Model suggests how life's code emerged from primordial soup

Aug 07, 2009

(PhysOrg.com) -- In 1953, Stanley Miller filled two flasks with chemicals assumed to be present on the primitive Earth, connected the flasks with rubber tubes and introduced some electrical sparks as a stand-in for lightning. The now famous experiment showed what amino acids, the building blocks of proteins, could easily be generated from this primordial stew. But despite that seminal experiment, neither he nor others were able to take the next step: that of showing how life’s code could come from such humble beginnings.

By working with the simplest and elementary RNAs, physicists led by Rockefeller University’s Albert J. Libchaber, head of the Laboratory of Experimental Condensed Matter Physics, have now generated the first theoretical model that shows how a coded genetic system can emerge from an ancestral broth of simple molecules. “All these molecules have different properties and these properties define their interactions,” says first author Jean Lehmann, whose work appears in the June issue of . “What are the constraints that allow these molecules to self-organize into a code? We can play with that.”

The is a triplet code such that every triplet sequence of letters on (mRNA) corresponds to one of the 20 amino acids that make up proteins. Molecular adaptors called transfer RNAs (tRNAs) then convert this information into proteins that can achieve some specific tasks in the organism. Let’s say that each triplet sequence on mRNA, known as a codon, represents an outlet that can only accept a tRNA with a complementary anticodon. Translation works because each codon-anticodon match corresponds with an amino acid. As each tRNA is plugged in, a chain of amino acids is formed in the same order as the codons until translation is complete.

However, primitive tRNAs were not as finicky as tRNAs are today and could load any amino acid known to exist during the time of prebiotic Earth. Without the ability of tRNA to discriminate between various amino acids, such a random system might not be able to self-assemble into a highly organized code capable of supporting life.

To find out if it could, Libchaber and Lehmann, together with Michel Cibils at Ecole Polytechnique Federale de Lausanne in Laussane, Switzerland, worked with a simple theoretical system. They took two of the simplest amino acids thought to exist billions of years ago, two primitive tRNAs and an RNA template with two complementary codons, and then developed an algorithm to incrementally change the concentration of each molecule. Their goal was to see which conditions, if any, could coax the system to specifically translate codons in a non-random fashion. They found that the properties of the molecules set the concentrations at which the molecules needed to exist for a coded regime to emerge.

At these concentrations, the scientists found that a vetting process began to unfold whereby the tRNA and the amino acid began to seek each other out. All in all, an elementary translation process depended on two time scales: the time during which a tRNA remains bound to its codon (hybridization) and the time it takes for the amino acid on that tRNA to form a new chemical bond with the amino acid next to it (polymerization).

“It takes a lifetime for the tRNA to dissociate from its codon,” says Libchaber, who is also Detlev W. Bronk Professor at Rockefeller. “If it takes the amino acid loaded on the RNA longer than a lifetime to polymerize to an amino acid nearby, the selection of tRNA and amino acid doesn’t occur. But when the two lifetimes are comparable, even when there is nonspecific loading of an amino acid, a selection process begins to take hold because some amino acids would be more adaptive during that time span -- and start what would be the beginning of a code.”

Although Libchaber and Lehmann point out that the analysis certainly does not provide a full picture of the problem, the work nonetheless brings us one step closer to understanding how Life first began. “The dream of physicists is to create elementary life,” Libchaber says. “Then we would know that we understand something.”

More information: PLoS One: June 2009

Provided by Rockefeller University

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User comments : 14

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E_L_Earnhardt
1.3 / 5 (3) Aug 07, 2009
O.K. so eliminate ALL "amino acid"! We have an idea of it's construction. Let's look for the rest!
Alexa
3 / 5 (10) Aug 07, 2009
..The dream of physicists is to create elementary life..
By AWT the life evolution follows an ancient Oparin's coacervate theory. Coacervates are tiny oily droplets, which are precipitating spontaneously from saturated solutions of various organic compounds, the racemic mixtures of amino-acids and sugars in particular. Under high concentration and some shaking so called reverse micelles or even double layered liposomes can be formed. Such liposomes can behave like walking droplets, described recently:

http://focus.aps..../v15/st7

We can imagine, such droplets were precipitated from waves of ancient lakes at places, where organic compounds were pre-concentrated by wind and solar radiation and they were thrown at coast surface, covered by various surfactants. The droplets are attracted to them, so they started to climb around coast, collecting these materials in their cells. The most successful droplets become so large by such way, they fragmented into smaller ones under impact of next breaker wave, and whole process has repeated many times. Blastulation can be considered as a rudiment of this process by now.
Alexa
3.4 / 5 (8) Aug 07, 2009
Note that liposome model explains chirality of life in easy and natural way. Every liposome is very small (i.e. of high surface curvature) and it has a double surface, formed by hydrophobic membranes. In such system, the surface tension phenomena cannot be neglected, because the highly concave surface exhibits so-called superhydrophobicity, so it repels the carbohydrate molecules with many -OH functional groups, which are collected preferably inside of liposome. While the building blocks of organic matter, i.e. the amino-acids with hydrophobic radicals should adsorb at the outer surface of liposome, preferably. This forms a natural condition for spatial arrangement of t-RNA components at the phase interface of liposomes. They probably should form spontaneosly in thin dispersion of lipides in solution of of aminoacids and ribose mixture.
brant
1 / 5 (1) Aug 07, 2009
My headlines;

"Model suggests how life's code emerged from primordial soup created by a alien genetic engineering company(F&B Ticker FAB on the Universal Stock Exchange) over a billion years ago."
SDMike2
1 / 5 (2) Aug 07, 2009
So, with all this theory, where is the lab produced life?
thales
5 / 5 (2) Aug 08, 2009
So, with all this theory, where is the lab produced life?

Yeah! Why doesn't experiment precede theory? Oh right, it goes the other way. Your bad.
Alexa
3 / 5 (4) Aug 08, 2009
But system of oily droplets fullfils many criterions of life. Such droplet grows by collecting of chemical from their exterior, they're spliting into smaller one after reching of critical size, while maintaining their composition. This is basically what the inheritance means.
Velanarris
4.7 / 5 (3) Aug 08, 2009
It's amazing that they think mRNA must be one of the original chains that led to life, when they have zero evidence for it.

The original strands of DNA could have been wholly different before mRNA came about. When an organism is that small, and reproduces that fast, entire systemic changes occur over single generations. Perhaps we're missing a primary intermediate.
superhuman
not rated yet Aug 08, 2009
By AWT the life evolution follows an ancient Oparin's coacervate theory.

It is much more likely that life started with a self replicating molecule in solution and only later got encapsulated in lipid particles.

I think it is possible that one day we may have a good idea of how it all started but to get there we will first need to develop instruments capable of analyzing single molecules of complex polymers with atomic precision. Such instruments could be used to screen 3-4 billion years old minerals for the presence of complex polymers capable of encoding information. Such polymers could then be tested in a variety of conditions to see if they are capable of self replication and simple enough to have formed spontaneously on ancient Earth. Certainly a monumental task but if we are lucky it may allow us to discover the missing link between a rock and life.
LuckyBrandon
not rated yet Aug 08, 2009
yea i found the last research done on this subject more convincing that this. they effectively have shown nothing until they get it in the lab and accomplish the task. Even if some constituents are not entirely accurate (such as the mRNA velanarris mentioned), if we can reproduce it with what we do have and suspect, it will be very good evidence that the same or a similar reaction could have occured in the primordial stew.
you can still make good firey ass chili with peppers or with the powder after all.... :)
Alexa
3 / 5 (6) Aug 09, 2009
..It is much more likely that life started with a self replicating molecule in solution and only later got encapsulated in lipid particles...
IMO both these mechanism are closely related together, as the lipid membrane provides inheritance and primitive natural selection mechanism in periodically changing environment (least stable membranes will collapse first, so they're opened to mutations). Reactions in homogeneous phase lacks the selection, mutation and inheritance mechanism.

In brief, we cannot prepare artificial life in lab without shaking of dispersion, because natural selection requires changes of environment. I presume, this isn't very artificial requirement here, because many lipids can be formed in natural processes as the least soluble fraction of primordial soap.
Velanarris
5 / 5 (1) Aug 09, 2009
we're missing a primary intermediate
This is indeed possible, but RNA itself is able to play a role of both organels, both enzymes in ribozymes and RNA precursors were revealed in cosmic space which simplifies theory of evolution.


However, this molecule is far more complex than is necessary.

As SH said,
It is much more likely that life started with a self replicating molecule in solution and only later got encapsulated in lipid particles.

And I agree. Simple self replicating chains of base pairs are a more likely beginning. Start simple.
Slotin
3.7 / 5 (3) Aug 09, 2009
Nobody says, it isn't. But not in pure state, as primordial soup was very complex mixture of chemicals of different consistency.
Birger
not rated yet Aug 18, 2009
Freeman Dyson states long ago that the original information carrier would have been simpler than DNA (and possibly simpler than RNA). Apparently, there are many helical molecules that might have served the purpose, but at the cost of more transcription errors.
Of course, closing the experimental gap will certainly take time. Kudos to Libchaber, Lehmann and Cibils for getting this far!

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