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Author Topic:   Abiogenesis
AZPaul3
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Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 10 of 305 (383013)
02-06-2007 4:54 PM


The Origin of Life
...would be a good start for an overview on the subject.

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 206 of 305 (396554)
04-20-2007 8:01 PM


Stirring the Soup
So after this restful respite we can stir the primordial soup once again.
Abiogenesis is most probably a purely chemical process. Although some metaphysical poofery cannot be said to be impossible (since we cannot prove a negative) there are approximately 0 data points in its favor. There are entire sets of disciplines from chemistry through Quantum physics with thousands of data points all pointing to a naturalistic, undirected, random-combination, chemical abiogenesis.
We do not know with precision how this would have happened. There are numerous hypotheses on probable vectors from RNA World, Metabolism-First, PNA/TNA/PAH, Cairns-Smith, in primordial soup pools, deep sea vents, shallow evaporating ponds, etc., all with their plusses and minuses. As is usual with these things one would not be surprised to learn that some combination of the above together with something as yet unknown were the real thing.
Some cite incredibly small probability within a linear mindset as opposition to a naturalistic abiogenesis. Given the known points of a pre-biotic atmosphere, the self-organization of aminos, organic compounds and fatty-acid limpid membranes, an abundance of water everywhere where literally billions of chance combinations occur each minute of every day for millions of years, it is indeed incredible to think that nothing would arise.
Keep in mind the only requirement of abiogenesis is a simple, short-chain chemical replicator. The process does not require, nor should it be expected to require, a complex chain, a complex mechanism or a complete code set, let alone the most disingenuous claim of opponents, a complete functional cell. Abiogenesis only requires a sustaining replicator of the most minimal function. Some contention in this thread that a completed set of digital genetic codes would be necessary for abiogenesis to occur, I think refers to the later stages of the process. Something we may not define as “living” but could sustain its replication over many thousands of generations could probably be achieved from a simple genetic code. Evolution would create the complexity of a more robust code over the millennia to come, resulting in the first pre-proto-cell and beyond.
There has also been expressed in this thread the thought that abiogenesis occurred once on this planet. By what reason do we assume the process occurred only once? On such a pristine planet with all the materials, all the time, why should we assume it happened once? Is it reasonable to speculate the process could have happened a few times, maybe a dozen, a hundred, a million? Could the first few hundred-thousand times some abiogenic process got started, it cycled out after a few minutes, hours, days, years? With our knowledge of the pre-biotic Earth and the mechanisms of chemistry involved we cannot reasonably limit the robustness of such a process, whatever it was, to just once.
By the same token, I submit, it is unreasonable to limit the process to just a pre-biotic Earth. This planet today is a more saturated bio-chemical soup than ever. The workings of chemistry have not changed. If an abiogenic event occurred 200k years ago or 50k years ago or last Thursday at 4:18am Phoenix time what is to be expected? Should we expect some one-eyed, half-green half-pink, sea monster to suddenly arise from the deep? No. An abiogenic process may, and probably has many times, reoccurred. But in a world already full of life, expecting such a process to cycle un-eaten through the millennia it takes to develop the most moderate complexity is not just unreasonable it is ludicrous.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 252 of 305 (397131)
04-24-2007 3:30 PM
Reply to: Message 249 by Fosdick
04-24-2007 1:41 PM


Re: And the principles are...?
Nothing, except they don't seem to be enough to make life from scratch like a pizza pie, which is what one might expect from the "principles of chemistry."
This may not be a reasonable expectation, Hooter. With all our advanced knowledge of medicine we have yet to conquer cancer and the common cold, yet we have a pretty good idea of the directions in which we should be looking for the answers. The same with abiogenesis. We haven’t the complete knowledge, yet, but everything we do have reasonably points to a chemical process and appears to point here to this planet as the source of our terrestrial life.
No, this does not mean that ALL life in the universe began here or only exists here. An abiogenic event on this planet does not preclude something similar happening elsewhere in the galaxy. And the chemistry of some other event may be totally different from what may have happened here (different genetic code set, structure, different aminos or nucleotides if these are even used at all, etc.)
You are, of course, correct in that at present we do not know enough about the how and where of abiogenesis to make any definitive statements, but the data points we do have seem to point to a purely chemical event of terrestrial origin. Until we see something that indicates otherwise, and points overwhelmingly away from this supposition, then this is where the evidence leads and we have not choice but to follow.
Panspermia is a reasonably plausible explanation for life on this planet, though it does force the question of how that seed developed to some other time and place. The evidence, however, incomplete as it presently is, does not lend this the greatest support. Our speculations must not just be reasonably plausible but also based on the directions the preponderance of the known evidence points. At his time that direction appears to be purely chemical and terrestrial.
you are the one who thinks genes are just collections of chemicals.
So what else would they be?
If you're thinking "digital code set" I have no objection. If you're thinking "essence of universal life force," well now we have a problem.

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 Message 249 by Fosdick, posted 04-24-2007 1:41 PM Fosdick has replied

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 262 of 305 (397155)
04-24-2007 6:39 PM
Reply to: Message 256 by Fosdick
04-24-2007 4:11 PM


Re: And the principles are...?
If it was only a chemical process, and if it happened here on earth, I would expect that we would know everything important about it by now.
And this expectation is based upon...what? Our incomplete but improving knowledge? Of all the trillions of combinations and permutations why do you think we should have hit on the formula by now? Why not by next Thursday or some Thursday 23 years from now?
If Earth is so damn bio-friendly then why can't I go into the woods, turn over a rock, and see abiogenesis making fresh copies of new chemical thingies right before my eyes?
I suggest that if you looked in the right place at the right time you probably could. The chemistry has not changed. Do you really think that if some short-chain chemical replicator came into being in your back yard this afternoon you would know it? Would you really expect it to survive for the following few months without being some bugs dinner?

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 Message 256 by Fosdick, posted 04-24-2007 4:11 PM Fosdick has replied

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 277 of 305 (397331)
04-25-2007 2:18 PM
Reply to: Message 270 by Fosdick
04-25-2007 11:02 AM


Re: Why?
Then, by your reasoning, abiogensis could never happen because life would simply eat itself to death. (After bug A eats bug B it starves to death, and the whole process has to start over.)
You’re almost right there, Hoot. After some millennia of replication and the development of a rudimentary genetic code by chemical trial and error some simple “bugs” would have been formed and would have eaten other replicators, scraps of partial replicators and other bugs just as they do today. It is a bug-eat-bug world out there. This is, after all, still a "Bacteria Planet."
I can't prove that it wasn't, but I can prove that life itself is more than just a collection of chemicals. (Clue: think genes”pure, digital information.)
So, Hoot, is it your contention that some simple rudimentary combination of molecules acting as a crude genetic code some 3.5 billion years ago could not have evolved into the elegant genes we know and love today? Would you share this proof you have that life is more than just a collection of chemicals?

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 Message 270 by Fosdick, posted 04-25-2007 11:02 AM Fosdick has replied

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 Message 284 by Fosdick, posted 04-25-2007 7:57 PM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 282 of 305 (397355)
04-25-2007 3:27 PM
Reply to: Message 279 by Woodsy
04-25-2007 2:32 PM


Re: Pure, Digital, Information
I wonder if Hoot Mon is trying to sneak souls in through the back door with this "more than chemistry" stuff.
He may be, but I don’t think so.
The Hooter will correct me if I am wrong here.
I get the impression that what Hoot is trying to convey is that our knowledge is so deficient to explain life (read: the complexity of a genetic code) yet our knowledge of chemistry is so vast that we must have missed something. I would not say he is looking toward some metaphysical poofery or “life force” or essence but more towards some grand universal organizing principle we just have not yet discovered, like some underlying imperative of an Information-based Universe. This is not to mean that there is some Intelligent Omniscient Being directing creation but more a meaning of a universe whose structure is not determined solely by some chart of particles and a few fundamental forces but rather by some basal information paradigm embedded in the fabric of the cosmos.
But, then again, I may be full of excremental dollops.
Edited by AZPaul3, : Oh, let's see...I added nothing actually. Subtracted nothing, either. Hopefully no one will notice any change so, on that hope, I'll not reveal my slight error and thus pretend there was none.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 283 of 305 (397365)
04-25-2007 4:41 PM
Reply to: Message 280 by Modulous
04-25-2007 2:58 PM


It's Alive! It's Alive! Or is it?
Most definitions of “Abiogenesis” evoke at least a primitive, cursory but functional cell in that it exhibits metabolism and replication. In this definition I agree that such a formation would be extremely rare on this planet today.
However, I do put forward the position that, shall we call them Replicator Events (?), still do happen on this planet; the serendipitous combination of chains of molecules that exhibit metabolism/replication where none was before.
I say this because this planet is a much richer “soup” than an abiotic planet with every nook and cranny now crammed full of the detritus of past life.
Take a drop of water from a pond, clear away all the plankton, flies toes, bug antenna, all that large stuff, and you will be left with small globs of cytoplasm, segments of cell membrane, scraps of nuclear membrane, husks of mitochondrial bodies, full proteins and chromosomes being rent by hydrostatic pressures flinging chains of aminos and fragments of helical nucleics everywhere. It is a bacterial smorgasbord to be sure. But, with all this biochemical stuff already half-formed and ready to go the probability of a replicator event is much greater now than on a pristine abiotic Earth. But, once spawned, having such a thing survive, progress and evolve in today’s world is dubious.

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 Message 280 by Modulous, posted 04-25-2007 2:58 PM Modulous has replied

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 294 of 305 (397529)
04-26-2007 11:27 AM
Reply to: Message 284 by Fosdick
04-25-2007 7:57 PM


Re: The chemical v. code test
Take two E. coli bacteria and put them in separate test tubes containing the same sterilized, healthy medium. Now, using your nanosurigical skills...
Been there. Thunk that. The first batch didn’t do so well, as you pointed out. It just sorta sat there and got dead. That second batch however grew into something hideous like something out of those Saturday afternoon matinees. The Thing That Eat Phoenix. I guess I didn’t get all the parts back in the right places. I had to nuke it before it spread.
The molecules in question are just chemicals. There is no denying that. The order of the molecules on the chain is important, obviously. No denying the order constitutes a code, and an elegant one at that, without which life sorta sits there and gets dead.
The development of this code is the interesting part. Molecular combinations in random trial and error over a few hundred million years or something more directed? Any speculations on this you can share with us?

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 Message 284 by Fosdick, posted 04-25-2007 7:57 PM Fosdick has replied

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 Message 299 by Fosdick, posted 04-26-2007 1:32 PM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 300 of 305 (397543)
04-26-2007 1:44 PM
Reply to: Message 299 by Fosdick
04-26-2007 1:32 PM


Re: The chemical v. code test
Wish I had a good one. Since I don't believe Goddidit, what are my options? Vitalism? Parallel universes? What ever it is that we don't yet know is HUGE.
Do you reject molecular combinations in random trial and error over a few hundred million years?

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 Message 299 by Fosdick, posted 04-26-2007 1:32 PM Fosdick has replied

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 Message 302 by Fosdick, posted 04-26-2007 3:01 PM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.2


Message 304 of 305 (397564)
04-26-2007 3:33 PM
Reply to: Message 302 by Fosdick
04-26-2007 3:01 PM


Big Number Abiogenesis?
I believe its was Hoyle and Wickramasinghe who calculated the probability of the first protein molecule to be on the order 1 in 10^120.
I don’t know about those two and I’m being lazy in not looking them up, but, seems to me the first question is “What first protein?” Proteins are chains of amino acids. Reasonable speculations indicate a whole slog of aminos in a pre-biotic Earth environment. Doesn’t seem to me to be so far fetched that two such thingies glom on to each other and viola . first protein. Probably doesn’t do much except float around looking for more candidates to join with.
10 to some big number seems a bit linear in thinking, doesn’t it? If we’re talking some large mega-protein like hemoglobin then I can understand the incredulity of its spontaneous generation, but, I hope this is not what is being offered here.
Cannot a simple chain of, say 5 aminos, or maybe even 50 aminos, not be considered a protein? The incredulity certainly lessens at this level. And if we take the reasonable assumption of many millions of trials daily over many millions of years, does this not lessen it even more?

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 Message 302 by Fosdick, posted 04-26-2007 3:01 PM Fosdick has not replied

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