Time factor in self assembly calculations?

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Originally posted by Tranquility Base:
. . . somewhere but not God - right? At least not a God who is at least as conscious as us? Why not?

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Somewhere verifiable....------------------
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All you do is simplification of the problem.
Since all natural (but glycine) aminoacids have an chiral C atom, they have two distinct L-or R-configurations ("mirror images" or "enantiomers"). Thus, any oligo-peptide of 10 aminoacids and composed of only one type of aminoacids (e.g. all alanine) will be spontaneously formed under abiotic conditions in 2(exp)10 different configurations. In life we only see the L-configuration of aminoacids (and we only find the R-configuration of the ribose and deoxyribose --that have 2 and 3 distinct chiral C-atoms and thus 4 and 8 enantiomers are possible-- in RNA and DNA, respectively). I've never seen a plausible solution to this problem. It's rather ignored.
Peter[This message has been edited by peter borger, 08-07-2002]

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Originally posted by blitz77:
Time since surface water became available and the first supposed bacteria. Unless you are supposing it didn't happen in water?

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Aren't you taking the latest possible date for the appearance of surface water and the earliest date for the arrival of bacteria? Nature - Not FoundEven if the organisms questioned in the cited article turn out to be organism, at worst there is a few hundred million years not 100 million.Haven't we been over this before?Secondly, some of the molecules involved need not have been formed on Earth at all-- certain amino acids for ex.Thirdly, your probability calculations assume complete randomness and chemistry isn't completely random. It follows rules.Fourthly, are you calculating the chance of that one series of reactions will produce a protein (I believe you were talking about proteins) or do you realize that there would have been hundreds of millions or billion of simultaneous reactions going on?Gene posted some applicable links : EvC Forum: Evolution vs. Thermodynamics------------------
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My main point was not about the meaningfulness of the earlier calculations- I was trying to highlight how sensitive the outcome is to the inital level of complexity considered. Start using large exponents and pretty much anything is possible.I think the real problem with the meaningfulness of these calculations is that they assume there was a single unlikely event which gave rise to a single self replicating molecule which was similar to a modern day biopolymer. The approach is only slightly better than trying to imagine how a whole cell or eyeball could have spontaneously formed. I think the real lesson from these exercises is that our imaginations are simply not up to the task of intuitively finding the path from nonliving to (modern) living matter.We have to "think outside the cells we live in" The selective use of L-amino acids in proteins and R-sugars in polynucleotides is probably already the result of selection which occurred an unimaginably long time ago. Is a more fundamental issue not the estimation of how probable spontaneous formation was but its impossibility? Does it only have to be possible in order to be a viable alternative?I just thought of an interesting question regarding quantum physics ie:1.If the observation influences the result,2. If a process which results in many quantum states creates observers as part of one of those states, does the act of observation cause the states to collapse into the one containing the observer?Sorry to pick a new tangent- the original thread was getting a bit thread bare. Does this count as "sleight of hand" on the part of an evolutionist? ;PShane

dear Shane,You state:
"I think the real problem with the meaningfulness of these calculations is that they assume there was a single unlikely event which gave rise to a single self replicating molecule which was similar to a modern day biopolymer. The approach is only slightly better than trying to imagine how a whole cell or eyeball could have spontaneously formed. I think the real lesson from these exercises is that our imaginations are simply not up to the task of intuitively finding the path from nonliving to (modern) living matter."But a freak event is still an event and the likelyhood of events occurring --unlikely or likely-- can be calculated. Ignoring that is ignoring that the accidental origin of life is an event. The same fallacious reasoning can be found in Dawkins' "The Blind Watchmaker". I don't buy it.And:
"We have to "think outside the cells we live in""Who are you? Richard Dawkins?And:
"The selective use of L-amino acids in proteins and R-sugars in polynucleotides is probably already the result of selection which occurred an unimaginably long time ago"Problem is the evolutionary rules of selection do not work at this level.Finally, you say:
"I just thought of an interesting question regarding quantum physics ie:1.If the observation influences the result,2. If a process which results in many quantum states creates observers as part of one of those states, does the act of observation cause the states to collapse into the one containing the observer?Sorry to pick a new tangent- the original thread was getting a bit thread bare. Does this count as "sleight of hand" on the part of an evolutionist?"....Ye, why not discuss Schrodinger's cat, (or was it Heisenberg's dog)?.Best wishes,
Peter

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Thirdly, your probability calculations assume complete randomness and chemistry isn't completely random. It follows rules.

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So what rules are you talking about-thermodynamics, increase in entropy, etc?

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Fourthly, are you calculating the chance of that one series of reactions will produce a protein (I believe you were talking about proteins) or do you realize that there would have been hundreds of millions or billion of simultaneous reactions going on?

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I did cover that-look at my numbers-I assumed that 10^93 different reactions were going on at the same time every second, each one producing an protein of 100 amino acids even without counting how many 100 amino acids could be produced at the same time (divide the 10^81 by
the number of atoms in a 100 amino acid chain.)

More fuel to the fire, though more concerned with energetics than statistics, and more to demonstrate how many fundamental pieces of the puzzle are still missing than to support peptides being the first form of "life":Free energies and equilibria of peptide bond hydrolysis and formation. Martin RB BIOPOLYMERS 45 (5): 351-353 APR 15 1998Abstract:
For every n amino acids linked in a protein there are n - 1 peptide bonds. The free energy of peptide bond hydrolysis and formation in aqueous solution defines the equilibrium position between peptide and amino acid hydrolysis products. Yet few experimental values exist. With a minimum of assumptions, this paper deduces the free energies of hydrolysis of a variety of peptide bonds. Formation of a dipeptide from two amino acids is about eight times more difficult than subsequent condensations of an amino acid to a dipeptide or longer chain. Condensation of an amino acid to a peptide of any size is five times more difficult than joining two smaller peptides of at least dipeptide size. Thus in an abiogenesis scenario there is a kind of
nucleation in peptide bond formation with the initial condensation of two amino acids to yield a dipeptide more difficult than subsequent condensations
to a growing chain.You replied:
"But a freak event is still an event and the likelyhood of events occurring --unlikely or likely-- can be calculated. Ignoring that is ignoring that the accidental origin of life is an event. The same fallacious reasoning can be found in Dawkins' "The Blind Watchmaker". I don't buy it."A probability will always be a very poor substitute for a detailed and at least partially demonstrable mechanism given the enormous assumptions they require to get off the ground. And even if we could precisely calculate the probability of life forming spontaneously on earth that wouldn't necessarily tell us if it did or didnt happen by the mechanism proposed. Anything you can calculate a probability of is possible, and anything that is possible could have happened. I am not using this as a way of arguing for abiogenesis- simply to highlight the limitations of probabilistic approaches. Life on earth could be an unimaginable fluke. Until we can look further afield we wont know if life is a common property of the universe. Until we understand fundamental behaviour of biomolecules we wont know what are reasonable assumptions (see paper above).And I am not Richard Dawkins but was complemented by the suggestion >>"The selective use of L-amino acids in proteins and R-sugars in
>>polynucleotides is probably already the result of selection which
>>occurred an unimaginably long time ago">Problem is the evolutionary rules of selection do not work at this
>level.I think this is an unreasonable assumption. It is quite reasonable to suggest a scenario where "organisms" using either or both arbitrary sets of chiral monomers (or currently unknown biomolecules) competed against each other. The example I posted on self replicating polypeptides could experience evolution if different starting materials were present allowing different product peptides with different selectivity and efficiency to be formed. The short answer is that no one has looked at these basic behaviours yet."....Ye, why not discuss Schrodinger's cat, (or was it Heisenberg's dog)?."Hmmm- I always suspected that uncertainty, and not curiosity, killed the cat....Shane

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Originally posted by blitz77:

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Thirdly, your probability calculations assume complete randomness and chemistry isn't completely random. It follows rules.

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So what rules are you talking about-thermodynamics, increase in entropy, etc?

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No, nothing that complicated. Chemicals react in different ways to different chemicals under different circumstances. It isn't a directed process but it isn't random either. It seems like this need to be taken into account. Forgive me if I miss some points you are trying to make. Admittedly, my chemistry could be better.[/b][/quote]I did cover that-look at my numbers-I assumed that 10^93 different reactions were going on at the same time every second, each one producing an protein of 100 amino acids even without counting how many 100 amino acids could be produced at the same time (divide the 10^81 by
the number of atoms in a 100 amino acid chain.)[/B][/QUOTE]Ok. Gotcha.------------------
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[QUOTE][B]I've never seen a plausible solution to this problem. It's rather ignored.[/QUOTE][/B]The amino acids found in meteorites are primarily left handed, due to selective destruction involving light. This is applicable because (1) the same thing could have been happening in the environment in which abiogenesis occured (2) the primary source of AA's in early Earth might have been from meteorites.[This message has been edited by gene90, 08-09-2002]

Oh... and does this mean that you are accepting points one and two as valid criticisms?------------------
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Dear Gene,You say:
"The amino acids found in meteorites are almost exclusively left handed, due to selective destruction involving light. This is applicable because (1) the same thing could have been happening in the environment in which abiogenesis occured (2) the primary source of AA's in early Earth might have been from meteorites."I say:
Show me the references and I will respond to that. I've heard these stories before and all they show is a 4:6 ratio R:L.
Ad 1) Acoording to recent insights the primordial atmosphere contained oxygen and thus ozone. This protects the putative biolocules from degradation through (UV-)radiation.
Furthermore, show me an experiment where is demonstrated that radiation (no matter what kind) specifically degraded/converts a racemic mixture of R and L molecules.
Ad 2) If 1) is true, how many meteorites would it take to build one simple organism (by chance?)?cheers
Peter[This message has been edited by peter borger, 08-08-2002]

[QUOTE][B]Furthermore, show me an experiment where is demonstrated that radiation (no matter what kind) specifically degraded/converts a racemic mixture of R and L molecules.[/QUOTE][/B]Right-handed polarized light preferentially degrades R AAs. I'm embarrassed to use a source as popular as ABCNews to answer your question, but you did ask.http://abcnews.go.com/...ce/DailyNews/lifeorigins980730.html [QUOTE][B] is true, how many meteorites would it take to build one simple organism (by chance?)?[/QUOTE][/B]Useless question. For one, meteorites vary by mass. For another, dust infall is also a factor. Finally, we don't know how many AA's are needed. All of the Creationist arguments here are invalid because they attempt to generate one protein, and reject all others.[This message has been edited by gene90, 08-09-2002]

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Originally posted by gene90:
For another, dust infall is also a factor. Finally, we don't know how many AA's are needed.

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Isn't dust infall somewhere in the range of 200 tons per year currently?------------------
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dear Gene,Apparently, you didn't read these articles. The authors conclude:"How did amino acids form? Why are they all left-handed? Although the two Science papers offer some tantalizing clues, evolutionary biologists still have two unanswered questions."Why is nobody reading the stuff they discuss?Peter

[QUOTE][B]"How did amino acids form? Why are they all left-handed? Although the two Science papers offer some tantalizing clues, evolutionary biologists still have two unanswered questions."[/QUOTE][/B]Clearly there is something here you do not understand. Science is tentative. This proposed mechanism is only one possible explanation*. That is what your quote means.* For another one, see "Magnetic Field Skews Molecular Handedness" by Charles Seife in Science Now, 6/21/2000By the way, I stand corrected, the L excess is between a lousy 2 to 9%.I also read a comment where a researcher stated that he thought the starlight mechanism was "too exotic" for his taste.I had to find both of these out on my own when it was your job to throw them at me.I hope this doesn't get too personal but you had a chance to show me up and you didn't even exert an effort. There's no fun in that kind of "debate". I thought you would check a journal or some science articles rather than getting a meaningless quote from my own "cite" but...that is too often what happens.[This message has been edited by gene90, 08-09-2002]