Does Contemporary Evolution use a Pseudo-Creationism schema?

Discussion in 'General Philosophy' started by wellwisher, Feb 10, 2016.

  1. PhysBang Valued Senior Member

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    This is certainly your assumption.

    But what is not taught to students is that water has the magical properties that you think it has, but for which there is no evidence.
     
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  3. Yazata Valued Senior Member

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    Perhaps.

    Ok.

    Darwin didn't know about genetics, certainly not modern molecular genetics, genomics and developmental biology. But his natural selection concept certainly seems to be sound, even if he didn't have any precise idea of how any of it worked.

    Ok. Organisms evolve so as to be better adapted to their ecological niches.

    Of course. Chemistry arises in several different ways. If we are talking about gene mutations, we have to understand what genes are (Darwin had never heard of genes). Chemical changes in genes are obviously going to be matters of gene chemistry, just by definition. Some mutations are changes in base sequences and some changes will be more likely than others just because of the chemistry. Many mutations aren't really chemical changes in the genes so much as they are portions of software code getting repeated or transposed to new locations in the genome. There are going to be chemical aspects to that too, since breaking and forming nucleic acid bonds is chemistry. (There are actually a suite of enzymes that do that.) All this chemistry stuff that's happening down on the genome level is likely to have phenotypic effects at the anatomical level, big ones if the changed genes control fetal development or something like that. A single mutation might cause a dramatic and sudden change in an organism's anatomy, which will have selective implications when that organism tries to survive in its environment.

    If we are talking about the initial formation of chemical replicators, chemistry is going to be the foremost topic of discussion. (Many people perceive chemistry as the most boring of the sciences, least involved with fundamental issues, but it's the doorway to understanding the origin of life.) Speculation about the formation of replicators is all about the formation of the precursors of RNA (or whatever the initial self-replicating material was) under prevailing natural conditions and their polymerization into chains capable of copying themselves. If that requires certain chemical conditions, we might imagine that this primitive replicator might have better chances if it can somehow foster those conditions. So replicators capable of surrounding themselves with a membrane might have selective advantages or replicators capable of producing chemical energy somehow. Replicators with these advantages would be better represented in subsequent generations.

    Ok. (More or less.)

    I think that's one of the defects of a great deal of astrobiological speculation. It's really most interested in reproducing Earth life, which as you say is supremely adapted to Earth conditions. Obviously Earth-life is the only example of life that we currently have. And just as obviously, the only exoplanets where we are going to have any chance of finding life identical to our own is on planets identical to our own. But if we start with chemical replicators capable of forming in alien conditions, in liquid methane perhaps, and then imagine them evolving in those conditions so that similar functions are met that increase the replicators' chances of successfully replicating, we might end up with evolved organisms very different from ourselves and perhaps more alien than anything that science-fiction imagines.
     
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  5. James R Just this guy, you know? Staff Member

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    wellwisher:

    The general idea is to search for life-as-we-know-it, whilst always keeping an open mind that other kinds of life might be possible.

    Liquid water is a convenient medium, and has a lot of quite singular chemical properties. For example, the hydrogen bonding in water molecules makes them reasonable stable, so that they don't tend to react in nasty ways with things that might form life.

    Quarks are largely irrelevant to chemistry. Ordinary matter only consists of protons, neutrons and electrons. The quarks that make up the protons and neutrons are all confined within those particles. The chemical properties of atoms are determined by the electrons, at a scale about 10,000 times larger than the scale at which the quarks are bound.

    How do quarks impact the formation of DNA? They impact it insofar as they determine the properties of protons and neutrons in the atoms that interact to form DNA ... and that's about it.

    What kind of "interface" are you expecting?

    You are not allowed to write in the science sections because, despite many warnings, you continued to post misleading untruths and half-truths in the science sections, together with quite a lot of unsupported nonsense. This was explained to you in the many warnings you received. Why do you seek to misrepresent things now?

    Nobody makes the assumption that replicators "just appear". If that were the assumption, nobody would be working on the problem of abiogenesis.

    Water is a medium in which chemical reactions conducive to life can take place. Once life is formed, water is a convenient solution in which the chemical processes of life can occur.

    Creationism isn't in any sense a scientific theory. It's mythology. It can't be tested. It is unfalsifiable. Science is nothing like that.

    What you don't seem to understand is that science is comfortable with gaps. In fact, scientific research at the limits of knowledge is fundamentally all about trying to filling gap.

    Creationism starts with the answer - God did it - and expands that answer with related mythology. Science starts with questions and works to find answers based on a careful examination of nature. And, crucially, scientists are always saying "We don't know yet" and "That's only a hypothesis at this point" and "This idea is yet to be confirmed". Creationists, in contrast, claim to have all the answers from the start, because for them there is only one answer: God did it all.
     
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  7. wellwisher Banned Banned

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    This is a pseudo-science tradition that is taught in school. I get censored via a dual standard of pseudo-science. Only the traditions get to use pseudo-science and call it science.

    Experiments, where water is removed from cells, and then replaced with all types of postulated solvents for life; to see what happens and/or to prove or disprove your premise, where shocked to find, that none of these solvents worked, properly, right down to the activity of individual enzymes. If some aspects of the cell had worked, what you say would be at least partially true. But when nothing works, that implies all things have been tuned to work in water. They could not replace water, like is taught as science, but is pseudo-science.

    It is like saying any key on the key chain can open any lock, because we assume we live in a world of randomness and probability. Given enough time, any key will have some small odds to work. Then we try the experiment with other solvents, to prove this, only to find, only the water key will work. Instead of saying probability is wrong, we double down and censor the truth.

    Water is the bio-physical-chemical source for the internal selection process within life on earth. Maybe if you started with another solvent, from day one, it would set its own unique environment for internal chemical selection. But you would not be able to change that oar in midstream. The idea that any solvent can replace water, at any time in earth's evolution, have been to be pseudo-science.

    You are suspended for one minute for teaching pseudo science, even if you honestly represent the randomness tradition and take the word of other you respect.

    Now that you are back;

    The value of water is water is not an ideal solvent. For its mass of only 18 grams/mole, water has an unusually high boiling point. In this series of molecules, with the same mass of 18 grams per mole, notice the difference in boiling points; CH4=-258C, NH3=-35C H2O=100C. The reason why the boiling point of water is so high is due to hydrogen bonding. Ammonia also has hydrogen bonding, but its significantly lower boiling point, reflects less internal binding strength within its hydrogen bonding.

    The hydrogen bonding in water can occur with up to four hydrogen bonds forming on each water molecule. This is loosely analogous to what carbon does with covalent bonds; four bonds. The result is water wants to form internal order, that is bound together with considerable strength. The high boiling point for something so small, reflects the high level of internal binding and order. When organics and other materials are present in water, cannot increase the potential of the water to much, or the water will segregate and expel them; oil and water. This is based on energy considerations.

    The binding in water is so strong, yet water is so light; 18 grams/moles, water is very picky due to own internal energy considerations, and it can enforce the rules, quickly, due to its tiny size and mass. The materials of modern cells have passed eons of scrutiny, by the strictest of solvent standards, but a tiny molecules with a high capacity to enforce the rules. Life has been refined in the furnace of water until it shines like gold.

    Water can form hydrogen bonding with organics, including oil, even though water and oil don't normally mix. However, it is much more stable for water to bind with other water, than to the oil. The term hydrophobic is sort of a misnomer, since organics do not fear water, since water can hydrogen bond to an organic, like oil, nearly as strong as the van der Waals bonds that bind the oil. The real problem is water can do much better hydrogen bonding with other water; energy advantage that favors self binding of water. The analogy is one can eat cheap steak but if given the choice they will eat fillet. The water can accommodate organics, if it has to, but it will segregate if given the water-water option. This allows the water to size up any organic, and then compare this to its own internal energy needs. If water has no choice but to form an interface with an organic, due to crowding, there is a unique energy profile, from the organic binding sites, back to the more stable bulk water. Water can finger print this way.

    Ammonia is a good degreaser and is often used as a cleaner to remove tough oil stains. The internal hydrogen bonding energy of ammonia is closet to the van der Waals bonds of oily organics, than water's hydrogen bonds are to oily organics. Ammonia it will not segregate, as quickly or completely, if given the option. This will can cause the protein structures of water based cells, to including too much ammonia. This may be useful on another planet, but not on earth.

    It is not coincidence that DNA are the most hydrated molecules in the cell. The water binds to the DNA almost as well as it can bind to itself. The DNA is like an adopted son to water. This was always the goal of water; peaceful coexistence where there is a sense of family. DNA was not a random thing but was a goal because it has the least energy potential with water, for a huge molecule. Not all changes on the DNA will have the same energy profile in the water. Some are not as favorable, while other make the adopted son even closer.
     
  8. origin Trump is the best argument against a democracy. Valued Senior Member

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    So you believe pseudo-science is being taught in school? You believe science is a tradition, like mythology? That is wierd since 95% of your information is science based and the rest is stuff you just made.

    I think you are purposely saying things like science is pseudo-science and science is tradition simply to inflame people - this is one of the classic methods of internet trolls.
     
  9. James R Just this guy, you know? Staff Member

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    wellwisher:

    Strange, then, that you spent the rest of your reply essentially repeating it.

    I didn't make any claim about being able to replace water with some other solvent. Are you trying to erect some kind of straw man here?

    Of course life on Earth is suited to water. It evolved in water.

    I don't know what you mean by that. What is it a source of, exactly?

    I agree with you!

    I mentioned hydrogen bonding in my previous post. I am aware of many of the interesting physical properties of water.

    Life is well suited to a watery medium, I agree.

    The strands of the DNA double helix are bound together with hydrogen bonds. Water does nice hydrogen bonding, as you've pointed out.

    You speak of water as if it is alive and has desires and goals all of its own. Is that what you think, or are you just constructing a colourful analogy?
     
  10. Yazata Valued Senior Member

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    I can't say that I understand Wellwisher's point, but I get the impression that he's convinced that water is the key to life, that life just naturally forms in the presence of water. That may be what his rather cryptic phrase "internal natural selection" is intended to mean - that water somehow 'selects', fosters and facilitates the kind of chemical events necessary for the appearance of life.

    If he does believe that life will just spontaneously form in the presence of water, he does seem to be giving it some pretty amazing qualities.
     
  11. wellwisher Banned Banned

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    Water self hydrogen bonds, with other water, with four hydrogen bonds, similar to way carbon will covalent bonds with four bonds. Water can form extended structures within itself, just like carbon can form polymers. For example, water forms an icosahedral (H2O)280 structures as seen below. This forms because it defines a state of lowered energy. When you add organics to water, there is surface tension. This cause the potential of the water to increase, therefore such structure can become more limited.


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    As an analogy say you form a club that discusses politics. If all the members of the club agree with you, you can stand on your soap box and preach in a spirited way. If new members appear that don't agree with you and/or who create tension, you will get bogged down, attempting to convince them. You would prefer to be up on your soap box to a friendly audience, where you are at your best. But you may find yourself pushing some to comply, while others will never change. Those who will never change may need to be expelled. Now the audience is friendly again, and you can get spirited. Water does the same thing.

    The high boiling point of water shows just how much stability is contained in the self binding of water. This is why water will expel oil to form two layers. It wants to preach to a favorable audience; lowest energy. But it can also expel other materials to a lessor degree; partial solubility of materials. Surface tension also creates energetics at surfaces that can act as activation energy for reacts that are seeking lower potential. Other solvents will also of this, but water has the most push as inferred by its high boiling point per mass. If all else is equal this extra push allows water to get to life faster, thereby giving water a selective advantage; if all the solvents work side by side.

    If you look at the folding of protein into perfect folds, this is driven by hydrophobic interacts. But like I said, hydrophobic is a misnomer since water can form a weak version of hydrogen bonds with any organic. However, this leaves potential in the bulk water; surface tension, since water can do batter by itself.

    Below is a 3-D energy diagram of an unfolded protein and the energy diagram of the final packed protein. The peaks on the left represent the energy potential between water and groups on the protein. These peaks are lowered by separating the water from the side groups of the protein as it packs. The water flows down these energy hills, toward lower potential, collapsing the diagram until the protein is folded into a smooth lowest energy; relative to water, structure. The perfect packing of protein is connected to the potential between water and the unfolded protein, with water forcing this interaction into a a state of minimal energy.

    Others solvents don't work as well because their interactions with the protein create a difference energy diagram. Their weaker self binding means smaller hills. Instead of water rushing down the streams of tall energy hills, the other solvents moves slower down gentle slopes and get entrained by the protein folding, but not the same each time.

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    The energy diagram of the unfolded protein; above, in light of the observation that DNA is the most hydrated molecule tells me something, which I have sense for years. The water around the DNA is at lower potential, than the water at the ribosomes were new protein appear with energy hills, needing to packed to lower the energy. There is an energy gradient in the cell water from the DNA to the ribosomes. The production of protein helps to induce this gradient. This is by design, since the gradient from DNA to the ribosomes, by making the water potential different, can be used for push/pull dynamics. If the potnetial is too high one way to lower this is to flood this area with lower energy organics like mRNA. RNA is less reduced than DNA; extra -OH group on the sugar and is therefore even more water friendly, making this help the most at the ribosome area.
     
    Last edited: Feb 16, 2016
  12. PhysBang Valued Senior Member

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    And what does any of this have to do with evolution?
     
  13. Yazata Valued Senior Member

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    I'm sure that water was very important in the origin of life, but how can water be the source of life itself if nucleotides won't polymerize in aqueous solution? I think that it's obvious that there was more to it than the simple presence of water.

    "The gas-discharge experiments only produce monomers (if conditions are right) but none produce the long chain molecules that are the ultimate basis for life on Earth...

    We want M1 + M2 -> polymer + H2O. But the reverse is more likely in the ocean (look at the reaction in reverse). So must get rid of liquid water and need energy source."

    http://www.as.utexas.edu/astronomy/education/spring05/scalo/lectures/309L-2DOriginLife.pdf

    And...

    " The polymerization of nucleotides in aqueous solution is an uphill reaction and does not occur spontaneously to a significant extent."

    http://bonhamchemistry.com/wp-content/uploads/2012/01/RNA_World.pdf
     
  14. origin Trump is the best argument against a democracy. Valued Senior Member

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    That proves that mutations are not random but are directed by Poseiden and Aqualad.
     
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  15. wellwisher Banned Banned

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    I agree that amino acids and nucleotides do not spontaneously polymerize in water. However, once these materials are polymerized, by whatever means, they will not work properly, if water is not present to fold them, and then help catalyze them. You cannot substitute other solvents, because water and organics are co-partners.

    The way the partnership works is, water has an impact on the secondary, tertiary, and quaternary structures of biomaterials. This will define their active shapes. The active organics; protein, are then able to catalyze primary structures; covalent bonds, such as needed for protein polymerization.

    Enzymes, via templates, can form raw protein. But these protein come hot off the press, without distinct folded form. The water induces the protein into a unique fold. Once the water makes this fold, the new protein is now active and is ready to deal with primary structures and covalent bonds. These reactions will not occur in other solvents, meaning the enzyme's covalent bonding forming and breaking action, also needs water. Water is part of the 3-D structure of the enzyme.

    If we remove water and use other solvents we will bottleneck protein folding, so there is no active shape. This makes the polymerization of protein by enzymes, stop working. If we start with already folded protein, we extracted from water and ten add another solvent, the enzyme still can't do its job, because water needs to be part of its catalytic structure. Water contributes any things including energy and entropy to the enzyme.
     
    Last edited: Feb 17, 2016
  16. wellwisher Banned Banned

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    Relative to evolution, even if you start with replicators, these will need water to work. Water is needed for the dynamic replicator structure and kinetics. If you ignore water being necessary and assume naked organics, you will need to substitute for the tangle water affects, with math magic. This is why I call this approach pseudo-creationism.
     
    Last edited: Feb 17, 2016
  17. origin Trump is the best argument against a democracy. Valued Senior Member

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    I think we can all agree that water is needed for life. Perhaps we can move on from this point.
    I do not see where you have addressed the issue of nonrandom mutations. You have said that the idea of random mutations is incorrect. How are mutations not random? What is making the mutation nonrandom?
     
  18. wellwisher Banned Banned

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    The randomness is the result of a working premise, used in biology, which underestimates the extent by which water contributes to life. Water is a copartner, with the organics in life. But the working premise is water is important, but it is only a solvent, which is minor, compared to the variety of organics. This assumption creates the randomness.

    Let me give you an analogy. The phases and properties of materials in nature are a function of both temperature and pressure. Say we assumed pressure is important (like water). However, it is no way near as important, as temperature. Therefore will define all physical properties of materials in terms of only temperature, since pressure is only a minor player.

    Since we don't control pressure, when we run temperature experiments, variations in pressure, due to temperature, will not be properly addressed, since pressure is not that important. But since we see what appears to be variations about temperature, we assume the properties of matter can be modeled with statistical variations about temperature. Randomness, in this case, is a result of an assumption that underestimates the co-dependence of pressure.

    The observed random is real in the sense of the assumptions used. However, it is not real in the sense of a theory that makes temperature and pressure co-dependent. The latter will not have this randomness.

    Proteins need to fold properly to work properly. This is induced by water. If you remove the water, for just this one step, all the organic steps are a moot point. Yet this is not important to the random model, since water is there for a free ride.

    My conclusion is all of biology and all of the life sciences that use randomness, are pseudo-creatiomism. They substitute a logical connection between water and organics, in favor of a soft connection between organics and randomness. This god of random tells them what they want to believe and think. This is oracle based on faith.

    I have been addressing evolution, over the years, because I was being polite about this global flaw in biology. I was hoping someone would get the hint, by addressing it indirectly via soft area of science. But I need to be more blunt.

    Maybe someone can form a mutation on the DNA, that would benefit evolution, without water. Water is not important so this should be easy to do.
     
  19. PhysBang Valued Senior Member

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    Do you have any evidence that water makes genetic mutations non-random, or just a feeling?

    Does your "water-based" biology have the ability to match the available observations about the natural world as well as the biology used in schools, universities, and labs?
     
  20. origin Trump is the best argument against a democracy. Valued Senior Member

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    An assumption cannot create randomness. How does water create nonrandom mutations?

    That analogy is not helpful in the slightest in helping to understand how water creates nonrandom mutations.

    That has nothing to do with anything. A dried out protien won't fold properly - so what?

    You still have given no reason for reaching that conclusion!

    Please be as blunt and clear as possible and answer the question of how water or anything casues mutations to be nonrandom!!

    No one is saying that, for crying out loud! Why do you keep harping on that!

    All you have to do is give a reason to why you think that mutations are not random. You write alot and discuss water alot but you have NEVER answered that question. Be blunt and answer the question - we can take your bluntness.
     
  21. PhysBang Valued Senior Member

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    I think that wellwisher never took biology, so doesn't realize all the experiments that are carried out in water and all the papers there are about reactions in water or in the very watery environment of bacteria and cell membranes.
     
  22. origin Trump is the best argument against a democracy. Valued Senior Member

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    Probably, it doesn't seem that he has taken many science courses at all. For some reason he objects to the idea of random mutations so he is trying to find some reason for the mutations to be nonrandom - with no luck apparently.
     
  23. PhysBang Valued Senior Member

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    I suspect it is because conservatives do not like the idea that the people who succeed in life do so because of random factors or because of the environment. They do not like the idea that the people who suffer in life do not suffer because they deserve it, they merely suffer because of circumstances. There is a lot of this ideology that pervades the history of biology.
     

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