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

[Karlos]

Quite; it's just that I am not entirely patient :-D

[blobrana]

Heres a link to evolutionary landscapePDF:

Or here

That may be key to asking the correct questions.

[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.

[bjjones37]

If I may take an opposing viewpoint, just for the sake of discussion and understanding. Consider the effect of entropy on a chemical reaction.  It is obvious that there is an inverse relationship between energy and entropy.  But this relationship has causal implications.  Within a closed system, the kinetic energy of the present substances affects more than simply the rate of reaction.  It is a known phenomenon that when two substances react, there are more than one or two products to the reaction. Take for instance H2 and O2.  2H2 + O2 yield 2H2O in theory.  In actuality, there will be H2O, H2O2, H2, O2, and possibly a variety of other by products to include O- and H+.  This is a result of the causal effect of the kinetic energy inducing the higher entropic state.  So one of the consequences of this increased state of disorder, at least from the standpoint of Chemistry, is actually the production of some more complex compounds. Granted these are produced in very minute quantities.  But they are produced nontheless.  

It has been some 20 years since I took chemistry so if there is some flaw in my reasoning, please point it out.

[KennyR]

Cymric wrote:
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.

It's more than that. It's structures in the quantum world that actually define chemistry. They ARE chemistry! Matter and its chemical interactions are just an expression of this quantum world. Change any tiny part of the underlying structure and perhaps neutrons wouldn't be stable, or electrons would have 100000 times the mass.

Just as quantum physics "just happened" to be perfect for physics, which allowed chemistry, which allowed biology. The formation of life, through whatever means, was as predetermined as the formation of quarks, protons, and atoms.

And every chemical reaction too, involves quantum physics directly. When molecules react, they don't do it like lego or clockwork. At the instant of a reaction, they exist in a quantum superstate, where simultaneously all of the possible products of the reaction exist, until something causes the quantum state to break down. Usually the most probable product of the reaction finishes up.

Chemists should already be familiar with quantum superstates via the benzene molecule. I was taught in high school that benzene constantly swaps its pi and sigma bonds. However it was also known for years that this does not fit what we observe of its properties. Chemists found out later that  all the possible configurations of the kekule ring structure exist at once. It's the same properties of conjugated bonds that allow some polymers to conduct electricty. Neither of these phenomena are chemical, both are quantum.

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.

[bjjones37]

KennyR wrote:

Chemists should already be familiar with quantum superstates via the benzene molecule. I was taught in high school that benzene constantly swaps its pi and sigma bonds. However it was also known for years that this does not fit what we observe of its properties. Chemists found out later that  all the possible configurations of the kekule ring structure exist at once. It's the same properties of conjugated bonds that allow some polymers to conduct electricty. Neither of these phenomena are chemical, both are quantum.

Oh how I regret missing out on quantum chemistry. This opens up a whole new line of thought.

 We just have to find out how it did it, and what "its method" was.

So very true.

[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..

[Karlos]

Cymric wrote:

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.

Ah, that's what's been causing my recent coding gripes :-D Must remember to sleep.

It's a fascinating problem. When I discovered prebiotic chemistry was available in as an option in my master's year I jumped on it. I generally like to keep abreast of developments in the field, despite giving up on chemistry as a career option. Life is just so fascinating at the microscopic level -  it irks me slightly to think I probably won't live to see it completely unravelled although I don't rule out the possibility.

[Karlos]

bjjones37 wrote:

Oh how I regret missing out on quantum chemistry. This opens up a whole new line of thought.

Yep, quantum mechanics has revolutionised understanding in may areas of chemistry from spectroscopy (probably the first area affected) right through to reaction and structure prediction. Really liked quantum mechanics. So simple in basic concept and yet so complex at the same time.

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 :-)

[the_leander]

fascinating stuff, I like the way Darwins theory is more firmly boardered to things once they get going, how it is described as a framework for understanding rather then the end in itself (after reading Darwin's work, it was blatantly obvious to me - a layman that he simply didn't have a clue wtf was going on with regards the mechanics of it.. iirc he suggested that blood of all things could be the stuff responsible, which to me was just ironic, since I believe that the red blood cell is the only cell in the body that doesn't come with its own dna).

I understand it in as much as the principles go, but my lack of higher education shows up blatantly when trying to dig into the detail of it all. I just wish that I could explain it in a way that even hardend fundies like my folks in law that even they couldn't dismiss it.
 
offtopic, the folks in law have recently gotten back from a trip that lasted a week, so its been bliss... I just wonder when this topic will rear its ugily head again.

@fluffy and Karlos:

Don't worry about the thread, it was good to include what you did because it put context to what caused the necessity for the thread.

I just wish that I had the education you guys did. I guess I will always be more of a mechanically minded person then one for theory :-)

[Karlos]

@KennyR

And every chemical reaction too, involves quantum physics directly. When molecules react, they don't do it like lego or clockwork. At the instant of a reaction, they exist in a quantum superstate, where simultaneously all of the possible products of the reaction exist, until something causes the quantum state to break down. Usually the most probable product of the reaction finishes up.

True. And that product is statistically most likely to be a virtually intractable oily brown crap that requires about 3 purification stages when it comes to any non-trivial organic synthesis, if my experience is anything to go by ;-)

[bloodline]

@karlos


Hahahaha! yeah, organic chemistry was never my fortè either :-D

[Karlos]

bloodline wrote:
@karlos


Hahahaha! yeah, organic chemistry was never my fortè either :-D

Yes, but it was mine :lol: The stuff I was doing at the time however, was entirely novel and was based on my bosses earlier research into (chirally) directed metallation by rotationally restricted amides. Great stuff, except removing the amide (in it's entirety) is next to bloody impossible without destroying whatever else you have in your substrate.

My task was to investigate using removable sulfone / sulfonamide derived systems instead of the above amides, since cleaving these off later is not particulalry difficult.

The first step was to prepare them and investigate their low temperature properties (to see if the sulfur based replacement for the amide sterically locks out and stops rotating). This alone took a few months :-/

Due to the size differences and bond angle issues, getting such a rotationally inhibited sulfonamide was not entirely straightforward. Having to wait weeks at a time for a set of low temperature NMR (getting the spectra for the same sample from say -80C to room temp in 5C increments) didn't exactly help.

Unfortunately, just as I was starting to get somewhere, those neer-do-well Japanese industrial chemists jumped in and published work they'd been secretivley working on, rendering all my work useless. Absolutely nobody awards a PhD for second place.

By then I was pretty disillusioned to say the least...

[blobrana]

Impressive,
Second place is still worth writing about though...(in CV)


Anyway, i noticed this:
"Two years ago, another team showed that polio viruses could assemble themselves from off-the-shelf chemical components mixed in a test-tube.

And several chemists are exploring the kinds of chemical reactions that may have preceded life."

from here...

[Karlos]

@blob

The theory was very impressive as was the existing work. I did enjoy it at the outset. A year of no results and then getting scooped just as I started to get some was a factor in my deciding to leave the subject (although not the only/biggest one).

About the prebiotics again:

The off the shelf components in question were themselves the product of biochemical synthesis (although some may be artificial of course). Even if they were not and were all present in abundence on prebiotic earth, getting your original polio virus structure in the first instance would be rather more miss than hit. It's an order of magnitude more complex than Lee's peptide. The test tube conditions themselves are likely not quite the conditions on prebiotic earth.

Still, self assembly is one of the critical factors in living systems so they are definately looking in the right place.

[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!