https://evolutionnews.org/2024/10/kinesins-nanoscale-molecular-motors-each-built-for-a-...

"Typically, kinesins are built with 1) a set of motor domains responsible for harnessing the energy from ATP and generating force, 2) a central stalk domain that holds the motor domains together, and 3) a tail domain with specialized functions for binding different cargo.

"What is amazing about kinesins is they all get their energy from the same place (ATP hydrolysis), but they seem to use it differently for different tasks inside the cell. Some kinesins are power walkers (like the one in the video above) — taking hundreds of steps along the microtubule before falling off. Others are hoppers — only taking a few steps before letting go of the track. Some kinesins walk forward, some walk backward, and some walk in both directions (trust me…this observation is still quite puzzling from a biophysical perspective). Other kinesins don’t walk at all, but somehow use their ATP energy to trigger the microtubule track to fall apart underneath them.

"Are these differences in function a result of random haphazardness — stochastic tweaking of gene sequences to give infinitesimally small perturbations of amino acids within the motor to eventually (over billions and billions of years) produce a smorgasbord of elegant machines like the kinesin family? Many in the scientific community have faith in this hopeless Darwinian theory. Thankfully, there are a number of scientists who view the nanoscale world with wonder and are open to the idea that molecular machines reflect purpose and design. They see molecular motors as intelligently designed for a reason. These machines must function properly for cells to divide, for essential cargo to be delivered, for biochemical energy to be converted from chemical gradients into stored energy for metabolism, for the propulsion of a cell in a given direction to avoid danger."

Comment: there are many videos available to see kinesins in action walking along the tubules while carrying a cargo. All constructed from amino acids in various folding patterns. dhw to the contrary, this is the proper level for discussion of cellular activity.

https://www.chemistryworld.com/news/ultracold-snapshots-reveals-in-exquisite-detail-how...

"A series of highly detailed images of the structures found in the whirling flagellum that powers a bacterium’s movement has revealed new insights about how microbes get to where they want to be.

"Using cryo-electron microscopy (cryo-EM) two different groups have uncovered the molecular architecture of, and interactions between, key components of the bacterial motor that powers bidirectional rotation of the flagellum.

‘The whole concept of chemotaxis is the ability to move away from danger and towards food sources and many bacteria are able to do this via the flagellum … either by changing the direction in which the flagellum rotates or by stopping it completely,’ explains Steven Johnson, staff scientist at the National Cancer Institute (NCI)...

***

‘'[Salmonella] has a very simple system of turn counterclockwise to go in a straight line, turn clockwise to just start tumbling on the spot, and by combining those two different modes of operation, you can bias the direction in which the bacteria is walking,’ Johnson explains.

"The motor in the flagellum is composed of multiple rings, one of which is the cytoplasmic ring (C-ring), or ‘switch’, which is responsible for switching the rotation of the flagellum between counterclockwise and clockwise.

***

‘'It has been known for decades that the rotation direction did change and … that it’s this giant [C-]ring structure in the cytoplasm of the cell that’s responsible for that change and … that there’s a whole host of signalling receptors that respond to the external signals that then signal for this one particular molecule which combines to the C-ring motor and changes the direction the rotation occurs,’ Johnson says. ‘We also know that this rotation was partly being driven by small external stators … we learned a couple of years ago that that’s likely due to a mechanism by which the stators themselves have tiny little rotary motors…. This led to the hypothesis that the tiny rotary motors on the outside are driving this giant cog on the inside.’

"However, Johnson says what they didn’t know was how to alter the C-ring and change the direction it rotates relative to these tiny external motors, because they’re rotating in one direction.

***

"They looked at both the clockwise and the counterclockwise rotating forms and were able to define a huge structural conformational change in the C-ring, enabling directional switching.

‘'This essentially means that these little rotating motors move from being on the outside [of the big cog] to the inside, so the direction in which they drive it is reversed because essentially there is a 180° swap in conformation,’ explains Susan Lea, chief of the Center for Structural Biology at the NCI, who led the team of researchers. ‘It’s this humungous change which really extends our understanding of how big a conformational change proteins are able to make,’ she adds.

***

"However, Iverson says the questions they were trying to answer evolved over the course of the study. ‘The first questions that we had seem so trivial now – which is that this motor is powered by a gradient across the membrane of protons – a proton flux. It’s a current that runs down, transverses the membrane and can turn the rotor one way or the other. In this case, the current that goes one way can turn the motor either way and so we asked, how do you have something that’s reversible? That really wasn’t understood.’

‘'What we see after this study is almost a trivial explanation, which is you have this giant motor and a piece of the motor that responds to the current just flips around to reverse the motor.’

"Morgan Beeby, a structural biologist at Imperial College London, in the UK, welcomed the findings of the two studies. ‘Both papers determine the actual molecular architecture of a part of the motor we call the rotor – the cytoplasmic ring … the rotor component is interesting because it can also switch from rotating clockwise to counterclockwise and that’s the basis for how bacteria navigate… The key insight is a very clear, molecular rationale for how the rotor rings switches between a clockwise and counterclockwise conformation.’

‘'In isolation this result may not be that exciting, but because we’ve now got the structure of the stator component as well … we can now start saying something quite intelligent about how the thing actually works.'’

Comment: this is a highly complex reversible rotary motor powered by a proton flow. See the videos to understand how mind boggling this motor is. And it appeared with bacteria early in evolution. We generally characterize evolution as developing from simple to complex. Not so according to this study. We are seeing highly designed motors from early on. Only a designer mind fits the issue of the source..

https://inference-review.com/article/bacterial-swimming

"STUDIES OF THE bacterial flagellar motor were some of the first to take advantage of cryo-EM. David DeRosier and Keiichi Namba used cryo-EM to study the basal body and the flagellar filament, respectively.10 Structural insight into the stator units around the basal body was restricted to negative-stain reconstructions, again with limited resolution.11 Tomography gave additional insight into their organization,12 but the limited resolution of these reconstructions prevented detailed molecular understanding of torque generation.

***

"To our great surprise, we found that the stator unit is a complex with a stoichiometry of 5:2 MotA:MotB, and not 4:2 as previously believed.16 This ratio introduces an asymmetry, as 4:2 stoichiometry would most likely have been symmetric. MotA has four helices spanning the inner membrane and a cytoplasmic domain. The part of this domain most distal from the membrane is well conserved and binds the rotor. The five MotA molecules make a nearly symmetric, ringlike structure surrounding the N-terminal helices of two MotB molecules, which contain a universally conserved aspartate residue. Each of the MotB N-terminal helices is followed by a plug helix that lies between two MotA molecules. The two plugs cross over and are thought, based on prior experiments, to block activity of the stator unit. As expected, the channel appears in closed conformation.

***

"...result can be explained if it is the rotation of MotA around MotB that drives the rotation of the motor. We proposed that one of the two MotB aspartates—call it MotB1—is protonated and anchored to MotA. This is a high-energy state for MotB1, which would drive MotA rotation were it not for the aspartate of MotB2. This aspartate is both negatively charged and unprotonated: the neutral surface of MotA cannot rotate across it. But when MotB2 accepts a proton from the periplasm, it is neutralized, and rotation of the hydrophobic MotA surface across the neutralized MotB2 aspartate can now occur. After rotation, MotB2 grabs on to MotA in this new position, and MotB1 releases its proton. MotB1 then waits at the cytoplasmic side to pick up a new proton. After these steps, a 36º rotation of the MotA ring around the MotB dimer has occurred. The whole structure is in the same state as before, except that MotB1 and MotB2 have switched roles, so the cycle can begin again.

***

"How does this miniature MotAB rotary motor power the rotation of a large flagellum? Upon incorporation in the motor, the C-terminal domains of MotB dimerize and bind to the peptidoglycan layer that forms part of the cell envelope. Peptidoglycan binding is accompanied by the unplugging of the MotAB ion channel, which allows ions to flow from the periplasm to the cytoplasm. Upon ion flow, MotA rotates clockwise around MotB. Given normal swimming conditions, the rotor is engaged at the proximal side of the MotA ring, and the clockwise rotation of MotA rotates the rotor counterclockwise. When all flagella spin counterclockwise, they form a bundle and swim in a straight line.

"Upon chemotactic signaling, a whole signaling cascade takes place and results in the phosphorylation of CheY. Phosphorylated CheY binds to the rotor and switches its conformation. The rotor now interacts with the distal side of the MotA ring. The same clockwise rotation of MotA around MotB induces a clockwise rotation in the motor. One or several flagella change their rotation direction, breaking up the flagellar bundle. The bacterium starts tumbling, until CheY is dephosphorylated and gets released from the rotor and all flagella again spin in the same counterclockwise direction and the bundle reforms.

"Researchers have come a long way since Antonie van Leeuwenhoek observed moving bacteria several centuries ago. They now know bacteria swim using long filaments powered by a bidirectional, rotary proteinaceous motor. They know the molecular makeup of the rotary motor, and that this bidirectional motor is itself driven by unidirectional miniature rotary motors. Yet several unanswered questions still remain. What is the exact energy consumption of the motor—how many ions are used per rotation of MotA around MotB? How can the motor use several stator units? Do they need to act cooperatively, or can single stator units drive rotation even in the presence of other bound but non-active stator units? A combination of single-molecule light microscopy, biophysical experiments, and cryo-electron tomography is likely necessary to answer these questions."

Comment: a microscopic bacterial motor just like the ones we make macroscopically, down to what each molecule does. This is the favorite ID example of what must be designed by a mind. The quality of design is the equal of what we create. If bacteria came first, can you imagine how complex first life was in the very beginning? Remember Archaea came first and they had flagella.

https://phys.org/news/2022-11-uncovers-bacteria-ancient-mechanisms-self-repair.html

"The findings, published today in Science Advances, show how the flagellar—the ancient motor that powers the swimming ability of bacteria—can also help these tiny organisms adjust to conditions where their motility is impaired.

***

"The researchers from the School of Biotechnology and Biomolecular Sciences are the first in the world to use CRISPR gene-editing technology to alter a flagellar motor. They used synthetic biology techniques to engineer a sodium motor onto the genome to create a sodium-driven swimming bacteria. They then tested and tracked the bacteria's ability to adapt when the environment was starved of sodium.

"Sodium is an ion, which means that it carries a charge. It is this charge that powers the flagellar motor via stators, or ion channels.

"The team found that the stators were able to rapidly self-repair the flagellar motor and restore movement. These findings could lead to new advances across the biological and medical science fields.

"'We showed that environmental changes can cause ion channels to react quickly," said lead author of the paper Dr. Pietro Ridone."

Comment: this shows active immediate adaptation. a must for a single cell organism. When bacteria first appeared this vital mechanism had to be present. Only by design.

https://www.sciencedaily.com/releases/2022/09/220927111326.htm

"It has been known that the propeller in bacteria is quite different than similar propellers used by hearty one-celled organisms called archaea. Archaea are found in some of the most extreme environments on Earth, such as in nearly boiling pools of acid, the very bottom of the ocean and in petroleum deposits deep in the ground.

"Using cryo-EM, Egelman and his team found that the protein that makes up the flagellum can exist in 11 different states. It is the precise mixture of these states that causes the corkscrew shape to form.

"Egelman and colleagues used cryo-EM to examine the flagella of one form of archaea, Saccharolobus islandicus, and found that the protein forming its flagellum exists in 10 different states. While the details were quite different than what the researchers saw in bacteria, the result was the same, with the filaments forming regular corkscrews. They conclude that this is an example of "convergent evolution" -- when nature arrives at similar solutions via very different means. This shows that even though bacteria and archaea's propellers are similar in form and function, the organisms evolved those traits independently.

"'As with birds, bats and bees, which have all independently evolved wings for flying, the evolution of bacteria and archaea has converged on a similar solution for swimming in both," said Egelman,"

Comment: it is not surprising that the flagella of bacteria and Archaea are similar. Similar
solutions abound in evolution.

https://phys.org/news/2022-08-motor-proteins-cells.html

"With the help of the Canadian Light Source (CLS) at the University of Saskatchewan, a research team led by John Allingham from Queen's University and Hernando Sosa from the Albert Einstein College of Medicine has shed light on a protein that regulates the intricate microscopic networks that give cells their shape and helps ship important molecules to diverse locations.

***

"n their published work, they are the first group to clearly describe the mechanism of action of a tiny motor protein called Kinesin-8 that enables it to control the structures of microtubule fiber networks inside the cell.

"Our recent paper in Nature Communications, co-first authored by Byron Hunter and Matthieu Benoit, shows how this specific type of kinesin motor protein has developed the ability to use microtubules as tracks for movement, guiding transport of cargo within the cell," said Dr. John Allingham, a professor at the Queen's School of Medicine, "in addition to being able to disassemble these tracks, controlling their length and location in cells."

"The Kinesin-8 proteins ensure that a cell's cargo is in the right place during cellular division and help to regulate cellular networks, making sure the microtubules do not grow too long."

Comment: this precision in delivery control of cellular protein products can only result from a carefully designed controlled process. Compare it to Amazon Prime receiving a Monday order and delivering it precisely on Tuesday.

https://www.cell.com/current-biology/fulltext/S0960-9822(21)00454-1#tbox1

"Summary
Cells need to be able to sense different types of signals, such as chemical and mechanical stimuli, from the extracellular environment in order to properly function. Most eukaryotic cells sense these signals in part through a specialized hair-like organelle, the cilium, that extends from the cell body as a sort of antenna. The signaling and sensory functions of cilia are fundamental during the early stages of embryonic development, when cilia coordinate the establishment of the internal left–right asymmetry that is typical of the vertebrate body. Later, cilia continue to be required for the correct development and function of specific tissues and organs, such as the brain, heart, kidney, liver, and pancreas. Sensory cilia allow us to sense the environment that surrounds us; for instance, we see as a result of the connecting cilia of photoreceptors in our retina, we smell through the sensory cilia at the tips of our olfactory neurons, and we hear thanks to the kinocilia of our sensory hair cells. Motile cilia, which themselves have sensory functions, also work as propeller-like extensions that allow us to breathe because they keep our lungs clean, to reproduce because they propel sperm cells, and even to properly reason because they contribute to the flow of cerebrospinal fluid in our brain ventricles. Not surprisingly, defects in the assembly and function of these tiny organelles result in devastating pathologies, collectively known as ciliopathies (Box 1). Thus, the proper function of cilia is fundamental for human health."

From Evolution News:

https://evolutionnews.org/2021/06/cilium-and-intraflagellar-transport-more-irreducibly-...

"Consider first how many players are needed to build a cilium. Pigino’s parts list begins with microtubules in a 9+2 arrangement going up the cilium from base to tip. The two center microtubules are singlets; the outer ring of 9 are in doublet pairs. Riding on those rails are two engines: kinesin-2, which travels from base to tip (anterograde), and dynein-2, which goes from tip back to the base. Kinesin-2 has a head, stalk, hinge and two “feet” (called heads) that walk on the microtubule while carrying a load; the engine contains six protein subunits. Dynein-2 also has a motor, stalk, linker and tail, and is powered by two AAA+ domains that spend ATP for power. Those are the two engine types, and they work in teams along the microtubules.

"IFT proteins are numbered, such as IFT8 and IFT176. IFT complexes, such as IFT-A, is composed of six IFT proteins. IFT-B, with 16 IFT proteins is another complex. These ride along the trains to the tip, acting as adaptors for the cargo, which include tubulin proteins, dynein parts, membrane proteins and other IFT proteins.

"At the base, a basal body structure called the BBSome forms out of eight BB proteins. It functions as the cargo adaptor for the anterograde train. It authenticates other molecules trying to enter the cilium and moves cargo exiting the retrograde train. Overall, “About 24 different proteins constitute the theoretical minimal functional unit of IFT,” Pigino says, although much needs to be learned.

***

"A precise sequence of amino acids is required for each protein’s function, and the longer the protein, the more improbable that chance could get it right. IFT proteins are large. For instance, BBS1 in the BBSome has 593 amino acid residues; IFT172 (part of the IFT-B complex) has 1,749. The improbability is exacerbated when proteins have to work together. It’s not necessary to belabor the point again, but it’s instructive that Pigino never mentions evolution in her article.

"Moving cargo up and down the cilium takes place in five steps. First, the train assembles at the base. Kinesins line up along a microtubule doublet, their “heads” touching the tracks. Parts of dynein (the return engine) are loaded so as not to touch the tracks, avoiding a “tug-of-war” between the engines. Membrane parts and other cargoes are loaded with the help of IFT-A and IFT-B. Like a well-organized monorail car, the completed train “walks” up the track aided by multiple kinesin-2 engines powered by ATP.

"At the tip, the third phase begins. Cargo is unloaded and ferried to the growing cilium (microtubules and membrane). Concurrently, the dynein engines are assembled in an “open configuration as an intermediate state to ensure a controlled activation.” The kinesins are disassembled for transport back to the base. The fourth stage activates the dyneins and starts the train moving, carrying both IFT complexes and waste products to the base. The fifth and final stage unloads the cargo, disassembles the retrograde train and recycles the parts. If you conceive of railcars in a narrow mine shaft carrying tools needed by miners at the far end, and returning the carts with waste products, the analogy seems apt — only the cell’s actions are all automated."

Comment: the study of the bacterial flagellum all over again evolved into helpful celia/hairs that are vital to health. Pure irreducible complexity requiring a designer.

https://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2021.1/BIO-C.2021.1

"Systems biology [1] employs methodology and techniques typical of systems engineering. Similarly, reverse engineering the features of biological organisms leverages both biology and engineering disciplines. Specifically, the systems engineering perspective on bacterial motility detailed in Parts 1, 2 and 3 studies the purpose, functions, components, and structure of a typical bacterial flagellum and the flagellum’s assembly stages. The dynamic operation and control of this motility organelle is also studied. This study takes two essentially independent approaches below. One is a constructive approach, which this
Part 1 covers; the other is an analytical approach to be covered in Part 2. The first, constructive approach is a top-down specification. It starts with specifying the purpose of a bacterial motility organelle, the environment of a bacterium, its existing resources, its existing constitution, and its physical limits, all within the relevant aspects of physics and molecular chemistry. From that, the constructive approach derives the logically necessary
functional requirements, the constraints, the assembly needs, and the hierarchical relationships within the functionality. The functionality must include a control subsystem, which needs to properly direct the operation of a propulsion subsystem. Those functional requirements and constraints then suggest a few—and only a few—viable implementation schemata for a bacterial propulsion system. The entailed details of one configuration
schema are then set forth. This constructive approach is analogous to how a myriad of
theorems, definitions, and constructions of plane geometry are derived from the few basic axioms and the rules of logic. A sincere attempt has been made to keep the elaboration of this constructive approach logical and as independent as possible from knowledge of the actual flagellar structure. The analytic approach of this study will be covered in Part 2 and is a bottom-up deconstruction of a typical flagellum. The bacterial flagellum is a well-researched molecular subsystem, and Part 2 draws its information from many cited papers. It documents the known 40+ protein components and the observed and inferred structure, assembly, and control of a typical flagellum. However, in Part 2 the protein and assembly relationships will be illustrated graphically in a form and detail not found in any previous paper. After the constructive and analytic approaches are presented, they will be compared in Part 3 along with a set of fresh concluding observations. The comparison is appropriate, because engineers regularly specify and design systems top-down, but they construct those systems bottom-up. Then the resulting implemented system is evaluated against the specification."

***

OBSERVATIONS
"Regarding the foregoing derivation of requirements and Figures 2 to 4, we see intricate coherence which is essentially irreducible. It is hard to imagine that a motility system (comprising control, propulsion, and redirection subsystems) could function at all without each of those details present. Current evolutionary biology proposes that the flagellum
could have been “engineered” naturalistically by cumulative mutations, by horizontal gene transfer, by gene duplication, by co-option of existing organelles, by self-organization, or
by some combination thereof [10, p. 210]. See the summary and references by Finn Pond [11]. Yet to date, no scenario in substantive detail exists for how such an intricate propulsion
system could have evolved naturalistically piece by piece. Can any partial implementation of a motility system be even slightly advantageous to a bacterium? Examples of a partial system might lack sensors, lack decision logic, lack control messages, lack a rotor or stator, lack sealed bearings, lack a rod, lack a propeller, or lack redirection means. Would such partial systems be preserved long enough for additional cooperating components to evolve? Further observations will conclude Parts 2 and 3. They will include suggestions for further research into the molecular details of proteins composing the bacterial flagellum, as detailed in Part 2."

Comment: I just copied out the beginning and the end of an enormous technical engineering can analysis of the flagellum. Note my bolds. The point of this paper is always the same as the poster child for design. There must be an engineering designer.

https://www.quantamagazine.org/bacterial-organelles-revise-ideas-about-which-came-first...

"for the past few decades, researchers have been quietly uncovering many complex structures within prokaryotes, including membrane-bound organelles. In contrast to eukaryotes, which all have a suite of organelles in common, different groups of prokaryotes showcase their own specialized compartments.

***

"And that list is only growing as scientists discover more and more compartments within supposedly simple bacterial cells. “Bacteria are a lot more complex, in other words, and may have a lot more similarities in their biology to eukaryotes than people have assumed in the past,” said John Fuerst, a microbiologist at the University of Queensland in Australia. The very existence of organelles in these bacteria, coupled with intriguing parallels to the more familiar ones that characterize eukaryotes, has prompted scientists to revise how they think about the evolution of cellular complexity — all while offering new ways to probe the basic principles that underlie it.

***

“'Historically, people have known about compartments in bacterial cells that carry out specific functions for a long, long time, going back to the 1800s,” said Arash Komeili, a microbiologist at the University of California, Berkeley. Yet, while eukaryotic organelles have been studied in great detail for many decades, it has only recently become possible to do so in prokaryotes. Bacteria are tiny: orders of magnitude smaller than typical eukaryotic cells, and sometimes even smaller than eukaryotes’ organelles. That made it extremely difficult to isolate and analyze bacterial compartments to get a sense of what they were — and what they were doing.

***

"A couple of decades ago, two-dimensional imaging by Fuerst and others seemed to indicate that the DNA of the bacterium Gemmata obscuriglobus was surrounded by a membrane, instantly raising comparisons to the eukaryotic nucleus. Those results have been called into question — imaging seems to indicate that the compartment isn’t entirely closed, meaning it does not satisfy the definition of an organelle — but experts remain excited about these bacteria. They have the most complex internal membrane system seen in prokaryotes to date, and they contain proteins that structurally resemble those that shape and maintain eukaryotic membranes. They also seem capable of processes that were thought to be unique to eukaryotes, such as digesting nutrients inside their cells and synthesizing molecules called sterols.

“'The problem is, we basically don’t know anything about [this membrane system],” said Damien Devos,

***

"Bacteria also seem to have a wide variety of enclosed structures that are bound not by a lipid membrane but by a protein coat. Take carboxysomes, which evolved in bacteria twice, independently, to fix carbon. They and smaller, self-assembling nanocompartments have a polyhedral structure that looks shockingly like a viral capsid, the protein shell that encloses viral genomic material.

"The catalog keeps getting longer: Komeili and his colleagues recently discovered a new lipid-bound organelle that accumulates iron, which they’ve dubbed the ferrosome. Bacteria seem to have a cornucopia of such organelles, with more waiting to be discovered."

Comment: These studies raise the issue of just how complex was original life if it started with so-called simple bacteria. Perhaps not so simple and required a designer.

https://oscillations.net/2018/11/06/on-the-frontline-allen-liu-the-mechanome-and-synthe...

“'The design of biological motors can be classified by cataloging the motor’s general structural features, fuel type, stepping distance, stall force, and other mechanical parameters. Detailed measurements of the motility cycles and underlying mechanisms for motility also provide information about how these mechanisms work. Ultimately ‘sequencing’ the mechanome will lead to the discovery of the design features of biological motors in general, enabling us to catalogue them and outline the rules that govern their behavior.”

***

"I think Matt had an important insight that if we measure the forces and displacements of proteins under forces, we may be able to decipher the design principle of molecular machines. If you think about all the proteins that sense or respond to forces, one can argue that in principle all proteins are sensitive to forces. This is because proteins are folded into three-dimensional structures by non-covalent interactions. And if you apply a force by grabbing onto a single molecule and extend it, the protein will unfold. So by their nature, all proteins are sensitive to forces.

"The key thing the field is trying to understand now is that if a force is applied, how does it change the energy landscape of the molecular interactions. How does that force facilitate binding or unbinding to other molecular entities? We still don’t know which proteins have cryptic sites that open upon physiological force applications. To a certain extent, we have not identified all the key molecular players in force transduction.

***

"An artificial cell that does not have any encoded components. It can still come from purifying a protein out of a host cell like E. coli. A major approach is based on protein reconstitution.

"The way that this could work is—if you think about the cells in our bodies that do not have a nucleus, like red blood cells and platelets. Although these cells do not have a nucleus, they perform very sophisticated functions. For instance, a platelet is just ~2-3 microns in size, yet it has all the protein machinery enclosed within its own cell membrane and can function in blood coagulation without having any genetically encoded components.

Comment: I think of this scientist as viewing the cell as I do. Where in the platelet is the intelligence to run its functions? The interview is about a ten minute read and opens up a new area of cell research looking at how the cell's automatic reactions are controlled in part by physical forces.

https://www.sciencedaily.com/releases/2018/05/180511102316.htm

"The group led by ICREA Research Professor Cayetano Gonzalez at the Institute for Research in Biomedicine (IRB Barcelona), in collaboration with Giuliano Callaini's team at the University of Siena in Italy, has published a study in The Journal of Cell Biology that identifies the critical role played by a protein called CENTROBIN in sperm tail development.

"In flies, as in humans, the sperm cell (spermatozoon) is made up of the cell body proper, also referred to as the sperm "head," and the flagellum. The flagellum, also called the sperm "tail," is a slender lash-like appendage that protrudes from the cell body. By beating their tails, sperm cells swim to the female reproductive cell (oocyte) and fertilise it. A bundle of microtubules that span the entire length of the tail is critical for flagellar beating. These microtubules are arranged in a characteristic radial symmetry that has been conserved throughout evolution and is templated by a small organelle called the basal body, which sits at the base of the flagellum.

"Using the vinegar fly Drosophila melanogaster as a model to study how the sperm tail develops, Gonzalez's Cell Division Lab has found that CENTROBIN plays a critical role in the assembly of a subset of microtubules within basal bodies. In the absence of CENTROBIN, basal bodies lack these microtubules, as do the non-motile tails that they template. Consequently, CENTROBIN mutant males are sterile.

***

"In summary, the recent article demonstrates that CENTROBIN, which is well conserved between humans and flies, is a positive regulator of normal flagellum development. Remarkably, a previous study by the same group showed that CENTROBIN exerts a negative effect in the development of primary cilia. Primary cilia are a shorter version of flagella that are present in certain neurons in the fly and in many cell types in humans, where they function as sensors of external stimuli. Like flagella, primary cilia contain a microtubule array that is templated by the basal body.

"Taken together, these results reveal the multifunctional nature of CENTROBIN, a protein that plays opposing roles in distinct cell types in the same organism.

Once again evolution must find just the right specialized protein for a specific function and this protein has two different functions in flagella and cilia. A chance form of evolution has little likelihood of finding just the right protein molecule. a

https://phys.org/news/2018-04-bacterial-propeller.html

"Many bacteria are equipped with a flagellum, a helical propeller that allows bacteria to travel. The flagellum is assembled in a highly organized manner involving the stepwise addition of each of its internal parts. However, there are many open questions as to how this orderly construction is achieved.

***

"'Flagellar assembly is a complex process involving more than 70 genes," lead author Naoya Terahara explains. "First, the basal motor is assembled, followed by the hook, and finally the helical filament. Each structure is built by sending a unique set of proteins to the site of assembly. The cell can somehow sense when each structure is complete, triggering a switch to export the next series of proteins. We wanted to develop a more detailed picture of how this switching occurs.

"The export machinery sits at the base of the flagellum, and is made from nine copies of a protein that form a ring. The ring acts like a gatekeeper, selecting which proteins will travel out to the growing flagellum. The ring is incredibly small—mere nanometers in diameter—making precise analysis relatively difficult. To gain insight into this machinery, the researchers used high-speed atomic force microscopy. The approach, conducted through a collaborative effort with researchers at Kanazawa University, allowed the team to directly visualize the ring. By then making mutations in the ring, they could pinpoint which regions were responsible for triggering the export switch.

***

"'Our findings suggest that subtle changes in the ring's shape determine which proteins are exported to the growing flagellum," lead investigator Tohru Minamino explains. "Once the hook has been assembled, contact points in the ring shift slightly, altering the ring's shape and allowing helical filament proteins to travel through."

"The proposed model may have a significant impact on research into bacterial infections: the flagellum shares many similarities to the injectisome, a needle-like structure used by infectious bacteria to deliver proteins to their host. The study may thus serve as a map to better guide infectious disease research."

Comment: Of course atheists believe this all happened by chance. Doesn't seem reasonable to me. 70+ genes just got together naturally. Really?

https://youtu.be/3hDQYzi1XGo

Too complex for anything but a designer

Superb! Thank you. I don’t know why some folk think it’s a slap in the face for Darwinism, but I would certainly acknowledge that it is a problem for atheism.

https://youtu.be/3hDQYzi1XGo

Too complex for anything but a designer

https://www.sciencedaily.com/releases/2017/09/170912093059.htm

"Researchers have discovered a new class of enzymes in hundreds of bacterial species, including some that cause disease in humans and animals. The discovery provides new insights into how bacteria invade their hosts.

***

"'What we found in this case is that many bacteria have repurposed their flagella to function as protein-degrading enzymes. There are thousands of these enzymes, making this potentially one of the largest enzyme structures known."

"Bacterial flagella are filaments composed of around 20,000 proteins that link up together and form structures about 10 micrometers long -- roughly one-tenth the width of a human hair. While they can differ structurally, most flagella help with propulsion, and in some cases, they can attach bacteria to host cells. The discovery of flagella as enzymes means that some of them can also break down tough bonds in cells and tissues.

"We think that these enzymatic flagella may help some bacteria degrade and move through viscous environments. Interestingly, scientists have tried engineering flagella with this functionality before, but until now, we didn't know that nature already did this," said Doxey, a member of the Centre for Bioengineering and Biotechnology at Waterloo.

"To test whether these new enzymatic flagella are active, scientists examined Clostridium haemolyticum, a pathogen that's highly fatal in cows and sheep, and isolated the flagella. This pathogen has numerous flagella on one cell. They found that the flagella are capable of breaking down proteins found in cow liver -- precisely where the organism infects.

"The researchers also found the enzymes in bacteria that inhabit the human gut. Further research is needed to determine whether they play a beneficial or harmful role in humans."

Conclusion from the study: http://www.nature.com/articles/s41467-017-00599-0

"our findings provide a fascinating and multilayered story of molecular evolution, involving not only protein domain recombination, but also lateral gene transfer. First, a collagenase-related gene appears to have inserted into a flagellin hypervariable region, presumably within a collagenase-containing lineage such as Clostridium. This is consistent with numerous studies that have documented intragenic recombination in flagellins, which serves as a mechanism for antigenic diversification. It is reasonable to assume that this domain insertion likely happened after the evolution of microbial collagenase and MMP-like proteins. The proteolytic flagellin gene then spread to other microorganisms through lateral transfer "

Comment: Enzymes are giant complex molecules. This one contains zinc. This adds to the known complexity of flagella. It cannot have developed by chance evolution, as it is irreducibly complex.

https://www.sciencedaily.com/releases/2017/04/170413141058.htm

"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 report the eludication 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?"

"Eli Cohen pursued the question of rod length control in Salmonella enterica using genetic tools with slow progress until, in one of his courses, he heard about the concept of the outer membrane tethering protein Lpp, that physically links the outer membrane to the cell wall. The Salmonella envelope is composed of an inner membrane and an outer membrane that interacts with the outside world. Between the two membranes is a space containing a cell wall called the periplasm. Cell biologists previously didn't know whether the LppA protein propped up the cell wall, like pillars prop up a roof, or whether the outer membrane was tethered to the cell wall.

"Cohen, Hughes, and their colleagues engineered strains of Salmonella to determine if LppA acted as a tether for the outer membrane and whether or not the outer membrane influenced flagellar rod length. They found that varying the length of the LppA protein varied the width of the periplasm along with the length of the rod.

"'The rod needs to touch the inside of the outer membrane," Cohen says. "So, if the outer membrane is farther away, the rod has to grow there to meet it."

"'This work ended up showing that it actually is a tether holding the outer membrane down," Hughes adds. "If you don't tether it down, the outer membrane explodes away from the cell.'"

Comment: There is no way chance mutations could produce this mechanism. Only a designing mind can do it. It has to be put together all at once.

http://www.nature.com/articles/ncomms13425#f2

Abstract: "The bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook from Campylobacter jejuni by cryo-electron microscopy at a resolution of 3.5 Å. On the basis of this structure, we show that the hook is stabilized by intricate inter-molecular interactions between FlgE molecules. Extra domains in FlgE, found only in Campylobacter and in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest that Campylobacter requires an unusually strong hook to swim without its flagella being torn off. This structure reveals details of the quaternary organization of the hook that consists of 11 protofilaments. Previous study of the flagellar filament of Campylobacter by electron microscopy showed its quaternary structure made of seven protofilaments. Therefore, this study puts in evidence the difference between the quaternary structures of a bacterial filament and its hook."

***

"Flagella are found in both gram-positive and gram-negative bacteria. Although flagellar hooks appear identical at first sight, the diversity of flagellar hook proteins suggests that the hooks have diverged to specifically fit the motility requirements of each bacterium.

***

"Flagella, although macroscopically similar, have evolved features that will make them specially adapted to particular tasks. The intestinal jejunum is a viscous environment where C. jejuni is adapted for swimming25,26. The results shown here tend to support the idea that additional strengthening of the hook in C. jejuni is necessary to enable motility in this viscous environment."

Comment: Please look at the diagrams and illustrations in the article. That is the easiest way to understand the enormous complexity of this bacterial motor. Bacteria did not self-invent these motors. That is self-evident.


> dhw:If cellular intelligence exists, it is what you call the controls. If ‘dabbles' exist, of course they are rearrangements. The question is how and why your God picks on individual organisms and physically rearranges their genome to produce a nose, a kidney, a wing, or mentally guides them to fly to warmer climes or to tie complicated knots. - It is all the process of God-driven evolution. We see evolution start with bacteria and end up with us. Success! Why bother with questions about the roadmap?
> 
> DAVID: Our mind is only a small reproduction of the complexity of His mind, a minor reflection of His mind. We are created to respond to Him and relate to him.
> 
> dhw: Difficult to respond and relate to someone who deliberately remains hidden, but in any case, why would he create us in order to have us respond and relate to him? Is he lonely? Bored? - Apparently He treasures faith.