title: Ribosomal accretion, apriorism and the phylogenetic method: a response to Petrov and Williams.
abstract: Historical (ideographic) and non-historical (nomothetic) studies of ribosomal accretion appear to arrive at diametrically opposite conclusions. Phylogenetic analysis of thousands of RNA molecules and protein structures in hundreds of genomes supports the structural origin of the ribosome in RNA decoding and ribosomal mechanics. Predictions from extant features in a handful of rRNA structural models of the large ribosomal subunit support its origin in protein biosynthesis. In recent correspondence, one of us reported that correcting dismissals of conflicting data and avoiding unwarranted assumptions of the nomothetic method reconciled conclusions. In response, Petrov and Williams dismissed our arguments claiming we did not understand their algorithmic model of ribosomal apical growth. Instead, they controverted the historical approach. Here we show that their objections to the phylogenetic method are unjustified, that their algorithm subjectively guarantees back-in-time molecular deconstructions toward the protein biosynthetic core, and that processes of ribosomal growth are much more complex. We prompt abandoning apriorism, decreasing ad hoc hypotheses and integrating historical and non-historical scientific methods.
authors.affiliation: Carl R. Woese Institute for Genomic Biology, University of Illinois , Urbana, IL, USA.
authors.forename: Derek
authors.initials: D
authors.lastname: Caetano-Anollés
authors.affiliation: Carl R. Woese Institute for Genomic Biology, University of Illinois , Urbana, IL, USA ; Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois , Urbana, IL, USA.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Caetano-Anollés
keywords: coaxial helical stacking; molecular evolution; rRNA structure; ribosome origins