Uncommon Descent Serving The Intelligent Design Community

VIDEO: A look at the ATP Synthase in action, courtesy Discovery Institute (and Wikipedia)

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DI has just released a video on the ATP Synthase in action (HT: ENV):

[youtube XI8m6o0gXDY]

The blurb at Youtube reads:

ATP Synthase is a molecular machine found in all living organisms. It serves as a miniature power-generator, producing an energy-carrying molecule, adenosine triphosphate, or ATP. The ATP synthase machine has many parts we recognize from human-designed technology, including a rotor, a stator, a camshaft or driveshaft, and other basic components of a rotary engine. This machine is just the final step in a long and complex metabolic pathway involving numerous enzymes and other molecules—all so the cell can produce ATP to power biochemical reactions, and provide energy for other molecular machines in the cell.

{Added, courtesy commenters below, here is another useful animation:}

[youtube H7P4xOUPYVw]

Wiki’s somewhat more schematic GIF animation, will help us see what is going on in each cycle of rotation, a little more closely:

Here, we have an enzyme made of a protein complex of subunits, constituting a rotary machine in the mitochondria of the living cell

A typical animal cell

 

. . . and responsible for providing the molecular energy batteries without which life would collapse.  And, it is recognisably a motor with a working head on its shaft.

What is the empirically grounded explanation for motors, again?

And, the spontaneous, chance and necessity model for its origin is ________, based on _______ as observational evidence?

Any takers? END

Comments
BA77's video link from #10 is a good one, and explains how the proton gradient is maintained in the context of photosynthesis system.Chance Ratcliff
January 26, 2013
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BA posted this inaccuracy:
In what I find to be a absolutely fascinating discovery, it is found that photosynthetic life, which is an absolutely vital link that all higher life on earth is dependent on for food, uses ‘non-local’ quantum mechanical principles to accomplish photosynthesis:
Not on this planet it isn't. Photosynthesis is impossible in the abyssal hot smoker ecologies. Not so absolutely vital for "higher life", apparently.timothya
January 26, 2013
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BA77@10, thanks for the links. I'll spend some time with them when I get the chance. :)Chance Ratcliff
January 26, 2013
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Mung,
"(Is that essentially the same as mechanical energy?)"
Yes, I believe so.
In what sense is energy stored in protons?
It's stored in the gradient itself, which is defined as a higher concentration of protons on one side of a membrane than the other. I'm picturing two air tanks, one pressurized and the other not, both connected together. The transfer of air from one to the other could be harnessed and converted to mechanical energy. From there converting to other forms would be straightforward. I think your water wheel is an appropriate metaphor. In order to keep it running, some process needs to bring water from the bottom back to the top. This is apparently what occurs in biological systems. See the quote I provided from your video at #8, which occurs around the three minute mark. This video might provide some insights, but I haven't had a chance to watch it yet.
How in the world could natural processes have “discovered” by trial and error that a proton gradient could be turned into another useful form of energy?
I take it that "natural selection" is not a sufficient explanation for you then. In fact, to me it doesn't seem necessary nor does it seem sufficient for the generation of biological novelty.Chance Ratcliff
January 26, 2013
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seems your favorite is the same as my broken link. =p
Hehe. I imagine many of us have that one in our list. ;)Chance Ratcliff
January 26, 2013
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For cells that lack mitochondria, where is the proton gradient created?Mung
January 26, 2013
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So maybe I am using the wrong metaphor, but so far it seems appropriate to me. Say there is a waterfall. A gradient. Some Intelligent Designer comes along and builds a water wheel. Now we have "rotational energy." (Is that essentially the same as mechanical energy?) And then we convert that energy into something else, maybe another "form" of energy. Where's the initial energy? We don't call it "water energy" do we? Or a "water gradient." In what sense is energy stored in protons? How in the world could natural processes have "discovered" by trial and error that a proton gradient could be turned into another useful form of energy?Mung
January 26, 2013
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lol chance. seems your favorite is the same as my broken link. =pMung
January 26, 2013
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ATP synthase structure and mechanism What does it mean to say that there is energy stored in a proton gradient?Mung
January 26, 2013
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Further fine tuning of light is discussed in the following videos and podcast:
Fine Tuning Of Universal Constants, Particularly Light – Walter Bradley – video http://www.metacafe.com/watch/4491552 Michael Denton: Remarkable Coincidences in Photosynthesis - podcast http://www.idthefuture.com/2012/09/michael_denton_remarkable_coin.html Intelligent Design - Light and Water - video http://www.metacafe.com/watch/4669620 Proverbs 3:19 "The Lord by wisdom founded the earth: by understanding He established the heavens;"
bornagain77
January 26, 2013
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As well, Please note the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape around the direction of travel as a 'hypothetical' observer moves towards the ‘higher dimension’ of the speed of light(Of note: This following video was made by two Australian University Physics Professors with a supercomputer.)
Approaching The Speed Of Light - Optical Effects - video http://www.metacafe.com/watch/5733303/
As well, it is very curious to note that it takes a infinite amount of information to give a complete description of a photon:
Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh Excerpt: In contrast to a classical bit, the description of a (photon) qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1) http://www.cas.umt.edu/phil/faculty/duwell/DuwellPSA2K.pdf Quantum Computing – Stanford Encyclopedia Excerpt: Theoretically, a single qubit can store an infinite amount of information, yet when measured (and thus collapsing the Quantum Wave state) it yields only the classical result (0 or 1),,, http://plato.stanford.edu/entries/qt-quantcomp/#2.1 Single photons to soak up data: Excerpt: the orbital angular momentum of a photon can take on an infinite number of values. Since a photon can also exist in a superposition of these states, it could – in principle – be encoded with an infinite amount of information. http://physicsworld.com/cws/article/news/7201
The following experiment actually showed that information can be encoded into a photon while it is in its quantum wave state,
Ultra-Dense Optical Storage – on One Photon Excerpt: Researchers at the University of Rochester have made an optics breakthrough that allows them to encode an entire image’s worth of data into a photon, slow the image down for storage, and then retrieve the image intact.,,, Quantum mechanics dictates some strange things at that scale, so that bit of light could be thought of as both a particle and a wave. As a wave, it passed through all parts of the stencil at once, carrying the "shadow" of the UR with it. http://www.physorg.com/news88439430.html
Now, I find the preceding to be absolutely fascinating! Light is found, in our experiments for special relativity, to be ‘eternal’. As well, a photon, in its quantum wave state, is found to be mathematically defined as a ‘infinite-dimensional’ state, which ‘requires an infinite amount of information’ to describe it properly, can be encoded with information in its 'infinite dimensional' state, and this ‘infinite dimensional’ photon is found to collapse, instantaneously, and thus 'non-locally', to just a '1 or 0' state, out of a infinite number of possibilities that the photon could have collapsed to instead! Moreover, consciousness is found to precede the collapse of the wavefunction of the photon to its particle state. Moreover, a non-local, beyond space and time, cause is needed to explain the 'harvesting of energy' in photosynthesis. Energy that all other complex biological life on earth is ultimately dependent on. Now my question to materialistic atheists is this, "Exactly what ’cause’ has been postulated throughout history to be completely independent of any space-time constraints (eternal), as well as possessing infinite knowledge, so as to be the ‘sufficient cause’ to explain what we see in the quantum wave collapse of a photon and in the non-local quantum coherence of photosynthesis??? ,,,In my personal opinion, even though this is not hashed out in exhaustive detail yet, and regardless of what atheists may think, all this evidence is about as sweet as it can get in experimental science as to providing empirical proof that Almighty God created, and sustains, this universe and all life in it.,,,
John 1:1-5 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind. The light shines in the darkness, and the darkness has not overcome it. Jeremy Camp – The Way (Official Music Video) http://www.youtube.com/watch?v=9q6o4sbndVE
Further notes: As well, it is found that light is extremely fine tuned to the atmosphere, to biological molecules and to water, for life to exist:
Extreme (1 in 10^24) Fine Tuning of Light for Life and Scientific Discovery - Richards, Gonzalez - video http://www.metacafe.com/w/7715887
Visible light is incredibly fine-tuned for life to exist. Though visible light is only a tiny fraction of the total electromagnetic spectrum coming from the sun, it happens to be the "most permitted" portion of the sun's spectrum allowed to filter through the our atmosphere. All the other bands of electromagnetic radiation, directly surrounding visible light, happen to be harmful to organic molecules, and are almost completely absorbed by the atmosphere. The tiny amount of harmful UV radiation, which is not visible light, allowed to filter through the atmosphere is needed to keep various populations of single cell bacteria from over-populating the world (Ross; reasons.org). The size of light's wavelengths and the constraints on the size allowable for the protein molecules of organic life, also seem to be tailor-made for each other. This "tailor-made fit" allows photosynthesis, the miracle of sight, and many other things that are necessary for human life. These specific frequencies of light (that enable plants to manufacture food and astronomers to observe the cosmos) represent less than 1 trillionth of a trillionth (10^-24) of the universe's entire range of electromagnetic emissions. Like water, visible light also appears to be of optimal biological utility (M.Denton; W.Bradley; G.Gonzalez; J.Richards).
Fine Tuning Of Light to the Atmosphere, to Biological Life, and to Water – graphs https://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMTljaGh4MmdnOQ
bornagain77
January 26, 2013
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A few notes: ATP synthase also lays at the heart of photosynthesis:
Electron transport and ATP synthesis during photosynthesis - Illustration http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.figgrp.1672 The Miracle Of Photosynthesis - electron transport - video http://www.youtube.com/watch?v=hj_WKgnL6MI
And we now have evidence for photosynthetic life suddenly appearing on earth, as soon as water appeared on the earth, in the oldest sedimentary rocks ever found on earth.
The Sudden Appearance Of Photosynthetic Life On Earth - video http://www.metacafe.com/watch/4262918 U-rich Archaean sea-floor sediments from Greenland - indications of +3700 Ma oxygenic photosynthesis (2003) http://adsabs.harvard.edu/abs/2004E&PSL.217..237R
Moreover there is no evidence of prebiotic chemical signatures
Dr. Hugh Ross - Origin Of Life Paradox (No prebiotic chemical signatures)- video http://www.metacafe.com/watch/4012696
And although the specifications of ATP synthase are enough to make any engineer worth his salt drool, and are surely indicative of vastly superior design, I would like focus in on photosynthesis itself. In what I find to be a absolutely fascinating discovery, it is found that photosynthetic life, which is an absolutely vital link that all higher life on earth is dependent on for food, uses ‘non-local’ quantum mechanical principles to accomplish photosynthesis:
Non-Local Quantum Coherence In Photosynthesis - video with notes in description http://vimeo.com/30235178 Quantum Mechanics at Work in Photosynthesis: Algae Familiar With These Processes for Nearly Two Billion Years - Feb. 2010 Excerpt: "We were astonished to find clear evidence of long-lived quantum mechanical states involved in moving the energy. Our result suggests that the energy of absorbed light resides in two places at once -- a quantum superposition state, or coherence -- and such a state lies at the heart of quantum mechanical theory.",,, "It suggests that algae knew about quantum mechanics nearly two billion years before humans," says Scholes. http://www.sciencedaily.com/releases/2010/02/100203131356.htm
Yet to explain quantum correlations, one must appeal to a beyond space and time cause:
Looking Beyond Space and Time to Cope With Quantum Theory – (Oct. 28, 2012) Excerpt: To derive their inequality, which sets up a measurement of entanglement between four particles, the researchers considered what behaviours are possible for four particles that are connected by influences that stay hidden and that travel at some arbitrary finite speed. Mathematically (and mind-bogglingly), these constraints define an 80-dimensional object. The testable hidden influence inequality is the boundary of the shadow this 80-dimensional shape casts in 44 dimensions. The researchers showed that quantum predictions can lie outside this boundary, which means they are going against one of the assumptions. Outside the boundary, either the influences can’t stay hidden, or they must have infinite speed.,,, The remaining option is to accept that (quantum) influences must be infinitely fast,,, “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,, http://www.sciencedaily.com/releases/2012/10/121028142217.htm
And since all higher life forms on earth are ultimately dependent of photosynthesis in order to receive their food, the implications should be obvious:
Psalm 104:14 He causes the grass to grow for the cattle, And vegetation for the labor of man, So that he may bring forth food from the earth,
But to further solidify the inference for a beyond space and time cause for photosynthesis, it would be worthwhile to reflect on light itself for a moment.,, Time, as we understand it temporally, would come to a complete stop at the speed of light. To grasp the whole 'time coming to a complete stop at the speed of light' concept a little more easily, imagine moving away from the face of a clock at the speed of light. Would not the hands on the clock stay stationary as you moved away from the face of the clock at the speed of light? Moving away from the face of a clock at the speed of light happens to be the same 'thought experiment' that gave Einstein his breakthrough insight into e=mc2.
Albert Einstein - Special Relativity - Insight Into Eternity - 'thought experiment' video http://www.metacafe.com/w/6545941/
That is to say, traveling at the speed of light will only get us to the place where time, as we understand it, comes to complete stop for light, i.e. gets us to the eternal, 'past and future folding into now', framework of time. This higher dimension, 'eternal', inference for the time framework of light is warranted because light is not 'frozen within time' yet it is shown that time, as we understand it, does not pass for light.
"I've just developed a new theory of eternity." Albert Einstein - The Einstein Factor - Reader's Digest "The laws of relativity have changed timeless existence from a theological claim to a physical reality. Light, you see, is outside of time, a fact of nature proven in thousands of experiments at hundreds of universities. I don’t pretend to know how tomorrow can exist simultaneously with today and yesterday. But at the speed of light they actually and rigorously do. Time does not pass." Richard Swenson - More Than Meets The Eye, Chpt. 12
bornagain77
January 26, 2013
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Yet another example that highlights the absurdity of blind, unguided and purposeless goo to you by way of the zoo fairy tale theory of neo Darwinian!! Intelligent Design is science and NDE is a myth .JoeMorreale1187
January 26, 2013
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From Gradients (ATP Synthases):
In biological systems however, a gradient is always maintained.
Is this because it provides a selective advantage? Of course, biological systems in which a gradient is always maintained have a definite reproductive advantage, I suppose.Chance Ratcliff
January 26, 2013
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Of course, this motor bears no resemblance to human design, because we know that God simply does not design things that way, because, he doesn't. Oops, wrong thread.Chance Ratcliff
January 26, 2013
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To note, with ATP Synthase, proton energy is used to convert mechanical energy into the chemical energy stored in ATP. This process can also run in reverse, hydrolyzing ATP to charge the proton gradient, if the concentration of ATP is high and the proton gradient low, as this video explains.Chance Ratcliff
January 26, 2013
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This association appears to have occurred early in evolutionary history, because essentially the same structure and activity of ATP synthase enzymes are present in all kingdoms of life.
Why is it assumed that this enzyme evolved? Are we not often reminded that evolutionary theory is supposedly separate from OOL? I gather that all ubiquitous proteins and systems "occurred early in evolutionary history." Here is one of my favorites for ATP Synthase, and still one of the best: http://www.youtube.com/watch?v=H7P4xOUPYVw Mung, thanks for the Gradients (ATP Synthases) link; it's also a goody. BTW, your "ATP synthase structure and mechanism" link is broken.Chance Ratcliff
January 26, 2013
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ATP Synthase is a molecular machine found in all living organisms.
Wikipedia:
ATP synthase is an important enzyme that provides energy for the cell to use through the synthesis of adenosine triphosphate (ATP). ATP is the most commonly used "energy currency" of cells from most organisms. It is formed from adenosine diphosphate (ADP) and inorganic phosphate (Pi), and needs energy.
It takes energy to make energy! But are we really converting one type of energy to another type of energy?
The evolution of ATP synthase is thought to be an example of modular evolution during which two functionally independent subunits became associated and gained new functionality. This association appears to have occurred early in evolutionary history, because essentially the same structure and activity of ATP synthase enzymes are present in all kingdoms of life. The F-ATP synthase displays high functional and mechanistic similarity to the V-ATPase. However, whereas the F-ATP synthase generates ATP by utilising a proton gradient, the V-ATPase generates a proton gradient at the expense of ATP, generating pH values of as low as 1.
Wow. One uses a gradient, another creates a gradient. All accidental like. Which came first, the gradient or the membrane? Gradients (ATP Synthases) Cellular Respiration (Electron Transport Chain) How many different types of energy are involved here!? Rotational energy: ATP synthase structure and mechanism And it works in reverse! This is stunning Intelligent Design, Eric! ;) ATP Synthase (FoF1-complex) Home ATP synthase is a huge molecular complex http://enzyme.expasy.org/EC/3.6.3.14 mahMung
January 26, 2013
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He should have been an artist Some would say he is, I suppose, of a flim-flam kind. 'O, that this too too solid flesh would melt, thaw and resolve itself into a dew!' It's that magic he yearns for. Not the magic of the supernatural. The kind whereby nothing turns itself into everything. And logic is only binding when you want it to be.Axel
January 26, 2013
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I was just going to say: 'Deceptive, eh? Looks as if it had been designed. I wonder what basis Ritchie has for questioning the reliability of our senses with regard to the natural world, solely with regard to design, the very concept upon which science, EMPIRICAL science, is based.Axel
January 26, 2013
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Whether Lab or Cell, (If it's a molecular machine) It's Design - Dr. Gauger - podcast http://intelligentdesign.podomatic.com/entry/2013-01-25T15_53_41-08_00bornagain77
January 26, 2013
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