Robust monomer-distribution biosignatures in evolving digital biota

Because organisms synthesize component molecules at rates that reflect those molecules' adaptive utility, we expect a population of biota to leave a distinctive chemical signature on their environment that is anomalous given the local (abiotic) chemistry. We observe the same effect in the distribution of computer instructions used by an evolving population of digital organisms, and characterize the robustness of the evolved signature with respect to a number of different changes in the system's physics. The observed instruction abundance anomaly has features that are consistent over a large number of evolutionary trials and alterations in system parameters, which makes it a candidate for a non-Earth-centric life-diagnosticComment: 22 pages, 4 figures, 1 table. Supplementary Material available from C

A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration

Improved genetic algorithm for multiple sequence alignment using segment profiles (GASP)

This paper presents a novel genetic algorithm (GA) for multiple sequence alignment in protein analysis. The most significant improvement afforded by this algorithm results from its use of segment profiles to generate the diversified initial population and prevent the destruction of conserved regions by crossover and mutation operations. Segment profiles contain rich local information, thereby speeding up convergence. Secondly, it introduces the use of the norMD function in a genetic algorithm to measure multiple alignment Finally, as an approach to the premature problem, an improved progressive method is used to optimize the highest-scoring individual of each new generation. The new algorithm is compared with the ClustalX and T-Coffee programs on several data cases from the BAliBASE benchmark alignment database. The experimental results show that it can yield better performance on data sets with long sequences, regardless of similarity

Defining Life

Any definition is intricately connected to a theory that gives it meaning. Accordingly, this article discusses various definitions of life held in the astrobiology community by considering their connected “theories of life.” These include certain “list” definitions and a popular definition that holds that life is a “self-sustaining chemical system capable of Darwinian evolution.” We then act as “anthropologists,” studying what scientists do to determine which definition-theories of life they constructively hold as they design missions to seek non-terran life. We also look at how constructive beliefs about biosignatures change as observational data accumulate. And we consider how a definition centered on Darwinian evolution might itself be forced to change as supra-Darwinian species emerge, including in our descendents, and consider the chances of our encountering supra-Darwinian species in our exploration of the Cosmos. Last, we ask what chemical structures might support Darwinian evolution universally; these structures might be universal biosignatures. Key Words: Evolution—Life—Life detection—Biosignatures. Astrobiology 10, 1021–1030

Transcription and translation in an RNA world

The RNA world hypothesis requires a ribozyme that was an RNA-directed RNA polymerase (ribopolymerase). If such a replicase makes a reverse complementary copy of any sequence (including itself), in a simple RNA world, there is no mechanism to prevent self-hybridization. It is proposed that this can be avoided through the synthesis of a parallel complementary copy. The logical consequences of this are pursued and developed in a computer simulation, where the behaviour of the parallel copy is compared to the conventional reverse complementary copy. It is found that the parallel copy is more efficient at higher temperatures (up to 90°C). A model for the ribopolymerase, based on the core of the large subunit (LSU) of the ribosome, is described. The geometry of a potential active site for this ribopolymerase suggests that it contained a cavity (now occupied by the aminoacyl-tRNA) and that an amino acid binding in this might have ‘poisoned’ the ribopolymerase by cross-reacting with the nucleoside-triphosphate before polymerization could occur. Based on a similarity to the active site components of the class-I tRNA synthetase enzymes, it is proposed that the amino acid could become attached to the nascent RNA transcript producing a variety of aminoacylated tRNA-like products. Using base-pairing interactions, some of these molecules might cross-link two ribopolymerases, giving rise to a precursor of the modern ribosome. A hybrid dimer, half polymerase and half proto-ribosome, could account for mRNA translocation before the advent of protein elongation factors