Natural Selection at the Nanoscale

Discussion in 'Alternative Theories' started by wellwisher, Dec 15, 2016.

  1. wellwisher Banned Banned

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    Darwin's theory of evolution and natural selection was originally based on observations at the macro scale of life; we can see with the eyes. Potentials in the environment, help define natural selection. If we were in the desert, this environment sets unique physical parameters which life needs to adapt to, to be selected. If there are genetic changes, in existing desert animals, changes that allow better adaptation to the desert, will be selected.

    The goal of this topic is to extrapolate Darwin Theory, and explore natural selection at the nanoscale instead of at the macro-scale. In this case, the nanoscale environment is the solvent; water. Water, as the dominant and continuous phase, will set unique environmental potentials, at the nanoscale, which will create a natural selection process for the evolution of life.

    If we remove the water from any cell or any level of life down to enzymes, these will not work and life will be gone. If we replace the water with another solvent, still nothing works properly, and there is still no life. The reason is life on earth has evolved in a water environment. All the chemical systems are optimize to the water environment. If we replace the solvent, it is like placing a polar bear at the equator. He will not be selected there. Other solvents will set a different nanoscale environment and would select different chemicals so they can be more functional.
     
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  3. origin In a democracy you deserve the leaders you elect. Valued Senior Member

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    OK
    I doubt anyone would disagree that water is necessary for life as we know it. Not sure how natural selection and water are related. This has been a reoccuring theme of yours, but you have never been able to successfully link the two.
    The same can be said of oxygen, chlorides, potassium, etc., etc.
    obviously.
    On the face of it this is clearly false. Maybe you mean something different than you wrote.
    No it would be like shooting a polar bear.
    Not just a different environment; an instantly deadly environment.
     
    Last edited: Dec 15, 2016
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  5. Yazata Valued Senior Member

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    Yes, in Darwin's time.

    In the case of multicellular organisms, selection occurs on the level of phenotypes, the macroscopic anatomical features of entire organisms. In a particular environment, some anatomical features are likely to have more selective value than others. But evolution happens with single-celled organisms too, and much more quickly there than with multicellular organisms. The phenotypic features of bacteria that confer selective advantage are microscopic and they aren't anatomical features, since all bacteria are anatomically similar. They are biochemical features, differences in metabolism. That's why bacteria are so diverse biochemically, why most of the diversity in chemical metabolism that's observed on Earth is observed in bacteria.

    I think that biologists in Darwin's time were aware of much of this, though I'm not sure how much they knew about bacteria. Darwin was certainly an acute observer of the 'macro-' (phenotypic) appearance of animals.

    What's new since Darwin's time is knowledge of the genotypic level, an even deeper molecular-biological level where evolutionarily relevant change occurs on the genomic level. Changes in the genes (through mutation) and in sets of genes (through transpositions and whatever) are what lead to differences in metabolism in bacteria and to differences in fetal development that lead to anatomical differences in multicellular organisms. So while it's the anatomical and metabolic differences that directly confer selective advantage in particular environments, it's difference in the underlying genetics that produce those selectively-relevant differences and it's the genetic differences that are passed on to succeeding generations.

    The real cutting edge at the moment is probably origin-of-life studies. That's where chemical evolution is most obvious, where genotypes become synonymous with phenotypes and where the replicators which possess or lack selective advantage are the molecules themselves and collections of those molecules, leading up to the appearance of the first cells. Unfortunately, most of this work is speculative, since the earliest chemical replicators no longer exist today and they apparently didn't leave fossils (at least ones that we recognize).

    Maybe. The contents of cells is mostly water molecules and most of early chemical evolution is imagined to have happened in water. But it's more complicated than that, since RNA won't spontaneously polymerize in water in the absence of appropriate ribosomes. So we have the chicken-egg problem of what came first, the RNA or the ribosomes. The ribosomes are large protein molecules and they won't form and fold properly without RNA. But the RNA chains won't form without the ribosomes. A way out of that little trap would be RNA first originating in a non-aqueous environment where the ribosomes aren't necessary.

    https://en.wikipedia.org/wiki/RNA_world

    That's all true for Earth life and it's one of the reasons why Earth life is as it is, biochemically speaking. I'm not convinced that something closely analogous to Earth life couldn't appear in more exotic extraterrestrial environments such as seas of liquid methane (which are known to exist on Saturn's moon Titan and probably on countless exoplanets as well). If it exists, theat kind of life would evolve in different biochemical directions though, both in the origin phase and at the metabolic elaboration phase.
     
    Last edited: Dec 15, 2016
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  7. wellwisher Banned Banned

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    Too many people on this site seems to assume that life can form in other solvents. Yet nobody, in all of science, has ever demonstrated this to be true. Do a search for proof! This claim should be called speculation and alternate theory, yet somehow it gets a pass. Why do the moderators allow a dual standard when it comes to speculation? Can anyone prove that life can form in other solvents? This unsubstantiated claim, allows other bad premise to appear to be true. This is why it is allowed; distraction. The claim that any solvent will do demonstrates ignorance of selection at the nanoscale.
     
    Last edited: Dec 15, 2016
  8. wellwisher Banned Banned

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    The thing is, RNA and ribosomes won't do anything, without water, since water is part of their structures. The water environment also allows these materials to assume the proper configurations and folds based on surface energy. Water even mediates the binding sites for mRNA and amino acids.
     
  9. wellwisher Banned Banned

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    This may be a good working example to explain what I mean by water as the nano scale environment for natural selection. Picture the ribosomes and mRNA as two nanoscale lifeforms living in an aqueous environment; analogy visualization for educational purposes. This water environment sets potentials for these two materials. As an analogy, the potentials are like a meadow at 40 degree latitude, setting the potentials for a blueberry bush (ribosomes) and some birds (RNA). The goal of the selection process is to minimize the potential of the ribosomes; thrive, and the mRNA; eat and procreate. It is also about selection that minimizes the potential of the union of the two; optimize the interface so both benefit. This allows the birds and blueberries to persist and thrive in that environment.

    Water has certain parameters that are persistent. But it also has parameters that can change, locally, due to the flora and fauna; hydrogen bonding variations. This is reflected in local environments, within the larger scale nano-environment. In the analogy the meadow forms little eco-system pockets, where the blue berry thrives in one place and where elderberries thrive somewhere else. Both are part of the same meadow, and each attracts it own birds. All have evolved in the meadow subject to the same parameters.

    If we take a ribosome, water will attach to its surface, based on the geometry of the ribosome and the character of its surface groups. This surface water, will also hydrogen bond to itself to form a surface netting, which will then hydrogen bond to the bulk water beyond the ribosome. This defines a very unique local water environment; ecosystem. This identifies the ribosome to approaching things, since the netting is seen, first. If we have another organelle nearby, this also has a water surface net, extended into the bulk water. Where the two extended waters meet, the water in the middle may or may not be at lowest energy. There can still be potential for selection, even if the local systems appeared to be optimized, since the goal is bigger than just one thing; needs of the entire global water.

    All I am doing now is painting a broad picture. Shortly I will add physical parameters to the water to define the nanoscale environment. If we had a rocky environment, this terrain places limits on the types of plants that will thrive. This is more conducive to shallow rooted plants. You may not see a lot of plant that need deep roots. Water is the same way in that this environment will not work for everything. It has parameters for a targeted selection process; rough in, before fine tuning. The shallow plants don't have to worry about the deep roots plant competition since they will not be able to persist. The dice are loaded.
     
    Last edited: Dec 16, 2016
  10. Kittamaru No more Staff Member

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    I would posit it is foolish to assume life cannot exist without water- it is just that we associate "life" with "carbon based life", which is heavily reliant (if not utterly so) on H2O. Can we prove life can form in other solvents? We can't "prove" it yet, but it has been thought about, recently too:

    http://www.dailymail.co.uk/sciencet...-thrive-Saturn-s-moon-Titan-claims-study.html

    http://news.cornell.edu/stories/2015/02/life-not-we-know-it-possible-saturns-moon-titan
    It is a fascinating thought experiment, and one that we may one day be able to execute once we can do more routine trips to mid and deep space.
     
  11. paddoboy Valued Senior Member

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    Any scientific theory was at one time speculation. There is nothing wrong in speculation in science as long as one accepts it is speculation, and/or still being researched. eg: I often speculate for reasons I have stated many times that the universe should/is full of lifeforms of various types, but as yet I also accept that at this time we have absolutely no hard evidence to support life off the Earth.
    And secondly you seem so quick to always use the word "proof"Perhaps you need to brush up on what a scientific theory is, and why science is a discipline in perpetual progress.
     
  12. origin In a democracy you deserve the leaders you elect. Valued Senior Member

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    Perhaps you did not realize that we are IN the Alternative Theory section!
     
  13. DaveC426913 Valued Senior Member

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    Life on Earth, as it has evolved (from water!), requires water to live, grow and reproduce.
    Does anyone disagree with this?

    What does that have to do with non-Earth life in-general, evolving in non-water environments?
     
  14. wellwisher Banned Banned

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    There is no tangible proof that life can evolve in non-aqueous environments. That is speculation, even if it is funded by science; blue sky research. It is all based on an erroneous random assumption that can created lottery jackpots out of thin air. If you take away the magic, there is no logic or evidence.

    Life in water has plenty of evidence, but the logic for evolution is blended with lottery winnings; random. I am trying to show that the co-partnership between water and organics allows the lottery winning assumption to be replaced with logic.

    Let me return to a basic foundation premise.

    If you compare water; H2O, to ammonia; NH3, and methane, CH4, although all these molecules have the same molecular weights, the boiling point of water is much higher than both of these. BP of water is 100C BP of ammonia is -33C BP of methane is -161C . The boiling point is a measure of the intermolecular forces that exist between these molecules in the liquid phase.

    This difference between methane and ammonia is due to stronger hydrogen bonding in ammonia. The difference between water and ammonia, since can both form hydrogen bonds and ammonia has more hydrogen bonding hydrogen, has to do with the symmetry of the hydrogen bonding within water; two donors hydrogen and two receiver groups. Ammonia which has three donors protons but only one receiver. Although both can form up to four hydrogen bonds, the symmetry of water allows it to form extensive 3-D networks. Ammonia can also form up to four hydrogen bond, but its asymmetry does not allow the same extensive networking. in many ways, water at the level of hydrogen bonding doe what carbon with covalent bonds; four bonds and polymerization.

    Hydrogen bonding has a property called cooperative hydrogen bonding. This is similar to a resonance state; benzene. Instead of making use of covalent bonds, like in benzene, it makes use of electron delocalization via the hydrogen bonds. Water extensive structuring allows for cooperative hydrogen bonding, adding a lot of stability; very high BP for something so small.

    What this translates to in terms of contribution to the partnership of life is, water tends to self cluster due to its high stability due or cooperative bonding. If there are organics present, these often become phase separated, so water can do its own thing. In cells, all the organelles and the many structure are separated phases, which is made easier because water is self binding to gain the energy advantage of cooperative resonance. Water will try to minimize surface contact since this adds energy; surface tension.

    The strong self binding of water is ideally suited to phase separate the large organic structures of life. Both ammonia and methane will solubilize many of these same structures or allow too much variation, since they do not self bind strongly enough.
     
  15. DaveC426913 Valued Senior Member

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    As stated, I doubt anyone would disagree.

    Research, by definition, occurs upon things that hav not ben discovered yet.

    Are you arguing that research, by definition, is unscientific?
     
  16. origin In a democracy you deserve the leaders you elect. Valued Senior Member

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    None of which has anything to do with evolution.
     
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  17. wellwisher Banned Banned

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    Blue sky research is about researching out of the box subjects. I enjoy this type of research. Most research does not fall that far from the known trees. Blue sky not only is outside the box, but can go all the way to ozone layer; thus the name blue sky. You may or may not be able to resolve the original goal. However, the pursuit of the goal will often lead to innovation in equipment and other discoveries, that were not part of the program. It can be useful as a staging area. Life in other solvents is blue sky research. It only has legs based on the random assumptions; math magic, not hard data. This is nevertheless important, because you never know what you will find along the journey. The journey of a thousand steps begins with the first step. It may bring us down new paths.

    There is no simple one liner I can give to explain this topic. Instead I am trying to develop a new branch of chemistry; biophysical chemistry. This is a very wide subject since all materials of life come in to contact with water. I am doing this in a systematic way, which involves first setting theoretical footings and foundation before building, vertically. My approach is state some of water's extreme properties; anomalies, to show how they are important to life at the nanoscale. I am basically defining the nanoscale environment seen by life and evolution at the nanoscale. If we know the environment we know some of the needs.

    Water has the highest heat capacity of any liquid

    Heat capacity is the number of heat units required to heat a body one degree. It take more energy to heat water, one degree, than any other liquid. This is also connected to hydrogen bonding. Water will form hydrogen bonds, with up to four neighbors. The symmetry of two donor and two acceptors groups allows water to polymerize into clusters, with the clusters able to form cooperative hydrogen bonding; resonance for added stability. As we add heat, all these layers of hydrogen bonding stability, have a lot of capacity to absorb energy. First, the cooperative resonance will become more and more limited, then larger clusters will become smaller, until finally local hydrogen bonds begin to break and reform.

    One of the values of water being able to absorb so much energy; heat, is this helps to regulate the entropy of the organics of life. Entropy needs heat; waste heat, for entropy to increase. The high heat capacity of water absorbs much of the waste heat. This makes it harder for the organic structures to gain entropy, thereby allowing order to persist over a wide range of temperature.

    For example, when proteins fold in water, they fold with very specific folds. This is due to the energy needs of 3-D hydrogen bonding of water. Water wants to go all the way to cooperative resonance. This need will first cause the hydrophobic groups to phase separate, one by one, based on their energy potential with the water. The water then also causes the hydrophilic groups to populate the surface, with water hydrogen bonded to these and to other surface water, forming a girdle around the surface of the protein. This girdle is under tension; surface tension. Protein can maintain their exact folds due to the water girdle.

    Proteins will begin to denature in water at about 41C or 105.8F. Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state. As we increase temperature from 98.6F (human body temperature), the high heat capacity of water is absorbing the heat energy. This is causing the cooperative resonance and larger scale clustering to diminish to some degree. The protein remains stable, since it can't gain enough entropy to denature. When we reach 105.8 F, the water has absorbed sufficient energy to where the larger scale 3-D girdle begins to split at the seams; smaller scale hydrogen bonding, and we get a protein muffin top.
     
    Last edited: Dec 18, 2016
  18. DaveC426913 Valued Senior Member

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    You are going about the scientific method backwards.

    You already have your conclusion (that water is essential to even exotic forms of potential life), and are now defining the premises that will show (to you) that its an inescapable truth.
     
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  19. wellwisher Banned Banned

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    If I had access to resources, I could do it the easy way, which is run a conclusive experiment. One does not even have to explain anything if the experiments gives the results you expect. It can be left for others. But since I do not have that access, I have to do this the hard way. I need to build a conceptual foundation using science I find around the house; science we already know, but used in a different way.


    Water expands when it freezes.

    Water expands when it freezes due to features of hydrogen bonding. Hydrogen bonding in water is primarily an electrostatic attraction, between the positive charge of the hydrogen protons and the negative charges on the oxygen of water. The electrostatic potential lowers as distance decreases; hydrogen and oxygen get closer. Yet, water expands when it freezes, giving off energy. When water freezes and expands the electrostatic attraction is going the wrong way. This should be endothermic, yet it is highly exothermic.

    The reason has to do with hydrogen bonding also showing partial covalent bonding character. For proper covalent bonding, the oxygen and hydrogen need to align and separate somewhat, so there is proper wave addition of the molecular bonding orbitals.

    In liquid water, hydrogen bonds exist in both states; polar and covalent, and can easily switch back and forth, since there is only a small energy difference between the two states. The average life of a H2O molecule in liquid water is about 1 millisecond before it break covalent bonds and switch hydrogen, all at room temperature. The hydrogen bonds starts as the polar state and the switch shifts to the covalent state. The accepting water, shifts one of its other hydrogen bonds from coolant to polar. The result is a balance of forces and new hydrogen partners. This helps with the cooperative resonance as well as quantum tunneling.

    The value of this is every hydrogen bond in the 3-D water matrix, is a binary switch. The dual nature of hydrogen bonding allows the switch to flip, without having to break the hydrogen bonding. Water can be attached to an enzyme; girdle, and by flipping the switch, change the local surface potentials, while retaining sufficient girdle strength not to allow protein muffin top.

    The polar hydrogen bonding benefits by minimizing distance, to minimize charge potential. The covalent aspect of hydrogen bonding is slightly more stable. It has to align and expand, relative to the polar state, to get proper orbital overlap. The net result is the binary switch is not just an on-off (P-C switch), but each switch setting has four different physical potentials. The covalent setting is more expanded (adds volume), adds pressure to the local surroundings, contains less internal energy (enthalpy) and contains less entropy. While the polar setting exerts a negative pressure on the surroundings (contracts), occupies less volume, contains more enthalpy and also exhibits more entropy. If we have an enzyme girdle and we switch the setting, we can add or take away free energy, as well as pull or push the enzyme. Or if we wish to shut off an enzyme, we only need the flip the water switch one setting and leave it there.

    Picture the water of the cell forming it own structuring, due to the hydrogen bonding of water, while also phases separating organelles and others features as separated things in the cell. These organelles have their unique surfaces with the water, which impart the aqueous hydrogen bonding girdle. Since these surfaces are unique and different, they have different impacts on the water. Each girdle can have a unique combination of switch settings, that define the surface, based on its energy, entropy, pressure, etc.
     
  20. joepistole Deacon Blues Valued Senior Member

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    If Wellwisher knew anything about chemistry she would know there is already a branch of chemistry devoted to chemistry of life. It's called biochemistry.
     
  21. wellwisher Banned Banned

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    I was very skilled at chemistry in college. I especially liked organic and physical chemistry. I became a materials expert; metals, ceramic and polymers, with polymers my speciality. Back in the day, I scored 93rd percentile in the graduate chemistry entrance exams, without test preparation. I have a good conceptual knowledge of biochemistry, since this is nothing but organic chemistry and polymers. However, I don't have the normal memory approach. My knowledge is more grass roots chemistry; nanoscale.

    My polymer background allows me to understand the correlation between 3-D macromolecular structures and their properties, for macromolecules beyond and including bio-polymers. My current approach is to add some physical chemical considerations, to organic chemistry and the chemistry of polymers, to develop the bio-physical chemistry of water and life.

    I was a development engineer, so I was paid to think outside the box, rather than recite the party line of what already is. I still do this, but without a lab and pilot plant area so I can test my theories and adapt to the experiments. I have to think to compensate.

    This topic deals with the interface between water and the second, tertiary and quaternary structures of the polymers of biochemistry; nanoscale environment. Biochemistry will deal with the DNA double helix. Whereas this aspect of bio-physical chemistry will deal with the DNA double helix, as well as the double helix of water, that exists in the major and minors grooves of the DNA double helix. This is not shown in biology textbooks, which renders the stock analysis, inaccurate and obsolete.

    This topic will also deal with the water beyond the double helix, connected to the phosphate groups, all the way into the bulk water. All this water is connected via hydrogen bonding, and is needed for bioactivity and gene recognition. The binary switch nature of hydrogen bonding, allows a way for information to be communicated, to the DNA, while also altering local physical parameters; pressure, volume, enthalpy and entropy via the double helix of water.

    The potential in the water is equal to the sum of its dissolved and surface interface parts.

    If we have pure water, the water molecules will hydrogen bond forming extended water structures. These can also form cooperative resonance for added stability. As we add materials to the water, different materials will impact water differently. The water will alter its structuring, to minimize energy, based on the material and the concentration, and how these impact the water.

    As an example, although sodium; Na+ and potassium; K+, cations both have a single positive charge, water responds differently to each cation in terms of its structuring. Sodium ions will bind to the oxygen of water stronger than the hydrogen of water can bind via hydrogen bonding. The impact of sodium is to create more order in water; kosmotropic. Potassium ions, although they also having a single positive charge, bind to the oxygen of water weaker than water binds to itself. This tends to disrupt the structures of water; chaotropic, adding potential energy.

    When cells pump and exchange sodium and potassium cations, the sodium ions accumulate on the outside and potassium ions accumulate on the inside. The purpose of this is to set up two distinct aqueous environments; with a water potential gradient between the two zones (order and disorder). The exterior sodium cation induction makes water more friendly to organic food materials. The reduced food material will add energy to water, due to the induction of surface tension. This is compensated by the order in water, induced by the sodium. Inside the cell, the potassium ions, by created chaos in water structuring, helps to loosen up the protein girdles, so the protein are more bioactive; move between conformations.

    If you remove the outer membranes from modern cells, so there is no cationic pumping mechanism, the naked interiors of the cell, will still concentrate potassium ions. They will extract potassium from the environment, up to normal cell concentrations. This is due to the potassium ions and the protein surfaces, balancing each other out, relative to minimizing water potential. The water is able to lower potential, due to the protein surfaces, by drawing in potassium ions.

    In terms of evolution (blue sky theory), if you had an empty volume, surrounded by a simple membrane with cation pumping and exchange, one could use this to extract specific protein from the environment, selected to compensate for the interior K+. The K+ and protein will form a team needed to minimize water potential. This is not random but based on energy in the water.

    Many scientists believe the cation pumps are no longer needed, but are there simply as a failsafe. However, active cationic pumping, by increasing the membrane potential higher, is still helpful for driving extractions in both directions; inputting and exporting materials.
     
    Last edited: Dec 20, 2016

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