Knowledge and subjectivity. Origin of life

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

  1. Fraggle Rocker Staff Member

    Depends on what you mean by "nothingness." If you allow for the existence of abstractions, like the Laws of Nature, something can indeed emerge from nothingness.

    The Second Law of Thermodynamics says that entropy tends to increase over time, asymptotically approaching a state in which there is zero organization. However, it also allows for spatially and temporally local reversals of entropy. This is our best bet for explaining the sudden appearance of our universe. There was no net increase in matter and energy because all the particles and antiparticles exactly balance each other, but there was a tremendous local increase in the organization of this region: a temporally and spatially local reversal of entropy, as the Laws of Nature allow.

    This organization has been continuously dissipating, as entropy has been continuously increasing, since that one moment.

    Many people go beyond mere anthropomorphism and postulate a universe that is anthropocentric. Some popular religions teach that Homo sapiens is God's greatest achievement, so the entire universe is designed as a home for us, full of teaching moments.
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  3. exchemist Valued Senior Member

    Actually, on this occasion I think you are seeing creationists under the bed.

    My reading of the OP is not at all that it supports intervention to explain abiogenesis. The first part makes a - more or less cogent - observation that the progress of mankind in understanding the world has been one in which Man's place in it has moved gradually from being central to being more and more marginal and incidental, as we progressively adopted the discipline of objectivity. Then it veers off into a fog of undecipherable nonsense, but I don't read any of it to argue against the value of objectivity. Rather the contrary.

    In fact, one of many strange things about the post is that it assumes the audience finds it unbelievable that life could have arisen naturally. It is almost as if it is a rather incompetent attempt at convincing a group of creationists of the error of their ways. So on a forum like this, it seems to be preaching to the converted!

    I don't get too hung up on the comments about "reversing" entropy. This is a term Fraggle Rocker used in fact, and he is not exactly known for his religious sympathies. I think it is just an infelicitous choice of terminology, to describe processes in which part of the system reduces in entropy, such as the formation of a crystal, for example.

    I was about to make the same comment as you have abut the magnitude of the enthalpy change in the ATP -> ADP process. It is not a lot, compared to most chemical reactions, but then if it were it would be hard to control in the delicate cellular environment.
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  5. wellwisher Banned Banned

    The main point I was making is ATP contains energy, but works at the product side, by lowering the energy floor of combustion. In combustion/fire, H20 is a terminal product, but in the case of ATP, water is reacted further, since the bottom (product side) is made even lower. ATP can squeak energy out of water. Fire can't react with water, like ATP, so the action of ATP does not show up as an energy source relative to fire/oxidation. This is subtle but ATP helps the cell store energy by making the working molecule slide under the radar of the environmental oxidation potential.

    Life and entropy is easier to see if you break the cell down into two separate but connected layers. One way to separate these experimentally, is too freeze daughter cells, and then thaw/freeze at various stages as they grow. The freezing will stop metabolism and thereby end the main dynamic layer of entropy increase. What will remain is the static or configurational source of entropy. The freezing will then allow one to compare the structural entropy before and after, based on the same atom counts.

    For example, we initially we will have more amnio acids or smaller molecules, which are loose in water, to maintain the atom count. These have more freedom to randomize than the large protein that will form later as the cell grows. The protein themselves, lose all sense of randomness with each forming unique folds. The unique folds of proteins is a good example of life having figured out a way to remove all traces of randomness so probability reaches 1.0. In terms of structural entropy, life has evolved to where all traces of entropy increase is removed protein to protein (same proteins). There is a sense of direction that is free from entropy and randomness. Water helps the cell tighten up.
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  7. Rav Valued Senior Member

    Such abstractions exist in the mind, and minds exist because neural architectures exist, and neural architectures exist because matter exists, and matter exists because some primordial state that some people like to call "nothingness" threw a quantum hissy fit and spat out a universe by dividing itself into perfectly equal amounts of positive and negative energy (mass-energy and gravity, or whatever).

    Now that's some pretty damned spectacularly awesome behaviour for something that, by definition, isn't even anything!
  8. wellwisher Banned Banned

    Another way to look at this, which is similar to RAV, are the laws of nature allow us to predict outcomes. Knowledge of these laws allows new technology and engineering. If we knew the natural laws behind life, we would be able to predict how life can and will form.

    The current consensus assumption of life is based on random, which is a bias of traditions. For example, proteins fold into unique folds and not average folds. Protein folding has nothing to do with randomness, but would need to follow cause and effect laws to get such consistent results. Yet the traditions insist on random. The traditions have build an elaborate design based on random, which if accepted, will bias the mind against any form of logical design.

    This bias persists even though unique protein folds, with protein constituting the bulk of the mass in life, is totally contrary to this assumption. I would trace this bias to it being an atheist counterpoint or mirror to Creationism. Creationism thinks in terms of cause and effect, but with God the singular cause. The general schema, of cause and effect, is dismissed due to this God connection (throw out the babu with the bath water). God can be ignored, if we assume Chaos rules using casino math, since periodic jackpots will appear. The entropy question is important because it is the dividing sword between logical and random, since increasing entropy means random while decreasing entropy implies order.

    The question becomes, how does a random model for life explain the well documented observation of unique folding of protein, with probably of 1.0? The entropy change of folding protein is zeroed with the reliability of cause and effect.

    I looked at the cell as two layers, so one can see this as separate. The random theory will often net total an increase in entropy, thereby appearing to prove that random is net at work. With two layers this is not a done deal.
  9. elte Valued Senior Member

    I think Fraggle's way of putting it seems good. Each time a DNA molecule is involved in building a new DNA molecule, there is a new and local organizing process going on in that construction. On that local level, entropy was reversed when organization was increased instead of decreased. Also, when the body builds energy stores by consuming energy sources in its environment, it is reversing entropy in that part of itself by concentrating the energy, which will later be dispersed. That's my two cents, anyways.
  10. exchemist Valued Senior Member

    Well, it's barely worth quibbling over, but all I'm saying is that most scientists would speak of entropy being "reduced" in part of the system in such cases, rather than "reversed".

    To me, "reverse" has something of a connotation of going "backwards" somehow, which is not appropriate, because it suggests something abnormal or even impossible. Personally I would try to avoid any such implication like the plague, as it could be taken as supporting the creationist notion that something extraordinary is going on. Whereas, on the contrary, reduction of entropy in parts of natural systems occurs all the time and is wholly unremarkable.

    Crystallisation of solids and condensation of vapours are two obvious examples. Thermodynamically, if I recall this correctly, these processes occur naturally when ΔG<0. ΔG =ΔH - TΔS. For a condensation or crystallisation, ΔH is -ve (system moves to lower enthalpy state, with evolution of Latent Heat), while ΔS is also -ve (entropy reduces). At the boiling or melting point, where you have the equilibrium state between the two phases, ΔG = 0. This occurs when ΔH = TΔS: if T goes down a bit, it condenses or freezes, as the TΔS term reduces and becomes outweighed by the enthalpy term. So, which "way" the process goes is thus a function of temperature. There is no "forward" or "reverse" direction.

    But I'm conscious I am rather labouring a minor detail of the best words to use. In any context other than the processes of life, I would not bother.
  11. elte Valued Senior Member

    I dunno, we often speak of reversing processes. Maybe it's not totally accurate to put it that way.

    One thing, however, comes to mind that we say can never be reversed, to my knowledge, which is time.

    On the other hand, with a battery, when we charge it up, that is basically a reverse discharge process. It doesn't identically reverse the discharge process, I admit.
  12. Yazata Valued Senior Member

    Hey, good post mjs. Welcome to Sciforums!

    I agree that the history of ideas shows a distinct tendency away from anthropocentrism.

    I'm not sure if the newer and more impersonal theories are always simpler though. Often the reverse seems to be true. Contemporary scientific theories have become so arcane that only scientists can fully understand them. (String theori, Higgs bosons, cosmic inflation, dark energy, and anything 'quantum'.) To most of the general public, science is just magic, a subject for faith, and not unlike religion.

    The ideas that the earth was flat and that the earth occupies the center of the universe aren't unreasonable. Wrong, as it turned out, but not stupid by any means. As you say, people figured that if the earth was moving, then why doesn't everyone fly off? And it's hard to think of anything more solid and immovable than the earth under our feet.

    I'm not convinced that we ever can, entirely. That doesn't mean that we can't (or shouldn't) try to produce scientific theories that address the entire universe, and not just our own subjectivities. But we will still be human beings, with all our limitations, producing those theories. They will still be human perspectives on an objective universe that's a lot bigger than we are.

    Yeah, life does seem to violate entropy, advancing from less-ordered to more-ordered. But that negentropy seems to be local, and comes at the price of a larger increase of entropy in the entire system.

    That it is. Very much so.

    Up through the 19th century, many people, including some famous biologists, argued strenuously that some mysterious vitalistic principle, whether divine intervention or an as-yet unknown life-force, was pushing biology to behave so differently from the rest of inorganic physics and chemistry.

    I don't believe that there is any external designer or inner force steering nature towards certain ends.

    It's an 'anthropic' perspective, that's for sure. The reason we can observe the processes that gave rise to us is because we, human beings, are here to do the observing.

    I'm not sure that I want to think of that as 'subjective' though.

    Take the sentence, 'Fish swim in the ocean'. That's an 'objective' statement, one that's true or false of its objects (fish and the ocean) independently of what the subject doing the speaking happens to believe about it. Now take the sentence, 'I like the taste of fish'. That one is 'subjective', it isn't really about fish at all, it's really about the speaking subject him/herself.

    I want to say that it's entirely possible to make objective statements (statements that are true or false about objects other than ourselves) from our own particular perspectives. (Human beings, at this point in history, here on earth, or whatever it is.)

    Yeah, that's more or less how I imagine it happened.

    That's an interesting point. It's our location here at the end of the historical process that makes us think that the process is directional, that makes it look like the whole evolutionary process was aimed at producing human beings like us. But that's probably just an illusory result of our perspective on things. I like it.

    Right. Every intermediate stage in our own ancestry, or in any branch of the entire evolutionary tree of life for that matter, could argue with just as much (and just as little) justification that the preceeding process that led up to them was directed squarely at producing them too.

    But that would probably just be an accident of perspective, the result of their perceiving themselves as being out at the end of that particular branch.

    I agree.

    Again, good post. I liked it, it has lots of stimulating ideas in it. An impressive debut.
    Last edited: Mar 19, 2014
  13. exchemist Valued Senior Member

    True, and one particularly hand-waving formulation of the 2nd Law that I've come across is that entropy is "the arrowhead on the direction of time", or words to that effect. Which is all very poetic, and sort of fair enough for a closed system, but most of the phenomena we encounter are in open systems, where it cannot be said. I think formulations such as this cause too many wrong ideas in the heads of laymen and should be avoided.

    When we charge a battery, we are reversing a discharge process, sure. But without knowing the cell reaction I would not care to comment on whether the entropy of the cell contents would be higher in the charged or discharged condition. All that can be said for sure is G (Gibbs Free Energy) will be lower in the discharged state. And you are right it is not an exact reversal, since entropy of the whole system will increase each time we do either -unless we do it under thermodynamically reversible conditions i.e. infinitely slowly etc, so that the change in S is zero - something we obviously cannot do in practice.
  14. Yazata Valued Senior Member

    I don't think that mjs was 'preaching'.

    He/she seemed to have been arguing against the idea, common among evolutionists (perhaps more so in the 19th century than today) that evolution is a directional process, from 'lower' to 'higher', ending in the highest being of all, the human being. In other words, the idea that nature has some impetus in it that drives it towards producing intelligent beings like ourselves.

    Mjs seems to be arguing that our sense that it's so, that all of evolutionary history was somehow focused on producing us, is probably the result of our human perspective from which we look at things.

    I think that's right.

    Or at least many of the better educated intellectuals didn't. But they weren't everybody.

    (I'll add that today, we are closer in time to the Hellenistic Greeks than they were to the ancient Sumerians. The Greeks already perceived that the world was ancient in their day. The antiquity of things like the pyramids impressed them.)

    Mjs' point seems to have been that the history of ideas appears to display a tendency in which at least the more advanced thinking has moved away from a local anthropocentric perspective in which people describe how things seem to them, towards a more universal perspective in which philosophy and science attempt to describe, in a more abstract fashion, how things behave, and the principles that govern that behavior, everywhere in nature.

    I agree with that too.
  15. Aqueous Id flat Earth skeptic Valued Senior Member

    Maybe I'm reading too much into it. I look at a statement like 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. That seems to minimize the phenomenal nature of the Copernican revolution, which cost Bruno his life and nearly waxed Galileo. In my mind Galileo alone epitomizes the victory of objectivity over superstition. To think that he put together the idea that he could shape glass into lenses, and then use his new invention to discover that Jupiter itself was a center of rotation . . . only to suffer examination and penalty under the Inquisition . . . well, I would hardly characterize him as "a part inside the system" or lacking in objectivity. The key ingredient that's been left out I think is tenacity. Not to mention bravery -- some of the the highest ideals we all aspire to, religious or not, and not nearly as confining as reducing all progress to a one-dimensional quest for objectivity. Objectivity is a natural tendency anyway which increases over time as we throw off the shackles of superstition.

    Maybe I'm overreacting. But once upon a time the fate of all science practically hung over the Church as a Sword of Damocles, in the form of incremental progress -- in folks like Copernicus, Kepler, Galileo, Brahe and Newton alone. While I agree that this progress changed the view that we're just parts inside a system, folks like them defy the other idea, that we couldn’t have an objective view of things. Being inside a system may pose a lot of difficulties but the only thing working agaist progress was superstition.

    Let me dissect the words 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. I've never been comfortable with that assessment; it has nearly purely religious pseudo-science motivating it. I think mjs started to develop from this raather nicely the idea of energy cycles, but then landed on this: Countless reactions, but not a single one is placed in chance. How extraordinary!! That does seem to me to suggest a retreat in the direction of intelligent design.

    Heh heh. I like his "redneck retard" characterization of fundie T-baggers. It's truly an American phenomenon, but I know you understand what I mean. For some reason the folks driven from England and similar hotspots to the presumed safety of the Americas obviously included a lot of nuts and windbags, and that DNA still lingers here.

    Sure. It's an intrinsic property of spheres that if you throw them randomly in a box they will align themselvels in the manner of a crystal lattice. I actually think the assumption that some folks make -- that this represents an increase in information -- is a sign that some of that lingering superstition is just too hard for some folks to shake off.

    Exactly. There is a zone where biochemical reactions are favored -- in the liquid phase of water at standard pressure, which rules out having nitroglycerin or hydrazine or some other highly energetic and unstable molecule as the batteries of life. (Besides the more obviously limitations.) The wellwishers of the world could have their demons driven out of them simply by looking at a table of enthalpies of formation for common reactions from a Chemistry 101 text. 30 kJ/mol would be within range of those numbers, which simply tells us that nothing even remotely resembling reversal of entropy, nor which violate the way generally nature works (mjs) is going on in any of the bioenergy cycles.

    Heck, we can measure the enthalpy change in the ambient as the sun rises and sets. That's a cycle unto itself which has a collosal Bunsen burner behind it. The naturally occurring difference between (pick a number) 273+x Kelvins and 273+y is some small deviation in the roughly 8 Joules of energy (nR) per mole of air alone. While that may seem insignificant to Creationists, admittedly it's only a tenth of a Joule or so, that's the amount per mole of air alone (or water or anything else affected by diurnal variation). That's an infinity to the scale of "mere mortal men". That to me is enough to wipe out any concerns about energy being created magically. It's pretty obvious where it's coming from.
  16. exchemist Valued Senior Member

    Well Yazata, you are capable of seeing things in the OP that I cannot. I do see - and have acknowledged it - that there is an observation about increasing use of objective thinking resulting in Man's position in the world being seen as less central. So far so good. But the main contention in the piece, so far as I can discern it, is that because Man is a product of life and more generally the working of the universe, our view of life and the working of the universe is somehow intrinsically subjective, i.e. we cannot be objective.

    This strikes me as an utter non sequitur. It is true that the goal of complete objectivity is unattainable, due to the various influences, conscious and unconscious, that affect any individual. That's why scholarship of any kind, including science, works best as a collective enterprise, where the biases of one can be compensated for by the different perspectives of others. But what is the basis for asserting that because we are products of the universe we cannot be objective in our perception of it?

    And if it were true, so what? The punchline seems to be " 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 first two sentences are simply statements of what scientists have been saying for over a century. The last seems an unrelated metaphysical point.

    Maybe I'm being thick, but I just cannot see this post as serious words of wisdom, I really can't.
  17. Fraggle Rocker Staff Member

    Evolution merely selects for traits that provide a survival advantage for the individual and, therefore, for the species. Intelligence is one of those traits so evolution often selects it.

    We're not the only ones; all of the Great Apes (humans, the two species of gorilla, the two species of chimpanzee and the orangutan) are extremely intelligent. So are the two species of elephant. So are many (if not most) of the dozens of species of dolphins, the dozens of species of crows, and the hundreds of species of parrots.
  18. RR Edwards Registered Member

    This is a logical fallacy - which cannot exist in a rational world. Therefore your "ultimate ancestor" has no chance of being real.
  19. wellwisher Banned Banned

    Going from higher to lower entropy happens all the time. When liquid water freezes into ice, the entropy will fall. The heat of fusion that is given off reflects, in part, the energy that the entropy will give up, as it lowers. In terms of a number H2O (entropy change for liquid to solid) -22.00 J mol-1 K-1 (0 °C)

    If you look at life, as having two layers, life has a logical explanation with respect to the laws of entropy and energy. The first layer is dominate and is dynamic. It is connected to metabolism and recycle, which net lowers energy and increases entropy. The second layer is a configurational or structural layer, where the cell is increasing stored energy and lowering molecular entropy. The second layer can be isolate by chilling a cell so all chemical activity stops. The dynamic layer goes to zero. What is left is the configurational layer which contains energy value which increases as life grows. It also defines lower entropy relative to the starting materials from which it stems. Fossils reflect the second layer since chemical activity is zero. As long as the sum of layer one and layer two has net increase in entropy, there is no violation of the second law of entropy.

    If we zoom into one of the proteins in the configurational layer, it has a unique fold, with probability equal to 1.0. This natural design of life reflects the configurations of life leaving the black box of statistics and entering the realm of cause and effect. The confusion many people have, appears to be connected to wanting to maintain the bias of the random traditions, in spite of this well documented observation. I have yet to hear anyone explain this in terms of random yet the random traditions persist and even work to silence this truth.

    If we look a one of these exactly folded proteins, with probability equal to 1.0, one will also notice it is held together with very weak bonding forces. Experiments of protein denaturation indicate that proteins are held together with only the equivalent of 2-4 hydrogen bonds worth of binding energy.

    Because protein are so unstable with respect to denaturation, with very little energy required to mess it up, it was reasonable to assume, in the early days, that folding had to be an average configuration, based on random assumptions. But as the technology was able to conclusively atom count and prove unique folding, was the rule, there was/is no explanation by the caretakers of the traditions to perpetuate the random myths.

    There should be much more entropy and variation within proteins, based on random assumptions, but there is not. This is swept under the rug to perpetuate the traditions for some unknown reason. I am not a creationist, but the protectors of the traditions need to maintain that misinformation so other misinformation is not challenged. Let us settle this, by anyone from the traditions, offering a random explanation of unique protein folding in spite of weak binding energies.
  20. exchemist Valued Senior Member

    And the "protectors of the traditions"?

    Would they be "liberals, by any chance?

    (My Wellwisher Bingo card is almost full….)
  21. wellwisher Banned Banned

    So, the answer to the question, how can proteins fold with probability of 1.0, appears to be because well-wisher is blaming liberals? That is a habit of mine, I will admit. But this does not make protein folding, unique. However, being liberal could make it harder to muster the critical thought spark needed to see the significance of this in light of traditions heavily invested in the randomness of evolution and life.

    I suppose change is hard, so I will not the push the issue.
  22. exchemist Valued Senior Member

    A very gentlemanly response to my remorseless teasing. I respect that.
  23. CHRIS.Q Registered Senior Member

    This is a good example

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