Matthew A. Carrigan

A statistical view of FMRFamide neuropeptide diversity.

FMRFamide-like peptide (FLP) amino acid sequences have been collected and statistically analyzed. FLP amino acid composition as a function of position in the peptide is graphically presented for several major phyla. Results of total amino acid composition and frequencies of pairs of FLP amino acids have been computed and compared with corresponding values from the entire GenBank protein sequence database. The data for pairwise distributions of amino acids should help in future structure-function studies of FLPs. To aid in future peptide discovery, a computer program and search protocol was developed to identify FLPs from the GenBank protein database without the use of keywords.

The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion.

Background Gene duplication is a source of molecular innovation throughout evolution. However, even with massive amounts of genome sequence data, correlating gene duplication with speciation and other events in natural history can be difficult. This is especially true in its most interesting cases, where rapid and multiple duplications are likely to reflect adaptation to rapidly changing environments and life styles. This may be so for Class I of alcohol dehydrogenases (ADH1s), where multiple duplications occurred in primate lineages in Old and New World monkeys (OWMs and NWMs) and hominoids. Methodology/Principal Findings To build a preferred model for the natural history of ADH1s, we determined the sequences of nine new ADH1 genes, finding for the first time multiple paralogs in various prosimians (lemurs, strepsirhines). Database mining then identified novel ADH1 paralogs in both macaque (an OWM) and marmoset (a NWM). These were used with the previously identified human paralogs to resolve controversies relating to dates of duplication and gene conversion in the ADH1 family. Central to these controversies are differences in the topologies of trees generated from exonic (coding) sequences and intronic sequences. Conclusions/Significance We provide evidence that gene conversions are the primary source of difference, using molecular clock dating of duplications and analyses of microinsertions and deletions (micro-indels). The tree topology inferred from intron sequences appear to more correctly represent the natural history of ADH1s, with the ADH1 paralogs in platyrrhines (NWMs) and catarrhines (OWMs and hominoids) having arisen by duplications shortly predating the divergence of OWMs and NWMs. We also conclude that paralogs in lemurs arose independently. Finally, we identify errors in database interpretation as the source of controversies concerning gene conversion. These analyses provide a model for the natural history of ADH1s that posits four ADH1 paralogs in the ancestor of Catarrhine and Platyrrhine primates, followed by the loss of an ADH1 paralog in the human lineage.

1 Setting the Stage: The History, Chemistry, and Geobiology behind RNA

TWO RNA WORLD HYPOTHESES Because they are organic molecules, ribonucleic acids can be understood using the language of organic chemistry. Those who accept the premise in the title of this book, however, regard RNA as very special organic molecules. Today on earth, given appropriate collections of catalysts from modern life, RNA can direct its own replication, where the replicates are imperfectly made, and where the imperfections are themselves replicatable. Such a combination of properties allows an organic system to support Darwinian evolution, the only process known to naturally generate functional behavior in chemistry. Only one other class of molecules, DNA, is known to be similarly special. In modern life on earth, DNA and RNA collaborate with a third encoded class of biomolecules, proteins, to support Darwinian evolution. This collaboration, in turn, generates the enormous range of life that today occupies nearly every habitable niche on the planet. Those interested in the origin of Darwinian evolution have for four decades speculated that RNA might have supported Darwinian evolution without other encoded molecules (Rich 1962), either DNA or proteins. The “RNA World” title has come to be associated with this speculation (Gilbert 1986). The notion of an RNA World relates to two classes of hypotheses. One class holds that an earlier form of life on earth used RNA as the only genetically encoded component of biological catalysis. Evidence for this is found within the details of the biochemistry of contemporary life on earth and appears to be reasonably well supported (Crick 1968;Visser...

The Nature of Life: Classical and Contemporary Perspectives from Philosophy and Science: Is there a common chemical model for life in the universe?

A review of organic chemistry suggests that life, a chemical system capable of Darwinian evolution, may exist in a wide range of environments. These include non-aqueous solvent systems at low temperatures, or even supercritical dihydrogen-helium mixtures. The only absolute requirements may be a thermodynamic disequilibrium and temperatures consistent with chemical bonding. A solvent system, availability of elements such as carbon, hydrogen, oxygen and nitrogen, certain thermodynamic features of metabolic pathways, and the opportunity for isolation, may also define habitable environments. If we constrain life to water, more specific criteria can be proposed, including soluble metabolites, genetic materials with repeating charges, and a well defined temperature range.