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Swift
2013-Jul-31, 08:49 PM
From R&D magazine (http://www.rdmag.com/news/2013/07/natural-affinities-may-have-set-stage-life-ignite?et_cid=3398205&et_rid=54734303&location=top)


The chemical components crucial to the start of life on Earth may have primed and protected each other in never-before-realized ways, according to new research led by Univ. of Washington (UW) scientists.

It could mean a simpler scenario for how that first spark of life came about on the planet, according to Sarah Keller, UW prof. of chemistry, and Roy Black, UW affiliate prof. of bioengineering, co-authors of a paper published online in the Proceedings of the National Academy of Sciences.

Scientists have long thought that life started when the right combination of bases and sugars produced self-replicating ribonucleic acid, or RNA, inside a rudimentary “cell” composed of fatty acids. Under the right conditions, fatty acids naturally form into bag-like structures similar to today’s cell membranes.

In testing one of the fatty acids representative of those found before life began—decanoic acid—the scientists discovered that the four bases in RNA bound more readily to the decanoic acid than did the other seven bases tested.

By concentrating more of the bases and sugar that are the building blocks of RNA, the system would have been primed for the next steps, reactions that led to RNA inside a bag.

“The bag is the easy part. Making RNA from scratch is very hard,” Keller said. “If the parts that come together to make RNA happen to preferentially stick to the surfaces of bags, then everything gets easier.”

The scientists also discovered a second, mutually reinforcing mechanism: The same bases of RNA that preferentially stuck to the fatty acid also protected the bags from disruptive effects of salty seawater. Salt causes the fatty acid bags to clump together instead of remaining as individual “cells.”

The researchers found that several sugars also give protective benefit but the sugar from RNA, ribose, is more effective than glucose or even xylose, a sugar remarkably similar to ribose, except its components are arranged differently.

The ability of the building blocks of RNA to stabilize the fatty acid bags simplifies one part of the puzzle of how life started, Keller said.

“Taken together, these findings yield mutually reinforcing mechanisms of adsorption, concentration and stabilization that could have driven the emergence of primitive cells,” she said.


Here is the journal abstract (http://www.pnas.org/content/early/2013/07/29/1300963110.abstract?sid=56c0db65-dbe0-4a86-a5ca-fd3e595b1128)

Selfsim
2013-Jul-31, 10:02 PM
In testing one of the fatty acids representative of those found before life began—decanoic acid …What is the evidence that decanoic acid existed before life began?

I suppose it would be no big surprise that such a molecule would be lying around if RNA molecules were also about .. but where is the evidence that it did?

Decanoic acid might seem so common thesedays, as to make the question seem like a nit-pick, but most present-day fatty acids are produced biotically. (Thus far, I've never seen primordial geological evidence for the existence of fatty acids … space-bound PAHs and meteoric amino acids-sure .. but fatty acids?)

John Mendenhall
2013-Jul-31, 10:06 PM
Wow. Great research.

Europa, what will we find there?

"Life will find a way." -Michael Crichton, through Dr. Ian Malcolm in Jurassic Park.

Selfsim
2013-Jul-31, 11:55 PM
Nobel Laureate Jack Szostak has been talking about this for quite some time.

He elaborates on what he calls the crucial major chemical steps for this phase of abiogenesis (7:30 min mark) as: (http://www.youtube.com/watch?v=U6QYDdgP9eg)

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

His step (i) above, posits stearic and oleic acids (18 carbon chains) as a starting point. Decanoic acid is an 8 carbon chain acid, so I suppose its a bit simpler. It is normally formed from the oxidation of another 10 carbon chain: 1-Decanol (a straight chain primary fatty alcohol). I suppose the latter, being in the same family as simpler alcohols like methanol, takes it further from bio-organic chemistry and brings the whole idea back to the inorganic origin point, (for the membrane component, that is.

My point being .. where might the decanoic acid have come from: Did it evolve alongside by bio-organics (maybe even a by-product of it), or did it evolve from inorganic predecessors?
(Everyone seems to like assuming the latter .. but where's the actual evidence for this?)

Selfsim
2013-Jul-31, 11:58 PM
..."Life will find a way." -Michael Crichton, through Dr. Ian Malcolm in Jurassic Park.But how did life find its own way in the first place? :)

Swift
2013-Aug-01, 02:03 PM
What is the evidence that decanoic acid existed before life began?

I suppose it would be no big surprise that such a molecule would be lying around if RNA molecules were also about .. but where is the evidence that it did?

Good question. I don't know the complete answer, but I did find this paper (http://astrobiology.gsfc.nasa.gov/analytical/PDF/Herdetal2011.pdf) where it and similar compounds were identified in the Tagish Lake carbonaceous chondrite meteorite.

I found several other references that describe using it as a model compound for making vesicles, as it seems to be one of the better compounds at doing so.

KhashayarShatti
2013-Aug-01, 06:47 PM
But how did life find its own way in the first place? :)

As far as the question is based on "How" and not on "Why" I think I can add some engineering bases for it. I think The analogy lies within the extrapolation of life form. Lets ask : How did governance or the first government appear?"
Now interpolation plays the key role to find an answer for this question. "How did a cell appear?" or interpolating it further "How did RNA come into existence?"
By extrapolating life form, I think governments are trying to make a DNA of themselves and replicate it as far as they can(nothing to do with politics). I interpret it as life form. And by analogy perhaps this may take place when the right combination of organo-community takes the right form. A process described as a change from "bottom-up" to a "top- down" formation.

Let us further prove this situation by a very good example:
I start with the difference between Bacteria and viruses. The difference is that bacteria cannot enter cells while viruses can enter cells. When a virus enters a cell core , disintegration of the cell DNA occurs and from the other side proteins try to decode genetic structure of The DNA of the virus and stick to it to create a new governance. All similar to what is actually happening at a much larger scale similar to the appearance of governance right at the current stage of life. Obviously the success depends on the self defensive system and by interpolation this could be analogous to how sub nano structures of life get formed.
I think the solution is based upon a similar systematic approach to decode the inputs and the outputs of salts or acids for the right stabilization of the organo-community structure.

Nick Theodorakis
2013-Aug-02, 01:08 AM
Just a couple of mntpciks:


As far as the question is based on "How" and not on "Why" I think I can add some engineering bases for it. I think The analogy lies within the extrapolation of life form. Lets ask : How did governance or the first government appear?"
Now interpolation plays the key role to find an answer for this question. "How did a cell appear?" or interpolating it further "How did RNA come into existence?"
By extrapolating life form, I think governments are trying to make a DNA of themselves and replicate it as far as they can(nothing to do with politics). I interpret it as life form. And by analogy perhaps this may take place when the right combination of organo-community takes the right form. A process described as a change from "bottom-up" to a "top- down" formation.

Let us further prove this situation by a very good example:
I start with the difference between Bacteria and viruses. The difference is that bacteria cannot enter cells while viruses can enter cells.


Not necessarily. Rickettsia and mycoplasmas are obligate intracellular parasites, and some pathogens such as Listeria can hide out within cells.



When a virus enters a cell core , disintegration of the cell DNA occurs ...

Again, not necessarily, and not even most of the time.

Nick

Selfsim
2013-Aug-02, 06:48 AM
Good question. I don't know the complete answer, but I did find this paper (http://astrobiology.gsfc.nasa.gov/analytical/PDF/Herdetal2011.pdf) where it and similar compounds were identified in the Tagish Lake carbonaceous chondrite meteorite.

Hmm ... (thanks for that .. interesting) ... lots of reading there, too.

A couple of comments on this paper (and as an aside): I notice the 'extra-terrestrial-ness' of the 0.04ppm decanoic acid, is somewhat ambiguous. They point out that the δ13C (carbon isotope ratio) is indicative of terrestrial ... (well and truly so too, I might add ... ie: (-24 ± 5), but the deuterium ratio, (δ D), is more non-terrestrial). Even assuming that it is non-terrestrial, there isn't very much of it! Gotta wonder just how often this kind of compound shows up, too .. even in present-day carbonaceous chondrite meteorites?
Also, from just one sample, (Tagish Lake), can one extrapolate from this with confidence, to conclude that there might be sufficient amounts to form the membranes of early cells? (I wonder ...).

The other thing which bugs me about the delivery-to-Earth-via-meteorite-impact hypotheses, is that if these chemicals AND amino acids were present in primordial LHB meteorites, then why not go the full distance and argue that cells already existed on the impacting meteorites?

These questions aside and being fair about it, I guess the OP study is really simply announcing the measured RNA affinity for decanoic acid (when compared with other similar fatty acids) .. which is fine, (and of interest).


I found several other references that describe using it as a model compound for making vesicles, as it seems to be one of the better compounds at doing so... Sure ...(yep) ..

Selfsim
2013-Aug-02, 07:01 AM
As far as the question is based on "How" and not on "Why" I think I can add some engineering bases for it. I think The analogy lies within the extrapolation of life form. Lets ask : How did governance or the first government appear?"
Now interpolation plays the key role to find an answer for this question. "How did a cell appear?" or interpolating it further "How did RNA come into existence?"
By extrapolating life form, I think governments are trying to make a DNA of themselves and replicate it as far as they can(nothing to do with politics). I interpret it as life form. And by analogy perhaps this may take place when the right combination of organo-community takes the right form. A process described as a change from "bottom-up" to a "top- down" formation.

Let us further prove this situation by a very good example:
I start with the difference between Bacteria and viruses. The difference is that bacteria cannot enter cells while viruses can enter cells. When a virus enters a cell core , disintegration of the cell DNA occurs and from the other side proteins try to decode genetic structure of The DNA of the virus and stick to it to create a new governance. All similar to what is actually happening at a much larger scale similar to the appearance of governance right at the current stage of life. Obviously the success depends on the self defensive system and by interpolation this could be analogous to how sub nano structures of life get formed.
I think the solution is based upon a similar systematic approach to decode the inputs and the outputs of salts or acids for the right stabilization of the organo-community structure.Sorry .. I have no idea of what you're trying to saying here.
(Might I suggest you start another thread, too ..?..)

Swift
2013-Aug-02, 09:39 PM
Also, from just one sample, (Tagish Lake), can one extrapolate from this with confidence, to conclude that there might be sufficient amounts to form the membranes of early cells? (I wonder ...).
The "one sample" might be an artifact of the amount of time I wanted to spend Googling this information (which was measured in minutes). For all I know there are more papers on more samples, or this may be the only one. Once I got to "not zero", I stopped searching. And no, I'm not interested enough to do any more searching. ;)


The other thing which bugs me about the delivery-to-Earth-via-meteorite-impact hypotheses, is that if these chemicals AND amino acids were present in primordial LHB meteorites, then why not go the full distance and argue that cells already existed on the impacting meteorites?
Two thoughts.

One, I don't know that this proves that decanoic acid was brought to Earth via meteorite. I think the main thing the Tagish Lake paper demonstrates is that this and similar compounds were present in the prebiotic solar system (your question as to whether they existed before life). For all I know, it may have also formed on the pre-biotic Earth. I think there are at least proposed (and lab demonstrated) mechanisms for amino acids to have formed on Earth. That may also be true for these fatty acids.

Second, it seems more likely that simply compounds could be transported by such a mechanism than whole organisms; I would image they would be more rugged and less likely to be destroyed for one thing. And the presence of such compounds in meteorites has been demonstrated. No one has found any evidence of an organism in such a meteorite.


These questions aside and being fair about it, I guess the OP study is really simply announcing the measured RNA affinity for decanoic acid (when compared with other similar fatty acids) .. which is fine, (and of interest).
That was my only intent. It is a piece of evidence of one step of one possible mechanism. That's it as far as I'm concerned.