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Thread: odds of functional proteins emerging by chance?

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    odds of functional proteins emerging by chance?

    I can count the probabilities of all events that happened a within a week before our conception that if were otherwise we would not be here. It would be probably higher than chances of life not to emerge from chemistry.
    For someone with IQ>100, this points not towards magical interference, but towards a perspective issue. Like for instance life being a huge system of evolving chemical reactions judged under the perspective of a tiny fraction of results (us) embedded inside the system

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    A slightly vague post, globali.
    Current biology such as us has little to do with abiogenesis w2hich starts with chemicals and goes up to the first cells, not the complex, multi-cellular animals that have evolved over billions of years.
    This points to the well known science of abiogenesis and evolution.

    The odds are not from "emergence by chance" (chemistry is not random). The 1 example of an habitable planet we have so far suggests the odds are 100% but of course we need more examples. Actual odds are educated guesses and vary a lot.
    ETA: Look at this Drake equation article. The estimated fraction of habitable planets that develop life ranges from 10^-9 to 0.13.
    Last edited by Reality Check; 2018-Dec-10 at 10:39 PM.

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    Quote Originally Posted by Reality Check View Post
    ... The odds are not from "emergence by chance" (chemistry is not random).
    (Re: my underline).

    Non-equilibrium thermodynamics can, in some cases, produce non-linear effects such as chemical oscillators. This class of reactions stand as demonstrations that chemical reactions do not necessarily have to be dominated by equilibrium thermodynamic laws. Such reactions often operate far from equilibrium, and remain so for a significant periods of time and typically evolve chaotically. They also serve as a model for sometimes unstable biological chemical phenomena.

    Examples are: the Belousov-Zhabotinsky reaction (BZ reaction), the Briggs-Rauscher reaction, the Bray-Liebhafsky reaction and the iodine clock reaction.

    Current abiogenesis hypotheses point towards auto-catalytic sets as a likely basis for pre-biotic chemistry, of which the above reaction classes form a subset.

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    My favorite analogy is the box of paperclips. Shaken up, the clips hook on to each other and form branching chains. A good example of adding energy to a chaotic system and getting order out of randomness.

    Now picture the same thing, on a planet wide scale, over millions of years.

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    I think the point I'm raising, (which is exemplified by the class of reactions indicated in my post#2), is that the appearance of order is abrupt, and often extremely difficult to predict. There are no simple formulas or models which can be said to produce consistent outcomes.

    The temporal 'volatility' in the appearance of order, (which could be viewed for example, as a collection of stable pre-biotic chemicals), represents neither randomness nor certainty.

    All of which questions the idea that Earth-like planets in the habitable zone, (having non-equilibrium thermodynamics, oxygen, liquid water, etc), leads anywhere definitive, when it comes to predicting the presence of life.

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    Quote Originally Posted by Reality Check View Post
    A slightly vague post, globali.
    Current biology such as us has little to do with abiogenesis w2hich starts with chemicals and goes up to the first cells, not the complex, multi-cellular animals that have evolved over billions of years.
    This points to the well known science of abiogenesis and evolution.

    The odds are not from "emergence by chance" (chemistry is not random). The 1 example of an habitable planet we have so far suggests the odds are 100% but of course we need more examples. Actual odds are educated guesses and vary a lot.
    ETA: Look at this Drake equation article. The estimated fraction of habitable planets that develop life ranges from 10^-9 to 0.13.
    Personally, I would think that it is at the 10^-9 end of the range, but then evolution is straightforward to technological civilizations.
    However, I read a book on Exobiology and SETI (I think it was The Great Silence) which referred to an article using Bayesian math (I did not look for the article, as I never took Bayesian math) which says if there are multiple events necessary for something to happen, each of which normally takes much, much longer than the time you have for them to happen, but you "force" them to happen, then the intervals between the events are evenly spaced, even if they are greatly different in how much time it takes on average for them to occur. The book used this to argue that life probably originated on Mars, since Mars cooled off sooner than Earth did and life seems to have originated too soon for it to have begun on Earth. But since the book was published estimates of first life ( and to a degree, the periods between the other events) have been expanding even more, so maybe abiogenesis is not the bottleneck and Great Filter I think it is.
    SHARKS (crossed out) MONGEESE (sic) WITH FRICKIN' LASER BEAMS ATTACHED TO THEIR HEADS

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    Quote Originally Posted by globali View Post
    I can count the probabilities of all events that happened a within a week before our conception that if were otherwise we would not be here.
    Well, that's different from counting the probability of one event happening within a billion years that ultimately led to life on earth.
    Everyone is entitled to his own opinion, but not his own facts.

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    it may sound heretic, but why do we take for granted that life is about order, or life should be divided in basic units? Isn't that too anthropocentric as a point of view?

    An isolated organism may appear to have order, but the only reason why every organism exists is the....the rest of other life. And i am not sure if you consider life as an entirety what is the thermodynamical status!

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    We say life is about order because we see that life is more ordered than non-life. A gas is a collection of particles randomly colliding, etc. A cell is a more ordered set of chemical reactions.

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    Quote Originally Posted by globali View Post
    it may sound heretic, but why do we take for granted that life is about order, or life should be divided in basic units? Isn't that too anthropocentric as a point of view?

    An isolated organism may appear to have order, but the only reason why every organism exists is the....the rest of other life. And i am not sure if you consider life as an entirety what is the thermodynamical status!
    It's a fallacy that order and chaos are opposites (thanks a lot, ancient Hellenes!) Everything has some order and some chaos in it.
    "I'm planning to live forever. So far, that's working perfectly." Steven Wright

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    Quote Originally Posted by globali View Post
    it may sound heretic, but why do we take for granted that life is about order, or life should be divided in basic units? Isn't that too anthropocentric as a point of view

    An isolated organism may appear to have order, but the only reason why every organism exists is the....the rest of other life. And i am not sure if you consider life as an entirety what is the thermodynamical status!
    These are very interesting viewpoints. For instance where one doesn't know exactly what one is searching for in an alien environment, then one would start by surveying the general landscape first ... then notice what contrasts with it.

    I notice you're still in the recent signup moderation queue .. shall be patient and await any follow-ups you may want to have (once you get to fully interactive status).

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    there has been interesting work on making DNA with more letters. The idea is that many more proteins could then be made offering the possibility of electric biology, for example. I see no fundamental reason why a different set of bases could evolve, or the same ones as we have here. If evolution is assumed then progress from simple to complex seems more likely as in the blind watchmaker analogy. It's rather like the Boltzmann's brains thought experiment (as to what is likely).
    sicut vis videre esto
    When we realize that patterns don't exist in the universe, they are a template that we hold to the universe to make sense of it, it all makes a lot more sense.
    Originally Posted by Ken G

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    Reality check: That is true, but even in the case of a highly disordered and chaotic system, if you just put a isolate a tiny part of it and consider it a separate unit, and have a camera only on that part, then you will certainly observe phenomena not explained by the rules of randomness. If these inconsistencies are you, then you would even consider them highly ordered. I am not saying this is true, but you got my point..

    Selfsism: Yes. Deep under the oceans there are organisms that have life cycles compared to geological ages. My guess is that if we find anything in another planet will resemble those organisms. Complex organic biomolecules can stick together in harsh conditions and form something like that. Don't forget that DNA with all the packaging is a stable way organics can be stored and preserved.

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    Quote Originally Posted by profloater View Post
    there has been interesting work on making DNA with more letters. The idea is that many more proteins could then be made offering the possibility of electric biology, for example.
    Electric biology? Please explain .. I'm curious.
    Quote Originally Posted by profloater
    I see no fundamental reason why a different set of bases could evolve, or the same ones as we have here. If evolution is assumed then progress from simple to complex seems more likely as in the blind watchmaker analogy. It's rather like the Boltzmann's brains thought experiment (as to what is likely).
    I think its important to keep clear the distinct phases here (at least in discussion pertaining to the overall process). Abiogenesis is distinct from Evolution and the usually agreed functional 'break-point' is self replication. Abiogenesis generally covers events prior to self replication.

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    Quote Originally Posted by Selfsim View Post
    Electric biology? Please explain .. I'm curious.
    I think its important to keep clear the distinct phases here (at least in discussion pertaining to the overall process). Abiogenesis is distinct from Evolution and the usually agreed functional 'break-point' is self replication. Abiogenesis generally covers events prior to self replication.
    I am quoting (from memory) from a New Scientist review of progress in making synthetic and alternative DNA bases. I do not have it in front of me but I will look it out and report back.
    sicut vis videre esto
    When we realize that patterns don't exist in the universe, they are a template that we hold to the universe to make sense of it, it all makes a lot more sense.
    Originally Posted by Ken G

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    New scientist 8 december p 40 “life rewritten” building on the work of Steven Benner others have tried adding codons, extra letters to the normal A T C G to make new proteins. They work in bacteria of course. Romesberg is another name, 2017 he created a six letter e.coli. The magnetic and conducting proteins foreseen are speculative but intriguing. His e.coli. Fluoresced. Commercial company: Synthorx.
    sicut vis videre esto
    When we realize that patterns don't exist in the universe, they are a template that we hold to the universe to make sense of it, it all makes a lot more sense.
    Originally Posted by Ken G

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    Quote Originally Posted by globali View Post
    Reality check: That is true, but even in the case of a highly disordered and chaotic system, if you just put a isolate a tiny part of it and consider it a separate unit, and have a camera only on that part, then you will certainly observe phenomena not explained by the rules of randomness. If these inconsistencies are you, then you would even consider them highly ordered. I am not saying this is true, but you got my point..
    I do not get your point. An unsupported story that a highly disordered and chaotic system will not be random in a "tiny part". A fancy that there are inconsistent "rules of randomness" and they are me?

    Consider a room full of gas. It is a highly disordered and chaotic system made up of very many randomly colliding particles. Isolate a tiny part of that room, say a tenth. There is still a highly disordered and chaotic system made up of many randomly colliding particles. Repeat. Eventually you get to a "tiny part" of the room with a lot of particles randomly colliding with each other. The system has not become ordered. We could keep dividing the room but then we pass out of the realm of thermodynamics and into the kinetics of a few colliding bodies and then the kinetics of a single body.
    Last edited by Reality Check; 2018-Dec-13 at 11:13 PM.

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    I don’t know how to explain it in a simple way. Lets say these colliding particles are randomly dispersed in the room. They won’t be dispersed exactly evenly, but there will be areas with high concentrations and areas that are empty. Let’s also assume that the molecules are a little bit sticky and they attach to each other for a while. Now suppose the observer is a group of molecules that came together inside the system. It may think that the purpose of this environment is to create objects like him that die and get reborn. He be like: Hey, why is this place full of objects like me if this place was supposed to be a total chaos if you take into account the initial ingredients and the conditions?
    Now this is a really silly example, but the aim is to show that you can still have a chaotic environment, but some insiders may have a really weird perspective. And life is definitely a weird system because we are definitely integrated inside the whole system of life.

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    Quote Originally Posted by globali View Post
    An isolated organism may appear to have order, but the only reason why every organism exists is the....the rest of other life. And i am not sure if you consider life as an entirety what is the thermodynamical status!
    I'm not exactly sure what you mean to say, but if you talk about thermodynamics, I think that life as a whole is not really in thermodynamic equilibrium. What is really happening is that life is using energy from outside (basically the energy generated by the sun, but perhaps also a bit from the cooling process of the earth) to create the order that is life.
    As above, so below

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    Quote Originally Posted by profloater View Post
    New scientist 8 december p 40 “life rewritten” building on the work of Steven Benner others have tried adding codons, extra letters to the normal A T C G to make new proteins. They work in bacteria of course. Romesberg is another name, 2017 he created a six letter e.coli. The magnetic and conducting proteins foreseen are speculative but intriguing. His e.coli. Fluoresced. Commercial company: Synthorx.
    Thanks for the follow up, profloater .. will check it out when I get the chance.

    I thought most earthly bio-organics (eg proteins) fluoresced when stimulated externally with particular wavelengths? That is actually one of the latest proposed detection technologies for detecting bio-molecules using onboard labs in remote rovers(?)
    I'm not so sure why that's such a special property in the engineered proteins? I'll have to read up further ..

    Cheers

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    Quote Originally Posted by globali View Post
    Reality check: That is true, but even in the case of a highly disordered and chaotic system, if you just put a isolate a tiny part of it and consider it a separate unit, and have a camera only on that part, then you will certainly observe phenomena not explained by the rules of randomness. If these inconsistencies are you, then you would even consider them highly ordered. I am not saying this is true, but you got my point..
    I agree with Reality Check's reply post on this one .. However, you did specified 'a highly disordered and chaotic system' which differs from 'a purely random system' in so far as the appearance of self-similarities at different scales. Is that what you meant?

    Quote Originally Posted by globali
    Selfsim: Yes. Deep under the oceans there are organisms that have life cycles compared to geological ages. My guess is that if we find anything in another planet will resemble those organisms. Complex organic biomolecules can stick together in harsh conditions and form something like that.
    Why do harsh conditions result in geological scale longevities? (Please explain reasons).
    Quote Originally Posted by globali
    Don't forget that DNA with all the packaging is a stable way organics can be stored and preserved.
    Hmm depends on your definition of 'organics'. I frequently argue that this term has no objective meaning in an alien landscape where there are no known currently or previous lifeforms evident.

    'Organics' carries objective meaning pertinent to planet Earth's biome however, because lifeforms here are already known to produce residual 'organics' as a by-product of already known and well-defined earth life processes. Where there is no evidence of such processes, (perhaps in an alien landcscape), 'organics' cannot carry that same objective meaning, (due to there being no supporting evidence in that environment).

    PS: I get your point however, about DNA being an effective storage repository for information .. provided its encapsulating environment permits this stability.
    Last edited by Selfsim; 2018-Dec-14 at 04:19 AM. Reason: PS

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    Quote Originally Posted by globali View Post
    I don’t know how to explain it in a simple way. Lets say these colliding particles are randomly dispersed in the room. They won’t be dispersed exactly evenly, but there will be areas with high concentrations and areas that are empty.
    There is a statistics program I used to use that had an opening quote: "Randomness comes in bunches". If particles are perfectly evenly dispersed, they are not random. Random collections of things have some clumps.

    I'm also not sure what this has to do with life or odds of functional proteins emerging by chance. Are you arguing some sort of creationism, that abiogenesis is not possible? I am not sure what your point is.
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    Quote Originally Posted by Jens View Post
    I'm not exactly sure what you mean to say, but if you talk about thermodynamics, I think that life as a whole is not really in thermodynamic equilibrium. What is really happening is that life is using energy from outside (basically the energy generated by the sun, but perhaps also a bit from the cooling process of the earth) to create the order that is life.
    Jens: You assume that life as a whole is about order, because it is a sum of ordered systems, so their sum must be order as well. However, my point here is that you can have some molecules in a room moving randomly, add external energy and not increase the order at all. However, there will be mostly some clumps and dead space. From a clumps perspective, the system consists and constantly creates other clumps like himself/herself. So it constantly creates ordered systems and so the sum of them is also order. So according to a clumps point of view, the entire system takes energy from the outside to create order,like life.

    Swift: Exactly, randomness comes in clumps. I agree.
    I do not support creationism. However, i am not comfortable with the current ideas that somehow organics formed by chance or by law the first self-replicating, self-sustainable magic bullet (cell), and through evolution we got what we have today. However, creationism is definitely not the answer. To me, whenever you have a series of events that seem to be luckily coincidents that always favor you, and you seem to be winning the lottery everyday, then you should check if there is an issue in your perspective. Or if you are dealing with self-fullfilling prophesy.


    Selfsim: Yes, i wanted to say disordered and chaotic system.
    Well, in harsh conditions complex "sticky" stereochemical reactions systems will probably evolve into a steady state where not many chemical reactions are happening. I quess that is the most stable state. I also quess cell division has alot to do with the abundance of molecules (result of nucleotide-driven cascade of reactions) inside the context of a membrane-layered system.
    Organics on earth mostly have to do with long molecules with unique stereochemistry. I think complex stereochemistry is key, because it makes equillibrium difficult. Don't know.

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    I think comparing self-organizing organic chemistry and biogenesis to winning a lottery is a misleading analogy. One in a million chance of winning, but if you have a billion players playing a million times each, the odds of no one winning at all are vanishingly small.

    The scale in time and places of the trial and error mixing and matching of molecules on early Earth, means that lots and lots of one in a billion chances actually happened. I'm not saying self replicating molecules were inevitable, just that in some form or another, they were probably not as unlikely as one event.

    Indeed, it seems likely that it may have happened more than once, and life is merely the most successful iteration.
    "I'm planning to live forever. So far, that's working perfectly." Steven Wright

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    Quote Originally Posted by globali View Post
    Jens: You assume that life as a whole is about order, because it is a sum of ordered systems, so their sum must be order as well. However, my point here is that you can have some molecules in a room moving randomly, add external energy and not increase the order at all. However, there will be mostly some clumps and dead space. From a clumps perspective, the system consists and constantly creates other clumps like himself/herself. So it constantly creates ordered systems and so the sum of them is also order. So according to a clumps point of view, the entire system takes energy from the outside to create order,like life.
    So? .. Just alter the study frame of reference .. I think this is all you're saying isn't it?

    Quote Originally Posted by globali
    Selfsim: Yes, i wanted to say disordered and chaotic system.
    Well, in harsh conditions complex "sticky" stereochemical reactions systems will probably evolve into a steady state where not many chemical reactions are happening. I quess that is the most stable state.
    I don't think one can generalise from a single example of one instance of sterochemistry found in such an environment (beneath deep oceans .. presumably also related to the stereochemistry inherent in all other forms of life).
    You need a non-earth sample to begin the process of extrapolating to the universal case.

    Quote Originally Posted by globali
    I also quess cell division has alot to do with the abundance of molecules (result of nucleotide-driven cascade of reactions) inside the context of a membrane-layered system.
    I would say in the example you're drawing from, the complexity of the molecules themselves, ultimately produces 'abundances'. For example, the subcellular molecules self-organise, prior to cellular division.
    Quote Originally Posted by globali
    Organics on earth mostly have to do with long molecules with unique stereochemistry. I think complex stereochemistry is key, because it makes equillibrium difficult.
    .. or more like "unique sterochemistry is key"?

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    The Earth was hotter long ago--so more smokers. Tidal forces greater. The planet was one big organic chemistry lab. I have this idea that water flow past any number of smokers with different shapes might have formed leeward vortices that spun up something.

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    Well the most difficult part is not to create self organizing chemistry, but to sustain it, at least initially.

    Selfsim: Yes. I think that by moving the reference frame away from separate biological units like us, there are some advantages, because to my opinion we can potentially get rid of concepts like fine tuning, luckily coincidents, self organization, self regulation, order, etc.

    Unique stereochemistry has several advantages because it can push the interactions not towards the most stable molecules, destroying their potential to become life-forming molecules, but towards the formation of the most stable 3D structures.And then complex stereochemistry can interact with simple molecules and create even more complex stereochemistry

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    Quote Originally Posted by globali View Post
    Selfsim: Yes. I think that by moving the reference frame away from separate biological units like us, there are some advantages, because to my opinion we can potentially get rid of concepts like fine tuning, luckily coincidents, self organization, self regulation, order, etc.
    I think understand your opinion here .. but good luck ... the force runs very strong in 'the hunters' of exo-life.

    Quote Originally Posted by globali
    Unique stereochemistry has several advantages because it can push the interactions not towards the most stable molecules, destroying their potential to become life-forming molecules, but towards the formation of the most stable 3D structures.And then complex stereochemistry can interact with simple molecules and create even more complex stereochemistry
    Just to clarify and cut-to-the-chase, you are speaking specifically about stereoisomers here? Homochirality, yes?
    When homochirality emerged in biology is not known.
    Positioning it as a cause is thus an expression of a reasoned opinion (apparently also derived from earth-life's currently unique case). As such, I can't see how this is consistent with your 'theme' of changing the frame of reference away from earthly 'biologicial units' (as per your first statement above)?

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    With stereochemistry i am referring to all the ways the spatial conformation or the 3D structure of a molecule can affect its activity. For instance, the unique way a protein folds in space has alot to do with which molecules and how it will interact. Remember the key-keyhole model of enzymatic activity.

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