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Sunday, March 20, 2011

Bacteria Flagellum not refuted


Casey Luskin raises some interesting points for those who are convinced that the bacteria flagellum is a poor example of intelligent design. The entire article is a bit technical but feel free to comment on it here. It appears that Luskin is personally engaging the public in the comment section below the article so feel free to direct a question towards him. I personally found the following comment to be quite interesting...

"I used to be anxious that taking a lot of Biology and Biochemistry classes would challenge my faith. Then I took Metabolism, Cell Biology, and Immunology. What I discovered was such mind-blowing complexity that it's impossible to believe there wasn't some kind of Designer anymore. More education caused me to become more religious. Professors will try to offer naturalistic explanations for everything, and it's tempting to believe them because the have a PhD. However, once you start asking yourself if their explanations really make sense instead of taking their word for it, purely naturalistic evolution starts looking like the biggest hoax in the history of science."

26 comments:

GentleSkeptic said...

Argument from Incredulity. Again.

Theological Discourse said...

Try reading the WHOLE ARTICLE instead of what was posted here GS. For such a 'skeptic' you sure do love to jump to conclusions without taking in ALL of the evidence.

To anyone that actually read the original article its quite obvious that the argument isn't this:


What I discovered was such mind-blowing complexity that it's impossible to believe there wasn't some kind of Designer anymore.


but instead is, well, the, the actual article instead of someone just COMMENTING on the article. The author of the real article is not using an argument from ignorance, he is clearly stating the following:

modern Darwinian theory -- as classically understood -- has come no where close to explaining the origin of this remarkably complex and sophisticated motor engine.'


For the logically inept such as GS I will break it down.

P: Behes Bacteria Flagellum argument has not been refuted.
P: gives reasons in the form of actual evidence like the following:

"Why exactly is flagellum biosynthesis so tightly regulated and orchestrated? Not only do the energy demands render the flagellum an extremely expensive system to run, but untimely expression of flagellum proteins may induce a strong immune response in the host system, something no bacterium wants to do.

What is the significance of this from the standpoint of evolutionary rationale? Well, flagellin monomers are somewhat potent cytokine inducers. If you are a Yersinia organism in possession of a Type-III Secretion System the last thing you want to do is display those flagellin peptides to the macrophages. Such would be liable to significantly countermand the Yersinia's anti-inflammatory strategy."


The above excerpt is not anywhere close to an argument from ignorance. It is not saying anything at all along the lines of "it's so grand and excellent that it was designed," etc. etc.
C: therefore Behes Bacteria Flagellum has not been refuted.

It's very clear that the "gentle" part of your name refers to "gentle on logic and critical thinking," since you are clearly unable to tell the difference between "therefore it was designed" and "therefore Behes Bacteria Flagellum argument has not been refuted."

Patiently awaiting for you to charge in here and prove my point, by either missing the point and trying to discuss what the articles evidence proves or by simply being completely intellectually dishonest and refusing to admit your error.

Jquip said...

"Argument from Incredulity. Again."

Yep. I'm pretty tired of it myself. Design guys say it hasn't been proven so it must be false. Dice guys say it hasn't been disproven so it must be true.

I think you'll agree that we should ask both ends of this debate to knuckle down and start doing some actual science. Put it on the lab table and evolve flagellar motors from scratch. The loser goes home with a broken theory. Until that happens this is all just interfaith bickering.

GentleSkeptic said...

What Jquip said. Sort of.

In short, it's not up to evolutionary theorists to show EXACTLY HOW the bacterial flagellum developed, because we CAN'T ever know for sure. All the evolutionary theorist has to do is show that the development of the bacterial flagellum is plausible given what we know; in other words, that it is not "irreducibly complex," a term made up by ID proponents.

More generally, the fact that today's biologists cannot provide a definitive account of how every single structure or organism evolved proves nothing about design versus evolution. Biology is still in its infancy, and even when our understanding of life and its history is far more complete, our ability to reconstruct what happened billions of years ago will still be limited.

Mr. Luskin, on the other hand, has his work cut out for him. He is making a positive claim: the bacterial flagellum WAS DESIGNED. Note that he never specifies how, or to what end, or even by whom, exactly. Instead of spending his time insisting that the other guys obviously have it all wrong, he really needs to get into a lab and propose and test a mechanism for the alleged design and a positive identity for the alleged designer. (Of course, we al know Who the Designer Is, but even the IDers can't come right out and say it, less the 'science' of ID actually begin looking like the religion that it is.) Even if he were to completely and single-handedly dismantle the ToE, it wouldn't count as evidence that his theory is right.

Patiently awaiting for you to charge in here and prove my point…

Get comfy. You're gonna be here awhile.

Theological Discourse said...


He is making a positive claim: the bacterial flagellum WAS DESIGNED.

No, he was making a positive claim: the bacterial flagellum argument was NOT REFUTED. See the title of the article and the conclusion of his article?

Now read where I wrote this:
you are clearly unable to tell the difference between "therefore it was designed" and "therefore Behes Bacteria Flagellum argument has not been refuted."


You are confusing 2 different arguments. The argument "therefore it was designed" is not hte same argument as "the BF argument was refuted" and more importantly the argument wasn't an argument from ignorance.

Theological Discourse said...

looks like I didn't have to wait very long, you proved my point in your very first response against it!

now, I don't expect you to admit you were wrong, I mean, even when evidence is plain and clear as day, punching you in your face, you still won't admit it, but it isn't usually for you, its for people reading it.

Jquip said...

"In short, it's not up to evolutionary theorists to show EXACTLY HOW the bacterial flagellum developed, because we CAN'T ever know for sure."

Absolutely, and that sword cuts both ways. If our definition of plausible is a just-so story that fits within our preconceptions? Tell me your preconceptions and I can make a plausible story up on the spot. I'm just not going to pretend I'm doing science by clowning Rudyard Kipling.

If it's to be science it needs to hop up on the lab table. And sure we will never be able to show `exactly` how some current artifact produced from historical postulates we don't have absent a time machine. But we can at least show that the proposed intermediates don't kill the critter or prevent fixation.

It's not sufficient, but it's the lowest possible expectation we can have and still call it science. This is true even if you're reading about the evolution of a protein under Dice as a fan of Dice yourself.

JD Curtis said...

No, he was making a positive claim: the bacterial flagellum argument was NOT REFUTED

I probably wasn't thinking of it at the time TD, but yes, this is an important destinction.

I would say that the arguments advanced by Luskin, Behe, et al "lend greater weight" to the idea that there was a Creator, than such structures, as cited up above, occurred in nature through strictly materialistic, undirected processes.

Justin Vacula said...

Yes, ID is junk science. The scientific community (the experts) have come to quite an overwhelming consensus based on evidence leading to the conclusion that evolution happened...and just because you can't explain something doesn't mean that you can jump to supernaturalistic explanations.

Here's all you need to know about the flagella:
http://www.talkorigins.org/indexcc/CB/CB200_1.html

JD Curtis said...

Yes justin,

Thank you for the obligatory talkorigins.org link dump.

You readily admit that the flagellum reference cannot be readily explained. Since when did anyone from the scientific community "create" one where there was none before?

qwer said...

What is Darwinian theory, anyway? Perhaps he means Evolution theory? This straw man fallacy states that, classically understood, it does not explain the origin of the flagellum. There is no reason why it should. Evolution theory explains the origin of species, not specifically its component parts - which are covered by other biological disciplines.

Behe's irreducible complexity argument most certainly has been refuted, and anyone that has read Jonathon Miller's book, Only a Theory, would know this.

"Not only do the energy demands render the flagellum an extremely expensive system to run, but untimely expression of flagellum proteins may induce a strong immune response in the host system, something no bacterium wants to do."

If this is the case, it is obviously a very poor design, and yet it exists both in its current form, AND its component parts in other applications.

To say that the irreducible complexity argument for the flagellum hasn't been refuted, is to say that you are ignorant of the refutation. It is, therefore, clearly an argument from ignorance.

Theological Discourse said...


Yes, ID is junk science. The scientific community (the experts) have come to quite an overwhelming consensus based on evidence

the same scientific community that came to an overwhelming consensus on global warming....oh wait....

Theological Discourse said...

Dropping a talk origins link is almost always a for sure indication that person is a sheep, a blind follower who possess the type of blind irrational faith that he accuses religious people in having, and the funny thing is, 9 times outta 10, the person dropping the link has little to no clue what the article is talking about.

Everytime someone drops a talk origins link I just drop a link to some creationist site, its just as effective.

GentleSkeptic said...

"Irreducible Complexity" IS the Argument from Incredulity, just fancied up a little.

"We just can't figure out how this structure might have arisen naturally, therefore it was designed." That's it.

And saying that "the bacterial flagellum argument was not refuted" is somehow different than saying that "our original argument—that the bacterial flagellum was designed—still stands" is not an important distinction. It is a distinction without a difference. And nothing is more tiresome that Internet Theologians who play self-congratulatory semantic games while dodging substance. But then, that's what theology is, really.

And JQuip's sword, while certainly sharp, does not, in fact, cut both ways.

If our definition of plausible is a just-so story that fits within our preconceptions? Tell me your preconceptions and I can make a plausible story up on the spot.

Great! Except that when dealing with the ToE in 2011, it's not just airy "preconceptions" that must be satisfied, it's compatibility with the mountain of existing evidence. The ToE proposes mechanisms for the development of of the BF that do both. (See that talkorigins dump.) ID, on the other hand, is saddled with only the airy preconceptions, and made-up ideas like Irreducible Complexity.

……………

But here's my real beef with the endless wrangling over the stupid bacterial flagellum.

Let's say, for the sake of argument, that YHWH is real and that he's the Designer. (Just cutting to the chase here.) Let's also agree that man is the Object of His Creation, the real story of life on Earth.

Why is it that Behe and Luskin must forever look at bacteria to find "irreducible complexity"? Why aren't the Creator's most beloved creatures irreducibly complex? I can remove your appendix, your spleen, a kidney, breasts, some lymph nodes, an eye, even a limb or two, and you will still function. Why do we have to focus almost exclusively on flagellar motors to reveal the glory of the Designer's design?

Theological Discourse said...


To say that the irreducible complexity argument for the flagellum hasn't been refuted, is to say that you are ignorant of the refutation. It is, therefore, clearly an argument from ignorance.

someone doesn't know what an argument from ignorance is....

JD Curtis said...

If this is the case, it is obviously a very poor design, and yet it exists both in its current form, AND its component parts in other applications

Youre basically conceding design, 'But I don't like the design'.

Justin Vacula said...

I'm not a scientist and neither are you. I don't have the relevant expertise regarding this issue, but only have lay knowledge. In matters scientific, you need evidence and reputable sources. Talk Origins is that source needed, thus I link it.

JD Curtis said...

"The basic puzzle is that the flagellum is made up of dozens of protein components, and deletion experiments show that the flagellum will not assemble and/or function if any one of these components is removed (with some exceptions). How, then, could this system emerge in a gradual evolutionary fashion, if function is only achieved when all of the required parts are available?" Link

Jquip said...

""Irreducible Complexity" IS the Argument from Incredulity, just fancied up a little."

Let's say that I hypothesize that some object was created through stochastic variation within an iterative process. Now we've all tested the iterative process already. Eh. Possibly, we are arguing on the internet. If our hypothesis fails then it means that stochastic variation doesn't account for our observations and we have IC. Flip the hypothesis over and you'll find the same thing. Easy task that as Charles Darwin already did that work in his first book on the subject.

Dice and Design are each the null hypotheses of the other.

So far that's all proper. When it becomes a statement that we *should not test the hypotheses* is when we have an argument from ignorance.

"The ToE proposes mechanisms for the development of of the BF that do both."

So here's your introspective litmus: Is your theory more important than measurement? Do you support putting the hypothesized mechanisms on the lab table?

Jquip said...

"I don't have the relevant expertise regarding this issue, but only have lay knowledge. In matters scientific, you need evidence and reputable sources."

I agree and I applaud you for knowing your unknowns. Most folks are too small to even whisper such admissions.

Talk Origins is a great place to use for finding better information -- much like Wikipedia. Unfortunately they are, as they claim, very much an advocacy site with all that entails.

This includes a very unfortunate habit of misrepresenting their opponents' arguments. They also have a dreadful habit of using ad hominems as an argument rather than fun color commentary to come with one. Sometimes, they also misrepresent their own argument for better strength.

For example: Responses 1b and 1c on the page you provided are considered incorrect within the Dice camp. Given phylology and homology it is widely considered that the T3SS evolved from the Flagella rather than the other way around.

The essential problem for Dice is that the flagella is indeed a very sticky wicket. And we have not, as yet, worked out the particulars. The best and furthest work I'm aware of is that they figured out the ordering of the cascade needed to get self-assembly of the rotor proteins. Which is a good start but not nearly sufficient to satisfy Dice or Design fans.

Theological Discourse said...



"We just can't figure out how this structure might have arisen naturally, therefore it was designed.

Too bad that quote nor that line of thinking isn't found anywhere in the article.

And saying that "the bacterial flagellum argument was not refuted" is somehow different than saying that "our original argument—that the bacterial flagellum was designed—still stands" is not an important distinction. It is a distinction without a difference.


Actually the distinction is important, it distinguishes reality from fantasy. You see the former (the bacterial flagellum argument was not refuted)is something the article actually said, which is reality, while the latter (our original argument—that the bacterial flagellum was designed—still stands) is something you clearly made up, which can be classified as fantasy, since that is not found in the article at all, pretty important distinction there. Not only is the distinction important, but contrary to your assertion of the two arguments are a "distinction without a difference," they are indeed different. One argument is there, the other is something you made up, again, a very important difference between the two. Not to mention, the former and the latter are the difference between your initial assertion of "Argument from Incredulity. Again." to be correct and incorrect. Again, another difference. Furthermore, the initial argument need only give evidence to support how the BF argument has not been refuted, while the latter argument must give evidence of the existence of a designer, how the designer designed it, etc. etc. Another huge difference. I could go on and on.

You see GS, what you are doing is attempting to build a straw man argument. You are attacking an argument of your own construction rather than the one the author has made. The authors argument is "BF argument has not been refuted." The argument of your attacks is not the one the author has made, rather it is one of your own construction, which would be, "our original argument—that the bacterial flagellum was designed—still stands."

Thank you GS, for giving me so much evidence that clearly shows your poor use of logic and critical thinking, your intellectual cowardice and dishonesty, and your inability to gather all the facts before coming to a conclusion. It really makes it easier to completely show anyone that might read your comments how you are not to be taken seriously at all.

GentleSkeptic said...

Is your theory more important than measurement?

Right back atcha. The ToE has been measured and tested across multiple disciplines every which way from Sunday, and continues to amaze with its simplicity and elegance and explanatory power… can you say the same for ID?

Do you support putting the hypothesized mechanisms on the lab table?

Of course I do, and I'd love to. (If only it were that easy, we'd have our definitive answer already, wouldn't we?) I certainly never said that we shouldn't test the hypothesis. To suggest, on the other hand, that our inability to force the development of one bacterial mechanism in a petri dish would somehow put Dice and Design on equal footing is disingenuous. The bacterial flagellum, and arguments about it, do not exist in a vacuum. They are arrayed against a backdrop of staggering evidence in support of one theory, and a great big empty spot where evidence for—or even a clear articulation of—the other "theory" ought to be. All other things being equal, taking into account the known unknowns, and given that the BF is indeed a relatively sticky wicket, it is eminently safe to continue on testing away and looking for a solution under the hypothesis that the broad proof of the ToE will be upheld.

And ID is not a null hypothesis in any sense of the phrase. I'd say it's the opposite of a null hypothesis, if there is such a thing. It posits a Hidden Entity with an order of complexity beyond what we can "measure" or test. It leverages mechanisms that can't be recreated or even guessed at. It makes no meaningful predictions. It is non-parsimonious and unfalsifiable. I don't think it meets the criteria for a "theory" at all, just a belief.

"The explanation of a lesser entity in terms of a greater one is a perversion of what it means to explain."

So here's your introspective litmus: Is your theory more important than measurement?

I will also admit to having only lay knowledge, because it's only fair and it's not like I'm ashamed of it. I used to be in the YEC camp: I have been persuaded by the evidence. I think what sits most wrongly with me about ID—religion fronting as science—is that it makes no predictions and produces no useful or applicable knowledge. Behe and Luskin haven't developed any life-saving drugs; all they do is deny the ToE, and they've made lucrative careers out of simply being incredulous and ideologically motivated naysayers. Real science advances understanding, ID just tries to justify itself.

Jquip, I have to say that you're a super-sharp guy. It seems like we disagree on a lot—although I actually can't tell where you come down on this one—but I always enjoy reading your entries here. For what it's worth.

GentleSkeptic said...

TD: nothing would make me happier than if you would stop taking my comments seriously.

Theological Discourse said...


TD: nothing would make me happier than if you would stop taking my comments seriously

I don't, but that isn't going to stop me from pointing out the flaws and shortcomings in your...reasoning (i use that term lightly when it comes to you) and expose your intellectual dishonesty for other people so they may join me in not taking anything you say serious, and rightfully so, since the evidence clearly shows no one should do so.

Theological Discourse said...


I think what sits most wrongly with me about ID—religion fronting as science—is that it makes no predictions and produces no useful or applicable knowledge. Behe and Luskin haven't developed any life-saving drugs; all they do is deny the ToE, and they've made lucrative careers out of simply being incredulous and ideologically motivated naysayers. Real science advances understanding

so you're saying you think ID is wrong because of the reason listed above?

Jquip said...

"Right back atcha. The ToE has been measured and tested across multiple disciplines every which way from Sunday ..."

Heh, I'm a theoretical nihilist. I don't *do* theories per se. Most theories have been wrong and I accept that most will continue to be wrong. They are useless as a point of belief but awesome as a heuristic for what to measure next. Sadly we too often forget the need and reasons for the hypothesis/theory and choose to accept it as a true fact about things we don't know yet.

Take the ToE. Which one? Wallace's? Darwin's? Neo-Darwinian Synthesis? Or the last with more electrolytes? Gould? The list goes on. It's worth remembering that Before Dice and After Dice is split over 1953 -- Watson and Crick -- or 1972; when we finally got around to genetic sequencing. It's very young and largely untested. What *is* tested out the ying are PopGen diffusion equations. There's generally no argument over those in broad measure despite that people are still breathlessly publishing papers about bits that should have been obvious from the assumptions built into those equations -- see the recent bits about fast frogs.

"Of course I do, and I'd love to. (If only it were that easy, we'd have our definitive answer already, wouldn't we?)"

And that's what makes you a far better man than a biologist. The PopGen/Genetics dichotomy isn't trivial despite the pundits on both sides making great hay blurring the two together. If we've tested the yang out of the ToE then we would have a definitive answer. No matter the camp we're in we all need to get out the warsticks and start beating people until they can start doing science properly. This is a general flaw of science during the last 80 years and is in no way restricted to evolutionary biology.

"I will also admit to having only lay knowledge, because it's only fair and it's not like I'm ashamed of it. "

Wrong answer, you should be proud of it. The entire point of the formalized scientific method is the presumption that no one has more than lay knowledge. That's the point of it all.

"It seems like we disagree on a lot—although I actually can't tell where you come down on this one ..."

No worries, I'm just a friendly curmudgeon. If disagreements meant anything then my standard street wear would include steak sauce, a mini-grill, and a chainsaw.