Self-archiving and open access

My dissertation is now available! (It's even had a flattering review.)
The main part of the dissertation is based around a survey of 430 or so people on whether they knew about self-archiving and whether they accessed journal articles online from sources other than the official publishers' website. Over 70% of respondents did, a higher proportion than in previous surveys, though it depended a great deal on subject area. People in the field of medicine had hardly heard of it at all and were very unwilling to trust self-archived material. Why should this be?

There's a possibility of a sample bias, but other studies have found a similar tendency in medicine (there is much less self-archived material available in medicine than in other fields, as well). I suspect two things: firstly, that many researchers in medicine spend a lot less time immersed in academia than people in other subjects, and the concept of open access hasn't spread beyond academia yet; and secondly, that there is a much greater need for papers in medicine to be seen as authoritative, as determining the trustworthiness of articles is both more important and more difficult. More difficult, because the trials and experiments described are often expensive, long-term, or subject to stringent ethical stipulations; more important, because of the consequences if, say, a doctor acts on incorrect advice.
Whether these attitudes will change as self-archiving increases in popularity (as I believe it will) remains to be seen.

Science as entertainment

Mark Liberman at the Language Log has been tackling for some time the misinformation in Luanne Brizendine's book The Female Brain. In the latest twist, despite Brizendine's retraction of the material in question, the popular press are still promulgating it as if nothing had happened.

The press appear to rarely bother to check scientific facts before posting something, and may not admit their mistakes (another example, this time with the BBC as the culprit, has been dealt with in depth elsewhere). Mark Liberman suggests that this is because science news is viewed as entertainment, rather than on the same level as current events stories.

In a way, of course, almost all news is entertainment. There's very little in the daily news that directly affects people's everyday lives. Instead, as C.S. Lewis famously had it, 'He reads daily, with unwearied relish, how, in some place he has never seen, under circumstances which never become quite clear, someone he doesn't know has married, rescued, robbed, raped, or murdered someone else he doesn't know.' And, while scientific discoveries do have the potential to affect everybody's lives, the chance of any individual discovery directly affecting any given individual person is quite small.

On the other hand, that shouldn't stop journalists from checking their facts.

GM potatoes

As a gardener, I welcome the announcement of UK trials of potatoes genetically modified to be resistant to blight, for reasons given below. I was rather less pleased at the reaction of the GMWatch spokeswoman on the Today programme. She used the event as a hook to hang a very standard anti-GM rant off, without dealing in any way with the specifics of this particular implementation – and this is not a standard GM trial.

There are several ways in which this particular GM trial differs from many others that have occurred in the past. The gene inserted is from a wild potato plant, not a gene from another species. The same effect might be attained through many years of careful cross-breeding in the traditional manner; genetic modification just gets it done more quickly and more surely.

The purpose of the gene transfer is to give the plants resistance to potato blight, which is a deadly disease for which there is no organic treatment (organic potato farmers are permitted to use Bordeaux Mixture, which is primarily copper sulphate, but this is a concession by the Soil Association to the fact that without using some sort of inorganic compound, it is impossible to grow potatoes in an area subject to blight.

Potatoes crop, and reproduce, not by setting seed but by producing tubers. There is therefore a much lower chance of 'contamination' with other plant species (especially as there are far fewer relatives of the potato in the wild than there are of grass-based plants such as wheat). And, as I said above, the gene is one that occurs in wild potatoes anyway, and confers resistance to a fungal infection, not a weedkiller or pesticide. So if the gene did start appearing in wild plants, what harm would it do anyway?

It is true that reports of a toxicology experiment in the past have claimed that rats fed a certain strain of GM potato had damaged immune systems. But the full results of that trial, when they were finally released, were inconclusive, and some claimed the design was flawed and the paper should not have been published. And in any case, this is a different strain and would be expected to behave differently. But how can we tell that for sure without doing the trials?

Sleepwalking into extremism

The President of the Royal Society, Lord Rees, said on the Today programme this morning that we were in danger of sleepwalking into a future of extremism unless we do more to promote a scientific worldview. In particular, he accused the news media of giving too much publicity to 'mavericks' in a misguided attempt to show both sides of any argument.


We've heard this before, of course. In relation to climate change in the US (another example here), and the MMR vaccine in the UK (as I posted about a few months ago).


But Lord Rees is talking not in terms of informing the public to enable people to make their own minds up about things, but in terms of educating the public so they can make decisions about science policy. I'm a little dubious about this. Call me a snob, but I'm not sure any change in media policy is going to educate most people sufficiently to enable them to make decisions about science, simply because most of them won't care enough to be bothered. Unless it's something scary that might do Bad Things to them directly. Then they're at least interested enough to buy the newspaper that tells them the bad news.

Long silence

Sorry I've not been around for a bit. I've been writing a dissertation on whether researchers (in science and other fields) use self-archived literature: research material that has been made available by its authors on websites or in archives (repositories) in addition to normal journal publication. I'll post the full results shortly.

China to name and shame dodgy researchers

In a bid to curb the apparently increasing tendency for fraud amongst research scientists in the far east, the Chinese government has unveiled a plan to evaluate the 'credibility' of the researchers it funds. Those individuals or groups who fail, through breaking the rules or making 'mistakes', will be made public.

Assuming this isn't another control bid by the Chinese government, along the lines of censorship, then I think this could be a good idea. This sort of thing should happen anyway under the peer review system, but so much research is being done these days, much of it highly specific, that it can take a long time for fraud or other forms of misconduct to be found out. On the other hand, there's no indication of what criteria will be used to judge the 'credibility' of scientists. Or of whether any punishment will be applied, aside from publicity.

Faking it and taking it

Taking responsibility, that is. Hwang Woo-Suk has admitted a part in the faking of cloning research in his lab. A part, that is, as he still maintains that the actual faking was done by underlings.

This is rather disingenuous. Either he was in charge of his lab or he wasn't. If he was genuinely supervising his research staff, he should have known what they were doing. Giving 'specific orders' is neither here nor there. If he didn't know what they were doing he obviously wasn't involved enough in the work to claim the credit for it.

My mother made me do it

On another blog, Janet D. Stemwedel gives her take on the news that sexuality may be determined in the womb. My reaction is somewhat different. I don't see something caused in the mother's womb as biological determination so much as environmental. It's certainly not genetic, as Andy Forrest from Stonewall, quoted in the BBC article, seems to think. The extension of this is that it's not impossible to foresee a time in the future when we will be able to advise pregnant women to eat certain things, or take certain pills, to reduce the risk of their child being born gay.

I'm not at all sure how I feel about this. On the one hand, there are disadvantages to being gay that most parents would want to spare their children: the discrimination and prejudice, the far narrower field of potential mates, the inability to have (or at least difficulty in having) genetic offspring. If it were a matter of taking a pill to reduce the risk of your child being born disabled or stupid, I can't see many parents refusing it – in fact, we already do it in the form of vitamin supplements and whatever it is the government is advising us to eat this week.

But what if it were a pill to reduce the risk of your child being born red-headed? Or, less obviously unacceptable, how about a pill to reduce the risk of your child being highly emotional? Emotional people (easily upset) can be put at great disadvantages in life too.

I don't agree that there's anything intrinsically wrong with saying that some states of being (such as being able to walk) are better than others (such as being paralysed), in the sense that the 'better' state is generally more enjoyable for the person concerned (not that the person in the 'better' state is intrinsically a 'better' person for it). But even with a continuum of characteristics with number of usable limbs at one end and hair color at the other, it's unclear where sexuality should come on the scale.

Misguided concepts of balance

A group of thirty leading paediatricians and vaccination experts have written an open letter calling for parents to allow their children to receive the MMR vaccination. (I can't find a copy of the letter itself, but it's widely reported throughout the news media.) They blame 'misguided concepts of balance' in the media for confusing people about the validity of the research that suggests a link to autism.

Done properly, the peer review system should work well at weeding out dodgy research. But it's a paradigm that's very unfamiliar to the mainstream media and to most of those who gain their information from it. 'Person B says that the thing Person A said last year was dangerous isn't so scary after all' isn't a very good headline. How can the reader weigh up the relative merits of the arguments in a very specialised field with a completely different worldview?

The reference to 'misguided concepts of balance' is, I assume, a suggestion that the normal 'two sides to every story' approach taken by the media is counterproductive in this case. It implies equal validity on both sides, and the writers of the letter believe that Dr Wakefield's research is invalid and should be treated in health reporting similarly to the way the BNP is treated in politics journalism. This seems sensible, given the large amount of research suggesting the vaccine is safe, but in a way I can see the point of the opposing argument. Are people not intelligent enough, do we not respect their independence enough, to let them look at the evidence themselves and make up their own minds?

Interestingly, though, the very BBC webpage publicising this story gives, under the 'related links' section, a link to JABS, a group which opposes the vaccine on the basis of Wakefield's evidence, but no site arguing the opposite view, or even a link to the full text of the letter. If it's an open letter, surely it can be republished?

Which comes first: the eagle, or the green energy?

I hadn't truly paid much credence to the idea that wind farms were a hazard to birdlife. But there seems to be evidence that a Norwegian wind farm has directly caused the death of a number of white-tailed eagles. So it seems we need to look to our priorities: is a charismatic, beautiful and evocative species more important than alternative sources of energy that will help stave off the greenhouse effect?

I think so, not because 'eagles' are 'pretty' (though they're certainly beautiful birds), nor because I believe in preserving the exact environmental status quo, but because if we forget why we're trying to save the environment then we've lost something in ourselves.

Whaling

Japan have gained an initial victory in its attempt to restart commercial whaling. In a way I think this could be a good thing: my natural honesty is offended by what they do in the name of 'scientific research'. Perhaps we should call it commercial whaling, but keep the limits exactly where they are now.

That petition

The pro-animal testing petition (the one that Tony Blair signed) is available here.
Interestingly, the BBC article quotes someone as saying that the petition only has 13,000 names. Less than a week after that article was published, there are now 18,000 names.