Prebiotic chemistry and origins of life (continued)...

[Cymric]

KennyR wrote:
The amino acid code for the simplest self-replicating molecule than can be thought up is Lee's peptide:

RMKQLEEKVYELLSKVACLEYEVARLKKLVGE

Where each letter corresponds to an amino acid. This is the best that theorists can come up with, and it's pretty simple. It is probably impossible to find simpler self-replicating molecules.

So supposing you had a system that allowed peptides to form and join up, which no naturally existing non-bioligical system today allows (because water and oxygen in excess don't favour peptide bonding - ask Karlos).

There are about 2000000000000000000000000000000000 different ways of forming a polypeptide that are exactly 32 long like the one above. Only one way will make that self-replicator.

Even if the earth was 20 times the size and covered by one huge "warm pond", this would not happen by chance. Clearly, pre-biotic chemistry has a long way to go.

The answer of course is probably that it's not by chance, and that some symmetry inhereted from the quantum fluff that makes up the foundation of the universe favours life. In fact, there's no doubting it: it does, or we wouldn't exist.

This in itself does not disprove the engineering of a higher power. Some would even say it proved it.

It took me a while to come up with a meaningful reply to this argument. The underlying assumption is that self-replicating molecules started out as single entities, which consisted of aminoacids which had to stuck together 'just so'. Which of course leads to very worn reasoning that it couldn't have arisen by chance. You demonstrated that easily enough.  

However, I draw the line at 'something inherited from the quantum fluff that makes up the foundation of the universe' for an explanation. We are dealing with chemistry, not with the space-time continuum (or if you prefer, quantum foam.) Okay, if you insist, then I admit that chemistry is an exceedingly low-energy manifestation of it. However, I simply refuse to introduce high-energy physics into the equation on the grounds that the energy available on the ancient Earth was simply not sufficient. (The temperature was below the melting point of rock; radiation levels were a lot higher, but still not high enough. Gravitation was probably equal.) There is not a single shred of evidence to indicate that under these circumstances the Schrödinger equation must be amended with G, as you do (in very complex ways) in quantumgravity theory.

Which leaves us with the question what happened then. We don't know yet. One also has to take into account that by current standards, the ancient Earth was a decidedly hostile place: hot, radioactive, bombarded with radiation from an emerging sun, and a reducing, poisonous atmosphere. I get the impression that non-equilibrium chemistry with autocatalytical limit-cycles is very popular these days. Clays laden with metal ions (which are famous for their catalytical properties) are likely to have played a role.

And then I will admit that there might be some truth in Karlos' original statement that clinging to the biological concept of Darwinian evolution might not yield an answer, although---supposing for a moment that life did arise from a limit-cycle---it raises interesting questions on what life and evolution are, exactly. Yet I don't think people in this scientific field are studying it in terms of evolution: they are studying it from a chemical viewpoint. (At least, I would.)

However, just as I draw the line at inheritance from quantum fluff as an explanation, I draw the line at anything hinting at intelligent design too. I've argued before that I consider that to be intellectual capitulation. We've only just begun to develop the tools needed to tackle this very complex problem, I say, give it another century or so. Or two.

[Cymric]

KennyR wrote:
In the same way, it's possible that all 2000000000000000000000000000000000 polypeptides existed at once, and some underlying symmetry made it more likely for our self-replicator to form. Well, it's not so far-fetched; it was the same kind of "bias" in the quantum world that allowed matter to gain the upper hand over antimatter.

What predetermined life? We could go for the anthropomorphic theory and decide that this was by total chance that, among an infinite number of infinitely varying universes, ours was special and allowed the creation of self-replicator - simply because if it hadn't, we wouldn't be here to see it. Or we could go running to God. Either way is just as useless at the moment, but there is no doubting that our universe was destined to develop life the moment it was created. We just have to find out how it did it, and what "its method" was. Why is better left to philosophy.

It's now way past my bedtime, so my thought processes are beginning to falter and wander off in random directions. If I suddenly write nonsense, you know what's causing it.

After a good deal of thinking and searching and remembering the weird chiral preference of the living nature, hypothesised to be caused by the chiral preference of the weak nuclear force, I am grudgingly forced to admit there is more to quantum chemistry than just electrons and quantum alone. And once you get to the weak nuclear force, you're touching upon hypothesised CP-violation (or CPT conservation, whatever you prefer), and you end up with very, very fundamental physics in something which is quite, for lack of a better word, normal. (With that I mean that students of today are not really surprised any longer about the quantum mechanical description of many chemical processes.)

However, the influence is seriously small, and I am quite hard-pressed to admit its influence on the scale you seem to be proposing. Chalk that up to my engineering, rather than scientific, background. I can dig chiral preference, I can dig the benzene molecule, I can dig the transition state of a molecule undergoing a reaction. I cannot dig without extremely good reason (read: Nobel prize-winning experimental evidence, which is what it would be anyway) transition states specifically favouring what we would now call replicating molecules. I just cannot see (which is definitely a non-authoratitive opinion, given my knowledge of the subject) what sort of fundamental physics would favour self-replication. Nature favouring matter over anti-matter is 'understandable' by comparison. In other words, you seem to be mixing various instantiations of the quantum thingie, and I'm not sure whether that is correct or even allowed.

In addition, I'm not sure you can say that this particular universe was 'destined' to produce life thanks to its particular setting of basic parameters. More correct would be to say 'life as we know it', and even more correct that this universe simply did. To be destined for something implies a broader knowledge of alternatives, and we don't know of any. We don't---heck, we wouldn't even---know if you can have a universe with a chemistry as ours, but no life from its 'beginning' to its 'end', whatever those may be. That implies knowledge of the solution to the problem we are trying to solve: how did inanimate matter become alive?

Me go sleep now. Brain shutdown imminentz.. zzz..

[Cymric]

Karlos wrote:
I have to confess that I was unable to keep a straight face in  one lecture (in a series on frontier orbital theory, a QM application used in explaining reaction pathways) when the completely sombre lecturer announced: "And here we see the end result of the backside attack of the HOMO on the LUMO".

It was very childish of me, I know :-)

You missed out on the wonderful world of chemical engineering then, where we had to learn about the backside attack of the HOMO and the outcome of the penetration theory.

Of heat, inertia and matter, you sickos. It's respectable science, not some g33k l33t pr0n course!