Life is a complex phenomenon embodying many aspects, both physical and metaphysical, the discussion of any one of which is usually carried out under the rubric “the origin of life (OL)”. The article by H. Krammer et al. [1] (see below) touches upon a small but important aspect of the OL problem.
Kramer et al. [1] appears to have demonstrated what may be called “the principle of the thermal energy gradient-driven replication” of segments of RNA hairpins (see Figure 1).
There are two kinds of RNA “replications” — “physical” and “chemical”. The former does not involve any chemical reactions (i.e., covalent bond formations) while the latter does. As the following quote indicates, Krammer and his colleagues “explore a physical, not chemical, replication mechanism . . .”. in their paper. “Physical replications” implicate conformational changes of pre-existing biopolymers, whereas “chemical replications” involve synthesizing complementary sequences starting from a set of monomers or small fragments. It is possible that the origin of life on this planet 3.5 billion years ago depended on both of these two kinds of replications of RNA molecules.
In 1991 [2], I proposed a “thermal energy gradient-driven” mechanism for replicating RNA molecules “chemically”, not “physically”, thus complementing the mechanism of RNA replication proposed by Krammer et al. [1]. This chemical mechanism was named the “Princetonator” in recognition of the original ideas suggested by P. W. Anderson and his coworkers at Princeton. What would be most interesting may be to apply the experimental technique developed by Krammer and his group to testing the validity of the detailed molecular steps proposed in the Princetonator model of the origin of life. The excerpt from my recent book [3] is attached below [4] where I describe the Princetonator and its relation to the concept of the conformon, the postulated driving force for all goal-directed molecular motions in the living cell, including the first living cell.
References:
[1] Krammer, H., Möller, F. M., and Braun, D. (2012). Thermal, Autonomous Replicator Made from Transfer RNA, Phys. Rev. Lett. 108, 238104.
[2] Ji, S. (1991). Biocybernetics: A Machine Theory of Biology, in : Molecular Theories of Cell Life and Death, Rutgers University Press, New Brunswick, 1-237. (see Chapter 13, Molecular Theory of the Living Cell, 2012).
[3] Ji, S. (2012). Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and Biomedical Applications. Springer, New York.
[4] Ji, S. (2012). Mechanisms of the Origin of Life, Chapter 13, Molecular Theory of the Living Cell, op. cit.
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http://link.aps.org/doi/10.1103/PhysRevLett.108.238104
Phys. Rev. Lett. 108, 238104 (2012) DOI:10.1103, “Thermal, Autonomous Replicator Made from Transfer RNA”, Hubert Krammer, Friederike M. Möller, and Dieter Braun.
Abstract: Evolving systems rely on the storage and replication of genetic information. Here we present an autonomous, purely thermally driven replication mechanism. A pool of hairpin molecules, derived from transfer RNA replicates the succession of a two-letter code. Energy is first stored thermally in metastable hairpins. Thereafter, energy is released by a highly specific and exponential replication with a duplication time of 30 s, which is much faster than the tendency to produce false positives in the absence of template. Our experiments propose a physical rather than a chemical scenario for the autonomous replication of protein encoding information in a disequilibrium setting.
http://physics.aps.org/synopsis-for/10.1103/PhysRevLett.108.238104 Synopsis: Thermal Cycling Drives a Fast RNA Replicator .
The steps by which molecules in the primordial soup came together to form the genetic backbone of life are largely unknown. One approach to finding out is to artificially create basic life functions in the laboratory and consider if such conditions might have been possible in the Earth’s past. Writing in Physical Review Letters, Hubert Krammer and colleagues at the Ludwig Maximilian University of Munich in Germany show they are able to drive the replication of segments of tRNA (transfer ribonucleic acid), the molecule responsible for translating genetic code into the production of specific proteins, using a purely thermal process. Krammer et al. begin by rapidly cooling a solution of four halves of tRNA from high temperatures to 10 degrees C so that the molecules form hairpins, ”a state where the strand forms a closed loop on itself, except for a snippet of a sequence of bases, called a “toe hold”. It is this toe hold, which, in principle, carries enough information to encode a protein, that the authors try to protect and replicate by using a thermal process to coax the hairpins to open and pair to a complementary strand. When Krammer et al. thermally cycle the solution between 10 degrees C and 40 degrees C, the energy stored in the hairpin (which prefers it to bind to a complementary pair instead of itself) compensates for the loss of entropy associated with the molecules pairing up with their partners. This thermally driven process occurs on a relatively fast time scale of about 30 seconds, an important factor since molecules need to replicate faster than they degrade. According to the authors, convection currents in prebiotic liquids could have provided the necessary quenching and thermal cycling. Jessica Thomas.
