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

[Karlos]

For fluffy :-)

Rather than continue hijacking the_leander's threads, I figured it would be rather better to create one...

So, going back to this one, lets take a stock check. Existing evolutionary models explain the diversification and origin of new species of entire organisms relatively well. I have no issue with this at all.

For me, as we have discussed, the problem is the biochemical level. Prebiotic chemistry is a fascinating area that I studied intensely for a while. Foregoing for a moment the argument about how it all started, let's think about it for a moment.

It seems to me that there has been no significant (bio)chemical evolution for a very, very long time. What do I mean by this? Well, there may be small improvements in cell chemistry here and there, but by and large your human internal cellular machinary is not far in advance of any other eukaryotic organism - just look at yeast and you will find the same chemistry going on. Eukaryotes are themselves a step up from prokaryotes that have new biochemical pathways added on top of the prokaryotic set but do not significantly change those they inherited.

If you look at the most primitive forms of viral life you can find (and arguably they are not even really living), you  find that they still use the same chemistry. They still use at least RNA to store their compositional make up and they use protein casings etc.

It seems therefore, that the biochemical complexity known today is largely unchanged in every organism known. Were still using the same nucleic acids, proteins, electron transport chains, photosynthetic systems since pa(ramecium) fell of the bus (to paraphrase X-Ray). Of course there are better examples of some metabolic systems, but fundamentally the chemistry has not changed.

This is one reason I don't think that existing evolutionary theory (as it applies to biology) applies to the chemistry that enables the biology to exist.

If we consider that biological evolution is taking place all around us, why do we not observe the same in chemistry? Once you have a self replicating, sustainable chemical system there is no reason to assume it would be completely replaced by a more efficient one, just as bacteria still exist in profusion, despite being biologically usurped by more sophisticated organisms competing for the same resources.

If the existing evolutionary models apply to chemistry, why are there no pre - nucleic acid / protein chemstry based organisms known? Just because the latter may be more efficient, the former system(s) capable of self replication should still exist. Yet none do.

So, the biochemistry we know - that is nucleic acid / protiens / sugars / redox / electron transport / photosynthesis - has been around relatively unchanged since life began, despite the vast changes in the biology it has enabled. In fact, the only variations we see are in how that chemisrty sources the energy it needs in order to drive itself (be it photosynthesis, iron-sulfur, carboyhdrate oxidation etc).

There is no evidence that the chemistry itself was ever any less sophisticated; there are no rival self-replicating chemistries known, no evidence any have ever existed and no evidence that the existing biochemistry has changed significantly or is changing. In short there is no tangible  evidence of "chemical evolution".

So the questions remain. Where did the present chemistry come from and how did it establish itself so quickly given that it appears to have moved so little since? After all, it is generally believed the first single celled organisms powered by this chemistry were happily replicating wihin 200 million years of conditions being favourable.

There are many other reasons why I don't believe the existing evolutionary paragdims (as applied to biology) apply to the underlying chemistry, the above are just a few.

In my opinion, there is so much more to discover - sticking to creationalism or darwinism are not going to get us far.


If the_leander is reading this, feel free to hijack - it is only fair :-D

[Karlos]

I know what you are saying, but I think you are missing my point. There is no available evidence to support the notion that the fundamental biochemistry we know of is evolved from anything less primitive - no matter how far back you go, find the same chemistry. There are no cousins, no other evolutionary offshoots, rivals or specialisations that you might expect to find given the way biological evolution appears to have worked.

[Karlos]

KennyR wrote:

RMKQLEEKVYELLSKVACLEYEVARLKKLVGE

What does that come out to as a triple word score in scrabble?

Seriously, Kenny is right - prebiotic earth, with its reducing atmosphere, abundence of base materials and energy etc. possibly did favour spontanous peptide formation - soemthing which today only works thanks to the biochemical machinery that performs it - but would still be extremely lucky to even get as far as Lees peptide within the lifespan of the planet today, let alone 3.5 billion years ago. You still have to arrive at RNA as a better source of self replication and cataltytic activity (there are known RNA strands that perform various self-splicing and self-assembly within biochemistry), let alone moving towards the dual protein / nucleic acid system we have today. Yet all this must have been in place within about 200 million years of the raw chemical precursors needed for their assembly.

[Karlos]

bloodline wrote:

By the way, you must be forgetting your crystal chemistry (or maybe you have sucessfully purged from your mind as I spend every waking hour trying to)... but Crystals are a classic example of a self replicating system and totally inorganic too!

No, I didnt forget at all. But I don't regard crystal self assembly as comparable to biochemical where different systems are involved in a complex symbiotic process - eg proteins replicate DNA and transcribe it, but the DNA stores the information required to assemble the proteins.

Symmetry (dictated by ionic/covalent concerns) and close packing hardly compare to the above.

[Karlos]

bloodline wrote:

I also don't see why life didn't "hitch a ride" on a Crystaline scafholding before the complex RNA/DNA structures developed.

For one, there are no vestigial remmenants of this. Whilst it is true that many complex clays can interact with biological systems and in some cases are used, it seems to be the case that biology has found a use for the clays *since* reaching it's present level of complexity and not during its origin.

[Karlos]

@Blob & bloodline

None of these arguments explain how the existing biochemistry came to be and especially in the timescale. This is the thing I don't think people realise. You to have evolved the near-present level of biochemical level of sophistication required to support the most primitive iron-sulphur bacteria *within* 200 million years of the conditions being suitable enough to allow the chemical agents required to exist. This implies that whatever "chemical evolution" occured in pre-biotic times must have been super accelerated, even if you allow for clays etc playing an active role in the initial stages of self replication.

If we simulate as best we can the environment the evidence suggests prevailed at this time we can observe the formation of guanine like heterocycles, primitive amino acids (and even oligiopeptides) and various other life related chemicals. Which is great, but these are the most elemental building blocks. We do not observe anything like Lee's peptide for example. Even if we did, the step up from that to RNA is as great as the formation of Lees in the first place, not to mention any symbiosis between the two.

If you perform any meaningful calculation on the likleyhood of these events, even making generous concessions to the probability of intermediate stages encompassing the change of function you end up with rediculous odds.

Kenny may well be right that the universe tilts odds into the favour of life via some as of yet unknown means because left to chance alone it is as good as impossible.

[Karlos]

FluffyMcDeath wrote:

Like I keep saying, just because we cannot apply darwinism to prebiotic chemistry does not mean that we have to throw it out all together.

And nowhere do I say we should. It's a matter of appropriate method. One does not use quantum mechanics to help explain everyday physics. We know that classical physics is essentially an approximation for h=0 and that works fine for us. Likewise we don't use classical physics to explain the microscopic world since it falls on its bum.

It's just that people do apply the existing evolution model to the problem at hand, glossing over the inadequacies and questioning the motive of anybody who disagrees, which is as dogmatic as any old school 'creationalist' and I believe is putting off people from seriously looking into it.

This is the creationists arguement, and you are not one, and therefore you should not be making an arguement which can so easily be mistaken by creationists as support for their position and then used by them, however erronously, to tear down your own position.

I'm just calling it as I see it. I do try to keep an open mind; I mean, if it were proven beyond reasonable doubt that there is some ID going on I like to think I'd be able to accept it.

They ask them with a specific agenda and that is to open the door to the "Creator" and make "Him" necessary. You can think of better questions yourself.

Well, that's just it. The people questioning it originally didn't have any such agenda. It has been taken up by those that do since, but it is now the case you cannot raise the qestion without being so accused.

Of course the other thing is, even if the questions are asked with an agenda behind them it doesn't make the (properly considered) answers any less important. After all there is no guarentee which 'side' the answer will support anyway.

[Karlos]

FluffyMcDeath wrote:

Karlos wrote:

It's just that people do apply the existing evolution model to the problem at hand, glossing over the inadequacies and questioning the motive of anybody who disagrees[...]

But what model is that? Evolution happened, evolution is happening, it can be seen to be happening, so anyone who says they have some information that brings evolution into doubt should be viewed with as much suspicion as the guy who finds a helium baloon and says it disproves gravity.

Yes, biological evolution that is, and I agree. However, as you said yourself earlier, it has no applicability to non-living systems.

As for the gullability remark, I hope that wasn't directed at me :-)

[Karlos]

@Bjjones

It is really a conundrum as far as I am concerned. The speed with which life "as we know it" took hold is staggering when one views it from the prebiotic position.

I wouldn't hope for an answer to the problem any time soon, however. Presently were are on the uphill curve - the more we find out about it, the more questions we end up with.

Still, I sure as anything hope I live to see the answer - it's driven me nuts for the best part of 11 years :-)

[Karlos]

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

[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 :-)

[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 ;-)

[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...

[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.