Powerful Supercomputer Peers Into the Origin of Life

ScienceDaily (Oct. 4, 2010) — Supercomputer simulations at the Department of Energy's Oak Ridge National Laboratory are helping scientists unravel how nucleic acids could have contributed to the origins of life.

A research team led by Jeremy Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at University of Tennessee, used molecular dynamics simulation to probe an organic chemical reaction that may have been important in the evolution of ribonucleic acids, or RNA, into early life forms.

Certain types of RNA called ribozymes are capable of both storing genetic information and catalyzing chemical reactions -- two necessary features in the formation of life. The research team looked at a lab-grown ribozyme that catalyzes the Diels-Alder reaction, which has broad applications in organic chemistry.

"Life means making molecules that reproduce themselves, and it requires molecules and are sufficiently complex to do so," Smith said. "If a ribozyme like the Diels-Alderase is capable of doing organic chemistry to build up complex molecules, then potentially something like that could have been present to create the building blocks of life."

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New research at Oak Ridge National Laboratory explains
how a ribonucleic acid enzyme, or ribozyme (pictured),
uses magnesium ions (seen as spheres) to accelerate a
significant reaction in organic chemistry.
(Credit: Image courtesy of DOE/Oak Ridge National Laboratory)

Calilasseia wrote:Interesting that this ribozyme works using Mg2+ ions. Aside from the fact that there are 1.3 grams of magnesium dissolved in every litre of seawater (source: Kaye & Laby's Tables of Physical & Chemical Constants), a rich source of magnesium ions is, wait for it ... montmorillonite clays. Which have been a staple substrate for abiogenesis research for something like two decades.

Calilasseia wrote:Interesting that this ribozyme works using Mg2+ ions. Aside from the fact that there are 1.3 grams of magnesium dissolved in every litre of seawater (source: Kaye & Laby's Tables of Physical & Chemical Constants), a rich source of magnesium ions is, wait for it ... montmorillonite clays. Which have been a staple substrate for abiogenesis research for something like two decades.

Abstract
One aspect of the multifaceted proposal by A. G. Cairns-Smith, that imperfect crystals have the capacity to act as primitive genes by transferring the disposition of their imperfections from one crystal to another, is investigated. Rather than examining clay minerals, the most likely crystalline genes in the theories of Cairns-Smith, an experiment was designed in a model crystalline system unrelated to the composition of the prebiotic earth but suited to a well-defined test. Plates of potassium hydrogen phthalate riddled with dislocations were studied in order to ascertain whether, according to Cairns-Smith, parallel screw dislocations could serve as an information store with cores akin to punches in an old computer card. Evidence of screw dislocations was obtained from their associated growth hillocks through differential interference contrast microscopy, atomic force microscopy, and luminescence labeling of hillocks in conjunction with confocal laser scanning microscopy. The dispositions of growth active hillocks were quantified by fractal analysis. ‘Mother’ crystals were cleaved and inheritance was evaluated by the corresponding patterns of luminescence developed in their ‘daughters’ after continued growth in the presence of fluorophores. Luminescence microscopy proves to be a versatile tool for studying the dynamics of growth active hillocks. In the aggregate, this work speaks to the need for molecular mechanisms of dislocation nucleation.