Is life only a system of evolving chemical reactions?

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    • #18200
      minasole
      Participant

      Is life only a system of evolving (and selected) chemical reactions over long periods of time?

    • #115856
      claudepa
      Participant

      Hi. Could the question be also: Is biology only a part of chemistry ? I have no answer but a personnal experience. A long time ago during my phD in biology I identified a new chemical reaction involving DNA. I had then a very interesting collaboration with organic chemists who successfuly reproduced this reaction with small molecules. This was a confirmation of my results. However we did not agree on the notion of affinity between molecules. At this time (may be it is different now in chemistry, I do not know) chemists had not this notion of affinity between molecules, only the notion of reactivity. (the reaction with DNA was much faster than with the small model molecules for an affinity reason). We of course know that the affinity between molecules (antibody-antigen, transcription factor-DNA sequence,…) is very important in biology.
      Is this also part of evolving chemical reactions ?

    • #115878
      minasole
      Participant
      quote claudepa:

      (the reaction with DNA was much faster than with the small model molecules for an affinity reason). We of course know that the affinity between molecules (antibody-antigen, transcription factor-DNA sequence,…) is very important in biology.
      Is this also part of evolving chemical reactions ?

      Yes! But most of all i think it reflects the different conditions that generated these molecules. Biological reactions we observe are a tiny part of a larger group of reactions in which they belong..
      If you search enough, there will be a pure chemical explanation for this difference in affinity (perhaps different stereochemistry?)

      quote claudepa:

      Hi. Could the question be also: Is biology only a part of chemistry ?

      Chemistry can break down into physics. However there are difficulties into breaking down biology into complex organic chemistry (although the latter can pose a great variability of isoforms, thus enhancing complexity, selection and evolution over time that will eventually favour reactions with sustainability in the long term). However, there is a problem mainly with respect to thermodynamics and creation of order…

      We think of life as a miracle and order because, for instance, some might say that a cell is much more ordered than its components, which means that a cell is an ordered and not a chaotic system.

      However, I am skeptical with this interpretation because don’t forget that a cell never exists in isolation.
      Imagine you have a flask with water that is heated with fire. The molecules of water will start speeding randomly toward various directions. Virtually, what you are doing here with the cell argument is ignoring the fire and the majority of other water molecules and focusing only on subset of 1 or 2 specific molecules. These molecules will be perceived as gaining speed without an obvious reason,..
      Maybe sometimes our fate is to focus on the tree rather than the forest..

    • #115879
      claudepa
      Participant

      claudepa wrote:
      (the reaction with DNA was much faster than with the small model molecules for an affinity reason). We of course know that the affinity between molecules (antibody-antigen, transcription factor-DNA sequence,…) is very important in biology.
      Is this also part of evolving chemical reactions ?

      Yes! But most of all i think it reflects the different conditions that generated these molecules. Biological reactions we observe are a tiny part of a larger group of reactions in which they belong..
      If you search enough, there will be a pure chemical explanation for this difference in affinity (perhaps different stereochemistry?)

      I agree that biological reactions and chemical molecules used by biology are selected among a much larger group. A good example is adenine used by cells for very different purposes. Other examples are D sugars and L amino acids. I indeed believe that the very high affinity between macromolecules has a stereochemical cause. When these macromolecules meet their surfaces is modified until a minimum of energy is reached. The point I raised was only a semantic one, it seems pure chemistry but may be is not involved in the sentence: chemical reactions.

      claudepa wrote:
      Hi. Could the question be also: Is biology only a part of chemistry ?
      Chemistry can break down into physics. However there are difficulties into breaking down biology into complex organic chemistry (although the latter can pose a great variability of isoforms, thus enhancing complexity, selection and evolution over time that will eventually favour reactions with sustainability in the long term). However, there is a problem mainly with respect to thermodynamics and creation of order…

      We think of life as a miracle and order because, for instance, some might say that a cell is much more ordered than its components, which means that a cell is an ordered and not a chaotic system.

      The more I advance the more I imagine (may be I am wrong) a cell as a very ordered system. When I see videos of viruses going from the membrane to the nucleus travelling on microtubules, when I know that vesicles going out of the Golgi are targeted for their destination, I really see the cell like a city with roads and highways.

      However, I am skeptical with this interpretation because don’t forget that a cell never exists in isolation.
      Imagine you have a flask with water that is heated with fire. The molecules of water will start speeding randomly toward various directions. Virtually, what you are doing here with the cell argument is ignoring the fire and the majority of other water molecules and focusing only on subset of 1 or 2 specific molecules. These molecules will be perceived as gaining speed without an obvious reason,..
      Maybe sometimes our fate is to focus on the tree rather than the forest..
      minasole

      Cell exist in isolation but may be they will not live a long time in this situation. I like a video showing islotated cell moving on a glass plate towards an amino acid for which they have receptors at the membrane. They look really like small animals.

      Garter
      Garter

      Posts: 23

      Joined: Tue Oct 16, 2012 10:08 pm

    • #115886
      minasole
      Participant
      quote claudepa:

      The more I advance the more I imagine (may be I am wrong) a cell as a very ordered system. When I see videos of viruses going from the membrane to the nucleus travelling on microtubules, when I know that vesicles going out of the Golgi are targeted for their destination, I really see the cell like a city with roads and highways.

      Have you ever thought that maybe this “magical” small city only differs from chaotic chemistry in the fact that this system you described sustains itself and all procedures are repeated (pretty much) the same again and again?? Don’t forget that one of the most important properties of a cell is self-sustainance.

    • #115887
      claudepa
      Participant

      I am nor a chemist nor a thermodynamician. I know only of the basic types of chemical reactions that take place in a cell. What is amazing is their number, around 1 million chemical reactions per second in a bacteria I believe (anyway a huge number). Also amazing the efficiency of the nanomachines: A DNA polymerase is able to associate thousands of DNA base pairs per second. And all this works perfectly well without interferences that we could imagine chaos would create. What about the dissipative (ordered) structures that chaos could generate if I remember not too wrongly Ilya Prygogine ?
      OK a cell repeats the same reactions but it also responds to the environment through numerous signals to the membrane and then expressing the required genes. In multicellular organisms, as we are, all the DNA program of the cell is here to insure the positive role of the cell in the body. If mutations occur a whole machinery is present to correct these mutations and prevent the cell going wrong. Nothing is perfect and only when this system is overflowed will problems such as cancer occur. Thanks to Louis Pasteur we know that every cell comes from an other cell. It therefore comes from very far, 3.5 billions years, may be 4 billions say now some researchers. Nobody knows if there are several origins of cells or only one. Chemists have not yet succeeded to artificially create a cell. Even when the genes are synthetic cytoplasm and membrane are not.

    • #115891
      BrianEvans
      Participant

      To be more specific, life is self-propagating information capable of detecting environmental conditions and responding to them. The chemistry of biological systems is a tool through which these responses are expressed. Some chemical arrangements, like lipid membranes, are used mostly for mechanical reasons like durability and polarity. Others, like neurotransmitters and receptor proteins, are employed because their interaction follows a specific algebraic function and thus computationally behaves as that function. This allows the lifeform to chemically represent and analyze external information internally and respond to it.

      The life isn’t actually in the chemistry. It’s in the genetic information that expresses a total design for a self-propagating and adapting chemical machine. This information’s form is an emergent property of nucleic acid structure, but nucleic acids are just very convenient substrates on which to represent a chemical instruction set. A completely accurate translation of this information structure to another medium (such as a digital electronic representation) would be "life" just as much as the one implemented through chemistry.

    • #115893
      claudepa
      Participant

      Life is in DNA ? Life is in chemical reactions ? Membrane only mechanical ? But ATP synthesis is linked to membranes! Difficult for me to know what is the most important, I mainly see that the whole system works perfectly well. In around 100 yeras of research it has been possible to identify how the system works (I consider that the discoveries of these 100 years are absolutely extraordinary, and even the discovery of cell existence is not so ancient in the history of science) . But DNA without proteins to read it is like a tape without tape recorder. And without DNA, no proteins. Researchers speak of a precellular RNA world where RNA would have had at the same time both the functions of DNA for information and of proteins as executive agents. But again this is only speculation. When chemists will (or if they succeed) succeed to create such chemical autoreproducting assemblies of molecules it will be much more convincing.

    • #115902
      minasole
      Participant
      quote BrianEvans:

      The life isn’t actually in the chemistry. It’s in the genetic information that expresses a total design for a self-propagating and adapting chemical machine. .

      What about prions? They don’t seem to have no genetic information at all.

    • #115903
      claudepa
      Participant

      Good point with the prion. It is autoreproducible without nucleic acid. But then it is a question of definition of life. Prion as well as viruses could probably be chemically synthetized. At this time it seems very difficult to do it for a cell. If we should define life as all organism composed of cells, including ones with only one cell, (not the usual definition!) the question would remain unsolved. Furthemore it seems that the actual theory is that viruses are very old but appeared after cells. There are therefore presumed as a product of cells.

    • #115925
      minasole
      Participant

      This is only a problem of semantics. I dont see why prions are not living material. They are excluded from our definitions because they don’t fit our DNA models of life. But my prediction is that more such entities (non DNA) will be discovered in the future. At this moment, prions are only different from the rest of life on the fact that they are a much more simple set of chemical reactions…
      Biology in theory can be reduced down to chemistry, which can be reduced down to physics, however, things grow tremendously complex and its not worth it.
      On the other hand, I think that mathematical models cannot apply to biological systems that easily. For instance, mathematical models cannot fully represent true biological phenomena because they don’t account for the spatial factor. Additionally, they only assume that all chemicals can react with each other without accounting for inhibitory events, or other kind of interactions such as adhesive properties, hydrophobic interactions, etc, etc….Moreover, they can be manipulated until they work.
      Some scientists (even legit ones) introduced some kind of these supposed models into computers, played with complexity and supposedly got some incredible hidden patterns that miraculously emerged, in other words, nothing less than bacteria, flowers, animals, etc…
      Now i think this is an example how wrong initial assumptions, when used in wrong ways, can lead us to monstruously misleading conclusions.
      If your approach in order to answer how from complex primordial chemistry we got to today’s life is this, then it is life answering to the question how from 1, 2, 5, 8 you got 5689 and you claim: Eureka!!! Its 1+2=15*5=3000*8=5689

      On the contrary, I think that in a complex chemical system, due to all the kinds of interactions which are unpredictable, the most sustainable combinations of interactions (or else the resulting mixture) will be slowly selected in a step-by-step fashion, brick by brick, until we get the final mixture that will be super sustainable because it was sculped and shaped by eons of struggles and competitions.

    • #115926
      chemnorm
      Participant

      What an interesting topic

    • #115955
      minasole
      Participant

      Apart from the solar energy, in a primordial soup of chemicals, the following factors can shape the fate of the system, or else the natural history of the events:
      1) By the different isoforms that organic stereochemistry pose, which adds to the diversity and mechanics that is needed to avoid equillibrium. Organic molecules are more stable. Thus, their number would slowly grow in the mixture….

      2)Hydrophobic interactions (hydrophobic bonds, spatial configuration, separation and isolation of chemical systems, membranes, etc.
      3)And apart from that, another crucial factor that shapes the system is the property of some molecules to strongly adhere to each other, or to membranes. In fact, if you put living cells and dead cells in a flask, then you can sort them easily because only the living ones will strongly adhere to the walls.
      To see the importance of stickiness, take for instance the sponges. Recent studies has shown that they were one of the first organisms on earth, along with corals.
      They don’t seem quite like the other animals. In fact, I would say that they are something in between, more like random chemical systems. However, the strong adhesions between molecules (as well as multiple other factors) in sponges makes those systems sustainable over time. In fact, they were created because they were not destroyed. They can sustain themselves for millennia and every sustainable chemical novelty can prevail and be selected.
      4)Slow reactions can sustain themselves for a longer time…

    • #115958
      Alisaworm
      Participant

      Wow, insightful theme! Above answers make sense. Great!

    • #115971
      minasole
      Participant

      I have previously described what will happen in a flask of chemical reactions in the long term. There is not a certain plan that is favored, however the system will continue happening. The final resulting reactions will appear to have survival capacities if the observers are exactly those resulting reactions. Everything that happened lead to them. So the final combination of reactions will be the most sustainable of all combinations, given the particular conditions, because that’s exactly what happened. Those reactions prevailed in the long term.
      The other factor that might help the system to sustain itself theoretically is repeatability. However, there is problem with repeatability. How can arbitrary reactions gain, or even more amazingly, sustain their repeatability? Although in theory a process that can protect some repeatable reactions can evolve and be selected, another option is possible, that personally I think is more likely to be the case.
      And the second thing is this: Are there trully repeatable processes in nature? For instance, if a descendant is 99% the same as its ancestor, and they are both composed of 100 trillion reactions, this means they differ by 1 trillion reactions. Also, if you have two systems of 100 organic compounds with various stereochemistries that interact with each other and they become increasingly complex to the point that each system becomes 100 trillions of different compounds, then one would expect that 99% percent of the compounds of one system will be somewhere present in the other system as well, only as a result of pure chance.
      Now if two systems of 100 trillion reactions or possible interactions are exposed to the same chemical laws and conditions (variability prevails, hydrophobic bonds, adhesive properties prevail, stable molecules prevail, influx of external substances, same temperature, etc etc, then the two systems that will be mainly composed of the same substances, will share approximately the same fate, at least to our eyes. Because if by 95% the same thing happens in both systems, this means they differ by many trillion reactions, but for us, it is enough to consider the two processes identical.
      So to conclude, anytime it may be possible for a group of organic chemicals to burst complexity and development, but this can’t happen indefinitely, because of various internal and external obstacles, so the process is regulated in a way. Only in some circumstances this happens (etc development, cancer, rehabilitation, etc). Theoretically, this can be the case everytime the process finds the opportunity.
      Any thoughts?

      M Sakellakis

    • #115972
      minasole
      Participant

      Important note: The numbers used (trillions etc) are rough approximations and their sole intent are to better explain my thoughts and underscore the effect of big numbers. Don’t focus on the particular values…

    • #115980
      minasole
      Participant

      One important question is why this specific organic stereochemistry that constitutes life prevailed and thrived so much, and from where did it come from. I can think of two logical ways:
      Organic stereochemistry didnt reach equillibrium due to variability of possible isoforms and thus, everytime they were created, they persisted and survived, adding to complexity. Additionally, everytime they reacted with other organic or inorganic material (eg water, CaCO3 etc), they corrupted the other materials, adding to stereochemical complexity, and thus constantly adding novel material into the available for life chemical machinery of organic stereochemistry. In a similar way that prions corrupt the chemistry of the host organisms. This constantly increasing organic stereochemical reservoir can in theory undergo evolution and selection of the most sustainable chemical systems and theoretically create amazingly sustainable chemical systems such as ourselves or the other living beings.

    • #115981
      claudepa
      Participant

      When first cells (or the first cell) were formed either there was no so many available organic molecules or a very small minority of available molecules was fitted for life. 2 examples: 1) Adenine is a molecule used by cells for different purposes: information, energy, neurotransmission, redox reactions. 2) Only one type of isomer is used for sugars in nucleic acids and only one type of isomer is used for aminoacids.

    • #115985
      minasole
      Participant

      Yes but without isomers, equillibrium would have been much more likely i think.

    • #116006
      minasole
      Participant

      And i think that tumor heterogeneity and clonal evolution is a perfect example in which this concept of metabolic evolution and selection applies, because metabolic diversity between cells determine to a great extent which neoplastic cells will have better chances to prevail.

    • #116007
      claudepa
      Participant

      The actual view is that uncontrolled cell proliferation in tumors is due to mutations in DNA. These mutations can affect proliferation and death of cells. Mutated oncogene proteins, such as RAS for instance, can then send constantly signals of proliferation to the nucleus instead of doing it only when receiving a signal from the environment. Mutated antioncogene proteins such as RB do not anymore stop the cell cycle. Also mutated proteins responsible of apoptosis such as P53 will not anymore trigger the death of cells with mutations.

    • #116037
      Kalysonb
      Participant
      quote minasole:

      If your approach in order to answer how from complex primordial chemistry we got to today’s life is this, then it is life answering to the question how from 1, 2, 5, 8 you got 5689 and you claim: Eureka!!! Its 1+2=15*5=3000*8=5689

      The bigger question is, how did absolute 0 produce 1?

      Wrong initial assumptions, used in anyway, will lead to monstrously misleading conclusions.

    • #116075
      missplat
      Participant

      Actually, life is just a distant repetition of the burning of gases that make our sun. Our planet was formed when a mass of burning gas was thrown off by the sun and, although cooling on the outside, has remained a molten mass on the inside.
      Cells, of which life is formed, are tiny bags of H2O and a few other chemicals, which replicate the original burning process using energy from the sun (conveyed in light waves from the sun and heat from the molten interior).
      Thus, we ‘eat’ to gain the fuel to continue the burning process. We say this process ‘gives us energy’ to do the work required to keep us alive, but it is simply continuing the burning process at a distance.

    • #116227
      minasole
      Participant

      In a system of complex stereochemical reactions, the chemical evolutionary history will lead to a gradual selection of systems or compounds that are more and more stable. Thus, they will be less vulnerable to changes. So, in a sense they will be more immune to their surrounding changes. They will achieve that not only due to their own inherent stability (bonds, hydrophobicity, etc), but also by exploiting peripheral chemical mechanisms that promote their own stability.
      The end characteristics of these more stable groups of reactions/compounds will be: a) They are highly conserved, with minimal changes over time, b)key regulators or central pathways of whole system expansion and growth, because those reactions or their precursors has been there in the whole interrelated system since the beginning c) expansion of these chemical systems will expand the whole system related to them, because since they are the most stable ones, the cascade of reactions that they will cause cannot cause a shrinkage of the whole surrounding system, but only an increase in terms of volume and collection of a diversity of chemicals.
      Also, since the different chemical compounds, although countless, they are similar everywhere, this means that similar rules should apply universally. So these stable chemical compounds and the reactions that modify them should be similar everywhere, yet no identical.
      I think that the best candidates for these characteristics are nucleic acid and especially DNA, together with accompanying chromatin (histones, etc).

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