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

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

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.

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

  1. Instead of inviting Darwinists to refute my arguments, I invite them to misrpresent my arguments to the best of their ability. I say that, because that’s what they tend to do anyway: misrepresent arguments vs. actually refuting them.

    Behe claimed a mouse trap is irreducibly complex. Darwinist misrepresented the argument he was making.

    I invite Darwinists to misrepresent my argument that the 3-glasses-3-knives system is irreducibly complex. It would be interesting to see how they will misrepresent my argument, because it would be likely their misrepresentation would be no different than their supposed refutations.

    So instead of challenging them to give a refutation, I challenge them to make up the most clever misrepresentation. Given their past history, there is little difference in their mind between the two. :-)

    Or better yet, how about the ID proponents here at UD do there best to imitate how the Darwinists will misrepresent my assertion that the 3-glasses-3-knives system is irreducibly complex. :-)

  2. Larry, Moe, and Curley were eating lunch together. Each was thirsty and took a drink from his water glass, before buttering his bread with his knife. As the three were dining as a trio, it was more probable than not that the glasses and knifes would be returned to the table as they were.
    Then…Shemp came in with a glass of beer.

  3. 3
    material.infantacy

    You forgot about co-option. Your “irreducibly complex” beer stand is composed of parts that are functional in other contexts, and even predate the stand itself. Hell, you could make a tie clip out of a couple of the knives.

    Extravagant beer stands are better at attracting mates, so it doesn’t preclude an evolutionary scenario.

    There may be thousands, millions, or billions of ways to make a beer stand — that’s the one natural selection just happened to stumble upon.

    That beer stand is no more complex than a bunch of dishes in your dishwasher.

    What, are you saying that designers just “poof” beer stands into existence? We might as well believe that pink unicorns drink beer.

    I see nothing in that “system” that isn’t composed of matter — therefore material forces are the best explanation.

    That configuration of parts is no more improbable than any other configuration of the same parts.

    The beer stand is vestigial. My beer doesn’t last long enough for there to be any need of setting it down. xp

  4. material

    can you produce a mouse trap in small steps, when each of the steps is functional by itself, and without any help of intellegent?

  5. 5
    material.infantacy

    Dammit mk, the tie clip preceded the mouse trap!!! Besides, I can imagine a precursor mouse trap starting off as a nice little place for a mouse to have lunch.

  6. material.infantacy:

    LOL! Great list of absurd materialist arguments! I especially liked the last one in #3! :)

  7. You guys don’t know what almighty Time can do.

  8. material.infantacy said:

    You forgot about co-option. Your “irreducibly complex” beer stand is composed of parts that are functional in other contexts, and even predate the stand itself. Hell, you could make a tie clip out of a couple of the knives.

    Ya know, I should have pointed out a similar line of reasoning by the Dover Poster boy himself:

    I then detached the spring from the hammer [of the mouse trap], and used the device as a keychain. If I had cared to, I might have used the base and spring (2 parts) as a paper clip, my tie clip (glued to a door) as a door knocker, the catch as a toothpick, or the base as a paperweight.

    Dr. Ken Miller
    http://www.millerandlevine.com.....etrap.html

  9. The chemistry governing beer fermentation is perfectly understood. No mystical “beer fairies” are required to explain it. The knives and beer trick is just a warm can of Budweiser in a cheap tuxedo.

  10. Ya know, I just realized that the 3-glasses-3-knives system is inferior in simplicity to a coaster, which can achieve the same obvious intent of protecting the table and insulating the beer with only 1 part:

    Take a look at this:
    Beer Coaster

    After all Ken Miller used such a line of reasoning to argue a 5-part mouse trap isn’t irreducibly complex:

    A series of drawings made by John MacDonald at the University of Delaware (left) show just how quickly the assertions behind Behe’s mousetrap analogy collapse upon inspection. It it remarkably easy to construct a mousetrap with just 4 parts, 3 parts, or even a mousetrap with just one part. As MacDonald himself was careful to note, none of these contraptions are nearly as good as the standard 5-part mousetrap, but that’s exactly the point. Working mousetraps don’t have to have each of the 5 standard parts to be functional. If they have fewer parts, they can still be made to work.

    http://www.millerandlevine.com.....etrap.html

  11. material.infantacy noted:

    You forgot about co-option. Your “irreducibly complex” beer stand is composed of parts that are functional in other contexts, and even predate the stand itself. Hell, you could make a tie clip out of a couple of the knives.

    Yeah, shame on me, and I should have pointed out Matzke uses the same misrepresentation, ahem, I mean argument:

    homologies between flagellar and nonflagellar proteins suggest ancestral systems with functions other than motility.

    http://www.talkdesign.org/faqs/flagellum.html

  12. 12

    Hey, it’s not my fault that Behe wrote,

    An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.

    …which makes it perfectly valid to impeach his argument by showing systems missing parts which are still functional.

    I don’t get into elaborate arguments about mousetraps and other analogies, these are at best dubious analogies for actual biology. Trying to turn the analogy around (e.g. “evolving” a mousetrap) just compounds the problem. In real biology, there is homology between parts, unlike in the analogies. If airplane wings looked like modified car doors, and if knives looked like modified forks, and if developmental and DNA information confirmed this pattern, then you’d be getting closer to something like what is actually observed in biology.

    Also, in real biology, multiple and alternative functions are observed out there in nature, used for practical and direct survival-and-reproduction-related functions nature without humans thinking up creative and arbitrary functions.

    Of course, it’s a lot easier to yammer about bartop tricks than to learn about the statistics of homology searches, phylogeny estimation, and the incredible diversity of actual biology. But until you do, you have no hope of ever convincing the scientific community of your arguments. We know this stuff, why should we listen to people who pretend it doesn’t exist, and rely on preposterous and misleading analogies instead of doing hard work?

  13. “We know this stuff, why should we listen to people who pretend it doesn’t exist, and rely on preposterous and misleading analogies instead of doing hard work?”

    Edison’s sweat notwithstanding, “doing hard work”, on the basis of grotesquely risible materialist conjectures is no substitute for elementary reasoning on the basis of plausible hypotheses.

  14. Oh my goodness. NICK! How are you, bud? Sooo nice to see ya!

    Gentleman, at UD, I know we may have axes to grind with nick, but I urge civility, since I want the dialogue to take place.

    it perfectly valid to impeach his argument by showing systems missing parts which are still functional.

    Nick, you clever weasel you. I have to credit you for your ingenuity in misrepresenting what Behe said.

    An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism)

    Err, did you notice what I highlighted. For direct Darwinian evolution, it has to work “by the same mechanism”, not a different one, as in co-option!!!!!

    Of course other parts of the system can be functional for other purposes and coopted for other purposes. That wasn’t the point he was making.

    When Behe said “non-functional” it was with respect to the same mechanism. That is to say, it has to be a flagellum to start with (the initial function) and then continuously imporoved to function as the same mechanism (motility via a flagellum). That is an irreducibly complex system.

    By way of contrast, finch beaks and peppered moths had the initial mechanism in place and was continuously “improved”. Even by your own advocacy of co-option of the flagellum, the route is NOT direct, and thus you ought not to be advertising co-option as some refutation of Behe’s concept.

    Behe did give you an out, and even described the elements of co-option. To your credit you took the out.

    An irreducibly complex system cannot be produced directly

    Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect circuitous route.

    Indeed Nick, yours and miller’s cooption route is non-direct. And thus is no counter-example to Behe’s claim of “no direct route”. So even your supposed refutation is no refutation at all, only a false claim. You had to appeal to indirect and circuitious means to find a solution, exactly as Michale Behe predicted, but you wouldn’t ever give him proper credit for stating the elments of co-option would ya?

    Unfortunately for the ID side, Judge Jones signed off on Millers false claims under oath.

    To be fair, you might argue you didn’t like his wording. But after all these years of clarifying the intended meaning, you are of course free to misrepresent the intended meaing to your advantage. But that would hardly be ethical, imho.

    I should mention Ken Miller’s simpler mouse trap example and Doolittles simpler blood clotting are not really arguments you want to stand on either. Neither do they refute irreducible complexity, but it poses other problems because it would seem reasonable Natural Selection would select AGAINST increasing complexity when simpler architectures are available. But that problem seems lost on Ken Miller.

    Darwin obviously saw the problem when he about vomited to ponder the peacock’s tail. Natural Selection would work against the sort of extravagance we see in nature. Why would selection go for complex and vulnerable and frail systems when simpler would work? He knew it, and so should you.

    Any way, thank you for visiting. I look forward to what you have to say.

    But until you do, you have no hope of ever convincing the scientific community of your arguments

    Convincing the scientific community of my arguments wasn’t my goal. I merely wanted to know if the world shows evidence of design for personal reasons and for the sake of my colleagues in the ID community.

    I thought Mike Behe made a good case, and I wanted to dialogue with the best and brightest Darwinists like you to see how credible his ideas were. The fact that you and Ken Miller have to resort the misrepresentations (and Miller even under oath) and the most uncharitable reading of Behe’s works, suggests to me your side han’t refuted his claims.

    If the scientific community would prefer to listen to yours and Ken Miller’s misrepresentations versus the real arguments that were put forward, it is their loss.

  15. By the way Nick, how does a Type 3 secretory system qualify as being “the same mechanism” as a flagelllum? :-)

  16. UD readers,

    Nick is something of martyr. He suffered at the hands of Richard Dawkins and Jerry Coyne and PZ Myers. He has my respect for standing up to all 3 of them.

    Here is Mike Gene’s Tribute to Nick:
    Speech vs. Religion Comment 267289

    Some excerpts:

    The Matzke/Dawkins feud is actually quite interesting to think about. It all began when Matzke made a comment buried deep in a thread over at PT which said that Dawkins plays the Nazi card against religion. The problem is that he didn’t have any solid examples to back this up, so the Gnus smelled blood in the water and pounced. Coyne started the attack by calling Nick a “nasty piece of work” and this encouraged his fans to pile on. Throughout the comments section of the blog that advertises itself as being about evolution, Matke is routinely called a liar and worse. Next, Dawkins himself joins in, and provides his own ultimate scorn by treating Nick as someone he does not know….
    …..
    Then PZ piles on, referring to Nick as sleazy

    So as it stands, the Gnus are viciously attacking Matzke’s character all over the cybertubes and the one road that would turn it all around is unavailable to him.

    BTW Nick, if you are reading this, I feel for ya. You were the one, the only one, who helped Dawkins escape from the trap he sprung on himself when circulating that petition on his blog a few years back. Some gratitude, eh?

    Nick,

    You’re welcome to hang out with us here Nick. We may argue, but we won’t treat you like those “friends” of yours who stabbed you in the back publicly.

    Thanks for visiting. I mean that.

  17. Nick Matzke

    Hey, it’s not my fault that Behe wrote,

    An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.

    …which makes it perfectly valid to impeach his argument by showing systems missing parts which are still functional.

    But you still have to explain those systems. Yet you can’t.

    I don’t get into elaborate arguments about mousetraps and other analogies, these are at best dubious analogies for actual biology.

    Actually too siple- biological configurations are much more complex and intricate.

    But anyway- I understand your anger when it comes to analogies as your position can’t even muster and argument via analogy.

    And tat is why you and your ilk are so afraid of legislation like that being considered in Tennessee.

  18. As NickMatzke_UD wrote, Behe said an irreducibly complex system cannot be produced directly “by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.”

    NickMatzke_UD then said that then it is “perfectly valid to impeach his argument by showing systems missing parts which are still functional.”

    Then you (scordova) responded by saying that Behe included the words “which continues to work by the same mechanism” and that NickMatzke’s response did not take this into consideration.

    But without a clearer and more detailed description of exactly what this line involving “same mechanism” means – and applying it to showing how the “same mechanism” must be in effect — I don’t see why Nick is not right.

    Take this example (not from detail of biological study but just as a principle of thought to explain what I mean): birds have wings which couldn’t evolve from half-wings (according to Behe) because half-wings cannot give flight (the “same mechanism”) so the half-wings could not have evolved either.

    But these half-wings could have had the purpose of allowing the organism to glide – and earlier (quarter-wings or eighth-wings) to obtain balance when sitting in trees, and so forth.

    The functions are different (they don’t work by the “same mechanism”) and yet when they are modified they make other functions possible.

    This seems perfectly reasonable to me as a general principle of thought (though I’m not claiming I know the biological details of how this would be possible).

    So why does evolution HAVE to progress by the “same mechanism”?

    Second, you keep returning to the idea of the flamboyant or extravagant effect — the peacock, or the Rube Goldberg contraption – and so are arguing that irreducible complexity is the realization that evolution could not create an extravagant design. Regardless of the merit of this argument, it seems to be a different argument than the one Behe is presenting in the passage I quoted.

    So how does the “simplicity” of beer coasters relate to Behe’s description of irreducible complexity as making “successive modifications of a precursor system” impossible?

  19. material

    a)how much parts you need for a minimal mouse trap?
    b)can this minimal mouse trap(or system that not yet a mouse trap)is functional in nature?
    c)in co option you still need a new binding sites

    nick, a cat is very impressive mouse trap.
    and no, its not an analogy…

  20. 20

    Sal, what are we talking about, exactly? You’ve made claims that are all over the map. Most of it has been thoroughly worked over many, many times, in the Kitzmiller case and elsewhere. The rest of it is just uninformed. E.g. you can’t bring up the peacock’s tail without even mentioning sexual selection. Well, you can, but you just aren’t doing a serious scientific discussion.

    You and others initially made claims about how removing parts wasn’t an answer to Behe. I pointed out that Behe himself set up that challenge — and heck, “irreducible complexity” invites people to see if systems are reducible. Now you are talking about direct vs. indirect routes, but reducibility is important evidence for both. Mixed in is a bunch of random unserious discussion about the flagellum, blood-clotting, immune system etc. I and others have written detailed papers on the evolution of these systems. If you want a serious discussion, dig into those details and then we have something interesting to discuss. Otherwise, what’s the point in going around the merry-go-round again when nothing really matters except the detailed science?

    I appreciate the remarks about other controversies. What people don’t realize is that it all comes from the same place. I get suspicious whenever it looks like emotion, wishful thinking, and rhetoric are getting ahead of detailed examination of the evidence. Creationists have this problem an awful lot, but other people have it sometimes also.

  21. NickMatzke:

    Most of it has been thoroughly worked over many, many times, in the Kitzmiller case and elsewhere.

    Perhaps in your mind, Nick. However, if we use the same standards that Jones used in Kitzmiller, there aren’t any peer-reviewed papers that demonstrate blind and undirected processes (natural selecton and drift are blind and mutations are undirected) can construct new, useful multi-protein configurations.

    You and others initially made claims about how removing parts wasn’t an answer to Behe. I pointed out that Behe himself set up that challenge — and heck, “irreducible complexity” invites people to see if systems are reducible.

    Umm some IC configurations do contain parts that can be removed. However just because some parts can be removed that does not mean the entire configuration is reducible.

    Mixed in is a bunch of random unserious discussion about the flagellum, blood-clotting, immune system etc. I and others have written detailed papers on the evolution of these systems.

    Hogwash- unless you mean imagined = detailed.

  22. UD commenters,

    Please be civil and welcoming to Nick. This dialogue is too important to break down. And as I pointed out, the guy deserves respect, he’s certainly taken more persecution from the GNUts than I have.

    Nick,

    I asked

    how does a Type 3 secretory system qualify as being “the same mechanism” as a flagelllum?

    and Behe wrote:

    An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism)

    And to this point:

    you can, but you just aren’t doing a serious scientific discussion.

    Discussion at UD aren’t that serious, these are informal exchanges, and that is why I’m all the more appreciative that someone of your caliber will dialogue with us.

    I’m not pretending we’ll ever agree, but the readers would like to hear each side represented well.

    To that end, I really don’t see how TTSS is “the same mechanism.” By way of contrast, a finch beak is the “same mechanism” which can be improved by getting thicker. Finch beaks are an example of Darwinian selection taking a direct route. TTSS is hardly a direct route, imho. Do you agree or disagree?

    but reducibility is important evidence for both

    Building a 4-part mouse trap doesn’t make the 5-part mouse trap irreducible. Irreducibility refers to the Depth of Integration for the system to work, Darwinists have equivocated “Irreducible” to mean that you can create a similar or adequate function with a “reduced number of parts”.

    That is not the sense of how the word IRREDUCIBLE is being used by Behe, but Darwinists have chosen to render the most uncharitable and misleading interpretation of what Behe meant. I credit you guys for your ingenuity, or shall I say disingenuity. :-)

    Rube Goldberg machines are IRREDUCIBLY complex because of the depth of integration of parts. Same for human blood clotting systems. Saying the that something is not irreducibly complex because you can find a solution with a “reduced number of parts” is a misrepresentation of what ID proponents mean. If you think we should use different words, fine. Objection acknowledged.

    The problem IC posses is that of a rube-goldberg machine. The function is accomplished with more parts than you need, and the parts are organized such that removal of one part destroys the system and reduces it to nothing with respect to “the same mechanism” originally in question and “the same architecture”.

    Of course one might conceivably build a comparable system with the remaining parts, but the issue is why would selection choose a rube-goldberg machine with such deep integration over simplicity? Why would it choose a complex architecture when a simpler architecture ought to be selected for. And that is the problem with existence of extravagance in nature, not the least of which is sexual reproduction (symbolized by the peacock’s tail).

    I posted this thread to object to the misrepresentations that have been promoted as somehow answering Behe.

    But, if you have an answer for TTSS, I would be appreciative. Thanks.

  23. I continue to be impressed by how Darwinists can misrepresent IC.

    Darwinist version:

    Something is IC if the same function can’t be achieved with fewer parts, therefore if a system can be built with a reduced number of parts to achieve the same function, it is not irreducible

    ID version:

    Something is IC if the same function via the same mechanism can’t be achieved with fewer parts, the system is not IC if the same function via the same mechanism can be achieved with fewer parts

    See the subtle distinction? :-) If not, look at the 3-glasses-3-knives system to see what it means to achieve a function via a specific mechanism. The problem is the intermediate steps to the creation of the mechanism are dysfunctional.

    Biology is rich with lock-and-key/login-password type systems. A 15 character login-password system is irreducibly complex because the access mechanism will fail if the wrong password is provided. One wrong charcter and the system fails to function (if access is desired). To say that a 15 character login-password system is not IC because some people have password systems that uses a “reduced number of characters (say 4 instead of 15)” is just plain silly. But such are the arguments of Ken Miller.

  24. Nick:

    I and others have written detailed papers on the evolution of these systems. If you want a serious discussion, dig into those details and then we have something interesting to discuss.

    Maybe we can begin here. You criticize Scott Minnich, who said that 30 of the TTSS flagellum contain proteins found nowhere else in living organisms. The table you provided at PT shows that 15 of the proteins are not found anywhere else.

    You conclude, among other things, that: “Scott Minnich, the leading flagellum expert in the ID camp, was severely wrong about the most basic data relevant to the origins of the flagellum, the flagship system of the ID movement.”

    So, instead of 30, it was actually 15. To my mind’s eye, Minnich’s analysis is still fundamentally correct, though the degree of his correctness is diminished: i.e., instead of being “astronomically” correct, he is only “extremely” correct. (Even though, technically, he is still “astronomically” correct–but let’s not get sidetracked.) You literally feel that because there was an “error” in the “basic facts” (as though the “basic facts” are fixed in time given modern WGA) this entitles you to dismiss the entire argument. T

    his, to me, is a bit mind-boggling. President Obama once said that he had visited “all 57 states” already. Should I dismiss everything else he says because of this error?

    A few questions: (1) Is an Igloo designed, yes, or no? (2) Is an Igloo “irreducibly complex”, yes, or no? Is a TeePee designed, yes, or no? Is a TeePee “irreducibly complex”?

    That the parts of an irreducibly complex system are present elsewhere, does not effect its status as being IC. This is the thrust of Hoyle’s comment about a “tornado passing through a junkyard” analogy to Darwinism. A “functional” pathway to IC must be shown. But, of course, if you can show a pathway to IC, then it is not IC. Has a sensible, rational, credible “functional” pathway to the bacterial flagellum been demonstrated? I’m curious.

  25. Correction: …..who said that 30 of the TTSS flagellum proteins are not found anywhere else . ……

    I hope this doesn’t take away all of my credibility.

  26. Rick Penner:

    Take this example (not from detail of biological study but just as a principle of thought to explain what I mean): birds have wings which couldn’t evolve from half-wings (according to Behe) because half-wings cannot give flight (the “same mechanism”) so the half-wings could not have evolved either.

    Behe could have selected from thousands of biological examples to buttress his claims about IC. You’ll notice he didn’t choose the “wing” of a bird. So, why argue from a case and an example that Behe has obviously overlooked?

  27. PaV-

    The fallacy Nick promotes is that if you can get the proteins you can get the required configuration. However Nick forgets that with any bacterial flagellum there needs to be muliple subunits of each protein, some numbering in the thousands.

    So not only do we need the right proteins, but we need the right amounts- oh and we need chaperones to guide some proteins to their destination otherwise they wouldn’t make it due to cross-reactions- that is they would bind where they aren’t needed. Add to that we need the proper configuration.

  28. However Nick forgets that with any bacterial flagellum there needs to be muliple subunits of each protein, some numbering in the thousands.

    Joe,

    Thank you. Do you have a citation we can link to?

    In the meantime, I’m hoping Nick will answer my question:

    how does a Type 3 secretory system qualify as being “the same mechanism” as a flagelllum?

    In the absence of Nick, any Darwinists willing to volunteer an answer? :-)

  29. I don’t believe that Behe’s point has yet been stated clearly enough. Let’s look at the bacterial flagellum. In the following, I will take it as accepted by all that this structure is IC in the sense that Behe has defined: if you remove any part, it completely ceases to function. Does this prove that it could not have evolved by Darwinian mechanisms? No, and Behe acknowledged this. However, it does present a prima facie case that it cannot have so evolved, because if you have all the components in place but one, the structure is not only useless to the organism, but detrimental, as its construction and maintenance diverts energy from other uses. Therefore if a biologist wishes to assert that it has evolved by Darwinian means, he or she must provide convincing evidence that there is in fact an indirect route by which it could have evolved.

    Pointing to the TTSS, which contains only 10 of the forty or so proteins necessary for the flagellum, and in which the functioning of those 10 would have to be altered for them to operate as part of the flagellum hardly constitutes an indirect route to the evolution of the flagellum. Such a route would have to show how each of the remaining necessary proteins as it appeared by random mutation (leaving aside the astronomical improbability of random mutation creating an entirely new protein) could have been incorporated into the TTSS or some other structure that would have increased the organism’s fitness, and how those structures could have been modified to eventually become the flagellum, where each stage of the modification increased its fitness. If anyone has or knows of such a demonstration, I would very much like to see it.

    Absent such a demonstration, the assertion that the flagellum arose by Darwinian means simply amounts to an article of faith.

    In other words, demonstrating that a particular biological structure is IC places the burden of proof squarely on the shoulders of anyone who wishes to claim that it arose through Darwinian mechanisms.

  30. PaV:

    So, instead of 30, it was actually 15. To my mind’s eye, Minnich’s analysis is still fundamentally correct, though the degree of his correctness is diminished: i.e., instead of being “astronomically” correct, he is only “extremely” correct. (Even though, technically, he is still “astronomically” correct–but let’s not get sidetracked.) You literally feel that because there was an “error” in the “basic facts” (as though the “basic facts” are fixed in time given modern WGA) this entitles you to dismiss the entire argument.

    I’m a teleologist, not a Darwinian, but I’d like to say that, in the first place, I believe Dr. Matzke’s point in that PT article is not to address if the argument of irreducible complexity has been answered. Rather, IMHO, his point was to provide evidence that the flagellum did in fact evolve from pre-cursor parts. In doing so, he also showed that several ID proponents were wrong about data on flagellar parts and the statistically significant sequence similarity (from which the inference of homology can be made) these parts share with non-flagellar parts. Many of the flagellar proteins are not, in fact, unique, to the flagellum. But the observation of homology of flagellar proteins and non-flagellar proteins is not in itself evidence that the flagellum arose through non-teleological evolution. One must also show that these non-flagellar proteins pre-date the flagellar system. For example, a good number of flagellar proteins only share homology with TTSS proteins. However, the TTSS is almost certainly not a pre-cursor system to the flagellum.

    Also, just for the record, some of the sequence similarity shared by flagellar proteins with non-flagellar proteins is kinda weak. E.g., the FliG/MgtE sequence similarity.

  31. A car might have homologous parts to parts in a motorcycle, but that’s not the same as saying a car co-opts an entire motor cycle. You can’t simply remove parts out of car and end up with a functioning motorcycle. You can pull out the spark plug, and you’d still have a functioning radio and light system, but not an entire motor cycle. So its not really correct to say that a car co-opts a motor cycle or a motor cycle coopts a car is it?

    Yet the NCSE asserts a comparably silly statement:

    Even if it turns out that the type 3 secretion system is derived from the flagellum, it will still prove that (a) Behe was wrong that reduced subsets of “irreducibly complex” systems “are by definition not functional”,

    NO! NO! NO! Co-opting homologous parts is not the same as co-opting entire functioning systems! All that is demonstrated is the sharing of some homologous parts, that’s absolutely not the same as one system (like the flagellum) containing an entire, fully functioning TTSS!

    This is like claiming a car co-opts an entire functioning motor cycle merely because it has homologous parts. TTSS and the flagellum have homologous parts, but that different than saying the flagellum co-opts a functioning TTSS!

    Let’s say for the sake of argument the flagellum evolved from the TTSS. It doesn’t mean the flagellum actually co-opts the TTSS!

    What is also a bit disingenous is that to the extent the flagellum resembles the TTSS, if the TTSS evolved into a flagellum, it would have to be a malfunctioning TTSS first before it became a functioning flagellum. Thus, removal of parts from a flagellum won’t leave you with a functioning TTSS, only a malfunctioning one at best. And hence, claims that you can remove parts of the flagellum and have a functioning system are false. The falsehood is concealed by not being very overt in pointing out that the co-opted parts have to be assembled in a certain way to achive a different function, just like the coopted glasses and knives in video above have to be assembled in a certain way to achive function.

    What is not adequately conveyed, imho, is the fact the parts shared between the TTSS and flagellum are assmbled differently, the TTSS is not really co-opted is it?

    One might make the case the flagellum evolved from the TTSS, but that’s not the same as saying the flagellum co-opted something previously functioning, only parts of something previously function. The distinction is very important.

    The reason it is important is that for the TTSS to evolve into working flagellum, it has to be malfunctioning TTSS first before it can be a working flagellum. And this problem will repeat itself again and again with IC systems that co-opt PARTS (not wholes) of other IC systems.

  32. Joe,

    Thank you. Do you have a citation we can link to?

    Flagellum evolution in Nature Reviews Microbiology (Pallen & Matzke)

    Robert McNab, “Flagella and Motility,” in Escherichia Coli and Salmonella: Cellular and Molecular Biology, 2 vols., ed. F. C. Neidhart et al. pages 123-145

    “Edge of Evolution” pages 261-268

  33. Thanks Joe!

  34. Genomicus:
    You wrote:

    I believe Dr. Matzke’s point in that PT article is not to address if the argument of irreducible complexity has been answered. Rather, IMHO, his point was to provide evidence that the flagellum did in fact evolve from pre-cursor parts.

    I disagree with your analysis. His main point seems to be that Scott Minnich, and all the IDers, are way wrong when it comes to representing the flagellum as discontinuous with other life forms. He says they’re “way wrong”, or something to that effect. He seems to be content in showing that there is more homology present than Minnich states; thus Minnich is wrong; and therefore, the ID argument falls apart.

    I think he’s being deceptive and, perhaps, intellectually dishonest—though, more likely, it is simply a bias on his part.

    Here’s a quote from the PT post that is taken from his Nature article:
    ID advocates say that their position is supported by discontinuities between the flagellum and the rest of the biological world, just as a designed entity like a watch differs from an undesigned entity, such as a stone. In support of this line of reasoning, Scott Minnich in his expert witness report claimed that “the other thirty proteins in the flagellar motor (that are not present in the type III secretion system) are unique to the motor and are not found in any other living system.” As our discussion shows, this is not true. Instead, we have detected sequence homologies linking flagellar components to the rest of the biological universe (Table 1).

    IOW, Minnich is wrong. It’s not 30 non-homologous proteins; it’s only 15. But, of course, they have no way of accounting for how the 15 proteins came about. Of course, as you point out, all of these proteins have to be hooked up, linked together in some functional way. All of this is just waved away. “An ERROR has been detected. All bets are off. Their argument doesn’t hold water.”

    In the search for the truth, this is an evasive type of thinking.

  35. Just like the problem of properly positioned co-opted parts to form the 3-glasses-3-knives system, in similar manner the evolution of the assembly instructions is what Matzke and Pallen COMPLETELY ignore!!!!!!!!!!!!!!!!!

    Minnich said in Unlocking the mystery of life, that even supposing all the proteins are co-opted, the synthesis of the assembly instructions are not!

    From Biologos

    http://biologos.org/blog/self-.....e-required

    Other scientists have looked at how the timing of the assembly process is controlled at the genetic level. The genes that contain the instructions for making all the protein components of the flagellum are organized in a number of clusters called operons. Each operon is read when its “master sequence” is activated like a light switch. When the switch is flipped, the genes in that particular operon are interpreted by the cell so that the corresponding proteins are made. It turns out that the genes needed to produce proteins in the base of the flagellum are activated first. Once the base is complete, a clever feedback mechanism flips the next switch, activating the next set of genes, which allows later stages of assembly to occur, and so on. (It’s actually more complicated than that, but you get the idea.) So the parts of the flagellum are made “just in time,” shortly before each piece is needed.

    Just like the 3-glasses-3-knives analogy, the parts have to be properly positioned. NOTHING in Matzke’s paper addresses the evolution of assembly instruction. NOTHING. The insinuation is if we have homology or sequence similarity in proteins, then we can suppose Darwinism can create the assembly instructions. In the paper, Matzke say something like “this structure part is similar to that structure, therefore it is plausibly evolved from that”. I would agree that many of his examples are the closest conceptual precursors possible, but it is yet a gigantic problem to create assembly instructions that:

    0. create the parts
    1. assemble part in the proper sequence
    2. assemble parts in the right 3D location
    3. assemble parts with the correct timing

    I mean, how much homology can you find to do that? NO calculations provided for the probability of evolving assembly instructions.

    See this video:
    http://www.youtube.com/watch?v=hLTFiekwFy8

  36. By the way, no disrespect intended to the very fine work done by Nick in his papers. It is first rate quality, and he is a first rate Darwinist. I’m merely pointing out, the paper does not demonstrate the level of detail that estimates the probability of formation of the flagellum via his model.

    I’m not saying his model is incorrect, but one ought to score the probability that evolution can follow that path.

  37. 37

    So, instead of 30, it was actually 15. To my mind’s eye, Minnich’s analysis is still fundamentally correct, though the degree of his correctness is diminished: i.e., instead of being “astronomically” correct, he is only “extremely” correct.

    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?

  38. How many of those 15 remaining proteins are actually required for flagellar function?

    Only 2 are unique according to your excellent paper!

  39. 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. :-)

  40. 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.

  41. 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.

  42. 42

    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?

  43. 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.

  44. 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.

  45. 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”.

  46. 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.

  47. 47
    material.infantacy

    “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.

  48. 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.

  49. 49

    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.

  50. 50

    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.

  51. 51

    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.

  52. 52

    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.

  53. 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

    or

    Nick completely and utterly slighted me, in what I viewed as a sexist manner

    Abbie Smith

    or

    Yeah, I’m looking at you, Nick Matzke. …sleazy.

    or

    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…..

  54. 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.

  55. 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.

  56. 56

    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.

  57. 57

    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.

  58. 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.

  59. 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.)

  60. Woops. Double post. Apologies.

  61. 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?

  62. 62

    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.

  63. 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.

  64. 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.

  65. 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”.

  66. 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!

  67. 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?)

  68. 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.

  69. Pav,
    DNA is instruction to build proteins. It’s not a representation of life. It doesn’t need a separate protocol/system to take the representation and build it. So it’s nothing like your picture of a bar stool.

  70. DNA is instruction to build proteins.

    No, DNA may contain the instructions to build proteins, but the DNA is not the instructions. And your position can’t account for DNA.

  71. lastyearon:

    DNA must be transcribed to RNA. This involves an extremely complex “machine” called the transcriptome. It involves numbers of proteins itself. Then the transcribed DNA, has to be built up into a protein using transfer-RNAs and the ribosome. A sequence of DNA “represents” the protein that is the final product of this process, but DNA consists of nucleotides, and proteins consist of amino acids.

    Now, when you say: DNA is instruction to build proteins. It’s not a representation of life, isn’t this equivalent to saying that the description of a bar stool is not a “representation” of a “bar.” I suppose that’s true. But I wasn’t talking about a bar. However, what would be a bar without any bar stools?

  72. No, DNA doesn’t really “represent” anything. Humans can think of it as a representation, but that’s misleading, because representations are human concepts. DNA is a molecule, with chemical properties that in certain circumstances result (indirectly) in proteins. The transcriptome isn’t intelligent. It isn’t reading the DNA the way we read blueprints, or books. It’s reacting chemically, via natural processes.

    A drawing of a bar stool doesn’t build a bar stool. The phrase “bar stool” doesn’t build a bar stool.

  73. 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.

    1. Art works just fine.

    2. I was commenting on the implication in Genomicus’ comment that components with no obvious antecedent in some way pose a problem for the evolution of the flagellum. Nick picked up on where I was going (even before my comment appeared!) and pointed out the problems that Genomicus’ line of thought holds for the concept of IC.

    PS
    (I don’t know why your comment was delayed. Do you get routed to some sort of moderation buffer or something?)

    Every time.

  74. Our PCs react electrically, via natural processes, but that doesn’t mean nature produced our PCs.

    In order to transcribe you require knowledge. In order to translate you require knowledge. The transcriptome is as intelligent as any computer program, which traces its intelligence back to its designer.

  75. 75

    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 don’t know about that. Imagine that you have a single individual self-copying polymer. Later, it copies itself. Now you have two such polymers. Where did the second polymer come from? Its “information” was present in the first polymer, but it had not yet been instantiated. If one is going to insist on using information-speak, it sure seems like molecule #2 was “represented” in molecule #1. It is also the case that molecule #1 and #2 are identical. These aren’t contradictory statements. Thus, in this case (which is at least conceivable, whether or not such a thing can exist in real life), represented = representation.

  76. Art:

    What unique irreducibly-complex structure(s) do these “many flagellar proteins” that have no obvious antecedent form?

    The flagellar proteins that have no known pre-cursor parts form (obviously) a flagellum. Not sure what you’re driving at here?

  77. 77

    This proceeds directly from Shannon’s work …

    Hi Sal,

    You are correct, but the issue also has physical entailments which must be satisfied. With due respect to all the brilliant research work, the direct-templating proponent will see variation coming from the environment (or elsewhere) and come to depend upon it for something it doesn’t have the capacity to give. This is exactly the position taken by Gerald Joyce. He designed a two part RNA that, if broken apart and fed sub-units, could replicate itself through each halve serving as a template for the other. He then introduced variant sub-units, and as sure as sunshine, they were incorporated into the process. This was, of course, heralded as ‘a step toward creating life’. The problem here is a physical one, and it’s the physicality that must be addressed.

    His results end with the same direct templating process it started with (trivially altered by a variant). But such systems do not achieve, and cannot demonstrate, the material architecture of the representational systems they are designed to mimic. A representation (to operate as a representation) requires a materially-isolated protocol to physically establish the relationship between the representation and the effect it represents within a system. Otherwise that relationship wouldn’t exist. Furthermore, that protocol does not (along with the representation itself) ever become the product of the system. Direct-templating proponents ignore these entailments, even as they visibly exist in the very systems they intend to replicate. And variation within the sequence itself has no material power to establish a physical protocol which (as demonstrated) it must be isolated from in order for the representation to even exist. It’s worth remembering here that the system operates by variation in the sequence as a normal part of the process, while the protocol remains constant. Variation in the sequence has no effect on the protocol, while variation in the protocol flirts with catastrophic failure of the system.

    Protein synthesis is solely dependent upon the sequence in DNA as that pattern is transcribed to mRNA, and then used to order charged tRNA within the ribosome. That chain of transfer falls under the determining control of interactions between bases. But the appearance of a particular amino acid at the binding site of the polypeptide is not determined by the interaction between bases (even as those interactions continue between codons and anticodons). The effect is therefore not inherent to the properties of sequence. They share a relationship established remotely by the aminoacyl synthetases, undetermined by the material make up of the original sequence itself (but instead, determined by the material make-up of the protocol).

    This is what I was trying to indicate to Nick; in direct templating, the product can be reduced to the constituents of the system which become that result, but that is not the case in the instance of a representational system; they are neither reducible to the constituents, nor do they become the result.

    One may say then, ‘we find it like this today, but it did not begin this way’. But that realization doesn’t change of word of the observations, it only highlights the supposed transition. How far up the chain of complexity can you get with nothing but physical information – without the representation-protocol-effect system we see at work today? However far that is, it’ll need to be capable of creating a semiotic state in order to go any further.

  78. 78

    LYO,

    No, DNA doesn’t really “represent” anything.

    If in one system we have something that is a genuine representation, and in another system we have something that only appears to be a representation, then surely you can look at the physical evidence, and point out that distinction. Will you please point out that distinction?

  79. If it was created by a human being for the purpose of representing something, then it’s a representation.

  80. 80

    LYO,

    I see you’ve reasserted your claim, but I don’t see where you’ve pointed out the material distinction between the two physical systems. Surely you envision a material difference in the two systems, otherwise they would operate the same.

  81. lastyearon @79:

    What a hoot! Only counts if it was created by a human. Gotta love the (il)logic. :)

  82. Nick Matzke:

    Imagine that you have a single individual self-copying polymer.

    Imagine? LoL! Nick, please demonstrate there is such a thing as “a single individual self-copying polymer”.

    Geez Nick, imagination is NOT evidence.

  83. Art:

    I was commenting on the implication in Genomicus’ comment that components with no obvious antecedent in some way pose a problem for the evolution of the flagellum. Nick picked up on where I was going (even before my comment appeared!) and pointed out the problems that Genomicus’ line of thought holds for the concept of IC.

    Except Nick doesn’t understand the concept of IC and he thinks imagination = evidence.

  84. If it was created by a human being for the purpose of representing something, then it’s a representation.

    1. biological creatures other than humans use representation to convey information —

    http://bihartimes.in/Maneka/animalmoms.html

    2. even if supposing we can’t formally prove something is a representation, the fact that we humans find it analogous to a linguistic system is something Darwinsim or the laws of physics cannot explain. It qualifies as specified complexity. The No Free Lunch theorems apply in demonstrating such analogies do not spontaneously arise in physcial systems where representation is in evidence. It doesn’t formally prove ID, but if formally refutes Darwinism.

  85. 85

    Joe writes,

    82
    JoeMarch 28, 2012 at 4:41 am

    Nick Matzke:

    Imagine that you have a single individual self-copying polymer.

    Imagine? LoL! Nick, please demonstrate there is such a thing as “a single individual self-copying polymer”.

    Geez Nick, imagination is NOT evidence.

    Joe, you are being extremely silly. This original sub-discussion was explicitly about what was conceivable. It started with this post:

    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?

    Go bug BiPed if you don’t like the setup.

    And PS: Sal — if you want to find a creationist and UD participant far, far worse than the Gnu Atheists have been to me, look no further than Joe and his blog:

    http://intelligentreasoning.blogspot.com/

    …which is obvious and well-known. Assertions of creationist purity and righteousness in the face of this kind of stuff, which is obvious and well-known, are just incredible.

  86. 86

    66
    scordovaMarch 27, 2012 at 5:55 am

    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!

    Sal, this is extremely silly. Of course phylogenies are phylogenies of the specimens you have. None of the speciments you have sitting here in the modern day is going to be ancestral to any other specimen sitting here in the modern day — after all, they are here in the modern day! This is just an automatic fact about phylogenies of molecular sequences.

    But to jump from this boring automatic fact about phylogenies and the fact that you only have the sequences that are living now, to the statement that this is evidence that the ancestors inferred on a phylogeny never existed, is mind-bogglingly wrong. It’s precisely like saying the following: a high percentage of central asians and Mongolians share an identical or nearly identical Y-chromosome sequence which is thought to trace back to Genghis Khan. But, because Genghis Khan doesn’t exist now, “the missing common ancestor is missing”, so we can be confident that Genghis Khan never existed, because he doesn’t exist today.

    Ugh. And I just spent valuable minutes of my life explaining something totally obvious to rebut a half-baked creationist objection (not even half-baked…1% baked!) which should never have seen the light of day, and wouldn’t have if you did a little thinking and reading instead of just tossing out uninformed-but-bizarrely-confident broadsides at evolution. I think I’m done with this thread. Get back to me when you can demonstrate interest in a serious, well-informed discussion.

  87. even if supposing we can’t formally prove something is a representation, the fact that we humans find it analogous to a linguistic system is something Darwinsim or the laws of physics cannot explain.

    A linguistic system needs human beings (intelligent agents) to create and understand it. DNA does not. It’s a chemical process, that results in protein (and therefore life). We can consider a gene to be a representation of a protein, but that is only for our own comprehension. So analogizing between DNA and language is misleading.

    Consider your shadow. It can be considered a representation of you, and it contains information about lots of things, like your shape, the season, the time of day. But that doesn’t mean it was intelligently designed, does it?

  88. to the statement that this is evidence that the ancestors inferred on a phylogeny never existed, is mind-bogglingly wrong.

    That’s not what I said! I merely pointing out you are appealing to links that are ALWAYS missing, not just in fact, but also in principle like the common ancestor protostomes and deuterostomes.

    The IC argument argues that missing links are missing not only because we can’t find them, but from a mechanical standpoint, they did’t exist even in principle. Gould said it well, “what good is half a wing”. Here here.

    And no, you’re not wasting your time here. You’re learning the truth. If you don’t, the truth will haunt you the rest of your life because you’ll be basing your arguments on missing links which will never be found, not because they are extinct and left no trace, but because they never existed in the first place.

    If you relied instead on the intended meaning of what ID proponents put forward versus your distorted misrepresentations of what you claim they said, maybe you’ll see the indefensibility of your position.

    That said, I admire and respect your hard work and excellent writings, they are a great contribution to science, but they fundamentally miss the point, and the day will come your own research my be used to refute your intended goal of proving Darwin correct.

  89. Nick Matzke:

    Assertions of creationist purity and righteousness in the face of this kind of stuff, which is obvious and well-known, are just incredible.

    LoL! Nick, I have more than had it with you and your ilk, Dawkins, Coyne, Scott, Branch, et al., and I am willing and able to get down in the mud with you guys. That is my short-coming- I will dish back and will not keep turning my cheeks.

    Thank you for letting me clear that up.

  90. Nick,

    Genghis Khan was real. Your common ancestors are imagined. With cladistics and phylogeny they- those alleged ancestors- will always be imagined.

  91. A linguistic system needs human beings (intelligent agents) to create and understand it. DNA does not.

    How do you know DNA does not need intelligent agents to create and understand it?

    But anyway DNA, as with a computer program, is useless without a system that recognizes and knows what to do with it.

  92. lastyearon:

    No, DNA doesn’t really “represent” anything.

    Take a look at this table giving the “genetic code”, and then please explain to me once again why DNA does not “represent” anything.

    Humans can think of it as a representation, but that’s misleading, because representations are human concepts. DNA is a molecule, with chemical properties that in certain circumstances result (indirectly) in proteins. The transcriptome isn’t intelligent. It isn’t reading the DNA the way we read blueprints, or books. It’s reacting chemically, via natural processes.

    You seem to be making the case for ID here. Indeed, a “representation” is a “human concept”; and humans are intelligent. And ID argues that anything that acts as a representation of something else is the product of intelligence.

    Further, when you say that the transcriptome “isn’t reading the DNA the way we read blueprints, or books,” you’re entirely correct. The transcriptome is “reading” the DNA like a computer processor reads computer code. But, once again, this requires intelligent agents to compose the code and to build the processor. How did the cell come about without the involvement of an intelligent agent?

    A drawing of a bar stool doesn’t build a bar stool. The phrase “bar stool” doesn’t build a bar stool.

    If you saw a drawing of a bar stool, what would you call it?

  93. NickMatzke:

    [It would be helpful if you put "PaV" before the blockquotes; it makes it easier to identify your responses. Thanks.]

    It is also the case that molecule #1 and #2 are identical. These aren’t contradictory statements. Thus, in this case (which is at least conceivable, whether or not such a thing can exist in real life), represented = representation.

    In mathematics, many differential equations have, e.g., x = 0, as a solution. But the solution is considered, and so-called, “trivial”, since it tells you nothing at all about the mathematics. It strikes me that self-copying is but a trivial example of one thing representing another. As you say above, they’re identical. So they tell us nothing new.

    Love=love; hate=hate; birds=birds, tigers =tigers, and so forth. But dictionaries have something else for the right hand side of the equations above. IOW, meaningful information.

  94. 94

    A linguistic system needs human beings (intelligent agents) to create and understand it.

    As already stated, when a bee returning to the hive dances in a particular way during flight, the other bees will see that dance and can respond to it by flying in the correct direction to reach the feeding grounds. They respond to the dance based upon the pattern it contains. A particular dance is mapped to a particular response. Does this communication require a human in order to operate?

    When you use your vocal chords to make the sound of the human word “heal” and your dog sits; did you communicate with yourself alone? The representation in this instance is the sound “heal”, the intended effect of that representation is to get the dog to sit. You then voice the sound and the dog sits. Did only you understand the representation? Or, has the dog acquired the protocol to actualize the representation for himself? How about in the case of the grunts and clicks of a whale? Did those require a human to understand them as well?

    Your position is an anthropocentric trainwreck.

    Linguistics is often referred to as the study of (specifically) human communication. If that is the extent to which you use the word, then the word “linguistics” is inappropriate to these observations (as can be repeatedly demonstrated from examples throughout the living kingdom). If on the other hand, you use the word to indicate (as some definitions provide) the study of communication through conventionalized representations then perhaps it is more acceptable. The point is that you can call this phenomena anything you wish; the observations being made here come from an inventory of coherently-understood physical processes. As such, those observations are not subject to definitional skirmishes over loaded terms, except to the extend that someone would willfully impose those loaded definitons above the material observations themselves. It is the operation of the material system that is at issue.

    And on that point, you have once again simply asserted that DNA does not follow the observations made, yet you failed (once again) to point out the material distinction in the two systems. Is it your intention to suggest; “The systems are operationally identical, but even so, one is different than the other based on an unknowable quality which can be neither seen nor described”.

  95. 95

    Nick, I understand that you do not intend to engage the issues raised here, particularly those in post #77 (and #57 before it).

    That is unfortunate.

  96. UBP,
    Substitute intelligent agent for human being, and my point still stands.

    Representations (or symbols) can be arbitrary. It takes an intelligent agent to recognize the representation for what it represents. A gene is not a symbol of it’s protein. It’s a molecule with physical properties which cause chemical reactions that lead to the synthesis of proteins.

  97. Pav,

    Take a look at this table giving the “genetic code”, and then please explain to me once again why DNA does not “represent” anything.

    What? So are you saying that because it can be represented in a table format, with letters representing the individual molecules, that DNA is therefore a code, and since all codes are designed, DNA must have been designed?

    Any regular physical process can be represented in a table format.

    You seem to be making the case for ID here. Indeed, a “representation” is a “human concept”; and humans are intelligent. And ID argues that anything that acts as a representation of something else is the product of intelligence.

    Except that DNA doesn’t act as a representation of something else. It is a molecule with physical properties which lead to something else.

    Further, when you say that the transcriptome “isn’t reading the DNA the way we read blueprints, or books,” you’re entirely correct. The transcriptome is “reading” the DNA like a computer processor reads computer code. But, once again, this requires intelligent agents to compose the code and to build the processor. How did the cell come about without the involvement of an intelligent agent?

    This is a completely different argument. We’re talking about whether DNA is a representation (which requires an intelligent agent to interpret). Not whether the interpretive system requires an intelligent agent to assemble.

  98. Properly formatted…

    Pav,

    Take a look at this table giving the “genetic code”, and then please explain to me once again why DNA does not “represent” anything.

    What? So are you saying that because it can be represented in a table format, with letters representing the individual molecules, that DNA is therefore a code, and since all codes are designed, DNA must have been designed?

    Any regular physical process can be represented in a table format.

    You seem to be making the case for ID here. Indeed, a “representation” is a “human concept”; and humans are intelligent. And ID argues that anything that acts as a representation of something else is the product of intelligence.

    Except that DNA doesn’t act as a representation of something else. It is a molecule with physical properties which lead to something else.

    Further, when you say that the transcriptome “isn’t reading the DNA the way we read blueprints, or books,” you’re entirely correct. The transcriptome is “reading” the DNA like a computer processor reads computer code. But, once again, this requires intelligent agents to compose the code and to build the processor. How did the cell come about without the involvement of an intelligent agent?

    This is a completely different argument. We’re talking about whether DNA is a representation (which requires an intelligent agent to interpret). Not whether the interpretive system requires an intelligent agent to assemble.

  99. 99

    LYO,

    Representations (or symbols) can be arbitrary. It takes an intelligent agent to recognize the representation for what it represents. A gene is not a symbol of it’s protein. It’s a molecule with physical properties which cause chemical reactions that lead to the synthesis of proteins.

    In post #77, I presented a short (obviously abbreviated) inventory of the controlling interactions involved in mapping a specific codon to the appearance of a particular amino acid at the peptide binding site in a ribosome. The physical make-up of the codon (the sequence pattern it contains) does not control the appearance of a particular amino acid. That is controlled in isolation by the physical make-up of the protocol instead. These observations are not even controversial.

    If you can point to those material observations, and show a distinction between the material relationships that a genuine representation would demonstrate, and those that a quasi-representation(?) would demonstrate – pointing out the material distinction between the two – then you will have at last supported your assertion.

    But frankly, I think you should just concede to the physical evidence. If it’s the term “representation” that you are choking on, then fine, call it a specifier, or a dingledorf instead – the material observations (of what it is and what it does) won’t change either way.

    - – - – - – -

    Outside of you pointing out the material distiction you claim exists, there is no need to continue beating this dead horse.

  100. Dr. Matzke:

    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.

    Quite true, and I am well aware of that. However, the evidence in favor of the “sister group hypothesis” is a bit weak. In my humble opinion, the strongest evidence in favor of the sister group hypothesis comes from the phylogenetic trees estimated by Gophna et al. (2003). But as Saier (2004) correctly pointed out, if TTSS genes accumulate mutations at a faster rate than flagellar genes, this would account for the long branch lengths of the TTSS gene lineages. When you consider that laterally transferred genes generally evolve at a faster rate than orthologous genes, Saier’s point is strengthened because TTSS genes have been distributed laterally far more frequently than flagellar genes. Aside from that, and Mike Gene noted this some years ago, if you take a look at the SctN/FliI tree of Gophna et al., it actually does seem like SctN is derived from FliI. Pallen’s parsimony argument is interesting, but I won’t go into an analysis of that argument here. Admittedly, however, the “flagellum evolved into TTSS” proponents do need to gather stronger evidence to support their position. But, since the issue is not yet settled, one can hardly say that the TTSS is evidence that certain flagellar proteins (like FliF, etc.) evolved from pre-cursor parts that formed an ancestral secretion system. Then again, it could be said that since the issue of the origin of the TTSS is not yet settled, one cannot cite certain flagellar proteins as evidence that the flagellum did not evolve. I’d be honestly interested in your opinion on this.

    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.

    …which is why I didn’t add FliI as one of the essential flagellar proteins for which there is no homology evidence that it arose from a pre-cursor part.

    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.

    This implies that FliM is the result of a fusion between CheC and FliN (or a proto-FliN). This does not in any way provide evidence that FliN arose from a pre-cursor part, which was exactly my point in my brief lil’ essay.

    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.

    I’ll let others judge the “fatality” of this concession. But it is a necessary admission, even though, unfortunately, I don’t see many ID proponents admitting that the bulk of the flagellar proteins (or their homologs) can function in non-flagellar contexts. The evidence in favor of this view has been compiled by Matzke and other researchers, and unless it is flawed (which I highly doubt), we’re gonna have to admit this.

  101. And more evidence that Nick Matzke misrepresents reality- as if we needed more evidence to that effect:

    Yet another Scopes Monkey Trial on the way in Tennessee

    Unbelievable- Nick do you ever properly represent anything? Do you realize that people who can read know you are lying?

    Nick- ever hear of Madeline Murray O’Hare? She had nothing on what I am going to bring down on you and your ilk…

  102. Nick- ever hear of Madeline Murray O’Hare? She had nothing on what I am going to bring down on you and your ilk…

    Joe,

    I know you’re angry, but I’d like for us to be moderately civil while confronting Nick here on my threads. When he visits, it like enemies under a flag of truce. There are other places where you can vent your hard feelings, and I thank you for your restraint so far in my thread.

    I value the dialogue with Nick and Art because they can help us refine our arguments and occasionally give us valuable corrections.

    I’m not out to win public debates on the net by never admitting when our arguments are weak or even wrong. The process of dialogue will help correct and improve what we have to say, and then the message will become stronger and reach more people.

    The facts will help us prevail, but we can improve published ID literature by the process of interacting with our critics.

    This thread is an example of what I mean. I’ve learned that the 3-glasses-3-knives system is a good candidate for illustrating IC. No Darwinists dared to criticize it with the same misrepresentations that they offered for the mouse trap. It gives me reason to keep marketing it as another icon of IC. Instead of “Behe’s mouse trap”, how about “sal’s beer trick”. :-)

    The other thing I learned in this thread:

    1. Nick didn’t answer my question about “is TTSS the same mechanism”. He didn’t answer, because I think he knew he was wrong.

    2. I asserted the TTSS wasn’t even a real example of co-option. Nick chose instead to go after peripheral issues. That suggests to me my assertion is correct, that the TTSS wasn’t even what Judge Jones billed it to be!

    Finally, I’d like to publicly thank Nick for his time in visiting here. If anyone wants to really get in Nick’s face, there are other places to do it.

    With that in mind, I’d also like to thank all the ID commenters for their civility toward Nick in this thread. We certainly treated him with far more respect than Dawkins, Coyne, Abbie Smith, PZ Myers and the GNUs.

  103. The physical make-up of the codon (the sequence pattern it contains) does not control the appearance of a particular amino acid.

    So are you saying that the chemical structure of a gene is arbitrary with respect to the protein it results in?

    What, are there tiny construction workers inside the cell that read the DNA sequence, and then decide to go about building the proteins based on what they read?

  104. LYO:

    So are you saying that because it can be represented in a table format, with letters representing the individual molecules, that DNA is therefore a code, and since all codes are designed, DNA must have been designed?

    I’m saying that biologists are telling us that certain nucleotide triplets (codons) are translated by the ribosome into particular amino acids. This isn’t an ID person making this claim. It’s main stream biologists who are doing so. They call it the genetic “code”. IDers didn’t invent this description. Biologists call it a code. So, with that, I’ll end with my agreement with you: Yes, “DNA is therefore a code, and since all codes are designed, DNA must have been designed.”

    LYO:

    Except that DNA doesn’t act as a representation of something else. It is a molecule with physical properties which lead to something else.

    But, in this sense, it’s much more than a mere “representation.” As you’ve already pointed out, the words “bar stool” can’t form a “bar stool”, but a codon can, within a very complex machinery–more complex than any human, at this point, can fully comprehend–give rise to a particular amino acid through some physical process. But this doesn’t make it any less than a representation, but, as I said, something more. So, in this sense, the “genetic code” is much, much more of an intelligent construct than, e.g., a computer program.

    Tell me, is a glass half-full, or half-empty? This is the kind of thought process that is taking place right now in our discussion about DNA. You simply want to deny signs of intelligence present in physical matter. I can’t stop you from doing that.

    LYO:
    This is a completely different argument. We’re talking about whether DNA is a representation (which requires an intelligent agent to interpret). Not whether the interpretive system requires an intelligent agent to assemble.

    But you said above: Any regular physical process can be represented in a table format. Obviously, then, intelligent agents can “interpret” any physical process. So the fact that material processes can only be “interpreted” by intelligent agents is a given—an operation that is entirely separate from the “process” being interpreted. The only pertinent fact in our discussion is the determination that certain base triplets can be associated with certain amino acids in a way that mimics/corresponds to a “coding system” used by intelligent agents. And, then, finally, it is quite apparent that in the world we live in, ONLY intelligent agents are known to use “coding systems.” What else are we left to conclude except that intelligence is behind this coding system?

    But I imagine you’ll disagree, and it is because you seem to want to draw a very significant distinction between a physical process and a mental process, a distinction that, in your mind, so it seems, seals off the physical from the mental. It would seem this leaves you with this problem: if you want to ‘seal off’ the mental from the ‘physical’, to compartmentalize them as non-intersecting sets, then how are you going to explain the origin of the ‘mental’ from the ‘physical’?

    And, anticipating the usual argument, if you want to say that “evolution” brought it about, with the understanding that “evolution” is brought about via Darwinian/neoDarwinian processes—which are “random”—then you’re telling us that “random processes” brought about Einstein’s field equations. Isn’t something wrong with that picture?

  105. Genomicus[100]:

    I don’t see many ID proponents admitting that the bulk of the flagellar proteins (or their homologs) can function in non-flagellar contexts. The evidence in favor of this view has been compiled by Matzke and other researchers, and unless it is flawed (which I highly doubt), we’re gonna have to admit this.

    Nick’s online paper relies heavily on BLAST searches. Having looked at the paper by Cascales, Lloubes and Sturgis, which presents evidence linking the MotA/B proteins to the TolQ-TolR and the ExB-ExD proteins, one can’t help but notice the somewhat minimal correspondence between the proteins. They are all most similar in their TM (transmembrane) sequences, but not that similar at the C and N terminal ends. The fact that membranes must by hydrophobic already puts a constraint on the a.a. sequence. So one would expect a certain amount of similarity between all TM proteins to some extent. If you look at Fig 4B, comparing TolQ-R and ExB-D and MotA, there are two sections that are similar. In one stretch, there are 10 out of 18 a.a.s are similar between ExbB and TolQ; in the same stretch, only 5 out of 18 a.a.s are similar. In the next stretch of sequence, there are 11 out of 18 a.a.s similar between TolQ and ExbD, and, again, only 5 out of 18 a.a.s in common between MotA and ExbD/TolQ. It’s even worse for the N-terminal ends for TolR/ExbD and MotB: There, Fig 4C, only 2 (!) out of 18 a.a.s match between all three, while between TolR/ExbD there are 9 out of 18 matches.

    MotB is 308 a.a.s long. If only 2 a.a. residues are the same, and fall in the same place on a stretch of 308 a.a.s (TolR is 480 aas), then how can this be construed as making MotB “homologous” to ExbD and TolR? So what does protein X being “homologous” to Protein Y mean exactly? And what does this mean for the picture that is being painted of “co-opted” proteins?

    Maybe you could comment on this, Genomicus.

  106. Genomicus[100]:

    I don’t see many ID proponents admitting that the bulk of the flagellar proteins (or their homologs) can function in non-flagellar contexts. The evidence in favor of this view has been compiled by Matzke and other researchers, and unless it is flawed (which I highly doubt), we’re gonna have to admit this.

    If we can get clarity on this issue, then indeed this discussion at UD will have done something to serve the intelligent design community, which is the purpose of UD.

    The internet is good for these sort of discussions as it will help ID authors contemplating writing articles and books to have more accurate information.

    And as a matter of fact Bill Demski said he uses the net to get some of his ideas vetted.

    To that end, I and johnnyb have something in the works. :-)

    So again, gentleman, thank you for being cordial to first rate Darwinists like Nick. I will be sure, along with the commenters at UD, are recognized if johnnyb and I get our project going.

  107. 107
    material.infantacy

    tta gct agt act tat gaa gct cgt caa aat gat caa gaa agt aat caa act ggt gaa act att act taa

  108. PaV:

    Nick’s online paper relies heavily on BLAST searches. Having looked at the paper by Cascales, Lloubes and Sturgis, which presents evidence linking the MotA/B proteins to the TolQ-TolR and the ExB-ExD proteins, one can’t help but notice the somewhat minimal correspondence between the proteins. They are all most similar in their TM (transmembrane) sequences, but not that similar at the C and N terminal ends. The fact that membranes must by hydrophobic already puts a constraint on the a.a. sequence. So one would expect a certain amount of similarity between all TM proteins to some extent. If you look at Fig 4B, comparing TolQ-R and ExB-D and MotA, there are two sections that are similar. In one stretch, there are 10 out of 18 a.a.s are similar between ExbB and TolQ; in the same stretch, only 5 out of 18 a.a.s are similar. In the next stretch of sequence, there are 11 out of 18 a.a.s similar between TolQ and ExbD, and, again, only 5 out of 18 a.a.s in common between MotA and ExbD/TolQ. It’s even worse for the N-terminal ends for TolR/ExbD and MotB: There, Fig 4C, only 2 (!) out of 18 a.a.s match between all three, while between TolR/ExbD there are 9 out of 18 matches.

    Actually, I’m a bit iffy of the proposal that MotAB is homologous to ExbBD and TolQR. If I recall correctly, Cascales et al. do note that the fact that the bulk of the sequence similarity shared among these proteins is found in the TM domains does highlight the real possibility that this sequence similarity is not the result of shared ancestry but rather convergent evolution. Pallen and Matzke’s 2006 research used multiple PSI-BLAST iterations under default conditions to find homologs of MotAB. I’m not quite sure what they did exactly – that part of the paper is quite vague, ’cause when I run multiple PSI-BLAST iterations of MotA, I don’t get any hits of ExbB or TolQ. I think it would have been a good idea if they (a) listed how many iterations they made and (b) how exactly they arrived at their ExbB/TolQ hits. I emphasized the fact that Pallen and Matzke used PSI-BLAST under default conditions. This is important, because if they really wanted to guard against the possibility that the sequence similarity is the result of convergent evolution (because of the constraints on the TM domains), they could have filtered low complexity regions. This would have helped to gauge the reliability of their conclusion of homology.

    Furthermore, when I BLAST MotA against, say, the bacteria phylum Nitrospirae, I get a couple of MotA hits, but no ExbB or TolQ hits. And when I BLAST ExbB against that same phylum, I get ExbB hits, but not MotA hits. This is interesting, since this phylum has both proteins, but BLAST fails to recover them when you use the sequence that is supposed to be homologous to the other.

    Still, these proteins may be homologous (ExbB and TolQ almost certainly are), but I don’t think it’s prudent to say anything definite on the matter. I believe Dr. Matzke might have some functional considerations in mind as well, to strengthen the argument that the two are indeed homologous, but I can’t say anything about that at the moment.

    Also, there’s the interesting story of FliG and MgtE. BLAST searches do not indicate any significant degree of sequence similarity AFAIK, but Pallen and Matzke list the two as homologous based on “structural or functional considerations.” But this certainly raises the spectre of the good possibility of convergent evolution at the functional level.

    Still, the majority of the flagellar proteins do not have unique functions. For example, FliF and FliI do not need to function in the context of motility. And the same goes for FlhA/FlhB. Etc. etc. And this needs to be admitted by any intellectually honest ID proponent.

  109. 109
    The physical make-up of the codon (the sequence pattern it contains) does not control the appearance of a particular amino acid.

    So are you saying that the chemical structure of a gene is arbitrary with respect to the protein it results in?

    What, are there tiny construction workers inside the cell that read the DNA sequence, and then decide to go about building the proteins based on what they read?

    LYO, why do you insist on sinking the conversation to absurdities? And why did you skip the very next sentence following the one you quoted?

    You ask: “ What, are there tiny construction workers inside the cell that read the DNA sequence, and then decide to go about building the proteins based on what they read?

    No I am saying exactly what I said in the very next sentence: “[the appearance of a particular amino acid at the binding site] is controlled in isolation by the physical make-up of the protocol instead”.

    - – - – - – - –

    Nucleic sequences in DNA (via mRNA) order tRNA molecules. They do not order amino acids; in fact, they don’t even interact with them. Which amino acid appears at the binding site in the ribosome is solely based upon the physical structure of the protocol (aaRS) not the physical structure of the nucleic sequence.

    You’ll remember: as in any other instance of recorded information transfer, the protocol is an isolated “arrangement of matter which establishes the relationship between the representation and the effect it represents within the system”.

    Otherwise, that relationship wouldn’t exist.

  110. Genomicus:

    Thanks for your last post. I am a little more cynical about what constitutes “homology” than you seem to be, but you obviously have in-depth knowledge of the field.

    Maybe you could comment on the E-value that was used by Cascales, which, IIRC, was E 10^-4, or something like that. It’s hard to really figure out what E is. I’ve looked at some papers, and it still seems a bit of a mystery. The 10^-4 figure seems to be a rather large number if it’s being used to eliminate matches due to “chance”, which I believe is the reason it is used.

    My cynicism tells me that if expectation value, E, is not set low enough, then proteins that are only vaguely similar will end up being termed “homologs”. There is so much obfuscation and equivocation already going on in evolutionary sciences, we don’t need any more. And finding false-positive “homologs” everywhere certainly won’t help.

    Thanks again, though, for your post, and the work that went into it.

  111. Genomicus:

    Perhaps you would like to comment on this: with Michael Behe’s recent work in mind, where he demonstrates that most organisms adapt through “loss of function”, what does this imply for the way phylogenies are constructed. It seems to me that the way they use molecular biology to construct these phylogenies, there’s no way of distinguishing between the possibility that proteins have been built up over time, and the very real possibility that proteins have “broken down” over time.

    IOW, how do we know that in order for the flagellum to come about, certain proteins ended up being “co-opted”? Isn’t it possible that the “flagellar” proteins themselves were co-opted by other systems through a kind of “loss of function”. Is there anything to this way of thinking?

  112. Our discussion made it to EvolutionNews!

    http://www.evolutionnews.org/2.....57831.html

  113. Regarding the beer glass trick:

    This irreducible structure can in principle be build by starting with something that supports the structure initially in the middle which is then later on removed.

    The remaining structure is then, of course, irreducible complex.

    Similar arguments can be made for other irreducible structures like the bridge in the EN&V article, which could have once been a full brick wall.

    This doesn´t prove that certain biological features evolved in this way. But it shows that irreducible complexity is not per se an indication that such a structure could not have evolved. Because in principle (!), it´s possible.

    Sure, irrducible structures give rise to interesting questions in biology. But I don´t think making an Designer of the Gap´s argument for irreducible structures is a good long term strategy. These gaps tend to shrink.

  114. But it shows that irreducible complexity is not per se an indication that such a structure could not have evolved. Because in principle (!), it´s possible.

    Sure, irrducible structures give rise to interesting questions in biology. But I don´t think making an Designer of the Gap´s argument for irreducible structures is a good long term strategy. These gaps tend to shrink.

    Agree it can evolve in principle, but why would nature pick the extravagant solution over the simple? The same problem exists with the peacocks tail. Selection tends to select for simpler not more complex.

    Such is the mystery of sexual reproduction.

  115. Selection tends to select for simpler not more complex.

    Simplicity might have benefits, but they can be outweighed by other advantages of complexity in certain situations.

    The peacock tail may be one of those situations. It attracts females and may also help to avoid fights with other peacocks or predators.

    “Irreducible complexity” is not enough to rule out evolution, complexity itself can therefore also not be a principal roadblock to evolution.

    The question why these things come into existence is interesting and the basis of nice research. Attributing them to some unknown “Designer” is not exactly moving the discussion forward, is it?

  116. Indium:

    The question why these things come into existence is interesting and the basis of nice research. Attributing them to some unknown “Designer” is not exactly moving the discussion forward, is it?

    You’re maybe missing the point of what ID, as a scientific project, has to offer. The point of ID is not say, “Oh, look, this can only be explained by a Designer; therefore Darwin is wrong, and the real explanation for everything is that God made it.” First of all, things aren’t that simple, Second, this would be the stuff of theology, more than science.

    The real point of ID, and it looks like you’ve just stepped around it, is that biological systems are “designed”. Leave the “Designer” out of the discussion. The point is that for science to have a productive way of understanding how life functions, it must first have a correct assumption of how it arose, and how it operates. The choices in this controversy are: (A) Random processes, as fine-tuned by differential death (reproduction, if you like), and (B) design by some intelligence.

    I’ve read a paper about present-day proteins versus the “ancient” form of that protein. The investigators wanted to trace out the pathway. They introduced changes to the protein. They couldn’t “evolve” the protein in the ‘forward’ temporal direction. It was impossible. But they could go ‘backwards’ in the temporal direction. Well, what they had really proved—so it seemed to me—was that random processes couldn’t get you from “ancient” to “modern”. But rather than live with that conclusion, they basically “spun” it to sound Darwinian.

    Isn’t this a big waste of time? How many researchers feel compelled to pound a square peg into a round hole? Maybe all of this is necessary simply because man is curious; but, if at some point are we ’tilting at windmills’? If ‘design’ is assumed, and if the active ‘ingredient’, so to speak, of ‘intelligence’ is searched for, maybe we could come up with better answers and more quickly.

    Basically Darwinism is now already dead. It is simply a matter of time when the scientific community gives up this ghost. Everyday research points away from randomness (A) and points to intelligent operations within the cell (B).

    As to discussions, when a child says, “Where did I come from?”, and this all leads backwards in time to the Big Bang, then what is the answer to the question: “Where did the Big Bang come from?” Some discussions simply end because there’s no where else to go. We might not like that; but sometimes we end up in mystery, a place that reason alone cannot penetrate.

  117. material.infantacy

    tta gct agt act tat gaa gct cgt caa aat gat caa gaa agt aat caa act ggt gaa act att act taa

    You’re right. LastYearOn doesn’t get it.

  118. 118
    material.infantacy

    hehe PaV, I wasn’t sure anyone would bother to translate it. Thanks.

    The missed point is this. Without an integrated, functional system for DNA processing already in place, there is no physical relationship of note between codons and amino acids. There is a huge taking-for-granted that occurs when crediting chemistry with the association between DNA and proteins — and that is the existence of a functionally integrated, irreducibly complex, highly contingent context, without which no chemical mapping would take place.

    So the observation that physics and chemistry are involved with a codon being converted to an amino acid within the context of a living system is akin to the observation that physics and chemistry are involved with converting the electrical impulses represented by the string 01100001 to the character ‘a’ within the context of a computer system. The correct response to that transparently obvious explanation is along the lines of, “yeah, so?”

    Personally I’m interested in the configuration and provenance of the systems which facilitate and perform such mapping, and completely unimpressed by trivial statements about the physicality of the medium. Proteins are physical. Yeah, so? Rather, explain by what physical, transformative process the proteins crucial for functional reproduction with sustainable variation in living systems are created; and do so without recursive referral to contingent mechanisms within the system itself.

  119. PaV:

    Thanks for your last post. I am a little more cynical about what constitutes “homology” than you seem to be, but you obviously have in-depth knowledge of the field.

    When considering the question of whether two proteins are homologous, there are several points worth considering, including significant structural/functional similarity, significant sequence similarity, and similar length in terms of amino acid residues – although note that this last criterion by itself is very weak, and is only worth considering when you tie it to other criteria. And structural/functional similarity (and even sequence similarity, depending on how significant the sequence similarity is) can result from convergent evolution. IMHO, convergent evolution has been severely underestimated as a mechanism for giving the appearance of homology.

    Maybe you could comment on the E-value that was used by Cascales, which, IIRC, was E 10^-4, or something like that. It’s hard to really figure out what E is. I’ve looked at some papers, and it still seems a bit of a mystery. The 10^-4 figure seems to be a rather large number if it’s being used to eliminate matches due to “chance”, which I believe is the reason it is used.

    If Cascales et al. used 10^-4 as their cutoff E-value, then I really have to suspect that we’re looking at a false positive here. The standard cutoff E-value used by most researchers is 10^-5. Anything above that can very well be meaningless noise (as you know, the lower the E-value, the better).

    My cynicism tells me that if expectation value, E, is not set low enough, then proteins that are only vaguely similar will end up being termed “homologs”.

    Quite true.

  120. PaV:

    Perhaps you would like to comment on this: with Michael Behe’s recent work in mind, where he demonstrates that most organisms adapt through “loss of function”, what does this imply for the way phylogenies are constructed. It seems to me that the way they use molecular biology to construct these phylogenies, there’s no way of distinguishing between the possibility that proteins have been built up over time, and the very real possibility that proteins have “broken down” over time.

    IOW, how do we know that in order for the flagellum to come about, certain proteins ended up being “co-opted”? Isn’t it possible that the “flagellar” proteins themselves were co-opted by other systems through a kind of “loss of function”. Is there anything to this way of thinking?

    There certainly is the possibility that flagellar proteins were co-opted for other uses. IMHO, this seems to be the case with the TTSS, which evolved from flagellar proteins. Dr. Matzke and others disagree with this view, and as he implied, researchers are split on the question of whether the TTSS evolved from the flagellum, or whether the TTSS and the flagellum share a common ancestor.

    However, in principle, phylogenies can tell if flagellar proteins are ancestral to their homologs, or if homologs of flagellar proteins are ancestral to the flagellum. I say “in principle” because we are talking about deep-time here, and phylogenies are less accurate the more divergent the protein sequences are. For example, Gophna et al. constructed phylogenetic trees of TTSS and flagellar proteins using a distance-based method. But if TTSS proteins have evolved at a faster rate, this can result in an incorrect phylogeny (this has been highlighted by Saier, 2004). And TTSS proteins probably have evolved faster than flagellar proteins.

    But it is indeed true that before one immediately assumes that a homolog of a flagellar protein implies that the flagellum evolved, one needs to collect data on the taxonomic distribution of the proteins under consideration, estimate phylogenies, etc. If it is shown that the flagellar lineage is more ancient, then we don’t have evidence of a Darwinian origin of the flagellum.

  121. Simplicity might have benefits, but they can be outweighed by other advantages of complexity in certain situations.

    But the fact something can be advantageous after it exists does not in any way imply selection will select for it or its precursors when the system doesn’t even exist in the first place. And that is the challenge IC poses. Evolution can select in favor of systems that are non-existent.

    How can selection select toward evolving an IC system? Answers:

    1. reduction of function
    2. co-option

    Reduction of function is not really a solution because it implies a evoluton devolving from something more complex (which is the creationist view of evolution).

    Co-option is the other route, it is not ruled out, but that different than saying it is proven. It is only accepted because it’s the last resort. And co-option optimistically avoids the issue that a co-opted system might have to be malfunctioning before it can be co-opted, and thus defeats the co-option argument.

    But as I pointed out, not even Miller demonstrated co-option happened, the equivocated the notion of co-option and insinuated systems that weren’t co-opted as examples of co-option. Many signed off on the equivocation, even Judge Jones. Notice, the problem of that TTSS must become a malfunctioning TTSS before it can become a functional flagellum isn’t even addressed but rather ignored.

    The question why these things come into existence is interesting and the basis of nice research. Attributing them to some unknown “Designer” is not exactly moving the discussion forward, is it?

    It moves the discussion in the right direction if indeed that is the what caused the design. Darwinists claimed they solved the problem, there lack of rigor would be unacceptable in most other scientific disciplines.

    Whether ID is true or not doesn’t change the fact the Darwinists have failed to theoretically and empirically defend their claims.

    The discussion is more specific than speculating how things came to existence. The discussion focuses on whether supposed solution like Darwinism agree with the facts in evidence. The claims of success are premature at best, falsified at worst, and certainly not as good as theories of gravity.

  122. Genomicus:

    But if TTSS proteins have evolved at a faster rate, this can result in an incorrect phylogeny (this has been highlighted by Saier, 2004). And TTSS proteins probably have evolved faster than flagellar proteins.

    This is precisely my concern. “Faster” and “slower” are obviously relative terms. Does an objective standard exist? From what I can see, the answer to this question is “no”. So that means you can come up with almost any kind of conclusion you want. And, if you’re pre-disposed to Darwinian evolutionary thought, then this is how it’s going to be presented. But the bottom line is: is any of this really worth anything? Are scientists basically gazing at their bellybuttons when they do this kind of work?

    Not to be too cynical, I realize, too, that sometimes all this kind of ‘dirty work’ has to be done prior to truly reaching a full understanding of the dynamics and the true phylogenetic histories. But in the meantime, evolutionists ‘make hay’ using “data” that, for the most part, doesn’t have a solid foundation, and worse, is susceptible to an entirely contrary interpretation. It’s one thing to be wrong; it’s another to be 180 degrees off.

    But it is indeed true that before one immediately assumes that a homolog of a flagellar protein implies that the flagellum evolved, one needs to collect data on the taxonomic distribution of the proteins under consideration, estimate phylogenies, etc. If it is shown that the flagellar lineage is more ancient, then we don’t have evidence of a Darwinian origin of the flagellum.

    I read just a part of an article that said–I think this was a 2001 article–when it came to bacterial phylogenies they didn’t really have a clue. That is was almost impossible to really build a true phylogeny. Hence my question. And when you say “If it is shown that the flagellar lineage is more ancient, then we don’t have evidence of a Darwinian origin of the flagellum,” this is what is in the back of my mind. Time will tell.

  123. Here’s a link to the Cascales paper.

    Cascales, et. al, make this comment, stressing in the paper the importance of the aspartate (D) residue (a.a.) in the MotB. It seems that simply on the basis of this ONE a.a., Cascales is finding TolR/ExbD and Mot B to be homologs.

    Here are the sequences. (BTW, the 10^-4 figure came from a different article. In Cascales’s paper, no mention is made of the E value. I looked up his “supplementary information” at the given website, and there is no E-value given there either.)

    N Terminal transmembrane helix of TolR, ExbD and MotB:

    TolR sequences: E.coli
    RGRGRRDLKSE*IN*IV*P*LL*DV*L*LVLL*L*IFM*AT*AP*II*T

    ExbD: E.coli
    LDDNGEMHD*IN*VT*P*FI*DV*M*LVLL*I*IFM*VA*AP*LA*T

    MotB Sequences: E.coli
    GAAHGSWKIAYA^D^FMTAMMAF^F^LVMWLISI

    MotB Sequence: a. hydrophila:

    ……………………..*ADF*TL*AMMAFF*M*V*L*W*ILAV

    You can see the tremendous similarities between TolR and ExbD sequences, and you can see tremendous similarities between the MotB sequences of E. Coli and a. hydrophila, but comparing these two sequences, there are only 2!!! a.a. that match up, one being the aspartate (D). For all we know, the aspartate (D) may be needed structurally in these kinds of loops, and so would be ‘generally’ conserved simply from a chemico/physico point of view.

    Here’s what they write:

    The consensus sequences show that the TolQ proteins are more strongly conserved than the ExbB proteins. The consensus derived for the C-terminal helical hairpin of TolQ, ExbB and MotA proteins (Fig. 4B) indicates that this region of the protein is particularly strongly conserved, arguing strongly for an important functional and/or structural role. Interestingly, in the MotA sequences, this region is less conserved, despite its presumed functional importance in the formation of an ion pore. Comparing the N-terminal regions of the TolR, ExbD and MotB proteins gives strong consensus sequences and, as in TolQ hairpin, it is possible to observe a homology between the different groups of sequences, in particular the aspartate present in the overall 90% consensus sequence (Fig. 4C).

    I just can’t buy that MotB is a homolog of TolR and ExbD. This is a stretch. And how many other examples of this kind of ‘science’ will we find it we take a closer look?

    Anyway, perhaps you can react to this.

  124. 124

    Short responses — the MotA ExbB-TolQ homology is easy, I got it just now on PSI-BLAST. And it is officially annotated as a protein superfamily by NCBI. The MotB-ExbD-TolR homology is indeed tougher. However, it is widely accepted in the literature — dozens of publications — and even used in several papers for modeling one protein based on information about another, for building models of MotAB stoichiometry and interaction (ans similar models of the homologs), etc. You can’t just scratch at it a tiny bit, ignore all the reasons people think it’s homologous, and claim that you’ve got a good reason for rejecting the conventional wisdom.

    I’m not gonna do your research for you this time. I challenge you to look it up and demonstrate that you’re interested in serious investigation. Hint: start looking at the similarities between MotAB, TolQR, and ExbBD treated as complexes. Then add in the sequence similarities.

    (PS: Also, MotB has an easily retrievable homology to OmpA and relatives, so whatever is concluded about ExbB and TolR, that doesn’t dispense with all evidence for the evolution of that protein.)

  125. Nick,

    In what way does declaring homology help your position? Even if the proteins are homologs, to get a flagellum you need more than homologous proteins diffusing throughout the cell.

    And the evolution of a protein does not mean that necessity and chance didit.

  126. Short responses — the MotA ExbB-TolQ homology is easy, I got it just now on PSI-BLAST. And it is officially annotated as a protein superfamily by NCBI. The MotB-ExbD-TolR homology is indeed tougher. However, it is widely accepted in the literature — dozens of publications — and even used in several papers for modeling one protein based on information about another, for building models of MotAB stoichiometry and interaction (ans similar models of the homologs), etc.

    thanks Nick.

    Sal

  127. Hey Nick- dare to try to answer Dr Behe’s question?

    Let’s turn the tables and ask, how could one falsify the claim that, say, the bacterial flagellum was produced by Darwinian processes?

    ((Professor Coyne’s remarks about a Precambrian fossil hominid are irrelevant since I dispute the mechanism of natural selection, not common descent. I would no more expect to find a fossil hominid out of sequence than he would.) If a scientist went into the laboratory and grew a flagellum-less bacterial species under selective pressure for many generations and nothing much happened, would Darwinists be convinced that natural selection is incapable of producing a flagellum? I doubt it. It could always be claimed that the selective pressure wasn’t the right one, or that we started with the wrong bacterial species, and so on. Even if the experiment were repeated many times under different conditions and always gave a negative result, I suspect many Darwinists would not conclude that the claim of its Darwinian evolution was falsified. Of complex biochemical systems Coyne himself writes “we may forever be unable to envisage the first proto-pathways. It is not valid, however, to assume that, because one man cannot imagine such pathways, they could not have existed.” (Coyne 1996) If a person accepts Darwinian paths which are not only unseen, but which we may be forever unable to envisage, then it is effectively impossible to make him think he is wrong.)

  128. Nick Matzke:

    The MotB-ExbD-TolR homology is indeed tougher. However, it is widely accepted in the literature — dozens of publications — and even used in several papers for modeling one protein based on information about another, for building models of MotAB stoichiometry and interaction (ans similar models of the homologs), etc. You can’t just scratch at it a tiny bit, ignore all the reasons people think it’s homologous, and claim that you’ve got a good reason for rejecting the conventional wisdom.

    Nick, ipso facto that out of 308 a.a. there is only a 25 a.a. stretch where two proteins match up in two loci, is enough for me to conclude we’re not dealing with “homology”. That’s the whole point.

    You can “define” homology anyway you want. But from a sequence level, this make no sense at all. It is quite clear that ExbD and TolR are “homologous”. But then to stretch this definition to something like that between ExbD and MotB, is hardly more than equivocation, and stops being science. Invent a new word, if you have to, but to lump the one sequence analogy along with the other? This makes no sense. How do you any longer do science when you start calling entirely different phenomena the same thing?

    I’m not gonna do your research for you this time. I challenge you to look it up and demonstrate that you’re interested in serious investigation. Hint: start looking at the similarities between MotAB, TolQR, and ExbBD treated as complexes. Then add in the sequence similarities.

    Who asked you to do the “research”? The comment was directed to Genomicus. You stopped responding quite some time ago; I didn’t even know you were paying any attention. BTW, it seems to me, the last time I posted a response to you I asked you to use PaV as an indentifier, which you didn’t do again. I’m getting the impression that you don’t want to do that. That seems strange, if true.

    As to MotAB and TolQR and ExbBD as complexes, what is there to look up. I suppose you mean that they’re both thought to be functionally similar. And then we add in the “sequence” similarity. Yes, similar a.a.s in the TM region constrained by hydrophobicity; and then the ONE aspartate a.a. that seems essential for the proton pump. Sequence similarity based on ONE a.a.? This, as I’ve already stated, is folly. It is ignorance masquerading as insight.
    You should instead be amazed, even stunned into disbelief, that NS could organize the 308 a.a.s in MotB and the 480 a.a.s in TolR and come up with similar function. Let me just point out: this defies the odds. Relying upon random variation and NS as generators of these similar functions via almost completely disparate a.a. sequences, is mind-numbing. This kind of fine-tuning would require the age of the universe to bring about. But, just like God, NS can do anything. It’s kind of like a miracle. But you say, “Oh, no, it’s no miracle; they’re ‘homologous’.” Another fine Darwinian tautology.

    (PS: Also, MotB has an easily retrievable homology to OmpA and relatives, so whatever is concluded about ExbB and TolR, that doesn’t dispense with all evidence for the evolution of that protein.)

    In an earlier post to Genomicus, I brought up the whole idea that no one really knows what bacterial “phylogenies” look like. You can presume that the flagellum is derived from other occuring proteins (though this is like saying that using the Eiffel Tower, you could easily build the superstructure of the Empire State Building. Let me reassure you, that won’t happen via random processes.) Or, you can presume that the flagellum was used to build other structures. I don’t see how biologists can effectively make a determination of which of these two alternatives happened until a true understanding of any real phylogenetic relationships is established. You can read Genomicus’ response. He agrees, but, of course, demurs as to the actual state of phylogenetic histories.

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