - #31347

September 22nd 2010

beaglelady (31330):

“Science works by inference to the best explanation.”

Stephen Meyer has been saying this for years now.  Welcome to the ID camp, beaglelady.


beaglelady - #31354

September 22nd 2010

No one, not even the stubbornest TE, would argue that a Taj Mahal on Pluto arose out of earthquakes or lightning etc.  No one would argue that “methodological naturalism” constrains scientists to explain a Taj Mahal on Pluto by chance.  Everyone would agree that the design inference was legitimate.

That’s because we are familiar with buildings and what sort of being might have built them and we can see how they are built..

btw, does the Star of India sapphire look designed?


beaglelady - #31355

September 22nd 2010

But at the academy, it’s:  “I respect your right to say it, but if you do say it, I’ll do everything in my power to make sure that you never get tenure, and if you have tenure, I’ll do everything in my power to make sure you never get any research grants, and I’ll also operate a private blog using university facilites where I smear your name by accusing you of academic incompetence and personal dishonesty.”

Well now, 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.


beaglelady - #31356

September 22nd 2010

Stephen Meyer has been saying this for years now.  Welcome to the ID camp, beaglelady.

And that leaves Johan out, I suppose.  Given the poor track record of supernatural explanations,  ID can hardly be considered a best explanation.


John - #31357

September 22nd 2010

Rich trotted out a smelly, old creationist canard:
“The Pluto illustration was meant to point out what everyone grants in the practice of their lives, i.e., that integrated complex structures don’t arise by chance.”

Evolutionary theory doesn’t posit that either, Rich, as natural selection isn’t chance. But you already knew that and decided to try and deceive your audience anyway.

“The debate between ID and Dawkins-Dennett-Coyne is about whether chance alone…”

Utterly, completely, false. Evolution doesn’t proceed by “chance alone,” and you know it. Why is repeatedly violating the Ninth Commandment acceptable to defend your political views? It sure can’t be to defend any truly Christian position.


Rich - #31359

September 22nd 2010

beaglelady (31356):

“Given the poor track record of supernatural explanations,  ID can hardly be considered a best explanation.”

beaglelady, are you deaf?  How many times have I told you that ID doesn’t employ supernatural explanations?  And I just went to great lengths to explain to you the difference between “design” and “supernatural intervention,” yet it’s clear the distinction has not registered.  You are confident that you can adjudicate between Pennock and Dembski, Miller and Behe, yet you cannot grasp a distinction that is *essential* to the whole debate.  Have you no sense at all that possibly, just possibly, you have not read enough serious ID writing, or have not understood serious ID writing well enough, to comment on the subject?  Were I in your position, that possibility would certainly occur to me.


Rich - #31369

September 22nd 2010

beaglelady:

“btw, does the Star of India sapphire look designed?”

Utterly irrelevant.  Design inferences don’t proceed on the basis of the superficial looks of something.  Once again, if you actually knew ID literature, you would know that.  But you continue to think that you can refute ID without knowing what it says.


John - #31378

September 22nd 2010

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

Dembski: “Indeed, intelligent design is just the Logos theology of John’s Gospel restated in the idiom of information theory.” - with A., Kushiner, James M., (editors), Signs of Intelligence: Understanding Intelligent Design, Brazos Press, Grand Rapids, Michigan, 2001.

Who is the spokesman for the ID movement: Dembski or Rich?


John - #31379

September 22nd 2010

Rich wrote:
“Design inferences don’t proceed on the basis of the superficial looks of something.  Once again, if you actually knew ID literature, you would know that.”

I do know “ID literature,” and I know that it is based on superficial appearances and superficial scholarship.


Bilbo - #31383

September 22nd 2010

Alan:  So it looks like there are genetic mechanisms in place that control the production of the appropriate proteins.

Yes…your point? 

Alan: I have to bow out for an indefinite period,

OK.


Rich - #31385

September 22nd 2010

“John”, whoever he is, knows the conditions under which I will answer any further of his posts.  They include: adoption of a tone suited to civilization; an apology for all past imputations of dishonesty; the name of the website of the “Rich” with whom he falsely identified me; an apology for continuing to identify me with “Rich” even when corrected, and for his embarrassing display of anger the whole time he assumed that I was that “Rich” without checking; and now—upping the price—an admission that he was flatly wrong about the “genome” claim in an earlier debate, and a link to a list of his alleged scientific publications, a list which identifies him by name and institution.  Otherwise, there will be no replies to his objections.  (They are easily refuted, but I will not engage in dialogue with someone who does not respect the customs of educated discourse.)

So keep typing until the cows come home, my friend, if you have so little to do in your “research” lab that you have this much time to spare on the internet.  You’ll be talking only to yourself.


John - #31391

September 22nd 2010

Rich,

What makes you think I’m expecting a substantive response to any of my comments? You never did before…

“So keep typing until the cows come home, my friend, if you have so little to do in your “research” lab that you have this much time to spare on the internet.  You’ll be talking only to yourself.”

So again, you responded! Amazing. Do you not think before you type?


beaglelady - #31400

September 23rd 2010

But at the academy, it’s:  “I respect your right to say it, but if you do say it, I’ll do everything in my power to make sure that you never get tenure, and if you have tenure, I’ll do everything in my power to make sure you never get any research grants, and I’ll also operate a private blog using university facilites where I smear your name by accusing you of academic incompetence and personal dishonesty.”

Again, 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?


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