Uncommon Descent Serving The Intelligent Design Community

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

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

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

irreducible complexity house of cards

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

What if a Darwinist said,

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Comments
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.PaV
April 2, 2012
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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.)Joe
April 2, 2012
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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. Salscordova
April 1, 2012
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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.Joe
April 1, 2012
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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.)NickMatzke_UD
April 1, 2012
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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.PaV
March 31, 2012
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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.PaV
March 31, 2012
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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.scordova
March 30, 2012
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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.Genomicus
March 30, 2012
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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.Genomicus
March 30, 2012
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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.material.infantacy
March 30, 2012
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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.PaV
March 30, 2012
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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.PaV
March 30, 2012
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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?Indium
March 30, 2012
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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.scordova
March 30, 2012
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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.Indium
March 30, 2012
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Our discussion made it to EvolutionNews! http://www.evolutionnews.org/2012/03/illustrating_ir057831.htmlscordova
March 29, 2012
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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?PaV
March 29, 2012
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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.PaV
March 29, 2012
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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.Upright BiPed
March 29, 2012
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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.Genomicus
March 29, 2012
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tta gct agt act tat gaa gct cgt caa aat gat caa gaa agt aat caa act ggt gaa act att act taamaterial.infantacy
March 29, 2012
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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.scordova
March 29, 2012
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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.PaV
March 29, 2012
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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?PaV
March 29, 2012
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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?lastyearon
March 29, 2012
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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.scordova
March 29, 2012
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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...Joe
March 29, 2012
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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.Genomicus
March 28, 2012
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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.Upright BiPed
March 28, 2012
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