Another argument as to how a complex metabolism “may have” self-assembled

_{Denyse O'Leary

October 22, 2020

Intelligent Design, Origin Of Life}

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This time it’s thioesters:

Life as we know uses energy to reproduce itself. Organisms build and break down larger molecules using a common set of reactive intermediate energy carrier molecules. These carrier molecules help chaperone the reactions which build life’s biochemical complexity and help push metabolic reactions to drive cellular reproduction. New research suggests that such compounds can be made easily in the environment in the absence of biology, providing a hint as to how life may have started. …
The team thinks it is especially fascinating that these kinds of reactions may create “cascade reactions” which make more and more complex molecules: pyruvate decomposes, helping form a thioester, which then allows peptides (smaller cousins of proteins) to form via the newly discovered thioester route. The team hopes to test this experimentally next and to create a system that can increase the number of components it contains and their complexity by itself, perhaps all the way to self-reproduction. Some modern microbes in fact use pyruvate decomposition and thioester formation assisted by FeS clusters in their metabolism, and it is possible that the reactions the team discovered recapitulate how early prebiological or biological evolution discovered them. As the lead investigator on this work, ELSI Associate Professor Shawn McGlynn says, “This work provides new connections between multiple prebiotic reaction components that may have been critical to establishing early energy metabolism on Earth.”
Tokyo Institute of Technology, “New study shows how complex metabolism may have self-assembled from simple precursors” at ScienceDaily

Paper. (paywall)

The critical question is, why isn’t life originating from nothing all around us then?

See also: The Science Fictions series at your fingertips – origin of life What we do and don’t know about the origin of life.

Comments

These people don't understand that entropy is asymmetrical. Entropy increase is easy while the kind of entropy decrease they propose is extremely hard if not impossible: http://nonlin.org/entropy/Nonlin.org_{October 23, 2020
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As the following article states, translation in biology is "about 100,000 times more efficient than a computer."
The astonishing efficiency of life - November 17, 2017 by Jenna Marshall Excerpt: All life on earth performs computations – and all computations require energy. From single-celled amoeba to multicellular organisms like humans, one of the most basic biological computations common across life is translation: processing information from a genome and writing that into proteins. Translation, it turns out, is highly efficient. In a new paper published in the journal Philosophical Transactions of the Royal Society A, SFI researchers explore the thermodynamic efficiency of translation.,,, To discover just how efficient translation is, the researchers started with Landauer's Bound. This is a principle of thermodynamics establishing the minimum amount of energy that any physical process needs to perform a computation. "What we found is that biological translation is roughly 20 times less efficient than the absolute lower physical bound," says lead author Christopher Kempes, an SFI Omidyar Fellow. "And that's about 100,000 times more efficient than a computer." https://phys.org/news/2017-11-astonishing-efficiency-life.html
The amazing energy efficiency possible with ‘reversible computation’ has been known about since 1973 when Charles Bennett first laid out the principles for such reversible computation, but as far as I know, (apparently due to the extreme level of complexity involved in actually designing such ingenious ‘reversible computation’ in our own computers), has yet to be accomplished in any meaningful way in our computers:
Reversible computing? Excerpt: Reversible computing is a model of computing where the computational process to some extent is reversible, i.e., time-invertible.,,, Although achieving this goal presents a significant challenge for the design, manufacturing, and characterization of ultra-precise new physical mechanisms for computing, there is at present no fundamental reason to think that this goal cannot eventually be accomplished, allowing us to someday build computers that generate much less than 1 bit's worth of physical entropy (and dissipate much less than kT ln 2 energy to heat) for each useful logical operation that they carry out internally.?http://en.wikipedia.org/wiki/Reversible_computing#The_reversibility_of_physics_and_reversible_computing
Thus, although the Darwinist, (that I showed the 'horrendously complex' metabolic pathway schematic to), said that such 'horrendous complexity' in the metabolism of the cell did not (absolutely) prove that such horrendous complexity was the result of Intelligently Design, never-the-less, I can sleep very well at night in my belief that such 'horrendous complexity' MUST be the result of Intelligent Design. Whereas, on the other hand, if I were a Darwinist, I would be not sleep very well at all, and it would disturb me very deeply, knowing that I honestly had no realistic clue how such amazing 'horrendous complexity' could possibly come to be by 'chemical accidents'. As Dr. James Tour, (who is considered one of the top synthetic chemists in the world), noted, "From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids, and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks let alone their assembly into a complex system. That’s how clueless we are. I’ve asked all of my colleagues – National Academy members, Nobel Prize winners -I sit with them in offices; nobody understands this."
“We have no idea how the molecules that compose living systems could have been devised such that they would work in concert to fulfill biology’s functions. We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids, and proteins, were made and how they could have coupled into the proper sequences, and then transformed into the ordered assemblies until there was the construction of a complex biological system, and eventually to that first cell. Nobody has any idea how this was done when using our commonly understood mechanisms of chemical science. Those that say they understand are generally wholly uninformed regarding chemical synthesis. Those that say “Oh, this is well worked out,” they know nothing, nothing about chemical synthesis – Nothing! Further cluelessness – From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids, and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks let alone their assembly into a complex system. That’s how clueless we are. I’ve asked all of my colleagues – National Academy members, Nobel Prize winners -I sit with them in offices; nobody understands this. So if your professors say it’s all worked out, your teachers say it’s all worked out, they don’t know what they’re talking about. It is not worked out. You cannot just refer this to somebody else; they don’t know what they’re talking about.” James Tour – one of the top ten leading chemists in the world The Origin of Life: An Inside Story - March 2016 Lecture with James Tour https://www.youtube.com/watch?v=_zQXgJ-dXM4
Verse:
John 1:1-4 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.
bornagain77_{October 23, 2020
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As to:
The team hopes to test this experimentally next and to create a system that can increase the number of components it contains and their complexity by itself, perhaps all the way to self-reproduction.
Lofty goal. And might I add that I hope, since I can currently jump over small mud puddles, to someday be able to jump across the Pacific Ocean to Hawaii. Anyways, back in the real world, achieving self-sustaining metabolism is a far bigger hurdle than they, apparently, falsely imagine it to be.
definition of metabolism - Metabolism is the process by which your body converts what you eat and drink into energy. During this complex biochemical process,
Here is a excellent website that gives us a glimpse some of the staggering complexity of the Metabolic Pathways for a, supposedly, 'simple' cell:
ExPASy - Metabolic Pathways - interactive schematic http://biochemical-pathways.com/#/map/1
Once I showed that particular metabolic pathway schematic to a Darwinist when he asked me for ANY evidence of intelligent design in biology. After showing it to him, his response upon seeing that schematic was something along the lines of, ‘Just because it is horrendously complex does not prove it was designed.’. ,,, To which I responded something along the line of, “Well maybe not ‘prove’ it was Intelligently Designed in the absolute sense, but such ‘horrendous complexity’ certainly does not bode well for the extraordinary claim from Darwinists that such ‘horrendous complexity’ can possibly be the result of ‘chemical accidents’ either! To further back up my claim that such 'horrendous complexity' in metabolic pathways must be the result of Intelligent Design, and not the result of chemical accidents, the 'simple' cell is found to be optimal in its metabolic efficiency. Specifically, researchers found that "metabolism, (for a 'simple cell") functions optimally for a system that seeks to accomplish multiple objectives."
Optimal Design of Metabolism - Dr. Fazale Rana - July 2012 Excerpt: A new study further highlights the optimality of the cell’s metabolic systems. Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition. http://www.reasons.org/articles/the-optimal-design-of-metabolism
In fact, to further back up my claim that the 'horrendously complex' metabolism of the cell must be the result of Intelligent Design, it is found that a "single cell in the human body is approximately 10,000 times more energy-efficient than any nanoscale digital transistor",
Cell-inspired electronics - February 25, 2010 Excerpt: "A single cell in the human body is approximately 10,000 times more energy-efficient than any nanoscale digital transistor, the fundamental building block of electronic chips. In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power." http://phys.org/news/2010-02-cell-inspired-electronics.html
Moreover, (as if that was not bad enough) the ATP molecular machine (which is found at the bottom of the metabolic pathway chart) is found to be 100% efficient:
Thermodynamic efficiency and mechanochemical coupling of F1-ATPase – 2011 Excerpt: F1-ATPase is a nanosized biological energy transducer working as part of FoF1-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms.,,?Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase. http://www.pnas.org/content/early/2011/10/12/1106787108.short?rss=1
As should be needless to say, the 100% efficiency found for molecular machines dwarfs anything that human engineers have thus far accomplished in terms of energy conversion efficiency for man-made machines,
Example(s) of energy conversion efficiency https://en.wikipedia.org/wiki/Energy_conversion_efficiency#Example_of_energy_conversion_efficiency
Moreover, in order to achieve such amazing energy/biochemical efficiency as it does, the integrated coding between the DNA, RNA and Proteins of the cell is, apparently, ingeniously designed and/or programmed along the very stringent guidelines laid out in Landauer’s principle, (by Charles Bennett from IBM of Quantum Teleportation fame), for ‘reversible computation’ ,
Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett - September 2003 Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.sciencedirect.com/science/article/pii/S135521980300039X Logically and Physically Reversible Natural Computing: A Tutorial - 2013 Excerpt: This year marks the 40th anniversary of Charles Bennett’s seminal paper on reversible computing. Bennett’s contribution is remembered as one of the first to demonstrate how any deterministic computation can be simulated by a logically reversible Turing machine. Perhaps less remembered is that the same paper suggests the use of nucleic acids to realise physical reversibility. In context, Bennett’s foresight predates Leonard Adleman’s famous experiments to solve instances of the Hamiltonian path problem using strands of DNA — a landmark date for the field of natural computing — by more than twenty years. http://link.springer.com/chapter/10.1007%2F978-3-642-38986-3_20
bornagain77_{October 23, 2020
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The anti-ID explanation for why life isn't originating all around us is that the living consumes the material before it has the chance to form a living organism. That is on Peaceful Science, no less.ET_{October 23, 2020
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"New research SUGGESTS that such compounds can be made easily in the environment in the absence of biology, providing a hint as to how life may have started. … "The team thinks it is especially fascinating that these kinds of reactions MAY CREATE “cascade reactions” which make more and more complex molecules: pyruvate decomposes, helping form a thioester, which then allows peptides (smaller cousins of proteins) to form via the newly discovered thioester route." "As the lead investigator on this work, ELSI Associate Professor Shawn McGlynn says, “This work provides new connections between multiple prebiotic reaction components that MAY HAVE BEEN critical to establishing early energy metabolism on Earth.” OK, interesting thoughts, but this is nothing more than a hypothesis at best so why the hype? May create, suggests, may have been, etc. - these types of words are really meaningless in science. We are not interested in them because they tell us nothing! Fortunately, they rescued the article with this sentence: "The team hopes to test this experimentally next and to create a system that can increase the number of components it contains and their complexity by itself, perhaps all the way to self-reproduction." OK, now that is science. Go do your testing and then come back and tell us what you found. Then you can do a big PR and get your accolades, but now is way way too early because we know nothing! If you keep your Materialistic beliefs to yourself and stick with science, I'm sure you'll be fine.tjguy_{October 23, 2020
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