October 23, 2014 / Arlin Stoltzfus / 3 Comments
In a recent QRB paper with David McCandlish, we review the form, origins, uses, and implications of models (e.g., the familiar K = 4Nus) that represent evolutionary change as a 2-step process of (1) the introduction of a new allele by mutation, followed by (2) its fixation or loss.
What could be surprising about these “origin-fixation” models, which are invoked in theoretical models of adaptation (e.g., the mutational landscape model) and in widely used methods applied to phylogenetic inference, comparative genomics, detecting selection, modeling codon usage, and so on?
Quite a lot, it turns out. (more…)
October 17, 2014 / Arlin Stoltzfus / 2 Comments
Getting stuff right
Early in the evolution of the Sequence Ontology, it was noted (by gadflies like myself) that SO asserts the relationship of mRNA to gene to be the “part of” relationship. This is obviously wrong. An RNA molecule is not part of a DNA molecule. Saying that mRNA is part of a gene is like saying that a CD with some audio chapters from a book is part of that book.
Ontologies are supposed to support formal reasoning: errors in representation will lead inevitably to erroneous results. For instance, if we are reasoning about the chemical composition of a cell using mRNA part_of gene as a constraint, we would conclude falsely that the mass of DNA must always be at least as much as the mass of mRNA, because the mass of a thing is always at least as great as the mass of some specified parts.
(more…)