Cells and entropy

Discussion in 'Pseudoscience Archive' started by wellwisher, Jan 17, 2011.

  1. wellwisher Banned Banned

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    Mod note: This is a dedicated thread for collecting and quarantining the numerous posts by wellwisher on his 'alternative hypothesis' that the entropy of cells explains anything and everything in biology. In addition to entropy spam posts, posts regarding wellwisher’s (mis)understanding of DNA function and evolution are also moved and quarantined here.
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    There are two types of entropy to consider within life. The first is connected to the entropy with chemical structures. Going from CO2 and H2O into a tree is lowering entropy since there is more order with cellulose. There are more degrees of freedom in the CO2 and H2O.

    The second aspect has to due with the impact of life on the environment. The animals eats grass to make CO2.

    If life is decreasing entropy, does that mean that evolution, as a whole, moves in the direction of net decreasing entropy? This is not to say that entropy does not promote change, but lowering of entropy implies change leading to less and less entropy.

    One possible way to explain this; the net lower of entropy is consistent with increases in efficiency. Efficiency means less wasted energy, thereby lowering entropy, since entropy benefits by wasted energy.

    The animal that can gather food faster is more efficient. He will have a selective advantage due to less wasted energy and entropy. The animal that is always looking for food, but can't seem to find what it needs, displays higher entropy within his searching parameters. This will not have selective advantage, unless this higher entropy leads to an overall lowering of entropy; he finds the mother load of food for a net gain in future search efficiency.
     
    Last edited by a moderator: Mar 7, 2012
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  3. wellwisher Banned Banned

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    In the process of a person's life, from infancy to old age, our bodies undergo various integrated system changes all using the same DNA. For example, the male child might start to grow facial hair starting in their teens, etc. Genes can switch on and off as part of a developmental plan to create the various life transitions as a function of time.

    If we collected fossil samples of two twins, but each fossil twin came from two different periods in their parallel developmental stages it may look sort of like mutations, but it would be based on developmental transitions using the same DNA.

    Relative to wisdom teeth, if we collected the fossil samples before say age 18, it may appear like evolution is causing these teeth not to form. If we collected fossil samples at 30 for the other twin, after the wisdom teeth drop, now evolution looks different since the same teeth have developed. Yet it will all be done with the same DNA. Chickens have the genes for grow teeth, but development does not normally use these genes. If development did use these genes, we may be tempted to say a mutation.

    If you looks at siblings from the same two parents, we can analyze the DNA and know who the parents are, yet there can be a wide range of differences in the siblings, from tall to short, thin to heavy, cute to ugly, smart to dumb, healthy to sickly, etc. The difference can represent a variety of integrated genes. Since all the genes are contained within the parent DNA pool, the gene pool can be quickly shuffled into different working integrated organizations, in a short time. One set of parent DNA can lead to a variety.

    If each different sibling bred with a similar person, but the developmental variety suddenly got tighter, so their children were in a tighter range of shapes closer to the parent, it would look loosely like speciation, but done quickly in just one generation. The amount of entropy within development can cause the same DNA to look the same or very different, with all resulting in fully integrated and functional offspring.
     
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  5. wellwisher Banned Banned

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    Biologyworks under the assumption that life, like the universe, moves toward lower energy and higher entropy. Therefore, life and the evolution of life is connected to random events, instead of any logical progression into expected states.

    But consider this situation. The cationic pumping in the cell membrane increases the energy within the cell membrane, while lowering its entropy. A random mixture of cations would satisfy maximium entropy and lowest energy. The cell uses energy to reverse this normal push of the universe, increasing the energy and lowering the entropy within the membrane by segregating the cations.

    Now we have a boundary condition, around all cells which defines higher energy and lower entropy; oppisite direction of the universe. The question becomes, does this boundary condition provide a push that will move the innards of the cell into this direction?

    One significant observation that says yes, is the observation that the materials of the cell show single handedness, instead of the normal equal amounts of left and right handedeness of chiral molecules. Left handed proteins have lost a degree of freedom compared to a blend of left and right; reflects lower entropy just like the boundary condition. Next, since only left handed proteins are used by life, do these contain higher energy than right handed proteins to reflect the other aspect of the boundary condition? Left handed proteins are more active; energy.

    The next logical question becomes, does the boundary condition extend all the way to the genetic material, such that evolution will show movement in the direction of lower entropy and higher energy?

    One of the first aspects of evolution did exactly that. The first life used RNA as the genetic material. Life then shifted to DNA. It turns out DNA is more reduced that RNA; contains more potential energy per unit. Also the DNA has fewer degrees of freedom than RNA; DNA is lower in entropy. The DNA forms a double helix, while RNA can be single, double and blends of the two offering more entropy. Going from RNA to DNA implied moving the genetic material in the direction of the boundary condition.

    The cells of the body with the strongest low entropy and high energy boundary condition are the neurons. If the theory is correct, what should happen relative to the evolution of the brain, is the input data that is stored in the brain should move in the direction of lower entropy. The data should become more ordered into increasing complex ordering and exhibit higher energy; potential to change nature.
     
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  7. wellwisher Banned Banned

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    Cancer cells exist at higher entropy and lower energy than healthy cells. Their higher entropy allows additional degrees of freedom, compared to the restictive nature of differentiated cells from which they may stem. Their lower energy is reflected in their high replication rates, making it harder to store energy like cells that don't replicate.

    The question becomes, how do we lower the entropy and increase the energy of cancers cells, so they are no longer technically cancer cells?

    The modern approach does no work this way. Rather, since the goal is to kill the cancer, its entropy increases even more and its energy lowers more. Death will cause it to become ground down into high entropy while digested into low energy. This approach has had success winning battls, but with new cancer just as active as ever, winning the war is far away.

    A theoretical approach, which is the opposite, would attempt to lower the cancer's entropy. This does not mean killing the cancer. Rather we would differentiating it into an inert state where it gets fat (gains energy). Then it is not considered a cancer.

    Let me explain the basic theory for how this is possible. The cell membrane sets up a boundary condition for the cell, that defines low entropy and high energy for the cell. This is due to the segregation of sodium and potassium cations.

    Cell cycles alter the boundary condition, so there is more ion pump reversal;boundary increases entropy and lowers energy. Equilibrium within the cell will reflect this change within the boundary condition. It will increase the internal entropy (synthesis diversity) and lower energy (higher metabolism to shift the energy economy of the cell).

    We need to change the boundary condition around cancer cells, so they move into lower entropy and higher energy mode.
     
  8. wellwisher Banned Banned

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    I think I have the smoking gun, which evolutionary theory needs, so it is closer to making future predictions. The cell membrane creates a boundary condition where sodium and potassium cations are separated. The result is higher energy and lower entropy within the membrane. If this boundary condition theory is correct, it should have in demonstratable impact on the inside of the cell, causing the inside of the cell to form an equilibrium. The inside will also lower entropy and gain energy.

    http://www.lsbu.ac.uk/water/cell.html

    The fact that cells, even without membranes, will partian the K+ and Na+, with K+ inside, implies the inside of the cell has been induced by evolution into lower entropy and higher energy than the outside. This configurational equilibrium allows it to induce the lower entropy and higher energy cation partition even without a membrane. As cells evolved, the simple boundary condition set a potential constraint on cells, where the innards needed to line up in a low entropy and high energy way.

    Even if the DNA was making random genetic changes for evolution, unless the proteins that result are in equilibrium with boundary constraint, they will not remain part of the evolution of the cell. If nonequiibrium proteins could be carried forward and accumulate 50/50, a cell without a membrane would not be able to partition the equilibrium cations in a way that makes the membrane appear sort of redundant. It needs to favor the proteins that reflect the boundary condition.

    If you had a protein that causing entropy to increase in the cell due to random output that is not very well integrated (low entropy), this will define nonequilibrium since equilibrium needs lower entropy (perfect fit).
     
    Last edited: Apr 21, 2011
  9. wellwisher Banned Banned

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    The boundary condition of a cell; lower entropy and higher energy, allows one to make predictions, since evolution has a dual potential to push life into a sense of order. For example, if we compare proteins, to RNA to DNA, this ordering is implicit of entropy decreasing. That should be the direction of evolution with simple proteins first. Proteins have higher entropy or more degrees of freedom since there are more amino acids than nucleic acids. RNA has fewer degrees of freedom than proteins, while DNA has even fewer degrees of freedom.

    The boundary condition push for evolution continues on the DNA. For example, methyation of DNA will add a reduced group to DNA increasing its potenital energy; reduction. Methylation limits genetic expression resulting in fewer degrees of freedom on the DNA.

    When abiogenesis began, if proteins were made via dehydration of animo acids on clay surfaces, proteins would have been a mixture of left and right handed. The boundary conditioned lowered entropy or degrees of freedom resulting in only left handed. The constraint of higher energy would make left more active than right. The template relations which evolved, used to make proteins, was an induction into fewer degrees of freedom, allowing repeatable proteins. It was a natural consequence of the boundary condition.

    Going from single to multicellular also represented evolution moving in the direction of lower entropy. If we compare X number of singles cells, to X cells stuck together forming an integrated multicellular system, the singles cells have more degrees of freedom. With multicellular, the DNA, by also being differentiated, result in each cell's DNA losing degrees of freedom; differntiated cells use fewer genes.

    The energy role of ATP is based on ATP withdrawing electron density away from an enzyme for example. This situation is optimized for the boundary. As enzymes gain potential energy, the reduced state of the -OH group gets better for ATP. As the bondary moves cellular structures into higher energy, ATP gets better and better.
     
    Last edited: Apr 23, 2011
  10. synthesizer-patel Sweep the leg Johnny! Valued Senior Member

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    is it just me or is that just word salad?
     
  11. Kennyc Registered Senior Member

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    If it's green and leafy....
     
  12. wellwisher Banned Banned

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    What separates humans from the apes is human subjectivity. Humans are able to detach from the objective reality of instinct. I suppose drugs can induce that unique place in the mind.

    An animal is objective to instinct in that a certain cause and effect will apply with respect to action and reaction. The subjectivity of humans increases the entropy or degrees of freedom that are possible. For example, the animal when hungry may eat its native food. Humans might add all types of subjectivity to that native food from spices and salt to presentation on china plates. That is not objective to the needs of the instinct, but appeases that subjective side.

    The advantage to this extra level of human subjectivity is in its diversity and variations. This diveristy is useful to the objective aspect of the human species since having this wide spectrum of choices, makes it easier to constantly evolve culture. The subjectivity sort of generate random possibilities, with the objective analogous to every dog having its day.

    Drugs would help the random generation stemming from subjectivity, but it might not explain the objective overlay, which filters and weighs all those choices into optimized systems for culture.
     
  13. wellwisher Banned Banned

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    If you compare a uniform stereo-isomer mixture of L and D amino acids to purified L-amino acids, one main difference that I noticed is the mixture of L and D, has a higher entropy (more degrees of freedom) than just L-amino acids. This means purified L-amino acids have lost entropy, compared to the mixture, since the degrees of freedom of the amino acids has decreased to half the original.

    The question becomes, does life actively create an equilibrium condition that results in loss of entropy (used to help form only L-amino acids)? The answer is yes. This is connected to cationic pumping at the cell membrane, where sodium and potassium ions are segregated by means of enzymes and energy input. These two cations, like L and D amino acids would prefer a uniform solution. But because energy is being used (up to 90% of the cell energy in neurons), these two cations are forced to lose their original degrees of freedom, segregating on opposite sides of the membrane. This boundary condition, which takes energy to create, defines a low entropy zone within the water, where various low entropy equiibria inductions will happen; L-animo acids.

    This low entropy boundary condition is even more fundamental to life than DNA, since it is also part of abiogenesis. With abiogenesis we need to go from chaos and disorder (high entropy) into higher and higher levels of order (low entropy). All we need is the proper boundary condition.

    For example, if we compare DNA to RNA, DNA is more reduced. This means, pound for pound, if we burnt DNA we would get more energy than RNA. DNA is a double helix, while RNA has more options. The movement from RNA to DNA genetics followed the boundary into lower entropy. Say we wanted to lower the entropy of the DNA further, using the low entropy boundary condition. One equilibrium induction is to pack the DNA so it loses even more degrees of freedom. Condensed chromosomes are also a logical result of the boundary condition induction. It is not magic or random genetic but a logical result.

    Before there were the more modern cationic pumps, there where proton pumps, which segregated protons across a membrane; lower entropy. The mitochnodria still use this older boundary technique. This boundary condition is different from the dual cationic induction. The mitochondrial chromosome is also different being round instead of rods.
     
  14. Fraggle Rocker Staff Member

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    As I've mentioned before, the most succinct definition of "life" I've ever seen is "a large local reversal of entropy." Life sucks the organization out of everything around it, leaving it in a state of chaos so that total entropy has not decreased.
     
  15. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    Just a technical correction. The DNA of the mitochondria is not called a 'chromosome'. It is a loose circular strand, quite similar to bacterial DNA. The word chromosome literally means "colored body", derived from the fact that early microscope studies of cells required staining of the cells, and the Chromosomes were great at picking up the staining colors. That is because of their tight winding, etc., making for many sites where the stains could adhere.
     
  16. wellwisher Banned Banned

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    In my experience, there are three main orientations when it comes to explaining the appearance and progression of life. We have evolution, creationism and scientific intelligent design. Whereas evolution is based on random genetic change,s flollowed by selective advantage, scientific intelligent design is much less random up front, compared to evolution, but will go along with selective advantage on the tail end.

    Scientific intelligent design is all about a higher ratio of logic up front. To reach this goal takes more intelligence than just assuming black box random, which is why it is called intelligent design. With black box random you can make anything up you want, as long as the black blox has to remain closed. With scientific intelligent design, since you will try to open the black box, you need to be logical.

    What tends to happen is scientific intelligent design is lumped into creationism, whereas it is actually much closer to evolution. Those who believe in scientific intelligent design get the feeling, that evolution makes use of bullying and politics to silence science, that is not black box enough. It seems like a religion to SID.

    One possible explanation for this reaction, is biology is observational empirical and makes a lot of use of statistics to fill in the blanks. On the other hand, there are other areas of science, such as applied science and engineering, that is more logical since that is the approach they are taught. Some of these scientists have tried to cross the discipline boundaries due to an interest in evolution, and brought with them their causual approach to problem solving. Maybe because these two science approaches are so different the empiriists assume this must be religion since it not black box enough.

    In many places in these forums, I have shown how ion pumping uses the lions shares of a cell's energy to lower the entropy and increase energy at the cellular boundary. The cell must think this is very important to devoye most of its energy. The logical question is, does evolution reflect the same direction as this induction? The answer is yes. Evoluiton is not as black box as taught by the more empirical aspects of science, but have a sense of direction.

    The thick skulled scientific intelligent design people, who can't seem to get with the black box program, resist because they expect a more logical or intelligent design than the black box. Lower entropy means in the direction of less random; goal of life. The cell, iyself, disproves the modern version of black box evolution by how it uses its energy.
     
  17. spidergoat pubic diorama Valued Senior Member

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    Usual gobbledygook. Intelligent Design is creationism, and it's not even a theory.
     
  18. Hercules Rockefeller Beatings will continue until morale improves. Moderator

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    I love how internet crackpots think that the mere act of posting their woo-woo hypotheses on internet forums constitutes both demonstration and widespread acceptance of said hypotheses.

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    It’s funny.

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  19. James R Just this guy, you know? Staff Member

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    wellwisher:

    Isn't scientific intelligent design an oxymoron?

    No. ID is only pushed seriously these days by Creationists who want to get their religion taught in US schools. ID is just Creationism under a new name.
     
  20. wellwisher Banned Banned

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    My problem with evolution is not with the idea of evolution, but with the random assumptions for its chemical mechanism. The random assumptions are the primary stumbling block for many critics. This stumbling blocks constantly shows its face when people give examples of the odds being too high at various areas in evolution. They are looking for a logical mechanism since the odds don't appear there.

    I think I figured out the source of the problem connected to the random assumptions. It came to light many years back during a project I did as an engineer. I forgot how this got me questioning evolution, as is. I was doing development work and had to invent a process to clean several milllon gallons of mercury contaminated water to less than 1PPB. I was able to come up with the invention in about three weeks, which worked very well in pilot studies.

    Because of the high visibility of the final cleanup project, I was assigned a mathematician, whose job was to model the process with a statistical design type analysis I objected at first, since I invented the stupiid thing and knew how it worked, chemically and logically, and didn't need any hand holding with gambling math. But I was ordered to let him do his analysis just in case things went south. He could soften potential problems during discharge with statistical magic that would be acceptable to the EPA.

    When it was all over, his statistical modelling actually did a very good job. I was old school, but could see the usefulness in what he did. Ironically, he was a mathematician and not a chemists or an engineer, yet his math analysis, without his having any of my expertise, worked well. That made me think, even without a real understanding of the chemical mechanisms, by simply using his math design, he was able to achieve good results that parallelled what I was doing. I was impressed because the blackbox worked better than I expected.

    The question that came to me was, since his statistical design was doing all the heavy lifting for him, using a randon assumption, would it have been possible for him to make up a mechanism, and then let the math do all the heavy lifting, and still have the result come out well?

    If we apply this question to evolution, is the random assumption there to allow the statistical math to do all the heavy lifting. My math friend seemed to demonstrate that even if his random assumption was not true in reality, it still worked. In other words, my mathematician was able to parallel a rational analysis, from a trained chemical engineer, using a random assumption without needing full knowledge of the detailed mechanism. Reality was not needed by him, since the math was doing all the heavy lifting using blackbox statistics.

    If evolution is letting the math doing all the heavy lifting, a random mechanism can be wrong within bio-chemical reality, but will be needed, so the math can do all the lifting. If you look at the DNA, it also contains a double helix of water. This reality is not needed when the math does the heavy lifting. Evolution can deny this and other reality and still get good results as long as it uses the assumptions needed by the math.

    One test we could do that can determine whether evolution has a real mechanism or its usefulness is really due to a mathematical tool, is to define evolution without the math, to see if the theory can do the heavy lifting. I don't think the theory can stand without the math tool. This is why there is always a fight to maintain the math tool requirements.
     
  21. origin Heading towards oblivion Valued Senior Member

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    For crying out loud, are you serious? You gave the statistician the parameters for your process he just modeled what you gave him. Could his model develop a process? Of course not it could only model what was already invented and tested. If you are a chemical engineer as you say then you GOT to be smarter than that!

    I can understand people who deny evolution because they fear that if they accept the obvious evidence for evolution god will be pissed off at them. Even though I understand it, it still creeps me out when an intelligent person buries their head that far into the sand.

    It is like that astronaugt going on expeditions into the mountains of Turkey to find Noahs Ark, yikes!:bugeye:
     
  22. iceaura Valued Senior Member

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    So quit making them.

    They always involve misconceptions of evolutionary theory anyway (along with incompetence in statistical calculation) so you might finally get the hang of the theory if you dropped the reinforcement of misconception inherent in all those "random assumptions".
     
  23. wellwisher Banned Banned

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    The point I was making is there are many ways to model things. For example, one can model rational processes using numerical methods based on iterations. Just because such a math model can give good results does not mean the mechanism of the phenomena is based on iterations. That would be putting the cart before the horse.

    Statistics is also a tool that helps us model reality, but it is not reality. I believe that evolution has put the statistical cart before the horse. This has been made harder to see because the horse was altered in the image of the cart.

    I am not against evolution, just the mechanism is tailored to the math thereby allowing one to lose touch with reality and still get results. For example, the DNA has a double helix of water. How does that water impact the genetic mechanisms of evolution and does evolution include this? It does not have to when the cart leads the horse since you mold life to the needs of the math.

    An analogy is developing a process in industry. One is then asked to model it and you chose one of many mathematical methods. If you can get better results by tweaking the math parameters, even this starts to leave conceptual reality, the model is still better in the practical. Industry is less concerned with reality as with high quality results, so if I conformed my theory to help the math perform better, it looks better evne if the cart is is leading the horse.
     

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