Friday, 17 August 2007

The Wonders of Modern Technology

I think I submitted a paper today, but I'm not sure. At least I tried to.

The problem was the electronic submission. I was sending the manuscript (it's on Bayesian variable selection, for anyone who cares) to a statistics journal, so they like things in LaTeX. I had prepared the manuscript that way (my co-author is a LaTeX guy as well, so it was a way of learning how to use it). But they wanted the initial submission as a .pdf.

LaTeX writes documents out as Postscript files, and the pdf maker on TeXmaker doesn't like my figures. So, I had to make a Postscript version, then found out I couldn't convert to pdf on my Windoze machine, so I moved over to my Linux box, and used ps2pdf to convert it. The manuscript looked fine in Acrobat. Then I tried to submit. OK, first I realised we had forgotten to write an abstract, so had to go back, do that, write a postscript version, move to Linux and convert to a pdf. When I (finally) uploaded the pdf, the journal's software tells me it's not a pdf! Wha? It looks like one to every pdf reader I can lay my hands on (which is 3 or 4 - isn't Linux great?). But for some reason...

In the end I just emailed everything to them, with an apologetic note, asking how I could convert my pdf to a pdf. They haven't answered.
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Wednesday, 15 August 2007

Turf War!

The latest from the Beeb:
BBC NEWS | Science/Nature | Chernobyl 'not a wildlife haven'

The back-story is that in 1986 a nuclear reactor in Chernobyl blew up, throwing radioactivity over a wide area. The Soviet authorities decided that the area wasn't safe, so they evacuated everyone from around it, and basically built a big fence and put up signs with "Keep Out" written on them (in Russian or Ukranian, presumably). This sort of site is irresistible to ecologists: except for the radioactive bits, the habitat should revert back to a natural state.

So, the conclusion of one group of ecologists is that everything is rosy around Chernobyl, with lots of rare species hiding from mankind under a protective mushroom cloud. In contrast, the BBC report another paper by Anders Pape Møller and Tim Mousseau, Species richness and abundance of forest birds in relation to radiation at Chernobyl. This is the abstract:
The effects of low-level radiation on the abundance of animals are poorly known, as are the effects on ecosystems and their functioning. Recent conclusions from the UN Chernobyl forum and reports in the popular media concerning the effects of radiation from Chernobyl on animals have left the impression that the Chernobyl exclusion zone is a thriving ecosystem, filled with an increasing number of rare species. Surprisingly, there are no standardized censuses of common animals in relation to radiation, leaving the question about the ecological effects of radiation unresolved. We conducted standardized point counts of breeding birds at forest sites around Chernobyl differing in level of background radiation by over three orders of magnitude. Species richness, abundance and population density of breeding birds decreased with increasing level of radiation, even after controlling statistically for the effects of potentially confounding factors such as soil type, habitat and height of the vegetation. This effect was differential for birds eating soil invertebrates living in the most contaminated top soil layer. These results imply that the ecological effects of Chernobyl on animals are considerably greater than previously assumed. (emphasis added)

Going on this (unfortunately I can't get access to the full paper), what the authors found is that individuals and populations suffer more in areas of higher radiation. Makes sense. But look at the bit I bolded. In a scientific paper, this is really sniffy and aggressive: it's tantamount to accusing someone of distorting reality.

But, if we look at the science of both groups, there doesn't seem to be any conflict in what they report. The people who are saying that things are going well are comparing the exclusion zone to what it would have been like without the accident. As one of them writes:
However, it cannot be said that radiation is good for wildlife. Instead, the elimination of human activities such as farming, ranching, hunting and logging are the greatest benefit, and it can be said that the world's worst nuclear power plant disaster is not as destructive to wildlife populations as are normal human activities.
In other words, the accident caused the creation of a thriving conservation area. It wasn't planned, but it still happened. Isn't that great?

What Møller and Mousseau show is that, within the exclusion zone, the biodiversity is lower in areas with higher radiation. But they make no mention of comparisons with areas outside the exclusion zone. As far as I can see, there is no conflict between the results of the two groups (but if I see the paper, I might revise that opinion!): the biodiversity could still be higher than outside the zone.

Why the fuss? I don't know any of the people involved, but it looks like a typical academic spat. One side's pronouncements have almost certainly bruised the others' large egos, and this is the response. Because of the way science is supposed to work, we can't write in our papers that such and such is a tosser (checks: there are 201 papers in Web of Science with Tosser as an author. 172 are by A. Tosser. Hmmmm), so we are reduced to using hints, insinuations and politeness. Once you are familiar with the literature it's clear what's going on (and the example here is really not subtle). But those involvedm can still get your name on the BBC website by claiming that there is a real controversy.

This sort of thing happens quite regularly, and the best thing to do is either to step in to calm things down, or sit back with some popcorn to watch. Get a front-row seat in the right conference, and the blood will be lovely...

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I have an immature Nature

The title of a correspondence in the latest issue of Nature:

Scientific bodies must take own action on emissions

'nuff said Read more!

I do sleep deeply

Apparently there was a big thunderstorm over Helsinki last night. And I slept through it all. Oddly, though, I did wake up last night - an insect tried to hide in my right ear. Read more!

Monday, 13 August 2007

Rove Move

BBC NEWS | Americas | Top White House aide Rove resigns
Just two thoughts:
  • Let's see how many "rat leaves sinking ship" comments this story gets.

  • I don't think anyone predicted him leaving before Gonzales.

Rejoice! Rejoice!

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