Author: Mike White

Genomes, Books, and Science Fiction

Time to (re)read Thomas Kuhn

I will admit that I’m a sucker for book anniversaries of any sort, and since this month marks the 50th anniversary of the publication of The Structure of Scientific Revolutions, here’s your excuse to finally read it. I’ve been looking for an excuse to re-read it, since the first go around apparently made no impression on my brain – I will admit that I can’t say a single, intelligent thing about it.

To get yourself jazzed up, you can read the appreciation in The Guardian, and you can buy yourself the swanky new 50th anniversary edition. As for me, I’m sticking with my less glitzy second edition with the cool, somewhat minimalist cover.

Here’s our schedule, with discussions on Fridays: Continue reading “Time to (re)read Thomas Kuhn”

Sunday Science Poem: Mitochondrial Mothers

Despite my experiences of crushing boredom studying cell trafficking pathways in grad school, there was no way I was going to just walk past a book of poems titled Cell Traffic without stopping. In this delightful book, poet Heid E. Erdrich mixes themes of genetics, motherhood, ancestry, and Native American mythology to produce poetry that feels very relevant in a day when we can read information about our ancestry from the text of our DNA.

Today’s Sunday Poem is “Seven Mothers.” The title refers to the seven major, maternally inherited mitochondrial haplogroups popularized by Bryan Sykes in The Seven Daughters of Eve. Since Sykes’ book was published, we have developed a greater ability to use genetic variation in our nuclear DNA to trace our ancestry, and mitochondrial DNA now plays less of a role in our efforts to understand human ancestry than it once did. But it’s hard to beat the impact of mitochondrial maternal ancestry on our imaginations. Continue reading “Sunday Science Poem: Mitochondrial Mothers”

Not being an experimentalist is no excuse for not understanding experiments

Why are so many non-reproducible experiments so highly cited? Part of the problem may be a growing cultural change in biology: not everyone does experiments now. More and more, biologists are divided into experimentalists and computational biologists. (I hesitate to say theorists, because computational biologists don’t theorize about biology any more than experimental biologists.) The reason for this division is because, thanks to the growing availability of big data sets, it is possible to learn something new by analyzing already available data.

This is a positive development, but the risk is that we create a class of biologists who don’t understand the subtleties of the experiments that produced the data they work with. Continue reading “Not being an experimentalist is no excuse for not understanding experiments”

Certifiably reproducible science… meh

A movement is afoot to create formal structures to reproduce experiments (Ars Technica):

Almost nobody goes back and repeats something that’s already been published, though.

But maybe they should. At least that’s the thinking behind a new effort called the Reproducibility Initiative, a project hosted by the Science Exchange and supported by Nature, PLoS, and the Rockefeller University Press.

John Timmer goes on to write about reasons why some people think this is a waste of time. I agree with all of these reasons. Continue reading “Certifiably reproducible science… meh”

Is scientific writing designed to suck?

I disagree with this at Scientific American:

The conventions of scientific writing have two goals: to convey authority, and to demonstrate the author’s objectivity. Conventions that convey authority include a standardized article structure (Introduction, Methods, Results, Conclusion); booster words (Scientific articles contain more booster words [clearly, obviously] than other research articles, but less hedge words [may, seem, possibly].); and invocations of doom (To justify experiments articles often begin with overblown sentences like “As we all know, all species are dying.”).

Conventions that convey objectivity include the erasure of scientists as actors in their own experiments via past passive voice (e.g. “the chemicals were heated” versus “I heated the chemicals”) and the use of nominalizations or zombie nouns, which make actions themselves less visible by presenting their results as states of being (Compare “The rate was a reflection of population density increases,” to “The rate reflects an increased population density.”). – “Scientists as Writers”, Laura Jane Martin

Let’s be clear that we’re talking about research papers here, and not popularization of science. The goals of scientific convention are to present your data and make arguments as clearly and efficiently as possible.

When I read a scientific paper I’m not asking myself, ‘are these authors objective?’ Frankly, I don’t care whether they’re objective or not. Objectivity is overrated. I want to 1) understand what the authors did, 2) judge whether their methodology is sound, and 3) decide whether I agree with their arguments about the data.

Actually, as Laura Jane Martin points out, “today’s conventions emerged in a seventeenth century attempt to make scientific writing clearer.” So in fact I don’t disagree with her. Continue reading “Is scientific writing designed to suck?”