Complete structure of the world’s smallest turbine, ATP, now described

_{Denyse O'Leary

September 14, 2020

Cell biology, Intelligent Design}

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Remember when they didn’t used to believe the living world had turbines and wheels and gears? The chemical ATP, which powers all life, has a turbine:

Rotation muddies the picture As the structure of the mushroom-like F1 soluble domain is known already, Sazanov and his team looked particularly at the Fo domain, embedded in the mitochondrial membrane. Here, protons are translocated at the interface between the so-called c ring, a ring made up of identical protein subunits, and the rest of Fo. Protons are moved across the membrane as each c subunit picks up a proton on one side of the membrane, rotates with the ring, and releases the proton on the other side. This c-ring is attached to the central shaft of F1 and its rotation generates ATP within F1. To solve the structure of the Fo domain and the entire complex, the researchers studied the enzyme from sheep mitochondria using cryo-electron microscopy. And here, ATP synthase poses a special problem: because it rotates, ATP synthase can stop in three main positions, as well as in substates. “It is very difficult to distinguish between these positions, attributing a structure to each position ATP synthase can take. But we managed to solve this computationally to build the first complete structure of the enzyme,” Sazanov adds.
Institute of Science and Technology Austria, “Structure of ATPase, the world’s smallest turbine, solved” at ScienceDaily

Paper. (paywall)

Ask a Darwinist and he’ll tell you that “natural selection, acting on random mutation” caused all that to just swish into existence. As if. If it took so much intelligence to understand the intricacy of the system, it should be no surprise if it took some intelligence to create it.

Comments

Chuckdarwin@21 "Every example Behe has presented, including his infamous flagellum, blood clotting and the immune system examples have been shown to have viable evolutionary pathways." This claim is an amazing example of what could charitably be termed delusional thinking. Evolutionary biologists and Darwin groupies have been claiming to have finally completely demolished, debunked, irreducible complexity, including all the prime examples such as the bacterial flagellum, the immune system, the blood clotting cascade system, and so on. Dr. Behe has answered all these objections in many places. In particular I refer you to the Appendix of his latest book, Darwin Devolves (2019), that devotes 30 pages to address multiple criticisms. Many others are addressed at Discovery Institute's website (go there and do an author search on his name), and at www.michaelbehe.com. However, I doubt you are interested enough in looking at the details to actually peruse this material. That would be bucking the strong confirmation bias, and detract from your cheerleading for Darwin..doubter_{September 19, 2020
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. Chuckdarwin, The reference to complementarity I mentioned above is related to the complementarity of rate-dependent laws and rate-independent rules. You’ll notice that the most detailed and accurate description of the structure of a DNA molecule would tell you absolutely nothing about what enzyme it might code for. But frankly, I think that discussion would be fruitless without some common ground. Perhaps we could find some common ground by discussing one of your follow-on comments. You say: “your reference to the notion that “evolution requires biological [molecules] to be specified among alternatives….” has nothing to do with irreducible complexity but appears to be a kind of weird truism” Biological evolution requires molecules to be specified among alternatives from a transcribable memory, and that requirement is not physically possible without irreducible complexity. Firstly, the ability to specify something from a memory requires the presence pf two objects for each individual thing being specified. Secondly, the relationships in those pairs of objects must be successfully established in a process in order to persist over time (making a system capable of biological evolution possible). Is it your position that there are no requirements for a system capable of biological evolution?Upright BiPed_{September 19, 2020
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Re #17 "It [irreducible complexity] is a matter of known physical properties of matter, as has been generously recorded in the physics and biology literature (Von Neumann, Pattee, Barbieri, etc, etc) where it is often referred to as irreducible complementarity. To my knowledge the term “Irreducible complementarity” does not appear in the biological literature. Complementarianism appears, but not in relation to Behe’s “irreducible complexity” idea. Complementarity in genetics, for example, is simply the notion that nucleobases A, T, G, and C in DNA and A, U, G, and C in RNA “complement” each other to allow purines and pyrimidines to bond to form base pairs. Complementarity can also exist in other areas of biology. For example, there is an entire area of biology that studies complementarity in anatomy and physiology where anatomical form follows a physiological function, and vice versa, such as the bones in the inner ear which create the fluid dynamics necessary to convert sound waves to neurological signals to the brain. But again, no biological literature on irreducible complexity. In fact, the term “irreducible complexity” in biology is completely idiosyncratic to Behe and those in his camp. Every example Behe has presented, including his infamous flagellum, blood clotting and the immune system examples have been shown to have viable evolutionary pathways. Finally, your reference to the notion that “evolution requires biological models to be specified among alternatives….” has nothing to do with irreducible complexity but appears to be a kind of weird truism and a (very) simplified historical description of the biological research related to the function of nucleobases in DNA replication, which again has nothing to do with irreducible complexity. It is ironic that you would cavalierly attempt to enlist Watson and Crick in your cause. Watson has been very clear in a number of interviews, that he finds the whole notion of ID ridiculous.chuckdarwin_{September 18, 2020
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ET@15 You forgot that at the same time, the blind Darwinian semi random-walk process had also to, in addition to creating the ATP machine design itself, create the separate (also probably irreducibly complex) machinery and precisely timed processes necessary to mass manufacture the ATP machine. I wonder if Darwinians will now ingeniously and imaginatively generate another typical fairy-tale just-so story. Probably not, since there are so many new irreducibly complex molecular biology mechanisms being discovered, they just can't keep up. Keep up the faith, Darwinians.doubter_{September 17, 2020
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. Hello Es58, Yes, Brenner! I have posted that link a few times myself here on UD. It is an excellent clip.Upright BiPed_{September 16, 2020
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UB@17: Thanks for mention Brenner, it reminded me of this link where he discusses how Von Neumann predicted the details of the self-replicating machine, including the necessity to for it to include the instructions for replication: https://www.youtube.com/watch?v=5Ictxz1XCiY&list=PLYuNh6icjzkx1t7obOPBtRfyrXLqL30m4es58_{September 16, 2020
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. #16
Vague references to “the entire planet of scientists”
Science has very clearly acknowledged that an act of intelligence can be inferred from an operational definition of intelligence, via SETI. This is not in dispute.
Vague references to ... “our universal knowledge of the physical evidence”
Biological molecules like ATPase exist because they are specified among alternatives in the gene system. We know the components of the system and the necessary roles they play. We’ve known this for half a century or more. This is not in dispute.
In fact, they do nothing but obscure things in keeping with the modus operandi of the Intelligent Design movement.
I can be painfully specific if you’d like, but something tells me that detail is not something you actually want to pursue.. However, I could be mistaken about that, and I look forward to your pursuit of detail if that is indeed your goal. We can start with this:
Spare me yet one more claim of irreducible complexity
The concept of irreducible complexity has not only NOT been “debunked”, it will never be debunked (no more than the fire triangle will be debunked as the physical requirements of the rapid oxidation of a terrestrial fuel source). It is a matter of known physical properties of matter, as has been generously recorded in the physics and biology literature (Von Neumann, Pattee, Barbieri, etc, etc) where it is often referred to as irreducible complementarity. Evolution requires biological molecules to be specified among alternatives using a linear sequence medium (codons in DNA) and a set of non-integrate constraints (aaRS). Both sets of objects are required for specification to occur. This paradigm has been known since (at least) the 1860’s. It was predicted to exist in autonomous open-ended systems (i.e. biology) in the 1940’s, and was confirmed via experimental results in the 1950’s and 1960’s by Crick, Watson, Brenner, Hoagland, Zamecnik, and Nirenberg, among others. Nobel awards were handed out. This is not in dispute either. I look forward to your detailed response.Upright BiPed_{September 16, 2020
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#15 Spare me yet one more claim of irreducible complexity (paragraphs 2-4). Behe was debunked in 2004 by Kenneth Miller, et al. and again at the Dover trial in 2008. See e.g. http://www.millerandlevine.com/km/evol/design2/article.html #14 Vague references to "the entire planet of scientists" and "our universal knowledge of the physical evidence" do not advance the discussion. In fact, they do nothing but obscure things in keeping with the modus operandi of the Intelligent Design movement.chuckdarwin_{September 16, 2020
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chuckdarwin:
How do ID proponents propose testing the hypothesis that ATPase arose as a result of ID rather than natural selection?
Easy. First off, there isn't any evidence for natural selection producing such a structure. There isn't even a way to test the claim. Therefore we can invoke the Hithchen's gambit- that which can be asserted without evidence can be dismissed without evidence. Next we see if it fits the design criteria: "Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.” Michael Behe If you take a look at ATP synthase you can see it consists of two major subunits (F0 & F1) that are connected together by an external tether. This tether doesn't have anything to do with the functionality of either subunit but without it no ATP synthase. The problem for evolution by blind and mindless processes is exacerbated. Not only does it need to produce the two subunits but one has to be embedded in some membrane so that a gradient can be formed. And the other has to be stably tethered to the membrane the proper distance away. The tether looks like the membrane subunit F0 somehow formed an external docking site the proper length with F1 forming an external mating site. Again these two different protein subunits, the tether and mate, have nothing to do with the function of the protein complexes they are attached to and tether together. And without them there is no way to get the two working subunits together to produce ATP. There you have it- A simple external tether that stably holds the major F1 subunit/ rotary motor the proper distance away from its F0 motor force is evidence for the Intelligent Design of ATP synthase. The two major subunits and how it works is just icing on the cake. Anything else?ET_{September 15, 2020
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. #13 >>> First, who or what designed ATPase? This is an old con. The entire planet of scientists and university science departments have already signed off on the validity of infering design from an operational definition of intelligence – alone, without any requirement whatsoever of knowing the source of the intelligence. >>> Second, how was the design implemented or deployed? Again, scientists and university science departments around the world have signed off on a valid methodology to infer design. Demanding to know exactly how a particular design was implemented is a double-standard pursued for the purposes of dismissing the physical evidence. Having said that, our universal knowledge of the physical evidence suggest that the designer assembled a set of symbols and constraints and used that system to specify the products of the design. >>> Third, what research program can ID offer to make testable predictions (I.e. what further hypotheses) regarding the structure, function and mechanism of ATPase in catalysis? Once again, this is un-necessary to infer design. But since you brought it up, it is notable that the design inference is a strong confirmation of a well-documented prediction. On what grounds do ID critics dismiss that prediction and its experimental confirmation? - - - - - - - - - - - - - - - - - - - - - And now let us turn your questions around: 1) What is the physical source of the organization of the semantic closure required for life and evolution to begin? 2) How did this physical source manifest itself at the origin of life? 3) If this physical source is merely a proposition, then what test can be employed to falsify that proposition?Upright BiPed_{September 15, 2020
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How do ID proponents propose testing the hypothesis that ATPase arose as a result of ID rather than natural selection? The ID proponents must answer three questions empirically. First, who or what designed ATPase? Second, how was the design implemented or deployed? Third , what research program can ID offer to make testable predictions (I.e. what further hypotheses) regarding the structure, function and mechanism of ATPase in catalysis?. If you want to play at being scientists, then you need to start acting like scientists.chuckdarwin_{September 15, 2020
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Pater K:
Seversky correctly points out the paradox of infinite regression inherent in the design argument, when based primarily on complexity.
No, it isn't. A simple artificial tone is enough for SETI to infer ETs.ET_{September 15, 2020
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seversky:
If a certain level of complexity is so improbable as to compel intelligent design as an explanation then who designed the designer?
Who says the designer required a designer?ET_{September 15, 2020
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to Seversky and the other Darwinian clowns when you watch the video, it is clear, that your whole EVO-theory is a very absurd and very offensive non-sense. Don't matter how many scientists worldwide BELIEVE in this theory. Don't matter what is the scientific consensus. They are death-wrong and most of them even know that, but are afraid to speak out, because of the Darwinian mafia. In 21st century, this theory (developed by biologists) is so offensive, that all engineers should stand up. and, to answer your other question "who designed the designer?" Actually, the answer is very simple, lets see if you will comment on this, Seversky, because the last time i answered this question, you did not. So, here is the answer: Since human brain/logic was also created by our Creator/Designer/Engineer/God, this question can't be answered using human brain/logic/arguments. In other words, humans don't understand what they are talking about when asking that question over and over again ...martin_r_{September 15, 2020
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Pater Kimbridge@8 ES58 in 2 correctly stated the basic point. It occurs to me that with this issue the sauce for the goose is also sauce for the gander. Meaning, your little argument by reductio ad absurdum also leads to reductio ad absurdum conclusions in the case of the 747. But in the case of the 747, it is obvious that human designers did in fact engineer this very complex mechano-electronic system of systems. This conclusion is as certain as that the sun will rise the next morning even if not at all considering the known history of the aircraft. It would be the virtually certain conclusion even if Boeing never developed this aircraft, but a crashed one was discovered in the middle of the Mojave desert. Its construction obviously screams that it was designed. The obvious design of it speaks overwhelmingly loudly regardless or any other evidence. Unless you want to claim it came about through a tornado in a junkyard for instance. You claim that if in the case of macro-evolution we also conclude design based purely on analysis of the construction of the complex biological systems, such a conclusion is void because we don't know who or what designed the designers, and who designed them, and so on ad infinitum. Firstly and most fundamentally, as in the case of the 747, the conclusion of design and the question of who designed the designers are completely independent and are not linked in any manner. Secondly, following your approach, the conclusion that the 747 was designed based purely on examining the nature of its construction would also have to be rejected on the same grounds since we don't ultimately know who designed the engineers that designed the 747, or who designed them, and so on. But wait, we know absolutely certainly that the 747 was designed, just based on examination of the artifact. So your generic argument leads to a logical contradiction: it is self-refuting and must be invalid. In principle your argument fails, unless you can present some naturalistic process that could really, plausibly, have produced, for instance, the Cambrian Explosion of complex animal body plans in an instant of evolutionary time. Good luck.doubter_{September 15, 2020
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Seversky correctly points out the paradox of infinite regression inherent in the design argument, when based primarily on complexity. This renders such an argument void by reductio ad absurdum.Pater Kimbridge_{September 15, 2020
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Seversky @ 1
If a certain level of complexity is so improbable as to compel intelligent design as an explanation then who designed the designer?
If the Pacific ocean is to vast for me to swim across then how is water made?awstar_{September 15, 2020
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And actually further on #5: Addressing #1 must be deferred until we find out in detail who, where, when and why typed whoever typed comment #1.EugeneS_{September 15, 2020
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Seversky "then who designed the designer?" Who painted the painter? Who typed the author of comment #1 ?EugeneS_{September 15, 2020
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Wow. First, it's a clearly written abstract. Kudos to the editor. I glaze over when confronted by lots of acronyms and long chemical names, but this piece made things clear. Second, it's amazing!!! Third, a better mechanical comparison would be a turnstile, not a turbine. The rotary motion seems to be selectively allowing entry, not providing power.polistra_{September 15, 2020
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You are right Seversky. It all happened by accident. Darwin said so. I wish I was so complacently sure of anything as you are of everything.Belfast_{September 14, 2020
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Any rational person would conclude that a 747 was the product of design by an engineer. That conclusion would be reached solely based on the study of the design itself. It would in no way be contingent on the completely independent question of whether they could prove that the engineer was also designed.es58_{September 14, 2020
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If a certain level of complexity is so improbable as to compel intelligent design as an explanation then who designed the designer?Seversky_{September 14, 2020
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