Flagellum, Behe's prime example of irreducible complexity

Flagellum, Behe's prime example of irreducible complexity

https://reasonandscience.catsboard.com/t1528-the-flagellum-behe-s-prime-example-of-irreducible-complexity

How can "some mutation" alone turn a secretory system into a flagellum? Think about this, the T3SS has over 25 proteins, over 60 structural and regulatory proteins are required for flagellum assembly and function. 3, and both share only 9 to 13 proteins. So, instead of a single "Crooked" mutation, the transition from one machine to another would require the novel evolution of over 50 proteins along with huge structural rearrangements (that would certainly disrupt the function of the system). Clearly, evolution seems plausible, UNTIL we try testing against actual, more detailed facts taken from molecular biology

Miller's refutation of irreducible complexity of the Flagellum through co-option is a prima facie example of a pseudo-scientific argument. Since Miller recognizes implicitly that a gradual evolutionary step by step development of the flagellum is not possible, he comes up with an ad hoc explanation, namely co-opting parts from other biological systems. That copying, modifying, and combining together preexisting parts, already operating in other systems, would do the job. But, is it really? Could it be, that super-evolutionary mechanisms would act that way, borrowing parts from other biological systems and assemble them to a flagellum with a new function, perfectly ordered, with perfect fits, and new functions, with the help of Saint time, that would do that miracle? Even thinking, that time, in this case, would rather be detrimental, than help? Would it really be, that the most perfect and efficient motor in the universe could arise by copy/pasta, by a supernatural pick and add, a molecular quilt and patchwork mechanism? The question that follows is what exactly did the recruiting? What provokes recruitment to another system? and you believe in Santa Claus, as well? That's not only insane but completely impossible.

Natural selection preserves or "selects" functional advantages. If a random mutation helps an organism survive, it can be preserved and passed on to the next generation. Yet, the flagellar motor has no function until after all of its 30 parts have been assembled. The 29 and 28-part versions of this motor do not work. Thus, natural selection can "select" or preserve the motor once it has arisen as a functioning whole, but it can do nothing to help build the motor in the first place. 1

Knockout experiments and tests provide empirical evidence that the flagellum is irreducibly complex, as Scott Minnich  testified at the Dover process: 

Kitzmiller Transcript of Testimony of Scott Minnich pgs. 99-108, Nov. 3, 2005, emphasis added

We have a mutation in a drive shaft protein or the U joint, and they can't swim. Now, to confirm that that's the only part that we've affected, you know, is that we can identify this mutation, clone the gene from the wild-type and reintroduce it by the mechanism of genetic complementation. So this is, these cells up here are derived from this mutant where we have complemented with a good copy of the gene. One mutation, one part knock out, it can't swim. Put that single gene back in we restore motility. Same thing over here. We put, knock out one part, put a good copy of the gene back in, and they can swim. By definition, the system is irreducibly complex. We've done that with all 35 components of the flagellum, and we get the same effect.
(Kitzmiller Transcript of Testimony of Scott Minnich pgs. 99-108, Nov. 3, 2005, emphasis added)

The argument of the flagellum
1. The flagellum (turning propeller for movement in the water) has about 40 different proteins facilitating the work of the flagellum. Every protein is a complex structure of about 300 atoms.
2. All particles are very important and one cannot exist without another just like parts of the car engine. And the proteins will disintegrate if they are not in the flagellum structure.
3. The proponents of evolution are unable to give any explanation how all these 1200 parts appeared simultaneously in the right position and started to work together out of the prebiotic soup. 
4. Therefore, the only option is creation. Just like no car engine has ever come out of an explosion in an oilfield or tank of gasoline.
5. The Supreme Ultimate creator is God.

The irreducible complexity of the flagellum
1. The flagellum has 36 different proteins essential for the function of the flagellum. Every protein is a complex structure of average 300 amino acids
2. All proteins are required and one has no function without another just like a piston of a car engine has no use without the other engine parts. 
3. Evolutionary biologists are unable to give any explanation on how all these proteins could have evolved in a gradual fashion to form the flagellum 
4. Therefore, the only option is set up by an intelligent designer. 

http://www.genome.jp/kegg-bin/show_pathway?eco02040


http://creationwiki.org/%28Talk.Origins%29_The_flagellum_has_30_or_so_unique_%28non-homologous%29_proteins

http://www.detectingdesign.com/flagellum.html

let's see the original Argument from Ken Miller:

http://www.millerandlevine.com/km/ev...1/article.html

This leaves us with two points to consider: First, a wide variety of motile systems exist that are missing parts of this supposedly irreducibly complex structure; and second, biologists have known for years that each of the major components of the cilium, including proteins tubulin, dynein, and actin have distinct functions elsewhere in the cell that is unrelated to ciliary motion.

Given these facts, what is one to make of the core argument of biochemical design – namely, that the parts of an irreducibly complex structure have no functions on their own? The key element of the claim was that: ".. any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional." But the individual parts of the cilium, including tubulin, the motor protein dynein, and the contractile protein actin are fully-functional elsewhere in the cell. What this means, of course, is that a selectable function exists for each of the major parts of the cilium, and therefore that the argument is wrong.

Models of flagella rotation - how does the rotor work?
http://iaincarstairs.wordpress.com/2013/03/25/as-smart-as-molecules/

The earliest forms of life, dating back perhaps three and a half billion years, are assumed to be bacteria, and as far as we observe, every cell comes from a cell. Under episodes of cell stress or genome shock, as Shapiro points out in Evolution, a cell “activates the molecular systems that restructure genomes” (ref. Jorgensen).  This intense scurry for novelty in response to an external threat, and the coding of solutions into DNA which is passed sideways to their peers, is an observed method of evolutionary progress, and as antibiotic researchers will tell you, it is very effective indeed.

These bacteria are some of the most complicated and smartest critters on the planet – the proof being their survival over eons and their central role even in the biology of human beings: you might not want to live with them, but you can’t live without ‘em.

A method of their locomotion so strongly conserved that it still exists today is the flagellar motor.  This cunning device rotates between 20,000 and 100,000 RPM, five times the speed of an F1 engine, and due to the high surrounding pressure at molecular levels (a severe difficulty in nanotech engineering) can stop immediately.  When you assemble these motors, they work automatically in response to signals from within the bacteria – there is no need to invoke the supernatural any more than there is to keep track of your electric fan.

The combination of molecules is so precise, and once correctly assembled, they are so sturdy and incapable of miss performing that they only require the context of the cell with its switches, endless supplies of recyclable fuel, and regulatory systems, to perform their specialized task.

Proton or sodium-driven, they are equipped with motor, clutch, bushings, washers, gearing, and even a tiny printed maintenance schematic

Revisiting Co-option

Is the flagellum like the Type III injectisome? This question was addressed in the film. (Evolutionists have tried to point to the TTSS machine as an intermediate; see "Two of the World's Leading Experts on Bacterial Flagellar Assembly Take on Michael Behe.") The new diagram shows some similarities between the two machines, but many differences, including the component parts. Here's their discussion:

   The flagellum and the virulence-associated injectisome share an analogous architecture and homologous T3S components. However, the structure and function of the rod are quite different in the two systems. The rod of the injectisome is formed by a protein (PrgJ in S. Typhimurium). Rod assembly is required for proper anchoring of the needle structure. The function of the injectisome rod is to provide a conduit for protein transport from the bacterial cytoplasm to the host cell (Fig. 6D). In contrast, the flagellar rod and its complex interactions with the MS ring, P ring, and hook (Fig. 6B) provide dual functions: a hollow channel for protein secretion and a sturdy drive shaft to transmit torque between the motor and filament.

So even if the flagellum "co-opted" parts from the TTSS, many parts are unique. As Minnich stated in the film:

   You're talking about a machine that's got 40 structural parts. Yes, we find 10 of them are involved in another molecular machine. But the other 30 are unique. So where are you going to borrow them from? Eventually, you're going to have to account for the function of every single part as originally having some other purpose. So you can only follow that argument so far till you run into the problem of, you're borrowing parts from nothing.

The new paper corroborates Minnich's remarks. In conclusion, the authors say,

   In summary, high-throughput cryo-ET, coupled with mutational analysis, revealed a complete series of high-resolution molecular snapshots of the periplasmic flagella assembly process in the Lyme disease spirochete. The resulting composite picture provides a structural blueprint depicting the assembly process of this intricate molecular machine. This approach should be applicable in determining the sequence of events in intact cells that generate a broad range of molecular machines.

Eleven years is a lot of time to refute the claims about flagellar assembly made in Unlocking the Mystery of Life if they were vulnerable to falsification. Instead, higher resolution studies confirm them. Not only that, research into the precision assembly of flagella is provoking more investigation of the assembly of other molecular machines. It's a measure of the robustness of a scientific theory when increasing data strengthen its tenets over time and motivate further research. Irreducible complexity lives!

Flagellum: Nature, it turns out, is an engineer 2

The bacterial flagellum is one of nature’s smallest motors, rotating at up to 60,000 revolutions per minute. To function properly and propel the bacterium, the flagellum requires all of its components to fit together to exacting measurements. In a study published in Science, University of Utah researchers reports the elucidation of a mechanism that regulates the length of the flagellum’s 25-nanometer driveshaft-like rod and answers a long-standing question about how cells are held together.

While the biomechanical controls that determine the dimensions of other flagellar components have already been determined, the control of the length of the rod, a rigid shaft that transfers torque from the flagellar motor in the interior of the cell to the external propeller filament, were unknown. “Since the majority of the machine is assembled outside the cell there have to be mechanisms for self-assembly and also to determine optimal lengths of different components,” says biology professor Kelly Hughes. “How does it do that?”

1. http://www.discovery.org/a/3059
2. https://uncommondescent.com/irreducible-complexity/flagellum-nature-it-turns-out-is-an-engineer/
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009794/

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

The function for a flagellum is a PROPULSION SYSTEM, complete with engine and propeller to spin the prop. If you remove a part of that assembly, the system in inoperable because the prop will not rotate.

The definition of irreducible complexity is a CONDITION that occurs with MOLECULAR MACHINERY in which (1) the removal of a gene (protein part) renders the machine inoperable, and (2) unselected steps are observable in its DNA sequence.

Any biochemical system is irreducibly complex if and when this occurs. Behe made the discovery, championed the hypothesis, made testable and falsifiable predictions based upon irreducible complexity, and those predictions remain unfalsified. As the author and finder of this hypothesis, Behe was entitled to call his discovery by any name.

If anyone desires to challenge or criticize Behe's work they are certainly invited to do so, but in order to do that they must recognize his definitions of the terms he uses to describe the hypothesis. If someone ignores Behe's definitions and dubs anything they think makes better sense to mean "irreducible complexity," they can do that if they want, but they are not talking about Behe's work anymore, they would be talking about something else.


Gram-negative bacteria (fitted with a T3SS injectosome protein appendage) cannot swim. That is why the bacterial flagellum is irreducibly complex.

The reason why Behe used the illustration of a mouse trap is because if any of it's parts are removed, the machine will be incapable of catching mice. So likewise, if any gene/protein is removed from a bacterial flagellum the bacterium will no longer be capable of swimming. The function of the flagellum operates as a propeller engine providing propulsion to enable the bacteria to swim. Remove any part, and it cannot swim anymore. Secondary functions are IRRELEVANT.

It is irrelevant someone can still use a broken mousetrap as a tie clip, and It is irrelevant if subparts of a molecular machine can serve a different function. The moment anyone discusses some different function, they are no longer talking about irreducible complexity, they are talking about something else. Behe already directly responded to this nonsense, stated himself that mentioning other functions is a strawman, and went on to comment that never once did he ever suggest that subparts could not have secondary functions. He never discussed them because those questions are irrelevant.

The scientific research and literature confirms Behe's predictions. The flagella are required for propulsion motility (ability to swim). The bacteria that do not have the device are limited to surface motility (crawling like a snail). Just because there are bacteria that do not have the machinery does nothing to falsify Behe's hypothesis. If anything, the bacteria that do not have the propulsion system have less parts, and indicates a loss of information.

Whether Archaea cells have their own flagella has not falsified Behe's work. Archaea flagella have been shown to have no evolutionary pathway with bacterial flagella. If there were an evolutionary trajectory of descent connecting the two 2 domains the Behe's hypothesis would be falsified. Convergent evolution is what it is, but there is nothing about convergence that falsifies IC.

The issue is not how silly or practical irreducible complexity might be. No one ever said this is some gamechangine breakthrough discovery. Had Behe not been so heavily criticized by his claims the concept might have just been set aside and long forgotten. The publicity of the criticism against Behe fueled the emphasis on his work, and amplified that he actually technically was never falsified. If the best argument against his work is a strawman, then that is very telling of how credible his work is. Whether the concept is silly is irrelevant.

Either the bacterial flagellum, cilia, blood clotting cascade, and vertebrate immune system are irreducibly complex when applying Behe's definition or they are not. If they are, then his prediction is correct regardless of how insignificant the discovery might be. Had Behen been ignored, that would have told us that the discovery was meaningless. It was the vigorous resistance to his work BY THE SCIENTIFIC COMMUNITY that set how significant the discovery is. If his work is nothing than just silly, then it should not have received any attention.

Behe claims his predictions are a design-inspired prediction because when he looked at bacterial flagella under a microscope it reminded him of an outboard motor he's seen on boats. In essence, a flagellum is a motor that spins a fillament in the same manner as a propellor. Had Behe not contemplated the mechanical engineering of propulsion he would have not discovered irreducible complexity or proposed the predictions he made in his book, "Darwin's Black Box" (1996).

more readings :

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002983
http://mic.sgmjournals.org/content/journal/micro/10.1099/mic.0.25948-0?crawler=true&mimetype=application/pdf




The Evolution of the Flagellum
http://www.detectingdesign.com/flagellum.html

Researchers discover bacteria propelled by a kind of rotary driver 1

The finding came as Abhishek Shrivastava, a postdoctoral fellow working in the lab of Howard Berg, the Herchel Smith Professor of Physics and a professor of molecular and cellular biology, was investigating how many types of bacteria, including F. johnsoniae, are able to move without the aid of flagella or pili. The discovery is described in a recently published paper in Current Biology.
"If you look at the diversity of the bacterial world, there are many bacteria—including F. johnsoniae—that do not have flagella or pili, yet they move quite easily over surfaces, and travel long distances. This movement is called 'bacterial gliding,'" Shrivastava said. "To move by this process, bacteria require a constant influx of energy. We wanted to find out how bacterial gliding takes place and what could be a motor for gliding."

Though researchers had long observed bacterial gliding, the precise mechanics underlying the behavior remained a mystery.
The first clues came a few years ago, Shrivastava said, when researchers discovered that the rod-shaped Flavobacteria are actually bristling with tiny filaments, made up of a protein called SprB. These filaments are required for motility.
Shrivastava and others used an antibody "glue" to pin one of the filaments down to a glass plate and found that when they are held down, the cells pinwheel around the point of attachment. If a small, plastic bead were attached to the filament, they found that it would also rotate. The torque generated by the gliding motor was calculated to be large, and comparable to torque generated by motors that drive flagellar filaments.
Though not the only one found in nature—a similar motor powers the flagella found on bacteria like E. coli—the rotary motor discovered by Shrivastava and colleagues appears to be distinct from others. "If you look at the genome sequence of this bacterium, it does not have the genes that make the proteins used to build the flagellar motor," Shrivastava said. "It could be that some of the components are similar, but we are probably looking at some novel proteins. So we want to understand what makes up the nuts and bolts of this motor."
Going forward, Berg said, researchers still have many questions to answer. "The flagellar motor has about 20 different kinds of parts, from a drive shaft to a rotary bearing and a universal joint—that kind of machinery is in this bug, but we have no idea what that is. What we need to do now is somehow pull it out and understand the architecture of this motor."

1) http://phys.org/news/2015-03-bacteria-propelled-kind-rotary-driver.html

more: http://www.evolutionnews.org/2015/01/a_third_rotary093141.html
http://www.cell.com/cell/abstract/S0092-8674(10)00019-X?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS009286741000019X%3Fshowall%3Dtrue

Mechanics of torque generation in the bacterial flagellar motor 1

The bacterial flagellar motor (BFM) is responsible for driving bacterial locomotion and chemotaxis, fundamental processes in pathogenesis and biofilm formation. In the BFM, torque is generated at the interface between transmembrane proteins (stators) and a rotor. It is well established that the passage of ions down a transmembrane gradient through the stator complex provides the energy for torque generation. However, the physics involved in this energy conversion remain poorly understood. Here we propose a mechanically specific model for torque generation in the BFM. In particular, we identify roles for two fundamental forces involved in torque generation: electrostatic and steric. We propose that electrostatic forces serve to position the stator, whereas steric forces comprise the actual “power stroke.” Specifically, we propose that ion-induced conformational changes about a proline “hinge” residue in a stator α-helix are directly responsible for generating the power stroke. Our model predictions fit well with recent experiments on a single-stator motor. The proposed model provides a mechanical explanation for several fundamental properties of the flagellar motor, including torque–speed and speed–ion motive force relationships, backstepping, variation in step sizes, and the effects of key mutations in the stator.

http://www.pnas.org/content/early/2015/07/24/1501734112.abstract

http://www.reasons.org/articles/the-provocative-case-for-intelligent-design-new-discovery-highlights-machine-like-character-of-the-bacterial-flagellum

The Flagellum and Bacterial Motility

1

The most common mechanism used by bacteria to swim through liquid media is the flagellum. The bacterial flagellum consists of 3 major domains: an ion driven motor, which can provide a torque in either direction; the hook, a universal joint which transmits motor torque even if it is curved; and the filament, a very long structure which acts as a propeller, and behaves differently depending on which way the motor turns.
When the bacterial flagellum is rotated by the motor, the filament forms a supercoil, giving it an overall corkscrew-like shape. Flagellated bacteria are able to undergo directed movement through changes in the rotary behavior of the flagellum. When the flagellum rotates clockwise, the filament forms a long pitch supercoil, allowing several flagella on a single cell to form a large bundle, which propels the bacterium along a straight line in a single direction. When the filament is rotated in the opposite direction, it forms a shorter pitch supercoil; this causes the flagellar bundle to disassemble, and the independent motion of several flagella on the cell cause it to tumble randomly. Using these two modes of motion, bacteria can move up or down a stimulus gradient by decreasing their tumbling frequency (if they are moving in the preferred direction) or increasing their tumbling frequency (if they are moving against the desired direction), allowing them to undergo a biased random walk.

Mechanisms of flagellar components

The mechanical properties of all three flagellar components are of interest to biologists (due to the application to pathogenic organisms) and for nanotechnology, since they may offer a template for useful atomic-scale structures. The hook (which acts as a nanoscale universal joint) and the filament (which can be mechanically switched) have been particularly well studied, with both x-ray crystal structures and cryo-EM maps available for both assemblies.
The switching of the supercoils in the flagellar filament is thought to be the result of polymorphic transitions in the filament, when the individual protein units slide against each other. The molecular mechanisms of the polymorphic transition remain poorly understood. It is even unclear which interactions are more important, the protein-protein or the protein-solvent ones. As the resolution in experiments with functioning flagella is not high enough, simulations are necessary to clarify this issue. Likewise, while recent experiments have suggested that the universal joint properties of the hook step from compressibility in the interactions of adjacent subunits along the length of the hook, but the time and length scales required to resolve this interactions are not simultaneously accessible.

Coarse-Grained Model of the Flagellum

Coarse-grained flagellar filament. (a): Single flagellin monomer, all-atom versus CG model. (b): Arrangement of the monomers in the filament, viewed from the side and from the bottom, all-atom (left) and CG (right). (c): Simulated segment of the filament (1100 monomers).
All-atom simulations presently cannot reach the time and length scales relevant to the transitions in the flagellar filament (milliseconds and micrometers). Instead, one should take advantage of coarse-grained molecular dynamics (CG MD) techniques. In a CG model, one uses a reduced number of degrees of freedom to describe the system. As a result, with a given computer power, one can simulate larger systems over longer times than what is possible with the all-atom representation.
A CG technique, called the shape-based CG method, has been developed by the TCBG scientists and applied to simulate the flagellar filament (as reported here). In this method, one chooses a number of CG beads that will represent a single protein, and a self-organizing neural networking algorithm is used to distribute the beads so that they optimally represent the shape of the all-atom protein. A single flagellin protein is represented by 15 CG particles (about 500 atoms per CG particle).
The effective potentials for interactions between CG particles were derived from all-atom MD simulations. A simple implicit solvent model, reproducing the dielectric constant and viscosity of water, was used to account for the solvent (the implicit solvent was also parameterized based on all-atom simulations). As a result, a half-micrometer-long segment of the flagellar filament could be simulated over the time scale of tens of nanoseconds. This system consisted of about 20,000 beads in the CG representation, while in the all-atom description it would amount to 70,000,000 atoms, which could not be possibly simulated on modern supercomputers, let alone reaching the microsecond time scales.
The developed CG model distinguishes drastically from the well-established all-atom models. Yet, the TCBG's programs VMD and NAMD could be used without any change to simulate the coarse-grained flagellum. Remarkably, the scaling of the parallel performance that NAMD demonstrated in these CG simulations was the same as normally found in the all-atom simulations. The same CG method was also successfully applied to study the dynamics of viral capsids.

Polymorphic transitions in the rotated flagellar filament

Rotating the flagellar filament.
Three simulations of a large filament segment (530 nm long, 1,100 subunits) were performed (mpg movie, 6.1M): with the torque applied in the direction corresponding to the running mode, to the tumbling mode, and with no torque applied, as a control. The torque was applied to 30 monomers at the filament's base; each of the three simulations covered 30 microseconds.
Without the torque, the structure of the filament is stable. When the torque is applied, the structure remains stable overall, but the unit proteins rearrange dramatically. As the torque is transmitted along the length of the filaments, parts of the filament start rotating, while other parts (those closer to the tip) are still in rest. In the straight filament, which is the starting structure for these simulations, the protofilaments form a right-handed helix with large helical period. When the torque is applied counterclockwise (as viewed from the base to the tip), the protofilamens remain arranged in right-handed helices, but the pitch of the helices rises; when the torque is applied in the opposite direction, the helices become left-handed. The filament also forms a supercoil as a whole. For the rotation corresponding to the running mode, the filament forms a left-handed supercoil, whereas in the simulation of the tumbling mode, it becomes a right-handed supercoil. The same difference in handedness between these supercoils is found in the living bacteria.
Thus, the simulation reproduces some details of the experimentally known flagellar structures, and also suggests that the rearrangement of the protofilaments upon the rotation is consistent with the previous theoretical models. The protofilaments slide against each other, so that the whole structure undergoes a polymorphic transition from one helical state to another upon the application of a torque. These transitions induce the changes in the supercoiling states of the whole filament, producing the forms that allow a bacterium to swim or tumble, depending on the direction of the torque.

Role of the solvent

Effect of the solvent.
Strong coupling between the protein units within a protofilament, as opposed to weaker interactions between the units in neighboring protofilaments, should be the reason why the protofilaments slide against each other so as to produce the observed polymorphic transitions. However, other interactions are also involved in the function of the complex molecular machine that the flagellum represents. Elucidation of the role of certain interactions is often a difficult task for an experiment, but it becomes easy when one takes advantage of numerical computations, where the system can be manipulated at wish of a scientist. The CG simulations of the flagellar filament suggest that the protein-solvent interactions are actually extremely important for the polymorphic transitions to arise, something that has not been taken into account in the most of previous studies of the flagellum.
Rotation of a short flagellar segment (220 monomers) was simulated to investigate the role of the solvent. The speed of rotation propagation, switching of the protofilament states and supercoiling of the segment are the same as in simulations of the 1,100-monomer segment, demonstrating that the observed behaviour is due to local interactions. The short segment was simulated with and without the solvent, which in the employed model means with or without the external viscosity. Without the solvent, the flagellum rotates as a rigid body, i.e., the mutual positions of monomers are frozen, as can be seen in the movies of the rotation for the running mode (mpg movie, 6.0M) and for the tumbling mode(mpg movie, 6.2M). Apparently, the solvent (friction) plays a crucial role in the switching between the arrangements of protofilaments and, consequently, in producing supercoiling along the entire filament.

Because the arrangement of the monomers in the flagellum features an intrinsic scoop-like curvature, one wonders if this curvature induces the polymorphic transition due to interactions with the solvent. In simulations where the rotation is applied over the whole length of a short flagellar segment, the monomers brush out for the tumbling mode, and become very smooth for the running mode, with the shape of the monomers being strongly affected by the rotation. Without the solvent (friction), segments look the same for both rotation directions. However, in reality the torque is applied only to the base of the flagellum; in such case, the difference due to rotation one way or another, as observed in the CG simulations, is not in the monomer shape (which is unaffected by the rotation), but in the mutual arrangement of monomers. Thus, the role of the solvent (friction) is not a direct coiling or uncoiling of the filament by rubbing against its ragged surface, but rather a facilitation of proper torque transfer over the filament (by providing friction) allowing the monomers to undergo a polymorphic transition.

Further possibilities.

The CG model applied to study the flagellar filament has been deveolped in a general form, and can be in principle used to simulate any macromolecular assembly of known structure. For the flagellum itself, the parts other than the filament should be studied, such as the hook - a universal joint transmitting the torque from the motor to the filament, the connector rings between the hook and the filament, and constituents of the basal body. Eventually, when the structure of all elements is known with the resolution satisfactory fo the CG model (which does not ahve to be an atomic-level resolution), dynamics of the whole flagellum, with its multiple composing prtoeins, can be simulated.


1) http://www.ks.uiuc.edu/Research/flagellum/

Cell Motors Play Together 1


 If one molecular machine by itself is a wonder, what would you think of groups of them playing in concert?  Recent papers and news articles are claiming that’s what happens in living cells: molecular motors coordinate their efforts.
    Science Daily led off a story on this by saying, “Even within cells, the left hand knows what the right hand is doing.”  Researchers at the University of Virginia said they “found that molecular motors operate in an amazingly coordinated manner” when “simple” algae named Chlamydominas need to move with flagella.  This contradicts earlier models that pictured the motors competing with each other like in a tug-o’war.  “The new U.Va. study provides strong evidence that the motors are indeed working in coordination, all pulling in one direction, as if under command, or in the opposite direction – again, as if under strict instruction.”  It almost requires imagining a conductor or foreman guiding the process.  Understanding it could help with treatments of neurodegenerative disorders.  The article did not mention evolution.  The researchers published their work in PNAS.1  
    Another cellular system reported by Science Daily refers to coordination of independent parts.  DNA transcripts made of messenger RNA emerge from the nucleus in 3-D clumps.  These need to be “straightened out” into a linear code that can be read by the ribosome.  Research at Rockefeller University shows that one of the 30 kinds of proteins in the nuclear pore complex “magnetically” attaches to the transcript when it passes through the gate, joining an unwrapping machine called a helicase “to form a machine that unpacks balled-up messenger RNA particles so that they can be translated.”  Here’s how Andre Hoelz described the action: “We found that the messenger RNA protein package and Nup214 competitively bind to the helicase, one after the other.” Each binding strips one protein off as it passes through.  “The process is akin to a ratchet mechanism for messenger RNA export,” Hoelz said.  Failures in the mechanism, again, were said to be implicated in disease.  Once again, also, the article said nothing about evolution.


1.  Laib, Marin, Bloodgood and Guilford, “The reciprocal coordination and mechanics of molecular motors in living cells,” Proceedings of the National Academy of Sciences USA, published online February 12, 2009, doi: 10.1073/pnas.0809849106.
The Darwinists have their chance to show up and explain the evolution of coordinated action of multiple parts needed for function, the failure of any component of which leads to disease or death.  The intelligent design team showed up.  Where’s the evolution team?  It’s like in sports.  Fail to show up and you forfeit. 


Molecular Motors In Cells Work Together, Study Shows 2

Even within cells, the left hand knows what the right hand is doing.
Molecular motors, the little engines that power cell mobility and the ability of cells to transport internal cargo, work together and in close coordination, according to a new finding by researchers at the University of Virginia. The work could have implications for the treatment of neurodegenerative disorders.
"We found that molecular motors operate in an amazingly coordinated manner when moving an algal cell one way or the other," said Jeneva Laib, the lead author and an undergraduate biomedical engineering student at the University of Virginia. "This provides a new understanding of the ways cells move."
The finding appears online in the current issue of The Proceedings of the National Academy of Sciences.
Laib, a second-year student from Lorton, Va., and her collaborators, U.Va. professors Robert Bloodgood and William Guilford, used the alga Chlamydomonas as a model to study how molecular motors in most types of cells work to move internal cargo, such as organelles associated with energy production and nutrient transport, or even the entire cell.
These motions are caused by a line of motors that pull the cell along, like the locomotive on a train. Previous studies had suggested that these motors pulled in opposite directions, like a game of tug of war. More recent studies indicated that the motors were working together rather than independently.
The new U.Va. study provides strong evidence that the motors are indeed working in coordination, all pulling in one direction, as if under command, or in the opposite direction — again, as if under strict instruction.
"We've found that large numbers of these molecular motors are turning on at the same time to generate large amounts of force, and then turning off at the same time to allow transport in the particular direction," said Guilford, Laib's adviser and lab director. "This insight opens up the possibility for us to begin to understand the mechanism that instructs the motors to pull one way or the other."
A greater understanding of cell motility and the ways in which cells move cargo within cells could eventually lead to therapies for neurodegenerative disorders such as amyotrophic lateral sclerosis (Lou Gehrig's Disease), diabetic neuropathy, and Usher syndrome, a progressive loss of hearing and vision. Neurodegenerative diseases can be caused by defects in the transport processes within neural cells.
"You basically get a logjam within the cell that prevents forward progress of these motors and their cargo," Guilford said. "So if we could understand how the motors are normally coordinated inside cells, we might be able to eventually realize therapeutic approaches to restoring transport for cell revival."
"There is some amazing cooperation going on among these motors," noted Bloodgood, a specialist in cell locomotion research. "When one set of as many as 10 motors turn on, another set turns off in unison. Understanding this process could help us to restore this locomotion when defects occur."


1) http://creationsafaris.com/crev200902.htm#20090227a
2) http://www.sciencedaily.com/releases/2009/02/090213161043.htm

Nanoscale-length control of the flagellar driveshaft requires hitting the tethered outer membrane 1

http://reasonandscience.heavenforum.org/t1528-the-flagellum-behe-s-prime-example-of-irreducible-complexity#5501



The bacterial flagellum exemplifies a system where even small deviations from the highly regulated flagellar assembly process can abolish motility and cause negative physiological outcomes. Consequently, bacteria have evolved elegant and robust regulatory mechanisms to ensure that flagellar morphogenesis follows a defined path, with each component self-assembling to predetermined dimensions.

This is one of the bitter fruits of methodological naturalism. Even when the evidence points to design, the authors must follow the pre-established track that no " supernatural " or " intelligent creator " can be hypothesized, since he does not dwell in what is considered to be natural, and therefore " rational " explanation. The problem of such inferences is obvious to any intended and not blinded mind: The regulation of flagellar assembly had to be fully setup and programmed right from the start. No trial and error would permit to find the correct regulation. Why would there even be trials, if the flagella bear only function, once its full setup and regulated? Any system, not fully developed, would a secure track to catastrophe and chaos, and no functional result at all. Morphogenesis of the flagella had to be precisely programmed, and so the regulatory mechanism, right from the start. The objection that different degrees of flagella advanced systems exist is evidence that even adaptation and variation within the flagella was pre-programmed.

The flagellar rod acts as a driveshaft to transmit torque from the cytoplasmic rotor to the external filament. The rod self-assembles to a defined length of ~25 nanometers. Here, we provide evidence that rod length is limited by the width of the periplasmic space between the inner and outer membranes. The length of Braun's lipoprotein determines periplasmic width by tethering the outer membrane to the peptidoglycan layer



Length determination of linear filaments poses a particular problem, some of whose known examples are solved by using molecular rulers. The bacterial flagellum is one such linear filament composed of a series of axial structures that must be assembled to precise specifications to enable motility.

Is it more reasonable to infer that precise specifications come from an intelligent agency, or are they rather the product of random trial and error processes? Did the single building blocks have the intrinsic drive and desire to structure themselves together to form a flagellum?

FlgG subunits must stack upon one another to reach the outer membrane. The self-stacking capability of FlgG poses a dilemma for the cell: Once initiated, what prevents continuously secreted FlgG subunits from polymerizing indefinitely?



The flagellum is a compromise on the absolute optimization of swimming ability in favor of a motility organelle that is optimized to function in harmony with other components of the cell and under various conditions.

Elucidating structure of bacterial flagellar motor protein Researchers reveal the 3-D structure of a bacterial propeller protein 3

Researchers used biochemical techniques and electron microscopy to uncover the structure of the bacterial MotA protein, which forms part of the propeller motor (flagellum). Three-dimensional analysis found it is composed of a transmembrane component and cytoplasmic domain, while MotA molecules were shown to form stable tetramer complexes with other MotA molecules. These findings will aid understanding of the mechanism underlying energy conversion during bacterial movement.



Many bacterial species use spiral propellers (flagella) attached to motors to move through a liquid environment. An interaction between the rotor and stator components of the motor generates the rotational force required for movement. The stator converts electrochemical energy into mechanical force after undergoing a structural change caused by a movement of charged particles (ions) through an internal channel. Previous studies investigated the stator and its interaction with the rotor by constructing mutant proteins and analyzing their functions. However, little was known about stator structure.

The stator is one of the most important parts for the proper functioning of the bacterial flagellar motor, and is believed to work as an energy-converting unit that transduces electrochemical potential gradient across the cytoplasmic membrane into mechanical force. Here, we report the first 3D structure of the MotA stator complex formed without MotB (Fig. 5). 



(A) A side view. (B) Another side view, with a 90° rotation compared to the one shown in A. The yellow area labeled TM indicates the membrane regions. (C) A view from the cytoplasmic side. (D) A view from the periplasmic side. An atomic model of the transmembrane region of MotA tetramer complex13 was fitted into the transmembrane domain in A,B and D. Four MotA molecules are shown in Cα ribbon representation, each colored in cyan, red, brown and magenta.



1. http://science.sciencemag.org.sci-hub.cc/content/356/6334/197
2. Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook
3. https://www.sciencedaily.com/releases/2016/09/160907113352.htm
4. https://www.nature.com/articles/srep31526

Further readings:
https://uncommondescent.com/irreducible-complexity/flagellum-nature-it-turns-out-is-an-engineer/
https://uncommondescent.com/irreducible-complexity/flagellum-nature-it-turns-out-is-an-engineer/

http://sciencerefutesevolution.blogspot.com.br/2017/01/seven-ion-flow-motors-synchronized-with.html


The book: The bacterial Flagellum, Springer protocols, Humana Press 2017

Mentioning  the words:  

evolution : 2x   ( not directly in regard of the flagellum. i couldnt believe it, i checked 3x )
natural selection :             0x
mutations:                        14x
design(ed)                        21x

In what a wonderfully evolving world we live.....

Congrats to Michael....

Sorry, Charly.....not this time....

The Flagellum, Behe's prime example of irreducible complexity

http://reasonandscience.heavenforum.org/t1528-the-flagellum?highlight=flagellum

How can "some mutation" alone turn a secretory system into a flagellum? Think about this, the T3SS has over 25 proteins, the flagellum has over 60 proteins, and both share only 9 to 13 proteins. So, instead of a single "Crooked" mutation, the transition from one machine to another would require the novel evolution of over 50 proteins along with huge structural rearrangements (that would certainly disrupt the function of the system). Clearly, evolution seems plausible, UNTIL we try testing against actual, more detailed facts taken from molecular biology

Centrin Scaffold in Chlamydomonas reinhardtii Revealed by Immunoelectron Microscopy
http://ec.asm.org/content/4/7/1253.figures-only

The ultrastructure of the Chlamydomonas reinhardtii basal apparatus: identification of an early marker of radial asymmetry inherent in the basal body
http://jcs.biologists.org/content/117/13/2663

Now, this is truly a funny article:

Evolution of higher torque in Campylobacter-type bacterial flagellar motors
08 January 2018

Understanding the evolution of molecular machines underpins our understanding of the development of life on earth. A well-studied case are bacterial flagellar motors that spin helical propellers for bacterial motility.

Diverse motors produce different torques, but how this diversity evolved remains unknown.

To gain insights into evolution of the high-torque ε-proteobacterial motor exemplified by the Campylobacter jejuni motor, we inferred ancestral states by combining phylogenetics, electron cryotomography, and motility assays to characterize motors from Wolinella succinogenes, Arcobacter butzleri and Bdellovibrio bacteriovorus.

Observation of ~12 stator complexes in many proteobacteria, yet ~17 in ε-proteobacteria suggest a “quantum leap” evolutionary event.

My comment: So after over 20 years, when Behe published the first time about the Flagellum, the authors of this paper in Nature admit, they have no clue how the flagellum diversified ( they could have also admitted to have no clue how it emerged in the first place ), to then, make literally a LEAP OF FAITH, by claiming that the " 12 stator complexes suggest a “quantum leap” evolutionary event. ".

The Flagellum -  prime example of irreducible complexity

https://reasonandscience.catsboard.com/t1528-the-flagellum-behe-s-prime-example-of-irreducible-complexity#6351

http://www.genome.jp/kegg-bin/show_pathway?eco02040






Despite differences, all bacterial flagella consist of the following basic structures: 

(1) the basal body, which anchors the flagellum in the bacterial cell envelope and contains the motor that powers flagellar rotation; 
(2) the hook, which is a flexible, curved rod that converts rotary motion into waves; and 
(3) the filament, which propagates the waves initiated by the hook and pushes against the surrounding medium to propel the bacterium forward

The basal body is the most complex of these structures, consisting of three ring structures in Gram-negative bacteria, a rod, a rotary motor, and a flagellar protein export apparatus. The export apparatus is a type III secretion system that is required for translocation of most of the flagellar proteins that localize outside the cell membrane. 

It is composed of 36 different proteins, subdivided in 8 functional sections to name:

- Early and late Gene products ( 4 proteins )
- Filament proteins ( 4 proteins )
- Hook-Filament junction ( 2 proteins )
- Basal body proteins ( 8 proteins )
- Bacterial Chemotaxis proteins ( 3 proteins )
- Motor/Switch ( 2 proteins )
- Bacterial secretion system proteins ( 7 proteins )
- Cytoplasmic chaperone proteins ( 6 proteins )

To build a flagellum, more than two dozen proteins need to assemble in an ordered process. 
The flagellar/motility/chemotaxis gene system constitutes a regulon, i.e, an integrated hierarchy of controlled expression of about 50 genes, excluding receptor genes of which there are perhaps 20.
The gene clusters encoding the components of the flagellum can include >50 genes,  the total of core genes to 24.  Some of the genes are known to be essential for proper functioning of the flagellar system in a particular species. 
The  flagellar filament capping protein is composed of the FliD protein and plays an essential role in the polymerization of the filament protein, flagellin
The FliC flagellar filament structural protein is essential for Flagellum Formation and Motility
The FlgL and FlgK  flagellar hook-filament junction protein are indispensable for the formation of the flagellum
The assembly of a flagellum occurs in a number of stages, and the “checkpoint control” protein FliK functions in this process by detecting when the flagellar hook substructure has reached its optimal length.
The FlgD flagellar basal-body rod modification protein FlgD is a scaffolding protein needed for flagellar hook assembly
Five proteins make up the flagellar rod: FlgB, FlgC, FlgF, FlgG and FliE.  The rod acts as a drive shaft to transmit torque from the motor through the flexible hook to the flagellar filament thus essential for allowing for bacterial locomotion
Five proteins (FliE, FlgB, FlgC, FlgF, and FlgG) are involved in assembly of the rod
The FlgG flagellar basal-body rod L-ring protein assembles around the rod to form the L-ring and protects the motor/basal body from shearing forces during rotation 
The FlgH flagellar L-ring protein is essential in Gram-negative bacteria
The N- and C-terminal regions of FlgF and FlgG play decisive roles in heteromeric interactions.
A disruption in FlgI causes a motility defect because the flagellar construction terminates at the rod structure.
Flagellar basal body protein FliE is required for flagellin production and to induce a proinflammatory response in epithelial cells.
The FlgB flagellar basal-body rod protein is required for the assembly of the flagellar hook and filament
The FlgI flagellar P-ring protein is known to be indispensable for P ring formation    
The flagellar basal body protein FliE is required for flagellin production and to induce a proinflammatory response in epithelial cells.
flgB flagellar basal-body rod protein
Rod assembly occurs by export via the flagellum-specific pathway of its constituent proteins and by their incorporation into the rod structure in the probable order of FlgB, FlgC, FlgF and FlgG
FlgC is one of four proteins that comprise the rod section of the basal-body assembly of the flagellar motor
FliF is the basic subunit that polymerizes to form the MS ring structure complex of the flagellar basal body
Charged residues of the rotor protein FliG essential for torque generation in the flagellar motor of Escherichia coli
The flagellar switch composed of three proteins, FliG, FliM, and FliN. The switch complex modulates the direction of flagellar motor rotation in response to information about the environment received through the chemotaxis signal transduction pathway.
MotA and MotB comprise the stator element of the flagellar motor complex. Required for rotation of the flagellar motor.
There are nine proteins (FliH, FliI, FliJ, FlhA, FlhB, FliO, FliP, FliQ and FliR) that are truly central to the flagellar export apparatus, in the sense that they participate in the export of all known substrates. Strictly speaking, only six of these components are essential when a broad range of flagellated species is considered; FliH, FliJ, and FliO are not always present.
There are at least three specific cytoplasmic chaperones, FlgN, FliS and FliT, which associate with their substrates, the hook-filament junction proteins, flagellin, and the filament capping protein, respectively. They do prevent substrate degradation
FliJ is essential for the export of flagellum building blocks
FlgA and flgI, are known to be indispensable for P ring formation. 
The flagellar fliR is needed for flagellation 
The FlhD/FlhC Complex, a Transcriptional Activator of Flagellar Class II Operons
The anti-sigma factor FlgM and the sigma factor FliA jointly control the expression of late flagellar genes in H. pylori, in particular of the major filament protein FlaA


Filament proteins
fliD flagellar filament capping protein
fliC flagellar filament structural protein

Hook-Filament junction
flgL flagellar hook-filament junction protein
flgK flagellar hook-filament junction protein

FliK  flagellar hook-length control protein
FlgD flagellar basal-body rod modification protein

Basal body proteins
flgG flagellar basal-body rod protein
flgH flagellar L-ring protein
flgF flagellar basal-body rod protein
flgI flagellar P-ring protein
fliE  flagellar basal-body protein
flgB flagellar basal-body rod protein
flgC flagellar basal-body rod protein
fliF flagellar basal-body MS-ring and collar protein

Bacterial Chemotaxis
fliG flagellar motor switch protein
fliM flagellar motor switch protein
FliN flagellar motor switch protein

Motor/Switch
motA motility protein A
motB motility protein B

Bacterial secretion system
fliH flagellar biosynthesis protein
fliI  flagellum-specific ATP synthase
fliO flagellar biosynthesis protein
fliP flagellar biosynthesis protein
fliQ flagellar biosynthesis protein
flhB flagellar biosynthesis protein
flhA flagellar biosynthesis protein

Cytoplasmic chaperones
flgN flagellar biosynthesis protein
fliJ   flagellar biosynthesis protein
fliS flagellar biosynthesis protein
fliT flagellar biosynthesis protein
flgA flagellar basal body P-ring formation protein
fliR flagellar biosynthesis protein

Early and late Gene products
flhC DNA-binding transcriptional dual regulator
flhD DNA-binding transcriptional dual regulator
fliA RNA polymerase, sigma 
flgM anti-sigma factor for FliA

To build a flagellum, more than two dozen proteins need to assemble in an ordered process. The accurate size and subunit composition of each substructure of this nanomachine is achieved by coupling gene expression to the assembly state.
http://www.els.net/WileyCDA/ElsArticle/refId-a0000301.html

Disruption of any flagellar component causes the assembly of flagellar structure to arrest
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885626/

The flagellar/motility/chemotaxis gene system constitutes a regulon, i.e, an integrated hierarchy of controlled expression of about 50 genes, excluding receptor genes of which there are perhaps 20.
https://www.sciencedirect.com/science/article/pii/S0167488904001016

The gene clusters encoding the components of the flagellum can include >50 genes.The bacterial flagellum has received attention as an exemplum of biological complexity; however, how this complexity and diversification have been achieved remains rather poorly understood. The actual series of evolutionary events that have given rise to the flagellum, as might be inferred from the relationships of all genes that contribute to the formation and expression of this organelle across taxa, has never been accomplished.Because present-day distributions of these three genes are attributable to secondary loss, they too should be considered as part of the ancestral set of genes specifying the bacterial flagellum, bringing the total of core genes to 24.  Some of the genes are known to be essential for proper functioning of the flagellar system in a particular species. The origins of complex organs and organelles, such as the bacterial flagellum and the metazoan eye, have often been subjects of conjecture and speculation because each such structure requires the interaction and integration of numerous components for its proper function, and intermediate forms are seldom operative or observed.

The evolutionary claim:
The flagellum originated very early, before the diversification of contemporary bacterial phyla, and evolved in a stepwise fashion through a series of gene duplication, loss and transfer events. The bacterial flagellum too originated from “so simple a beginning,” in this case, a single gene that underwent successive duplications and subsequent diversification during the early evolution of Bacteria.

https://www.pnas.org/content/104/17/7116

Michael Behe's response to the paper:
DARWINISM GONE WILD: Neither sequence similarity nor common descent address a claim of Intelligent Design
https://evolutionnews.org/2007/04/darwinism_gone_wild_neither_se/

Filament proteins
The  flagellar filament capping protein is composed of the FliD protein and plays an essential role in the polymerization of the filament protein, flagellin
https://www.ncbi.nlm.nih.gov/pubmed/8683574

The FliC flagellar filament structural protein is essential for Flagellum Formation and Motility
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045070

Hook-Filament junction
The FlgL and FlgK  flagellar hook-filament junction protein are indispensable for the formation of the flagellum
https://www.nature.com/articles/s41598-018-32460-9

FliK  flagellar hook-length control protein 
The assembly of a flagellum occurs in a number of stages, and the “checkpoint control” protein FliK functions in this process by detecting when the flagellar hook substructure has reached its optimal length.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206646/

The FlgD flagellar basal-body rod modification protein FlgD is a scaffolding protein needed for flagellar hook assembly
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC205349/

Basal body proteins
Five proteins make up the flagellar rod: FlgB, FlgC, FlgF, FlgG and FliE.  The rod acts as a drive shaft to transmit torque from the motor through the flexible hook to the flagellar filament thus essential for allowing for bacterial locomotion
http://vm-trypanocyc.toulouse.inra.fr/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=FLGF-FLAGELLAR-MOTOR-ROD-PROTEIN 

Five proteins (FliE, FlgB, FlgC, FlgF, and FlgG) are involved in assembly of the rod
https://pdfs.semanticscholar.org/167d/061efff99608b7fbb2e98f8c4aebe638453a.pdf

The FlgG flagellar basal-body rod L-ring protein assembles around the rod to form the L-ring and protects the motor/basal body from shearing forces during rotation 
https://string-db.org/network/360105.CCV52592_0104

The FlgH flagellar L-ring protein is essential in Gram-negative bacteria
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895218/


The N- and C-terminal regions of FlgF and FlgG play decisive roles in heteromeric interactions.
https://jb.asm.org/content/198/3/544

A disruption in FlgI causes a motility defect because the flagellar construction terminates at the rod structure.

Flagellar basal body protein FliE is required for flagellin production and to induce a proinflammatory response in epithelial cells.
https://www.ncbi.nlm.nih.gov/pubmed/11821427

The FlgB flagellar basal-body rod protein is required for the assembly of the flagellar hook and filament
http://www.subtiwiki.uni-goettingen.de/v3/gene/view/1C6C8DB02E10EAC0588389D9F0D3AF3E19172C5C

The FlgI flagellar P-ring protein is known to be indispensable for P ring formation    
http://www.microbiologyresearch.org/docserver/fulltext/micro/146/5/1461171a.pdf?expires=1544265470&id=id&accname=guest&checksum=2ECAB0B7AA0F00F5526FF431D590956F

The flagellar basal body protein FliE is required for flagellin production and to induce a proinflammatory response in epithelial cells.
https://www.ncbi.nlm.nih.gov/pubmed/11821427

flgB flagellar basal-body rod protein
Rod assembly occurs by export via the flagellum-specific pathway of its constituent proteins and by their incorporation into the rod structure in the probable order of FlgB, FlgC, FlgF and FlgG
https://www.uniprot.org/uniprot/P0ABW9

FlgC is one of four proteins that comprise the rod section of the basal-body assembly of the flagellar motor
https://www.ncbi.nlm.nih.gov/pubmed/2181149

FliF is the basic subunit that polymerizes to form the MS ring structure complex of the flagellar basal body
https://www.ncbi.nlm.nih.gov/gene/946448

Bacterial Chemotaxis
Charged residues of the rotor protein FliG essential for torque generation in the flagellar motor of Escherichia coli
https://www.ncbi.nlm.nih.gov/pubmed/9102466

The flagellar switch composed of three proteins, FliG, FliM, and FliN. The switch complex modulates the direction of flagellar motor rotation in response to information about the environment received through the chemotaxis signal transduction pathway.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC178617/

Motor/Switch
MotA and MotB comprise the stator element of the flagellar motor complex. Required for rotation of the flagellar motor.
https://www.uniprot.org/uniprot/P28611

Bacterial secretion system
There are nine proteins (FliH, FliI, FliJ, FlhA, FlhB, FliO, FliP, FliQ and FliR) that are truly central to the flagellar export apparatus, in the sense that they participate in the export of all known substrates. Strictly speaking, only six of these components are essential when a broad range of flagellated species is considered; FliH, FliJ, and FliO are not always present.
https://www.sciencedirect.com/science/article/pii/S0167488904001016

Cytoplasmic chaperones
There are at least three specific cytoplasmic chaperones, FlgN, FliS and FliT, which associate with their substrates, the hook-filament junction proteins, flagellin, and the filament capping protein, respectively. They do prevent substrate degradation
https://www.sciencedirect.com/science/article/pii/S0167488904001016

FliJ is essential for the export of flagellum building blocks
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024577/

FlgA and flgI, are known to be indispensable for P ring formation. 
http://mic.microbiologyresearch.org/content/journal/micro/10.1099/00221287-146-5-1171

The flagellar fliR is needed for flagellation
http://europepmc.org/abstract/MED/9324257

Early and late Gene products
The FlhD/FlhC Complex, a Transcriptional Activator of Flagellar Class II Operons
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC197124/pdf/jbacter00041-0229.pdf

The anti-sigma factor FlgM and the sigma factor FliA jointly control the expression of late flagellar genes in H. pylori, in particular of the major filament protein FlaA
https://jb.asm.org/content/191/15/4824

To build a flagellum, more than two dozen proteins need to assemble in an ordered process. The accurate size and subunit composition of each substructure of this nanomachine is achieved by coupling gene expression to the assembly state.
http://www.els.net/WileyCDA/ElsArticle/refId-a0000301.html

More than two dozen proteins need to assemble means it cannot be less than that. In other words, if this number is reduced, the function is lost. By definition, this means the system is irreducibly complex. 

Disruption of any flagellar component causes the assembly of flagellar structure to arrest
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885626/

That sentence speaks for itself. Any of the 36 protein components are necessary, and cannot be disrupted, or the systems will not assemble. 

The flagellar/motility/chemotaxis gene system constitutes a regulon, i.e, an integrated hierarchy of controlled expression of about 50 genes, excluding receptor genes of which there are perhaps 20.
https://www.sciencedirect.com/science/article/pii/S0167488904001016

The gene clusters encoding the components of the flagellum can include >50 genes.The bacterial flagellum has received attention as an exemplum of biological complexity; however, how this complexity and diversification have been achieved remains rather poorly understood. The actual series of evolutionary events that have given rise to the flagellum, as might be inferred from the relationships of all genes that contribute to the formation and expression of this organelle across taxa, has never been accomplished.Because present-day distributions of these three genes are attributable to secondary loss, they too should be considered as part of the ancestral set of genes specifying the bacterial flagellum, bringing the total of core genes to 24.  Some of the genes are known to be essential for proper functioning of the flagellar system in a particular species. The origins of complex organs and organelles, such as the bacterial flagellum and the metazoan eye, have often been subjects of conjecture and speculation because each such structure requires the interaction and integration of numerous components for its proper function, and intermediate forms are seldom operative or observed.


The author openly admits that evolutionary explanations are not satisfactory, and the core genes is 24. That means, if one of these 24 genes is removed, genesis of the flagellum cannot occur. That, once again, demonstrates irreducible complexity. 

Bacterial flagellar biosynthesis is a complex and ordered process requiring the coordinated and temporal regulation of dozens of genes via a transcriptional hierarchy.

https://reasonandscience.catsboard.com/t1528-flagellum-behe-s-prime-example-of-irreducible-complexity#6355

The organization of flagellar genes varies greatly among bacteria. In some bacteria the flagellar genes are arranged within a few operons that are clustered together within the chromosome (e.g., Sinorhizobium meliloti). In contrast, the flagellar genes in Helicobacter pylori are arranged in over 20 operons that are scattered around the chromosome. Temporal regulation of flagellar genes ensures that the structural proteins of the flagellum are produced as they are needed for assembly of the nascent flagellum. In the assembly pathway, the basal body is generated first, followed by the hook and then the filament.

Sequential expression of flagellar genes is achieved through the integration of regulatory networks that control the expression of different sets of flagellar genes. These regulatory networks are responsive to specific checkpoints in flagellar biosynthesis which helps coordinate flagellar gene regulation with assembly. Temporal regulation of flagellar genes is also subject to developmental control in many bacterial species that exhibit a dimorphic lifestyle

MASTER REGULATORS
In traditional flagellar gene transcriptional hierarchies, the first genes to be transcribed encode regulatory proteins that initiate transcription of the early structural genes. This regulator is referred to as the master regulator,
and it recognizes elements in the promoter regulatory regions of genes whose products are required at the earliest steps of flagellar assembly. Traditionally, genes encoding the master regulator are termed class I genes.

FlhDC is the most extensively studied master regulator. Expression of flhDC is controlled by several regulators including but not limited to the heat shock proteins DnaK, DnaJ, and GrpE, which respond to changes in temperature
H–NS, which responds to changes in pH, OmpR, which responds to osmolarity ( Osmotic concentration is the measure of solute concentration )  and cAMP–CAP, which responds to the availability of carbon sources. Additional signals that affect flhDC expression include quorum sensing ( quorum sensing is the ability to detect and to respond to cell population density by gene regulation ).  flhDC is not unique with regard to the multiple environmental signals that mediate its expression through global regulators. Thus, transcription of other master regulator genes is likely also regulated in a cell cycle-dependent fashion similar to E. coli flhDC.


Regulation of the flagellar master regulator FlhDC. 
Multiple regulatory proteins influence the expression of flhDC in response to various environmental factors, andstill other regulators influence mRNA stability, protein stability, or activity. Arrowheads indicate a positive effect while blunt-ends indicate a negative effect.

FlhDC recognizes sites located approximately 28–88 bp upstream of the transcriptional start site of its target genes, which overlap the -35 promoter elements of these genes. FlhDC activates transcription of genes whose products include components of the flagellar protein export apparatus, basal body, hook, and the regulatory proteins FliA and FlgM.


https://royalsocietypublishing.org/doi/full/10.1098/rsos.171854
More:
https://evolutionnews.org/2011/03/michael_behe_hasnt_been_refute/

At low speeds, the flagellum rotation proceeds in steps

The bacterial flagellar motor is a highly efficient rotary machine used by many bacteria to propel themselves. It has recently been shown that at low speeds its rotation proceeds in steps. The storage of energy in protein springs accounts for this stepping behavior as a random walk in a tilted corrugated potential that combines torque and contact forces. The absolute angular position of the rotor is crucial for the step properties, in particular the observation that backward steps are smaller on average than forward steps.  The storage of energy in protein springs by the flagellar motor may provide useful general insights into the design of highly efficient molecular machines. Many species of bacteria swim to find food or to avoid toxins. Swimming motility depends on helical flagella that act as propellers. Each flagellum is driven by a rotary molecular engine–the bacterial flagellar motor–which draws its energy from an ion flux entering the cell. Despite much progress, the detailed mechanisms underlying the motor's extraordinary power output, as well as its near 100% efficiency, have yet to be understood. Surprisingly, recent experiments have shown that, at low speeds, the motor proceeds by small steps (∼26 per rotation), providing new insight into motor operation. A simple physical model can quantitatively account for this stepping behaviour as well as the motor's near-perfect efficiency and many other known properties of the motor. Torque is generated via protein-springs that pull on the rotor; the steps arise from contact forces between static components of the motor and a 26-fold periodic ring that forms part of the rotor.

Bacteria swim by virtue of tiny rotary motors that drive rotation of helical flagella. These motors are powered by a transmembrane proton or sodium ion  flux which is converted into torque. At low speeds, the bacterial flagellar motor proceeds by steps. The free-energy source for the motor is an inward-directed electrochemical gradient of ions across the cytoplasmic membrane, the protonmotive force or sodium-motive force for H+-driven and Na+-driven motors, respectively. 1  There is a stepping motion of a Na+-driven flagellar motor at low sodium-motive force and with controlled expression of a small number of torque-generating units. We observe 26 steps per revolution, which is consistent with the periodicity of the ring of FliG protein, the proposed site of torque generation on the rotor. 

At low speeds, the bacterial flagellar motor proceeds by steps. This stepping is stochastic in nature, as manifested by the occurrence of occasional backward steps even for motors locked in one rotation direction. What is the origin of motor steps and how can these steps be reconciled with the near perfect efficiency of the motor observed at low speeds?  Steps, including backward steps, are an inevitable consequence of the physical structure of the motor—a stator driving a “bumpy” rotor through a viscous medium. Torque is generated by the passage of hydrogen ions (or in some organisms sodium ions) through the cytoplasmic membrane. Torque is applied to the rotor, including the flagellum, by the stator, which is comprised of independent torque-generating units (MotA/B complexes) anchored to the peptidoglycan cell wall. The maximum torque in the high load, low speed regime tracks the electrochemical potential difference or proton motive force (PMF) across the membrane, and the motor operates with nearly perfect efficiency.

Other molecular motors have shown stepping behavior, including the actin-myosin motor, the dynein-microtubule motor, and kinesin. In these ATP-powered motors, which are less powerful than the bacterial flagellar motor by orders of magnitude, stepping is a built-in and essential part of motor operation. By contrast, we have argued that in the bacterial flagellar motor the observed stepping arises solely from steric hindrance. 2


Model for stepping of the flagellar motor
A. Side view of the flagellar motor. 
B. Top view of the motor highlighting the model's essential ingredients. The passage of  across the inner membrane causes the stretching of protein “springs” which link the peptidoglycan-anchored stator complexes (MotA/B) to the rotor (FliG, etc.). In the schematic, stretched springs are attached to a stator at one end, and to an attachment site (represented by blue dots) at the other end, and apply a torque to the rotor. Contact forces between the stators and the rotor also produce a potential of interaction, which is approximately 26-fold periodic due to the 26 FliG subunits. The 26-fold periodicity of FliG and the 11-fold periodicity of the hook and filament are represented.  represents the absolute angular position of the rotor. 
C. Left: Rotation of the rotor as a whole corresponds to a viscously damped random walk in a tilted corrugated potential  arising from the combined torque and contact potential. Right: Example of a trace generated by the model (blue) and the inferred steps (red) between local potential wells (shown with purple shading).




1. http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/16208378
2. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000540#pcbi.1000540-Sowa1

A motor within a motor!! Really? The more the bacterial flagellum is understood the less it look a "hobbled together" through happenstance evolution."

"Quite surprisingly, the team shows that the stator unit itself is in fact also a tiny rotary motor. This tiny motor powers the large motor, which makes the threads rotate, causing the bacteria to move. The results contradict existing theories on the mechanism of the stator unit, and this new knowledge might be useful in the fight against bacteria-based diseases."

Even the "icon of intelligence design " continues to speak to the greatness of the designer.

https://phys.org/news/2020-09-tiny-protein-motor-fuels-bacterial.html?fbclid=IwAR0RYSyGliYbWYo1-PBK-ah8okvvhvkTkZBNlmOUJWnnnCNUzbUMJU1ZoQE

Architecture of a flagellar apparatus in the fast-swimming magnetotactic bacterium MO-1

Not a new story, but so awesome, that worth being brought to attention again. This is a prime example of irreducible complexity over irreducible complexity.

One motor is fine, thanks, but how about seven, all hooked up in parallel? The MO-1 bacteria has a sheathed stack of seven flagella, interspersed with counter-rotating elements which reduce friction. This system was analyzed by Osaka University in 2012 (see below). With this multiple motor, it swims at a rate of 300 micron/sec, slightly more than one meter/hour. A grain of talcum powder is about 10 microns in diameter.

The seven filaments are enveloped with 24 fibrils in the sheath, and their basal bodies are arranged in an intertwined hexagonal array.. ..this strongly suggests that the fibrils counter- rotate between flagella in direct contact to minimize the friction of high-speed rotation of individual flagella in the tight bundle within the sheath to enable MO-1 cells to swim at about 300 μm/s.

..http://www.osaka-u.ac.jp/en/news/ResearchRelease/2012/11/20121127_1

These bacteria are about 225 nanometers wide, slightly less than a quarter of a micron – 44 side by side would be no wider than a grain of talcum powder – so if scaled up to the size of a small speedboat, perhaps 3 meters long, its proportional speed would be in excess of 14,000 kph – about ten times the speed of sound.

https://www.pnas.org/content/pnas/early/2012/11/21/1215274109.full.pdf

40:18
Claim: Notice what he says."An irreducibly complex system can't be produced the way that evolution works, by numerous successive slight modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional."
Reply: Definition of Irreducible Complexity
Michael Behe's  Definition — [an irreducibly complex system is] "a single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning." (Darwin's Black Box, page 39, 1996)

The basic function of the system must be kept. Where the basic function is lost, that is the threshold of irreducible complexity. So if you remove 40 or 50 proteins as Dr. Kenneth Miller says, the basic function is lost.

42:32
Claim:  But the argument is that evolution can't produce the parts because the individual parts have no function of their own. That's what irreducible complexity means
Reply: What function does each of the 36 proteins employed in the flagellum play on their own?

42:43
Claim:  Well, ever since Darwin, we've had a very good explanation. And that is these complicated machines,they don't arise from scratch.They arise from combinations of components that have different functions, functions of their own, and the components originate with functions of their own as well. Let's take 40 of its 50 parts away. The parts are all gone, and I have left 10 parts that span the membrane.
What are left behind are 10 proteins in the base of the flagellum. Now if irreducible complexity is right, this should be absolutely functionless. What is left behind is the type three secretory system, and it is fully functional.
Reply: The type three secretory system is irreducible on its own right.

Qualified answers have already been given:
Why the Type III Secretory System Can’t Be a Precursor to the Bacteria Flagellum
https://evolutionnews.org/author/cluskin/

Then you have to ask, how do you go from the secretory system to the flagellum where an additional number of proteins are required, which are by themselves also only functional in the assembly of the flagellum in its entirety?

Claim:  almost every protein in the bacterial flagellum is strongly homologous to proteins that have other functions elsewhere in the cell.
Reply:  For a working biological system to be built, the five following conditions would all have to be met:
C1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time, they are needed.
C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if subsystems or parts are put together in the right order, they also need to interface correctly.
( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)


Question: How did the assembly processe emerge ?

Bacterial flagellar biosynthesis is a complex and ordered process requiring the coordinated and temporal regulation of dozens of genes via a transcriptional hierarchy.

The organization of flagellar genes varies greatly among bacteria. In some bacteria the flagellar genes are arranged within a few operons that are clustered together within the chromosome (e.g., Sinorhizobium meliloti). In contrast, the flagellar genes in Helicobacter pylori are arranged in over 20 operons that are scattered around the chromosome. Temporal regulation of flagellar genes ensures that the structural proteins of the flagellum are produced as they are needed for assembly of the nascent flagellum. In the assembly pathway, the basal body is generated first, followed by the hook and then the filament.

Sequential expression of flagellar genes is achieved through the integration of regulatory networks that control the expression of different sets of flagellar genes. These regulatory networks are responsive to specific checkpoints in flagellar biosynthesis which helps coordinate flagellar gene regulation with assembly. Temporal regulation of flagellar genes is also subject to developmental control in many bacterial species that exhibit a dimorphic lifestyle

MASTER REGULATORS
In traditional flagellar gene transcriptional hierarchies, the first genes to be transcribed encode regulatory proteins that initiate transcription of the early structural genes. This regulator is referred to as the master regulator,
and it recognizes elements in the promoter regulatory regions of genes whose products are required at the earliest steps of flagellar assembly. Traditionally, genes encoding the master regulator are termed class I genes.

FlhDC is the most extensively studied master regulator. Expression of flhDC is controlled by several regulators including but not limited to the heat shock proteins DnaK, DnaJ, and GrpE, which respond to changes in temperature
H–NS, which responds to changes in pH, OmpR, which responds to osmolarity ( Osmotic concentration is the measure of solute concentration )  and cAMP–CAP, which responds to the availability of carbon sources. Additional signals that affect flhDC expression include quorum sensing ( quorum sensing is the ability to detect and to respond to cell population density by gene regulation ).  flhDC is not unique with regard to the multiple environmental signals that mediate its expression through global regulators. Thus, transcription of other master regulator genes is likely also regulated in a cell cycle-dependent fashion similar to E. coli flhDC.


Regulation of the flagellar master regulator FlhDC. 
Multiple regulatory proteins influence the expression of flhDC in response to various environmental factors, andstill other regulators influence mRNA stability, protein stability, or activity. Arrowheads indicate a positive effect while blunt-ends indicate a negative effect.

FlhDC recognizes sites located approximately 28–88 bp upstream of the transcriptional start site of its target genes, which overlap the -35 promoter elements of these genes. FlhDC activates transcription of genes whose products include components of the flagellar protein export apparatus, basal body, hook, and the regulatory proteins FliA and FlgM.


https://royalsocietypublishing.org/doi/full/10.1098/rsos.171854
More:
https://evolutionnews.org/2011/03/michael_behe_hasnt_been_refute/

https://communities.springernature.com/posts/let-slip-the-cogs-of-war

From The Origin of Species to the origin of bacterial flagella
https://pubmed.ncbi.nlm.nih.gov/16953248/

Evolution of the spirochete endoflagellum, the smallest known, feasible? 

The spirochete endoflagellum, particularly in the genus Spirochaeta, represents the simplest known flagellar system in biology. This unique motility structure, also called a periplasmic flagellum, is located between the outer membrane and cell wall of these bacteria. Its minimalistic design consists of just three main protein components: a filament protein (FlaB), a hook protein, and a motor protein complex. This simplicity stands in stark contrast to the more complex external flagella found in other bacteria, which typically involve over 40 proteins. The spirochete endoflagellum's total protein count ranges from 5 to 10, depending on the specific species. This streamlined structure is possible due to its unique periplasmic location, which allows for effective motility with fewer components.  Each of its components is essential for function, creating an integrated system where the removal of any part would render it non-functional. This characteristic highlights the system's irreducible complexity. These proteins are highly specific to their roles within the flagellum and lack individual functions outside this system. This specificity precludes their co-option for other cellular purposes. The assembly of even this simplest flagellum requires additional proteins, estimated at 5 to 7, along with genetically encoded assembly information. The endoflagellum's structure presents challenges to conventional evolutionary explanations. Its irreducible complexity, where all components are simultaneously necessary, makes gradual evolutionary scenarios difficult to propose. The absence of functional intermediate forms between simpler structures and the complete flagellum further complicates gradual evolutionary explanations. 

Consequences of the removal of any of the proteins composing the flagellum. We focus on Borrelia, Brachyspira, and Leptospira.

1. Borrelia burgdorferi:
- FlaB: Forms the entire PF filament. Removal would likely result in complete loss of the filament structure.
- FlaA: Localized near the base of the filament. Its removal might affect the connection between the filament and the motor, potentially disrupting force transmission.

2. Brachyspira hyodysenteriae:
- FlaB1, FlaB2, FlaB3: Form the core filament. 
  - Double knockout of flaB1-flaB2 affects PF synthesis and swimming motility.
  - Double knockout of flaB1-flaB3 or single knockout of flaB3 has less impact, suggesting some functional redundancy.
- FlaA: Forms the sheath. Its removal might affect the final morphology of the PF, potentially altering its mechanical properties.

3. Leptospira species:
- FlaB1, FlaB2: Form the core filament. Removal would likely result in loss of the core structure.
- FlaA1, FlaA2: Involved in sheath synthesis, but their deletion doesn't affect sheath formation.
- FcpA: Major sheath component. Its knockout results in lack of sheath and likely affects PF coiling.
- FcpB: Sheath protein localized along the outer curve of the PF. Its removal might affect PF coiling.

General consequences


1. Loss of cell shape: In many spirochetes, PFs are crucial for maintaining the characteristic spiral or wave-like cell shape. Removal of key proteins could result in straightening of the cell body.
2. Loss of motility: As PFs are essential for spirochete motility, removal of key structural proteins would likely result in loss of swimming ability.
3. Altered cell-end morphology: In Leptospira, PF depletion affects the bent morphology of cell ends, which is crucial for their unique swimming mechanism.
4. Impaired pathogenicity: As motility is often a virulence factor, loss of PF function could reduce the pathogenicity of disease-causing spirochetes.
5. Structural instability: Proteins like the crosslinked FlgE in T. denticola provide structural stability. Their removal could lead to a less stable flagellar structure.

Proteins unique to spirochete periplasmic flagella (PFs) 

Proteins that appear more specific to spirochete PFs:

1. FcpA and FcpB (Leptospira species):
These proteins are described as specific components of the Leptospira PF sheath. The document doesn't mention any homologs in other systems, suggesting they might be unique to spirochete PFs. FcpA is described as a major sheath component crucial for coiling, while FcpB is localized along the outer curve of the PF. Their specialized roles in PF structure and function suggest they may have evolved specifically for this purpose in spirochetes.

2. FlgE with self-catalytic crosslinking (Treponema denticola):
While FlgE (flagellar hook protein) exists in other bacteria, the self-catalytic intersubunit crosslinking between conserved lysine and cysteine residues is described as a feature of T. denticola FlgE. This specific modification appears to be an adaptation for the spirochete PF, providing additional structural stability.

Proteins that are less likely to be unique:

1. FlaA and FlaB proteins:
These are flagellin proteins, and while they have specific roles in spirochete PFs, flagellins are common in many bacterial flagella. The document mentions that species with more complicated flagella often have multiple flagellins (e.g., Campylobacter jejuni, Caulobacter crescentus). Therefore, FlaA and FlaB proteins, while adapted for specific roles in PFs, likely have homologs in other bacterial systems and could have been co-opted and modified for their current function.

2. Motor components:
While spirochete flagellar motors have some unique features, they share fundamental parts (rotor and stator units) with externally flagellated species. This suggests that the basic motor structure could have been co-opted from a common ancestor and then modified for the specific needs of spirochetes.


The structural disparities between these flagellar types are substantial. Spirochete flagella, while composed of a filament, hook, and basal body, lack the additional components found in E. coli. The hypothesized evolutionary pathway must account for the emergence of new proteins and structures, such as the C-ring (FliG, FliM, FliN, FliY) and additional motor proteins (MotA, MotB) in E. coli flagella. These proteins have no clear counterparts in spirochete flagella, raising questions about their supposed gradual development. Genetic and regulatory aspects present further obstacles to evolutionary explanations. While both organisms organize flagellar genes in operons, E. coli exhibits a more elaborate hierarchical regulation system. The claimed evolution would require not only the emergence of new genes but also the development of complex regulatory networks to control their expression and assembly. This transition demands explanation at both the hardware (physical structures) and software (genetic and regulatory systems) levels. Recent quantitative studies have shed light on the magnitude of these differences. High-resolution cryo-electron microscopy has revealed detailed structures of flagellar components, emphasizing the precision required in their assembly and function. Comparative genomics analyses have highlighted the extensive genetic differences between spirochete and E. coli flagellar systems. These findings underscore the challenges in proposing a gradual evolutionary pathway between the two.

The relocation of flagellar assembly from the periplasmic space to the cell exterior represents a fundamental shift in cellular organization. This change would necessitate modifications to the cell envelope, new protein trafficking mechanisms, and altered assembly processes. The supposed evolutionary pressure driving this transition remains unclear, as both flagellar types confer motility advantages in their respective environments. Current theories attempting to explain this transition often invoke intermediate forms or co-option of existing cellular machinery. However, these hypotheses struggle to account for the functionality of partial structures or the coordinated genetic changes required.  The interdependence of flagella with other cellular systems further complicates evolutionary scenarios. Changes in flagellar structure and function would necessitate corresponding adaptations in chemotaxis systems, cell envelope composition, and energy metabolism. This interconnectedness challenges the notion of gradual, step-wise evolution.

Persistent gaps in our understanding include the lack of clear fossil evidence for intermediate forms and the limited examples of transitional flagellar types in extant species. Current evolutionary theories often resort to speculative mechanisms that lack empirical support.

Future research directions to address these challenges might include comprehensive comparative genomics of diverse bacterial flagellar systems, experimental studies attempting to recreate aspects of the supposed transition, and detailed biophysical modeling of flagellar function in various configurations. However, these approaches must be pursued with recognition of the fundamental questions that remain unanswered regarding the mechanisms and drivers of such a complex transition.

Divergent Origin of Bacterial and Archaeal Flagella

Flagella are whip-like appendages that allow bacteria and archaea to move through their environment. Despite their similar function, the structure and composition of bacterial and archaeal flagella are distinctly different. Bacterial flagella are typically composed of a single protein, flagellin, which forms a hollow tube. In contrast, archaeal flagella are composed of multiple proteins and have a more complex structure, homologous to bacterial type IV pili proteins.

Comprehensive phylogenetic analysis of flagellum-related genes from bacteria and archaea reveals that they form distinct clades, indicating the absence of a common ancestor. This supports the theory that the flagella of Bacteria and Archaea emerged independently. The lack of universally conserved flagellum-related genes across both domains further suggests distinct genetic bases for flagellum biogenesis and function. Protein sequence comparisons highlight significant differences between bacterial and archaeal flagella. Bacterial flagellin has a characteristic "D0" domain, which is absent in archaeal flagellins. Conversely, archaeal flagellins possess a unique "N-terminal" domain not found in their bacterial counterparts. The functional mechanisms of these flagella also differ. Bacterial flagella operate using a rotating mechanism driven by a motor at the base, while archaeal flagella, although also rotating, are structurally and compositionally distinct. Cryo-electron microscopy (cryo-EM) has provided further insights into the structural differences between bacterial and archaeal flagella. Bacterial flagellar filaments have 11 distinct protofilament conformations, whereas archaeal flagellar filaments are composed of 10 protofilaments in different conformations, with a notable seam absent in bacterial counterparts.

The lack of homology in proteins, distinct structural features, and independent pathways strongly support that bacterial and archaeal flagella do not share a common ancestor. Instead, they emerged independently. This highlights the importance of considering distinct histories when studying complex cellular structures across different domains of life.

Distinct Emergence and Convergence from a Polyphyletic Creation Perspective

The differences between bacterial and archaeal flagella are evidence of polyphyletic creation. This perspective suggests that the specialized structures of both bacterial and archaeal flagella were intentionally designed and created independently, rather than evolving from a common ancestor.

Key Points Supporting Polyphyletic Creation:

1. Distinct Protein Composition:
    - The unique protein compositions of bacterial and archaeal flagella, with no homology between them, could be seen as a result of independent creation events. Each type of flagellum was designed with specific proteins suited for its function, rather than evolving from a single ancestral protein.

2. Phylogenetic Distinctiveness:
    - Comprehensive phylogenetic analysis reveals distinct clades for flagellum-related genes in bacteria and archaea, which are evidence that these structures were created separately. The lack of a common ancestor in the phylogenetic trees supports the idea of multiple, independent origins.

3. Unique Structural Features:
    - The presence of unique domains in bacterial (such as the "D0" domain) and archaeal (such as the "N-terminal" domain) flagellins, which are not found in each other, can be viewed as a hallmark of distinct design principles applied to each domain of life. This suggests that each flagellum type was independently designed to meet the specific needs of the organism.

4. Functional Mechanisms:
    - The different mechanisms by which bacterial and archaeal flagella operate—both involving rotation but with distinct structural and compositional bases—are evidence of designed convergence. Each system was independently crafted to achieve similar functional outcomes (motility) through unique design strategies.

5. Cryo-EM Structural Insights:
    - The structural differences revealed by cryo-EM, such as the different numbers and conformations of protofilaments and the presence of a seam in archaeal but not bacterial flagella, point to intentional design features. These differences suggest that each flagellum type was created with its own distinct structural blueprint.

The complexity and specificity of these structures are best explained by multiple, separate acts of creation, each tailored to the needs and environments of the respective organisms. This interpretation aligns with the idea that complex cellular structures across different domains of life were individually and purposefully designed.

Convergent Evolution: A Challenge to Traditional Evolutionary Theory

The concept of convergent evolution presents significant challenges to the traditional evolutionary framework. Convergences are instances where organisms exhibit similar morphological traits despite having distinct genetic backgrounds. This phenomenon is often observed in frogs, lizards, or herbs that appear structurally identical but differ genetically. Here are key points that illustrate why convergence poses a challenge to the traditional evolutionary narrative:

Biologists have documented numerous cases where organisms cluster together based on their morphology, yet are genetically distinct. This implies that these organisms, which look almost identical, must have emerged independently, acquiring similar traits through separate pathways. This contradicts the expectation that such striking similarities should arise from a common genetic heritage. Stephen J. Gould, in his book Wonderful Life: The Burgess Shale and the Nature of History, uses the metaphor of “replaying life’s tape” to argue that evolutionary outcomes are nonreproducible. If one were to rewind and replay the history of life, the results would be entirely different each time, due to the highly contingent nature of evolutionary processes. This suggests that identical morphological traits arising independently in separate lineages is highly improbable under traditional evolutionary mechanisms. The essence of the evolutionary process, according to Gould, is that it proceeds through a series of highly improbable stages. Any slight alteration in early events would cascade into vastly different outcomes. Therefore, the occurrence of "repeatable" evolution, where similar traits emerge independently in different lineages, is inconsistent with the established mechanisms of evolutionary change.

Paleontologist J. William Schopf highlights that biochemical systems are composed of many interlinked components. As such, any fully developed biochemical system is too complex to have evolved more than once. This implies that the similar traits observed in convergent evolution could not have independently evolved multiple times, suggesting a different explanation for their origin. The phenomenon of convergence, where similar morphological traits arise in genetically distinct organisms, challenges the traditional evolutionary explanation. The complexity and improbability of these traits evolving independently multiple times suggest the need for an alternative understanding of biological diversity. This perspective considers the possibility of distinct origins for similar traits, rather than attributing them to repeatable evolutionary processes.

“…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel. "  Stephen J. Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York, NY: W.W. Norton & Company, 1989), 51.

Gould’s metaphor of “replaying life’s tape” asserts that if one were to push the rewind button, erase life’s history, and let the tape run again, the results would be completely different. The very essence of the evolutionary process renders evolutionary outcomes as nonreproducible (or nonrepeatable). Therefore, 

“repeatable” evolution is inconsistent with the mechanism available to bring about biological change. Paleontologist J. William Schopf, one of the world’s leading authorities on early life on Earth, has made this very point in the book Life’s Origin. Because biochemical systems comprise many interlinked pieces, any particular full-blown system can only arise once…Since any complete biochemical system is far too elaborate to have evolved more than once in the history of life, it is safe to assume that microbes of the primal LCA cell line had the same traits that characterize all its present-day descendants.

https://www.cell.com/cell/fulltext/S0092-8674(22)00996-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867422009965%3Fshowall%3Dtrue

[url=Nature's Incredible ROTATING MOTOR (It’s Electric!) - Smarter Every Day 300]Nature's Incredible ROTATING MOTOR (It’s Electric!) - Smarter Every Day 300[/url]



https://www.youtube.com/watch?v=PRROQdEdCnc



https://www.youtube.com/watch?v=gjOEK1CTmfk