Uncommon Descent Serving The Intelligent Design Community

Amazing machine animations


Recently I came across some amazing animations of various kinds of engines and other machines at the following Web sites, which I thought I might share with readers:

Here, here, here, here and here.

Two questions to ponder:

(1) How many of these machines have analogues in the world of living things?

(2) What predictions does Intelligent Design theory make regarding which of these machines will be found in organisms?


Suck eggs Eric! :) Mung
Dionosio and UB: Too kind, but thank you. Happy Easter! Eric Anderson
Flailing Blindly: The Pseudoscience of Josh Rosenau and Carl Zimmer - Jonathan Wells - April 17, 2014 Excerpt: Kinesin (a motor which hauls protein cargo around the cell) is considerably more energy efficient than man-made machines. It has been called "a stunning example of cellular nanotechnology" and "positive evidence for design." kinesin moves quickly, with precise movements, to get from one place to another. A kinesin molecule takes one 8-nanometer "step" along a microtubule for every high-energy ATP molecule it uses, and it uses about 80 ATPs per second. On the scale of a living cell, this movement is very fast. To visualize it on a macroscopic scale, imagine a microtubule as a one-lane road and the kinesin molecule as an automobile. The kinesin would be traveling over 200 miles per hour! The fact that the cell's cytoplasm is quite crowded makes this even more remarkable -- like an automobile going 200 miles per hour through a traffic jam. http://www.evolutionnews.org/2014/04/flailing_blindl084521.html bornagain77
A metaphor I have adopted for the issue of design in nature is the double play in baseball as described at: http://ayearningforpublius.wordpress.com/2012/03/25/darwin-and-baseball/ Hard to understand how undirected forces could arrive at the machine that was Tony Kubec > Bobby Richardson > Moose Scowron ayearningforpublius
Pity American baseball clubs are able to offer immeasurably more to West Indian players, KF, as I believe most of your most gifted cricketers or potential cricketers 'took the President's shilling', so to speak. Your cricket team were regular world-beaters at one time, weren't they? Axel
EA: Spot on, keep that line and length. Under that kind of pressure, sooner or later you will get an edge, and the ball will duly be caught in slips or gully. KF PS: For BH, line towards wicket, & length of the point of bouncing up from the pitch are main tactics of the bowler. A batsman under pressure tends to err, and if the ball is struck by the edge not the sweet spot "meat" of the bat, it tends to pop up, an easy catch for the five most aggressive fielding positions. "Catches win matches." PPS: The force of the minimal, core ID claim is why clever and ruthless Darwinist objectors so often try to divert focus or obfuscate the issue. kairosfocus
Axel @ 13: Batting on the back foot . . . a cricketing expression. Let's enlighten the benighted heathen -- look, even Piltdown man was playing Cricket. [The hint is deliberate.] On the back-foot, one is forced to play defensive strokes against aggressive bowling; as the batting stance has -- for RH batsman, L foot forward, R back, somewhat sideways to the bowler at the other end of the pitch and with head turned to watch the bowler, bat gripped in hands to stroke at the ball and defend the wicket behind. On the defence, one is simply stopping the ball, not trying to hit it some distance to run or if it crosses the boundary, an automatic 4 or 6 . . . 6 if you hit cross the boundary without the ball touching the ground inside the boundary once it has been hit. Though, once, Sir Vivian Richards (next island over) turned such a stroke into a 6. KF kairosfocus
#19 I agree, Eric is a sharp (and even-handed) resource on UD. Upright BiPed
Eric Anderson @ 17 Thank you so much for taking the time to explain the subject so clearly. I'm learning quite a bit from what some of you write in this blog. Dionisio
Hi everyone, Here are a few more links I've dug up: http://www.nature.com/nnano/archive/subject_nnano_s4_012013.html Molecular machines and motors archive http://www.icmr.ucsb.edu/programs/documents/GarciaGaribay2.pdf (Excellent slides; contrasts between macroscopic and molecular machines) http://www.gracevalley.org/teaching/2002/Lifes_Molecular_Machines.html (Two-stroke engine ATP) http://www-als.lbl.gov/index.php/holding/316-rotary-firing-in-ring-shaped-protein-explains-unidirectionality.html (Rotary or radial engine) http://www.evolutionnews.org/2013/01/spectacular_new_1068501.html (ATP) http://www.evolutionnews.org/2013/04/are_we_right_to071511.html http://www.evolutionnews.org/2013/03/car_motor_cell070451.html http://www.gracevalley.org/teaching/2002/Lifes_Molecular_Machines.html (F1 Rotary motor) No biological analogues of 4-stroke engines, Stirling engines, Boxer engines or Wolfhart engines, so far. vjtorley
Dionosio @12:
Is that a general prediction based on the empirical fact that all complex specified purpose-oriented functional information we know of, has been produced only by intelligent causes?
Basically, yes. Think of it this way: What is intelligent design? In essence, intelligent design is the claim that certain things are best explained as the result of intelligent activity rather than unintelligent natural processes. And what kinds of things fall in that category? Things that exhibit complex specified information. So we can reword slightly and say: ID claims that things which exhibit complex specified information are the result of intelligent activity. That's it. Nothing about the designer. Nothing about what kinds of designs might be implemented in particular cases. If we reformulate the ID claim as a prediction, and formulate it in a way that is falsifiable, then we can say: ID predicts that we will not find complex specified information arising solely from unintelligent natural causes. But that is it. ID doesn't, nor can it, predict anything about the identify of the designer, which designs will be implemented in particular cases, whether (in addition to design) there might be some broken machines, messiness, natural processes at work in the world. It is true that once we have concluded design in a particular case we might -- based on our general understanding of design approaches and processes -- put forward some hypotheses, some working assumptions, some research questions that can guide us in further inquiry. For example, I have personally stated on this forum that I anticipate only a small percentage of DNA (5-10% or less) will end up being non-functional. But that is based on my experience with and understanding of what is required for an information-rich, highly-functional, robust, engineered system. It is not a "prediction" of ID. And I try to be careful when sharing such working assumptions or engineering expectations that I am not presenting them as flowing from, or being predictions of, ID. Without a desire to step on anyone's toes, I would just reiterate that I think every ID proponent should use similar caution. The design question is very limited and specific. Implications, expectations, additional avenues of inquiry may flow from an affirmative answer of design. But we must not conflate the latter with the former. That is why the answer, the only correct answer, to vjtorley's second question in the OP is "None." Eric Anderson
It is not even as if it were a question of their having their own facts, in lieu of their own opinions. It seems a hilarious irony that the likes of Lewontin, in the forays into Quantum Mechanics I imagine he is obliged to make, on occasions, simply CANNOT avoid thereby allowing God 'a foot in the door'. So what do they do they? Effectively stick their fingers in their ears, and chant, 'Woo-Woo! Woo-Woo! Woo-Woo!' Axel
Yes, BA77. That is the pivot, and the key to QM identified by the very founders of QM, Planck, Bohr, and seemingly unwittingly, by Einstein in his work relating to light and its observer. 'Axel, I certainly think that many findings of Quantum Mechanics should receive much more acclaim than they have so far.' I think you are far too diffident, BA. Is it not a single-answer question: yes or no? Is it not beyond the conjectural, beyond the theoretical (for all practical purposes (in a very literal sense, seemingly, also. Ironically, it has to be said, in view of its evocations of woo-woo, in the materialist's wee bonce ...!!!), and has now long been established as an iron-clad truth. In short, for them, it's 'the elephant in the living-room'. 'Off the dial' scandalous. Imagine if a high-school student refused to accept quadratic equations, or a grade-school pupil, the first half of the alphabet! I understand that in science, as in any professional field, one would have to go along to get a long, to a certain extent, so I understand your patience and diffidence with said 'ostriches'. Nevertheless, I am absolutely dumbfounded that 'our friends' have been permitted to get away with ignoring this primordial physical fact, very much concerning matter, as well as mind, of course, and to freely range the heavens in gratuitous flights of metaphysical fancy, all of which latter seem to signally fail to throw any light at all on anything. Axel
Axel, I certainly think that many findings of Quantum Mechanics should receive much more acclaim than they have so far. They certainly turned my simplistic materialistic notions of reality upside down,,,, There are only two options really to consider. Consciousness is either foundational to material or material is foundational to Consciousness. And from every angle, some angles more clear than others, Consciousness is found to be foundational in quantum mechanics. And that is the one thing that materialists either can't, or refuse, to see and has Naturalists invoking all sorts of bizarre scenarios trying to deny the reality of their own, and God's, mind,,, "Anyone who is not shocked by quantum theory has not understood it." Niels Bohr bornagain77
It strikes me, BA77, that 'OID', for Optimal Intelligent Design' should be substituted for 'ID', in references to the innumerable sublimely-sophisticated designs evidenced in the natural world. It seems that eventually, all Nature's designs prove to be not just smarter than man's, but optimally so. Such a neologism would ratchet up the adversarial assertiveness of your contentions, aiming to put them in their rightful place: 'on the back foot'. Remember, this blog has an enviable 'cachet' among the denizens of dirt-worship, since rejection of their posts here seems to cause them anxiety and petulance. As in the history of science up to the present day, if the truth be told, the best brains in science who post in the English language, post here and to kindred theistic blogs. Which brings me to another matter: You are often accused by the more thoughtless noggin-heads of materialism of spamming, as, again and again, you are reduced to repeating what seems to me to be the findings of QM, founded entirely on a mathematical basis, i.e. mathematically proven, checked and double-checked. Is it not high time you and similarly competent boffins collaborated in drafting a comprehensive compendium of the unfalsified, indeed, de facto, unfalsifiable, truths of physics, the theistic implications of which the aforesaid, irrational materialists refuse, point blank, to accept, manifestly on purely religious grounds - and IN THE TEETH OF MATHEMATICALLY-VERIFIED PHYSICS. In terms of the ultimate study of matter, the days of classical, Newtonian, mechanistic physics are long past, now, and they must be forced to get over it. Hinting that QM is weird, woo-woo, and can't really be seriously taken into account from a theoretical viewpoint. Eugene Wigner et al are not conjectural 'outliers', just eccentric mavericks with a woo-woo 'bee in their bonnet', are they? Mathematical proof of the human mind's ability to influence the past, surely merits the closest, most assiduous attention on the part of all physicists; yet it is marginalized by the dirt-worshippers in favour of unalloyed nonsense, such as the infinitely 'shape-shifting' multiverse. Should it not be broadcast, popularized as a sovereign achievement of science, by the mainstream media, as were Einstein's findings? Axel
Eric Anderson @ 11
unintelligent causes on their own will never be shown to produce complex specified information.
Is that a general prediction based on the empirical fact that all complex specified purpose-oriented functional information we know of, has been produced only by intelligent causes? Is the Darwinian theory based on the scandalous extrapolation of the Galapagos finch adaptation story? Does modern science show that such adaptation is associated with the built-in adaptive mechanisms present in the biological systems? Can unintelligent causes produce those sophisticated built-in adaptive mechanisms present in the biological systems? Can unintelligent causes produce the elaborate molecular and cellular choreographies and orchestrations observed within the biological systems? Does this debate continue only because there are two opposite irreconcilable worldviews? Dionisio
(2) What predictions does Intelligent Design theory make regarding which of these machines will be found in organisms?
None. One might, of course, offer one's speculations about what kinds of things another designer might do. But it would not be a "prediction" flowing from ID. Furthermore, and I say this knowing some may get upset to hear it, ID is not primarily about making predictions. Nor is Darwinism. Both ID and Darwinism (or "evolution" more broadly) are primarily attempts to use current evidence and observations to explain historical events or to explain current artifacts we see around us. True, we might perhaps be able to come up with a couple of predictions here and there that would be inevitable predictions of the theories. However, they would be general to the theory.* But for the most part, neither one says much of anything what specific kinds of organisms or features of the natural world or biological characteristics will be discovered. And, unfortunately, many of the enthusiastic attempts to tie such suppositions and predictions to ID as though they flow inevitably from the design inference do ID a disservice. ----- * For example, ID "predicts" that unintelligent causes on their own will never be shown to produce complex specified information. But ID doesn't predict anything about whether this or that organism will have a particular gene, or a particular molecular machine, or any other specific biological feature. ID and Darwinism/evolution share quite a bit in this regard, because they both play a similar role. Eric Anderson
a few more notes: William Bialek: More Perfect Than We Imagined - March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://darwins-god.blogspot.com/2013/03/william-bialek-more-perfect-than-we.html Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail." http://www.sciencedaily.com/releases/2009/06/090616103205.htm Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.html Learning from Bacteria about Social Networking (Information Processing) - video Excerpt: I will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers. http://www.youtube.com/watch?v=yJpi8SnFXHs "To grasp the reality of life as it has been revealed by molecular biology, we must first magnify a cell a thousand million times until it is 20 kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would see then would be an object of unparalleled complexity,...we would find ourselves in a world of supreme technology and bewildering complexity." Michael Denton PhD., Evolution: A Theory In Crisis, pg.328 bornagain77
Dionisio @ 8 Follow-up to comment #2 by tragic mishap Dionisio
I refuse to read this post because vjtorley was wrong about something [science-related] once and is therefore not a credible source for anything.
I would not mind to have the scientific knowledge Dr. Torley has, and be wrong about something [science-related] once ;-) I've been wrong about many things many times :( Dionisio
A few comments on the complexity being dealt with:
We have always underestimated cells. Undoubtedly we still do today.,,, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines." (Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92 (February 6, 1998): 291-294) Venter: Life Is Robotic Software - July 15, 2012 Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said (Craig) Venter. http://crev.info/2012/07/life-is-robotic-software/ How we could create life - The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell - Paul Davies - 11 December 2002 Excerpt: Instead, the living cell is best thought of as a supercomputer - an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff - hardware - but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won't work because it addresses the problem at the wrong conceptual level. http://www.theguardian.com/education/2002/dec/11/highereducation.uk "No human contrivance operates with either the degree of complexity, the precision, or the efficiency of living cells." James A. Shapiro, "21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering," Gene, Vol. 345: 91-100 (2005) Bio-Mechanics - Don't the Intricacy & Ubiquity of Molecular Machines Provide Evidence for Design? by Casey Luskin - Spring 2012 Excerpt: molecular machines use components we commonly recognize in human machinery. They may have joints, gears, propellers, turnstiles, brakes, and clutches, which form motors, tweezers, vehicles, assembly lines, transportation networks, intelligent error-checking systems, and much more. But biomolecular machines have a major difference that distinguishes them from human technology: their energetic efficiency dwarfs our best accomplishments. One paper observes that molecular machines "are generally more efficient than their macroscale counterparts,"7 and another suggests that the efficiency of the bacterial flagellum "could be ~100%."8 Human engineers can only dream of creating such devices. http://www.salvomag.com/new/articles/salvo20/molecular-machines-evidence-for-design.php The Origin of Life on Earth Excerpt: Every living cell, even the simplest bacterium, teems with molecular contraptions that would be the envy of any nanotechnologist. As they incessantly shake or spin or crawl around the cell, these machines cut, paste and copy genetic molecules, shuttle nutrients around or turn them into energy, build and repair cellular membranes, relay mechanical, chemical or electrical messages—the list goes on and on, and new discoveries add to it all the time. It is virtually impossible to imagine how a cell’s machines, which are mostly protein-based catalysts called enzymes, could have formed spontaneously as life first arose from nonliving matter around 3.7 billion years ago. Dr. Jack Szostak - Nobel Laureate and leading Origin of Life researcher who, despite the evidence he sees first hand, still believes 'life' simply 'emerged' from molecules http://www.scientificamerican.com/article.cfm?id=origin-of-life-on-earth Problems with the Metaphor of a Cell as "Machine" - July 2012 Excerpt: Too often, we envision the cell as a "factory" containing a fixed complement of "machinery" operating according to "instructions" (or "software" or "blueprints") contained in the genome and spitting out the "gene products" (proteins) that sustain life. Many things are wrong with this picture, but one of the problems that needs to be discussed more openly is the fact that in this "factory," many if not most of the "machines" are themselves constantly turning over -- being assembled when and where they are needed, and disassembled afterwards. The mitotic spindle...is one of the best-known examples, but there are many others. Funny sort of "factory" that, with the "machinery" itself popping in and out of existence as needed!,,, - James Barham http://www.evolutionnews.org/2012/07/problems_with_t062691.html Biochemical Turing Machines “Reboot” the Watchmaker Argument - Fazale Rana - July 2012 Excerpt: Researchers recognize several advantages to DNA computers.(7) One is the ability to perform a massive number of operations at the same time (in parallel) as opposed to one at a time (serially) as demanded by silicon-based computers. Secondly, DNA has the capacity to store an enormous quantity of information. One gram of DNA can house as much information as nearly 1 trillion CDs. And a third benefit is that DNA computing operates near the theoretical capacity with regard to energy efficiency. http://stevebrownetc.com/2012/07/02/biochemical-turing-machines-%E2%80%9Creboot%E2%80%9D-the-watchmaker-argument/
Although the page is a bit disorganized, Perhaps you can find a few more useful notes here Dr. Torley:
Molecular Machines https://docs.google.com/document/d/1EudghOv3c_ktHIU-z_sEHz6SSqzLxIwllqhflBNMzws/edit#
Of course much more is out there on the web Dr. Torley, but hopefully this will provide a good start to answering your questions, bornagain77
Journey Inside The Cell – Stephen Meyer http://www.youtube.com/watch?v=1fiJupfbSpg The Ribosome of the cell is found to be very similar to a CPU in a electronic computer: Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf Endoplasmic Reticulum: Scientists Image 'Parking Garage' Helix Structure in Protein-Making Factory - July 2013 Excerpt: The endoplasmic reticulum (ER) is the protein-making factory within cells consisting of tightly stacked sheets of membrane studded with the molecules that make proteins. In a study published July 18th by Cell Press in the journal Cell, researchers have refined a new microscopy imaging method to visualize exactly how the ER sheets are stacked, revealing that the 3D structure of the sheets resembles a parking garage with helical ramps connecting the different levels. This structure allows for the dense packing of ER sheets, maximizing the amount of space available for protein synthesis within the small confines of a cell. "The geometry of the ER is so complex that its details have never been fully described, even now, 60 years after its discovery," says study author Mark Terasaki of the University of Connecticut Health Center. "Our findings are likely to lead to new insights into the functioning of this important organelle.",,, ,, this "parking garage" structure optimizes the dense packing of ER sheets and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell. When a cell needs to secrete more proteins, it can reduce the distances between sheets to pack even more membrane into the same space. Think of it as a parking garage that can add more levels as it gets full.,,, http://www.sciencedaily.com/releases/2013/07/130718130617.htm Programming of Life – Eukaryotic Cell – video http://www.youtube.com/watch?v=WVCwDOMCpXY Ben Stein – EXPELLED – The Staggering Complexity Of The Cell – video https://www.youtube.com/watch?v=zl0NXSbeeqg
The following article has a list of 40 molecular machines in the cell:
Molecular Machines in the Cell - http://www.discovery.org/a/14791 Simplest Microbes More Complex than Thought Excerpt: The smallest, simplest cells are prokaryotes.,,,One of the papers in Science to which PhysOrg referred said that some 200 molecular machines are found in this little microbe. http://www.creationsafaris.com/crev200912.htm#20091229a The Closest Look Ever At The Cell's Machines - 2006 Excerpt: The study combined a method of extracting complete protein complexes from cells (tandem affinity purification, developed in 2001 by Bertrand Séraphin at EMBL), mass spectrometry and bioinformatics to investigate the entire protein household of yeast, turning up 257 machines that had never been observed. It also revealed new components of nearly every complex already known. http://www.sciencedaily.com/releases/2006/01/060123121832.htm
Bacteriophage T4 Assembly - Assembly Of A Molecular "Lunar Landing" Machine - video https://www.youtube.com/watch?v=Ofd_lgEymto
The first thought I had when I saw the bacteriophage virus is that it looks similar to the lunar lander of the Apollo program. The comparison is not without merit considering some of the relative distances to be traveled and the virus must somehow possess, as of yet unelucidated, orientation, guidance, docking, unloading, loading, etc... mechanisms. And please remember this level of complexity exists in a world that is far too small to be seen with the naked eye.
"Acrobatic" molecular machine has now been elucidated; Excerpt: The researchers wanted to find out how MRN “can repair DNA in a number of different, and tricky, ways that seem impossible for ‘standard issue’ proteins to do,” the press release said. These proteins are not static balls of amino acids; they have dynamic, interactive, moving parts. The motor in the complex, Rad50, “is a surprisingly flexible protein that can change shape and even rotate depending on the task at hand.” http://www.creationsafaris.com/crev201103.htm#20110327b Even the Cell's Dumpster Is an Intricate Machine - February 10, 2012 Excerpt: This "massive proteolytic machine" (1.5 million atomic mass units, or 1.5 Mega-daltons) is composed of numerous protein subunits arranged in functional complexes, and is capable of degrading a wide variety of protein types. The barrel portion of the machine, where protein degradation occurs, had already been described in more detail. Inside the barrel (a stack of four rings with a cavity in the middle, composed of 28 protein parts), active sites on the inside walls cleave polypeptide chains into short segments about 7-9 amino acid units long, which can be reused by the cell directly, or further degraded into individual amino acids for recycling. Obviously, this dangerous interior must be protected, lest it run amok like a chainsaw murderer. That's why an elaborate lid structure, composed of 19 more protein parts, guards the entry gate and checks the credentials of each protein that enters. http://www.evolutionnews.org/2012/02/even_the_cells056231.html Cell Machinery Untangles Misfolded Proteins - April 2, 2013 Excerpt: biologist Helen R. Saibil, provides a model diagram of this "highly dynamic" machine and descriptions of what the parts do. There are channels, toggles, linkers, mobile lids, and dockers. One of the primary parts looks like a stack of 3-tiered rings with a channel down the middle. The other part looks a little like Pac-man, biting down on a "hot spot" on the side of the rings, accompanied by other moving parts. Each of the primary parts is further composed of several protein domains. Multiple ATP "energy pellets" power the operation at three locations. The cell first has to identify the misfolded aggregate, find a loose end, and feed it into a slot on the side-mounted machine. The docking point acts as a regulator that can reprogram the side-mounted machine according to the stage of the operation. Once threaded into the right position, the loose end is fed into the central channel of the three-tiered machine, so that untangling can proceed. The untangled polypeptide exiting the central channel can then be refolded by other chaperone machines at the ready. Only dim details of this operation are understood so far. The "mechanism" by which the strand is "handed over" from one domain to the other is "unclear," Saibil writes. It's also not clear how the tangled mess of peptide pictured in the model diagram can avoid snags as it passes through the machinery. Yet it works. Rightly, Dr. Saibil praises "the remarkable ability of cells to reverse protein aggregation." http://www.evolutionnews.org/2013/04/cell_machinery070411.html Laser Spotlight Reveals Machine 'Climbing' DNA - (Oct. 26, 2012) Excerpt: New imaging technology has revealed how the molecular machines that remodel genetic material inside cells 'grab onto' DNA like a rock climber looking for a handhold.,, The molecular machines in question are called Structural Maintenance of Chromosome (SMC) complexes: they remodel the genetic material inside every living cell and work along similar principles to a large family of molecules that act as very small motors performing functions as diverse as trafficking vital material inside cells to allowing muscles to contract.,, Up until now conventional techniques of biological physics or biochemistry have not been sufficiently fast or precise to monitor such tiny machines inside living cells at the level of single molecules.,, http://www.sciencedaily.com/releases/2012/10/121026110747.htm Molecular Biology Animations – Demo Reel http://www.metacafe.com/w/5915291/ DNA - Replication, Wrapping & Mitosis - video (notes in description) http://vimeo.com/33882804 Regulating DNA Repair Mechanisms Excerpt The DNA repair mechanisms themselves are fascinating from a design perspective. The list above includes ten different tools (more like high powered machines) that the cell has available for DNA repair, http://www.evolutionnews.org/2010/11/regulating_dna_repair_mechanis040801.html Inner Life of a Cell w William Dembski commentary - video http://www.youtube.com/watch?v=jNs5kBE66Xo
DNA helicase - molecular machine - video http://www.youtube.com/watch?v=YzNuLsqMqyE Myosin - video http://www.youtube.com/watch?v=j8F5GGPACkQ Bacterial Flagellum - A Sheer Wonder Of Intelligent Design – video http://tl.cross.tv/61771 Bacterial Flagellum - video http://www.youtube.com/watch?v=Ey7Emmddf7Y Bacterial Flagellum: Visualizing the Complete Machine In Situ Excerpt: Electron tomography of frozen-hydrated bacteria, combined with single particle averaging, has produced stunning images of the intact bacterial flagellum, revealing features of the rotor, stator and export apparatus. http://www.sciencedirect.com/science/article/pii/S096098220602286X Electron Microscope Photograph of Flagellum Hook-Basal Body http://www.skeptic.com/eskeptic/08-08-20images/figure03.jpg Souped-Up Hyper-Drive Flagellum Discovered - December 3, 2012 Excerpt: Get a load of this -- a bacterium that packs a gear-driven, seven-engine, magnetic-guided flagellar bundle that gets 0 to 300 micrometers in one second, ten times faster than E. coli. If you thought the standard bacterial flagellum made the case for intelligent design, wait till you hear the specs on MO-1,,, Harvard's mastermind of flagellum reverse engineering, this paper describes the Ferrari of flagella. " Instead of being a simple helically wound propeller driven by a rotary motor, it is a complex organelle consisting of 7 flagella and 24 fibrils that form a tight bundle enveloped by a glycoprotein sheath.... the flagella of MO-1 must rotate individually, and yet the entire bundle functions as a unit to comprise a motility organelle." To feel the Wow! factor, jump ahead to Figure 6 in the paper. It shows seven engines in one, arranged in a hexagonal array, stylized by the authors in a cross-sectional model that shows them all as gears interacting with 24 smaller gears between them. The flagella rotate one way, and the smaller gears rotate the opposite way to maximize torque while minimizing friction. Download the movie from the Supplemental Information page to see the gears in action. http://www.evolutionnews.org/2012/12/souped-up_flage066921.html The Bacterial Flagellum: A Paradigm for Design - Jonathan M. - Sept. 2012 Excerpt: Indeed, so striking is the appearance of intelligent design that researchers have modelled the assembly process (of the bacterial flagellum) in view of finding inspiration for enhancing industrial operations (McAuley et al.). Not only does the flagellum manifestly exhibit engineering principles, but the engineering involved is far superior to humanity’s best achievements. The flagellum exhibits irreducible complexity in spades. In all of our experience of cause-and-effect, we know that phenomena of this kind are uniformly associated with only one type of cause – one category of explanation – and that is intelligent mind. Intelligent design succeeds at precisely the point at which evolutionary explanations break down. http://www.scribd.com/doc/106728402/The-Bacterial-Flagellum Astonishing Molecular Machines – Drew Berry http://www.metacafe.com/w/6861283
Although, I don't know how to answer your questions properly at this time, here are a few notes that may be helpful to you in regards to meaningfully answering them in the future.
Miniature Molecular Power Plant: ATP Synthase - January 2013 - video http://www.youtube.com/watch?v=XI8m6o0gXDY ATP: The Perfect Energy Currency for the Cell - Jerry Bergman, Ph.D. Excerpt: In manufacturing terms, the ATP (Synthase) molecule is a machine with a level of organization on the order of a research microscope or a standard television (Darnell, Lodish, and Baltimore, 1996). http://www.trueorigin.org/atp.asp Your Rotary Engines Are Arranged in Factories - August 2011 Excerpt: As if ATP synthase was not amazing enough, a team of scientists in Germany now tells us they are arranged in rows with other equipment to optimize performance. From electron micrographs of intact mitochondria, they were able to detect the rotary engines of ATP synthase and other parts of the respiratory chain. Their diagram in an open-source paper in PNAS looks for all the world like a factory.,,, “We propose that the supramolecular organization of respiratory chain complexes as proton sources and ATP synthase rows as proton sinks in the mitochondrial cristae ensures optimal conditions for efficient ATP synthesis.” The authors had virtually nothing to say about how this might have evolved, noting only that the structure is “conserved during evolution” in every sample they examined (3 species of fungi including yeast, potato, and mammal). What this means is a lack of evolution over nearly two billion years, in the standard evolutionary timeline. http://crev.info/content/110817-your_rotary_engines_are_arranged_in_factories Piston Engine Joins Rotary Engine in Cells - September 2010 Excerpt: The mechanism proposed by Leonid Sazanov’s group at the Medical Research Council in Cambridge is “almost completely unexpected,” ,,, Unlike the ATP synthase, which “drives protons across the membrane in a rotary turbine-like motion,”,,, the transfer of electrons from NADH cause a slight widening of one part of the complex, forcing the long helix to move like a row of pistons that shove the protons across the membrane.,,, One faculty member “predicts that it will become one of the most cited papers in respiratory chain research, as important to our complete understanding of energy generation as is the mechanism of ATP synthase.” http://www.creationsafaris.com/crev201009.htm#20100922a Molecular picture of the 'Piston' Engine is here http://www.the-scientist.com/article/display/57654/ Powering the Cell: Mitochondria - video http://www.youtube.com/watch?v=RrS2uROUjK4 Molecular Machine - Nuclear Pore Complex - Stephen C. Meyer - video http://m.vuclip.com/w?cid=172103441 Dr. Jonathan Wells's Centriole Hypothesis - video https://www.youtube.com/watch?v=NNvXTassmHM Kinesin Linear Motor - Video http://www.youtube.com/watch?v=kOeJwQ0OXc4
I refuse to read this post because vjtorley was wrong about something once and is therefore not a credible source for anything. j/k <3 vj. :D tragic mishap
Very interesting. Thank you for posting this. Dionisio

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