Monday, 10 July 2017

Reading forwards

I wrote recently about publishing the results of my PhD thesis research. That paper in the Journal of Biogeography was a second attempt to get my stuff into print: an earlier draft had been rejected by a slightly more prestigious and definitely more main-stream population genetics journal. Many previous papers had been published showing that gene frequencies of domestic cats differed among different populations, but my paper was the second that was a sort of meta-analysis comparing the results from several different earlier studies. It was rejected for two reasons 1) serious population genetics research was then carried out on Drosophila fruit-flies and mice not on domestic cats 2) A key part of my analysis used a 1973 paper by Lewontin and Krakauer to show that one could detect natural selection in the populations. I was happy to cite that paper because Richard Lewontin [bloboprev] was a giant of population genetics and the L&K analysis was so clearly expressed and convincingly argued. Their contention was that if you have a bunch of populations cross-tabulated against a bunch of genetic traits you can carry out an analysis of variance. If one of the traits has more variance than the others, a likely explanation is that differential selection is driving the gene frequencies for that trait apart. It was neat, I had the data, I was computer literate so could apply the LK test and so I did.

In his interview Eugene Garfield developed the idea of citation consciousness. It is the requirement that, if you are going to cite an earlier paper, you have to ensure that it is still valid: by using Garfield's citation tools to work forward from that key paper to see who else has cited it and to what effect. I, publishing my thesis in 1983, had conspicuously failed to carry out this necessary validation task. It turned out that in the months after Lewontin and Krakauer published, there was a shit-storm of criticism from Masatoshi Nei, Alan Robertson [BIG cheeses in the field] and other savvy population geneticists who haven't made it into Wikipedia yet. Nei & Co rubbished the L&K paper, exposing its false assumptions, tendentious findings and specious reasoning. I was totally unaware of this slag-fest because I was living in a bubble. The referees for the journal where I submitted my first attempt were up to speed with the literature of theoretical population genetics 1973-1983, saw that I wasn't and that cast a wider doubt upon my competence: consequence? reject!

Later on, I moved away from bigger-than-a-breadbox population genetics and into biological sequence analysis, that was a more recent field and there were no 10 year-old papers for me not to know about. Apart from that my boss was ambitious, and really on the button and wasn't going to allow me to be vague about the literature or anything else.

It was embarrassing to be caught with my trousers round my ankles and I think I blamed my thesis committee for not putting me right when I came to defend my thesis. That was quite unfairly shifting the burden of responsibility: when you get a PhD you are - finally - an adult. You can't blame Mammy anymore for deficiencies in your scientific practice. I could have decided then that I was unable to carry out the basic tasks of science and gone off to be a carpenter. I'm glad I didn't, and I think I've been a net contributor to the task of making sense of the World.

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