Uncommon Descent Serving The Intelligent Design Community

mouse trap illustration vs. 3-glasses-3-knives illustration — Irreducible Complexity, Depth of Integration

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Darwin once remarked the tail of the peacock made him sick because the unnecessary extravagance of nature was suggestive of Intelligent Design. What made Darwin sick then still holds true today, he never solved the problem, and it is more in evidence by the problem of Irreducible Complexity (IC).

To illustrate extravagance, consider the simple goal of getting a card to lie horizontally. This goal is easily achieved. Simply let a card fall down on a table. But one can take the same card and get it to lie horizontally by making part of the flat roof of a house of cards like this one.

irreducible complexity house of cards

Cleary one could argue there is an irreducibly complex core of this system, namely the cards on the lower levels. Removal of a single card from the lower levels would cause a breakdown of the system.

What if a Darwinist said,

the system does not have an irreducibly complex core because I can get a card to lay down horizontally without such an elaborate infrastructure. Further the house of cards is not evidence of intelligent design because the same task of getting a card to lie horizontally is inefficiently achieved. It is bad design because it is frail, and therefore it is not intelligently designed. Therefore the house of cards does not have an irreducibly complex core and further it is evidence of bad design since the same goal can be achieved more simply.

Would we think the objection is silly x 10? Of course we would! Yet Darwinists have made such silly objections, and worse, people like Judge Jones accepted similarly silly objections as valid science in his ruling against Intelligent Design.

What is spectacular about a house of cards is not that the goal can be achieved with the fewest parts, but the goal is achieved with MANY interdependent parts with a great depth of integration. This even more the case with Rube Goldberg Machines. From wiki:

A Rube Goldberg machine, contraption, invention, device, or apparatus is a deliberately over-engineered or overdone machine that performs a very simple task in a very complex fashion, usually including a chain reaction. The expression is named after American cartoonist and inventor Rube Goldberg (1883-1970).

Michael Behe even referenced the Rube-Goldberg machine in his book to describe irreducible complexity.

But Behe also used the a mouse trap consisting of 5-parts to illustrate the notion of irreducible Complexity (IC). A missing part would render the 5-part trap dysfunctional. Darwinists responded by saying mouse traps can be built with 4 parts, therefore, a 5-part mouse trap is not irreducibly complex since 4-part traps can be made. But Darwinists refute an argument that Behe never made. They don’t refute the concept of irreducible complexity, but only a straw man misrepresentation of Irreducible Complexity (IC).

I would argue Rube-Goldberg machines are far more illustrative of the problem irreducible complexity poses for Darwinism than mouse traps. Given the Darwinists misrepresentations, I suggest instead of mouse traps, ID proponents illustrate IC via a 3-glasses-3-knives system (depicted below). I suggest it because it will better resist Darwinist misrepresentations.

Consider the goal of letting a glass of beer be oriented vertically such that the beer doesn’t spill out. This simple goal can be achieved with minimal effort by simply placing the glass of beer on a level table. However the same goal can be achieved by letting it rest on an irreducibly complex system of 3 knives-and 3 glasses arranged in such a way that there is depth of integration in the parts. A video is worth a thousand words:

And that is the real problem irreducible complexity poses, the extravagance involved in doing tasks that can be done more simply.

Despite this, we have Darwinists saying the human blood clotting system is not Irreducibly Complex because there are creatures that implement blood clotting with fewer parts than humans. They also say that the flagellum is not irreducibly complex because we find existence of flagellum proteins in other systems. They might also argue that having extra parts is evidence of imperfect design because the same goal can be achieved with fewer parts.

But such arguments are as silly as saying the 3-glasses-3-knives system in the above video is not irreducibly complex because a glass of beer can remain vertical without such an elaborate system, or that the 3-glass-3-knife system is not irreducibly complex because knives have been co-opted to be used for other purposes, or that the system is not evidence of intelligent design because it is frail and unstable and thus an imperfect design, etc. etc.

Yet similar arguments are in promoted by Darwinists like Ken Miller and Nick Matzke and then accepted by Darwinists like Judge Jones. They seem unwilling or unable to discuss the real arguments being made. So I’m presenting this 3-glasses-3-knives illustration to help cure them of the injuries with Darwinism has inflicted on their ability to think clearly. If they are willing to take the medicine, perhaps they can be cured of their misconceptions!

I think in light of the misrepresentations put forward by Darwinists, the 3-glass-3-knife illustration can be used instead of mouse-traps since it illustrates the Rube-Goldberg concept which Behe put forward.

The problem IC poses for Darwinism is the extravagance of nature. Darwin perceived the problem the extravagance of nature posed for his theory and it made him sick. The problem is not that goals are achieved via the simplest means, but via extravagant and irreducibly complex means with great depth of integration.

Comments
Sorry to jump in, but NickMatzke, in response to UBpd, wrote: As for (2), it is possible to conceive of a self-copying polymer, or an auto-catalytic system, in which the “representation” and “what it represents” are one and the same. From a strictly logical point of view, if a physical configuration is a "representation" of something else, and you "copy" the "representation", then it is no more than a second "representation"; it is certainly NOT that which is "represented". I can write the words "bar stool". This conjures up an image of what a bar stool is: a flat rectangular surface, supported by four legs located at each right angle of the flat surface, and which, near the bottom, are interconnected to one another using horizontal bars. And, of course, there is an actual "bar stool" out there somewhere. Both the description of a "bar stool," and an actual "bar stool" are "what is represented" by the physical configuration of the English language that are the words "bar stool". Certainly "bar stool" is NOT the same as my "description" of what a bar stool is. These are two, entirely different "physical configurations" of the English language. And, of course, "bar stool" and an actual bar stool, are two, completely different physical realities.PaV
March 27, 2012
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What unique irreducibly-complex structure(s) do these “many flagellar proteins” that have no obvious antecedent form?
Dr. Hunt, Do you agree with Nick's count of 2 unique and essential? I see no reason, yet, to disagree except on the grounds that the BLAST searches found sequences that aren't expressed. Thanks for you input. Sal PS (I don't know why your comment was delayed. Do you get routed to some sort of moderation buffer or something?)scordova
March 27, 2012
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Thus, if the T3SS group is a clade sister to a flagellum clade, then there is a common ancestor on that phylogeny with the 10 or so T3SS proteins that is not reconstructed as a flagellum. This looks pretty much like a secretion system.
But ya see Nick, the missing common ancestor is always MISSING! Don't you recall our conversation loong time ago about transformed cladists who fell out of favor with Dawkins for pointing out we see all related as sister groups with no one ancestral to another! But if you say TTSS is not ancestral, your co-option argument collapses unless you appeal to non-existent entities! Logic, my good man, logic!scordova
March 27, 2012
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Firstly, for one thing to represent another thing (as agreed in #1), it must be separate from it. An auto-catalytic structure does not transfer recorded information as described in #1. This again is conflating recorded information with physical information, where the state of an object is deemed as “information” in order that it be calculable to human observers. To say that information has been transferred in an auto-catalytic structure is to step in as an observer and simply assert that it has.
This proceeds directly from Shannon's work -- information is the measure of reduction of uncertainty. If there were no uncertainty in the physical outcome of a process, there would be no opportunity for reduction of uncertainty. This simple fact is lost upon the OOL community! The most elmentary illustration is a fair coin. I conveys 1 bit of information. Darwinist like Jack Kreb then argued, "what about a 2 headed coin, that will reduced the improbability". True, but then it can convey only 0 bits of information. By appealing to self-ordering, you're looking for mediums of information storage that have almost zero capacity in terms of bits. Therefore, autocatalysis is not the way to solve OOL despite the millions of hours of time spent on this "solution".scordova
March 27, 2012
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Since the whole point of the original IC argument was that IC systems couldn’t evolve,
Mike Gene liked your paper. Because he, like Behe, accept front loaded evolution. Even cretionists do to some extent. Incidentally, OOL does not have co-option to complicate the analysis. That's one reason I like the subject. ID is quite in evidence there. And incidentally, I was indeed cheering your detractors on. Not because they were right, but I felt you needed to get a little taste of your own medicine, err, remember all that stuff you fabricated about an evolutionary biologist by the name of Richard Sternberg. scordova
March 27, 2012
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Nick Matzke:
Since the whole point of the original IC argument was that IC systems couldn’t evolve,
Nope, that is incorrect. Since the whole point of the original IC argument was that IC systems couldn’t evolve via blind and undirected chemical processes, ie darwinian/ NDE processes. IOW once again Nick Matzke erects a strawman and tilts at it. Also Nick cannot tell the difference between homologos and homoplasy- that is between what proteins are related and what proteins converged- or what proteins are similar due to a common design. IOW Nick's "argument" is one from ignorance.Joe
March 27, 2012
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Reply to Genomicus -- actually, about half the papers/researchers say that the T3SS and flagellum are sister groups. The phylogenies, such as they are (quite uncertain; relationships that are billions of years old are difficult to resolve definitively) at least allow this. Sister is not the same as ancestor, but then, nothing on a phylogeny is an ancestor of everything else -- phylogenies represent sister group relationships. But, what phylogenies allow you to do is reconstruct shared traits in common ancestors. The homologous proteins are shared traits. Thus, if the T3SS group is a clade sister to a flagellum clade, then there is a common ancestor on that phylogeny with the 10 or so T3SS proteins that is not reconstructed as a flagellum. This looks pretty much like a secretion system. Furthermore, whatever the resolution of the T3SS relationship, there is another homologous system, possibly sister to the whole flagellum/T3SS clade (it's an extremely long branch), that has homologs of at least FliHIJ, FlhA, and FliF IIRC. And then, a further sister (definite this time) of all of the above is the F1Fo-ATPase and relatives, which has homologs of at least FliHIJ. As for FliM/FliN -- actually, the chunk of FliM which is not homologous to FliN is homologous to CheC and relatives, which IIRC are widely distributed in sensory cascades and not just in flagella. But this is the key point:
IMHO, it has been convincingly demonstrated by Matzke et al. that the majority of flagellar proteins do not have unique functions (i.e., they can and do function in non-flagellar contexts).
Since the whole point of the original IC argument was that IC systems couldn't evolve, because partial systems would allegedly be "by definition nonfunctional", and thus could not be preserved by selection, this is a huge and fatal concession.NickMatzke_UD
March 27, 2012
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At the same time, however, there are many flagellar proteins (over half) for which there is no evidence that they arose from pre-cursor parts. Just. Saying.
What unique irreducibly-complex structure(s) do these "many flagellar proteins" that have no obvious antecedent form?Arthur Hunt
March 26, 2012
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Woops. Double post. Apologies.Genomicus
March 26, 2012
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A few notes on the essential proteins in flagella and their homology with other proteins: ------------------------------------------------------------ Protein:----------Homologs: FlgBCFG----------FlgBCEFGK FlgD-------------- None FlgE-------------- FlgBCFGK FlgK-------------- FlgBCEFG FlgL-------------- FliC FlhA-------------- LcrD; YscV FlhB-------------- YscU FliC-------------- FlgL, EspA FliE-------------- None FliF-------------- YscJ FliG-------------- MgtE FliI-------------- YscN; AtpD; Rho FliK-------------- YscP FliM-------------- FliN; YscQ FliN-------------- FliM; YscQ FliP-------------- YscR FliQ-------------- YscS FliR-------------- YscT MotA-------------- ExbB; TolQ MotB-------------- ExbD; TolR; OmpA ------------------------------------------------------------ The above "diagram" lists the proteins that seem to be essential to flagellar function, along with their homologs (if any). Data taken from Dr. Matzke's PT post referenced above by PaV. The first thing to note is that out of 23 proteins, only 2 have no known homologs. However, another 7 proteins only share homologs in the type III secretion system (TTSS). The TTSS is not a pre-cursor system to the flagellum, so these homologies cannot be evidence for the evolution of these flagellar proteins from pre-cursor parts. The origin of the TTSS is, in fact, a matter of debate. However, no specialist in the field is proposing that the TTSS is a pre-cursor system to the flagellum (i.e., that the flagellum evolved from the TTSS). Finally, we have proteins like FliM/FliN that share homologs in the TTSS and are homologous to each other. This means that for one of these proteins, there is no evidence that it evolved from a pre-cursor part. In other words, FliN may have given rise to FliM, accounting for the homology between the two proteins, but this means that there is no evidence that FliN arose from a pre-cursor part. And if it is argued that the two proteins are derived from a common non-flagellar ancestor, there is no evidence for the existence of this common ancestor. Thus, for one protein in the FliM/FliN pair, there is no homology evidence that it evolved from a pre-cursor part. The same goes for FlgL/FliC and FlgBCEFGK. Conclusion: For 12 out of 23 essential proteins in the flagellum (or about 52% of the proteins), there is no evidence that they evolved from pre-cursor parts. The Point My point here is simply to provide some perspective on the bacterial flagellum and homology. From a Darwinian perspective, there are two important reasons (IMHO) for searching for homologs of flagellar proteins: 1. To determine if a given flagellar protein can only function in a flagellar context. 2. To provide evidence that a given flagellar protein arose from pre-cursor parts. IMHO, it has been convincingly demonstrated by Matzke et al. that the majority of flagellar proteins do not have unique functions (i.e., they can and do function in non-flagellar contexts). At the same time, however, there are many flagellar proteins (over half) for which there is no evidence that they arose from pre-cursor parts. Just. Saying. (Hopefully, that diagram came across well and is fairly easy to understand.)Genomicus
March 26, 2012
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A few notes on the essential proteins in flagella and their homology with other proteins: ------------------------------ Protein: Homologs: FlgBCFG FlgBCEFGK FlgD None FlgE FlgBCFGK FlgK FlgBCEFG FlgL FliC FlhA LcrD; YscV FlhB YscU FliC FlgL, EspA FliE None FliF YscJ FliG MgtE FliI YscN; AtpD; Rho FliK YscP FliM FliN; YscQ FliN FliM; YscQ FliP YscR FliQ YscS FliR YscT MotA ExbB; TolQ MotB ExbD; TolR; OmpA ------------------------------ The above "diagram" lists the proteins that seem to be essential to flagellar function, along with their homologs (if any). Data taken from Dr. Matzke's PT post referenced above by PaV. The first thing to note is that out of 23 proteins, only 2 have no known homologs. However, another 7 proteins only share homologs in the type III secretion system (TTSS). The TTSS is not a pre-cursor system to the flagellum, so these homologies cannot be evidence for the evolution of these flagellar proteins from pre-cursor parts. The origin of the TTSS is, in fact, a matter of debate. However, no specialist in the field is proposing that the TTSS is a pre-cursor system to the flagellum (i.e., that the flagellum evolved from the TTSS). Finally, we have proteins like FliM/FliN that share homologs in the TTSS and are homologous to each other. This means that for one of these proteins, there is no evidence that it evolved from a pre-cursor part. In other words, FliN may have given rise to FliM, accounting for the homology between the two proteins, but this means that there is no evidence that FliN arose from a pre-cursor part. And if it is argued that the two proteins are derived from a common non-flagellar ancestor, there is no evidence for the existence of this common ancestor. Thus, for one protein in the FliM/FliN pair, there is no homology evidence that it evolved from a pre-cursor part. The same goes for FlgL/FliC and FlgBCEFGK. Conclusion: For 12 out of 23 essential proteins in the flagellum (or about 52% of the proteins), there is no evidence that they evolved from pre-cursor parts. The Point My point here is simply to provide some perspective on the bacterial flagellum and homology. From a Darwinian perspective, there are two important reasons (IMHO) for searching for homologs of flagellar proteins: 1. To determine if a given flagellar protein can only function in a flagellar context. 2. To provide evidence that a given flagellar protein arose from pre-cursor parts. IMHO, it has been convincingly demonstrated by Matzke et al. that the majority of flagellar proteins do not have unique functions (i.e., they can and do function in non-flagellar contexts). At the same time, however, there are many flagellar proteins (over half) for which there is no evidence that they arose from pre-cursor parts. Just. Saying.Genomicus
March 26, 2012
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Nick,
As for (2), it is possible to conceive of a self-copying polymer, or an auto-catalytic system, in which the “representation” and “what it represents” are one and the same.
Firstly, for one thing to represent another thing (as agreed in #1), it must be separate from it. An auto-catalytic structure does not transfer recorded information as described in #1. This again is conflating recorded information with physical information, where the state of an object is deemed as “information” in order that it be calculable to human observers. To say that information has been transferred in an auto-catalytic structure is to step in as an observer and simply assert that it has. There is also a physical distinction between a) a representational arrangement of matter being transferred, and b) the state of an object (serving as a template) being deemed “information” by an observer. That distinction can be elucidated in the physical properties of the systems and their products. One of them can be reduced to those properties, while the other cannot (without the actions of the second arrangement of matter). Both structures exist in nature, but one does not explain the other. Now, if you can conceive of transferring a representational arrangement of matter (as agreed in #1) that does not require a second arrangement of matter in order to establish the relationship between representation and what it represents, then I am interested in hearing it.Upright BiPed
March 26, 2012
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Sal, Apparently my memory and google skillz are better than yours. In this thread, you write:
Whatever my personal shortcomings may be, it doesn’t have relevance to the facts and ideas at hand. And however low a person you may view me to be, I’ve never stooped to the level of backstabbbing and demonization your colleagues like Jerry Coyne, Richard Dawkins, and PZ Myers stooped to with regards to you. Not that I’m suggesting we become bosom buds, but c’mon, you can’t say I’ve been as bad as them! I mean, I’ve never said these things of you: [quotes]
But back on April 23, 2011, you wrote:
Matzke’s attacks on ID are fundamentally based on misrepresentation, strawman arguments, equivocation, distortions, etc. Well, it seems his way of doing business has finally caught up with him. There is poetic justice in his public humiliation at the hands of fellow Darwinists. [smiley]
It looks like you were cheering them on. Now, maybe this was just a dumb joke, but that wouldn't be apparent to most readers.NickMatzke_UD
March 26, 2012
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At least Sal gets it, that’s progress.
Awe shucks, thanks Nick. Over at PT you said us ID guys were clueless. Well, that's why we need bright scientists like you to set us straight. With respect to the 2 unique proteins, I think you've argued your point well-enough, that at least for me, I would be dissuaded from using the "unique protein" argument for the flagellum. Such a line of reasoning is not needed anyway! I've outlined that the assembly instruction critique is much more forceful, and it was one Dr. Minnich argued as more important. So you work will hopefully get my colleagues to pursue the assembly instruction angle far more vigorously than trying to demonstrate proteins are unique.scordova
March 26, 2012
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Gee, the lack of homologous proteins sure seemed quite interesting to ID advocates back when they thought that homology accounted for “only 10? flagellar proteins.
It is still interesting, Nick. And your position can't account for any of the required proteins nor their alleged homologs. And you sure can't account for the correct quantities nor the correct configuration- not wrt necessity and chance. As for the OoL- well Nick, if the OoL is not reducible to matter, energy, necessity and chance, then neither is the evolution of any flagellum. IOW, Nick, if living organisms were designed then the inference is flagella were either directly designed or were designed to evolve/ evolved by design. That is why the OoL is critical to any talk of evolution- you cannot discuss evolution without a discussion of the OoL. I know you want to separate them but that is just deceptive at best.Joe
March 26, 2012
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Sal — you’ve been acting OK in this particular thread, but for years you’ve been famous amongst us evolution-debaters for any number of creationist shenanigans which were vile or idiotic if taken seriously, and juvenile/unserious/unprofessional if taken as jokes.
That's true. That's me, but I'm not a scientist like you. ID is my hobby, whereas Darwinism is your profession. Whatever my personal shortcomings may be, it doesn't have relevance to the facts and ideas at hand. And however low a person you may view me to be, I've never stooped to the level of backstabbbing and demonization your colleagues like Jerry Coyne, Richard Dawkins, and PZ Myers stooped to with regards to you. Not that I'm suggesting we become bosom buds, but c'mon, you can't say I've been as bad as them! I mean, I've never said these things of you:
[Matzke is] a nasty piece of work … Matzke has apparently made stuff up Jerry Coyne
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Nick completely and utterly slighted me, in what I viewed as a sexist manner Abbie Smith
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Yeah, I’m looking at you, Nick Matzke. …sleazy.
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Nick Matzke is a deliberate, intentional, unrepentant liar. Richard Dawkins
I'd say by comparison, your opponents on the ID side have never treated you with such disrepect, and even a scoundrel like me never stooped so low to call you such things (and I didn't even include the stuff the GNUs said about you on the blogs). So no, you don't have to take me seriously. I'm merely pointing out, I don't have quite the axe to grind against you that Richard Dawkins does. I've never seen you stoop to their level, and I respect that. And finally, I really do think you are among the brightest of the lot of them. Good luck with your science career, and I would sincerely hope you show those guys up. Then I can boast that I once debated the great Darwinist Nick Matzke! Your Flagellum paper was one of the best evolutionary papers I've ever read. Right up there with some of Haldane's work and Kimura in my list of good evolutionary reads.....scordova
March 26, 2012
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We’ve had this discussion with Nick in some detail in the past. Homologous proteins are interesting. That is about it. They do not in any way demonstrate an evolutionary origin for the flagellum.
Gee, the lack of homologous proteins sure seemed quite interesting to ID advocates back when they thought that homology accounted for "only 10" flagellar proteins. They made this argument dozens of times, in court, in books, etc., again and again. Heck, ID people have emphasized this argument from the 1990s right up until...*this very thread*. You can't just turn around and pretend like this didn't happen. At least Sal gets it, that's progress.NickMatzke_UD
March 26, 2012
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42 Upright BiPedMarch 26, 2012 at 1:50 pm Nick, the last time I approached you on the topic of biological information, you side-stepped the issue like a cowgirl on a dance floor. I wonder if you might try to enagage in earnest this time. Will you bring your advanced intellect to bear on these three pertinent questions regarding the existence of information within a material universe: 1) In this material universe, is it even conceivably possible to record transferable information without utilizing an arrangement of matter in order to represent that information? (by what other means could it be done?) 2) If 1 is true, then is it even conceivably possible to transfer that information without a second arrangement of matter (a protocol) to establish the relationship between representation and what it represents? (how could such a relationship be established in any other way?) 3) If 1 and 2 are true, then is it even conceivably possible to functionally transfer information without the irreducibly complex system of these two arrangements of matter (representations and protocols) in operation?
This is much clearer than whatever you were asking in that link you provided. I agree with (1). As for (2), it is possible to conceive of a self-copying polymer, or an auto-catalytic system, in which the "representation" and "what it represents" are one and the same. (3) answers itself once you've got my answer to (2). However, this thread is not about the origin of life, it is about the origin of the flagellum, so please start a new thread if you want to discuss the origin of life. I won't discuss the OOL further here, at least, the thread is already confusing enough.NickMatzke_UD
March 26, 2012
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PS By the way Nick, now you’ve had a chance to taste how we in the ID community perceive the behavior from your side of the ailse. Evolutionary biologists like Coyne and Dawkins aren’t as objective, dispassionate, and fair with the facts are they? Hang out with us. We may disagree, but at least for myself I won’t stoop so low as your GNU “friends”.
Sal -- you've been acting OK in this particular thread, but for years you've been famous amongst us evolution-debaters for any number of creationist shenanigans which were vile or idiotic if taken seriously, and juvenile/unserious/unprofessional if taken as jokes. Start with various quote mines of Darwin and others, then move over to junk like the "Darwin beat a puppy" story removed of context, then move to your refusal to acknowledge reality even on ultra-simple matters like the age of the Earth, and finally the Darwin-Nazi stuff -- and that's just what I remember off the top of my head. You've got a lot of work to do before you're going to convince us that you are serious, constructive, and nice person, or even one who actually follows what are supposed to be Christian values in your online persona.NickMatzke_UD
March 26, 2012
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I’d like to commend Nick on his research on the flagellum. Nick’s figure of 2 unique and essential proteins deserves some notice since it is a number that disagrees with Scott Minnich’s claim of 30 unique and essential.
So where's the retraction and correction from Casey Luskin, who still cites Minnich and his testimony as authoritative? Where's the correction in the ID textbook Explore Evolution, which repeats this statement? How about the other several dozen prominent videos and publications where leading ID guys have used this or a very similar talking point? And, why was it like pulling teeth for me to get this point recognized in this blog post? It's been settled since, let's see, 2006. Other stuff very briefly: Re: the malfunctioning system argument -- (a) It's not true that a proto-flagellar system would be a defective secretion system. Flagella even today can serve both motility and secretion functions. T3SS effectors ("toxins") can even be secreted through flagella, IIRC. The flagellum is basically a type 3 secretion system with a bunch of duplicated and specialized pilus proteins, and a motor complex (itself homologous to 2-protein ion transport systems) stuck on the outside to turn it. (b) Even if it were true, which it isn't, that modifying a T3SS in a flagellar direction must make it nonfunctional as a secretion system, this still doesn't matter much, because the changes could happen in a duplicated version of the system, with one duplicate retaining the ancestral function unchanged. There are bacterial genomes encoding 2 whole distinct flagellar systems, and holding 2 or even 3 (IIRC) nonflagellar T3SS. Re: the regulation of flagellar assembly -- please tell me what the universally required parts of the assembly system are supposed to be. The problems you will discover: (a) flagellar assembly -- the gene order and operon structure, the regulatory proteins, etc. -- is even less conserved than the core structural proteins. Several of those 13/15 nonessential proteins are the assembly/regulation ones in the standard model systems of E. coli/Salmonella. (b) Furthermore, even in systems where a particular regulatory protein seems essential (even though it is absent in other flagellated species), usually a scan for compensatory mutations will turn up the fact that alternative, simpler expression solutions -- such as constituitive expression, i.e. "the gene is always stuck in the 'on' position", work OK as substitutes. As I wrote back in 2003 (!), as you folks would know if you would read evolution stuff more carefully,
The evolution of the organization of flagellar genes and operons also deserves attention, although the precise organization found in modern bacteria is probably not essential (Kalir et al., 2001).
Which is a reference to this passage in Kalir et al. (2001):
The precise order of transcription of the various operons is probably not essential for assembling functional flagella. This is suggested by complementation experiments in which the motility of flagella mutants was rescued by expression of the wild-type gene from a foreign promoter (1). The detailed transcription order could, however, function to make flagella synthesis more efficient, because parts are not transcribed earlier than needed.
This is confirmed by the immense diversity in flagellar operon structure (see the second article by Liu & Ochmann; they had a dubious article on flagllum evolution, but they had a quite good one on the evolution of operon structure) and by the non-universality of flagellar regulatory proteins. So again, what exactly is the IC system in flagellar assembly? Random other stuff: Sal writes,
incidentally Nick, do you know for a fact that the supposed homologues found in your blast searches actually result in protein expression. If not, then well, maybe those proteins are unique and not found in living systems.
What are you suggesting, that these homologous genes are all pseudogenes? What's your evidence? Typically pseudogenes have early stop codons and the like. These don't. Bacterial genomes almost always have very little junk DNA anyway. And in the cases where the genes occur in model organisms (e.g. E. coli) they have been purified & studied to some extent. E.g. the MotAB homologs ExbBD and TolQR. So yes, they are virtually certain to be expressed.NickMatzke_UD
March 26, 2012
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To understand the nuance in my criticism of the TTSS not being really co-opted, here is an illustration. The flagellum and TTSS operate in 3 dimensional space, but let me try to illustrate with a 1 dimensional example: a password-login system. Consider that you were trying to break into a computer account of 40 characters. Say the password is:
SUperCalifragilisTICEXpialidocious
Suppose we were clued in that there were co-optible parts to the password like:
SUper Cali fragilisTIC EXpiallidocious
Then the breaking of the password would be much easier! However if we had the above fragments a bit scrambled:
pSUer aCli fragTICilis suoicEXpiallido
and further the fragments were agumented with extra parts and diminished with some missing parts
pSUerzt aClilmo fragTilis suoipiallido
claims that you can co-opt the parts become more and more dubious!!!! You might only be clued in that something resembling the fragments might solve your password problem. Clearly there is a lot of homology (as in they use most of the same letters in upper and lower case), and maybe even some grouping is generally in the right direction, but that's about it. Further say that the above fragments are functional passwords to other login-systems. Alteration of the sequence characters in the above fragments would be fatal obviously to the functioning of the fragments as passwords in their respective systems. Thus, altering the fragment in order to co-opt it would be selected against. It can be done, but the probability of it happening is reduced.... The TTSS gets about the right subset the protein "alphabet" and maybe even 1 or 2 components in the right place. Sure it is a candidate for a pre-cursor, but it is disingenous to say it was co-opted as a functional intermediate because for it to be incorporated into a flagellum it would mostly likely have to be rendered dysfunctional. Consider the necessary transformation to "co-opt" the precursors in our illustration:
pSUerzt -> SUper aClilmo -> Cali fragTilis -> fragilisTIC suoipiallido -> EXpiallidocious
Think I'm overstating the difficulty. The illustration is only re-arrangement of parts in 1-dimension! It is quite another thing not only to re-arrange protein parts in 3-dimensions, get them to connect to each other, but to also write assembly instructions for the cellular factory that accomplish the positioning. The instructions must: 1. express the proteins 2. position the proteins Anyone who has written process or factory control software can appreciate the difficulty of doing this right! Think about some one giving you directions to another city. Consider then, if he misprinted just one instruction, like turning left, when you should turn right. Get the picture? Yet the Darwinists have misrepresented the TTSS as somehow being co-opted. The only thing that was co-opted was maybe some subset of a parts listing. It is very disingenous to say that NS co-opted a functioning TTSS, if it co-opted it, it would have to be malfunctioning first! Not exactly a solution! Clear some on the Front Loading spectrum of the ID community suspect there is an evolutionary relationship between the TTSS and the flagellum. I'm fine with that, but evolving via front loading is quite different from evolving in a Darwinian manner. One might object to this analysis as employing a 'single-target' fallacy, that there are numerous ways to make a flagellum. That objection is correct, but this illustration was provided merely to point out that claims that the TTSS was co-opted are untrue.scordova
March 26, 2012
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"This is a useful observation, as far as it goes. But it does not in any way refute Behe’s point, nor does it obviate the need for infusion of complex specified information to get from point a to b."
Eric, just as I see it. Noting sequence similarity does not further understanding of the process by which sequence A is transformed into sequence B. There's nothing about the observation of sequence similarity that precludes design, lacking an empirically verifiable mechanism with empirically verifiable limits of capability in traversing the space between A and B. There must exist a function that transforms A into B -- this is inarguable. This function must be extrinsic or intrinsic, or some combination of the two. Extrinsic functions include necessity/chance and design. Intrinsic factors would rely on the configuration and operation of the system in question -- the myriad integrated systems which comprise the organism (for instance, a type of transformation may be possible via an internal heuristic). However if one appeals to the operation of the system in question in order to explain its origin, one is begging the question, perhaps even committing a category error. In order to be logically consistent then, one must consider only extrinsic factors as causal phenomena in regards to origins. Either necessity and chance are culpable, or agency is. If there is another option that doesn’t refer back to the system in question, I don’t know what it is. Sequence similarity does not address the issue, except to suggest that there is some point at which the similarity falls within the purview of a random search. If we're to believe that sequence similarity is suggestive of an evolutionary relationship between sequences, which is accountable via a blind external mechanism, we could really stand to know what that mechanism is, and how it accounts for relatedness. How does the “evolutionary mechanism,” independent of the functional configuration of the system in question, account for a transformation from sequence A to sequence B in cases of relatedness? If a given transformation falls within the capabilities of random search, I'm all for crediting Darwin. If a given transformation can be mapped to physical necessity, then natural processes are capable of achieving it. However, appeals to the internal configuration and operation of the system in question as evidence for what blind processes can accomplish, should not be abided. I'm hopeful that this distinction will be emphasized as the debate progresses. Right now it appears that the term “evolution” is strongly aligned with the sophisticated operation of a vastly integrated system of functional configuration. The term “evolution” apparently stands in for “the operation of the system in question.” Any definition which relies on that which an organism is configured to do as a result of its internal specification, is at the least, an unfortunate equivocation.material.infantacy
March 26, 2012
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All of the above comments reinforce the point I made in #29, above: if a biological structure or process has been shown to be irreducibly complex by Behe's definition, then the burden of proof of its evolvability by Darwinian mechanisms lies with the Darwinian and nowhere else. Clearly, Dr. Matzki has not yet met that requirement with respect to the flagellum, since the observation that proteins homologous to those used in the flagellum exist in bacteria does not constitute an evolutionary path to its existence. Much more is required to show that a step by step path to a functioning flagellum, each step of which has a reasonable probability of occurring and increases its fitness, is possible. Absent that requirement having been met, the assertion that it did in fact so evolve is a statement of faith, not science.Bruce David
March 26, 2012
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I'd like to commend Nick on his research on the flagellum. Nick's figure of 2 unique and essential proteins deserves some notice since it is a number that disagrees with Scott Minnich's claim of 30 unique and essential. UD is organized to serve the intelligent design community. I think we would be doing the ID comminity a disservice if we didn't recognize Nick's fine work. Maybe this data point provided by Nick is one of the few objections to ID literature that may be right (most of it is nothing more than equivocation and misrepresentation), but I thought Nick's fine research ought to be recognized, and to the extent it is correct, appreciated. (we certainly have trashed some of his other offering for sure). Personally, my focus has been on OOL. The question of co-option in OOL is rather moot in that case :-). That's why I like the topic. IC works beautifully there! So this is the first time I've really visited the flagellum. And in the process, I've become quite appalled by misrepresentation the Darwinist have put forward. They argue the TTSS could have been co-opted, and that is patently NOT true. Only parts of the TTSS have been co-opted, not that entire TTSS. And that is a very very important distinction, becuase to evolve a TTSS to a flagellum, it has to be evolved to a malfunctioning TTSS first! Yet the Darwinists have said a functioning TTSS was co-opted, whereas the truth is a malfunctioning TTSS had to be co-opted, not a functioning one. That's highly disingenuous, imho. That said, I think Nick has done a great service to science for his research on the flagellum. I will probably never agree with him about evolution, but it does the ID community no good to not recognize his hard and meticulous work, despite the fact we disagree with him. Given how badly he has been persecuted by the evolutionary community on the internet (Dawkins, Coyne, PZ Myers, the GNUs), he almost ought to be recogized as an honorary creationist -- something I'm sure he'd be delighted to put on his resume. :-) PS By the way Nick, now you've had a chance to taste how we in the ID community perceive the behavior from your side of the ailse. Evolutionary biologists like Coyne and Dawkins aren't as objective, dispassionate, and fair with the facts are they? Hang out with us. We may disagree, but at least for myself I won't stoop so low as your GNU "friends".scordova
March 26, 2012
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Joe:
IOW it isn’t just enough to say you can get the right parts- you need the correct quantities and the correct configuration.
Exactly. Which is why finding all the parts around elsewhere (which hasn't been done yet) is not an "explanation" of the flagellum's origin. Further, it is also why ideas like co-option, horizontal gene transfer, gene duplication and the like are impotent to account for complex systems (that is not to say such things do not occur; they just can't actually do much by themselves, and certainly don't represent an answer to irreducible complexity). Everything has to be integrated into a functional whole, and then the instructions for the whole process -- building the parts from scratch and integrating them into a functional whole -- have to be preserved and made available to be passed down to the next generation. Finding homologous proteins to those in the flagellum is interesting. But it is about as interesting as finding homology elsewhere (camera-type lens in different creatures; pendactyl limb structure; etc.). It is not an explanation for the origin of the system in question.Eric Anderson
March 26, 2012
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In "Unlocking the Mystery of Life", Jonathan Wells says that not only is the physical part- the bacterial flagellum (any/ all of them) is irreducibly complex but so are the assembly instructions. IOW it isn't just enough to say you can get the right parts- you need the correct quantities and the correct configuration.Joe
March 26, 2012
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Nick, the last time I approached you on the topic of biological information, you side-stepped the issue like a cowgirl on a dance floor. I wonder if you might try to enagage in earnest this time. Will you bring your advanced intellect to bear on these three pertinent questions regarding the existence of information within a material universe: 1) In this material universe, is it even conceivably possible to record transferable information without utilizing an arrangement of matter in order to represent that information? (by what other means could it be done?) 2) If 1 is true, then is it even conceivably possible to transfer that information without a second arrangement of matter (a protocol) to establish the relationship between representation and what it represents? (how could such a relationship be established in any other way?) 3) If 1 and 2 are true, then is it even conceivably possible to functionally transfer information without the irreducibly complex system of these two arrangements of matter (representations and protocols) in operation?Upright BiPed
March 26, 2012
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We've had this discussion with Nick in some detail in the past. Homologous proteins are interesting. That is about it. They do not in any way demonstrate an evolutionary origin for the flagellum. Nick's "explanation" is not an explanation at all. It is simply an observation that there is some similar stuff out there. This is a useful observation, as far as it goes. But it does not in any way refute Behe's point, nor does it obviate the need for infusion of complex specified information to get from point a to b.Eric Anderson
March 26, 2012
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NickMatzke: You’re doing better than most, but you’re not there yet. Keep reading. How many of those 15 remaining proteins are actually required for flagellar function? I suppose, looking at Table 1, you mean "how many of these 15 remaining proteins are 'indispensable'." And you seem to define "indispensable" based on whether or not other bacteria are functioning bacteria despite the absence of one, or several, of these 15 proteins. It's not clear how pertinent, or reliable, this definition is. For example, for the L-ring and P-ring proteins, apparently they're not in gram-positive bacteria. But it is beyond a doubt that if these proteins were not present in TTSS, then the flagellum would not be able to work. So, it is "indispensable" in that sense. Likewise, you consider proteins to be "indispensable" if they are present in a mutant form. If there are no homologies, then the fact that the protein is present in a mutant form only tells us that there is a certain flexibility in the protein sequence; it's not telling us that the entire protein is "indispensable". This seems to me to be a bit of a stretch, and there are two examples of this. Further, some of these "unique" proteins are not found in other types of flagella. But if they were present, then, as I understand the method you employed, they wouldn't have even been 'unique', since a homologous sequence would have shown up in the BLAST search. Finally, your argument seems to assume that other types of flagella are not IC. But all bacterial flagellum are IC. They're just as much IC as the TTSS, and dependent on the presence, and purposeful arrangement, of these essential proteins just as they are in the case of the TTSS. .......................... Yet, all of this seems to miss the point almost entirely. I asked you above---and you haven't answered---if an Igloo is 'designed'. Ice is everywhere during the winter. It's not the presence or absence of the ice that determines whether or not an Igloo is designed. It is the arrangement of the pieces of ice into a functional whole that gives evidence of design. I can only suppose this obvious truth is why you chose not to answer the question. In terms of the ID perspective, it is not really all that pertinent whether a protein is "indispensable" and "unique" to a living organism. Rather, it is the assembled ensemble that points to IC. If I'm driving on the highway, and I see a gathering of rocks formed into the shape of a 'cross', though the rocks come from nearby beds, the shape---the assembled ensemble---tells me that design is present. You seem to be defining IC as creatio ex nihilo. While creatio ex nihilo is a separate, and very germaine, issue, that is not the principal concern of ID in its claim of IC. You remember that I also asked about the TeePee. Wooden branches and sewn hides: these are already created objects; they're readily available. The "design" of the TeePee, the IC of the TeePee is not based on the branches and the skins being "created from nothing", but is, rather, constituted by the placing of all of these thing together in a particular form that, in its own specified way, provides function---and which, in this case, represents IC, and, hence, "design." The branches have been chosen; they are of a particular length and size. The hides are sewn together to form a particular shape so that they can be fitted together with the branches. The whole point of the bacterial flagellum---which, conveniently for Darwinists---gets lost in this entire discussion is the fact that it looks almost exactly like an "outboard motor." We KNOW that outboard motors have been designed. We KNOW the functional relationships that exist between the various parts of the assembled ensemble, and we KNOW why these various parts have been chosen and purposely formed into a functional whole. And we also KNOW that if you take just "one" essential part away from an outboard motor, that it won't function. I knew the man who first put a "supercharger" onto a race engine. He took it from a tractor. He didn't "invent" it. He didn't "create it out of nothing." But, of course, via this process he "designed" the race engine of the future. Race engines had "evolved"! The ID/IC argument is that if you have 30 plus proteins that come together to form an arrangement that is "functional", and that resembles known objects of human design, and whose system (the assembled ensemble) is rendered "function-less" by the removal of any essential protein/s, then you have an IC system. And that means what you're looking at has been "designed." It is NOT the result---cannot be the result---of random processes. If we found bacteria that had, let's say, 10 proteins, assembled together to fashion a functioning flagellum; and then another protein with the same, or similar, proteins, plus the addition of 5 more proteins, and now forming a more "fit" flagellum; and so forth in increments of 5 proteins, all the way up to the TTSS flagellum, then I would say that the argument for IC is weakened, and the argument for Darwinian mechanisms having brought this about, strengthened. But this isn't what we see. We see "design". Just ask Richard Dawkins.PaV
March 26, 2012
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incidentally Nick, do you know for a fact that the supposed homologues found in your blast searches actually result in protein expression. If not, then well, maybe those proteins are unique and not found in living systems. And if the flagellum parts are actually ancestral to the hologues (the reverse of you evolutionary model), then if the proteins are no longer expressed, it only shows, that co-option doesn't work so well. :-)scordova
March 26, 2012
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