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Spin Flagellum, Spin

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This month in Current Biology Vol 18 No 16, Howard C. Berg writes a “Quick guide” to the Bacterial Flagellar motor. In it he outlines what is currently known of these amazing structures.

“The flagellar motor is a remarkably small rotary electric motor that includes a stator, drive shaft, bushings, mounting plate, and a switch complex. The motors are powered by protons or sodium ions, that flow through channels from the outside to the inside of the cell. Depending upon the configuration, the rod, hook, and filament are driven clock wise or counter clock wise. Other components include a rod cap, discarded upon rod completion, hook cap, discarded upon hook completion, hook-length control protein, and a factor that blocks late-gene expression.”

As “nothing in biology makes sense except in the light of evolution”, Berg concludes with a few brief comments.

“Is the flagellar motor unique? Yes and no. As a device that powers flagellar rotation, yes. As a device composed of rings, rods, and external filaments, no. There is a homologous structure, called the needle structure, assembled by the same kind of transport apparatus, used by pathogenic species (such as Salmonella) to inject virulence factors into eukaryotic cells. Some argue that the flagellar rotary motor evolved from the needle structure, but it was probably the other way around, since flagellated bacteria existed long before their eukaryotic targets. Perhaps they evolved from a common ancestor. What was the rotary motor doing before the helical propeller was invented, if indeed that was the order of events? Serving as a secretory apparatus that acquired the ability to spin? Packaging polynucleic acids into virus heads? Food for thought.”

Recently Nature Reviews Microbiology volume 6 June 2008 p 455 has a review of the regulation of Flagellar construction, where the authors say “The bacterial flagellum, one of the most remarkable structures in nature: a complex self-assembling nanomachine” where “dozens of proteins, many of which have intrinsic self-assembly properties, need to come together in an ordered assembly process to complete these molecular nanomachines.”

These authors also need to remind us of the inescapable compelling logic of evolutionary biology:

“Finally, it seems that the bacterial flagellum is a structure of great complexity. In an attempt to understand why, it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system. We only need to be reminded that evolution demands that changes occur on the existing structure — no starting from scratch. It is fair to say that we are at long last making a dent in our understanding of how this evolutionary process might have occurred for the reducibly complex bacterial flagellum and the beautiful result it has produced.”

The flagellum is obviously too complex to have been designed. It must have evolved. The logic is inescapable.

Comments
successive generations of microorganisms developed portions of the flagellar motor piece-by-piece according to some pre-existing non-NDE plan, but the entire structure was not operational all at once
That "might" be viable if there exists a realistic indirect pathway. A recent conversation on UD where the hypothetical indirect pathway of the bacterial flagellum is discussed: https://uncommondescent.com/intelligent-design/chance-law-agency-or-other/#comment-289741 The end of this conversation puts the problem in perspective: https://uncommondescent.com/intelligent-design/chance-law-agency-or-other/#comment-290187 Other major points: https://uncommondescent.com/evolution/behes-multiple-mutations-needed-for-e-coli/#comment-290408 https://uncommondescent.com/intelligent-design/chance-law-agency-or-other/#comment-289702 https://uncommondescent.com/philosophy/id-and-catholic-theology/#comment-212175 But while Darwinian mechanisms have trouble making leaps in the "islands of functionality" a designed plan "shouldn't" have that issue since even large informational/functionality gaps can be bridged.Patrick
September 8, 2008
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what is THE ID hypothesis
Before anyone discusses this further I want to note there isn't such a thing as "THE ID hypothesis" but there are ID-compatible hypotheses. So despite this question being outside the scope of core ID it is a valid question. Considering the timescales involved, the hard part is determining which hypothesis is correct. So it's a matter of examining the evidence and attempting to narrow down the possibilities until one, or as few as possible, remains. More on this topic: How does the actor act?Patrick
September 8, 2008
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If the flagellar motor was designed and not evolved step-by-step over time via natural selection what is the ID hypothesis of how it got into prokaryotes in the first place? Was it placed whole within an existing strain of microorganism? (i.e., there was a generation of prokaryotes without flagellar motors followed by a generation of prokaryotes _with_ fully functioning, fully formed flagellar motors) Or did the structure build up slowly over time, according to non-natural selection rules? (i.e., successive generations of microorganisms developed portions of the flagellar motor piece-by-piece according to some pre-existing non-NDE plan, but the entire structure was not operational all at once.) Or is there some other method that I'm missing? This is not something I've seen a lot of discussion about. Given that structures like the flagellar motor are irreducibly complex how are they instantiated in the creature that contains them?Trimbach
September 8, 2008
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First, since a subset of its components exhibits an altogether different (protein exporting) function, then the flagellum can obviously not be “irreducibly complex” (!)
That is a very common misconception. Read: https://uncommondescent.com/comment-policy/put-a-sock-in-it/ http://www.discovery.org/scripts/viewDB/index.php?command=view&id=1831Patrick
September 8, 2008
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parlar You're still either not up to speed on the evidence or not willing to acknowledge the bits that don't support your case. Far, far more prokaryote species have flagella than have a T3SS which was also evidence presented to Matzke before he submitted his hypothesis for publication. And here's another paper explicitely suggesting that the t3ss is a descendent of the flagellum.DaveScot
September 8, 2008
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OFF: Could you guys recommend me some articles about using parts of the flagellum motor in nanotechnology?MaxAug
September 8, 2008
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tragicmishap, es58: It is actually true that many pathogens demonstrate evidence of degenerative processes acting on their genomes: Some examples are Yersinia pestis (bubonic plague), Bordetella pertussis (whooping cough), Francisella tularensis (rabbit plague), Mycobacterium leprae (leprosy). The list is long. Common for all such pathogens is also that they are more specialized than their undegenerated relatives. Taking it to the extreme, bacteria that are intracellular endosymbionts (being extremely specialized and restricted) all have extremely small genomes.parlar
September 7, 2008
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trag @11: Somewhere online (no link) I had read a paper where the author discussed the previous 3 (at that time) simplest (smallest genome) life forms that had yet been discovered. Each originally had been touted as possibly the earliest independent life, but had eventually been determined to have devolved from more complex life forms. The author wanted to suggest that all viruses had actually been parts of previously viable independent life forms that eventually had devolved to viruses. No idea if that is in any way supportable, but might fit in with the idea that originally there hadn't been "negative" organisms. However, even in the sea, where 1 life form eats another, not quite sure what means bad and good.es58
September 7, 2008
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Another clarification of the last statement (very important!). The phylogenetic tree of T3SS sequences and flagella sequences contains two major branches: One major branch with T3SS sequences and one major branch with flagellum sequences. These major branches coalesce at the root. This provides a good indication that these branches have different origins.parlar
September 7, 2008
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DaveScot: Ok, relatively speaking. The point being that there would be both more deeply diverging as well as more recently diverging branches of flagella sequences. Of course, the same argument goes for T3SS preceding the flagellum, which is likewise unsupported by the data. Instead, the tree demonstrates two major branches that coalesce at the root.parlar
September 7, 2008
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T3SS would exist as a recently diverging branch in a flagellum tree Recently? A billion years ago is hardly recently.DaveScot
September 7, 2008
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DaveScot, Thanks for pointing me to this interesting paper. I think, however, that you may partly have misunderstood its conclusions and implications. The paper you refer to does not in any way demonstrate that flagellum preceded the T3SS. First of all, let me say that your statement about devolution, as you call it, being simpler than evolution indeed is very correct. The paper actually provides a good demonstration of this. What it shows is that genes required to build the flagellum are lost in an environment where the flagellum is no longer needed (in this case, inside another cell). In fact, in bacteria that establish host-restricted and less complex lifestyles, a large array of gene functions are always found to become degraded and ultimately lost. This is because gene functions need to be maintained by selection - otherwise they are unavoidably inactivated by random genetic drift. The interesting point in this paper is, however, that some genes in the flagellum apparatus are consistently (conspicuously!) retained, namely those shared with the T3SS. Note that it does NOT convert the flagellum to a T3SS. The T3SS is a specialized apparatus with a needle structure that can inject effectors (proteins) through membranes into different cellular compartments. The retained genes can merely move proteins out of the bacterium. The authors speculate that the retained genes might support symbiotic interactions by exporting proteins out from the bacterium to the host organism. If the conclusions in the paper are true, two things are evident: First, since a subset of its components exhibits an altogether different (protein exporting) function, then the flagellum can obviously not be “irreducibly complex” (!). Second, in agreement with phylogenetic data, it suggests that this primitive protein export system existed first and that that the flagellum and the T3SS independently evolved from it. Just to clarify this point, if the T3SS evolved from the flagellum, we’d expect from phylogenetic analysis that the T3SS would exist as a recently diverging branch in a flagellum tree. This is not the case.parlar
September 7, 2008
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parlar Nice try but no cigar. I have an even newer paper (2008) finding that the T3SS, just like we said all along, came from the flagellum, not an ancestor they both had in common. You can read it here.DaveScot
September 7, 2008
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As a software engineer I can't count the number of times I've worked on someone else's code (or even my code that I had not visited in a long time) and thought, "Why did he (or I) do it that way? There's a much simpler, more efficient way to do it." So I modify the code and the program goes down in flames. Upon further inspection I realize that the "inefficient, unnecessarily complex" code was actually the only way to do it, for reasons that were not immediately evident. So, when I hear Darwinists in their infinite wisdom making claims about how biological systems are inefficient and unnecessarily complex (as in "too complex to have been designed"), and that they know it could have been done better, I can only assume that they have no experience in designing complex, functionally integrated systems. I imagine they would be more than happy to offer their opinion about how write a computer program when they know nothing about software engineering.GilDodgen
September 7, 2008
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Devil's Advocate sez: The TTSS injects eukaryotes now but back then it injected other prokaryotes. And BTW those prokaryotes are no longer around. (However we still cannot explain how the TTSS came about because it is irreducibly complex.)Joseph
September 7, 2008
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Penitents of denial, the proud, always "Nature" incurred, insanity-littered was fella reconsidered just flagella Instance for another smelling like turd Evidence in for theory that was backward. OK, I was just trying to see what else besides logic could run backward. I happened to choose a limerick. See? No problem, as long as you are willing to TORTURE IT TO DEATH to meet your needs. Don't worry Darwinists, anything can go backward . . . everything will be fine . . . peer review is just weiver reep going the other way, it will all make sense (ignore for now that it makes little sense); it will all be fine. . . it just takes time.Tim
September 6, 2008
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Hi Bornagain, That's been a favourite point of mine. Of course if you use it in an argument you will hear the lament "well, I don't see how the design perspective was necessary...anyone could have made the prediction." The point is, of course, that we know the design perspective was central because the man who made the prediction said it was, and we know that he is the one who did make the prediction independently. And then his work becomes twisted as evidence against design. Funny.Charlie
September 6, 2008
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Make that the 6:00 minute mark of the first video,,, it is also very interesting that Dr. Minnich is very frank in stating that his "design" perspective allowed him to make the "correct" prediction!bornagain77
September 6, 2008
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You guys might find this interesting: Scott Minnich actually predicted that they would find the Flagellum doing "double duty" as a secretory mechanism for virulence. Look around the 8:30 mark on the video: Bacterial Flagella - A Paradigm for Intelligent Design 4/6 http://www.godtube.com/view_video.php?viewkey=392e50560876f8304ecf Bacterial Flagella - A Paradigm for Intelligent Design 5/6 http://www.godtube.com/view_video.php?viewkey=7f327f064614bc8d6337bornagain77
September 6, 2008
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DaveScot, You’re absolutely right about the lack of logic that T3SS should have evolved before the eukaryotic targets in which it injects effectors. According to the literature, it appears however that the evolutionary scenario which has most support is that both systems (flagellum and the type III secretion system) evolved independently from an ancestral system involved in bacterial protein export. Wong et. al. (2007) wrote a review that touches on this [1] and so did also McCann and Guttman [2], if you want to learn more about their arguments. Mark Pallen and Gophna U Volff has also written a book chapter that addresses this issue [3]. 1. Wong T, Amidi A, Dodds A, Siddiqi S, Wang J, Yep T. Evolution of the Bacterial Flagellum. MICROBE-AMERICAN SOCIETY FOR MICROBIOLOGY, 2007 2. HC McCann, DS Guttman. Evolution of the type III secretion system and its effectors in plant-microbe interactions. New Phytol, 2008 3. Pallen MJ, Gophna U. Bacterial Flagella and Type III Secretion: Case Studies in the Evolution of Complexity. Genome Dyn. 2007parlar
September 6, 2008
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Portishead re; function of t3ss only to prey on eukaryotes Yes, that is correct. See here.DaveScot
September 6, 2008
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"it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system"
This is the obligatory bow of the Darwinist brain's normal reasoning faculties to the absurdities of the Darwin idol. What have real designers fashioned in real life? Electric motors that look uncannily like the somebody ripped off the original plans for the flagellum. The design is so obvious that Crick just had to say, "Biologists must constantly keep in mind that what they see was not designed, but rather evolved." Darwinian 'logic' here is tantamount to insanity. For mentally ill folks usually live in some deep form of denial of reality or inability to distinguish reality from imagination. That's exactly what we witness here in the article.Borne
September 6, 2008
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DaveScot, Thanks for the note at (12) - fascinating stuff. I take it that T3SS is a part of prokaryotes that is only used for predating on eukaryotes (i.e. it doesn't work on other prey, only eukaryotes)?Portishead
September 6, 2008
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For people who claim not to believe in ID or a designer, they seem to know plenty about what this designer couldn't, shouldn't, and wouldn't do. Do you think they acquired this knowledge scientifically?Adam23
September 6, 2008
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I thought someone would say that, but I know it's not necessary. It's perfectly reasonable that pathogens were designed to do exactly what they do. Any Christian (as I am), reading through the Old Testament would have to immediately come to grips with God being responsible for killing people. My point is that it makes sense that the original blueprints of a designer did not include pathogens. So in order to make pathogens, the designer drew upon pre-existing structures. It might be possible that they evolved through Darwinian or other evolutionary means (front-loading perhaps) as well. But either way this is a question ID can pursue that Darwinists won't. As to specific pathogens, that's my point exactly. The natural limits on these pathogens are being removed, suggesting a loss of specificity. That is something we know Darwinian processes can do. A designer could do it just as well, sure. What we have not seen is any increase in specificity or information, even though it appears to us as if pathogens are "evolving".tragicmishap
September 6, 2008
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@11. I am not sure what perspective you are coming from, but *if* there is a designer, he/she/it/they are responsible not only for designing the 'good things' in biology, but also many of the 'bad things' in biology. Behe says as much in EoE regarding Malaria, and there are many more examples of complex 'negative' organisms (Parasitology comes to mind). It is not necessary for pathogens to have originated from a 'positive' organism from either a design or evolutionary point of view. Re: "species specific" pathogens. The worry with many pathogens is that they become zoonotic, animal diseases infecting humans. This is the worry with Avian Influenza, that a strain that can infect humans will mutate and spread (has it yet? I have not kept up with the news). "More information means more specification" -> actually, it is possible this is not the case. See the thread on UD (and TT) about the 'universal genome'. However, more expressed information means more specification (which is probably what you meant, rendering this last para useless:/ heh). https://uncommondescent.com/intelligent-design/universal-genome-in-the-origin-of-metazoa/Avonwatches
September 6, 2008
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portishead can you explain more fully the reasoning behind your objection to Matzke’s logic on T3SS? Was he actually saying that there were no prey around? Many people, including me, pointed out to Matzke (before he submitted for publication) that the T3SS is a weapon used by predatory prokaryotes to inject toxins into their eukaryote prey. The commonly accepted order of phylogeny is that prokaryotes were around for about 2 billion years before the first eukaryote showed up on the scene. During all those 2 billion years prokaryotes had strong survival need for locomotion to move upstream in nutrient gradients. The flagellum thus, in any reasonable explanation, preceded the T3SS by billions of years. Matzke pointedly ignored that in his desperation to find a simpler precursor for the flagellum so he went right ahead with a fatally flawed thesis that the flagellum descended from the much simpler T3SS when everyone and his brother had pointed out to him that was almost certainly not true. Nature went right ahead and published the nonsense as well such is their zeal to cast doubt on anything that comes out of the ID camp. DaveScot
September 6, 2008
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Is it possible that the T3SS did evolve from the flagellum? Since the T3SS has fewer of the components of the flagellum, it's possible that evolution did in fact destroy several components leading to the new structure. And there wouldn't have to be any new structures involved to simply secrete something. That could involve transport mechanisms that already existed for the virulent factors. I find it interesting that the simpler T3SS may have evolved from the flagellum and is also pathogenic. I've been wondering if every pathogen is actually an evolutionary derivative of something created for a positive biological purpose. All pathogens could have started out performing a function, but a random mutation knocks out a key system which specifies the structure's function. More information means more specification. If you knock out some information, the system becomes less specified and able to infect species it was never meant for, causing a disease. Am I making sense?tragicmishap
September 6, 2008
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This reminds me of phlogiston logic. Phlogiston is given off during combustion, so the ash weighs less than the original material. When it was demonstrated that a metal (like zinc or tin), when heated and combusted in a bell jar filled with oxygen, yielded ash that weighed more than the original metal, it was proposed that phlogiston could have negative weight. So, phlogiston has positive weight except when it has negative weight. By similar logic, Darwinian mechanisms produce a result, except when they produce the opposite result, and when something is too complex to have been designed, it must have evolved by Darwinian means.
Finally, it seems that the bacterial flagellum is a structure of great complexity. In an attempt to understand why, it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system.
An Intel CPU is a structure of great complexity, so surely a designer would have fashioned a simpler structure? What kind of logic is this? If anything is the enemy of science, it is Darwinian logic.GilDodgen
September 6, 2008
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This must be understood, the "this system in nature is so staggeringly complex in form and function that it renders speechless our best engineers, therefore it can only be a creation of natural selection and random genetic mutation and aren't these IDist idiots to even consider an alternative" non-thinking is not an abberation, an anomaly in evolutionary thinking, it is evolutionary thinking. That is it is evolutionary logic in a nutshell. It applies across the board in the natural sciences. But how to make sense of this counter-intuitive "thinking" in evolutionary biology? Well it is a psychological necessity, I mean to even consider abandoning their god of scientific materialism, simply unthinkable, so they don't think... Even (in fact especially) ten year old children yet to be indoctrinated into a scientific materialist worldview get how counter-intuitive such mental convolutions are when describing ever more complex systems in nature, yet the PhDs' from Cornell, Stanford and Berkeley are the last people to get it naturally. As the saying goes "you have to have your PhD before you don't get it." The Native Americans were right, the Trickster Coyote's shadow looms over every aspect of the world and humanity and in the discipline of evolutionary biology his shadow looms large, Coyote stands a hundred feet tall and his howling can be heard for hundreds of miles around, but you have to know how to listen...zephyr
September 6, 2008
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