Making research open to all

I've written before on the important issue of public access to research and data sets that have been supported by public funding. The Obama administration has taken an important step in the direction of expanding access. On February 22 John Holdren, Director of the Office of Science and Technology Policy, issued a policy statement, available here, instructing federal agencies with research budgets of more than $100 million to make the research results available within 12 months of publication. As the journal Nature puts it:

The policy applies to an estimated 19 federal agencies, which each spend more than US$100 million on research and development. It would roughly double the number of articles made publicly available each year to about 180,000, according to the Scholarly Publishing and Academic Resources Coalition, an open-access advocacy group in Washington DC, which called the memo a “landmark”. Until now, only the US National Institutes of Health (NIH) has required its research to be publicly available after 12 months.

You can read Nature's assessment of possible approaches in the US here.

But don't expect things to happen too quickly. The policy statement gives agencies six months to come up with a draft plan, and doesn't specify an implementation date. The new US policy meets what Nature calls the green standard: research results and data sets must be available within one year of publication. The gold standard, which the UK alone is pursuing, is to make research available immediately. You can read more about the issues involved in the difference here.

Flu surveillance news - and using data to do it

Update, March 8: The New York Times has run an article about companies using similar searches to identify unreported drug interactions.

A few weeks ago I posted a link to the Google Flu Trends website, along with links to the research Google cites stating that Google Flu trends does a good job anticipating flu surveillance data. A couple of weeks ago, though, the journal Nature published an update titled "When Google got flu wrong." It seems that Google's algorithms suggested a sharp uptick in flu prevalence in the US in early January 2013 - which the surveillance data did not bear out. That has prompted some comments and columns in the press about the accuracy of the Google site.

How to interpret all this? I think it's inaccurate to say, as Nick Bilton did in his Times column, that Google's algorithm was looking only at the numbers, not the context of the search results. Only humans can look at context - that's why it's important to review numbers, not take them at face value. That's exactly what the author of the first column I cited did - he raised questions. But it's not as if the Nature article says that everything about Google Flu Trends or other crowd-sourced flu information. Declan Butler writes:

Google Flu Trends has continued to perform remarkably well, and researchers in many countries have confirmed that its ILI estimates are accurate. But the latest US flu season seems to have confounded its algorithms. Its estimate for the Christmas national peak of flu is almost double the CDC’s (see ‘Fever peaks’), and some of its state data show even larger discrepancies.

It is not the first time that a flu season has tripped Google up. In 2009, Flu Trends had to tweak its algorithms after its models badly underestimated ILI [influenza-like illness] in the United States at the start of the H1N1 (swine flu) pandemic — a glitch attributed to changes in people’s search behaviour as a result of the exceptional nature of the pandemic (S. Cook et al. PLoS ONE 6, e23610; 2011).

Google would not comment on thisyear’s difficulties. But several researchers suggest that the problems may be due to widespread media coverage of this year’s severe US flu season, including the declaration of a public-health emergency by New York state last month. The press reports may have triggered many flu-related searches by people who were not ill. Few doubt that Google Flu will bounce back after its models are refined, however. [Links in original]

One of the US websites is Flu Near You. You join the website (you can use your Facebook login, and as far as I can tell they don't send an annoying notice to everyone you know that you've joined.) And then you report weekly on the flu status of some or all of your household. That's a screenshot of its recent reports in the northeast. According to its website, Flu Near You has more than 44,000 participants in the US; Nature reports that the participants are representative in terms of age distribution. And this is only the beginning:

Already, web data mining and crowdsourced tracking systems are becoming a part of the flu-surveillance landscape. “I’m in charge of flu surveillance in the United States and I look at Google Flu Trends and Flu Near You all the time, in addition to looking at US-supported surveillance systems,” says [Lyn] Finelli. “I want to see what’s happening and if there is something that we are missing, or whether there is a signal represented somewhat differently in one of these other systems that I could learn from.”

Our genetic quirks

Two stories came out last week about two curious features in our body chemistry. On Wednesday,  the journal Nature explained the age old mystery: why do our fingers and toes wrinkle during a bath? So we can pick things up, of course!

Laboratory tests confirmed a theory that wrinkly fingers improve our grip on wet or submerged objects, working to channel away the water like the rain treads in car tyres.

On Thursday, the Atlantic.com ran this story about the iron we need - and that can poison us. Some of us carry a hereditary condition called hemochromatosis:

a genetic disease leading to a toxic accumulation of iron in his organs. A modern manifestation of an ancient DNA mutation, this disorder can be traced to a single unknown ancestor who lived millennia ago. This mutation allowed her (or him) to more readily absorb iron from food, which may have unexpectedly aided survival in lean times -- possibly at the expense of iron-overload in later generations. . . . [The mutation is found in] nearly one in ten individuals of northern European ancestry.

There are lots of mysteries: why did the mutation arise? Do you need two copies to develop the disease, or just one? Where did it arise and how did it spread? Why is is so common in people of Northern European descent? It's a great story - evolutionary medicine with a modern example.

An interactive guide to energy use

The journal Nature has published an interactive guide to the world's energy use, available here.
You can find out which countries are using which resources (in 2011). There are some surprises. For example, I knew that mainland China and the US are large consumers of coal and oil energy. But they are also the largest consumers of hydro and renewable energy as well. I expect that's because the largest consumers of energy are going to be the largest consumers regardless of the source. If you think I'm wrong, please let me know via the comments.

You get a sense of the issue in these screenshots:


Coal:

Oil:

Hydro/Renewable

It's an interactive guide, and I selected a few countries to illustrate what I found. I tried to be reasonably representative of established and emerging economies while keeping the charts small enough to see. (Note - you will have to click through to the Nature page to interact with the data yourself.)