PvM posted Entry 2798 on December 22, 2006 11:29 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2788



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

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Comment #151542

Posted by Andrew McClure on December 23, 2006 12:12 AM (e)

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

Comment #151551

Posted by Mark Studdock, FCD on December 23, 2006 12:32 AM (e)

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

Comment #151560

Posted by Bob O'H on December 23, 2006 1:47 AM (e)

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

Comment #151572

Posted by djlactin on December 23, 2006 5:56 AM (e)

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

Comment #151574

Posted by Katarina on December 23, 2006 6:12 AM (e)

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.

Comment #151575

Posted by Katarina on December 23, 2006 6:19 AM (e)

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

Comment #151583

Posted by Karl Lembke on December 23, 2006 8:02 AM (e)

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

Comment #151584

Posted by Larry Moran on December 23, 2006 8:05 AM (e)

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.

Comment #151586

Posted by Frank J on December 23, 2006 8:14 AM (e)

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.”

Comment #151591

Posted by Steverino on December 23, 2006 8:34 AM (e)

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

;-)

Comment #151608

Posted by Frank J on December 23, 2006 10:09 AM (e)

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.

Comment #151613

Posted by wamba on December 23, 2006 10:48 AM (e)

Drat, Steverino beat me to the obvious joke.

Comment #151616

Posted by Bruce Thompson GQ on December 23, 2006 11:23 AM (e)

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)

Comment #151618

Posted by PvM on December 23, 2006 11:44 AM (e)

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

Comment #151622

Posted by Katarina on December 23, 2006 12:35 PM (e)

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.

Comment #151625

Posted by WinstonEwert on December 23, 2006 1:17 PM (e)

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.

Comment #151633

Posted by Torbjörn Larsson on December 23, 2006 2:47 PM (e)

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/postmonth/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!

Comment #151641

Posted by Jake on December 23, 2006 3:25 PM (e)

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

Comment #151670

Posted by Katarina on December 23, 2006 6:10 PM (e)

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.

Comment #151672

Posted by David B. Benson on December 23, 2006 6:21 PM (e)

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

Comment #151683

Posted by Popper's ghost on December 23, 2006 8:58 PM (e)

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/contentmgr/showdetails.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.

Comment #151684

Posted by Popper's ghost on December 23, 2006 9:07 PM (e)

‘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.

Comment #151687

Posted by Popper's ghost on December 23, 2006 9:32 PM (e)

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”.

Comment #151688

Posted by Popper's ghost on December 23, 2006 9:51 PM (e)

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.

Comment #151689

Posted by Popper's ghost on December 23, 2006 9:54 PM (e)

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.

Comment #151690

Posted by Popper's ghost on December 23, 2006 9:56 PM (e)

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

Comment #151691

Posted by Popper's ghost on December 23, 2006 9:59 PM (e)

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.

Comment #151692

Posted by Popper's ghost on December 23, 2006 10:12 PM (e)

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.

Comment #151694

Posted by Popper's ghost on December 23, 2006 10:24 PM (e)

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.

Comment #151695

Posted by Popper's ghost on December 23, 2006 10:44 PM (e)

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.

Comment #151708

Posted by Nick (Matzke) on December 24, 2006 12:59 AM (e)

Glad people are enjoying this. It doesn’t seem to have showed up at YouTube, but I tried to post a comment there that noted there are some simplifications and mistakes in the video (i.e.: it’s not that 40 of 42 proteins have known homologs, it’s that 40 of 42 proteins are either inessential and/or have homologs), but it is worthwhile nonetheless for getting some of the basic ideas across.

Larry Moran was asking about the latest version of the flagellum evolution model. The official maintained version of the flagellum evolution essay is at TalkDesign.org here. An update from September 2006 is here, with several important links to PT posts and journal articles. The background page was also updated in September.

Comment #151710

Posted by PvM on December 24, 2006 1:02 AM (e)

Seems Dembski is already trying to trivialize the video. I guess we will soon see him distance himself from the DVD video projects of the Discovery Institute as well :-)

It’s funny to see his faithful followers still making some pretty silly comments about the evolution of the flagellum.

In the mean time our scientist wannabe Casey is arguing how much science ID has done… Somehow he seems to think that evidence that shows how science has some problems finding robust phylogenetic trees in some instances is evidence of ID.

I will have to find the Dawkins segment where he ridicules the ID argument…. Yes, we have something that does not explain anything but since Darwinian theory is having some problems, this scientifically vacuous idea should suddenly gain credibility?

Intellectual laziness, that’s what ID has come to be.

And then there is Junk DNA, which somehow was predicted by ID to have function. Of course there is no foundation for such claims that ID predicts DNA having function.

I invite any ID proponent to explain how ID predicts finding function in junk DNA. There is no scientific foundation for such claims to be found in ID since ID does not deal in explanations or predictions beyond: Darwinian theory cannot explain it.

Comment #151719

Posted by Torbjörn Larsson on December 24, 2006 3:12 AM (e)

Katarina wrote:

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?

I think the problem here may be that a creationist may point to a system and proclaim it IC. But it often turns out that there are subsystems that work in the same (blood clotting) or different function (secretion system), and these are related by evolution (surprise, surprise). Then the new subsystem becomes labeled IC by IDiots. And the game starts anew. These predictions leaps like a butt propellar moved by the divine wind.

Katarina wrote:

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.

As I understand it, Muller used it as a prediction of evolution. But the ID ‘use’ fails consistently - you would not expect IC systems to be unevolvable, but evolvable. And since evolution is known to happen, the ID expectation is slightly less belieavable than a god.

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.

All:

God Jul/Good Yule !

Comment #151724

Posted by Popper's ghost on December 24, 2006 4:43 AM (e)

I explained below why the concept is a prediction of evolution, and why it is falsified when used in Behe’s strawman of evolution.

Sorry, but you write so imprecisely as to be nearly nonsensical, and it results in errors. The ToE predicts (per Muller) that IC systems will arise; that is very different from “the concept is a prediction”; as I said, that’s a category mistake. And it’s Behe’s strawman theory of evolution, that all evolution occurs by incremental additions, that is falsified, not “it” (IC) “when used in Behe’s strawman”, whatever the heck that’s supposed to mean. And Behe’s strawman is falsified not just by his purported IC examples but by many many many cases to the contrary of his silly restriction to linear additions; that’s why it’s such a ridiculous strawman.

Comment #151725

Posted by Popper's ghost on December 24, 2006 4:46 AM (e)

A totally failed concept, object, property or method is falsified in my book.

You should throw out your book, then. Only theories are falsified, and they are falsified by evidence that contradicts their predictions.

Comment #151735

Posted by Steverion on December 24, 2006 7:38 AM (e)

I really am enjoying this thread. Not being a scientist, this has made the top so much more understandable.

Question: ID’ers seem locked on IC as the hingepin to their entire argument. Where is the science/evidence that says IC (if you can actualyly prove something really is IC) proves design?

That seems to me, to be nothing more than a leap of faith.

Comment #151743

Posted by Larry Moran on December 24, 2006 8:56 AM (e)

Nick wrote:

Glad people are enjoying this. It doesn’t seem to have showed up at YouTube, but I tried to post a comment there that noted there are some simplifications and mistakes in the video (i.e.: it’s not that 40 of 42 proteins have known homologs, it’s that 40 of 42 proteins are either inessential and/or have homologs), but it is worthwhile nonetheless for getting some of the basic ideas across.

This is an important point. There are quite a few errors* but that doesn’t mean the video isn’t useful. Let’s be careful not to claim that it’s the best scientific evidence we have.

Does anyone know who made it?

*For example, the ATPase activity would not have been part of the primitive secretion mechanism: only the rotor part is needed.

Comment #151758

Posted by darwinsuncle on December 24, 2006 10:26 AM (e)

PvM and Nick Matzke,

Positively brilliant! Right down to the use of the music of Boston. Do keep up the good work.

Comment #151759

Posted by PvM on December 24, 2006 11:53 AM (e)

On UcD ID apologetics are blowing their fuses. Quite amusing…

As people on this thread have pointed out, such videos are very instrumental in bringing science to the layman, helping them understand the vacuity of Intelligent Design and help them appreciate the science of evolution.

Probably worse, these videos may lead to ID apologetics to come to realize how scientifically vacuous their ideas really are.

Comment #151760

Posted by PvM on December 24, 2006 12:07 PM (e)

IDnet.au ‘responded’ on UdC

If IC is an argument from ignorance “Because I cannot imagine how something evolved, it must not have”, then Darwinism is an argument from imagination. “Because I can imagine how something evolved, it must have.”

No need for experimental evidnce when we can make a video simulation.

Why don’t we watch X Men instead because it proved mutations produce valuable evolution.

Does anyone realize how silly this argument is?

1. ID can only exist when there is ignorance, the moment a scientific hypothesis is presented, the hole in which it was hiding has been closed.

That by itself is sufficient to lay to rest the silly idea that IC cannot evolve.

Now ID proponents may want to argue that the proposed hypothesis does not meet the requirements, but that would mean a lot of scientific hard work, something mostly unfamiliar to ID defenders.

What is even more ironic is that it is ID which attempts by showing a video animation of the flagellum to argue that it must have been designed.

The irony…

This video has revealed a lot more of the ignorance amongst ID activists. Well worth it.

Comment #151761

Posted by Nick (Matzke) on December 24, 2006 12:10 PM (e)

Does anyone know who made it?

CDK007 is all I know. Maybe he is a fan of cell division protein kinases.

*For example, the ATPase activity would not have been part of the primitive secretion mechanism: only the rotor part is needed.

Please explain if you get a chance over the holidays. I tend to think that the fact that many related hexameric ATPases tend to thread DNA or protein through a hole in the middle of them while burning ATP indicates that perhaps the proto-F1Fo-ATPase at the based of the flagellum did something similar. This may have been more of a unfoldase activity than direct transport (then and now). This may have incidentally caused rotation in the structure, or not.

The whole question of the nature of “proto-F1Fo-ATPase” in structures ancestral to the flagellum is a bit different than I proposed in 2003; I tend to think now that perhaps the modern F1Fo-ATPase was derived *from* an F1Fo-ATPase-like system that used both ATP and protonmotive force to conduct active export across the inner membrane.

But I am being called to decorate cookies…

Comment #151764

Posted by steve s on December 24, 2006 12:45 PM (e)

Question: ID’ers seem locked on IC as the hingepin to their entire argument. Where is the science/evidence that says IC …proves design?

There’s no science or evidence for that, it’s just another handy wavy BS claim. The claim that ‘if not direct evolution, then ID’ is what Judge Jones referred to as “the same flawed and illogical contrived dualism that doomed creation science in the 1980’s”

Comment #151765

Posted by Bruce Thompson GQ on December 24, 2006 1:19 PM (e)

PvM asks:

Does anyone realize how silly this argument is?

Incredibly silly.

UDs magical retort, “(n)o need for experimental evidnce when we can make a video simulation” misses the whole point of a hypothesis. By providing a hypothesis new questions and tests are derived. In comparison a designed flagellum is pretty much just natural history.

Delta Pi Gamma (Scientia et Fermentum)

Comment #151805

Posted by Katarina on December 24, 2006 11:20 PM (e)

Pops,

First let me get this out of the way: I apologize for my rudeness (and bad jokes) in previous threads. I have no excuse.

Second, I’m struggling to understand some parts of what you’re saying and if you’re willing, I could use clarification.

1. Regarding the concept evolutionary robustness, you’ve used the term thus:

IC systems can’t maintain function if any of their parts are destroyed – therefore, they are evolutionarily robust.

and

IC systems are evolutionarily robust, because any mutation that destroys the function of some component destroys the function of the system

and in this thread,

..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.

I get that all IC systems are evolutionarily robust, but I have trouble with the concept itself: I’m not sure what else you would consider evolutionarily robust, and that doesn’t help me understand what the term means. Maybe if you could point me to some references.

2. Your response to Winston Ewert’s comment, that the unevolvability of IC is a stronger claim than its evolvability is puzzling. I must be in the dark about what actually makes a claim strong. Especially since, later on, you say

Answering the second question [whether IC systems can be evolved] in the affirmative is a much more powerful strategy [than whether something is IC]..

So can a strategy be powerful if the claim behind it is not powerful?

3. I have a problem with your house with stilts example. Sorry, but I have trouble comparing biological systems with man-made ones on principle, when it comes to evolution. Evolution typically works gradually, not by abrupt addition of new parts, or with forethought, e.g. support of a failing part while a new one is being made. Of course you are perfectly well aware of this, which is why I am not sure why you chose that example, but I’m probably missing something as usual.

What I do understand is your main argument, and I am converted: The superiority of the strategy that uses known evolutionary mechanisms and homologues to explain how an IC system - whether it is truly IC or not - evolved. Even though some systems are IC and some are not, the demonstration of evolvability works for both. It makes sense to choose one approach or the other, not both, to avoid confusion.

Comment #151809

Posted by Popper's Ghost on December 25, 2006 1:38 AM (e)

If IC is an argument from ignorance “Because I cannot imagine how something evolved, it must not have”, then Darwinism is an argument from imagination. “Because I can imagine how something evolved, it must have.”

We don’t call these people IDiots for nothing. “Because I can imagine how something evolved, it may have” is enough to counter the IDiots’ claim that it must not have.

Aside from that, we don’t merely “imagine” how; this didn’t come out of thin air, it came from the evidence provided by homologues.

No need for experimental evidnce when we can make a video simulation.

I suppose that we have to reject Kepler’s conclusion that the planets sweep elliptical orbits because it wasn’t based on experimental evidence.

Comment #151820

Posted by Popper's Ghost on December 25, 2006 3:06 AM (e)

I get that all IC systems are evolutionarily robust, but I have trouble with the concept itself: I’m not sure what else you would consider evolutionarily robust, and that doesn’t help me understand what the term means.

By “evolutionarily robust” I simply mean resistant to change. For other examples, consider basic cell mechanisms that have been around, pretty much unchanged, for billions of years. They’re robust because even the slightest change has radical consequences that are most likely to be fatal. What these have in common with the components of IC systems is that the function of other components depend on them. But these basic cell mechanisms are truly robust, far more so than the components of a flagellum, since a flagellum can shift in its function and possibly still be useful, or may become less valuable if, for instance, the organism becomes sessile.

Your response to Winston Ewert’s comment, that the unevolvability of IC is a stronger claim than its evolvability is puzzling. I must be in the dark about what actually makes a claim strong.

Apparently so. The phrase is common in law, philosophy, and in fact anywhere where people are engaged in making and disputing claims. The more a claim asserts, the stronger it is; stronger claims are less obvious, require more support, and are more radical in their implications. “That’s such a strong claim” applies to things like “All Republicans are racists” and “Bush knew all along that Saddam didn’t have WMDs”. OTOH, “Some Republicans are racists” and “Bush may have really believed there were WMDs” are weak claims.

So can a strategy be powerful if the claim behind it is not powerful?

How can a claim be powerful? Arguments are powerful, not claims. “strong” doesn’t mean powerful here, it means something more like “intense”, or “high amplitude”. Strong claims – claims that assert a lot – are argumentatively weak because it takes less to refute them. The most powerful strategy is the one that offers up claims that are the hardest to refute – such as “this may have evolved”, vs. “this cannot have evolved”. The people who offer up the latter are losers.

I have a problem with your house with stilts example. Sorry, but I have trouble comparing biological systems with man-made ones on principle

The example was simply to help you think about how one gets from one IC blood clotting system to another IC blood clotting system; I can’t help you if you reject it before even thinking about it. The explanation in the TO article provides the exact same logic, but in a more complex framework; I just tried to simplify it for you. The fact that one system is biological isn’t relevant here (and on a far-reaching aside, humans are biological systems, operating on memetics; even the intentional/non-intentional divide isn’t one of principle – not if you’re a materialist; it’s material all the way down – or up).

Evolution typically works gradually, not by abrupt addition of new parts, or with forethought, e.g. support of a failing part while a new one is being made.

But these aren’t relevant differences here. In the blood clotting case we have a mindless gene duplication. In the table case, someone has to intentionally supply a support, because table legs don’t mindlessly dupicate themselves. Different mechanisms resulting in redundancy, but redundancy in both cases, and it’s the redundancy that is relevant to whether something is IC, not whether components were placed or removed intentionally or gradually. Understanding that different mechanisms – particularly mindful goal-oriented human activity vs. mindless non-goal-oriented evolution – can produce the same result is crucial to responding to the argument from design; see Dawkins’s chapter in The Blind Watchmaker on the remarkable similarity between echolocation in bats and SONAR.

What I do understand is your main argument, and I am converted: The superiority of the strategy that uses known evolutionary mechanisms and homologues to explain how an IC system - whether it is truly IC or not - evolved. Even though some systems are IC and some are not, the demonstration of evolvability works for both. It makes sense to choose one approach or the other, not both, to avoid confusion.

Actually, my main argument is that, when it comes to ID and IC, we shouldn’t talk about flagella or blood clotting systems at all – to do so gives the appearance that Behe’s IC argument could be a legitimate concern for ToE. But, his argument is rubbish; per Muller, IC systems confirm ToE, they don’t falsify it; Behe’s argument is sheer fallacy. Aside from that, it’s perhaps fun and interesting and informative and enlightening to work out the details of the evolution of the flagellum and the blood clotting sequence, but we shouldn’t use that as our argument against ID/IC. The former approach is based on a much weaker (less assertive) claim – that Behe’s argument is fallacious. It’s weak because it requires no evidence at all, and is a consequence of simple logic; airtight refutations were published shortly after Behe’s book appeared. The claim that the flagellum really did evolve, and evolved just so, is a much stronger (more assertive) claim; it requires a lot more work, gathering a lot of evidence, considerable reasoning and room for error, much easier to find a flaw in. Stronger claims are harder to defend, and thus it’s not a good idea to base your strategy on them – ask any lawyer (note that “there is no reasonable doubt” is a much stronger claim than “there is reasonable doubt”).

Comment #151822

Posted by Popper's Ghost on December 25, 2006 3:37 AM (e)

Katarina, here is an introductory essay about evolutionary biology that uses the terms “weak claim” (claims less) and “strong claim” (claims more). You will find this usage throughout science and philosophy, so it’s a good idea to become familiar with it.

Comment #151832

Posted by Katarina on December 25, 2006 8:45 AM (e)

Pops,

For the stilt example - still doesn’t help me. The blood clotting system wasn’t failing when the gene duplication occured, and remained IC for its function of the moment.

For the rest, it did clarify things for me, not only about your arguments but about arguments in general. Thank you.

BTW, I picked up “Freedom Evolves” by Daniel Dennet as you recommended. Really enjoying it.

Your fan

Comment #151850

Posted by PvM on December 25, 2006 2:54 PM (e)

I believe that this whole exercise has shown at least one important result: ID activists are terrified to see science put in simple understandable graphics. After all, knowledge is contrary to ID which has to insist on people remaining in ignorance.

Teach the controversy I tell you… IC debunked…

Comment #151863

Posted by Popper's Ghost on December 25, 2006 4:27 PM (e)

For the stilt example - still doesn’t help me.

Your problem, not mine.

The blood clotting system wasn’t failing when the gene duplication occured

Again not a relevant difference; the example was merely to illustrate how one IC system can transform into another IC system via a non-IC step. None of your objections (except the next, which is so far off base that I wonder if you’ve been drinking or something) have anything to do with that.

and remained IC for its function of the moment

Huh? No system with a redundancy is IC! What part of “irreducible” don’t you understand?

Comment #151864

Posted by Popper's Ghost on December 25, 2006 4:36 PM (e)

BTW, I picked up “Freedom Evolves” by Daniel Dennet as you recommended. Really enjoying it.

Cool; but it’s Dennett.

Your fan

Ah shucks.

Merry Mythmas!

Comment #151894

Posted by Katarina on December 26, 2006 4:31 AM (e)

What part of “irreducible” don’t you understand?

[Slaps palm on forehead, hard] Nooooow I get it. Looking for needles, I missed the obvious. The double gene is redundant before it further mutates.

Oops, Dennett. Right.

Yes, professor Pops, thanks for having the patience to correct me again. Now that you’ve tamed me you must keep me!

Comment #151898

Posted by k.e. on December 26, 2006 8:23 AM (e)

Crikey am I on the right page?

PvM and PG NOT trying to rip each others arms off?

hehehehehe

Happy New Year!

PG noted.

The only reason we have for why an “intelligent designer” would have done things like that [allow a believer to conceive the idea that some artifact may be IC] is to fool us into thinking they evolved.

That designer was obviously too intelligent for Behe and his rabble of idolaters, which oddly ,include his other self.
But then so were the plaintiff’s lawyers and the Judge.

Where Behe and Dembski fall down in this little spat is their inability to capitalize on the stupidity of their followers.

Behe and Dembski instinctively know that a great number of people in the post literate age are incapable of deconstructing creationist nonsense. The post logically and historically literate will fall for subjective platitudes and line in the sand biblical authoritarianism of ‘True Believers’ but a great number of them are susceptible to clear ideas expressed through video literacy. The DI had great success with their DVD ‘flagellum fallacy’ and science visualizers are playing catch up. There must be more opportunities for education of people by this means who are beyond traditional methods.

For Behe and Dembski et al. to respond to that video by offering their alternative hypothesis may indeed be a step beyond their ability.

Comment #151907

Posted by Popper's Ghost on December 26, 2006 10:41 AM (e)

The double gene is redundant before it further mutates.

Actually, strictly speaking, you were right (sorry about that) that the system remains IC when the gene duplication occurs, since the duplicate genes express exactly the same system; the genotype is redundant but the phenotype is not. The system only becomes non-IC when the gene mutates to produce two different components performing the same general (but not specific) function. From the TO article:

(B) Now have a gene duplication for the protease. This is a reasonably common process in evolution; an entire section of the genome gets doubled; so that now there are two genes, both producing the same protease protein. There is no difference to the working of blood clotting; as all the proteins involved are the same.

© Now have a small modification to one of the duplicated genes. There are now two slightly different forms of the protease. Call them protease-A and protease-B. Either one would manage fine for blood clotting. In that sense, the system of three proteins is no longer irreducible; it has redundancy.

(D) Now suppose that there are mutations to protease-A which give it a capacity to activate protease-B. That is, both proteins get activated at the break in a vessel by contact with tissue proteins; but protease-B gets additional activation from the activated protease-A. This kind of additional activation can have some selective benefits, in speeding up the response of the whole system.

At the point, the system is still not IC. It only becomes IC when the original component’s function, the one that has been duplicated and modified, ceases:

(E) Finally, now that protease-B is activated by protease-A, it no longer depends on activation from the tissue proteins, and further modifications can reduce this activation pathway. This makes the whole system “irreducible” again, because all three proteins are now required for clotting.

Comment #151908

Posted by Popper's Ghost on December 26, 2006 10:43 AM (e)

PG noted.

The only reason we have for why an “intelligent designer” would have done things like that [allow a believer to conceive the idea that some artifact may be IC] is to fool us into thinking they evolved.

Uh, no, your bit in brackets has nothing to do with what I wrote. “things like that” are “exactly the sorts of correlations we would expect if the ToE is valid”.

Comment #151929

Posted by Katarina on December 26, 2006 4:07 PM (e)

k.e.:

PvM and PG NOT trying to rip each others arms off?

Did you miss this?

Popper’s ghost:

Actually, my main argument is that, when it comes to ID and IC, we shouldn’t talk about flagella or blood clotting systems at all – to do so gives the appearance that Behe’s IC argument could be a legitimate concern for ToE.

The whole point of the flagellum animation is to present a reasonable scenario for the gradual evolution of an IC system. While PG thinks it’s fun and OK to do so, he doesn’t think it works well as the main strategy. While he presents his argument soundly, I don’t think it justifies picking a fight. I think it doesn’t hurt to buttress the weak claim with the strong one. In practice, the illustration is still very important as a reference, and adds substance to the “weak claim.” Every bit helps. (On the other hand questioning whether something is IC in the first place, as I tried to do earlier, may be counterproductive.)

According to the introductory essay by Alexey Kondrashov PG linked to, the weak claim of evolution is that the further back into the lineage of a species one ventures, the more different the progenitors will look. In other words, change over time. This argument was first proposed by Lamarck, according to the essay. The strong claim of evolution is that all species are related, and this was the claim made by Darwin.

Lamark’s weak claim may have been enough to logically infer relatedness if one looked around enough, but Darwin’s strong claim required evidence. True, the more substance you have, the easier it is to poke holes through it, and this is a problem. But there is evidence, which makes the strong claim more convincing. This doesn’t mean we should discard the weak claim: it is a starting point and is compatible with the strong claim. Together, they help us see the big picture. Likewise, PG’s strong and weak claims are compatible, and in this student’s lowly opinion, should both be part of the strategy.

Pops:

the genotype is redundant but the phenotype is not

I don’t see why (I know, my problem). Why would the phenotype not be redundant in part B? The phenotype’s function would not be disrupted if the newly duplicated gene disappeared, right? It would only have one less protease, so the rest of the proteases would not cease to do their job. It’s still reducible, until, as you point out, after enough mutations have taken place to make the proteases’ functions interdependent.

Which brings me back to this: Are IC systems really evolutionarily robust, that is, “resistant to change?” To stay with the example we are discussing, do you agree that blood clotting was IC before each doubling mutation, as well as after subsequent mutations that made the other parts dependent on the new protease? And doesn’t that show that IC systems change without the organism losing viability?

(I beseech you, keep your hand light; my bottom is still bruised from your last reprimand)

Comment #151962

Posted by Popper's Ghost on December 27, 2006 3:36 AM (e)

Likewise, PG’s strong and weak claims are compatible, and in this student’s lowly opinion, should both be part of the strategy.

I would note that many people on “our side” aren’t familiar with or don’t grasp the weak claim – that the existence of IC systems is no challenge to ToE. I think we would be more effective if they did, and if we all made that argument consistently whenever the IC nonsense is mentioned, until it sinks in.

the genotype is redundant but the phenotype is not

I don’t see why (I know, my problem). Why would the phenotype not be redundant in part B?

Because the phenotype in part B is exactly the same as it is in part A, before the gene was duplicated. As the article says, “There is no difference to the working of blood clotting; as all the proteins involved are the same”.

And doesn’t that show that IC systems change without the organism losing viability?

I said resistant, not immune. Gene doubling events do occur, but not nearly as frequently as arbitrary mutations.

Comment #151972

Posted by fnxtr on December 27, 2006 9:26 AM (e)

175 years ago today, Chuck looked out the window in England and said “Screw this, I’m not spending another winter in England! Where’s that boat?”

Comment #152017

Posted by Katarina on December 27, 2006 10:53 PM (e)

Pops, you’re not getting tired of this conversatin, are you?

I think we would be more effective if they did, and if we all made that argument consistently whenever the IC nonsense is mentioned, until it sinks in.

But it’s difficult to talk about a shaky concept - IC - which isn’t used in biology, and isn’t well defined, even if Muller did talk about interlocking “parts” (atoms are parts, so are amino acids, genes, proteins, protein complexes, tissues, organs, limbs, etc.) Which is the main reason our conversation got muddled, I think.

Because the phenotype in part B is exactly the same as it is in part A, before the gene was duplicated.

Yes. And it would be exactly the same if the double gene were to be removed. Remember this?

IC is well understood to refer to a system that can’t function if any of its components is removed… The “reduction” of complexity here refers to the removal of a component; the “ir” means that the system no longer functions if such a reduction occurs.

Will the blood still clot if the doubled gene, or the double protein is removed? Yes. Has the function of blood clotting been lost? No. Unless you wish to amend your comment above, according to you, blood clotting is not IC immediately after gene duplication.

I said resistant, not immune

And of course I went after the strong claim, not the weak one you actually made - because was easier to refute (see, I remember what you teach me) - or perhaps because I still had this in mind:

IC systems are unlikely to evolve further, because any change to them is non-viable

I should have said that any change to them is either non-viable or most likely useless; still, they can evolve, due to a shift in function or a change in environment that makes a previously useless feature sueful, as is true of most of evolution.

According to this comment and its amendment, the only options for change in an IC system are:
1. Non-viability,
2. Uselessness,
3. Shift in function due to environmental demand
Number 3 is a nice save, though it leaves little room for the description “resistant to change;” still it does fall short of a contradiction.

Gene doubling events do occur, but not nearly as frequently as arbitrary mutations.

Yeah, but they are responsible for so much! According to P.W. Hochachka and G.N. Somero in their book “Biochemical adaptation: Mechanism and process in physiological evolution,” Oxford University Press 2002, there are 5 types of highly conserved genes in eukaryotic cells:
1. Those that code for enzymes functioning in DNA replication, repair, transcription, protein synthesis,
2. Those that code for metabolism-related proteins (glycolysis, Krebs cycle, ETS, etc.)
3. Those for ion channels, ion pumps, transporters/exchangers,
4. Those that code for intracellular motors, microfilaments, sacroplasmic reticulum, mitochondria, other organelles,
5. Those that code for the function of sensing the extracellular environment and then communicating conditions and changes to the intracellular environment. They are also responsible for cell signaling in multicellular organisms.

Evolution in the last one, #5, is hypothesised by the authors to be important to the rise of multicellular life. And the way that genes in that category mutate is by gene duplication! Here’s their own brief summary:

To reiterate, the implications of these new studies are: (i) that unity of biological systems derives mainly from the conservation of ‘core’ genetic programs (involving perhaps several thousand genes) for ‘core’ cellular-level functions and structures; (ii) that the complexity and diversity of physiological systems arise in large part from genes that are involved in internal communication and in interfacing the organism with its environment;

There’s more, but this bit summarizes my point. Which isn’t to contradict anything you’re saying, but I did not want anyone to think we are trivializing gene duplication. The evolutionarily robust systems which you referred to in answer to my question of what else is considered that, are the highly conserved genotypes. But I don’t see why an IC system is necessarily evolutionarily robust. But this brings me back again to the arbitrary definition of IC, which blocks progress in this conversation, and in thinking about IC in the context of evolution at all.

And alas, (I don’t see a way around it) the looseness of the definition of IC causes trouble for the specific claim that “IC systems are an evolutionary prediction.” Therefore I’m going to have to change sides and go with the strategy of describing the evolution of each system, instead of bothering to talk about IC at all. I know it’s more cumbersome, but at least it is clearer. You said it: imagining how the system might have evolved is enough to refute Behe’s claim that it could not have evolved.

[this is where I duck and cover]

Comment #152019

Posted by Popper's Ghost on December 27, 2006 11:08 PM (e)

, you’re not getting tired of this conversatin, are you?

Yes; you’re too much work. Good luck.

Comment #152020

Posted by Katarina on December 27, 2006 11:19 PM (e)

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

Comment #152053

Posted by Katarina on December 28, 2006 8:19 AM (e)

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.

Comment #152143

Posted by Inoculated Mind on December 29, 2006 2:27 AM (e)

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?

Comment #152173

Posted by Katarina on December 29, 2006 7:05 AM (e)

Can you dig up the reference?

Comment #152231

Posted by Torbjörn Larsson on December 29, 2006 5:11 PM (e)

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.

Comment #152235

Posted by Torbjörn Larsson on December 29, 2006 5:35 PM (e)

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. ;-)

Comment #152237

Posted by Torbjörn Larsson on December 29, 2006 6:38 PM (e)

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/postmonth/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.)

Comment #152243

Posted by Katarina on December 29, 2006 9:08 PM (e)

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).

Comment #152249

Posted by Torbjörn Larsson on December 29, 2006 9:47 PM (e)

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?

Comment #152252

Posted by Katarina on December 29, 2006 10:37 PM (e)

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_ReplyToCritics_121201.pdf

Comment #152254

Posted by Katarina on December 29, 2006 10:55 PM (e)

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.

Comment #152256

Posted by Katarina on December 29, 2006 11:06 PM (e)

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?

Comment #152415

Posted by Torbjörn Larsson on December 30, 2006 10:43 PM (e)

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.

Comment #152483

Posted by Katarina on December 31, 2006 7:49 AM (e)

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.

Comment #152948

Posted by Chuck on January 2, 2007 5:23 PM (e)

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.