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Theory of Intelligent Design, the best explanation of Origins » Intelligent Design » Irreducible complexity » The Flagellum, Behe's prime example of irreducible complexity

The Flagellum, Behe's prime example of irreducible complexity

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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, 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

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.

let's see the original Argument from Ken Miller:

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?

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?”


further readings:

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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 :

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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."



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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.

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The Flagellum and Bacterial Motility


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.


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6 Cell Motors Play Together on Mon Dec 07, 2015 9:30 am


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."


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

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.

2. Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook

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