Are ATP energy cycles essential for life?

_{David L. Hagen

January 19, 2008

Biology, Evolution, Intelligent Design, Irreducible Complexity, Self-Org. Theory, The Design of Life}

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“The energy in the ATP molecule powers all biological processes. Thus, the synthesis of ATP is essential for life.”

Sir. John Walker, The ATP Synthase Group, MRC Dunn Human Nutrition Unit

ATP Synthase has been frequently discussed at Uncommon Descent including Intelligent Engineering or Natural Selection 15 July 2006

“Our job is to follow the money, track and document the flow of funds, and thereby help prove the underlying criminal activity.”

Eileen Mayer, Chief, Internal Revenue Service, Criminal Investigation Division

I propose that one of the most important concepts in Intelligent Design vs evolution is to “follow the energy trail“.

This will be especially important in examining the origin of life.

Energy processes are central to design of dynamic systems.

The improbability of bio energy systems by abiogenesis or stochastic processes will likely be a key method to distinguish Intelligent Design from Neo-Darwinian evolution.

Jerry Bergman wrote a very detailed article ATP: The Perfect Energy Currency for the Cell Vol. 36, No. 1 of the Creation Research Society Quarterly. Bergman describes ATP as irreducibly complex. Cornelius Hunter in : ATP Synthase: Paley’s Secret Spring shows ATP is the “secret spring” expected by William Paley.

I posit that:
1) ATP energy cycles are essential to self reproducing biochemical life.

2) ATP energy cycles require biochemical gradients and membranes.

3) Mutations in ATP energy cycle or related membrane formation genes degrade or destroy ATP energy cycle function, causing disorder or death.

Predictions:

4) Unknown biological systems will depend on ATP formation and supply for function.

Inferences

5) An ATP energy cycle is essential for self reproducing life and must exist before natural selection can occur.

6) ATP synthase is irreducibly complex and cannot be formed from abiotic systems by Neo-Darwinian mechanisms.

Do these statements need to be modified or are they universally general? e.g. do they apply to ocean vent biological systems?

Are there any detailed Neo-Darwinian mechanisms for the origin of ATP synthase?

Comments

[...] sentiments exactly. Judge for yourself. You might like to have a look at these links here and here, on Uncommon Descent, where ATP synthase has been highlighted previously, as evidence for [...]The video that proves Intelligent Design | Uncommon Descent_{November 22, 2010
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How could ATP synthase have evolved from helicase when helicase requires the energy from ATP to operate? ATP synthase therefore must have come first.Jonathan Sarfati_{February 8, 2008
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jerry Thanks for pointing out the complexity of ATP synthase. My reason for using "ATP energy cycles" was to include ATP synthase, photosynthesis and the other very complex components of those energy cycles.DLH_{January 25, 2008
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two things "in the cytoplasm by photosynthesis" Shouldn't this be glycolysis? If it isn't then there should be an additional method for glycolysis and how about fermentation and the creatine phosphate system? Also ATP is a relatively simple molecule but ATP synthase is immensely complex. So when discussing this, the distinction should be made. GTP is also a relatively simple molecule.jerry_{January 20, 2008
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In commenting on Behe's response to critics, Nelson Alonso says:
As defined by Dr. Behe, this system fits the definition of irreducible complexity. For F1 to work, all five parts, denoted by Greek letters alpha, beta, gamma,delta, and epsilon, are needed. For F0 to work all three parts a, b, and c are needed.
DLH_{January 20, 2008
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In his article, Jerry Bergman wrote:
Now that scientists understand how some of these highly organized molecules function and why they are required for life, their origin must be explained. We know only four basic methods of producing ATP: in bacterial cell walls, in the cytoplasm by photosynthesis, in chloroplasts, and in mitochondria. No transitional forms exist to bridge these four methods by evolution. According to the concept of irreducible complexity, these ATP producing machines must have been manufactured as functioning units and they could not have evolved by Darwinism mechanisms. Anything less than an entire ATP molecule will not function and a manufacturing plant which is less then complete cannot produce a functioning ATP. Some believe that the field of biochemistry which has achieved this understanding has already falsified the Darwinian world view (Behe, 1996).
DLH_{January 20, 2008
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DHL, I do not know of systems that use GTP but that could be attributed to my ignorance. I do not claim to be a metabolic expert. My conjecture is that there are no design benefits to ATP over GTP. Presently, it is only a hunch. Actually, I see the use of a nucleotide to be somewhat in the favor of the Darwinists since it could be an example of co-option (information storage and metabolism). But I think cooption is a weak argument for Darwinists because ubiquitously using something that works well is good engineering. It would be an interesting line of ID research to figure that out. Although I wouldn't pursue it because I expect it to be a null result. Much more rewarding work could be done by further characterizing the irreducible complexity of the simplist ATP energy cycle.paul_{January 20, 2008
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Paul "I see the choice of ATP vs GTP as the foundation for cellular energy . . " Interesting conjecture. Are there design benefits of ATP over GTP that suggest why ATP over GTP? Are there bio systems that ONLY use GTP and NOT ATP? Are there any self reproducing cells that operate only on GTP and not ATP? If so, how can we generalize the hypotheses?DLH_{January 20, 2008
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Objectives behind this post: 1) Identify systems essential to life. 2) Identify irreducibly complex systems. 3) Apply reverse engineering to these systems to identify design principles. 4) Explore ID predictions vs Neo-Darwinian predictions.DLH_{January 20, 2008
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No doubt the ATP energy system used by terrestrial life is irreducibly complex. But, it is not a coincidence that many explosives and ATP use phosphate chemistry. I think using a polyphosphorylated nucleotide is more a fine tuning argument like why carbon chemistry and water are necessary for life. However, I interpreted Bill's first proposition to specifically require ATP for life. I don't think this is necessarily true. Why not a different polyphosphorylated nucleotide? I see the choice of ATP vs GTP as the foundation for cellular energy as similar to the use of yellow as gender neutral baby cloths instead of green. Then the irreducible complexity of the systems that use ATP was built around that specific molecule.paul_{January 20, 2008
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For more good descriptions see: F₁F_o ATP Synthase - Molecular Biochemistry I, Rensselaer ATP synthesis - Davidson College This describes the following Photosynthesis - ATP synthesis system: See: Animation movies of ATP synthesis: Hypothesis: This combination Photosynthesis - ATP synthesis system is essential to self reproducing biochemical life and is also irreducibly complex. (Welcome links to studies demonstrating that proteins involved in photosynthesis and ATP synthase are essential.) For technical details on ATP synthase and its differences ("Orthologs") see: ATP Synthesis Orthologs Note: This description assumes common descent. This can also be basis for common design. See Ortholog ISCID For neutral definitions of sequence and spatial similarity see: Sequelog and SpalogDLH_{January 20, 2008
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Greetings! This stuff is over my head, I knew about ATP, but I never gave it much thought. Looks like I going to have to do some research. Thanks for the post...Unlettered and Ordinary_{January 19, 2008
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The Nobel Prize in Chemistry 1997 was given to Paul D. Boyer, Dr. John E. Walker, "for their elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)" and to and Jens C. Skou,"for the first discovery of an ion-transporting enzyme, Na + , K + -ATPase." This includes a good review & bibliography A recent review is given by: Catalytic and mechanical cycles in F-ATP synthases: Fourth in the Cycles Review Series Peter Dimroth, Christoph von Ballmoos, and T Meier EMBO Rep. 2006 March; 7(3): 276–282. Identification of Two Proteins Associated with Mammalian ATP Synthase Björn Meyer et al. Molecular & Cellular Proteomics 6:1690-1699, 2007. Data on ATP synthase proteins can be found in the: Orientations of proteins in membranes database ATP Synthase proteins F1F0 ATP synthase (PS bFast, the link is in the main post.)DLH_{January 19, 2008
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Now, what happens during reproduction? The cell still needs to maintain itself so how can it do both?ari-freedom_{January 19, 2008
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I remember a similar discussion on this board a few months back. In the discussion a new poster said that he moved from an evolutionary to an ID position when he did his doctoral thesis on ATP Synthase. I asked him what his religious perspective was. He responded that he began his education as a content athiest, but that he is now a confused agnostic (or something like that.) Bottom line is that this ATP synthase stuff is enought to turn any honest athiest into a good IDer.bFast_{January 19, 2008
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Gotcha I edited that sentence into smaller statements. Does that help? Engineers include energy systems as essential to designing dynamic systems. Abiogenic systems dissipate energy.DLH_{January 19, 2008
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Wow, this system is not irreducibly complex, it is super-irreducibly complex! I have checked, and it is so complex that it would be more than enough to falsify ten different theories of evolution... Just the alpha subunit precursor is 533 aminoacids long! And it is only a small part of the system... Talking of Dembski's UPB: here we have, for the mere alpha subunit precursor, a level of complexity of... well, I don't know, Excel can't do the math, it's a number far too big (20^533). And you are perfectly right, how can one even imagine a living replicator, be it the simplest in the fantasctic world which is the mind of a darwinist, without an efficient source of energy exchange, which means at least the ATP system... Ah, but I must be sidetracked by my obvious prejudices. Wikipedia very simply explains that ATP synthase probably evolved from the convergence of DNA helicases and... guess who? "the flagellum"! It's ironic, isn't it?gpuccio_{January 19, 2008
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[...] https://uncommondescent.com/evolution/are-atp-energy-cycles-essential-for-life/ I propose that one of the most important concepts in Intelligent Design vs evolution is to “follow the energy trail“, especially as it relates to the origin of life as one of the key strategies to identify Intelligent Design. [...]» Gotcha, but state it without ID!_{January 19, 2008
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Evolutionists are beginning to address the importance of the energy cycle and feedback. e.g., The most important concept I see in Robert Saphiro's comments on the origin of life is the essential need for feedback and particularly for energy feedback:
Life had to start with the mess—a miscellaneous mixture of organic chemistry to begin with. How do you organize this? You have to have a preponderance of some chemicals or lacking others would be against the second law of thermo-dynamics—it violates a concept that as a non-physicist that I barely grasp called 'entropy'. You get the idea that life could start in mixtures of simple molecules, provided that the organization of these molecules was intimately connected to the release of some energy as heat if there was coupling.

. . . they found that the energy wouldn't be released unless some chemical transformations took place. If the chemical transformations took place then the energy was released, a lot of it is heat. If this just went on continuously, all you do is use up the energy. Release all of it and you've converted one chemical to another. Big deal. To get things interesting, you have to close the cycle where the chemicals can be recycled by processes of their own, and then go through it again, releasing more energy.

Well the fact that this cycle, this energy-driven cycle, was working would suck the material out of all these other side-reactions into the main cycle. . . . The main idea is that you get a network of reactions, which would feed into each other, and the net result would be that the latent energy would be released.

One doesn't need a freak set of perhaps a hundred consecutive reactions that will be needed to make an RNA, and life becomes a probable thing that can be generated through the action of the laws of chemistry and physics, provided certain conditions are met. You must have the energy. It's good to have some container or compartment, because if your products just diffuse away from each other and get lost and cease to react with one another you'll eventually extinguish the cycle. You need a compartment, you need a source of energy, you need to couple the energy to the chemistry involved, and you need a sufficiently rich chemistry to allow for this network of pathways to establish itself. Having been given this, you can then start to get evolution.

. . . in the origin of life we have a problem that can be solved not too difficultly in a laboratory, by getting the right set of molecules, by getting an appropriate source of energy—okay, we cheat a little bit, we use a beaker as the container rather than some membrane, which is perhaps more difficult to achieve than is commonly understood, . . .
--------------------- Can the jumps from Shaphiro's "mess" to energy feedback cycles, to ATP synthase be quantified and shown to be beyond the Universal Probability Bound? e.g., probability of < 1 in 10^120?DLH_{January 19, 2008
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