"In order to carry out this diabolical work, bacteria must not only produce the protein toxins that bring about the demise of their hosts, but they must efficiently inject them across the cell membranes and into the cells of their hosts. They do this by means of any number of specialized protein secretory systems. One, known as the type III secretory system (TTSS), allows gram negative bacteria to translocate proteins directly into the cytoplasm of a host cell (Heuck 1998). The proteins transferred through the TTSS include a variety of truly dangerous molecules, some of which are known as "virulence factors," and are directly responsible for the pathogenic activity of some of the most deadly bacteria in existence (Büttner and Bonas 2002; Heuck 1998).
At first glance, the existence of the TTSS, a nasty little device that allows bacteria to inject these toxins through the cell membranes of its unsuspecting hosts, would seem to have little to do with the flagellum. However, molecular studies of proteins in the TTSS have revealed a surprising fact – the proteins of the TTSS are directly homologous to the proteins in the basal portion of the bacterial flagellum. As figure 2 (Heuck 1998) shows, these homologies extend to a cluster of closely-associated proteins found in both of these molecular "machines." On the basis of these homologies, McNab (McNab 1999) has argued that the flagellum itself should be regarded as a type III secretory system. Extending such studies with a detailed comparison of the proteins associated with both systems, Aizawa has seconded this suggestion, noting that the two systems "consist of homologous component proteins with common physico-chemical properties" (Aizawa 2001, 163). It is now clear, therefore, that a smaller subset of the full complement of proteins in the flagellum makes up the functional transmembrane portion of the TTSS.
Stated directly, the TTSS does its dirty work using a handful of proteins from the base of the flagellum. From the evolutionary point of view, this relationship is hardly surprising. In fact, it's to be expected that the opportunism of evolutionary processes would mix and match proteins to produce new and novel functions. According to the doctrine of irreducible complexity, however, this should not be possible. If the flagellum is indeed irreducibly complex, then removing just one part, let alone 10 or 15, should render what remains "by definition nonfunctional." Yet the TTSS is indeed fully-functional, even though it is missing most of the parts of the flagellum. The TTSS may be bad news for us, but for the bacteria that possess it, it is a truly valuable biochemical machine.
The very existence of the Type III Secretory System shows that the bacterial flagellum is not irreducibly complex. It also demonstrates, more generally, that the claim of "irreducible complexity" is scientifically meaningless, constructed as it is upon the flimsiest of foundations – the assertion that because science has not yet found selectable functions for the components of a certain structure, it never will. In the final analysis, as the claims of intelligent design fall by the wayside, its advocates are left with a single, remaining tool with which to battle against the rising tide of scientific evidence. That tool may be effective in some circles, of course, but the scientific community will be quick to recognize it for what it really is – the classic argument from ignorance, dressed up in the shiny cloth of biochemistry and information theory."
------------------ Occam's razor is not for shaving with.
I'll try to target this means to the end of thread directly next time, meanwhile this was my answer on another board (NO ANSWERS IN GENESIS)
As for the standard natural biology I was refering to COLLEGE ZOOLOGY by Robert Hegner ~1931p69 "Changes such as these, that are inherited, are required for the evolution of new species, and it seems probable that the investigators who have observed heritably diverse pure lines areise from a single pure line have actually followed a process that is in part responsible fro the origin of species." And I, BSM, was on my way to show you the visualization that may even help to determine if there is more friction on the inside or outside memebrane of bacteria flagella but instead you chose to think you could not understand what I said.
Point start(see Wolfram NewKIndof Sciencep536to537only) ONe- "But so far as one can tell the details of thos do not work out" BECAUSE THERE IS A DIFFERNCE A LA HUXELY ETC GOULD ETC ETC OF PRE-MITOTIC, MITOTIC AND MEIOTIC (THE MATERIALISM FOR ANY NATURALISM INVOLVED)(UNLESS MY SPECULATION THAT WOULD BE IN THIS THREAD OTHER STUFF OF MINE AS PER MINED OTHER DUMP ETC ETC ETC) tWO- "But why exactly does matter have to be introduced explicity at all? BECAUSE THE BIOLOGY OF SPECIAL RELATIVITY INTERPRETS UP TO CENTRIFUGAL FORCE SO! three- "everything we call matter is actually made up of pure gravitational energy or of something" (me taking out comma) "like gravitational waves" This did not have all biology in mind while it could have all chemistry of the older Roland Hoffman type (Chemistry Imagined Reflections on Science (which may or may not have included a conversation I had with him or else he like Boyd talks to all students regardless of interest alike) where there is a continual thought to search the literature never finding the holy grail. The issue is how chemically the ionic vs temperature template topology to be coordinated (in terms of figures of centrifugality which are centripetal actually)(sorry the mistake in the second denotation of "centrifugal" should have been word 'centripetal' my mind had already left the board). I had this idea of gravity waves in high school. That is what I had been known by my brothers both physicists for. But as Wolfram points in that this reasoninig never worked in and one had to have matter already in but because the inorganic environs of bacteria have more information contnent than viruses if... more Brad stuff... (it may be that only viruses and gravity can be part of bent space...)
Regardless this IS clear. I struggle only to express my self from this say Einstein "The principle of inertia, in particular, seems to compel us to ascribe physically objective protperties to the space-time continuum. I work with accelerations both in reprodution and locomotion of protozoans into a insecet food web GIVEN a Lotka-Voterra of bacteria-virus man-made stable (by hygiene) then this compulsion depends in part not only on physics 5th force but also on Mendel arthmetic no matter the mechanism.
That is why there is NOT MECANISM in evolution thinking only MECHANICAL thought. Qutam theory makes this actually easier to understand but Hoffman refused to talk with me until I took a course in QM. WOlfram does not go this far he only speaks oF Quantum Field Theory for as Eisntein said in "What is the theory of relativty", "The special theory of relativity...pointed beyond itself, however." But not the general one. The proportionality from which the Albert spoke need not be the same for an Lotka-Volterra of fox and hares compared evolutionarily with bacteria-virus.
I am no master. Yoda is not either. The force need not be with the Carteisnism EITHER for a techonology of thelogic involved etc-- stuff not put in.
The basic prediction the article makes (correct me if I am wrong) is that TTSS is homologous to the bacterial flagella, at the molecular level, and thus the flagella evolved from TTSS and itself is a "type of TTSS"(Mcnab).
Now this is nothing but the modified version of the EFM (Export-Filament-Motility) hypothesis, already once mentioned by Miller. The flaw(s) in this hypothesis is excellently summarised by Gene in his response to Miller. He outlines a point that is very vital to be taken in consideration.
Is there any reason to think the type III export system, complete with the ancestors of flhA, flhB, fliR, fliQ, fliP, fliI and others, existed as a "cooptable part." Thus far, the answer is no, as there are good reasons to think the type III system evolved from pre-existing flagella.
The evidence for the above claim:
1. The bacterial flagellum is found in both mesophilic and thermophilic bacteria, gram-positive and gram-negative, high GC and low GC content bacteria, and spirochetes. Type III systems seem to be restricted to a few gram-negative bacteria. That is, if we look at the sequenced genomes from the various groups cited above, we can find the genes for the bacterial flagellum but not the type III system genes.
2. Independent evidence suggests the type III system is recent. It is not only restricted to gram-negative bacteria, but to animal and plant pathogens. In fact, the function of the system depends on intimate contact with these multicellular organisms. This all indicates this system arose after plants and animals appeared. In fact, the type III genes of plant pathogens are more similar to their own flagellar genes than the type III genes of animal pathogens. This has led some to propose that the type III system arose in plant pathogens and then spread to animal pathogens by horizontal transfer.
3. It's much easier to envision the evolution of the type III system from flagella than vice versa. For starters, evidence has surfaced that the basal body of the flagellum already works to secrete proteins other than the flagellar proteins, including virulence factors. Thus, the basal body is already poised to evolve into a type III system from the start. Evolution apparently would only have to duplicate and tweak the type III virulence protein secretion activity already existing in flagella. . In my opinion, this view is far more parsimonious than to propose that something like the type III system evolved long ago, was lost by all bacteria but gram-negative animal/plant pathogens and then was used to evolve the flagellum so that horizontal transfer could spread flagella far and wide (despite the lack of evidence for such transfer).
Thus, it should not be surprising that the scientific opinion has been converging on the notion that the export machinery evolved from the flagellar machinery. (5,7)
Is there any evidence that supports transporting this system, or something like it, back in time? The type III system is one of at least four different bacterial protein transport systems. And it appears to be the most complex of the bunch. The key here is that the type III/flagellar cytoplasmic export system does not show clear homology with any of these other transport systems. But we also know that evolution builds on and modifies what already exists rather than create de novo. Thus, if these other transport systems were already in place (and they probably were), why didn't evolution simply build on one of the simpler versions rather than create a whole new method of protein secretion de novo? The type III-from-flagellum scenario better fits with what we know about evolution - that it uses what already exists rather than inventing de novo. Thus, not only is there no evidence to support putting this transporter (or something closely homologous) back in pre-flagella days, there is reason to think it wouldn't be there.
Another fundamental problem with the first step of the EFM hypothesis is that it assumes IC to explain IC. Consider that the flagellum is composed of about 20 different proteins. Of those twenty, ten are homologous to the type III export machinery. Thus, this hypothesis begins its attempt to explain the origin of a 20-part IC system by assuming the existence of half of it (10 parts).
Let's briefly consider the 10 parts of the type III export machinery, where I'll use the flagellar gene names. There is FliI, an ATPase that is anchored to cytoplasmic face of the inner membrane. It may provide energy for the synthesis of the export machinery or transport of secreted proteins. It is thought to capture proteins in the cytoplasm for transfer to the secretory apparatus. There are several proteins that span the inner membrane and probably make up the protein conducting channel, including FlhA, FliP, FliQ, FliR, and FlhB. There is FliF, which in flagella, form the MS ring. And there is FliN and FliG, which in flagella, make up the C ring (located beneath the MS ring). Finally, there is FliH, with an unknown function.
Whether all 10 proteins are required for type III transport is unknown, but it appears most are essential:
quote:Several proteins essential to secretion including LcrD, YscD, R, S, T, and U, are known or predicted to reside in the inner membrane (10,12,48-50). At the outer membrane, only one protein, YscC (48), and two lipoproteins, YscJ and VirG (51,52), appear essential for proper secretion. The roles and subcellular locations are not known for several more essential proteins, YscE, F, G, I, K, and L (9,48,51). How all of these proteins interact with one another to form the secretion apparatus is not yet understood. It is clear, however, that correct assembly of the apparatus is required not only for secretion, but also for normal synthesis of effector molecules (47,48). If one component of the export machinery is missing, production of the effector molecules is altered. 
There is yet another interesting aspect to all this. Since evolving from some flagellum, the type III transport system appears to have lost its ability to engage in rotary transport. The flagellar motor is composed of five proteins: MotA, MotB, FliG, FliN, and FliM. We'll discuss this more below, but right now it is worth pointing out that the type III systems have no homologs for MotA, MotB, or FliM. The Mot proteins are essential components of the motor, as they are membrane proteins that fulfill two functions: they transport ions to provide the energy for rotation and serve as the stator against which the rotor (FliG, FliN, FliM) moves. What's more, the type III rotor components have significantly changed. The type III homolog of FliN shares sequence similarity only with in its C-terminal 80 amino acids. And the sequence similarity between the FliG homologs are almost non-existent. Furthermore, there have been significant changes in FliF. FliF forms the MS ring (the "mounting plate"), which is associated with and above the C-ring composed of FliG, M, and N. FliF in flagella is composed of 500+ amino acids, but in the type III homolog, both the C- and N-terminal domains thought to be involved in forming the MS ring are missing. All that is left in common between them is a central region of about 90 amino acids.
Here we find another reason to recognize the significance of the flagellum-to-type III system evolution. Type III systems have apparently lost their ability to rotate. Thus, we can't think of type III systems as something pre-adapted to rotate, as all the rotary information has been lost. To argue that the type III system could reacquire the ability to rotate, as the flagellum does, is to essentially violate Dollo's Law, which states: "evolutionary change manifested at any level higher than the genetic is irreversible, and that anatomical structures or functions once lost cannot be regained."  Yet by proposing that the flagellum once existed as a type III system and later acquired the ability to rotate is not hardly any different that proposing type III systems could reacquire the ability to rotate and violate Dollo's Law.
A Summary of the problems of Miller's hyothesis:
There are good design reasons for building the flagellum around a transport system and attempts to assign historical significance to this are completely unsupported.
We have the ability to imagine simpler initial states for designed systems where our imagination does not reflect reality. Thus, the mere ability to imagine simpler states is rather meaningless.
The data suggest that not any transporter is good enough for evolving something like the bacterial flagellum. This is important because the EFM never addresses the origin of the transporter itself. It seems quite plausible that selection pressures for evolving a good transporter would steer the system away from being preadapted to form something like the flagellum (which is why bacterial flagella are monophyletic).
There is no evidence that anything like the type III system predated the flagellum. The type III system itself most likely evolved from a flagellum.
Because it is known that evolution borrows, rather than invents de novo, proposing the de novo evolution of a type III transport system among bacteria that already had several transport systems in place makes little sense.
The type III system itself is IC, perhaps with ten IC components. No attempt is made to explain its flagella-independent origin.
In light of the evolution of the type III system, proposing a type III-to-flagellum evolution appears to violate Dollo's Law.
(5)Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH Jr. 2000. Phylogenetic analyses of the constituents of Type III protein secretion systems. J Mol Microbiol Biotechnol Apr;2(2):125-44.
I still do not know if it is necessary for me to go any deeper in the primary literature. I read a paper in NATURE about OCt 17, I think that spoke of ion channels in bacteria of the same "strong conservation" genetically (by base pair analysis) with ones found in NEURONS. Now we all know that bacteria are not neurons unless Margulis is going to tell me otherwise etc so re-use of systems IS an issue for me becuause while the science literature permits this to be writ up with 'phlylogenic' intentionality I have begun to make a circle around this kind of thinking that could show that it in physico-chemistry has nothing to with common or not descent. ( I have already said somewhere else on this board that I thought that NEURONS have been 'turned' in the imagination of scientists 90degrees or more from the representation that posses in the skin) and this article only confirms what I think the evidence will be on my visualzation of biology.
I wanted to explain how the opposite directums of motion (baceterial cell turning vs appendge motion) could be A MECAHNICAL RESULT of bioentropisms but I am far from having the statistical mechincis of this worked in(out of Wolfram's "science"etc) such that If this workd I would have predicted which "ring" has more of the friction measurable in it. ( I am still wondering if this is a problem like Maxwell's on magentic inertia that science did not have even the equimpement to test until the 60s or not). But since I have not clicked on the link yet in this thread I do not know if my interest is commensurate with your "getting" what I say. Perhaps I move to another loom herein.
I can guarentee you that it is not a physico-chemistry answer.
I have worked on voltage gated potasium channels and I can assure you that the origin of similarity between human neuronal potasium channels and bacterial potasium channels is either evolution or creaiton. It is not physico-chemical.
There is a huge variety of distinct families of channels but each family is undoubtedly related within itself by E or C history. They have incredibly conserved sequences that are inconceivable to imagine arriving convergently or by absolute necessity. They have the same pore helices and voltage sensing helices. God or evolution has clearly reused the basic deisgn.
But the biochemical funciton is essentially identical. The voltage gated channels in bacteria act as voltage gated channels. There are more reasons to have channles than being a neuron. Every cell in your body has ion channels in it to maintain ion concentrations.
[This message has been edited by Tranquility Base, 12-10-2002]
I have to bother with this beacuse I am not sure I am thinking about adapations on the base of free path length variance or if you maybe did not catch my intro to a my own concept of bioentropisms.
What I am visualizing is a sphere that would underlay any network notion of space that Wolfram wishes to devolve (into you c or e?)that would be where PERVERSIONS which by Gibbs are turnings symmetrical but since I need to first make sure only symmetry phyiscs is what I would have isolated I can not be sure as to physico-chemical or chemical-physico.
I am not saying the that "chanels" per say are evo or creatons etc but I am trying to keep solid the manipulation of any FARADY lines of force in the physical lines of force that you might be correct that I abadon since physicists have said thinking along these lines PHYSICALY made less than more sense. But I also know that reasoning from the limited matter that physics and chemistry deals with IS NOT THE SAME as thinking of nuclei and mitosis etc. I do need a materialism that is specific to reproduction even if this IS NOT (necessarily) the kind Wolfram visualized. What i gleaned from my grandfathers papers on classic genetics was about temperature and the turning of associationsand dissociations of ions on this sphere (the size of which if true would be between millions and billions)& I think this notion of science in terms of temperature templates CONSTRAINTIHNG this underlying gentetically expressed channelling of ions and all this is clearly readable by me with marginal notes of Fourier, Lavoiser and Faraday coming up to date.
The reason I do not consider this of phylogenetic value is that this is the point or sphere from which I can fluidly explain why I differ from Dobshansky in visualizing the gene pool. It would be a "vapor" rather. The issue of logic is indeed materializing here but one needs the way out perspective of Wolfram to begin to grasp the more conservative position I expouse. I think that Mayr's notion of proximate and ulitmate was just an excuse to cover up his reluctance and you could include just about every biologist at Cornell at this,to enter the kind of deterimiate thoughts I have WITHOUT being a dialectica biologist of determist interpretor of the IQ controversy.
I dont doubt you know more of the mole bio on this than me. I still am from the "old" school that is trying to talk or in my case not talk of PHENOTYPES. I did not know I had to already be speaking FROM einsteins experience of geometry and I fully expected natural history to not really be but history.
Again, that would be saying the same thing but on the class and not individual level. There is philosophy for this but it gets tiring to remeber it all.
It may be that words such eisode and exode (not anode and cathode) that Faraday was toying with are more important on the base you mention of common volatge-gated materiality but by then I would have as well explain an idea I have for using biology to extend ANALYTICAL CHEM for which I tried to not get into the psychology of all this yet remain purerely in the physical not mental area.
1) The flagellum descended from a basically modern type III secretion system
2) The existence of the T3SS greatly weakens the argument for ID based on the theoretical ICness of the flagellum, and makes the hypothesis of an ancestral T3SS-like system ancestral to the flagellum a plausible idea (strengthened by various other points listed in the article).
#1 is not supported by available data, #2 is, and they should not be confused although IDists usually argue against point #1 while failing to deal with point #2.
1) The flagellum descended from a basically modern type III secretion system [/QUOTE][/B] Well, your "1)" made me think about some Cornell biologists who talk about a "circulation between the endoplas and goglgis" not any creationism as I was about to show how (trying to imagine what you materially denote by "secrection" but it seems that you say not to even bother with this thought which for me is MORE physical having to do with erogicity and the difference between weight and visocosity both in and out the (any)cell which IS NOT the issue I raise as to calculating which bacteria membrane has the most friction. [QUOTE][B] 2) The existence of the T3SS greatly weakens the argument for ID based on the theoretical ICness of the flagellum, and makes the hypothesis of an ancestral T3SS-like system ancestral to the flagellum a plausible idea (strengthened by various other points listed in the article).[/QUOTE][/B] So I guess if I am "reading" you correctly, you are saying that by classing DNA base pairs IN GROUP that this in and of it self argues against some form of Dembski or Johnson supported Intelligent Design for any Paley? The problem I have is that we do not have a good idea BIOLOGICALLY of "homology" for the functioning physiology we do know let alone in that area where molecular motion and motion of molecules is part and parcel so I see no way to discrimate where GOD is or Was Not. This problem like the one Humphries experiences in Cosmology seems to be the assumption which the common descent seems to be implying (correct me if I read something into the words you did not say or imply or induce etc) a common homogenity of the natrualism for a variable material involved. If that IS what you think then you could know my position is that the homogenity and any future on-going regime of "ideology" used to continue funding this work is only about the nano to millions of meter divisions and does not cover everthing material let alone everything social. My work does not give the final psychological twist however. I was only looking for a principle vision from which to deduce correct biology. That was lacking execpt the mecahincal thought that gene frequencies change was sufficent. I did not think this when I first found Rene Thom's 1975 book on Catastrophe Theory and I continue to think this way since ~1982 I may have thought differetly a bit beofre but then again I also did not think my idea of gravity waves and the mind could acutally only be about the body. I did not and never have been able to support some notion of a dualism of mind and body. My brain and me are one and the same but I KNOW I am not a baceteria however I think Medicine is useless if it can only prescibe ANTI-bacterials and cut tissue. I do not have a better program for "disease" but I have some priciples that might devolve such. [B][QUOTE] #1 is not supported by available data, #2 is, and they should not be confused although IDists usually argue against point #1 while failing to deal with point #2.[/B][/QUOTE]
What I am indicating is that by using science to show where we are going to explore rather than where nature may have already come from is a better distribution of financial resources and that this may mean that pragmatically one can not afford evolution thinking and insistence on all teaching going into the CONCEPT of a common lineage because this is MORE mypoic requireing all the thinking to fall into one line biologically which with computation in parralell we may man-made do otherwise and I think indeed this is WISE.
I am sorry my interest as TB warned me is not specifically with your use of the same evidence. i DO NOT know what I am doing diffently that prevents me from previewing correctly.