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.
Highlights
Frontiers in GeneticsThere is little corroboration content in grand hypotheses that have not yet endured severity of test, such as the rooting of the tree of life, the origin of the catalyzed peptide bond, or the structural origin of the ribosome [see Lienau and DeSalle (2009, 2010), for discussions]
Reviewed by: Nikhil Tyagi, University of South Alabama, USA Hemant K
The study was based on the identification of insertions of “branch” helices onto preexisting coaxially stacked “trunk” helices in a handful of crystallographic models (Petrov et al, 2014). This information was used to build a model of growth that added concentric layers around structures of the peptidyl transferase center (PTC), which were considered the origin and most ancient “heart” of the molecule. This “onion” model ordered “ancestral expansion segments” (AES) of rRNA in time using universal statements of ribosomal accretion: (i) “an helix will appear before an adenosine stack in an A-minor motif of rRNA” (Bokov and Steinberg, 2009), and (ii) “a coaxially stacked helical trunk will appear before its inserted branch” (Petrov et al, 2014)
Summary
There is little corroboration content in grand hypotheses that have not yet endured severity of test, such as the rooting of the tree of life, the origin of the catalyzed peptide bond, or the structural origin of the ribosome [see Lienau and DeSalle (2009, 2010), for discussions] In defense of their nomothetic method, they treated the phylogenetic approach exemplified by the work of Harish and Caetano-Anollés (2012) disdainfully using the Garbage-in Garbage-out (GiGo) computing adagio, implying that the parsimony method of phylogenetic systematics does not follow the principle of evidence, content and degree of corroboration.
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