A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons.

http://link.springer.com/content/pdf/10.1007/978-1-4684-4988-4_7.pdf

Evolution of Ribosomal DNA

The procedures of review and revision of a scientific article can be seen as part of the negotiation of the status that the scientific community will assign to the text's knowledge claim. This study locates some textual features of this negotiation by considering two articles by two biologists, the comments referees and colleagues made on them, and the authors' responses to these comments. The articles illustrate contrasting problems in the creation of a persona-one author is a well-known researcher in his field, and the other is publishing his first article in what is for him a new area. But they both have disagreements with journal editors and referees over the placement of their findings in a hierarchy of claims. And they both revise their articles to make them more conventional in form. Each article was reviewed five times before being accepted: while the long review makes the cases atypical, the layers of criticisms and responses allow us to see in detail processes that are usually compressed and dec...

https://www.jstor.org/stable/pdfplus/285398.pdf

Texts as Knowledge Claims: The Social Construction of Two Biology Articles:

Case studies of two proposals for research funding serve as examples of how scientific texts are the products of a community of researchers. Comparisons of successive versions of the proposals show...

The Social Construction of Two Biologists’ Proposals

The ribosome as a missing link in the evolution of life.

A model is proposed for the early evolution of the coding mechanism. A primordial RNA embodies the functions of today's nucleic acids in a single molecule. The molecule is generated by successive rounds of self-priming and -templating. After proximity is assured by enclosure in a cell, the functions can be partitioned among more efficient specialized molecules. The prediction of sequence homologies in later forms prompted a search for matches between t- and r-RNAs. These are described. Their distributions offer clues to their origins. The existance of overlapping homologies indicates an approach to the reconstruction of an ancestral molecule.

tRNA-rRNA sequence homologies: a model for the origin of a common ancestral molecule, and prospects for its reconstruction

Many tRNAs ofE. coli and yeast contain stretches whose base sequences are similar to those found in their respective rRNAs. The matches are too frequent and extensive to be attributed to coincidence. They are distributed without discernible pattern along and among the RNAs and between the two species. They occur in loops as well as in stems, among both conserved and non-conserved regions. Their distributions suggest that they reflect common ancestral origins rather than common functions, and that they represent true homologies.

Robert Widdowson

Papers

tRNA-rRNA sequence homologies: a model for the origin of a common ancestral molecule, and prospects for its reconstruction

tRNA-rRNA sequence homologies: Evidence for a common evolutionary origin?