Thermodynamic Efficiency of Cellular Computation

_{Jonathan Bartlett

November 22, 2019

Intelligent Design}

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I haven’t had time to read this yet, but it sure looks interesting. A new paper came out across the pond discussing the thermodynamic efficiency of various cellular processes/computations.

An interesting snippet from the abstract:

Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound.

Of course, various scientists assure us that selectionism is a failed concept and that no biologist today takes it seriously, right? Oh wait, also from the abstract:

This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection)

No evidence needed – of course it was done by selection! But, try to point out the limits of selectionism, and people cry foul because “scientists don’t believe that anymore.”

Comments

EricMH@3: Behe and Snoke came up with a genetic program that included recombination, duplication and such. That was in 2004. The numbers they came up with were fatal to Darwinian mechanisms and roundly denounced by the Darwin-believers. Nevertheless, the denouncers haven't come up with a program to prove Darwinian evolution via random causes will work. But don't hold your breathe--on either their coming up with one that will pass scrutiny, or, them changin their minds.PaV_{November 23, 2019
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JB, thanks for paper. Found full PDF of paper: Looks like a slightly earlier version... https://arxiv.org/pdf/1706.05043.pdf The interesting paragraph …
These results illustrate that translation operates at an astonishingly high efficiency, even though it is still fairly far away from the Landauer bound. To put these results in context, it is interesting to note that the best supercomputers perform a bit operation at roughly 5.27×10?13 (J) [77, 78]. In other words, the cost of computation in supercomputers is about 7 orders of magnitude worse than the Landauer bound of kT ln(2) = 2.87×10?21 (J), which is about 5 orders of magnitude less efficient than biological translation. Biology is beating our current engineered computational thermodynamic efficiencies by an astonishing degree.
Indeed, all by random mutations and accidental bumps in the night. Nothing engineered here. Carry on. https://en.wikipedia.org/wiki/Landauer%27s_principleDATCG_{November 22, 2019
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The paper in the OP is very interesting and being from 2017 is indeed relatively recent.PavelU_{November 22, 2019
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Perhaps a better phrasing would have been "someone pointed this out to me, I hadn't heard of it before, and I was too lazy to look at the date" :)johnnyb_{November 22, 2019
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PavelU, since you yourself have made many wildly inaccurate and false claims for papers that you have cited, don't you think others might find it more than a bit hypocritical on your part in you trying to parse exactly what the author meant by 'new paper' to see if you can find fault? The imbalance of measured judgement on your part, in rightly assessing a paper, is similar to a stumbling drunk claiming he is ballerina.bornagain77_{November 22, 2019
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The OP says: “ A new paper came out...” But the paper was published two years ago. How old can a paper be to be considered “new” ?PavelU_{November 22, 2019
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Darwinists, with their reductive materialistic paradigm, simply have no clue how any particular organism might achieve its basic form, much less how it might achieve a state that is so far out of thermodynamic equilibrium.
Darwinism vs Biological Form – video https://www.youtube.com/watch?v=JyNzNPgjM4w
Whereas advances in quantum biology now prove that quantum coherence is ubiquitous within life,,, i.e "in a wide range of important biomolecules",,,
Quantum criticality in a wide range of important biomolecules – Mar. 6, 2015 Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say. That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.” The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one (biomolecule) that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,, “what exactly is the advantage that criticality confers?” https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552
,,, that fact, coupled with the fact that quantum coherence is a thoroughly 'non-local' beyond space and time affair,
Looking beyond space and time to cope with quantum theory – 29 October 2012 Excerpt: “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,” http://www.quantumlah.org/highlight/121029_hidden_influences.php
,,, gives Christian Theists evidence that it must be God who is imparting that massive amount of 'positional information' into our bodies during embryological development and 'forming' our bodies to be so far out of thermodynamic equilibrium. Verse:
Psalm 139: 13-16 For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well. My frame was not hidden from you when I was made in the secret place, when I was woven together in the depths of the earth. Your eyes saw my unformed body; all the days ordained for me were written in your book before one of them came to be.
And of course, there is another implication for us personally. The implication for us personally of finding 'non-local', beyond space and time, and ‘conserved’, quantum information in molecular biology on such a massive scale, in every important biomolecule in our bodies, is fairly, and pleasantly, obvious. That pleasant implication, of course, being the fact that we now have very strong empirical evidence suggesting that we do indeed have an eternal soul that is capable of living beyond the death of our material bodies. As Stuart Hameroff states in the following article, the quantum information,,, isn’t destroyed. It can’t be destroyed.,,, it's possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.”
Leading Scientists Say Consciousness Cannot Die It Goes Back To The Universe - Oct. 19, 2017 - Spiritual Excerpt: “Let’s say the heart stops beating. The blood stops flowing. The microtubules lose their quantum state. But the quantum information, which is in the microtubules, isn’t destroyed. It can’t be destroyed. It just distributes and dissipates to the universe at large. If a patient is resuscitated, revived, this quantum information can go back into the microtubules and the patient says, “I had a near death experience. I saw a white light. I saw a tunnel. I saw my dead relatives.,,” Now if they’re not revived and the patient dies, then it's possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.” - Stuart Hameroff - Quantum Entangled Consciousness - Life After Death - video (5:00 minute mark) https://www.disclose.tv/leading-scientists-say-consciousness-cannot-die-it-goes-back-to-the-universe-315604
Verse:
Mark 8:37 Is anything worth more than your soul?
bornagain77_{November 22, 2019
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Work done in the area of quantum information theory, (apparently by scientists who could care less for the artificial restriction of methodological naturalism, (an artificial restriction on science which rules agent causality out of bounds before any investigation has even occurred)), has now proven that entropy is "a property of an observer who describes a system.”,,, As is touched upon in the following video,
Darwinian Materialism vs. Quantum Biology – Part II https://www.youtube.com/watch?v=oSig2CsjKbg
,,, it was shown, via advances in quantum information theory, that “an object does not have a certain amount of entropy per se, instead an object’s entropy is always dependent on the observer.”
Quantum knowledge cools computers: New understanding of entropy – June 1, 2011 Excerpt: In measuring entropy, one should bear in mind that an object does not have a certain amount of entropy per se, instead an object’s entropy is always dependent on the observer. http://www.sciencedaily.com/releases/2011/06/110601134300.htm
Moreover, in 2010 the Maxwell’s demon thought experiment, which was originally devised by James Clerk Maxwell in 1867, was finally experimentally realized. As the following paper highlights, it has now been experimentally demonstrated that knowledge of a particle’s location and/or position converts information into energy.
Maxwell’s demon demonstration turns information into energy – November 2010 Excerpt: Scientists in Japan are the first to have succeeded in converting information into free energy in an experiment that verifies the “Maxwell demon” thought experiment devised in 1867.,,, In Maxwell’s thought experiment the demon creates a temperature difference simply from information about the gas molecule temperatures and without transferring any energy directly to them.,,, Until now, demonstrating the conversion of information to energy has been elusive, but University of Tokyo physicist Masaki Sano and colleagues have succeeded in demonstrating it in a nano-scale experiment. In a paper published in Nature Physics they describe how they coaxed a Brownian particle to travel upwards on a “spiral-staircase-like” potential energy created by an electric field solely on the basis of information on its location. As the particle traveled up the staircase it gained energy from moving to an area of higher potential, and the team was able to measure precisely how much energy had been converted from information. http://www.physorg.com/news/2010-11-maxwell-demon-energy.html
And as the following 2017 article states: James Clerk Maxwell (said), “The idea of dissipation of energy depends on the extent of our knowledge.”,,, quantum information theory,,, describes the spread of information through quantum systems.,,, Fifteen years ago, “we thought of entropy as a property of a thermodynamic system,” he said. “Now in (quantum) information theory, we wouldn’t say entropy is a property of a system, but a property of an observer who describes a system.”,,,
The Quantum Thermodynamics Revolution – May 2017 Excerpt: the 19th-century physicist James Clerk Maxwell put it, “The idea of dissipation of energy depends on the extent of our knowledge.” In recent years, a revolutionary understanding of thermodynamics has emerged that explains this subjectivity using quantum information theory — “a toddler among physical theories,” as del Rio and co-authors put it, that describes the spread of information through quantum systems. Just as thermodynamics initially grew out of trying to improve steam engines, today’s thermodynamicists are mulling over the workings of quantum machines. Shrinking technology — a single-ion engine and three-atom fridge were both experimentally realized for the first time within the past year — is forcing them to extend thermodynamics to the quantum realm, where notions like temperature and work lose their usual meanings, and the classical laws don’t necessarily apply. They’ve found new, quantum versions of the laws that scale up to the originals. Rewriting the theory from the bottom up has led experts to recast its basic concepts in terms of its subjective nature, and to unravel the deep and often surprising relationship between energy and information — the abstract 1s and 0s by which physical states are distinguished and knowledge is measured.,,, Renato Renner, a professor at ETH Zurich in Switzerland, described this as a radical shift in perspective. Fifteen years ago, “we thought of entropy as a property of a thermodynamic system,” he said. “Now in (quantum) information theory, we wouldn’t say entropy is a property of a system, but a property of an observer who describes a system.”,,, https://www.quantamagazine.org/quantum-thermodynamics-revolution/
Again to repeat that last sentence,“Now in (quantum) information theory, we wouldn’t say entropy is a property of a system, but a property of an observer who describes a system.”,,, That statement about entropy being a property of an observer who describes the system, for anyone involved in the ID vs. Darwinism debate, ought to send chills down their scientific spine. Simply put, these developments go to the very heart of the ID vs. Evolution debate and directly falsify, number one, Darwinian claims that immaterial information is merely ’emergent’ from some material basis. And number two, these experimental realizations of the Maxwell’s demon thought experiment go even further and also directly validate a primary claim from ID proponents that an Intelligent Designer who imparts information into a biological system is necessary in order to circumvent the second law. As William Dembski himself stated in 1999, “It is CSI (Complex Specified Information) that enables Maxwell’s demon to outsmart a thermodynamic system tending toward thermal equilibrium”
“It is CSI (Complex Specified Information) that enables Maxwell’s demon to outsmart a thermodynamic system tending toward thermal equilibrium” William Dembki – Intelligent Design, pg. 159
And as David Abel stated in the following article, “A kinetic energy potential cannot be generated by Maxwell’s Demon from an ideal gas equilibrium without purposeful choices of when to open and close the partition’s trap door.”
MOVING ‘FAR FROM EQUILIBRIUM’ IN A PREBIOTIC ENVIRONMENT: The role of Maxwell’s Demon in life origin – DAVID L. ABEL Abstract: Can we falsify the following null hypothesis? “A kinetic energy potential cannot be generated by Maxwell’s Demon from an ideal gas equilibrium without purposeful choices of when to open and close the partition’s trap door.” If we can falsify this null hypothesis with an observable naturalistic mechanism, we have moved a long way towards modeling the spontaneous molecular evolution of life. Falsification is essential to discount teleology. But life requires a particular version of “far from equilibrium” that explains formal organization, not just physicodynamic self-ordering as seen in Prigogine’s dissipative structures. Life is controlled and regulated, not just constrained. Life follows arbitrary rules of behavior, not just invariant physical laws. To explain life’s origin and regulation naturalistically, we must first explain the more fundamental question, “How can hotter, faster moving, ideal gas molecules be dichotomized from cooler, slower moving, ideal gas molecules without the Demon’s choice contingency operating the trap door?” https://www.academia.edu/9963341/MOVING_FAR_FROM_EQUILIBRIUM_IN_A_PREBIOTIC_ENVIRONMENT_The_role_of_Maxwell_s_Demon_in_life_origin
In other words, it is now experimentally shown that it is the free will choices of an intelligent agent that allows a system to bypass the second law and achieve a state that is far from thermodynamic equilibrium (such as the far from equilibrium state that we observe in life). The information content that is found to be in a simple one cell bacterium, when working from the thermodynamic perspective, is found to be around 10 to the 12 bits,,,
Biophysics – Information theory. Relation between information and entropy: – Setlow-Pollard, Ed. Addison Wesley Excerpt: Linschitz gave the figure 9.3 x 10^12 cal/deg or 9.3 x 10^12 x 4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits. Morowitz’ deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6 x 10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures. http://www.astroscu.unam.mx/~angel/tsb/molecular.htm
,,, Which is the equivalent of about 100 million pages of Encyclopedia Britannica. ‘In comparison,,, the largest libraries in the world,, have about 10 million volumes or 10^12 bits.”
“a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong – The Creation-evolution Controversy ‘The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica.” Carl Sagan, “Life” in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894
Thus since Bacterial cells are about 10 times smaller than most plant and animal cells.
Size Comparisons of Bacteria, Amoeba, Animal & Plant Cells Excerpt: Bacterial cells are very small – about 10 times smaller than most plant and animal cells. https://education.seattlepi.com/size-comparisons-bacteria-amoeba-animal-plant-cells-4966.html
And since there are conservatively estimated to be around 30 trillion cells within the average human body,
Revised Estimates for the Number of Human and Bacteria Cells in the Body – 2016 Abstract: Reported values in the literature on the number of cells in the body differ by orders of magnitude and are very seldom supported by any measurements or calculations. Here, we integrate the most up-to-date information on the number of human and bacterial cells in the body. We estimate the total number of bacteria in the 70 kg “reference man” to be 3.8·10^13. For human cells, we identify the dominant role of the hematopoietic lineage to the total count (?90%) and revise past estimates to 3.0·10^13 human cells. Our analysis also updates the widely-cited 10:1 ratio, showing that the number of bacteria in the body is actually of the same order as the number of human cells, and their total mass is about 0.2 kg. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002533
Then that gives us a rough ballpark estimate of around 300 trillion times 100 million pages of Encyclopedia Britannica. Or about 300 trillion times the information content contained within the books of all the largest libraries in the world. Needless to say, “Someone” has been very busy making 'purposeful choices' bringing our material bodies to a state that is so far out of thermodynamic equilibrium.bornagain77_{November 22, 2019
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Eric - Along those lines - one of my favorite papers from the evolutionary computing area: Why Evolution is Not a Good Paradigm for Program Induction Which dovetails well with a paper I wrote on the same question about biology: Irreducible Complexity and Relative Irreducible Complexity: Foundations and Applications It's funny. Over and again I find numerous researchers basically agreeing with all of the points of basic science that ID makes. They just make sure you don't accidentally put them all together on the table at the same time.johnnyb_{November 22, 2019
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EricMH@3 The answer is that the science does not sell without the ideology. We're the bad guys here. BTW I looked at English's objection to your paper that there is in infinity where the sets objects don't match. I can't however see any real biological case where an infinity would occur. Am I thinking about this right?bill cole_{November 22, 2019
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If all these marvels are done entirely through natural selection, why do genetic algorithms suck so bad? What is the mismatch between random Darwinian evolution and its presumably faithful replication with genetic algorithms? What is the source of the outstanding performance of Darwinian evolution, if not in the mere operations of crossover, variation and selection? The field of genetic algorithms has been researching this question for decades, and the only gains it makes is by rejecting Darwinian mechanisms and including more teleological approaches like differential evolution and particle swarm optimization. What gives?EricMH_{November 22, 2019
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I clearly did not get enough sleep last night. Updated the page to have the link. It is here: https://royalsocietypublishing.org/doi/10.1098/rsta.2016.0343johnnyb_{November 22, 2019
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Is there any link to the paper? I found this one: https://ui.adsabs.harvard.edu/abs/2017RSPTA.37560343K/abstractPavelU_{November 22, 2019
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