To share or not to share?

Big data is great. I don’t think anyone can argue against the benefits of making datasets, whether they are from independent, controlled experiments, or from large-scale projects such as the Earth microbiome, publicly available. Depositing your data in one of the databases available, such as figshare or MG-RAST, can only ever help science. It progresses science by preventing fraud, making the process more transparent, and allowing for crosschecking of results. Sharing facilitates discussion. I have never heard of unethical use of shared data.

Nothing new there. In fact, sharing data might prevent masses and masses of unpublished data from getting lost forever, and thus has the potential to save millions of pounds of public money being spent on experiments that have already been done, but that no one knows about. Think about all those PhD thesis chapters, all analysed and written up, that never get published, and are therefore potentially lost for science forever. Similar to their open access strategy, research councils and funding agencies should perhaps set up a system that obliges PhD students to deposit their data before they can get their doctorate. Continue reading

A very short history of creativity in science

Is science creative? I know that the process of scientific discoveries can be, or ought to be – is inherently? – creative. You can find some interesting opinions here, but it boils down to having to be resourceful and imaginative to design experiments for answering difficult, or big questions. I agree. However, I think that increasingly, the process of scientific discovery is constrained and pushed into a straight jacket, with implications for the creativity that is necessary to come to great scientific discoveries. Who still has time to wander through nature, observing and thinking? To have long discussions during coffee breaks, and philosophise about new ideas and approaches?

Yet this is what early scientists did. They studied the patterns they observed in nature, through spending time in nature. Think about Newton being sat under a tree when the apple fell on his head, or about Darwin and his voyage on the Beagle. Think about their books, that read like adventure novels. In the early days of the Royal Society, in the 1600’s, science and philosophy, or metaphysics, were inseparable, and doing science consisted for a large part of talking about it. Later, there were close ties between poets and scientists, and romanticism had a major impact on 19th century science. For example, the romantic poet Samuel Coleridge travelled to Germany and presumably influenced natural scientists such as Alexander Humboldt. Coleridge and his friend Wainwright got their inspiration while going on long and exhausting walks, often for weeks on end, and having opium-fuelled discussions through the night. Continue reading

Cheating in academia?

It’s been all over the media in the past weeks – Oprah Winfrey’s interview with Lance Armstrong, in which he admitted having used EPO, blood transfusions, and hormones. Having been a semi-professional mountain biker for years, I have been following the accusations that preceded the interview, the buildup to the interview, and the (media) response after the interview. One thing I found particularly interesting is that Lance Armstrong didn’t feel he was cheating, because (at the time?) everyone was using doping.

After having read a recent blog post on Retraction Watch, I couldn’t help starting to compare cheating in sports with cheating in academia. There are quite a few parallels – for example, Tyler Hamilton, a convicted doping user, has written a book about his years in Lance Armstrong’s team, giving insight in the systematic drug use in the peloton. One of the most notorious committers of scientific misconduct, Diederik Stapel, has written a book about his fraud, and I am sure others will follow his example. After all, once your career is over because of cheating, writing a book about it is a good way to make money as well as coming clean, which must be a massive relief after having lived a lie for many years. Continue reading

A little bit of background on my latest paper

In my latest paper, Extensive management promotes plant and microbial nitrogen retention in temperate grassland, published in PLoS ONE last month, we show that traditionally managed, species rich haymeadows lose less nitrogen with drainage water from their soils than more intensively managed grasslands. This is important, because nitrogen that leaches from the soil can pollute ground and surface water, reduce plant species diversity, and cause problems for human health if concentrations in drinking water are getting too high.

In this paper, we used both extensive field observations and a mechanistic glasshouse experiment to show that traditional haymeadows have lower nitrogen leaching because of more uptake of available nitrogen in plant roots and in microbes. Specifically, we found that a greater biomass of soil fungi increased microbial nitrogen uptake, and that this in turn increased the retention of nitrogen retention in soil.

These results confirm an ecological theory, namely that ecosystems with a more fungal-dominated microbial community are more efficient in their nitrogen cycling, and have thus lower nitrogen losses. This is not a novel theory at all – in fact, it is often assumed to be true, but it has never before been experimentally tested. To illustrate this, in this Science paper, it is said that ‘Because fungal-based soil food webs promote less leaky nutrient cycles that are more retentive of nutrients than do bacterial-based food webs…’ and subsequently, a paper by Coleman et al. from 1983  is cited. However, on further inspection, this appears to be a review paper, which by no means proves that this theory is correct. Moreover, it is not possible to adequately test this theory, since it is not possible to take the microbial community out of its environment, and thus it is impossible to test whether it is the composition of the microbial community that is responsible for lower nitrogen leaching, or its environment, for example the amount of organic matter in the soil.

Continue reading