Abiogenesis discussion

[Paul Wally]

I'm interested in discussing abiogenesis or chemical evolution, the processes leading up to the emergence of life.
This is not only a very interesting field, in my opinion, but also relevant to the discussions going on about the probability of life and intelligence
emerging in the universe at large. I believe that if we could understand how abiogenesis works and the conditions under which it is possible, then we should get some idea of how likely it is to happen elsewhere.

For the purpose of this discussion I will define abiogenesis as chemical processes leading to the emergence of self-replicating and evolving complex molecules.
I choose this, perhaps narrow, definition so that we don't get into arguments about the definition of life or at what point in time life begins and abiotic chemistry ends. It is also a convenient definition in the sense that once molecules become self-replicating, we can already begin to use terms like species and populations of molecules, and it would then make sense to apply the principle of natural selection to them. So here, life is defined as that to which the theory of evolution through natural selection applies.

So the question is basically: How does self-replicating and evolving complex molecules emerge naturally in chemical processes. This is a discussion of possibilities implicit in chemistry, physics and planetary sciences. So it's very much a theoretical issue but it's also an issue of experimental methodology. What is the most effective methods for investigating the phenomenon empirically and quasi-empirically; experimental, computational or observational?

I'm looking forward to an interesting and creative discussion on this topic.

[John Jaksich]

Does the discussion extend into chirality? If it does then--it may be noted that experimentation on the growth of crystals and the preference of left-handed peptides over the right in noted lab experiments--rather than a 50/50 mixture.

[Paul Wally]

Does the discussion extend into chirality? If it does then--it may be noted that experimentation on the growth of crystals and the preference of left-handed peptides over the right in noted lab experiments--rather than a 50/50 mixture.

If you think it could be relevant, by all means share your knowledge. It could be that this chirality is an analogue for the kinds of processes involved in abiogenesis.

[John Jaksich]

Prof. Breslow and a co-worker ( Levine )- (at Columbia University) attempted a racemization procedure of phenylalanine (that possessed a 1 percent enantiomeric excess of the left-handed
isomer) their procedure was to slowly crystallize out 500 mg of an aqueous solution.

Out of the original 500 milligram solution--the solution left behind a 90 percent left-handed mixture (in solution) out of an original 1 percent left handed excess.

The point is that the original solution contained a nearly 50/50 mixture --but after crystallizing out of the solution---the result was to leave 10 percent only of the right-handed enantiomeric excess.

The citation is from Proceedings of the National Academy of Sciences USA (2006) Vol 103 pg 12979

[John Jaksich]

Here is the link to the paper:


http://www.pnas.org/content/103/35/12979.full

[John Jaksich]

Prof. Breslow and a co-worker ( Levine )- (at Columbia University) attempted a racemization procedure of phenylalanine (that possessed a 1 percent enantiomeric excess of the left-handed
isomer) their procedure was to slowly crystallize out 500 mg of an aqueous solution.

Out of the original 500 milligram solution--the solution left behind a 90 percent left-handed mixture (in solution) out of an original 1 percent left handed excess.

The point is that the original solution contained a nearly 50/50 mixture --but after crystallizing out of the solution---the result was to leave 10 percent only of the right-handed enantiomeric excess.

The citation is from Proceedings of the National Academy of Sciences USA (2006) Vol 103 pg 12979

I apologize for the cryptic writing?

The direct link should be better.

[John Jaksich]

I will be back---later

Sorry I cannot be of more assistance--currently!

[Paul Wally]

Thanks John, for that link. I find that there are quite a number of technical terms, which are such that if I understood their meaning, I would understand the paper.
I know at least that there are not many kinds of amino-acids and that they combine to form all the different proteins.

I'll look up most of the terms. Just a few questions.
The amino-acids found in the meteorites, are they conclusive evidence that amino-acids can form in space? How do amino-acids form, by the way?
The other question is, what does enantiomeric mean. I know chiral symmetry has got to do with mirror symmetry, right?

Thanks

[eburacum45]

An eniantomer is simply a compound which is a mirror image of another compound. Perhaps the presence of molecules of one particular handedness sometimes causes that handedness to predominate during racemization.

Racemization is any process which is supposed produce a mixture with equal numbers of left- and right-handed molecules (a racemic mixture). Obviously a procedure which fails to produce such a mixture is not really racemization; but biochemistry on Earth has a definite bias, so obviously something has caused this to occur. Maybe some alien biochemistries have opposite handedness to Earth biochemistry; perhaps some biochemistries are even racemic, and include equal mixture of both. Or perhaps all biochemistries have the same handedness- nobody knows.

Not until someone finds an alien lifeform, that is.

[marsbug]

I'm interested in discussing abiogenesis or chemical evolution, the processes leading up to the emergence of life.
This is not only a very interesting field, in my opinion, but also relevant to the discussions going on about the probability of life and intelligence
emerging in the universe at large. I believe that if we could understand how abiogenesis works and the conditions under which it is possible, then we should get some idea of how likely it is to happen elsewhere.

For the purpose of this discussion I will define abiogenesis as chemical processes leading to the emergence of self-replicating and evolving complex molecules.
I choose this, perhaps narrow, definition so that we don't get into arguments about the definition of life or at what point in time life begins and abiotic chemistry ends. It is also a convenient definition in the sense that once molecules become self-replicating, we can already begin to use terms like species and populations of molecules, and it would then make sense to apply the principle of natural selection to them. So here, life is defined as that to which the theory of evolution through natural selection applies.

So the question is basically: How does self-replicating and evolving complex molecules emerge naturally in chemical processes. This is a discussion of possibilities implicit in chemistry, physics and planetary sciences. So it's very much a theoretical issue but it's also an issue of experimental methodology. What is the most effective methods for investigating the phenomenon empirically and quasi-empirically; experimental, computational or observational?

I'm looking forward to an interesting and creative discussion on this topic.

We have parts of the picture for sure: we know from water altered carbon bearing meteorites that even simple early solar system bodies either had in them, or had chemical processes in them that could give rise to, a plethora of amino acids (building blocks of proteins in case anyone didn't know) and nucleobases (building blocks of DNA/RNA). What’s more these meteorites carry many more amino acids than life uses, and nucleobase-like molecules as well as actual nucleobases. This suggests to me that the intervening steps between these chemical mixes and the earliest known life had some Darwinian component whereby the best chemical system for life was selected. One intermediate step may have been evolving molecular replicators like these. In fact I think that the RNA molecules mentioned in that last article fit your (deliberately widened to avoid arguments I know) definition of life.

How we get from chemical mixes like those found in meteorites to something akin to RNA replicators (if that was indeed an intermediate step) is a mystery still.

[marsbug]

A few more bits on pre-biotic chemistry on small bodies, from the stardust mission:

Comet wild 2 contains a mix of heated and unheated material

Comet wild 2 has amino acids

Comet wild 2 has seen liquid water

Comet wild 2 has long chain hydrocarbons and has never seen liquid water

The story is still unclear but the indications are that parralels to prebiotic chemistry on Earth could be frozen in small solar system bodies.

[John Jaksich]

A few more bits on pre-biotic chemistry on small bodies, from the stardust mission:

Comet wild 2 contains a mix of heated and unheated material

Comet wild 2 has amino acids

Comet wild 2 has seen liquid water

Comet wild 2 has long chain hydrocarbons and has never seen liquid water

The story is still unclear but the indications are that parralels to prebiotic chemistry on Earth could be frozen in small solar system bodies.

Given our tendency for carbon chauvinism---I would say that we, as a species, need to look more deeply at all of previously analyzed data. As our technology evolves and becomes more sophisticated and sensitive, there will be areas of focus that were initially missed by even the best of analysts.

One area is that is being pursued is the re-analyzing of meteors for carbon-bearing materials. The Murchison meteorite has been analyzed over and over again--and some feel that it may have been over-analyzed.

Of late, there has been a new technique in Mass Spec analysis that was able to differentiate enantiomeric amino acids---and of particular importance was the finding of DL-2,3-Diaminopropionic acid, as well as DL-2,4-Diaminobutyric acid....

The analytic technique is also being used by the Rosetta mission.

More to post . . . upcoming

[John Jaksich]

The authors of the article (cited link---):

http://www.pnas.org/content/101/25/9182.full.pdf

perform an admirable analysis (IMO)

Calling to question whether non-protein amino acids were the progenitors of an RNA life forms

[Paul Wally]

A few more bits on pre-biotic chemistry on small bodies, from the stardust mission:

Comet wild 2 contains a mix of heated and unheated material

Comet wild 2 has amino acids

Comet wild 2 has seen liquid water

Comet wild 2 has long chain hydrocarbons and has never seen liquid water

The story is still unclear but the indications are that parralels to prebiotic chemistry on Earth could be frozen in small solar system bodies.

These findings suggest interesting possibilities. One such possibility being that the process of prebiotic chemistry already starts in the primordial nebula, perhaps some kind of exotic chemistry is possible under those early conditions. Of course we must also consider the most "boring" possibility, and that is that the material was simply ejected from the Earth billions of years ago, but then I don't know whether such a possibility is consistent with the Carbon 13 isotopes and also the findings of exotic amino acid in meteorite/s. The idea of mixing of materials in the early solar system suggests to me that the process leading up to life could be more spatially (beyond Earth) and temporally extended (before Earth) than we may originally have thought, and that the Earth is merely the central locus of that activity.

[marsbug]

The authors of the article (cited link---):

http://www.pnas.org/content/101/25/9182.full.pdf

perform an admirable analysis (IMO)

Calling to question whether non-protein amino acids were the progenitors of an RNA life forms

Fascinating, thank you. As I understand the paper they have found diamino acids for the first time in a carbanaceous chondrite. The propose a pathway from the diamino acids to PNA, a proposed precursor to RNA. Do I understand that aright?

[John Jaksich]

Fascinating, thank you. As I understand the paper they have found diamino acids for the first time in a carbanaceous chondrite. The propose a pathway from the diamino acids to PNA, a proposed precursor to RNA. Do I understand that aright?

If I remember correctly--the paper is dated--but in my opinion what I found intriguing was that the instrumental technique is being used in the current ESA Rosetta mission. But, the Stardust mission also made use of it--and it basically crashed in the Utah desert--I am unaware of the results from it.

As for synthetic schemes--the paper is (as I said) dated--it is significant for the fact that it did detect a precursor to a (one of more ?) pre-biotic RNA.


The polycondensation reactions mentioned in the paper---give a "retro-synthetic" analysis (or IMO --a "synthon" ).

The trends in elucidating biosynthetic schemes have gone toward understanding how metals (in the "soup") could have catalyzed the syntheses.

There has been quite a bit of work in that area--try googling a recent Nobelist:

K. Barry Sharpless


and there have been many others

in somewhat recent memory---->

E. J. Cory

J. D. Roberts

R. B. Woodward

Despite what may seem to be an industrial "chemistry" flavor to my
l
cited individuals----most of the chemists which I have personally dealt with have all expressed a desire to know

"Where did it all come from?"---chemically speaking


If you look closely at their work (above) ---there is the idiosyncratic flavor of genius working in many different levels of abstraction----they know how to put and answer questions that have many layers of meaning.

[marsbug]

I wish I had the time to give your reading list half the time it deserves John! Are you reffereing to time of flight mass spectrometry? I build those! Not the rosetta one, and I'm an engineer so my knowledge of chemical analysis techniques isn't as good as my knowledge of the mechanism and physics behind it, but I'm happy to help with any questions if you have them.

[Paul Wally]

An eniantomer is simply a compound which is a mirror image of another compound. Perhaps the presence of molecules of one particular handedness sometimes causes that handedness to predominate during racemization.

Racemization is any process which is supposed produce a mixture with equal numbers of left- and right-handed molecules (a racemic mixture). Obviously a procedure which fails to produce such a mixture is not really racemization; but biochemistry on Earth has a definite bias, so obviously something has caused this to occur. Maybe some alien biochemistries have opposite handedness to Earth biochemistry; perhaps some biochemistries are even racemic, and include equal mixture of both. Or perhaps all biochemistries have the same handedness- nobody knows.

Thanks for these explanations. Just to get these concepts clear in my mind: A water molecule is not an eniantomer, because it's mirror image is itself, because it's symmetrical. So an actual eniantomer is asymmetrical, i.e. there is no way to rotate the molecule in 3-D space and get it's mirror image, to get it's mirror image it has to be rotated through 4-D space, analogous to the L in the game of Tetris.

So is there as of yet no explanation for the bias? I have the suspicion that it's got something to do with the analogy of a ball on a hill that can role both ways, but once it roles the one way then there's a kind of cascade effect, but why would it then cascade all over the planet? Is it perhaps an early form of heredity? Or perhaps it's simply a function of the chemical environment.

[John Jaksich]

Thanks for these explanations. Just to get these concepts clear in my mind: A water molecule is not an eniantomer, because it's mirror image is itself, because it's symmetrical. So an actual eniantomer is asymmetrical, i.e. there is no way to rotate the molecule in 3-D space and get it's mirror image, to get it's mirror image it has to be rotated through 4-D space, analogous to the L in the game of Tetris. So is there as of yet no explanation for the bias? I have the suspicion that it's got something to do with the analogy of a ball on a hill that can role both ways, but once it roles the one way then there's a kind of cascade effect, but why would it then cascade all over the planet? Is it perhaps an early form of heredity? Or perhaps it's simply a function of the chemical environment.

As a fairly good citation of a pre-print from the e-print--Today I noticed a technique employed :Spectro-polarimetry of the bright side of Saturn’s moon Iapetus⋆ C. Ejeta , H. Boehnhardt , S. Bagnulo and G.P. TozziMax-Planck-Institut fO r Sonnensystemforschung, Katlenburg-Lindau, Germany ----(Authors---C. Ejeta & Boehnhardt)Institut f Or Geophysik und extratrrestishe Physik, TU Braunschweig, Germany -----(Author: C. Ejeta) Armagh Observatory, College Hill, Northern Ireland, UK-----(Author: Bugnulo) INAF - Oss. Astrofisico di Arcetri, Firenze, Italy ------(Author: Tozzi)

The crux of the method is that polarimetry is a standard for measuring the rotation of how plane-polarized light interacts with a medium which normally contains molecules that could account for enantiomers.As alluded within the conclusion and results section----> Iapetus is or contaiins water vapor (?) that rotated the light after standardization ----to a "negative" angle--it may be concluded that (?) there is a possible mixture within the ice that would possibly contain organic matter that could account for it.Please note that there are also inorganic species ( ---off the top of my head---Co ---some Cobalt complexes are known to have hundreds enantiomeric species that could rotate plane polarized light)really seems to be an outstanding article (with references) --

IMO Here is the citation:http://arxiv.org/abs/1110.3163v1. ABSTRACT:Context Measurements of the polarized reflected sunlight from atmosphereless solar system bodies, over a range of phase angles,provide information about the surface structure and composition.Aims. With this work, we provide analysis of the polarimetric observations of the bright side of Iapetus at five different phase angles,and over the full useful wavelength range (400-800nm), so as to assess the light scattering behaviour of a typical surface water ice.Methods. Using FORS2 of the ESO VLT, we have performed linear spectro-polarimetric observations of Iapetus’ bright side from2009 to 2011 at five different phase angles, in the range from 0.80 − 5.20◦ , along with one circular spectro-polarimetric observationat one phase angle.

Results. By measuring, with high accuracy (∼ 0.1 % per spectral bin for each Stokes parameter), the spectral polarization of thebright trailing hemisphere of Saturn’s moon Iapetus, we have identified the polarimetric characteristics of water ice, and found that itslinear degree of negative polarization decreases with increasing phase angle of observation (varying from −0.9 % to −0.3 %), with a clear dependence on wavelengths of observation.Key words. Iapetus: polarization – Iapetus: bight side – methods: Polarimetry...

[tnjrp]

While all this talk of the meteorites and whatnot is interesting of course, the RNA world hypothesis actually might be able to explain something about the process itself as it occured on Earth and it does seem to be "evolving" towards a full-fledged theory of abiogenesis:
http://www.newscientist.com/article/...eplicator.html
http://genetics.mgh.harvard.edu/szos..._2011_PNAS.pdf

It is of course an entirely different question as to how strong standing it will ever have, given that we cannot observe it happening in certifiably correct conditions in order to fully replicate the process.

Further reading on the subject of abiogenesis:
http://www.rationalskepticism.org/ch...45.html#p47054

[marsbug]

Here's a thought: it's been speculated that the moon could hold quite a lot of well preserved material (ejected via giant impacts) from Earth. Given that the rate of giant impacts was much higher in the early solar system could there should be disproportionate amount of material from Earths deep past - likely some older than any extant rocks on Earth. Could some of that maybe hold clues on conditions at the time abiogenesis took place?

[John Jaksich]

marsbug:


I find that to be a good question--but I am sure that the harshness (or lack of atmosphere along with cosmic radiation) would make the reasons to dig very deeply into the crust one easier (?) path to analyze for traces of the past solar system history (including abiogenesis).

[marsbug]

I would have thought the lack of atmosphere would be a plus? The weather amd presence of life throughout Earths crust are big stumbling blocks to look for preserved pre-biotic chemistry in Earths rocks. As ais our surface having an active geology to warm and alter even those rocks that have lasted 4 billion years. Somewhere like the lunar cold traps may have been cold, airless, lifeless, and geologically inert for billions of years - perhaps a terrestrial meteorite there would be better preserved? Ok landing will damage it but thats one event the effects of which could be be modelled and accouned for. And as for launch: I believe that rocks launched from the spallation zone around an impact can be meters across and only get heated to centimeters depth, though I can't remember where I read that.

I can't say it makes more sense to look on the moon for signs of terrestrial prebiotic chemistry for sure but my firs impression is hat it's an alterative worth investgateing. We see well preserved evidence of prebiotic chemistry in meteorites that are in the moon like conditions of deep space, for example.

[John Jaksich]

I would have thought the lack of atmosphere would be a plus? The weather amd presence of life throughout Earths crust are big stumbling blocks to look for preserved pre-biotic chemistry in Earths rocks. As ais our surface having an active geology to warm and alter even those rocks that have lasted 4 billion years. Somewhere like the lunar cold traps may have been cold, airless, lifeless, and geologically inert for billions of years - perhaps a terrestrial meteorite there would be better preserved? Ok landing will damage it but thats one event the effects of which could be be modelled and accouned for. And as for launch: I believe that rocks launched from the spallation zone around an impact can be meters across and only get heated to centimeters depth, though I can't remember where I read that.

I can't say it makes more sense to look on the moon for signs of terrestrial prebiotic chemistry for sure but my firs impression is hat it's an alterative worth investgateing. We see well preserved evidence of prebiotic chemistry in meteorites that are in the moon like conditions of deep space, for example.

I posed the question (similar to yours) several years ago to an expert (whom I cannot recall) from Arizona State University in regards to Martian samples and the Prof. stated that any type of organic molecules would be more readily found beneath the Martian soil.

[marsbug]

Makes sense.... the sunlight at the surface is much more UV heavy on Mars, and the moon would be ten times worse. Did he mention any other reasons or how deep any preserved chemistry would need to be to last?

[John Jaksich]

Makes sense.... the sunlight at the surface is much more UV heavy on Mars, and the moon would be ten times worse. Did he mention any other reasons or how deep any preserved chemistry would need to be to last?

I really don't believe he mentioned anything to me in the e-mail--however--in the meantime I will attempt to find the "link" that I used to e-mail him.

The site was a "ask a NASA scientist"--and that was how it came about.

I believe that one can only infer how deep the "drilling" needs to be---by what current missions are slated.

I will get back to you on this.

[marsbug]

Thans John. My first instinct is that to find preserved prebiotc chemistry will need a location that is not only well preserved and protected but which has been sterile since said chemistry was emplaced. However I'm guessing - it my be easier or harder than I imagine!

[allyjack]

Do creationists realize that even if somehow abiogenesis was debunked, that wouldn't falsify evolution?
Evolution isn't about "coming from nothing" unless you piece it together with abiogenesis, but the two theories (evolution may as well be a fact in my opinion) aren't completely attached to each other like so many creationists these days claim it is. Evolution is evolution, abiogenesis is abiogenesis. There's the lesson of the day for the ignorant creationists on here. Educated creationists clearly don't need this, though, so don't feel offended by this if you already know.

Pentru fanii mei care vorbesc limba romana vreau sa le spun am deschis o afacere cu haine. Daca doriti putem colabora sub mai multe aspecte.

[Clive Tester]

[B]evolution may as well be a fact in my opinion.

Only time will tell, and be prepared for some possible surprises along the way. The quest to understand the nature of the atom in the 20th century provides a good example, of how our notions of what we think is right and our notions of what we are capable of understanding can be put into a startling new perspective, when we gain the ability to search a little further.

[Cougar]

Finding life's building-block molecules in meteorites is one thing. How they are combined into a replicating life or pre-life form is quite another.

Stuart Kauffman studied this for about 20 years. He modeled generic molecules, making reasonable assumptions consistent with known chemical properties... and let them react, as molecules will do. I cannot do justice to his findings in a few sentences or paragraphs. But IIRC, if you get a large enough number of different molecules together, all reacting with each other differently, at some point you get emergent order. He essentially quantified it.