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Defending the Christian Worlview, Creationism, and Intelligent Design

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Defending the Christian Worlview, Creationism, and Intelligent Design » Molecular biology of the cell » Metabolism » Transformation of Energy to Maintain a Low Entropy State and Perform Work

Transformation of Energy to Maintain a Low Entropy State and Perform Work

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Otangelo


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Transformation of Energy to Maintain a Low Entropy State and Perform Work

A biological system in a state of energetic equilibrium is dead. The consumption of energy is required to drive and maintain the system far from equilibrium. That prerequisite is needed in order to allow the system to promptly change its configuration, according to the system's needs. In turn, the dissipative energy provides the thermodynamic driving force for the self-organization processes.

A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed.  Living cells accomplish this by using the compound adenosine triphosphate (ATP).  ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery. When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The energy is used to do work by the cell, usually by the released phosphate binding to another molecule, activating it. Since ATP plays a key role in the vital activities of all organisms, analysis of abiogenesis pathways for this compound becomes an important issue within the context of the problem of the origin of life.

Cell metabolism is impossible in the absence of nucleoside triphosphates because transcription and translation processes depend on them. ATP occupies a special place, because it was selected for the role of universal energy currency, that is, for coupling catabolic and anabolic reactions in the cell. 

Modeling of Abiotic ATP Synthesis in the Context of Problems of Early Biosphere Evolution May 13, 2014
https://sci-hub.ren/10.1134/S0016702914130084
The pathway of adenosine triphosphate (ATP) synthesis in living organisms consists of two autonomous stages; The first stage is construction of an adenine heterocycle linked to a ribose-5-phosphate molecule to yield AMP, while the following stage is the attachment of phosphoryl residues to the nucleotide molecule by macroergic phosphoanhydride bonds. Involvement of the same set of precursor molecules in both de novo biosynthesis of AMP and abiogenesis of this nucleotide is a very important issue for the analysis of metabolic pathways. 

Phosphoanhydride bonds in ATP and other nucleoside phosphates, as well as some other types of bonds with high hydrolysis energy, are referred to as high-energy (or macroergic) bonds in the biochemical literature. The presence of such bonds accounts for the involvement of ATP in intracellular transfer of chemical energy. However, strictly speaking, the energy balance between the molecules of the initial participants and products of the
reaction, rather than the energy of the bond itself, is relevant, since the breakage of any chemical bond is an endergonic process.

The complete biosynthetic pathway from ribose-5-phosphate to AMP consists of 13 consecutive “steps,” i.e., individual enzymatic reactions. None of the intermediate reaction products have an independent value in metabolism.  Photophosphorylation during photosynthesis, oxidative phosphorylation coupled to cellular respiration, and substrate-level phosphorylation  are the three principal ATP sources in living organisms.
Implementation of the first two mechanisms requires the presence of a lipid membrane incorporating the ATP synthase which catalyzes the attachment of a phosphoryl residue to ADP. The energy of the transmembrane electrochemical ion gradient (usually proton gradient) is the immediate source of energy for this process.

Abiotic formation of nucleosides in a chemical reaction of the bases with sugar molecules turned out to be quite problematic. The yield of purine nucleosides in such reactions was low, while pyrimidine nucleosides were not formed at all. The absence of a realistic mechanism for the specific synthesis of ribose under abiogenous conditions constituted an additional problem.  The absence of a realistic mechanism for the specific synthesis of ribose under abiogenous conditions constituted an additional problem, arising both from the low specificity of the formose reaction (which is usually considered an abiotic pathway of sugar formation) and instability of the “desirable” configurations of carbohydrate molecules under the conditions of a model experiment. This complication has not been completely circumvented even today.

Spontaneous instantaneous emergence of multienzyme complexes that are capable of catalyzing a series of sequential reactions resulting in the conversion of a substrate into the target product is highly unlikely. The modern views on the development of such multistep metabolic pathways imply gradual replacement of abiotic synthesis by more efficient biocatalytic reactions in protobionts. The occurrence of identical reactions during the chemical (abiogenic) and enzymatic conversion of the precursor molecules into the product molecule is a prerequisite for such substitution, that is, a reaction catalyzed by the newly formed enzyme can only replace a chemical reaction involving completely analogous substrates and products. Therefore, the initial substrates for abiogenic synthesis and biosynthesis of the final product (specifically, AMP) must be the same in this case.

The structure of the biochemical pathways is completely determined by the genetic machinery of the cell. The existence of profound structural differences between abiotic and enzyme driven systems is an important issue. 


Maintenance of the low entropy state of living systems requires the persistent infusion of energy (Morowitz 1968), first, to enable the system to maintain its complex organization and resist dissipation toward randomness. The second requirement for an input of energy derives from the fact that living processes perform work by growing and retracting, moving through the environment, emitting energy, counteracting concentration gradients, transforming materials, erecting and breaking down structures, and other endogenous activities. While energy transformations are characteristic of all dynamic physical and chemical systems, energy flow in non-living systems tends to result in greater disorder among all elements of the system. Energy released through different stages of the rock and water cycles, for instance, generally erodes land and distributes water to increase the entropy of the total collection of water and land toward equilibrium (lower mountains, more dispersed water and soil). The energy transformations of living systems, on the other hand, serve primarily to harvest and store the levels of free energy necessary for maintaining the highly ordered structure of the organism and performing the work that living cells carry out. The net effect for living systems, in contrast to that for non-living systems, is to maintain and often increase order at local levels and on microscopic scales.

There are two consequences to the way in which life transforms energy. One is that much of the energy is used to create and sustain a level of complexity that supports emergent functions that in their totality exceed the sum of the parts of the system. A mountain may be structurally complex but its role in the rock cycle is not dependent on the detailed organization of its individual rocks and sediments. The mountain is in essence a simple conglomerate of its component parts. The function of a living organism, on the other hand, depends critically on precisely how it is put together. Its component parts function in a coordinated manner, to generate a complex array of emergent properties, both structurally and functionally. The generation and maintenance of this complexity is one of the primary uses of the energy that living systems transform. A second consequence of biological energy transformations is to create one or more additional microenvironments within the natural environment. The Eh (redox-potential), pH, solute composition, and structural complexity of the living cell is maintained at levels different from the extracellular environment because of the autonomous functions carried out by the cell, but not in the abiotic environment surrounding the cell. New environments can also be created on a larger scale by colony forming organisms such as stromatolites and corals, which can alter the topography of large amounts of habitat.

Life-induced changes can occur even on a planetary scale, such as the change in atmospheric oxygen composition brought about by oxygen-producing microbes on Earth, beginning with the emergence of photosynthesis as a uniquely biological form of energy transformation (Knoll 1999; Schopf 1994). This innovation enabled life to become autotrophic (manufacturer of its own food from the simple and abundant molecule, CO2) on a global scale. Thus, not only is the transformation of energy a characteristic of life, but so is the ability of life to alter conditions in the natural environment. Note the dual requirement of living systems: to resist an increase in entropy, and to perform work. Both requirements are essential for the definition of a living entity. Any fabrication or machine is, for the time being, at a lower state of entropy than, and in disequilibrium with, its environment. Indeed, such objects are known to exist on other worlds: the lifeless Huygens lander rests on Titan, and the surfaces of Mars and the Moon are littered with man-made objects. When a cell or organism can no longer maintain steady disequilibrium conditions it approaches equilibrium with its environment and therefore dies



Last edited by Otangelo on Sun Feb 07, 2021 9:58 am; edited 2 times in total

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2Transformation of Energy to Maintain a Low Entropy State and Perform Work Empty Thermodynamics and science predictions Sat Jun 08, 2019 12:34 pm

Otangelo


Admin
Thermodynamics and science predictions

https://reasonandscience.catsboard.com/t2572-transformation-of-energy-to-maintain-a-low-entropy-state-and-perform-work#6856

It is often praised, how science-based on methodological naturalism serves to make accurate predictions. Let's imagine that we would be aliens, being part of a super-intelligent civilization. visiting early earth four billion years ago with a spaceship. We would find a hostile environment, no life, just spewing volcanoes etc.

We would leave, returning to our own planet, run a computer simulation, and make a prediction of how the earth would look like, 4 billion years later, and trying to simulate the effects that the four known forces of physics would have on every atom and every subatomic particle on our planet.

If we ran such a simulation out to the present day, would it predict that the basic forces of Nature would reorganize the basic particles of Nature into libraries full of encyclopedias, science texts and novels, nuclear power plants, aircraft carriers with supersonic jets parked on deck, and computers connected to laser printers, CRTs and keyboards?

If we graphically displayed the positions of the atoms at the end of the simulation, would we find that cars and trucks had formed, or that supercomputers had arisen? Certainly, we would not, and adding sunlight to the model would not help much.

The argument of thermodynamics was popular and often used by creationists, over a decade ago, but has gone a little bit abandoned in more recent Facebook times. The standard answers by atheists were that the earth is not closed, but an open thermodynamic system, receiving constantly energy through sunlight, which could decrease rather than increase entropy, so the argument is moot.

The Earth is an open system, it receives energy from the sun and entropy can decrease in an open system, as long as it is ‘‘compensated’’ somehow by a comparable or greater increase outside the system.

Isaac Asimov replied through an article at the Smithsonian journal:
You can argue, of course, that the phenomenon of life may be an exception [to the second law]. Life on earth has steadily grown more complex, more versatile, more elaborate, more orderly, over the billions of years of the planet’s existence. From no life at all, living molecules were developed, then living cells, then living conglomerates of cells, worms, vertebrates, mammals, finally Man. And in Man is a three-pound brain which, as far as we know, is the most complex and orderly arrangement of matter in the universe. How could the human brain develop out of the primeval slime? How could that vast increase in order (and therefore that vast decrease in entropy) have taken place?

Asimov concludes that the second law is not really violated, because: Remove the sun, and the human brain would not have developed . . . . And in the billions of years that it took for the
human brain to develop, the increase in entropy that took place in the sun was far greater; far, far greater than the decrease that is represented by the evolution required to develop the human brain.

Similarly, Peter Urone, in College Physics, wrote:
Some people misuse the second law of thermodynamics, stated in terms of entropy, to say that the existence and
evolution of life violate the law and thus require divine intervention. . . . It is true that the evolution of life from inert
matter to its present forms represents a large decrease in entropy for living systems. But it is always possible for the
entropy of one part of the universe to decrease, provided the total change in entropy of the universe increases.

The Theism VS Atheism debate is ALL about probability.

The reason natural forces can turn a computer or a spaceship into rubble and not vice versa is the probability: of all the possible
arrangements atoms could take, only a very small percentage could add, subtract, multiply and divide real numbers, or fly
astronauts to the moon and back safely.

If an increase in order is extremely improbable when a system is closed, it is still extremely improbable when the system is
open, unless something is entering which makes it not extremely improbable.

The claim that the second law does not apply to open systems was invented in an attempt to avoid the evident implications and logical inference of a creator.

The missing ingredient is information.

Norbert Weiner - MIT Mathematician - Father of Cybernetics

"Information is information, not matter or energy. No materialism which does not admit this can survive at the present day."

Life is permeated by codified information. Not only genetic but mostly, epigenetic information. Complex blueprints, which direct how the most complex high-tech factory complex of the universe, biological cells, have to be built, and how to error check and repair themselves all along the production process of higher molecular machines, how to generate energy in the form of ATP molecules, how to import the basic, life-essential elements, purify them, use them to build the basic building blocks of life like RNA, DNA, amino acids, carbohydrates, and fatty acids, how to create a homeostatic ambiance permitting information exchange and signaling networks to operate, how to react to ecological cues, how to develop, and how to respond to nutritional demands. And it had all to be pre-programmed and set up in advance for life to kick off - without evolution.

This coincides with the REMARKABLE, awe -, well, actually the God-inspired beginning of the Gospel of John:

1 In the beginning, was the Word, and the Word was with God, and the Word was God. 2 He was with God in the beginning. 3 Through him all things were made; without him nothing was made that has been made.

Science and religion are not at war, but actually complimentary. One informs the other, and vice-versa. They are the same coin, one side showing the face, and the other side the numbers. Both point to God. A God that does not hide himself, but made himself known to us. John continues in verse 14:

The Word became flesh and made his dwelling among us. We have seen his glory, the glory of the one and only Son, who came from the Father, full of grace and truth.

What a remarkable revelation !! Praise the Lord.

What is remarkable as well about the above text is that it was essentially formatted as a scientific paper.

The article, ‘‘A Second Look at the Second Law,’’ by Dr. Granville Sewell, Professor of Mathematics at University of Texas at El Paso, was submitted on October 21, 2010 to the Journal of Applied Mathematics Letters. Dr. Sewell’s article was peer-reviewed and accepted for publication on January 19, 2011.

On March 2, 2011, the Editor-in-Chief of Applied Mathematics Letters, Dr. Ervin Rodin, decided to withdraw the article without consultation with the author, not because of any errors or technical problems found by the reviewers or editors, but because the Editor-in-Chief subsequently concluded that the content was more philosophical than mathematical and, as such, not appropriate for a technical mathematics journal such as Applied Mathematics Letters.

Truth is, the REAL problem was that it was Intelligent Design-friendly. Then , afterwards:

Applied Mathematics Letters, which agreed to apologize to Intelligent Design-friendly Texas professor Granville Sewell and have its publisher, Elsevier, pay $10,000 in legal fees, has posted the text of its apology

http://retractionwatch.com/2011/06/13/applied-mathematics-letters-posts-apology-for-retracting-intelligent-design-friendly-paper/

The Journal of Applied Mathematics Letters and its Editor-in-Chief, Dr. Rodin, provide their sincere and heartfelt apologies to Dr. Sewell for any inconvenience or embarrassment that may have been caused by their unilateral withdrawal of his article, and wish Dr. Sewell the best in the future and welcome Dr. Sewell’s submission of future articles for possible publication.

Dr. Sewell’s article as accepted by Applied Mathematics Letters can be viewed at:
http://www.math.utep.edu/Faculty/sewell/AML_3497.pdf


Take proteins.
The natural tendency of proteins is to fall apart; for proteins to be synthesized, the reaction must be driven up the thermodynamic hill, away from equilibrium. The same is true of other biochemical processes: the transport of nutrients against a concentration gradient, the generation of physical force or electrical potentials, even the accurate transmittal of genetic information, all represent work in the thermodynamic sense. They can take place only because of cells couple the work function to a source of energy. This, in fact, is how energy is defined: it is the capacity to do work. Bioenergetics revolves around the sources of biological energy and the mechanisms by which energy is coupled to useful work

https://reasonandscience.catsboard.com/t2572-transformation-of-energy-to-maintain-a-low-entropy-state-and-perform-work#6856

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