Jan 252009

The other book I read over Christmas was “Dry Store Room No. 1: The Secret Life of the Natural History Museum” by Richard Fortey. This is an interesting tour of some of the past and present personalities behind the Natural History Museum, London. I found it a really interesting light read.

A good motto put forward in the book is “never throw anything away”, I was thinking that has some relevance for my recent experiences of computer files.

At times I thought Fortey’s views on museums a little old-fashioned, but then the very next sentence would launch into the importance of DNA sequencing in a modern museum and I would be slightly embarrassed to have doubted him. On the whole I was convinced by his views. He is very keen on the importance of naming species in the modern world, which although I don’t entirely disagree with think may ultimately be a bit of a distraction from the most important work of describing the big picture of diversity and the processes generating it. But he would probably agree with this too (he writes that we need to name things to understand their stories), its just that he talks about naming a lot and the importance of the processes generating biodiversity much less.

In previous eras he describes how keen amateurs became world experts by collecting all the relevant taxonomic literature on a group. In the recent past however, because of the amount of publications needed, amateurs could not hope to have access to enough literature to become experts on the taxonomy of any group. Now, he suggests, the internet may be reversing this trend as much more of the relevant literature is easily available. A great argument for open access publishing.

When discussing species status and hybridisation (pg 315-316) he has a quote that I like

“Since evolution is still happening all around us it would actually be rather surprising if there were not such difficulties of definition in nature.”

A light and entertaining read, worth the effort.

“Dry Store Room No. 1: The Secret Life of the Natural History Museum” Richard Fortey
Harper Press, 2008
ISBN: 978-0007209880

Jan 252009

Ben Goldacre is one of my favourite writers, I turn to his column in the Guardian each Saturday before anything else. I read his excellent book “Bad Science” over Christmas, and I really recommend it. He looks primarily at the reporting of science in the media but also about the science (lack of) in everyday life. He discusses for example homeopathy, the placebo effect and the MMR vaccine “hoax”. He writes really well, the book is funny (while at the same time being a bit scary) and its actually an important book. Important? Well, its more likely than anything I have seen to get people thinking about how we know what we know. That leads to a consideration of evidence, the scientific method and reduces the likelihood of been taken in by trendy but vacuous rubbish that can actually (as he discusses) be very dangerous.

It isn’t an academic text its a general book, but Bad Science is informative and interesting (and fun) even if you are a “proper” scientist who already knows about the scientific method, statistics and evidence.

One of his themes is that while science journalists are usually OK, when ridiculous “science” headlines appear in newspapers they are usually determined by an editor with a background in humanities who steers the story away from the trained science journalist to a general newspaper hack.

He is critical of humanities graduates who are journalists and know nothing of evidence and the scientific method. But I really wonder if modern biology graduates are so different, do they really learn this stuff on modern degree programs, or are they just sort of expected to assimilate it independently somehow? I have a colleague who was suggesting that we entirely abandon the first semester curriculum of the usual first year courses (diversity of life, ecology and evolution etc) and just teach the scientific method and experimental design. A very interesting idea.

Ben Goldacre’s blog http://www.badscience.net/

“Bad Science”
Ben Goldacre
Fourth Estate, London, 2008
ISBN: 978-0-00-724019-7

Sep 052008

I just received a copy of “Reading the story in DNA; a beginner’s guide to molecular evolution” by Lindell Bromham, OUP 2008, ISBN: 978-0-19-929091-8
I have only looked at it quickly but it is very impressive. I like the writing style. It is well produced. Figures are excellent. The parts I have read are full of common sense. It has a good mix of simplicity and depth. It seems at a good level for undergraduate students and some postgrads. It feels modern- a very very rare thing indeed for evolution books, as I often complain. It has “Techbox” sections describing such things as Genbank records, primer design, maximum likelihood methods. It has case studies- solving the mystery of the Chilean blob, using bioinformatics to describe endogenous retroviruses, horizontal gene transfer between parasitic plants and their hosts. Interestingly it also has “Heroes of the Genetic Revolution” boxes detailing the careers of some of the greats. Who would be your heroes?
OK so as I type this skimming through the book saying how much I like it I come across a nice picture and section on some work I contributed to on cryptic speciation in Brachionus rotifers[1]. So now it just looks like I’m sucking up, but I didn’t even know that was there when I started this post.

Anyway, it looks a great book.

1.Gómez A, Serra M, Carvalho GR & Lunt DH (2002) Speciation in ancient species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera). Evolution, 56(7):1431-1444, doi:1431-1444. 10.1111/j.0014-3820.2002.tb01455.x

Feb 122008

OK, so I was going to write about bioinformatics and phylogenetics in this blog, and here is my second post already that ignores both!
I just read a paper testing the relationship between beer consumption and publication output of ecologists in the Czech Republic. Apparently the higher your consumption the lower your total number of publications, total number of citations and citations per paper. Damn.
One of my colleagues just said she was very surprised that there wasn’t a positive relationship. I wouldn’t have been entirely surprised if the relationship had been the other way either- I’ve always thought most “thought science” was actually done in pubs and coffee rooms. But it seems that might not promote actually doing the experiment or writing the stuff up.

Grim, T (2008) “A possible role of social activity to explain differences in publication output among ecologists” Oikos, doi: 10.1111/j.2008.0030-1299.16551.x
“Publication output is the standard by which scientific productivity is evaluated. Despite a plethora of papers on the issue of publication and citation biases, no study has so far considered a possible effect of social activities on publication output. One of the most frequent social activities in the world is drinking alcohol. In Europe, most alcohol is consumed as beer and, based on well known negative effects of alcohol consumption on cognitive performance, I predicted negative correlations between beer consumption and several measures of scientific performance. Using a survey from the Czech Republic, that has the highest per capita beer consumption rate in the world, I show that increasing per capita beer consumption is associated with lower numbers of papers, total citations, and citations per paper (a surrogate measure of paper quality). In addition I found the same predicted trends in comparison of two separate geographic areas within the Czech Republic that are also known to differ in beer consumption rates. These correlations are consistent with the possibility that leisure time social activities might influence the quality and quantity of scientific work and may be potential sources of publication and citation biases.”

Feb 032008

So I don’t hate all books. Over Christmas I read Michael Lynch’s new book “The Origins of Genome Architecture”. One of the best books I have read in a long time. Well-written, clearly argued, well referenced and important. If you like molecular evolution, genomics or related topics you should definitely read this. I learned a lot about topics I already thought I understood well. The book is in some ways similar to his 2007 PNAS paper “The frailty of adaptive hypotheses for the origins of organismal complexity” but much more extensive in both depth and breadth. I have been very frustrated by comparative genomics and some of molecular evolution for a very long time. This book made me feel I wasn’t alone. The logic is simple, clear and devastating, providing an intellectual framework that will be useful to many wanting to look at genomic data.
If you are annoyed by the ease with which adaptationist explanations for pretty much anything in genomics are published you might also like to check out Jonathan Eisen’s “Adaptationomics awards“.

[Michael Lynch “The Origins of Genome Architecture”, 2007, Sinauer Associates, ISBN 9780878934843]
Strangely the UK Amazon site lists this book as authored by Michael Lynch and Bruce Walsh, although there is no mention of Walsh on my actual copy of the book. The US Amazon site lists only Lynch.