Your Proton Pump Working Inside Your Inner Power Plant

A research team from the Freiburg Institute for Biochemistry and Molecular Biology uncovered the best look at one of the body’s largest enzymes known as Mitochondrial Complex I…It contains four major parts with a function to transmit the energy in the food we eat into mechanical energy by using a proton pump inside our inner power plant.

Interesting news has come out of this research…

“In a laboratory experiment, hydrogen and oxygen gas would react in an explosion and the energy contained would be released as heat.  In biological oxidation, the energy will be released by the membrane bound protein complexes of the respiratory chain in a controlled manner in small packages.

“Comparable to a fuel cell, this process generates an electrical membrane potential, which is the driving force of ATP synthesis.  The total surface of all mitochondrial membranes in a human body covers about 14.000 square meter.  This accounts for a daily production of about 65 kg of ATP.”

The energy produced across that 14 square meters of mitochondrial membrane enables the  ATP synthesis to work which keeps all of us and every living thing from bacteria to giraffes – alive! Studying these mechanical devices which there are trillions of in the body that look something like coupling rods has added years to previous research in trying to understand how Mitochondrial Complex I works! Look how science daily compares it to a railway vehicle that provides power to a train…

“The now presented structural model provides important and unexpected insights for the function of complex I.  A special type of “transmission element,” which is not known from any other protein, appears to be responsible for the energy transduction within the complex by mechanical nanoscale coupling.  Transferred to the technical world, this could be described as a power transmission by a coupling rod, which connects for instance the wheels of a steam train.  This new nano-mechanical principle will now be analysed by additional functional studies and a refined structural analysis.”

Great news in learning about the respiratory transport chain in mitochondria which includes coupling rods that act like little locomotives. These locomotives work 24 hours a day, seven days a week in the body. So what was the significance of using evolution to understand this discovery? Darwinian evolution denies designed with intelligence and a purpose in nature. In reality, it had no explanatory power whatsoever, engineering models are being used instead to understand the control principles of this biological phenomenon! So let’s get rid of the storytellers and hire the engineers!

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19 thoughts on “Your Proton Pump Working Inside Your Inner Power Plant

  1. First:

    1) Blog readership numbers ?

    (2) Your qualifications to discuss any scientific subject, in response to the challenge to Olorin.

    (3) A substantive review of Signature in the Cell, promised for August 2009.

    (4) outstanding question from Upson Downes on mitochondrial Eve

    Also,

    I still want you to refute me on what I show about the bacterial flagellum. . . .

    . . . the flagellum IS NOT EVEN IRREDUCIBLE. — G. Kuwajima was able to remove ONE-THIRD of the 497 amino acids from the flagellum, AND IT STILL WORKED PERFECTLY!!!!! . . . Also, we know that the L and the P-rings can be taken away from the flagellum, and it will STILL work. . . .

    Still waiting for a refutation . . . .

    Failure to refute can be taken as an indirect admission.

  2. You beat me again, krissmith777 !

    So Michael, when are you finally going to answer these questions ?!?!?

    Michael: “So let’s get rid of the storytellers and hire the engineers!”

    Why should we get rid of you then ? Your stories are mediocre, but getting rid of you is a bit harsh, isn’t it ?

  3. Hey, I have one too.

    Michael, why do creationists in general, and you in particular, hate dark matter?

    It seems puzzling. Just state your reason—no contumely will accrue.

  4. The energy produced across that 14 square meters of mitochondrial membrane enables the ATP synthesis to work which keeps all of us and every living thing from bacteria to giraffes – alive! [emphasis supplied]

    Do we really need any further evidence of Michael’s astounding ignorance of matters biological? Well, here it is anyway.

    Guess what, Michael. BACTERIA DO NOT HAVE MITOCHONDRIA. Michael may plagiarize sciency-sounding techno-dazzlers from his eminence grise, but his own ignorance of the most basic, elementary, and fundamental facts in biology makes scientists laugh.
    .

    Yet, just in case, here is a chance for Michael to redeem himself. Especially since he claims to have “had chemistry” at some point. OK. The Science paper mentions that the stoichiometry of Mitochondrial Complex I is “4H+/2e-“. What does this mean?

  5. Michael, do yourself (and all of us) a favor, and please answer our questions. They’re good questions. They’re not going to bite.

    You’ll be doing yourself a favor by showing that you PROBABLY do know what you are talking about.

  6. Look how science daily compares it to a railway vehicle that provides power to a train…

    ….

    Great news in learning about the respiratory transport chain in mitochondria which includes coupling rods that act like little locomotives.

    ……….

    … engineering models are being used instead to understand the control principles of this biological phenomenon!

    Michael grasps desperately at straws again. Any biological mechanism that can even be superficially analogized to a human-designed artifact is somehow “evidence” that the biological referent is also designed in the same manner..

    But the purpose of this analogy, like most in this field, is merely to provide a convenient mental picture to readers who do not have the technical background to understand the actual configuration of the transmission element. Biologists, among themselves, use “cartoons” such as Fig. 4 in the Science paper to convey functional descriptions of cellular structures. This cartoon has a bar representing a membrane. Two adjacent rectangles pierce the bar; two other rectangles are linked to one of the membrane rectangles via two helices, representing electron densities. Sorry, Michael, this looks nothing like a little locomotive. The locomotive analogy is inappropriate in other ways—for example, no physical part of the complex actually moves during proton pumping. All of the action is strictly chemical, involving proton and electron densities along the element.

    Marshall McLuhan famously said that the map is not the territory. Here, Michael mistakes the analogy for the the real thing. A biological complex “is” a human contrivance, merely on the ground of an analogy created to give the layman a mental picture to hang onto like a subway strap.

    .

    Following the lead of this blog, “New Discoveries and Comments About Creationism,” we can ask, in what way does this Science paper fit the topic? Do we have in this paper a higher level of complexity? No. Do we have here a result that contradicts any previous knowledge or theory? Again, no. Do we have any indication whatever that this structure was specially created? Don’t be silly.

    Michael, in his ignorance, seems to think that this paper reports the discovery of some previously unimagined machine for converting energy in the cell. Wrong. Scientists have known about Mitochondrial Complex I (MCI) for years. They have known it is one of the largest and most complex bodies in the cell. That’s why it took so long to noodle it out by X-ray crystallography.[0]

    And that is the subject of this paper—the structure of this long-known body has been mapped. Now we can begin to figure out how the structure produces the function. (And perhaps even what it came from.)

    The authors themselves made a beginning on this next task. An interesting helix was found to provide a “transmission element” along with electrons pass between proton pumps. Its Fe-S makeup works somewhat differently from, but homologously to, the sodium proton pump of other cellular structures. This is significant—but it is not a big discovery or a head-scratcher that requires modifications to any other knowledge. It’s as though someone discovered a gasoline engine that used rotors instead of cylinders—The discovery does not affect the theory of internal combustion; it merely provides a different way of doing it.

    Actually, this discovery supports evolution rather than design. Why would a designer implement several different structures for proton pumping, when a single one would do? (This might be a creationist research project :-)
    Further, MCI is not entirely good news. Even Michael has no doubt heard of the health claims for “anti-oxidants” to prevent everything from aging to bunions. These nostrums counteract the “reactive oxygen species” (ROS) created during metabolism. Guess where these evil ROS come from? MCI generates them. That’s right—this complex engineering miracle is also the source of an aging process. Maybe we could analogize it to the black sooty smoke from the MCI’s locomotive.

    .

    Michael hangs his creationism argument on a superficial analogy. He confuses a sop for the layman to an actual biological structure. The analogy for this MCI structure could just as easily have been, say, an artesian spring connecting an underground aquifer to a surface stream.[1]. But then artesian springs are natural, not designed, so the MCI structure would not have been designed, and Michael’s source would have flipped past it as irrelevant. When the basic nature of a thing varies depending upon the analogy you use to visualize it, then it’s time to give up the analogies as the ultimate guide to reality.[2]

    Michael’s more significant false analogy, however, is to analogize the ways of God to the ways of human design.

    ===============

    [0] Hint: X-ray crystallography is not a Hogwartian magic lantern where you plop in a blob of goo, make an incantation, and wait for a picture to issue forth. DNA took months of effort with the world’s then leading expert.

    [1] Actually, this is a much better analogy than a locomotive. The MCI structure is literally a pump for a fluid, and not at all like a mechanical linkage that drives a mass at the other end.

    [2] Does science employ analogies? Of course. Light is a “wave.” Or a “particle.” Or…both?? This example illustrates both the use and the limitations of analogies.

  7. Saturday morning I’m off to James Peebles’ birthplace, to visit relatives and friends. Back on Thursday. Don’t let Michael get away with anything.

    (I really do want to know why he denies dark matter! It seems so irrational.)

  8. Olorin: “(I really do want to know why he denies dark matter! It seems so irrational.)”

    But Olorin ! Any dogmatic belief system, including christianity, is irrational. So this is not surprising …

    Do enjoy your trip to Jim Peebles’s birthplace – should be pleasant in summer !

  9. Olorin,

    Paley’s pocket watch comes to mine. He lived during the time of Darwin, neither man could imagine the specified complexity with mechanical workings of molecular machines being observed in the cell. Paley who argued in favor of intelligent design using a watch has been found also in bacteria…

    “The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally.”

    Something you wish Darwin could have done…lol…You state, “Actually, this discovery supports evolution rather than design. Why would a designer implement several different structures for proton pumping, when a single one would do?” This is what one calls, “begging the question” without evidence and this discovery is brand new and took ten years to find this function. The production of ATP in mitochondria requires so many steps, and your saying it can be done all in one step, so it couldn’t be a designer, right? Like you could build one better, right? No human technology even comes close to what is being discovered in the cell…This is why “biomimetics” is getting more popular and evolution is not used in that field…In biominetics they look for design in understanding productivity like using engineering in understanding the cell…

    Have a safe trip!

  10. “Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Therefore Design.”

    – PZ Myers

  11. Michael :Olorin,
    Paley’s pocket watch comes to mine. He lived during the time of Darwin, neither man could imagine the specified complexity with mechanical workings of molecular machines being observed in the cell. Paley who argued in favor of intelligent design using a watch has been found also in bacteria…

    Michael, watches are irrelevant to talking about biological complexity.
    Watches do not reproduce, they do not mutate, they are not natural oranisms, so natural selection cannot work on them.

    Paley’s watch, Behe’s moustrap are both irrelevant.

  12. Michael, welcome to the discussion!

    Why would a designer implement several different structures for proton pumping, when a single one would do?” This is what one calls, “begging the question” without evidence and this discovery is brand new and took ten years to find this function.

    Michael, you should review the definition of “begging the question,.” Where is the answer assumed before the reasoning begins? Where is the circular reasoning from that prior assumption back to the answer?

    .

    I’m not sure what discovery you claim to be “brand new.” Mitochondrial Complex I, and its overall functions have been known for may years; the authors provide the background as: “It is the entry point for electrons from NADH into the respiratory chain and couples electron transfer to ubiquinone with vectorial proton pumping across the inner mitochondrial membrane.”[1] No new discovery there.

    The discovery reported in the paper is the atomic configuration of this huge structure. This is noteworthy because x-ray crystallography becomes much harder as the subjects become larger. Probably no larger structure has ever been successfully analyzed. But larger is not “more complex.” In fact, rather than finding a complex unitary configuration, the authors found a number of smaller, simpler components hooked together. No discovery of new “complexity” here.

    So what is the “new discovery”? (Besides merely the crystallographic configuration of MCI.) The discovery that your source fawns over seems to be that electron and proton transfer are effected by a different method. Instead of sodium-based and other pumps that were previously known, MCI uses a Fe-S based chemistry. This pump is generally homologous to the previously known methods. It is not more complex than they are, merely bigger and different.

    So why is this discovery a revelation to design? Why any more than dozens of other pumps? Why is the MCI pump more complex than, say, the sodium-potassium pump driven by ATP hydrolysis? Or the pumps that neurons employ to convey neurotransmitters across synapses? Or, for that matter, the pump that secretes gastric acids to give you heartburn?[2]

    How is the structure of this pump any more relevant to creationism than previously known structures of the same kind? Does “bigger” imply more design? Does “different” imply more design?

    I think your anonymous source has set you up for a disappointment. There is nothing in this paper that anyone knowledgeable in the field would consider to advance an argument—even the complexity argument—for special creation.

    ============

    [1] Hunt, et al., “Functional Modules and Structural Basis of Conformational Coupling in Mitochondrial Complex I” Science Express, 1 July 2010 (10.1126/science.1191046), first graf.

    [2] The cure is Omeprazole, which is a “proton pump inhibitor.” (Marketed as Prilosec.)

  13. Paley’s pocket watch comes to mine.[sic] He lived during the time of Darwin, neither man could imagine the specified complexity with mechanical workings of molecular machines being observed in the cell.

    This is the key to the entire creationist argument, in a nutshell: “I can’t imagine how evolution could have happened, and I am the smartest person in the world, except, of course, for God. Therefore, God must have done it.” This is called the argument from ignorance, and it has no probative weight—not in science, not in law,[1] not even in theology.

    The argument from ignorance in evolution has steadily lost ground since Darwin’s time. Darwin didn’t know how trait inheritance worked. Now we do. The neo-Darwinian population geneticists figured out gene spread, even though they didn’t know what genes were. Now we do. Darwin bemoaned the lack of fossils. Month by month we are filling in the record—not only for humans, but for whales, horses, birds, and hundreds of other lineages. Genetic analysis confirms the fossil record with detailed variations.

    Let me anticipate. Michael remonstrates, “But hold! Every new discovery brings a new mystery at a lower level. Scientists may have figured out what cells do, but now we probe into the interior of the cell and find yet more unknowns.”

    Nevertheless, the onslaught has been continuous. The unknowns continue to become known, down through the multiple levels. Last month, no one knew what Mitochondrial Complex I looks like. Now we know, and have a start on how it works. Knowing these things can then lead to researching its ancestry.[2] If you know the history of creationism,[3] you will notice a gradual yet constant retreat from claims in the face of new knowledge. Answers in Genesis, for example, keeps a list of claims that creationists should no longer make. It is significant that new discoveries in biology, paleontology, geology, and biogeography seem to continually strengthen scientists’ acceptance of the fact of biological evolution, rather than weakening it. Evolution is just plain not “a theory in crisis” among scientists; even some creationists are advocating dropping this claim.[4]

    Further, the argument from ignorance cannot ever provide positive evidence for any theory. Again imagine our criminal defendant in the dock. The prosecutor thumps the table and intones, “Yer Honor, we are totally ignorant as to who perpetrated this heinous crime. Therefore, hence, and ipso facto, the prisoner, Judas J. Jingleheimer-Schmidt, MUST HAVE DONE IT.”[5]

    The argument from ignorance can by definition not provided positive evidence. And, when ignorance continues to fall, the proponents of the argument are pushed into smaller and smaller corners of darkness.[6]

    ==============

    [1] Would you convict a defendant of a crime on the basis of no evidence except, “Yer Honor, we don’t know who else could have done the dirty deed.”?

    [2] in the same way, perhaps, that a 450My old protein was reconstructed from its modern variants across numerous genera—and the reconstructed ancestor was found to be functional.

    [3] From, e.g., Numbers’ book, The Creationists.

    [4] You may believe a world-wide conspiracy of half a million researchers if you desire. However, it is somewhat difficult to imagine such a conspiracy being maintained by so many for so long. Even the Illuminati would be jealous of such success.

    [5] Well, maybe there was some evidence: The Bible, after all, mentions a Judas who was an arch criminal.

    [6] This does not necessarily result in a decreased resistance. It is said that a zealot is one who redoubles his efforts when he has lost sight of his goal.

  14. Paley’s pocket watch comes to mine.[sic] He lived during the time of Darwin, neither man could imagine the specified complexity with mechanical workings of molecular machines being observed in the cell.

    Intelligent design and creationism seem to have a death grip on “complexity.” As Tim Cooley notes above,

    “Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Complexity. Therefore Design.”

    – PZ Myers

    Is complexity, in and of itself, an indication of design? The argument is that biological systems are “like” artifacts designed by humans. Soooo what? Do you claim that life was designed by humans? I don’t think so.

    Designed by some kind of intelligence than, that is “like” human intelligence? This argument rests entirely upon two grounds: (a) the argument form ignorance—we don’t know how else it was done, and (b) the existence of such na intelligence and evidence of his/her/its actions.

    The previous comment addresses the argument form ignorance.

    As to the evidence for intelligence—

    Even hardened opponents of evolution admit that “evolution” exists. Speciation has been observed too often. (Ring species, for example.) Natural selection can be observed directly even over short periods of time. (For example, as moose and wolf populations change.) Heritable variation can no longer be denied. (Mutations, gene duplications, etc.) Therefore, THERE IS INDISPUTABLE EVIDENCE THAT THERE IS SUCH A THING AS EVOLUTION. The argument is over the magnitude of the changes it can produce—microevolution v. macroevolution.

    On the other hand, NO ONE HAS EVER SEEN DESIGN TAKING PLACE. There is no direct evidence at all for an act of design.

    Stephen Meyer plays a shell game with this in Signature in the Cell. His entire thesis is based upon the argument that living organisms are “like” human artifacts, and he argues that intelligence is required to produce these. Meyer, entirely ducks the issue as to whether a disembodied intelligence has exited or even could exist. He asserts that something whose existence he cannot show is a “best explanation”! He never ever gets around to showing any evidence that such an intelligence exists, or is even possible. He merely assumes its existence. He does not even speculate as to how such an intelligence could have or did infuse “biological information” into a living cell, or may have guided it thorough mutational changes, or any other mechanism. That is, his argument is purely theological.

    .

    Complexity seems to be the final frontier of the intelligent design crowd. Despite William Dembski, complexity—even specified complexity, whatever that may be—is not an indication of design. As I noted at excessive length in my comment of July 5, 2010 at 10:10 pm | #6 (Michael’s post dated July 5, 2010), theorists who study complex systems have found through experimentation that (a) evolved systems are usually more complex than designed systems for solving equivalent problems, (b) evolved systems are easily capable of generating and communicating information in furtherance of their goals, and (c) evolved systems tend to develop patterns that persist over time in the face of at least minior disruptions.

    Meyer and Dembski apparently have never heard of this work. (University of Michigan, Santa Fe Institute, and other locations.) And, if we get right down to it, biological systems “look” much more like non-von Neumann data-processing architectures than they look like the von Neumann computers that humans design. Non-von Neumann systems are exactly the ones that show evolutionary advantages over designed systems. Furthermore, non-von Neumann structures are easily built from simple components, and do not require an overall controller. They also have been proven (by von Neumann himself) to be capable of reproducing themselves.

    The complexity of life is truly awesome. It is, in fact, too complex to have been designed.

  15. Actually, moriahbetha, earlier mitochondrial analyses showed that there was no interbreeding of humans and Neandertal. (The variational ranges were separate.) The intermixing had to wait until just recently, when nuclear Neandertal DNA became available. And then, only some modern humans showed interbreeding—Europeans and Asians. This, however, is even stronger evidence against creationism.

  16. I’m not trying to prove creationism actually. I’ve just been reading a lot about mitochondria lately and I think it’s interesting.

  17. Mitochondria are very interesting animalicules. Reading about them is fun. Michael should try it sometime.

    Tracing male ancestry through Y chromosomes is also interesting. One of my 5th cousins runs a Y-chromosome project for our extended family.

  18. Science Daily:

    “In a laboratory experiment, hydrogen and oxygen gas would react in an explosion and the energy contained would be released as heat.

    ….

    “Comparable to a fuel cell….

    I hate to disagree with Science Daily, the National Inquirer of the technoworld. BUT. That statement is a laugh. Apparently the SD writer has never seen an actual fuel cell at work. Quietly, almost stealthily combining hydrogen from the fuel and oxygen from the air, and dribbling electrons out onto a wire. (And water, too, of course.) No explosion. Not much heat.

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