Logic and philosophy
evolvingthoughts | June 18, 2006
The second main approach to a natural conception of microbial species (by which I mean, as opposed to operational, practical or conventional ones, collectively called "artificial" conceptions) is what I will call the Quasispecies Model. According to the concept developed by Manfred Eigen for viral species, a quasispecies ("as-if-species") is a cluster of genomes in a genome space of the dimensionality the number of loci. A quasipecies is in effect a cloud of genomes, clustering around a "wild-type" coordinate (that is, genome) that may or may not actually have an extant or extinct instance…
evolvingthoughts | June 17, 2006
The cluster of genomes of asexual organisms forms what is called a "phylotype" (Denniston 1974, a term coined by C. W. Cotterman in unpublished notes dated 1960; I like to track these things down). Phylotype is a taxon-neutral term, though, that is determined entirely by the arbitrary level of genetic identity chosen. For example, "species" in asexuals might be specified as being 98%+ similarity of genome, or it might be 99.9%+ (I have seen both in the literature). A phylotype of, say 67% or 80% might be used for other purposes (such as identifying a disease-causing group of microbes).
The…
evolvingthoughts | June 16, 2006
Reposted from the old blog.
OK, this is one of a series of posts in which I will play with ideas that might will become a paper.
The problem is this: usually we define a species as a group of related organisms that share genes (or a gene pool, which amounts to the same thing). Sometimes we include also ecological considerations (either in the form of natural selection, or in terms of sharing a niche).
But many microbial species either do not share genes to reproduce, or they can but do not need to. So, the question is sometimes raised whether microbes (of this kind) form species at all…
evolvingthoughts | June 10, 2006The Ask a Seedblogger question this week is
Assuming that time and money were not obstacles, what area of scientific research, outside of your own discipline, would you most like to explore? Why?
That's an easy one: the one area I most miss having done well is: mathematics. Statistics, calculus, you name it, I don't know it. I actually did quite well as school but I had bad teachers and curricula (except for my last one, but I left school before year's end), and didn't see the point, quite frankly. Now I do. You can't address any area of knowledge without coming into contact with mathematics…
evolvingthoughts | June 10, 2006
Originally, science began when people started to give their papers and results publicly, for discussion and correction. Back in the days of the Royal Society and other subsequent bodies, a talk would be read to the society and then published in their proceedings, and there was an immediate live feedback. Nowadays the process is much more ossified - research, give talks to your research group, present posters and if you are really lucky a talk at a major conference, then send in the paper for peer review. Sometimes it works, sometimes it doesn't. Any researcher has played reviewer roulette in…
evolvingthoughts | June 8, 2006
Darwin, evolution, and Popper Creationists often appeal to authority in the person of the well-known philosopher, Sir Karl Popper, who said, they say, that evolution is not scientific. Mark Isaak's marvellous Index to Creationist Claims is in the process of adding a section on this. I responded, and so I thought I'd add it to my blog, in part because it is interesting how Popper actually saw evolution.
Popper originally said that evolution (by which he meant natural selection) was a "metaphysical research programme". Popper, unlike the logical positivists he opposed, held that…