Knowledge and subjectivity. Origin of life

Discussion in 'Biology & Genetics' started by mjs, Mar 17, 2014.

  1. mjs Registered Member

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    The entire history of revolutions in human thinking is full of examples in which complicated human-centered theories gave its place to simple explanations in which human is just a part inside a system and because of this fact, he has a subjective view. In the beginning, people thought the earth was flat, because that was what everybody observed. However, there were fundamental inconsistencies with this model, both mathematical and logical. Additionally, human couldn’t feel the motion of the earth and thus, believed their eyes and tried to explain the skies with the assumption that earth was the center of the universe. However, things were getting far too complicated, and finally this model was replaced with the heliocentric which made things easy and clear. In all cases we were a part inside the system and we couldn’t have an objective view of things. However, can we say that today we got rid of all thee subjectivities? Is there still way to go? I believe the latter is the case.
    Take for instance the phenomenon of life. All that is there is a complex system of countless chemical reactions. These reactions seem to have some amazing properties that violate the way generally nature works, because as we know, nature tends to simplify things by increasing entropy and moving toward lower energy states. What we have in life instead, is a system of sophisticated and stochastic reactions that lead to more and more sophisticated organisms with higher organization. These organisms are self-sustained through a complicated process that is called homeostasis. The complexity of the latter becomes more and more evident as we try to study every aspect of it in detail. For instance, acid base balance in an organism depends on a series of events that are cooperating in a way that if a single procedure was not there, then the whole system would be malfufunctiong. Even a relatively simple process such as Krebs cycle is composed of such a complex system of reactions, including upregulators and downregulators that ensures that the cycle is self regulated. Countless reactions, but not a single one is placed in chance. How extraordinary!!
    How can all these occur spontaneously? My question is: Can human subjectivity help us find a more simple explanation? In fact, can we make this extremely simple and assume that all the reactions that compose life on earth are actually random? Can they just be reactions that with the help of external sources of energy like sunlight are simply becoming more and more complex over time?
    Before you say that the answer is no, just think who is the observer of all these. WE. The end results. A part inside the system that judges this system from the inside. The causes judged by the result. In other words, subjectivity on its extreme.
    Think about it: Even if there were only random chemical reactions what would happen on primordial earth? The reactions with repeatability that occur in a cyclic manner would not eventually lead to a dead end and eventually would go on indefinitely in the long term (what we perceive as reproduction?). In addition, some reactions with specific characteristics would eventually survive, either because they promote their own existence, or they give them survival advantage toward others. This fact, with a little help of repeatability would lead to the creation of reactions with three characteristics: survival capacity, complexity and repeatability. If the reference frame is the results of these, or else ourselves, the whole process is actually perceived as evolution. To put it mathematically, evolution is called the study of the random series of events that lead to the transformation of A to B, where B=[B1,B2,B3,….Bv], when things are viewed through the perspective of either B1, or B2, or B3, …….or Bv.
    In other words, we exist not because a conspiracy force promotes our evolution, but because our reactions continue to occur. We are the ones that give value to our existence.
    The importance of this viewpoint is that apart from the fact that it answers previously unanswered questions, it assumes that living beings are actually complex systems of reactions, and can thus be manipulated in predictable ways under chemical laws. This means that apart from the fact that the theory is testable and falsifiable, it indicates major implications for medicine.
     
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  3. Fraggle Rocker Staff Member

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    You misunderstand entropy. The Second Law of Thermodynamics tells us that entropy tends to increase over time. However, spatially and temporally local reversals of entropy are not only possible but quite common.

    Life is simply a spatially local reversal of entropy. Living things destroy the organization of the things around them, deconstructing them into their basic chemical compounds, which we then consume, breaking them down even further so that we can use them to increase our size, or breaking them down further still so that we can use the energy in their chemical bonds to provide energy for our own biological processes and (in the case of animals) to provide energy for actual movement, as well as other metabolic processes such as temperature regulation and thought.

    Indeed there is a decrease in entropy in the creature that consumes the food or fuel, but there is a much larger increase in the entropy of its surrounding space. In the long run, the Second Law will prevail as it always does. When the sun runs out of fuel and stops filling the environment around us with energy, we will be forced to stop metabolizing our surroundings and we will die. (Unless we've mastered interstellar travel and have found a new place to rebuild our civilization--which would be merely another temporary reversal of entropy that can't last forever.)

    There's no contradiction here, merely a misunderstanding of entropy.

    The Big Bang itself can be seen as merely a spatially and temporally local reversal of entropy. There was no net increase in matter and energy (since they both sum to zero), merely a temporary increase in its organization, and as we speak the universe is slowly returning to its original state of maximum entropy/zero organization.

    Note that the Second Law places no limit on the size of a reversal of entropy.
     
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  5. origin Trump is the best argument against a democracy. Valued Senior Member

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    I have never agreed with this line of thought. A reversal of entropy would be occuring if a person were to spontaneously form out a bunch of chemicals, but that does not happen. From the moment of conception there is a tremendous amount of energy that is expended by the mother into the growing child. This expenditure of energy is not 100% effecient, there are lots of losses. If we look at the system of mother and growing fetus we will see that the mother is consuming energy at a rate that exceeds the amount that is needed to produce the chemical reactions and the growth of the fetus. In other words for the mother/fetus system, entropy increases.
     
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  7. exchemist Valued Senior Member

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    Who are you preaching to? The only people I've come across who think it is impossible life to arise without "violating" the way nature works are creationists. There aren't many of these here.

    You seem to think you have some special insight that solves a problem in science, but I honestly can't make out what.

    By the way, who in history believed the Earth was flat? Certainly from the time of the Hellenistic Greeks onward, nobody in Europe did.
     
  8. wellwisher Banned Banned

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    The easiest way to see the entropy balance within life, is to look at life as two separate but overlapping observations. First, metabolism breaks down larger food molecules into smaller and smaller molecules, all the way to CO2 and H2O, thereby increasing entropy. This satisfies the needs of the second law. Along with this, is the second observational layer. This is connected to life growing and adding organized structures, beginning with smaller units like animo acids that are built up into protein. In this layer, entropy is decreasing. As long as the first layer is higher than the second layer, there is no violation of the second law. The second law deals with the net value of entropy.

    What makes life different, is the second layer, where there is a concerted effort to decrease the rate of net entropy increase, for growth. If we burned the materials used by metabolism in a fire, we would get roughly the full 100% entropy increase. But with life being 85% efficient, based on the energy output of metabolism, life nets closer to 15% net entropy increase.

    This brings up to the second characteristic of life which makes it unique. The second layer also builds internal energy value when life grows. We can burn a tree because of stored energy, with bigger trees, due to growth, having more energy content. Normally energy is supposed to decrease to near zero, like in the fire, with the output energy gong into the higher entropy. With life, instead of fully going into entropy, the cell turns the energy of metabolism into work and stored structural energy. All forms of life will give off energy in a calorimeter.

    If you look at a mutation on the DNA, this is another example of entropy increase; disorder. But this is the exception to the rule since most of the template will have perfect matches, so there is minimal change of entropy at the template. In this case, the improper base pair is at higher energy than a proper base pair, with the extra energy going into structural entropy.
     
  9. origin Trump is the best argument against a democracy. Valued Senior Member

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    Entropy is increases. It is like saying that contructing a car decreases entropy. That would be an absurd statement, when a car is made the entropy of the universe increases and likewise with life.

    Your numbers are just made up but the bottom line is correct that entropy increases.

    Energy is stored, big deal. Entropy increases. When the sun shines on the ocean the temperature of the ocean increases and energy is stored, again big deal.

    Is that a poke at evolution? Improper base pairs and proper base pairs - sounds like a judgement call to me. How come you get to decide which base pair is 'proper'.

    By the way if you had just added liberals into your post I would have had BINGO. Maybe next time.

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  10. wellwisher Banned Banned

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    Water plays an important role with respect to the second layer of life, which allows entropy to decrease. If you mix oil and water, these will phase separate into two layers. This separation into two, lowers the energy of the two phases, but will cause the entropy to decrease. There is higher entropy within a solution of these two components, than there is if the two components separate out. Life's structures phase separate from each other, and from the water, to form lower entropy zones, compared to pure solutions. Polymerization plays a role in this. Water does this to the organics. Proteins will fold in ways to minimize the energy with the water, but doing so become organized into lower entropy phases.

    The DNA is the most hydrated molecule in the cell with Beta-DNA, the predominant form of DNA, the most hydrated of all the DNA conformations. This chemical design is a result of the need to increase entropy, by making a better solution with the water; more hydration. The membrane material (lipids) is the opposite, in that it reminds phased separated from the water and therefore exists at lower entropy. Water can freely migrate through the membrane, but as a second phase that only loosely binds to the membrane. These two bookends, with respect to the water-oil analogy, define the second layer structural entropy poles of the cell, with all the rest of the structure, in the middle with respect to entropy.

     
  11. wellwisher Banned Banned

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    The difference is the warming of the ocean, once the heat source or sun is gone, will lose heat at night, like any inanimate object, if there is a thermal gradient. The cell is different in that may continue to grow, by converting the energy of the day, into stable structural energy that will persist in spite of energy gradients. The next day the ocean is cooler but the cell is fatter.

    Once life dies, and become inanimate, it acts more like the ocean at night, losing energy.
     
  12. origin Trump is the best argument against a democracy. Valued Senior Member

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    So if I pour water into a bowl and then I pour oil into the same bowl you seriously think that I have decreased entropy? My god, after all this time you are still completely baffled by entropy.
     
  13. origin Trump is the best argument against a democracy. Valued Senior Member

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    So the difference is the time scale - so what.
     
  14. wellwisher Banned Banned

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    If we mix oil and water in one beaker and water and alcohol in another beaker, which has more entropy? The alcohol and water, since these blend into one solution instead of two phases of pure substances. Life uses water as its main component, with the organics of life not always able to blend into water to form solutions. This is useful since phase separation will result in lingering loss of entropy ,compared to the ideal solution. Evolution will be driven by the need to increase entropy further, with the DNA, for example, the best way so far for merging water and organics via extreme hydration.
     
  15. origin Trump is the best argument against a democracy. Valued Senior Member

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  16. Fraggle Rocker Staff Member

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    Entropy does not have to be studied at the level of the entire universe. It is quite reasonable to observe the interesting phenomenon of decreasing entropy inside an organism, in contrast to the accelerated increase of entropy in its immediate surroundings.

    In fact it is important to observe this phenomenon, because at the level of the entire universe, living organisms accelerate entropy and are hastening its decay toward (but never quite reaching) a state of complete disorganization.

    I would suppose that knowledge of the true shape of the Earth was first discovered in the Bronze Age, which began around 3000BCE in Mesopotamia, a bit later elsewhere, and less than 2,000 years ago in South America. The metal blades made possible by metallurgy were used to build the first precise, wooden wheels. (Of course stone and ceramic potters' wheels came first and undoubtedly inspired the vehicular wheel, but they were too small, heavy and irregular to be of much use on a cart.) Wheeled vehicles full of supplies and drawn by the first domesticated horses made it possible for people to travel rather long distances rather quickly. It surely didn't take long for them to notice that the stars seemed to have slipped a little out of their normal positions.

    Metal tools also made large ocean-going sailing ships possible. They covered distance even faster than horses, so sailors, who had to navigate by the stars anyway, would have quickly made a science out of charting the heavens and deducing the fact that the earth was spherical.

    So indeed, by Columbus's time every sailor knew that the world is round, and so did the better-educated landlubbers. But despite that knowledge, Columbus was terrible at reckoning, and figured that the shores of Asia were only a few thousand miles from Iberia--which is why he assumed that the people he met on Hispaniola were "Indians." If the continents of the New World did not exist, his crew would have run out of food long before they were even halfway to Asia.

    I'm not going to copy your entire post, merely say that it's a very good explanation. Let's hope that the two of us together were able to disabuse Origin of his misunderstanding of entropy.

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  17. exchemist Valued Senior Member

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    Regarding curvature of the Earth's surface, ANY seagoing nation able to go out of sight of land would have understood that departing ships appear to go down below the horizon - and that you can see them for longer from the top of a tall object (mast, cliff, etc). So I quite agree, knowledge of the Earth's curvature, if not necessarily of it being spherical, must have been very widespread from a fairly ancient date.

    As for the presentation of entropy by Origin vs. yours and wellwisher's, I think you are agreeing with one another. It seems to me that all of you are saying overall entropy increases during the processes of life and I don't think Origin is denying that it may decrease locally within a growing organism, at the expense of the far greater increase in the organism's surroundings of course.

    It may be the use of your slightly unusual term "reverse" that is problematic. "Reverse" could possibly be read to imply something going against what is normally unidirectional. But of course there are plenty of natural processes in which entropy locally decreases (condensation and crystallisation being two).

    Anyway, I think we are all in agreement.
     
  18. kx000 Valued Senior Member

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    There is one ultimate ancestor of all things. From life, to thoughts. It's more likely this ancestor created itself that occurred by random.
     
  19. wellwisher Banned Banned

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    If you had a sugar water solution in one beaker and a sugar water solution with yeast, in a second beaker, the second beaker, containing life, will increase entropy at a much higher rate, than the beaker without life. Life causes an acceleration within the rate of entropy increase. The question becomes why?

    The structural components of life, are based on lowered entropy, implicit of elaborate order, instead of disorder. This structural order is increasing as the cell grows. The structures of life represents a zone of entropy deficit, compared to inanimate matter with the same type and number of atoms. If the cell was to die and become inanimate, the structural entropy will increase. To make up for the deficit of entropy in the volume defined by the live yeast, entropy will be generated at much higher level; reflects the entropy potential.

    Water plays a pivotal role in this, via phase separation of organics into order. If the cell could fully dissolve all the structures into water, the rate of needed entropy would go down, since this would satisfy much of the entropy potential. If we take out the water from the beaker and the yeast and add alcohol as the solvent, the rate of entropy goes way down. The entropy potential, that had been in the water, is now substantially satisfied by alcohol and organic interactions. The yeast will appear dead and nearly all enzymatic activity will cease, since there is little potential.

    Liquid water, itself, is not an ideal solution, but rather is highly ordered due to hydrogen bonding, into high and low density domaines. Like the example above of the yeast beaker, water itself defines entropy potential compared to an ideal solution. This makes it the universal solvent plus many other things needed by life such as the need to spontaneous dissociation indicative of pH. The pH effect increases entropy.

    In physical chemistry, entropy is a measured quantity needed to close all energy balances. It is not just an imaginary concept base on disorder. Defining entropy in a clear way is often the main problem people have with the concept. But measuring the changes in entropy is well established. The measured value are not about opinion, but experimental verification.
     
  20. wellwisher Banned Banned

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    Besides lowering entropy into order, the cell also builds increasing energy value within its structures. An interesting molecule connected to this building of energy value is ATP. ATP is considered an energy rich molecule, but not in the way most people think. There is already a lot of stored energy in the cell, via its many structures, so ATP was designed to work in conjunction with this structural energy potential, while not directly adding to it.

    View attachment 6965

    The triphosphate moiety of ATP, is where the energy is. If you look at the triphosphate, you have the highly electronegative oxygen and the positively charged phosphorous induced by the oxygen. These are both strong election acceptors, not electron givers like octane or lipids. What this implies is ATP is energy rich in the sense of adding energy as an electron acceptor.

    In the general reaction diagram below, the purpose of ATP is not so much an energy rich molecule on the reactant side, but rather it is energy rich via the product side, with the electron withdrawing nature of ATP lowering the floor on the product side. This is useful and necessary to the cell, because it expands the energy value, without adding more reactant based energy to the cell, allowing more structural energy storage.

    As an analogy, it is like having a ball at height H. We need to make the ball more potential energy, but we can't add any more height. The work around is we dig a hole for the ball fall into, thereby gaining more energy potential, while not adding any height. By digging this hole, inside the cell, the environment does not see this potential, yet we have more energy.

    If ATP was an electron giver, on the reactant side, then it would add to the cell's energy profile, as seen by the environment. Now you have more potential for spontaneous oxidation and other reactions if the cells gains too much additional structural energy. But if we dig the hole, within the cell, the environment does not see this hole, but normalizes the structures to background products outside the cell.

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  21. Rav Valued Senior Member

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    Nonsense. Self-creation is a logical absurdity. So is the idea that something emerged from true philosophical nothingness. What is more likely is that somethingness is the only possible state of affairs, and that this scientific nothingness that everyone is discussing these days is simply the most foundational or fundamental layer of those affairs. And a whole lot more substantive and remarkable than the label of "nothingness" would suggest given what it can obviously manifest.

    Some people anthropomorphize it. Some don't. I don't. Philosophically speaking I just don't need the need, or the requirement.
     
  22. exchemist Valued Senior Member

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    For any readers with the stamina to have persisted this far, there is a somewhat clearer exposition of what Wellwisher seems to be on about here:

    http://chemwiki.ucdavis.edu/Physica...ase_Studies/Case_Study:_Thermodynamics_of_ATP

    The ATP +H2O -> ADP +HPO4- (or whatever, biochemists are very sloppy in making their reactions add up) process yields about 30kJ/mol.

    (This has bugger-all to do with the original topic, of course, but since "liberals" have yet to make an appearance in this thread we must be grateful for small mercies.)
     
  23. Aqueous Id flat Earth skeptic Valued Senior Member

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    The OP mentioned the Krebs cycle and wellwisher woke up like a germ-detecting robot to come sanitize the biology threads of any lingering ideas that thermodynamics disproves the existence of God.

    I actually have no idea what this thread is about. The OP resembles wellwisher's protracted rambling vagueries, minus his repetitive nonsensical analogies. I have it in mind that the Creationists who troll here have divvied up the work, with wellwisher specializing in the insinuation of intelligent design in some hackneyed pseudo-biochemical nonsense.

    The only technical remark in the OP that I recall, buried in that mess of verbiage, was some unspecified indictment of the Krebs cycle in some vague connection to human subjectivity, as if to suggest that science (objectivity I suppose) has some unspecified flaw of some kind. This seems to me to invite the plague of nonsense from wellwisher about reversal of entropy (creation) and water (waters separated by God in Genesis?)

    Obviously the biotic energy cycles are no more capable of reversing entropy than any heat engine. I actually haven't yet heard anywhere a single plausible case to support the idea that organisms demonstrate entropy reversal. As we well know, life could not exist without copious energy taken up from solar, chemical, and geothermal sources. The only person I recall even trying to argue it is wellwisher (chronically). I realize there is some pop science fare and perhaps a few academics who address this from a philosophical standpoint. But the way wellwisher mangles it, the Creationist pseudo science is easily taken to the shed for a walloping, for deliberately leaving out the requirement that systems (ah that was touched on in the OP: something about systems--) are defined in thermo. according to boundaries. The wellwishers of the world are pretending that this very essential piece of information can be "disappeared", leaving them to gloat about how magically easy it is to harp on an abundance of entropy reversal just by ignoring system boundaries.

    I guess that leaves us to figure out if wellwisher wrote the OP or if "mjs" was just making a driveby. There probably are some good technical discussion points that could develop. 30 kJ/mol sounds plausible -- if I'm not mistaken that's about 1/1000th the energy of burning an equivalent amount of gasoline. That certainly would seem to be a realistic order of magnitude for biochemical processes anyway.

    It's striking that the ADP-ATP cycle has relegated Phosphorus to this very specialized task of energy conversion. It's as if it found a niche there, to be exploited because, ignoring the rather peculiar presence the adenosine radical (but causally connected to other biological processes) there is an elegant simplicity to phosphate chains and their ability to make the cycle work -- as a matter of intrinsic chemical properties of course, obviously not by "design", and as we well know, not at all through reversing entropy. That simplicity meets the test of Occam's Razor, which, combined with the plausible 30 kJ/mol number, makes the theological argument come across as especially frivolous. As far as I can tell, this POV is completely relegated to the Anabaptists who seem to be the only denomination who got stuck on this issue, probably when energy cycles were covered, to their chagrin, in their high school life science classes.
     

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