Fundamental questions in evolution concern deep divisions in the living world and vertical versus horizontal information transfer. Two contrasting views are: (i) three superkingdoms Archaea, Eubacteria, and Eukarya based on vertical inheritance of genes encoding ribosomes; versus (ii) a prokaryotic/eukaryotic dichotomy with unconstrained horizontal gene transfer (HGT) among prokaryotes. Vertical inheritance implies continuity of cytoplasmic and structural information whereas HGT transfers only DNA. By hypothesis, HGT of the translation machinery is constrained by interaction between new ribosomal gene products and vertically (...) inherited cytoplasmic structure made largely of preexisting ribosomes. Ribosomes differentially enhance the assembly of new ribosomes made from closely related genes and inhibit the assembly of products from more distal genes. This hypothesis suggests experiments for synthetic biology: the ability of synthetic genomes to “boot,” i.e., establish hereditary continuity, will be constrained by the phylogenetic closeness of the cell “body” into which genomes are placed. (shrink)

The epistemology of the historical sciences has been debated recently. Cleland argued that the effects of the past overdetermine it. Turner argued that the past is underdetermined by its effects because of the decay of information from the past. I argue that the extent of over- and underdetermination cannot be approximated by philosophical inquiry. It is an empirical question that each historical science attempts to answer. Philosophers should examine how paradigmatic cases of historical science handled underdetermination or utilized overdetermination. I (...) analyze such a paradigmatic case, Darwin’s phylogenetic inferences. Darwin proceeded in three consecutive stages. The initial inference that there was some common cause of homologies was usually overdetermined. The final inference of the character traits of ancestor species was usually underdetermined. The second stage inference of the causal net that connected the species that share some common cause was inbetween. A comparison with Comparative Historical Linguistics demonstrates similar three stages of inference that move from the over- to the underdetermined. (shrink)