Ode to the Flagellum

| 75 Comments


The evolution of the flagellum Youtube video based on Nick Matzke's hypothesis by CDK007

75 Comments

In order for one to even remotely consider a system as irreducible complex one must show that an exhaustive search of that system through diverse organisms and homologies of the proteins making up that system give no information as to how that system evolved.

Congratulations; I am fairly certain that this is the longest sentence ever posted on youtube.

Smexy!!! ^_^ XD XD

Very well Designed!

Is there any way that Behe or Minnich could be invited to take a look at this video. I would love to read what they have to say in comment.

MS

Wow! That’s great: now I can read Nick’s articles and have an idea about what’s going on.

I guess the other side will criticize the vieo as a just-so story, but I can’t see how to avoid that in such a short presentation, I assume the gaps, and explanations of intermediate function, have been filled in. Or most of them anyway!

Bob

‘just-so story’ or not, at least it’s a hypothesis! beats’ ‘poof’ anyday!

It’s great to have a visualisation tool like this.

In order for one to even remotely consider a system as irreducible complex one must show that an exhaustive search of that system through diverse organisms and homologies of the proteins making up that system give no information as to how that system evolved.

Does it follow from the statement above that an IC system is necessarily not an evolved system? Or could a system be IC even if it is evolved of simpler parts, those parts having abandoned or modified their previous functions?

I’m not trying to be difficult - I am only asking because I’ve made an assertion similar to that quoted above, but I’m not sure about it, because I’m not sure if there is any IC biological system. Or if we would consider it as losing function as it loses parts, or as it gains parts, as Popper’s ghost suggested. I suppose the function just changes or improves in either case. Icefish lost their red blood cells, but their circulatory system improved for their environment. And the type-III secretory system gained parts, but its function now serves the greater system of the flagellum.

So why isn’t a current system considered just as IC as an older version or a newer version? It appears IC is meaningless, or else it’s meaning just isn’t very applicable to any kind of argument.

Mark - I’m glad to see you paying attention. Please stick around!

I never spotted the link to the technical details in the video. Was there supposed to be a URL included somewhere?

Who produced the video? I’d like to have the proper attribution. Also, could Nick point us to the best reference to his hypothesis? Is it the talkreason article from 2003?

The idea that bacterial flagella evolved from secretion complexes has been around since 1997 (at least). The IDiots keep ignoring the fact that plausible explanations for irreducible complexity have been proposed. I think this is fundamantally dishonest—but that’s why I call them IDiots.

Mark Studdock Wrote:

Is there any way that Behe or Minnich could be invited to take a look at this video. I would love to read what they have to say in comment.

Without a doubt some variation of Dembski’s “It’s not ID’s task to match your pathetic level of detail.”

I’m not sure they will understand it without the fart sounds.

;-)

Katarina,

My take on IC is that it is a rhetorical strategy that went even better than IDers planned, because from the start, critics divided into “it’s not IC” and “it’s IC but evolved, like Muller’s concept.” Whatever you call it, there’s a testable, and increasingly successful, evolutionary explanation, and no non-evolutionary explanation.

What I think IDers did plan on was deliberately not differentiating between (1) origin of an IC system from another IC system and (2) origin of an IC system from an non-IC system. IOW a subtler version of the creationist conflation of abiogenesis and evolution.

IDers have no interest in impressing scientists, because they know that they have no alternative explanation to offer. But by making critics sound confused or intolerant, they score points with their target audience.

Drat, Steverino beat me to the obvious joke.

Appropriate music and provides nice testable intermediates. Hope it goes viral.

I guess the other side will criticize the vieo as a just-so story

The continual complaints of “just so stories” always seemed foolish since it misses the mark. A proposed explanation as a disguised hypothesis from which experiments can be derived provides a framework for future research. The inability to grasp this concept by the ID crowd has no.…..

Stop, sorry, kill that train of thought. I forgot, the underlying premises of ID 1. design is quantifiable 2. the designer is testable

are untestable, so of course they are reduced to calling anything else a “just so story”

Delta Pi Gamma (Scientia et Fermentum)

Updated with links. Note to self: When using HTML, do not use KwickXML link syntax :-)

Hi Frank J,

..critics divided into “it’s not IC” and “it’s IC but evolved, like Muller’s concept.”

Yeah, guess I’m still stuck in the “it’s not IC” stage, or rather, the “there is no IC” stage. But maybe that’s because I need to study Muller’s IC better.

What I think IDers did plan on was deliberately not differentiating between (1) origin of an IC system from another IC system and (2) origin of an IC system from an non-IC system.

Since their premise is that evolutionary explanations are inadequate, I bet they don’t even think they need to consider the difference.

But by making critics sound confused or intolerant, they score points with their target audience.

Well, they can’t make us sound anything we’re not, but there’s something to what you say. A person who over-simplifies issues and is sure of his or her intuitive conclusions probably sounds more confident than one who is still actively seeking to understand how the natural world works. Guess that’s one reason religion is so popular.

Terminology…

An irreducibly complex system is one which none of the parts can be removed without the whole system ceasing to function. Thats cleary the case with the flaggelum. If this video is right (my knowledge of the area is too limited to judge) then its not that the flaggelum is not IC, but rather that IC can evolve, a much stronger claim.

Hopefully the other CDK007 videos are as interesting and well made.

Katarina Wrote:

It appears IC is meaningless, or else it’s meaning just isn’t very applicable to any kind of argument.

‘Irreducible complexity’ isn’t like other misguided concepts in the creationist toolbox, since it isn’t meaningless or unfalsifiable. Muller claimed 1918 that interlocking complexity is an expected result of evolution. Interlocking complexity is “a system of mutually independent parts that requires all those parts to be present for the system to work” ( http://www.talkorigins.org/origins/[…]h/sep06.html ).

Behe is of course using it in a strawman argument where evolution works by adding single parts. If he sees an interlocked system he thinks it couldn’t evolve and is an example of ID. By this misapplication he has moved a naturalistic concept into the religious creation domain.

But there are plenty of evolutionary mechanisms that doesn’t add single parts like exaptation and scaffolding. So nothing prohibits interlocking system to evolve.

I believe Behe et al went on to propose variants that erects other strawmen of evolution. But that they have also been falsified by specific examples.

Perhaps he needs to bite the bullet. He could introduce ‘little green men complexity’. Surely no green marsian has evolved on earth!

Was a soundtrack by Boston completely necessary? You know, coulda been Hank Williams, Jr. Just sayin.

Torbjorn Larsson,

So.. the blood clotting cascade in humans is considered IC, given the simple definition of loss of function with any of the interdependent parts removed? That is what I gather from the TO article. And the blood-clotting cascade of dolphins, even though it lacks a part that the human one has, is also considered IC? Meaning each intermediate step that it took to get to one IC system may also be considered IC if it has enough interlocking “parts?” Can someone correct me on this if I’m wrong?

I should probably apologize to Popper’s ghost for challenging his comments in an uninformed way - guess that’s what happens when ye’r too sure of y’self. I made the mistake of conflating evolvability with IC, which he tried to point out; but I’m slow to catch on.

I still have a little trouble seeing the utility of using IC for any arguments, though as a descriptive term apparently it is considered valid by biologists.

Perhaps he needs to bite the bullet. He could introduce ‘little green men complexity’. Surely no green marsian has evolved on earth!

No, but maybe it’s time they acknowledge that the Intelligence hypothesis may just as likely be the Marsian hypothesis, or the Robot hypothesis, or the Spaghetti Monster hypothesis.

Katarina — That’s HER noodliness, The FLYING Spaghetti Monster…

In order for one to even remotely consider a system as irreducible complex one must show that an exhaustive search of that system through diverse organisms and homologies of the proteins making up that system give no information as to how that system evolved.

This strikes me as rather confused, and incorrectly yields ground to IDiots like Behe by suggesting that IC is a meaningful or useful concept, even in theory. The statement would be true if IC meant “could not have evolved”, but that’s not what it means, that’s just what Behe falsely claims about it. An irreducibly complex system is defined as a system that can’t function if any of its components is removed. But that makes IC uninteresting/irrelevant for two reasons: 1) IC systems are no challenge to the ToE, since the evolutionary predecessor of the system need not have been that system minus some component; addition of a component is not the only – or even a common – way that evolution proceeds, and 2) “can’t function” is hopelessly normative; the IC system with a component removed surely can perform some function in some context. And even if it could not perform any function at all, it can be passed along as long as its presence isn’t fatal; the are numerous examples of benign mutations and useless systems (that may have once been useful); evolution, the inveterate cobbler, may find a way to make use of such useless components.

According to http://www.ideacenter.org/contentmg[…]s.php/id/840 Behe’s notion of irreducible complexity is a response to Darwin’s statement

If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.

But “could not possibly” is not the same as “I’m too blinded by my ideology to think of one, even though the evolutionary literature is full of relevant examples”. The fact is that Darwin lived long ago and is not the ultimate authority on the ToE or the philosophy of science, and his statement is not a very good falsification criterion for the ToE, precisely because of that “could not possibly”, which would require proof of a universal negative. But we have much better falsification criteria – for instance, there might have been no correlations between homologous structures among different species and the locations of the controlling genes in their genomes, but in fact we see exactly the sorts of correlations we would expect if the ToE is valid. The only reason we have for why an “intelligent designer” would have done things like that is to fool us into thinking they evolved.

‘Irreducible complexity’ isn’t like other misguided concepts in the creationist toolbox, since it isn’t meaningless or unfalsifiable.

Concepts are neither falsifiable nor unfalsifiable; that’s a category mistake. As for whether it is “meaningless” – who cares? The creationists use plenty of meaningful but irrelevant and misguided concepts; IC certainly isn’t the only one.

Muller claimed 1918 that interlocking complexity is an expected result of evolution.

I have pointed this out numerous times at PT, most recently in my exchange with Katarina about IC, when I repeatedly noted that such systems are evolutionarily robust, because most mutations will result in less viability; IC is thus a “fixed point” or an “attractor” of sorts for evolution. But because evolution isn’t teleological and is sensitive to an ever-shifting environment, nothing is truly “irreducible”.

Meaning each intermediate step that it took to get to one IC system may also be considered IC if it has enough interlocking “parts?”

Suppose you have a house on a platform on four stilts, and one of the stilts is rotten and needs to be replaced. You add some temporary supports, replace the old stilt with a new one made with improved modern materials, and remove the temporary supports. The old and new platforms are both IC – you can’t remove a stilt without the house falling down. In between, though, it wasn’t IC.

its not that the flaggelum is not IC, but rather that IC can evolve, a much stronger claim

That’s not a strong claim at all. The strong claim is the IDiotic one that IC systems can’t evolve.

(Where “can’t evolve” really means “can’t be the result of evolution”.)

Since their premise is that evolutionary explanations are inadequate, I bet they don’t even think they need to consider the difference.

Not only that, but they don’t even think of the difference. Their premise that evolutionary explanations are inadequate requires that remain ignorant (often willfully) of what the evolutionary explanations and data are.

My take on IC is that it is a rhetorical strategy that went even better than IDers planned, because from the start, critics divided into “it’s not IC” and “it’s IC but evolved, like Muller’s concept.”

It’s a false dichotomy; there are two different sorts of questions – whether some specific system, such as the flagellum or the blood clotting system, is IC, and whether IC systems can be evolved. Trying to answer the first plays right into the IDiot’s hands. Answering the second question in the affirmative is a much more powerful strategy, and some people were quick to point it out and that therefore Behe’s whole IC argument is fallacious (this was again pointed out, to great effect, in Dover). Sadly, we still have a lot of people who aren’t familiar with or don’t understand that answer, and are thus still attempting – not just pointlessly, but to our detriment – to answer the first question.

Is there any way that Behe or Minnich could be invited to take a look at this video. I would love to read what they have to say in comment.

Read the Kitzmiller transcript and you’ll know everything you need to about how Behe responds.

I guess the other side will criticize the vieo as a just-so story

Which demonstrates their intellectual bankruptcy – as well as how badly people on “our side” need an education in logic. Even a “just-so” story with no evidentiary support, but mere feasibility, refutes the IDiotic claim that the flagellum could not have evolved. The IDiot’s demand for details is utterly dishonest – they have been blown out of the water even without any. And here we have plenty of details that make this story not just feasible, not even just plausible, but likely.

A “just-so” story is one that is invented in order to support one’s favored thesis, rather than flowing from the evidence. That’s not at all what we have here; here, the existing homologues guided the development of the story.

Gee, thanks a lot. I think I preferred name-calling!

I’ve learned at least this from this conversation: Whatever Popper’s ghost’s profession, where I’m sure he shines, he’s no biologist. He did a good job of teaching himself the general bits one needs for commenting here; however this isn’t enough to propose the best strategy for dealing with Behe’s IC. I am disappointed he has run away instead of admitting as much.

The video says that removing any one of the 42 proteins results in zero function. However, I read a flagellum paper that commented on IC, saying that they got their flagellum down to 29 different proteins, and still functioning. Am I missing something here? Different flagellum?

Can you dig up the reference?

Torbjörn Larsson Wrote:

PG Wrote:

Concepts are neither falsifiable nor unfalsifiable; that’s a category mistake.

I explained below why the concept is a prediction of evolution, and why it is falsified when used in Behe’s strawman of evolution. Concepts, objects, properties, methods are part of models and predictions and thus falsifiable when used. A totally failed concept, object, property or method is falsified in my book. (Note: any of these can still have use some other time. But I wouldn’t bet on it.)

Perhaps you are trying to make an elaborate distinction between a concept and its use in models and thus predictions. Popper tried to solve the demarcation problem too, seems that is why his ghost is still around.

This is of course wrong. (Note to self: Never post when transportation is due any minute.)

Naive falsification concerns the theory. Even if the concept may in reality be applied in a weakening scale towards debunking and on parts or methods of a theory it is not clear what that would mean. (For an example of failed parts, take phlogistons in phlogiston theory.) As I noted they don’t need to be totally failed because the theory is falsified.

So it is I, not PG, who is making the larger proposal on demarcation. Which is especially bad since I unnecessarily tried to be cute to fit the format of the rest of the Yule comment. My apologies.

PG Wrote:

Sorry, but you write so imprecisely as to be nearly nonsensical, and it results in errors.

Exactly, this was a mess.

PG Wrote:

Only theories are falsified, and they are falsified by evidence that contradicts their predictions.

Yes.

As I noted in my earlier comment I believe that its use isn’t quite as restrictive, since repeated falsifications of theories where for example a particular method is used lends some weight on the value of that method. But it seems wise to restrict the term as originally intended. We have problems associated with the use of these concepts as it is. (I still haven’t read Popper. Would you believe the inanity of relying only on practice? Yes, you probably would. ;-)

Katarina Wrote:

the looseness of the definition of IC causes trouble for the specific claim that “IC systems are an evolutionary prediction.”

My initial reaction was as yours. I think it is a weak claim.

Muller Wrote:

… Most present day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect which it produced upon the “reaction system” that had been brought into being by the many previously formed factors in cooperation; thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous elementary parts or factors, and many of the characters are factors which, when new, where originally merely an asset finally become necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery; …

( http://www.talkorigins.org/origins/[…]h/sep06.html )

But again, weak claims have their uses. :-)

Regards PG’s claim on robustness, it seems intuitively correct since interlocking gives constraints on evolutionary paths. (Ie gene duplication works, arbitrary mutations probably not.)

I think the problem here is that logical claims about IC, i.e. evolutionary robustness, presuppose that either something is IC or it isn’t. There’s a false dualism going on here. According to Behe in his revision to the definition of IC, there are degrees of IC. If IC were absolute, no alteration at all would be allowed. In the same breath it would imply a perfectly efficient system. Yet most things found in biology are sub-optimal. At best biological systems asymptotically approach IC and efficiency.

Popper’s ghost said that duplications are rare, which is correct, but rare mutations are exactly the kind that generate variety for natural selection to work on, and are therefore necessary for evolution to take place.

And it isn’t just gene duplication or arbitrary mutations (there’s the dualism again); there are many kinds of mutations that can provide material for evolution, and all of these can alter systems which aren’t absolutely IC. See talkorigin’s 29 Evidences for a list:

Extremely extensive genetic change has been observed, both in the lab and in the wild. We have seen genomes irreversibly and heritably altered by numerous phenomena, including gene flow, random genetic drift, natural selection, and mutation. Observed mutations have occurred by mobile introns, gene duplications, recombination, transpositions, retroviral insertions (horizontal gene transfer), base substitutions, base deletions, base insertions, and chromosomal rearrangements. Chromosomal rearrangements include genome duplication (e.g. polyploidy), unequal crossing over, inversions, translocations, fissions, fusions, chromosome duplications and chromosome deletions (Futuyma 1998, pp. 267-271, 283-294).

Katarina Wrote:

it would imply a perfectly efficient system.

What is efficiency here?

I don’t think one can establish absolute efficiency anyway, besides the minimality of interlocking. A selected system is obviously more functionally efficient than those who weren’t. A minimal system should be more metabolically efficient than a non-minimal. But those are relative properties, and non-interlocked systems share some of them. OTOH, if a few percents difference in fitness is enough to fix genes in large populations it could be a partial or full explanation. So you are probably on to something.

But I think you are correct in that we are discussing a possible relative robustness for interlocked systems and not Behe’s absolute unevolvable IC. And I think that possible robustness could also be due to some evolutionary constraints that interlocking poses, regardless of how many remaining paths there is. Point mutations (“base substitutions, base deletions, base insertions”) seems to be some of the possible paths the constraints could restrict.

Intriguing. Has anyone studied fixation and evolvability of interlocked systems?

Good question: I meant not energy efficiency, but economic, that is, productive efficiency. We only have the parts we need to make the product - no more, no less. Though I don’t know, maybe the energy efficiency would go up too.

I did imply that robustness is relative, and more: this leaves plenty of room for evolution to work, since it is the improbable events that evolution relies on. The concept is not all that intuitive.

Behe didn’t say IC is absolute, he said it comes in degrees. I’m puzzled by why he did that.

Michael Behe Wrote:

An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.

(A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March, 2002; iscid.org/) http://www.iscid.org/papers/Behe_Re[…]s_121201.pdf

Has anyone studied fixation and evolvability of interlocked systems?

I think more in mathematics than biology (which explains why PG uses it), though the implications carry over somewhat.

http://www.santafe.edu/~krakauer/index.html

Of great interest is the way in which robustness mechanisms contribute to structural complexity. Many features of organisms go above and beyond their primary adaptive function and reflect additional mechanism whose role is to stabilize, insulate or render resistant, adaptations to noise or assault. Part of the interest in robustness mechanisms lies in their value in explaining the evolution of complexity.

Collegue of PG’s?

Katarina Wrote:

I meant not energy efficiency, but economic, that is, productive efficiency.

Well, in this case I don’t think one can distinguish between interlocked and non-interlocked systems, as I discussed above. Interlocked systems could be metabolically more efficient, both in producing/breaking down parts and driving reactions.

Katarina Wrote:

I did imply that robustness is relative,

OK. I was responding to “perfectly efficient”.

Behe Wrote:

The degree of irreducible complexity is the number of unselected steps in the pathway.

I think Behe later qualified his IC, since people found systems that could bridge evolutionary gaps with neutral (unselected) drift. So he adjusted what is effectively a gods-in-the-gaps assumption when the gap changed. I think he has done this several times.

You are right, efficiency the way I meant it doesn’t differentiate IC from non-IC; I didn’t use the right word.. Thanks for making that clearer for me. I think I need more sleep.

I’m glad to see my video has generated such interest. Again, thanks to Nick Matzke for the actual idea. I simply turned it into a cartoon. Check out my other videos at www.youtube.com\cdk007 I’m sure this group will find them interesting.

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This page contains a single entry by PvM published on December 22, 2006 11:29 PM.

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