Abiogenesis

[CraigS]

I am starting this thread as a follow-on from the latter discussion stages of the ‘Not sure what I saw’ thread.

One of the factors influencing the ‘chances of exo-life in the universe discussion', which is of primary importance, is how life can start from pre-biotic chemicals. There is no firm answer to this, (& there probably never will be unless of course, neutrinos actually do violate causality and we can go back in time to find out .. ), but theory might give us a glimpse into it all.

So here goes … what is 'Abiogenesis' ? ...

Wiki defines Abiogenesis as ...

In natural science, abiogenesis or biopoesis is the study of how biological life arises from inorganic matter through natural processes, and the method by which life on Earth arose.

Most amino acids, often called "the building blocks of life", can form via natural chemical reactions unrelated to life, as demonstrated in the Miller–Urey experiment and similar experiments that involved simulating some of the hypothetical conditions of the early Earth in a laboratory.

In all living things, these amino acids are organized into proteins, and the construction of these proteins is mediated by nucleic acids, that are themselves synthesized through biochemical pathways catalysed by proteins. Which of these organic molecules first arose and how they formed the first life is the focus of abiogenesis.

So, since the Miller-Urey experiment, Wiki lists about 10 'models', (or tentative statements/hypotheses), all having varying degrees of evidence or scientific rationale behind them.

Given that:

- these 'models' are science's best attempts at describing how it all started;
- the basic environments described by these 'models' ultimately give rise to our present definitions of past and present 'Habitable Zones' and;
- the most likely process leading to life follows the sequence: bio-monomers, bio-polymers then finally molecules to cells;
- life metabolises, regulates its internal environment, grows, responds to stimuli, contains information, replicates and evolves;

1) What does the reader think might be the closest model so far developed for abiogenesis and how simple does this mean 'exo-life' might be, (ie: as far as for the purposes of searching for it) ?

2) How close have we come to making an exo-life discovery, so far ?

3) How much significance does the presence of these 'models' add to the confirmation of discovered exo-life, should such a discovery occur ... and why? (Eg: can a discovery ever be claimed without them ?)

Cheers

[CraigS]

To Peter (Poita);

Re: you last post on the other thread …
... I don't think a protein is needed in order to declare life, as I don't think this is necessarily what they're looking for … (although it would be awesome to find one)!

I think this thread will explain what I mean. They've got a few more cards up their sleeve(s) than I first thought, also.

I'll elaborate more when I get the chance. Plenty of thought and care is needed for this thread and preparation time might be a bit longer than is needed in the other forum.

Cheers

[CraigS]

Ok .. so, to throw a little more fuel on the fire, try this one out …

This is a Youtube slideshow presentation called:
The origin of Life – Abiogenesis – Dr Jack Szostak.

Szostak was awarded the 2009 Nobel Laureate in medicine for his work on telomerase. He is thus a highly credible scientist in the field.

Summarising, these are what he says are the crucial major steps described in his theory on how abiogenesis can lead to 'life' (my summary ... of his slides):

Abiogenesis steps (~7:30 minute mark)

- monomers diffuse into a fatty acid vesicle;
- monomers spontaneously polymerise and copy any template;
- heat separates strands, increases membrane permeability to monomers;
- polymer backbones attract ions increasing osmotic pressure;
- pressure on the membrane drives its growth at the expense of nearby vesicles containing less polymer;
- vesicles grow into tubular structures;
- mechanical forces cause vesicles to divide;
- daughter vesicles inherit polymers from the parent vesicle;
- polymer sequences that replicate faster will dominate the population.

Thus the beginning of evolution.

Early genomes were completely random and therefore contained no information. (Ie: way, way simpler information content than modern DNA/RNA).
It was their ability to spontaneously replicate, irrespective of the sequence that drove growth and division of the fatty acid vesicles.
Any mutation that increases the rate of polymer replication would be selected for.

Mutation + Natural Selection = Increased Information

Early beneficial mutations would include:

- change sequence to contain only the most common nucleotides;
- don’t form secondary structures that block replication;
- form sequences that are stable, yet separate easily;
- form secondary structures that show some enzymatic activity ;
- Just like RNA, early nucleotides could both store information and function as enzymes.

Early polymer enzymes would:

- enhance replication;
- use high energy molecules in the environment (near thermal vents) to recharge monomers;
- synthesize lipids from other molecules in the environment;
- modify lipids so they don’t leave the membrane.

AND THAT’S IT … a simple two component system that spontaneously forms in the pre-biotic environment, that can eat, grow, contain information, replicate and evolve.

Simply through thermodynamic and electrical forces.

The long chain organic molecules he starts with, are the fatty acids: 'Stearic Acid' (an 18 Carbon saturated fatty acid) or 'Oleic Acid' (18 Carbon unsaturated fatty acid). These are rather ordinary long chain organic molecules comprising C, H and Oxygen.

So, according to his theory, all one needs is a warm, wet planet and some long chain organic molecules in order to declare: 'LIFE' (as we know it).

The question is: can we find some long chain organic exo-molecules ?

Interestingly, this is exactly what the MARS MSL/Curiosity rover is equipped to look for !

Cheers

[adman (Adam)]

Poita, if you have a jar full of the required amino acids, and let it sit and watch and wait, yes the odds of a functional protein appearing are astronomical (and more). But this getting dangerously close to the irreducible complexity argument of the ID proponents, who like to say that the appearance of life is analogous to a strong wind blowing through a junkyard and randomly assembling a Boeing 747.

Functional proteins are almost certainly a much more recent development in the processes of life, and as Craig says above the main initial requirement for kick-starting life is the appearance of self-organising and self replicating non-living 'cells' or vesicles. These entities have a much more palatable chance of appearing - indeed given the right mixture, are almost inevitable. It is my belief that the 'universe geared towards life' you were talking about is nothing more exotic than molecules simply following the path of least thermodynamic resistance (so to speak).

Adam

[renormalised (Carl)]

Yes, but self organisation and replication, in any system, doesn't make it alive....does it

There are plenty of systems which are self replicating and organising given the right conditions (crystal growth, for example), even proteins and other organic molecules. Let alone other inorganic, non biological systems. Doesn't mean they're necessarily alive. To be brutally honest about it, we don't have a clue about what life is. All we do know is some very limited, functional appreciation of the mechanics of it all. However, we've got plenty of time to figure this one out

[adman (Adam)]

No not at all - but that wasn't my point. It was that the odds of constructing a functional protein from its constituent amino acids is not representative of the chances of life appearing elsewhere in the universe.

[Poita (Peter)]

Originally Posted by adman

Functional proteins are almost certainly a much more recent development in the processes of life, and as Craig says above the main initial requirement for kick-starting life is the appearance of self-organising and self replicating non-living 'cells' or vesicles. These entities have a much more palatable chance of appearing - indeed given the right mixture, are almost inevitable. It is my belief that the 'universe geared towards life' you were talking about is nothing more exotic than molecules simply following the path of least thermodynamic resistance (so to speak).

Adam

Have you thought about what that really means?
That you can crank out 'life', i.e. a system that defies the 2nd law of thermodynamics by molecules following a set of simple rules that follow the 'path of least thermodynamic resistance'.

That the simple reductionist laws of physics have within them a 'formula' for creating life is a total 180 over current thinking, it would mean that life is either not as complex or information rich as we think it is (that we are the equivalent of Pi for instance - looks information rich, aperiodic and random but is in fact a simple calculation), or that how we believe the universe works is wrong.

People make the statement all that time, that a simple process that follows the known laws of physics can lead to life, without thinking of the ramifications of that statement.

Szostack's work has not yet been successful, despite years of work and extremely contrived conditions, he has not yet managed a spontaneous basic RNA replicator from scratch. This is despite hand picking in vitro combinations from trillions of unlikely ones. http://www.hhmi.org/research/investigators/szostak.html

His work is important, it shows potentially more simple "life forms" than anything that exists today, but even the model he proposes still has greater than astronomical odds of forming randomly.

We know bugger all about life, or about how it may have begun. There may be some basic protocell that will spontaneously form and have enough complexity to have a 'software' system that can push against the 2nd Law of Thermodynamics, but if there is, then it means we need some new theories of physics to explain it.

[avandonk]

We are only barely starting to understand the complex molecular processes of life.
Do not forget compared to what we know there is an infinity of unknown.
My lust for things whether sexual, food or bright shiny things cannot be pointed to by reductionist means.
To denigrate any attempts at a rational elucidation of what makes us tick is both pointless and absurd.

I prefer to think that the whole of our 'reality' is even stranger than we can imagine. As a devout atheist I think that the devil dodgers have at least got one thing correct. This is that at some fundamental level such as quantum mechanics and what we do not yet know everything is connected.

What we see as complexity could just be the eddies in some cosmic lattice of so called order.

It is up to us to try and discover what is real. Making up fairy tales leads nowhere. Only science based evidence that is peer reviewed works.

Bert

[CraigS]

Guys, this conversation only works if we don't dig in too much on either side.

The fact is that no-one has ever cracked this nut … and they may never crack it. There are gaping holes in both arguments.

My personal aim is to stand as close to the middle-road as I can (and its not easy .. I have views/beliefs and opinions as well) .. and again, my aim is to expose my own opinions for myself, and recognise them for what they are … ie: pure opinions.

The points raised so far, are all valid points.

I'm not particularly of the view that one can cite any specific Law of Thermodynamics, (like the 2nd Law), and apply it to the overall life emergence process. I think the thermodynamic argument needs to look holistically at the applicability of all the Laws across the whole theorised process, and then pose the question: exactly where are they applicable to specific parts of the end-to-end complex system (such as the theorised emergence process). This allows for recognition of the non-determinstic (ie: random) components and to look at teh effects these may have on the overall theorised process.

This approach may aid Peter's colleagues' argument in uncovering some of the mysterious "statistical fluke" aspects. It also provides more depth of insight into exploring the other side of the coin, also. The interaction of deterministic sub-processes, (on the basic chemistry side), and the random pure chance mutation/natural selection-over-vast-time sub-processes on the evolutionary side should also not be underestimated (?)

Also, I'm not presenting Szostack's theory as be-all and end-all theory. There are others … however, it does represent a fairly comprehensive and well thought out biological sciences view of the topic. (At the very least, it seems to provide some useful tools as the basis for discussion).

I recommend moving on to examining more evidence and probing the question: "What's the closest we've come to discovering exo-life"

I'll attempt that in another post.

Cheers & thanks for some interesting views. Hopefully this one won't go south .. like so many others have on this topic.

[adman (Adam)]

First of all - nothing 'defies' the 2nd law of thermodynamics - not even life. In a closed system entropy will increase to a maximum, yes. But living things are not a closed system. They are, in part at least, machines for consuming energy and changing it into different forms, and once you start to add energy to any system it accordingly permits localised decreases in entropy. No Laws are defied in the process. Most things we see in the universe are localised descreases in entropy, stars, solar systems, planets galaxies etc - all very unlikely if you are trying to create one randomly from their constituent parts, and yet there they are.

The fact that Szostack has not been successful means nothing. The composition of earths early atmosphere may have been different to what our models show, his suppositions about the mechanisms of the appearance of early life (about which you correctly say we know very little) may be a little (or even way) off. But by far the biggest problem is time - Szostack has had a few years, and a laboratory, whereas life had a few billion years and the entire earth to generate those first steps towards life.

Like you said - we know bugger all about life, and even less about how it started. I think we need to know more before we go altering our view of how the universe works

Adam

[CraigS]

So, the next piece of the puzzle would be to look at some of the evidence. In pre-emption of being accused of cherry-picking, I’ll state upfront that my reason for zooming in on this bit, is that I just like it ... it intrigues me ... there is objectivity behind it, the results have been scrutinised and peer-reviewed, and the source is reasonably reputable.

So ... onto the 2006 results of the Stardust Probe Return Sample ...

In 2006, the probe returned samples to Earth, taken from the coma of comet Wild 2:

In December 2006, seven papers were published in the scientific journal, Science, discussing initial details of the sample analysis.

Among the findings are: a wide range of organic compounds, including two that contain biologically usable nitrogen; indigenous aliphatic hydrocarbons with longer chain lengths than those observed in the diffuse interstellar medium; abundant amorphous silicates in addition to crystalline silicates such as olivine and pyroxene, proving consistency with the mixing of solar system and interstellar matter, previously deduced spectroscopically from ground observations; hydrous silicates and carbonate minerals were found to be absent, suggesting a lack of aqueous processing of the cometary dust; limited pure carbon (CHON) was also found in the samples returned; methylamine and ethylamine was found in the aerogel but was not associated with specific particles.

However, in 2009 the following was announced:

Glycine amino acid discovered in Comet Wild 2 sample:

From Wiki:

Glycine (abbreviated as Gly or G) is an organic compound with the formula NH2CH2COOH. Having a hydrogen substituent as its 'side chain', glycine is the smallest of the 20 amino acids commonly found in proteins. Its codons are GGU, GGC, GGA, GGG.

So there was some question about contamination of the sample. However, this was answered by isotopic analysis:

Isotopes are versions of an element with different weights or masses; for example, the most common carbon atom, Carbon 12, has six protons and six neutrons in its center (nucleus). However, the Carbon 13 isotope is heavier because it has an extra neutron in its nucleus. A glycine molecule from space will tend to have more of the heavier Carbon 13 atoms in it than glycine that's from Earth. That is what the team found.

"We discovered that the Stardust-returned glycine has an extraterrestrial carbon isotope signature, indicating that it originated on the comet," said Elsila.

Very interesting, eh ?

For me, this is pretty close to the mark (but still arguably, by no means, conclusive).

Cheers

[renormalised (Carl)]

Originally Posted by adman

No not at all - but that wasn't my point. It was that the odds of constructing a functional protein from its constituent amino acids is not representative of the chances of life appearing elsewhere in the universe.

Of course

[CraigS]

Originally Posted by renormalised

Of course

But it is representative of the way science works.

Looking for something unknown, not knowing where to look for it, in an infinite universe, is about as close as it gets to being a feebly based, disruptive waste of time and resources, in my view. (.. And yes, that is an opinion unworthy of further argument).

The 'dream' is not what motivates the search .. scientific process involving hypothesis, theory and objective evidence (perhaps, preceded by the dream), is. (Yep .. another opinion unworthy of further argument)

Cheers

[CraigS]

So, looking at:

i) post #3 (Szostak's abiogenesis theory, requiring long chain organic compounds like stearic or oleic acids) … and;

ii) post #11, the actual confirmed discovery of extra-terrestrial Glycine, (an organic compound and an amino acid, probably found in the coma of comet Wild 3);

… might we have what one could call one of the closest approaches so far of discovering something which might have a snowball's chance in a hot place, of evolving into something which could be called exo-life ?

There is a little inference in my above question .. and thus its legitimacy might be debatable, but my purpose in raising this, is to try and gain visibility of the 'best case' for abiogenesis that I can come up with. It would seem that going much further than this, would probably rely on heavier doses of inference .. and all its associated shortcomings.

Its quite an interesting perspective, though.

I also find it interesting that perhaps by co-incidence, this aligns with the organic molecule and C12/C13 isotope detection technologies, being built aboard the Mars MSL/Curiosity rover, due for launch shortly.

So, given that there's quite a pile of 'reasonably' based biological theory and objective, peer reviewed evidence behind the scenario implied, I wonder what the outcome might be if MSL/Curiosity discovered long chain organic molecules ?

Well, I guess I'm back onto speculation here again, so to bring 'er back on track', but remaining in the same 'groove', the question left for me is:

"How much significance does the presence of these 'models' add to the credibility of a hypothetical discovery of long chain organic molecules (LCOMs) in a 'habitable zone' (HZ), should such a discovery occur ... and why?

For example: Would a discovery of exo-LCOMs in an HZ, mean anything without theories like Szostack's, and evidence such as Stardust's coma sample ? If these do carry some significance, and add enough 'weight' to the situation, perhaps significant enough to justify say, a manned mission to Mars, then does a 'non-discovery' of an LCOM in an HZ carry the same weight ? And if so, what could possibly be the consequences of a non-discovery (or multiple non-discoveries) ?

In consideration of 'weight' aspects mentioned above, are our expectations really objective?

Cheers

[adman (Adam)]

Originally Posted by CraigS

"How much significance does the presence of these 'models' add to the credibility of a hypothetical discovery of long chain organic molecules (LCOMs) in a 'habitable zone' (HZ), should such a discovery occur ... and why?

For example: Would a discovery of exo-LCOMs in an HZ, mean anything without theories like Szostack's, and evidence such as Stardust's coma sample ? If these do carry some significance, and add enough 'weight' to the situation, perhaps significant enough to justify say, a manned mission to Mars, then does a 'non-discovery' of an LCOM in an HZ carry the same weight ? And if so, what could possibly be the consequences of a non-discovery (or multiple non-discoveries) ?

Well - from a purely objective point of view, until we know the exact mechanism by which life or 'proto' life came into being, we don't even know whether these types of molecules were required at the very beginning or whether life just took advantage of them once it had come into being. So finding these molecules on Mars will just add to the complexity of the speculation.

From a more human point of view it would be fantastic to find them, and will certainly be a leverage point for more funding!

Adam

[renormalised (Carl)]

Originally Posted by CraigS

But it is representative of the way science works.

Looking for something unknown, not knowing where to look for it, in an infinite universe, is about as close as it gets to being a feebly based, disruptive waste of time and resources, in my view. (.. And yes, that is an opinion unworthy of further argument).

The 'dream' is not what motivates the search .. scientific process involving hypothesis, theory and objective evidence (perhaps, preceded by the dream), is. (Yep .. another opinion unworthy of further argument)

Cheers

Yes, it is an opinion...and, have you actually ever worked as a scientist?? So how do you know how science works??? Stick to your subject at hand, Craig. You're starting to get into territory you're not familiar with.

[Poita (Peter)]

Originally Posted by adman

First of all - nothing 'defies' the 2nd law of thermodynamics - not even life. In a closed system entropy will increase to a maximum, yes. But living things are not a closed system. They are, in part at least, machines for consuming energy and changing it into different forms, and once you start to add energy to any system it accordingly permits localised decreases in entropy. No Laws are defied in the process. Most things we see in the universe are localised descreases in entropy, stars, solar systems, planets galaxies etc - all very unlikely if you are trying to create one randomly from their constituent parts, and yet there they are.

Adam

I understand how the 2nd law works, but the formation on stars, solar systems planets galaxies and so forth are easily explained by the existing laws of physics, they are not at all unlikely events to happen. They don't go against chemistry or physics to occur, they are, for the most part, 'powered' by gravity and easily understood physical and chemical reactions etc. none of their increase in order or complexity defies the 2nd law, neither does evolution or processes that occur once you get DNA based life forms.
They are in fact inevitable formations due to the known laws of physics.

The formation of something complex enough to become life doesn't fit that mould. I haven't seen any research that as even proposed an basic organism that doesn't have stupendously large odds against occurring, even the simplest ones proposed run up against the error catastrophe problem. Once you get to a DNA type system, natural selection, mutation etc. can kick in, but until you do, you don't have Darwinism to act as the method of swimming upstream against the current so to speak.

Anyway, all of that is really by the wayside, my point is that if life is bound to happen given certain conditions, i.e. that we have a bio-friendly universe, then that is an incredibly profound, and shocking statement, and I don't see how it could be codified or incorporated into the current theories of physics. I'm not at all saying the universe isn't that way, I agree that it could be, we just don't know, but if it is then that would turn current theories on their heads. I don't think I'm communicating my point clearly, I'll have a re-think.

[Poita (Peter)]

Originally Posted by CraigS

So, looking at:

i) post #3 (Szostak's abiogenesis theory, requiring long chain organic compounds like stearic or oleic acids) … and;

ii) post #11, the actual confirmed discovery of extra-terrestrial Glycine, (an organic compound and an amino acid, probably found in the coma of comet Wild 3);

… might we have what one could call one of the closest approaches so far of discovering something which might have a snowball's chance in a hot place, of evolving into something which could be called exo-life ?

There is a little inference in my above question .. and thus its legitimacy might be debatable, but my purpose in raising this, is to try and gain visibility of the 'best case' for abiogenesis that I can come up with. It would seem that going much further than this, would probably rely on heavier doses of inference .. and all its associated shortcomings.

Its quite an interesting perspective, though.

I also find it interesting that perhaps by co-incidence, this aligns with the organic molecule and C12/C13 isotope detection technologies, being built aboard the Mars MSL/Curiosity rover, due for launch shortly.

So, given that there's quite a pile of 'reasonably' based biological theory and objective, peer reviewed evidence behind the scenario implied, I wonder what the outcome might be if MSL/Curiosity discovered long chain organic molecules ?

Well, I guess I'm back onto speculation here again, so to bring 'er back on track', but remaining in the same 'groove', the question left for me is:

"How much significance does the presence of these 'models' add to the credibility of a hypothetical discovery of long chain organic molecules (LCOMs) in a 'habitable zone' (HZ), should such a discovery occur ... and why?

For example: Would a discovery of exo-LCOMs in an HZ, mean anything without theories like Szostack's, and evidence such as Stardust's coma sample ? If these do carry some significance, and add enough 'weight' to the situation, perhaps significant enough to justify say, a manned mission to Mars, then does a 'non-discovery' of an LCOM in an HZ carry the same weight ? And if so, what could possibly be the consequences of a non-discovery (or multiple non-discoveries) ?

In consideration of 'weight' aspects mentioned above, are our expectations really objective?

Cheers

I'm not sure what relevance of the presence of glycine is to the argument?

I'm not being facetious, I'm just missing the significance...I haven't had a lot of sleep and am running on slo-mo today.

[CraigS]

Originally Posted by Poita

Anyway, all of that is really by the wayside, my point is that if life is bound to happen given certain conditions, i.e. that we have a bio-friendly universe, then that is an incredibly profound, and shocking statement, and I don't see how it could be codified or incorporated into the current theories of physics. I'm not at all saying the universe isn't that way, I agree that it could be, we just don't know, but if it is then that would turn current theories on their heads. I don't think I'm communicating my point clearly, I'll have a re-think.

Peter;
Consider that life on Earth exists …

Hope this helps ..

Cheers

[CraigS]

Originally Posted by Poita

I'm not sure what relevance of the presence of glycine is to the argument?

I'm not being facetious, I'm just missing the significance...I haven't had a lot of sleep and am running on slo-mo today.

Well .. its an organic molecule … I don't think it could be classified as a long chain organic molecule .. but its not a simple one, either.

I don't know what steps might turn it into one .. I guess Szostack doesn't know either, eh ?

Cheers