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Author
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Topic: Back to the Topo II - where does it end?
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Nel
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Member # 614
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posted 09. May 2003 17:50
Nic,
Let me see if I can make my discussion of adhesion organelles a bit clearer. Pili are not homologous to flagellar filaments. They are not even analogously homologous. It isn't the filament that rotates in the bacterial flagellum
in fact, any filament may not even be enough, but the rotation mechanism is in the motor, with its driveshaft connected to the filament by the hook. Furthermore, the folding of pili seems to be IC. Even if type III systems were relevant, they don't convince me that selection would likely be able to do it, in that no subset of the parts carries out an alternative function.
quote:
This must set another record for self-contradiction! If there are alternative functions "all the way to the flagellum" then the "sea of nonfunctionality" either doesn't exist or is crossed by a land bridge.
No. Because each alternative function has a subset of parts that are required for that function, and between each alternative machine, you have nothing but random chance events. Too many in fact. This is what H. Allen Orr was referring to by air conditioners suddenly working with engines.
Dembski's calculation shows this, it's not just an all at once calculation. It is not enough that a subset or analog or homolog simply has an alternative function, if those alternative functions requires several parts to function, then there are still unselectable steps which is nothing but random assembly. I don't know why Darwinists characterize any statistical test as "all-at-once"(tm) even though they have never even looked at the calculation. What in the world would an all at once calculation need with an identity factor as Dembski's calculation needs? An identity factor pretty much tells you that it is easier to get the word "this" from "thi" then it is to get from "th". And that points to non-functionality. When there is non-functionality, there is nothing for natural selection to do. ]
Now, you assert that the evidence for co-option is common, but where's the plasticity among these systems?
Furthermore you attempt to cite some evidence from the literature
In these threads I see a few theoretical papers inferring evolution from some data that does not directly associate with complex specificity through co-option (i.e. genome patterns), and some that don't even have anything to do with Darwinian evolution at all. One of these threads also has a great deal on sequence repeats which has absolutley nothing to do with co-option. Please don't hurdle hundreds of citations at me. Pick one, or a few, and lets argue it. Everytime you show me a list of citations, the first few turn out to be a wild goose chase, as with the Spa47 paper. Feel free to link to your voluminous citations but pick a few, and fully discuss them, because eventually I plan to address all of your assertions and citations (I already have some interesting information on your chemotaxis citations).
You write:
quote:
There are lots of kinds of pili based on lots of kinds of transport systems, you keep bringing up one specialized system (based on a Type I transporter) over and over like it was some kind of talisman. Type III virulence systems (called Type III pili in some articles, like this the Cornelius and Van Gijsegem paper mentioned earlier).
Well lets talk about those unaddressed counterarguments. In my view the P pilus is a talisman. And the very reason for this is the logic of the parts, there is no evidence that simple repeats would do, the paper you cite, once again relies on an imaginary system. Note, there is a logic here for the required components. In fact, PapD has no function outsie the P Pilus. Here is Mike Gene:
quote:
The 3-D structures of PapD complexed with PapG (the adhesin on the tip) and PapK (one of the adaptors) have been solved. PapD forms a boomerang-shaped protein with two immunoglobulin-like (Ig-like) domains (a structure composed of layers of antiparallel beta sheets). The N-terminal end of PapK is also an Ig-like domain, but it lacks a C-terminal beta sheet that normally contributes to the hydrophobic core of the domain. This produces a cleft that exposes the hydrophobic core, which is what makes it so sticky and prone to aggregation by itself. The chaperone PapD masks this exposed region in a most fascinating manner - it donates one of its beta strands to complete the Ig-domain in PapK (Fig 1). But it does so in an atypical fashion, as the beta strand it donates runs parallel, not antiparallel, with its neighboring strand. Thus, PapD provides at least two essential functions captured in one very elegant act - by donating one of its beta strands, PapD simultaneously prevents aggregation of PapK while providing the missing steric information for proper folding of PapK.
http://www.idthink.net
So repeated subunits would be unlikely to form a functional pilus.
Which type III pili secrete proteins from the top? Please don't show me a secretory system because I'm going to tear my hair out. Archael flagella are irrelevant as they represent a seperate kingdom and their flagella are completely different from eubacterial flagella. So I don't know why you even call this a counterargument to the fact that pili are built completely differently from eubacterial flagella.
Can you show me in the peer reviewed literature how natural selection and random mutation built either the flagellum or the immune system? And I already showed why ExbB, or Spa47, or any other imaginary systems shouldn't have been taken into account by Dembski at all. It's irrelevant. Also as I showed in the immunity thread, there is a lot more evidence in the literature about the abrupt appearance of both these systems rather then it's Darwinian evolution. So I have no idea what you mean by "respecting" the literature, if anything , you are completely ignoring it.
Your diffusion coefficients seem to support my point about flagella and how anything less would be useless, after all, you are showing me fully functioning flagella. The reason why flagella can't go from point A to point B directly and do go through tumbling is because of brownian motion, a wiggle will most likely not even be able to induce movement. However, I would like to see the quotation for myself, and why you think it's relevant, before I fully discuss it.
As I already showed, Dembski's calculation is not like assembly a plane through a tornado in a junkyard. It is precisely attempting to find a forward-chaining of events that would have selection as the driving force all the way up mount improbable. But since only co-option and not direct evolution, can be invoked in the Darwinian pathway of the bacterial flagellum, it's nothing but random chance, especially since you are invoking multi-part IC machines with alternative functions (although I only see one such alternative machine, the type III secretory system, which seems to have evolved from the flagellum). Since each step does not depend on the last in indirect stories, you are telling nothing more than a tornado in a junk yard story.
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yersinia
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Member # 324
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posted 09. May 2003 21:27
Arrgh, this is becoming pointless. Apologies to the original people in the thread BTW, we kind of took it over.
I'm not sure there's much point in repeating myself again on various points, but Nelson continues to make a mistake-a-minute and I suppose at least the newer ones should be pointed out.
quote:
Let me see if I can make my discussion of adhesion organelles a bit clearer. Pili are not homologous to flagellar filaments. They are not even analogously homologous.
The term "analogously homologous" makes no sense at all. It's like saying "white black".
quote:
It isn't the filament that rotates in the bacterial flagellum in fact, any filament may not even be enough, but the rotation mechanism is in the motor, with its driveshaft connected to the filament by the hook. Furthermore, the folding of pili seems to be IC. Even if type III systems were relevant, they don't convince me that selection would likely be able to do it, in that no subset of the parts carries out an alternative function.
Actually, Blocker et al 2003, previously discussed, argue that the hook protein FlgE is homologous to the Type III pili needle protein MxiH/PrgI. See Figure 1.
And, this pili appears to have only two parts external to the cell, MxiH/PrgI and "CaoX?" (which presumably is questionable). Deja vu all over again as I pointed this out before. This pili is not made up of five parts.
As I'm already repeating myself I shall move on...
quote:
Everytime you show me a list of citations, the first few turn out to be a wild goose chase, as with the Spa47 paper.
Since I just mentioned Blocker et al. 2003 above, let's discuss Spa47. Previously you said about Spa47:
quote:
I read the paper last night, and it seems you are quite wrong about this. There is no evidence for a Spa47 protein complex, a fliI that is homologous to the b[eta] subunit of the F-ATP synthase. What is shown in green in fig 3 in the paper is only an imaginary model of Spa47 based on the F1 structure and that model can be successfully docked to the real NC outline where they would imagine it would have to sit to pump secrete proteins into the channel. The evidence here is pretty weak.
But you are completely ignoring the 33% amino acid sequence identity between the beta subunit of F1 and Spa47/FliI. This is statistically significant sequence similarity, so they said "hey, we bet that the structures are similar also, what happens if we plug the F1 beta subunit structure into our model" and, despite the millions of ways that a protein could not match the model, it fit quite well. This confirmed prediction strengthens the already strong homology inference based on sequence. Here is what they said about it:
quote:
How might these ATPases catalyze processive protein export? Spa47 (the Shigella FliI homolog) shares 33% amino acid identity with the -subunit of F1-ATPase. Proteins with >30% sequence identity have a high probability of sharing similar structures (69). Active F1-ATPase is a heterohexamer consisting of alternating alpha- and beta-subunits with a gamma-subunit inserted in a central channel where it rotates during the catalytic cycle (70). No equivalent of the alpha-subunit of F1-ATPases is found within flagellar or TTSS-encoding operons, so we assume that the type III export motor is a homohexamer. When modeled on the F1 structure, Spa47 fits at the inner membrane base of our NC structure (Fig. 3). It would contain a central channel aligned with the one found within the NC and of similar diameter to it, through which the proteins could be secreted.
However, if you think they are wrong, you are free to predict that future discoveries will not confirm the idea that Spa47/FliI form a homohexamer in their respective systems. Is this what you are predicting? At any rate, you can't reasonably say that there is "no evidence" (your italics) for Spa47/FliI/F1-beta homology.
Moving on to new mistakes:
quote:
Which type III pili secrete proteins from the top?
All of them. This seems like an important thing of which to be aware, given your previous dogmatic assertions about pili, doesn't it?
quote:
Can you show me in the peer reviewed literature how natural selection and random mutation built either the flagellum or the immune system? And I already showed why ExbB, or Spa47, or any other imaginary systems shouldn't have been taken into account by Dembski at all. It's irrelevant. Also as I showed in the immunity thread, there is a lot more evidence in the literature about the abrupt appearance of both these systems rather then it's Darwinian evolution.
LOL! We shouldn't re-start the immune discussion here, but I'm happy to direct people to the threads, and they can decide for themselves about the literature and Dembski, and whether or not Nelson ever even reached a stable, coherant position. The first thread and second thread.
Finally,
quote:
As I already showed, Dembski's calculation is not like assembly a plane through a tornado in a junkyard. It is precisely attempting to find a forward-chaining of events that would have selection as the driving force all the way up mount improbable.
LOL! How could Dembski's calculation even hypothetically find a "forward-chaining of events"?? He did no homology searches, no examination of analogs to see if simpler alternative functions were selectable, and did not look for which parts of the flagellum could be derived from other parts of a proto-flagellum. Here is a brief summary of the equation, tell us where "forward chaining" could possibly be "found":
quote:
Dembski tells us to multiply three partial probabilities to arrive at the probability of a "discrete combinatorial object":
pdco = porig × plocal × pconfig
plocal is the probability of a suitable collection of proteins being drawn from a set of existing proteins which includes the ones required. Dembski assumes that the proteins are randomly drawn from among the 4289 proteins coded for by E. coli's DNA, that 5 copies are needed of each of 50 different proteins (making 250 proteins altogether), and that, in each case, there are 10 different proteins that would be acceptable (i.e. there are 9 possible substitutes for the real protein. In effect, we have to make 250 draws, and at each draw we have a 500/4289 probability of picking a useful protein, giving an overall probability of (500/4289)250.
pconfig is the probability that, given the right collection of proteins, they will form a viable flagellum if arranged at random. Dembski aims to draw from a uniform probability distribution over all the possible ways of arranging the selected proteins:
Strictly speaking, the configuration probability for a discrete combinatorial object that exhibits some function is the ratio of all the ways of arranging its building blocks that preserve the function divided by all the possible ways whatsoever of arranging the building blocks. [pp. 294-295]
Since he can't calculate this directly, he uses an approximation that he calls a perturbation probability. We need not concern ourselves with the details.
porig is the probability of all the individual proteins forming by random combination of amino acids, and is again based on a perturbation probability.
source
There are a million other things wrong with this calculation but just show me the bit about looking for "forward-chaining".
Nelson writes regarding cooption:
quote:
But since only co-option and not direct evolution, can be invoked in the Darwinian pathway of the bacterial flagellum, it's nothing but random chance,
As for co-option citations, you've got to admit there are a lot of them, this isn't something that biologists came up with yesterday. I just noticed that one of my links was screwed up, here it is:
The Origin of "Information" via natural causes
Here are a few examples of co-option, sometimes even producing multiple-parts-required systems:
quote:
Here is a list, just off the top of my head. References can be found easily by searching PubMed so I trust you will not mind if for the purposes of space I just list some of the cases I know about without giving refs for all of them.
The recent-origin Drosophila genes jingwei and sdic
Nylon degradation genes (multiple independent origins)
Recent origin of antifreeze genes in fish (and plants)
Antibiotic and antipesticide genes
Here is a case of the origin of an autotransporter (AT) gene, lav by domain shuffling; I quote just a bit, the whole rather long article with all of their documenting evidence is freely online at pubmed:
quote:
A mosaic origin for lav was inferred from a G+C content transition at the boundary of its presumed passenger domain with the linker and -barrel domains. Similarly, the junction of nonhomology between lav and las coincides with the G+C transition and inferred domain boundaries of both genes. On the basis of quite different evidence (discordance between phylogenies based on individual domains), Loveless and Saier have proposed that AT proteins evolve by domain shuffling (28). A functionally novel AT can arise by linking a new passenger activity to a generic -barrel pore. Our analysis provides independent evidence for the combinatorial origin and subsequent reshuffling of at least one AT protein.
[...]
As biotype aegyptius strains and Int1 belong to different phylogenetic subgroups, it is unlikely that they inherited lav from a common ancestor. Rather, it is likely that the first H. influenzae clade to acquire the gene passed it to one or more other clades by transformation and homologous recombination within flanking DNA. Once a laterally transferred fragment has been acquired by a population of naturally transformable bacteria, it can readily be assimilated into the species by co-opting linked homologous sequence and uptake signals. Interstrain and interspecies transfer implies a shared selective advantage in certain host environments.
For the evolution of multigene systems, even those with multiple-parts -required, see:
Mortlock, R. P., editor (1992). The Evolution of Metabolic Function Boca Raton Fla., CRC Press, pp. 1-339.
Table of contents:
quote:
1) Experiments in the Evolution of Catabolic Pathways Using Modern Bacteria
2) Natural and Experimentally Evolved Pathways for the Utilization of D-Arabinose in Enteric Bacteria
3) The Development of a Catabolic Pathway for Ethylene Glycol
4) Evolution of [alpha]-Aminoadipate Pathway for the Synthesis of Lysine in Fungi
5) Common Ancestry of Escherichia coli Pyruvate Oxidase and the Acetohydroxy Acid Synthase of the Branched-Chain Amino Acid Biosynthetic Pathway
6) Evolution of Bacterial Alcohol Metabolism
7) Microbial Metabolism of Mandelate: Occurence, Function, Properties, and Evolution of Mandelate Dehydrogenases and Other Enzymes of the Mandelate Pathway
8) Evolution of the Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System
Section I: Physiologic and Organismic Considerations
Section II: Molecular Considerations
9) An Emerging Outline of the Evolutionary History of Aromatic Amino Acid Biosynthesis
10) Life Before DNA: The Origin and Evolution of Early Archean Cells
11) The Prebiotic Evolution of Complex Molecules: A Central Role for Catalyzed Cells
...and lots of articles published since 1992, e.g.:
On atrazine resistance (lots of articles here)
The degradation of pentachlorophenol by the recent assembly of a multiple-parts-required pathway, e.g.:
Copley SD. Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends Biochem Sci. 2000 Jun;25(6):261-5.
Anandarajah K, Kiefer PM Jr, Donohoe BS, Copley SD. Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol. Biochemistry. 2000 May 9;39(18):5303-11.
An even more sophisticated example is Johnson et al.'s (2002) article, "Origins of the 2,4-Dinitrotoluene Pathway". 2,4-dinitrotoluene (DNT) is another recently human-introduced compound, and yet bacteria have assembled a quite complex pathway for its degradation. The summary of the reconstructed evolution of the pathway is also quite complex (and detailed):
quote:
Inferences from the comparison of the structural genes of the 2,4-DNT pathway suggest that the pathway came together from three sources. The initial dioxygenase appears to have originated from a naphthalene degradation pathway like that of strain U2 (17). A large portion of the salicylate hydroxylase oxygenase component is retained but is not functional. The MNC monooxygenase was probably derived from a pathway for degradation of chloroaromatic compounds. The presence of the vestigial (with respect to 2,4-DNT degradation) ortho-ring fission dioxygenase is consistent with its recruitment from a pathway for chloroaromatic compounds. The true ring fission enzyme for 2,4-DNT degradation has a different origin. The sequence of DntD is quite dissimilar to all other described meta-ring fission enzymes, including those from naphthalene and chloroarene degradative pathways. The distinctive sequence of the ring cleavage enzyme reflects the substrate specificity observed for the THT oxygenase (28). The distant relationship between homogentisate dioxygenase and DntD and the association with homologs from amino acid metabolism (dntE and dntG) indicate that the lower pathway operon arose from a gene cluster for amino acid degradation.
The disparate origins of the various dnt and associated genes described in this study are consistent with the difficulties that bacteria face to achieve efficient metabolism of synthetic compounds like 2,4-DNT. The organization of the pathway genes suggests there is a progression towards a compact region en-coding the entire pathway. In that progression, remnants from assembly persist, such as the benzenetriol oxygenase (ORF3), putative maleylacetate reductase (ORF10), and putative trans-posase (ORF4). No role in nitroarene degradation is apparent for the remnants; their presence might indicate an intermediate point in the evolution of an optimal system or perhaps some of the proteins could be used in other pathways when another substrate is available.
And numerous review articles that review the topic of cooption:
Otto SP, Yong P. The evolution of gene duplicates. Adv Genet 2002;46:451-83 Related Articles, Links
Betran E, Long M. Expansion of genome coding regions by acquisition of new genes. Genetica. 2002 May;115(1):65-80.
Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. Selection in the evolution of gene duplications. Genome Biol 2002;3(2):RESEARCH0008 (free online)
Eizinger A, Jungblut B, Sommer RJ. Evolutionary change in the functional specificity of genes. Trends Genet 1999 May;15(5):197-202
Hughes A. Adaptive evolution after gene duplication. Trends Genet 2002 Sep;18(9):433
Ganfornina MD, Sanchez D. Generation of evolutionary novelty by functional shift. Bioessays. 1999 May;21(5):432-9.
Long M. Evolution of novel genes. Curr Opin Genet Dev 2001 Dec;11(6):673-80
True JR, Carroll SB. Gene Co-Option in Physiological and Morphological Evolution. Annu Rev Cell Dev Biol. 2002
It's not just some random internet poster's idea.
[ 09. May 2003, 21:31: Message edited by: yersinia ]
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Nel
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posted 10. May 2003 16:06
Nic,
By the way, I am one of the "original" people in this thread.
The Blocker et. al. paper discusses the type III secretory system. What is the % sequence similarity between FlgE and and the Type III secretory system's needle protein MxiH/PrgI? Speaking of Deja Vu, it appears that even if you want to call the needle complex of the type III secretory system - "pili", it requires 5 parts to function: MxiD, MxiG, MxiJ, MxiH and MxiI. Remove any one of these parts, you don't have a needle, it can't even secrete proteins. That is, even the needle complex of type III secretory systems are irreducibly complex!
Mol Microbiol 2001 Feb;39(3):652-63
Nic writes concerning Spa47:
quote:
so they said "hey, we bet that the structures are similar also, what happens if we plug the F1 beta subunit structure into our model" and, despite the millions of ways that a protein could not match the model, it fit quite well. this confirmed prediction strengthens the already strong homology inference based on sequence.
Nic, there is no such thing as a protein complex of Spa47. It's ficticious, imaginary, like Santa Clause, the Easter Bunny, Pumpkin Head, the Matrix, X-men, spider-man, super-man, echo and the bunnymen(actually they exist). It's made up. Of course it fits, the whole thing is imaginary. How can it be a confirmed prediction? Once the post-doc finds it (or something like it) then the prediction that the model makes can be confirmed.
quote:
LOL! We shouldn't re-start the immune discussion here, but I'm happy to direct people to the threads, and they can decide for themselves about the literature and Dembski, and whether or not Nelson ever even reached a stable, coherant position.
Nic, I would call the abrupt appearance of aquired immunity a stable coherent position.
With respect to Dembski's calculation this is how he can, more than hypothetically,do a forward-chaining, showing how a simpler flagellum could not only work, but be selectively advantageous. The Pperturb and Plocal calculations do this nicely. I think that I have shown that these homologs and analogs are quite irrelevant, and don't make up much of the chain anyway towards a flagellum. All keep doing is showing me type III secretion systems and irrelevant gram-negative specific functions that are consistent with the problems associated with getting a bacterial motor. A forward chaining of events would be showing how there are selectible functions, say, just for starters, from the M ring to the rod. There are none.
Nic writes:
quote:
There are a million other things wrong with this calculation but just show me the bit about looking for "forward-chaining".
I don't think that there is anything wrong with the calculation, although there is a lot more work to be done (which is a good thing). What the calculation does is actually attempt to show a Darwinian forward-chaining of events by doing a a backward-chaining search when it looks at the structure-function of the bacterial flagellum, to see what natural selection might have been able to select. That bit is right here:
quote:
But neither he nor anyone else in the biological community can do this. So an alternative approach is to try a backward chaining search that preserves function. What I show through my perturbation probabilities is that such searches face huge probabilistic hurdles. What this means is that if a forward chaining search succeeds, it does so as a highly specific and isolated path through genomic space. In that case the step-by-step probabilities moving forward from A_i to A_(i+1) could still be large enough not to overturn my universal probability bound. But absent a successful forward chaining search, there is no reason to think that success is even possible. Successful forward chaining assumes that a sequence like A_1 through A_n and can be made explicit. There is no evidence of this.
Response to Miller
It's kind of funny, to me, to see critics who say that it's nothing but random assembly, but they don't seem to notice that it's nothing but random assembly because natural selection can't select anything.
With respect to co-option, you cite papers that bear no relevance to the type of co-option you are invoking with the bacterial flagellum through a Darwinian means. None of these are multi-protein machines being added fortuitously through random mutation and natural selection to another multi-protein machine to make a completely new multi-protein machine.
For example, do you really think that this:
"Life Before DNA: The Origin and Evolution of Early Archean Cells"
is an example of multiple-part co-option that are "common"?
Or what about this:
"11) The Prebiotic Evolution of Complex Molecules: A Central Role for Catalyzed Cells"
Given that these chapters are probably not talking about how they have solved origin of life problems (looks more like a review), or that they have actually observed co-option of multi-part machines resulting in new machines by Darwinian natural selection, do you see how important it is for you not to hurdle citations at me? You should instead discuss them.
Here are some more examples, you cite:
Nylon degradation genes which is not an example of multi-part machines, it's just a single frameshift. Same with antifreeze and antibiotic resistence examples, simple and irrelevant.
More examples. The 2,4-DNT pathway, it doesn't seem as though this is the result of random mutation and selection. It is clear that the initial operon was from the naphthalene degradation pathway. The origin of the second operon is less clear, but seems distantly related to chlorophenol and nitrophenol degradative pathways. The origins of the remainder of the genes can only be proposed based on their nearest matches as indicated in the tables in the paper. Rearrangement and integration of segments from existing functional determinants, not through random events and selection of them, but a lot of these pathways, which also result in the lab, are due to DNA rearrangements which James Shapiro includes in Natural Genetic Engineering. This type of co-option is quite teleological.
The most ironic thing about your laz example is that it states:
quote:
As biotype aegyptius strains and Int1 belong to different phylogenetic subgroups, it is unlikely that they inherited lav from a common ancestor.
Instead what they are proposing is what looks like directed co-option through homologous recombination (which is IC) and lateral gene transfer, which is very complex mechanism in and of itself.
[ 10. May 2003, 16:35: Message edited by: Nelson_Alonso ]
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Pim van Meurs
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posted 10. May 2003 16:30
Nelson: With respect to Dembski's calculation this is how he can, more than hypothetically,do a forward-chaining, showing how a simpler flagellum could not only work, but be selectively advantageous. The Pperturb and Plocal calculations do this nicely.
At the risk of becoming repetitive i would like to repeat that Nelson continued claim about what Dembski's calculation did a forward chaining cannot be supported by either a mathematical analysis of Dembski's approach not a logical analysis of Dembski's approach.
Perhaps if Nelson can show us in detail how Dembski incorporate selection, co-option and other relevant mechanisms in his perturbation calculations then we may be able to explore his comments in more detail but so far any such claim seems imho to be erroneous and certainly not supported by the evidence.
Thus when Nelson states that: A forward chaining of events would be showing how there are selectible functions, say, just for starters, from the M ring to the rod. There are none.
Nelson at most could be stating that no forward chaining that shows a detailed selectable series has been shown which is far different from the conclusion that "there are none". In order to do the latter the ID proponent has the hard task of actually showing that there are none rather than assert. And surely the use of Pperturb and Plocal are not helpful in this endeavour.
As is argued Here for instance
quote:
. What Dembski computed instead is P(flag|dco), the probability that the flagellum could form by pure chance alone as a discrete combinatorial object.
But, of course, no biologist has ever taken the bacterial flagellum to be a discrete combinatorial object that self-assembled in the manner described by Dembski.Dembski has not defeated any actual biological proposition. He has slain nothing more than an imaginary dragon - a fictitious adversary that Dembski himself has fabricated from a stack of rhetorical straw.
and explained in more detail and quoted by Nic I believe at this location
quote:
Dembski tells us to multiply three partial probabilities to arrive at the probability of a "discrete combinatorial object":
pdco = porig ¥ plocal ¥ pconfig
*
plocal is the probability of a suitable collection of proteins being drawn from a set of existing proteins which includes the ones required. Dembski assumes that the proteins are randomly drawn from among the 4289 proteins coded for by E. coli's DNA, that 5 copies are needed of each of 50 different proteins (making 250 proteins altogether), and that, in each case, there are 10 different proteins that would be acceptable (i.e. there are 9 possible substitutes for the real protein. In effect, we have to make 250 draws, and at each draw we have a 500/4289 probability of picking a useful protein, giving an overall probability of (500/4289)250.
*
pconfig is the probability that, given the right collection of proteins, they will form a viable flagellum if arranged at random. Dembski aims to draw from a uniform probability distribution over all the possible ways of arranging the selected proteins:
Strictly speaking, the configuration probability for a discrete combinatorial object that exhibits some function is the ratio of all the ways of arranging its building blocks that preserve the function divided by all the possible ways whatsoever of arranging the building blocks. [pp. 294-295]
Since he can't calculate this directly, he uses an approximation that he calls a perturbation probability. We need not concern ourselves with the details.
*
porig is the probability of all the individual proteins forming by random combination of amino acids, and is again based on a perturbation probability.
Does Nelson agree with these definitions?
Dembski himself seems quite clear here
quote:
The idea is to take a functional system, perturb it, and determine how perturbation affects the probability of retaining function. If the probability of retaining function is high, then this would constitute evidence that a Darwinian pathway could readily lead to the system in question.
Note the use of retaining function.
Dembski continues
quote:
Miller's task, to vindicate Darwinism in regard to the flagellum, is to exhibit a forward chaining search through genomic space that issues in a genome coding for the flagellum. But neither he nor anyone else in the biological community can do this. So an alternative approach is to try a backward chaining search that preserves function.
It is clear that Dembski's calculations are not FORWARD searching and that he believes that it is up to Darwinists to provide a forward looking probability estimate to 'vindicate' Darwinism. But Dembski assumes that 1) this is the only way to vindicate Darwinism 2) that there is a need to vindicate Darwinism based on his strawman calculations of backwards probabilities that retain function.
[ 10. May 2003, 16:39: Message edited by: Pim van Meurs ]
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Nel
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posted 10. May 2003 16:41
Pim,
I noticed that you all you did was quote other people's arguments and you didn't even address why I think the calculation is a backward-chaining that a Darwinian pathway needs for each function to be selectable. Can you address this? For example, can you show me a selectable function within the subset of the type III needle comlex? What about within the subset of the export machine of the flagellum? If you can't, do you see what I mean by a backward chaining?
Also I only have time to partially respond to Rex, but if you post those definitions over at the "responses" thread I'll give you my opinion on it eventually. Suffice it to say that Porig has nothing to do with Pperturb!
[ 10. May 2003, 16:43: Message edited by: Nelson_Alonso ]
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yersinia
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posted 10. May 2003 19:29
Nelson writes,
quote:
Speaking of Deja Vu, it appears that even if you want to call the needle complex of the type III secretory system - "pili", it requires 5 parts to function: MxiD, MxiG, MxiJ, MxiH and MxiI.
The first three are parts of the base. MxiH makes up at least most of the needle. MxiI isn't mentioned in Blocker et al. 2003. Your citation (Mol Microbiol 2001 Feb;39(3):652-63), aka Blocker et al. 2001, says that MxiI "may cap at the external needle tip", but in Blocker et al. 2003 they say "No cap has been identified in any TTSS." So the picture is ambiguous regarding the presence of a cap protein (which they represent as "CaoX?" in Figure 1 of the 2003 paper, without further explanation).
quote:
Remove any one of these parts, you don't have a needle, it can't even secrete proteins. That is, even the needle complex of type III secretory systems are irreducibly complex!
The "needle complex" is the type III secretory system -- base, needle, etc. I don't deny that many parts are needed in the base in order to produce the extracellular pili/needle. But what you were arguing was that even just the extracellular pili required five parts in order to form a pili, because that was how the "simple" P pilus did it. Let's review your previous claims:
quote:
Nelson, page 2
I'm not familiar with a flagellum serving as an adhesion organelle, although I'm familiar with pili that do. With that you continue to introduce more unselectable steps, the irreducible complexity of the folding of P Pilus, not to mention the sophisticated mechanisms, donor strand exchange and donor strand complementation. The pilus itself is made up of 5 parts, PapK PapA,PapE,PapK, and PapG. Furthermore, the pilus doesn't seem to be able to secrete proteins, and the biggest difference between flagella and pili is that flagella are built from the top to the bottom, whereas pili are built from the bottom to the top.
====
Nelson p. 3
For example, you have the problem of the 6 part export machine. There is no evidence that any subset of this export machine carries out alternative function. And as I stated with the pili, With that you continue to introduce more unselectable steps, the irreducible complexity of the folding of P Pilus, not to mention the sophisticated mechanisms, donor strand exchange and donor strand complementation. The pilus itself is made up of 5 parts, PapK PapA,PapE,PapK, and PapG. Furthermore, the pilus doesn't seem to be able to secrete proteins, and the biggest difference between flagella and pili is that flagella are built from the top to the bottom, whereas pili are built from the bottom to the top.
====
Nelson, page 4:
In my view the P pilus is a talisman. And the very reason for this is the logic of the parts, there is no evidence that simple repeats would do, the paper you cite, once again relies on an imaginary system. Note, there is a logic here for the required components. In fact, PapD has no function outsie the P Pilus. Here is Mike Gene:
quote:
The 3-D structures of PapD complexed with PapG (the adhesin on the tip) and PapK (one of the adaptors) have been solved. PapD forms a boomerang-shaped protein with two immunoglobulin-like (Ig-like) domains (a structure composed of layers of antiparallel beta sheets). The N-terminal end of PapK is also an Ig-like domain, but it lacks a C-terminal beta sheet that normally contributes to the hydrophobic core of the domain. This produces a cleft that exposes the hydrophobic core, which is what makes it so sticky and prone to aggregation by itself. The chaperone PapD masks this exposed region in a most fascinating manner - it donates one of its beta strands to complete the Ig-domain in PapK (Fig 1). But it does so in an atypical fashion, as the beta strand it donates runs parallel, not antiparallel, with its neighboring strand. Thus, PapD provides at least two essential functions captured in one very elegant act - by donating one of its beta strands, PapD simultaneously prevents aggregation of PapK while providing the missing steric information for proper folding of PapK.
http://www.idthink.net
So repeated subunits would be unlikely to form a functional pilus.
Which type III pili secrete proteins from the top?...
====
Another quote from the same section Mike Gene's essay which you quoted:
quote:
The P Pilus
The P pilus is a very thin filament, whose outer diameter is only about 7 nm with a hollow core about 2 nm in diameter. The rod is thicker near the membrane and thins as it nears the tip. It functions as an attachment organelle, that is, it can reach out and anchor bacterial cells to other cells. The end of the filament has a protein that specifically binds to certain sugar molecules found on kidney cells.
Although the P pilus is among the simplest of attachment filaments, it is encoded by 11 genes. The filament itself is a heterogeneous structure. The primary subunit is PapA (it forms the thicker rod near the membrane). But as we get near the tip, we find another protein, PapE, forms the thinner filament.. At the very end, is PapG, the specific adhesin that binds to sugars on other cells. PaPG binds to PaPE through an adaptor protein, PapF. And PapE binds to PapA through another adaptor protein, PapK. Thus, the pilus itself is composed of five different proteins that are assembled in a fixed order (PapA - PapK - PapE-PapK-PapG, proximal to distal).
[bolds and italics added]
Again and again, you (citing your Mike Gene source) claimed that the extracellular pili extension is IC, was made up of five parts, etc., apparently just because one particular pili, the Type I secretion-based P pilus, does things that way. But, the Shigella Type III pilus only has one identified extracellular part, MxiH, and perhaps a cap protein (although as Type III pili continue to secrete virulence proteins and a cap might block this, maybe they don't have a cap at all).
Just like that, the "required parts" list for the extracellular extension went from 5 parts to 1-2 parts. Only now, finally, after repeating your mantra several times in the face of contradictory evidence, have you accepted on some level that the extracellular extension in fact need not be so complex. But did you forthrightly acknowledge this, and change the size of the parts list for the extracellular extension?
No, you changed the subject. You brought in the base of the needle complex, instead of just talking about the extracellular needle, which was what was being discussed regarding the P pilus:
quote:
Speaking of Deja Vu, it appears that even if you want to call the needle complex of the type III secretory system - "pili", it requires 5 parts to function: MxiD, MxiG, MxiJ, MxiH and MxiI. Remove any one of these parts, you don't have a needle, it can't even secrete proteins. That is, even the needle complex of type III secretory systems are irreducibly complex!
You need to show that the actual needle of the Shigella needle complex is made up of five parts, or else your incessantly repeated citation of the five parts that make up the extracellular extension of the P pilus has been debunked.
yersinia
PS: Plus, you will note that Shigella's Type III pili is built from the top and secretes from the top, like you repeatedly claimed (in the above-quoted material) was impossible, based on the P pilus.
[ 10. May 2003, 19:48: Message edited by: yersinia ]
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yersinia
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posted 10. May 2003 19:47
I just realized that the "CaoX?" of figure 1 in Blocker et al. 2003 is probably actually "CapX?", the p looking like an o either due to a typo or the somewhat degraded graphic in the pdf.
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yersinia
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posted 10. May 2003 20:07
quote:
Nic writes concerning Spa47:
quote:
[...] so they said "hey, we bet that the structures are similar also, what happens if we plug the F1 beta subunit structure into our model" and, despite the millions of ways that a protein could not match the model, it fit quite well. this confirmed prediction strengthens the already strong homology inference based on sequence.
[note: Nelson added a bold to the last sentence]
Nic, there is no such thing as a protein complex of Spa47. It's ficticious, imaginary, like Santa Clause, the Easter Bunny, Pumpkin Head, the Matrix, X-men, spider-man, super-man, ...
[italics original]
Your complete failure to deal with the 33% sequence identity is acknowledged.
Regarding Santa Claus et al., let me know when a hexamer model of one of them, based on a structure inferred from on sequence homology, just happens to fit snugly at the base of a Type III secretion system. It's like a puzzle piece fitting in a puzzle.
quote:
echo and the bunnymen(actually they exist).
Who?
quote:
It's made up. Of course it fits, the whole thing is imaginary. How can it be a confirmed prediction? Once the post-doc finds it (or something like it) then the prediction that the model makes can be confirmed.
Which of these is imaginary: the dimensions of the T3SS, the 33% sequence identity between Spa47 and beta-F1, the fact that the F1 subunit is a hexamer of F1-beta and its homolog, F1-alpha, or the fact that that hexamer fits at the base of the T3SS?
Are you going to stick your neck out with a better model, Nelson? Or keep talking about Santa?
yersinia
PS: Nelson writes, "Nic, I would call the abrupt appearance of aquired immunity a stable coherent position." -- LOL! You could never even decide if the "IC system" originated before the shark branch, the tetrapod branch, or the mammal branch. Similar difficulties to those you're having here...
[ 10. May 2003, 20:08: Message edited by: yersinia ]
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Pim van Meurs
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posted 10. May 2003 20:20
Nelson: I noticed that you all you did was quote other people's arguments and you didn't even address why I think the calculation is a backward-chaining that a Darwinian pathway needs for each function to be selectable.
Why should a Darwinian pathway be limited to retaining function? And as the Adami, Lenski, Pennock paper has shown forward and backward pathways me be quite different due to co-option, hitchhicking etc. I do not think that backward chaining calculations even as limited as Dembski's have any real relevance to RMNS pathway probabilities.
I also quoted other people's arguments, including Dembski's to help us determine common ground. Perhaps Nelson can tell us with what definitions he agrees and disagrees and why?
[ 10. May 2003, 20:57: Message edited by: Pim van Meurs ]
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Nel
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posted 11. May 2003 12:31
Only have time for a few comments again today (going to a big dinner).
Nic,
Calling the entire type III secretory system "pili" (or just the external needle, as you seem to be doing now) seems moot seeing as how type III secretory systems seem to have evolved from flagella. You havn't really justified why you are calling it that, but it may be irrelevant anyway. You never answered my question about the % sequence similarity between pili and the filament of flagella, but that seems moot as well, seeing as how any similarity between type III secretory systems and bacterial flagella are explained by the fact that t3ss evolved from the flagella.
Also, it doesn't make sense for you to point to a "two-part" pili when talking about the external needle, because, as you point out, the whole thing is the needle complex. It seems pretty arbitrary to call 2 parts the pilus but then continuously refer to the entire structure as "type III pili". The pili I was refering to that don't secrete any proteins are things like P-type Pili.
But if pili is the needle complex, then even this pili requires at least 5 parts to function. If you are arbitrary distingishing between the secretory system and the external needle, and that just the external are required, then you are wrong. The 3 parts at the transmembrane domain and the cytoplasmic bulb are just as required as the parts at the external needle.
You write,
quote:
But what you were arguing was that even just the extracellular pili required five parts in order to form a pili, because that was how the "simple" P pilus did it.
No I argued no such thing. I argued that the needle complex requires 5 parts to function.
As I stated:
quote:
it appears that even if you want to call the needle complex of the type III secretory system - "pili", it requires 5 parts to function: MxiD, MxiG, MxiJ, MxiH and MxiI.
Again Nic, remember that rule of thumb, if you can't quote me, then you're probably wrong about what you think I said.
In fact if you remove any one of those 5 proteins, the thing can't secrete anymore. I cited Mike Gene concerning the p Pilus, which is extremely different from type III secretory systems. The P Pilus requires 5 parts to function. You come back and say that the extracellular needle only requires 2 parts, you are wrong. Even if I removed one of the proteins that you call the "base", the thing can't secrete proteins. So regardless of how you partition the needle complex of type III secretory system, all 5 parts are required, just like the P pilus:
quote:
Mutants lacking either of these proteins formed needleless secretons and were unable to secrete Ipa proteins
This is regardless of whether Mxil acts as a cap and regardless of how you verbally partion it.
Nic also writes:
quote:
Nelson writes, "Nic, I would call the abrupt appearance of aquired immunity a stable coherent position." -- LOL! You could never even decide if the "IC system" originated before the shark branch, the tetrapod branch, or the mammal branch. Similar difficulties to those you're having here...
Actually I could decide and did so quite explicitely in that thread. The IC system, I clearly stated, showed up abruptly in sharks. The mammalian system, however, seems to have shown up just as abruptly, with it's high specificty state, and I held up the minimal function of the immune system and pattern of Vs Ds and Js as evidence. You never responded.
Now, can you show how I'm doing something "similar" in this thread?
The protein complex of spa47 is imaginary, and I've said this about 3 times now. If you don't think it's imaginary, show it to me. If you show me fig 3, then I'm afraid this is over your head. They are guessing at the structure of spa47, and thats all the paper is, a guess. It's not a "confirmed prediction", how can it be? Why would you think so? What does this have to do with whether I have a better model than they do? Are you willing to fund me?
[ 11. May 2003, 13:43: Message edited by: Nelson_Alonso ]
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yersinia
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posted 11. May 2003 16:12
Sigh, well now any detailed response really would be repeating myself.
In no particular order:
1) I quoted you extensively regarding the P pilus. The continual "five parts" refers to the extracellular pili being made of five parts. I.e.:
Type I secretion system:
P-pilus base: lotsa parts
P-pilus itself (outside the cell): 5 parts
We were thus supposed to infer:
Ancestral pre-flagellum secretion system base: lotsa parts
Ancestral pre-flagellum extension: 5 parts
However, the T3SS under discussion has:
Base: lotsa parts
Extension: 1-2 parts
...but you obfuscated to get 5 parts for the T3SS extension by including parts from the base, which is not what you were doing with the P-pilus. Your original claim was that the extracellular extension considered by itself would require 5 parts, but this is false.
2) You still haven't showed how a hexamer of Santa Claus would fit snuggly in a T3SS, like the Spa47 model complex does. You didn't identify any of my 4 points as imaginary.
3) Regarding the immune system, you just proved my point again: your "abrupt" appearance spans hundreds of millions of years. You say I never responded in the immune threads, but I am happy to let people decide that for themselves by looking at the relevant threads: immune 1, immune 2.
I think we're going in circles at this point. You can have the last word if you like.
yersinia
PS: I had better call my mother! :-)
[ 11. May 2003, 16:14: Message edited by: yersinia ]
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Nel
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posted 13. May 2003 14:44
Nic,
I find your complaint that you find the need to repeat yourself quite odd, as at times, you repeat yourself with no regard to my counterargument, and sometimes you simply drastically change your argument. Since you posted your ending summary for this thread, and recently edited previous replies, let me post a summary of what I think we have accomplished, in no particular order, but I don't want to quote too much, any doubt in what I am summarizing here, simply refer to the previous pages in this thread.
There is no such thing as a simpler organism that doesn't require a topoisomerase. E. coli, a gram-positive bacteria (there is evidence that gram-positives are basal), requires a topoisomerase in order to replicate it's DNA.
With respect to bacterial flagella, an entirely different topic, you attempted to show evidence of homologous structures that may point to a simpler precursor of flagella, you wrote:
quote:
the homology between FliI and F1F0 ATPase
But not only does the Fo component of the F-ATP synthase have nothing to do with FliI, but the F1 component is not just composed of alpha and beta, it's also composed of gamma, epsilon, and delta, not only that, but the entire F1Fo ATP synthase is irreducibly complex in that it requires 8 parts to function.
quote:
IIRC there's another ExbBD pair homolog that acts on something else. And motAB act on fliG in a similar fashion.
With respect to ExbB/D only MotA is homologous to ExbB (and the homology, in my opinion is not very impressive.) You then stated that the model for ExbB/D is simpler then the electrostatic model for the bacterial motor that Mike mentions in his essays at http://www.idthink.net. However, I showed that the model for both systems still requires quite a bit of specificity between the rotor and the stator, regardless of where the proton-binding site resides. Thus the complexity of each is still a big problem for any stochastic process to overcome. Furthermore, the function of ExbB/D/Ton is restricted to gram-negatives, MotA is much more widely distributed. You had asserted that both were equally widely distributed. You attempted to show this by linking to a tree, but that tree was based on a hypothetical protein, which is almost as irrelevant as your Spa47 assertion. Speaking of which, you wrote:
quote:
the assumption of homology seems to be confirmed by the fact that the resulting protein complex fits well into their model of T3SS structure.
But there is no such thing as a "protein complex" of Spa47. The protein complex proposed by the model is imaginary, so of course the imaginary protein complex fit well with their model, they made it up. You said that I didn't answer your question concerning the homology that Spa47 has with the b subunit of the F-ATP synthase, but in fact I did when I mentioned that fliI was only homologous to the beta subunit of the F-ATP synthase and not to the whole structure. So what do you mean by having to repeat yourself?
Well you try to tell me in your summary:
quote:
You still haven't showed how a hexamer of Santa Claus would fit snuggly in a T3SS, like the Spa47 model complex does. You didn't identify any of my 4 points as imaginary.
So why do I have to make up a protein complex of my own to show that the protein complex made up by the authors is imaginary? And as for your 4 points you write:
quote:
the dimensions of the T3SS, the 33% sequence identity between Spa47 and beta-F1, the fact that the F1 subunit is a hexamer of F1-beta and its homolog, F1-alpha, or the fact that that hexamer fits at the base of the T3SS?
Are you saying that the beta subunit fits at the base of the T3SS? Can you show me this data from the paper? But thats irrelevant. Since I heavily discuss the dimensions of the T3SS, then of course thats not imaginary. Since I discussed the homology as I mentioned above, thats not imaginary. That F1-beta might fit at the base of the Type III secretory system seems to also be imaginary.
What I am sure of, is that the protein complex that you referred to as a "confirmed prediction" is completely imaginary. It doesn't exist. And this is regardless of whether I can come up with a better model of Spa47. How you think that this is a confirmed prediction is beyond me.
You often interchange, for no particular reason (other than to support whatever particular point you have conjured up), the terms bacterial flagella, pili, and type III secretory system, which can be very misleading. You even do this within the type III secretory system, arbitrary calling only a small portion of it "pili". However, each of these three systems are very different from eachother, not only that, the type III secretory system most likely evolved from bacterial flagella, furthermore, both secretion systems and pili seem to require quite a few parts to function.
You write:
quote:
but you obfuscated to get 5 parts for the T3SS extension by including parts from the base, which is not what you were doing with the P-pilus. Your original claim was that the extracellular extension considered by itself would require 5 parts, but this is false.
However, this is simply false and the peer reviewed paper I referenced shows how you are wrong.
I stated:
quote:
it appears that even if you want to call the needle complex of the type III secretory system - "pili", it requires 5 parts to function: MxiD, MxiG, MxiJ, MxiH and MxiI.
This is not an obfusucation. What does the paper call the needle complex?
quote:
Electron microscopy (EM) indicates that the TTSSs of Shigella flexneri are composed of: (1) an external needle; (2) a transmembrane domain; and (3) a cytoplasmic bulb. EM analysis of purified and negatively stained parts 1, 2 and a portion of 3 of the TTSS, together termed the 'needle complex' (NC),
What I clearly stated was that the needle complex requires 5 parts and that there is absolutely no reason to regard the external needle as a "2-part system" when it is actually a "5-part system":
quote:
Five major [needle complex] components, MxiD, MxiG, MxiJ, MxiH and Mxil, were identified by N-terminal sequencing, MxiG and MxiJ are predicted to be inner membrane proteins and presumably form the base. MxiD is predicted to be an outer membrane protein and to form the outer ring. MxiH and Mxil are small hydrophilic proteins. Mutants lacking either of these proteins formed needleless secretons and were unable to secrete Ipa proteins
Type III systems require at least 5 parts which includes the 2 parts you arbitrary call pili.
With regard to the immune system, which is yet another topic entirely, you say that my assertion of abrupt appearance for aquired immunity spans hundreds of millions of years, and yet we don't see any acquired immunity nor any of it's required components until we see sharks. If you are referring to the mammalian system, of course what I said was abrupt here was the high specificity requirement and the Wu-Kabat pattern that seems paradoxical if the mammalian pattern arose step by step. Intelligently Designing Immunity
[ 16. May 2003, 14:40: Message edited by: Nelson_Alonso ]
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David L. Rice III
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posted 23. May 2003 12:32
This is to Nelson and Yersinia:
First, Yersinia you have done an excellent job of reviewing the literature on the questions I posed on the topo II enzyme. However I'm still not getting the proposition of living systems that don't require topo II. In the first place this is a hypothesis. If your hypothesis is true and there actually is a living system out there that can replicate without the topo II then that settles it. But all of the conditions that I know of for life require the enzyme NOT BECAUSE THE ENZYME ITSELF EXHIBITS IRREDUCIBLE COMPLEXITY but because the enzyme inhabits a functional space that must be filled for replication to proceed. Don't forget about the organism. It has to replicate.
Nelson's comments were good too and they also reveal some substantial questions that need to be answered. I'm more inclined to agree with Nelson simply because the verdict is not in for Yersinia's hypothesized replicator that does not need the topo II. Thank you guys!
David
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yersinia
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posted 12. June 2003 03:58
Just a short note, in the unlikely event that others were following the details of this thread. Earlier in this thread Nelson expressed severe doubts about Blocker et al's (2003) model of Spa47/FliI as a hexamer, corresponding to the hexamer shape of the F1 subunit of F1F0-ATPase:
quote:
Nic, there is no such thing as a protein complex of Spa47. It's ficticious, imaginary, like Santa Clause, the Easter Bunny, Pumpkin Head, the Matrix, X-men, spider-man, super-man, echo and the bunnymen(actually they exist). It's made up. Of course it fits, the whole thing is imaginary. How can it be a confirmed prediction? Once the post-doc finds it (or something like it) then the prediction that the model makes can be confirmed.
(this was important as a hexamer of Spa47/FliI would be yet another similarity between these ATPases (Spa47 in a T3SS, FliI in a flagellum) and the F1 ATPase subunit)
Anyhow, I just came across a brand-new article which would appear to empirically confirm the hexamer model:
quote:
Mol Microbiol. 2003 Jun;48(5):1349-55.
Oligomerization and activation of the FliI ATPase central to bacterial flagellum assembly.
Claret L, Calder SR, Higgins M, Hughes C.
Cambridge University Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK.
FliI is the peripheral membrane ATPase pivotal to the type III protein export mechanism underlying the assembly of the bacterial flagellum. Gel filtration and multiangle light scattering showed that purified soluble native FliI protein was in a monomeric state but, in the presence of ATP, FliI showed a propensity to oligomerize. Electron microscopy revealed that FliI assembles to a ring structure, the yield of which was increased by the presence of a non-hydrolysable ATP analogue. Single particle analysis of the resulting electron micrograph images, to which no symmetry was applied, showed that the FliI ring structure has sixfold symmetry and an external diameter of approximately 10 nm. The oligomeric ring has a central cavity of 2.5-3.0 nm, which is comparable to the known diameter of the flagellar export channel into which export substrates feed. Enzymatic activity of the FliI ATPase showed positive co-operativity, establishing that oligomerization and enzyme activity are coupled. Escherichia coli phospholipids increased enzyme co-operativity, and in vitro cross-linking demonstrated that they promoted FliI multimerization. The data reveal central facets of the structure and action of the flagellar assembly ATPase and, by extension, the homologous ATPases of virulence-related type III export systems.
Here is their graphic:
http://groups.yahoo.com/group/aefiles/files/FliI_ATPase_image.gif
From their conclusion:
quote:
A previous report has indicated that His-tagged FliI can exist in monomeric form (Minamino and Macnab, 2000a), and our gel filtration and multiangle light scattering analysis of the native soluble enzyme confirmed this earlier work; all FliI was recovered as the monomeric form. However, when we incubated the enzyme with its substrate ATP, it was evident that FliI has a tendency to oligomerize. Electron microscopy and two-dimensional image processing of FliI stabilized by the non-hydrolysable ATP analogue AMP-PNP revealed that the ATPase assembles to ring structures that exhibit a strong sixfold symmetry around a central cavity, which may represent a central channel. The data, achieved without the application of any symmetry, indicate that FliI is possibly a homohexamer. Such a structure would be comparable to that of the ATPases of the distinct type IV protein export pathway in Helicobacter pylori and E. coli, ascertained by comparable means (Krause et al., 2000a,b). Our data also revealed that ATPase activity of FliI displays positive co–operativity, indicating interactions between subunits, i.e. FliI oligomerization is coupled to activation of the enzyme.
[ 12. June 2003, 03:59: Message edited by: yersinia ]
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Mike Gene
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posted 12. June 2003 23:11
Since I violated my self-imposed 50 rule on another thread, why not lose control. ![[Smile]](smile.gif)
Excellent find by Yersinia, as it strengthens the plausibility of common design. And I’m kicking myself for not making a public ID prediction about this stuff. Let me explain.
First, we can drop the Spa47/FliI similarity, as it’s pretty clear the TTSS evolved from the flagellum. Standard descent explains this similarity (but not in a way that helps Yersinia’s speculations about flagellar origins).
The truly interesting stuff comes from the FliI and F ATPase subunit comparison. The essence of their similarity revolves around the ATP-binding domain. At first glance, this doesn’t seem too useful in distinguishing between common design and common descent, as one might expect ATP-binding motifs to be reused in different contexts from either perspective. But what seemed to indicate a hodgepodge use of this motif was that it appeared to be used as a monomer in the flagella. There didn’t seem to be any type of design logic behind its reuse.
Looking back, it should be clear now. First, ATP binding on the F-ATPase takes place at the interface between the two subunits. Having fliI work as a monomer spoke to a jury-rigged solution. Second, and more importantly, another bacterial protein complex shares the same ATP-binding architecture – rho transcription terminators. And what’s more, they form homohexamers, where three of the six sites are weak-binders and three are strong. To this structure is attached an N-terminal RNA binding domain and a C-terminal region that mediates communication between the RNA and ATP binding domains. This should have led me to predict that FliI would likewise draw from this design logic, as we now have a conceptual tie between all three different ATPases – they form rings where the ATP binding/hydrolysis is associated with work within the ring. Actually, the later part holds true for the F-ATPases and rho, so consider it a design prediction for FliI. ![[Wink]](wink.gif)
Heck, I’m even leaning toward a spinning wheel model for all three.
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