NYTimes and CauseScience discuss #ASAPbio -preprints in biology

The New York Times features an article today about ASAPbio (previous blog posts about ASAPbio). The purpose of the meeting was to accelerate the usage of preprints in biology. This comes in efforts to rescue the biomedical research system from its numerous flaws- including the difficulty in publishing (previous posts on the issues in academic publishing).

ASAPbio brought together numerous biologists- including Nobel Laureates, senior PIs, journal editors, junior faculty, and postdocs (including me!)- to try and establish a system in biology to publish in an open-access, quick manner online to supplement the current publishing system.

Check out the full NYTimes article. Here are some highlights:

On Feb. 29, Carol Greider of Johns Hopkins University became the third Nobel Prize laureate biologist in a month to do something long considered taboo among biomedical researchers: She posted a report of her recent discoveries to a publicly accessible website, bioRxiv, before submitting it to a scholarly journal to review for “official’’ publication.

Why use preprints at all? One of the major issues with the current publishing system:

Unlike physicists, for whom preprints became a default method of communicating discoveries in the 1990s, biomedical researchers typically wait more than six months to disseminate their work while they submit it — on an exclusive basis — to the most prestigious journal they think might accept it for publication. If, as is often the case, it is rejected, they try another journal. As a result, it can sometimes take years to publish a paper, which is then typically available for a time only to colleagues at major academic institutions whose libraries pay for subscriptions. And because science is in many ways a relay, with one scientist building on the published work of another, the communication delays almost certainly slow scientific progress. .

One of the benefits of preprints is that the work can be featured immediately without waiting year(s) to go through peer review publication process. Another benefit is that this work is open access, which is a huge problem internationally, especially in developing countries (previous posts on open access).

Unfortunately, some journals and scientists don’t support the idea of preprints. One potential issue is that work will get “scooped” (although, physics has been doing preprints for 20+yrs and has not had this issue):

Some journal editors say that preprints would be detrimental to science. Emilie Marcus, the editor of Cell, told scientists at the #ASAPbio conference that in conversations with more than 100 scientists Cell editors had found that the main reason they wanted to use preprints was to scoop competitors, which she suggested would cause the quality of papers to decline as everyone rushed to post first: “Is that the direction that we want to go?’’ Others have argued on Twitter that allowing research to reach the public without being reviewed before publication would be irresponsible.

Preprint advocates counter that scientists care too much about their reputations to publish shoddy work, and posts to bioRxiv are clearly marked to indicate that they may contain information that “has not yet been accepted or endorsed in any way by the scientific or medical community.’’ Others note that plenty of peer-reviewed papers in high-profile journals have proved to be wrong, and some argue that carrying out peer review after a paper is published would provide a more rigorous and fair vetting of papers, anyway.

There are lots of major flaws in the current system of publishing (as it stands, scientists have to pay to submit their work to journals, that work is then reviewed FOR FREE by other scientists, and after the paper is accepted, you must pay to access it. WTF). The aim of ASAPbio is not to totally overhaul the publishing system, but to take a step in fixing the issues. If work is a) open access and b) accessible to the public on a quicker timeline, this will advance science in a huge way. Personally, if this system is to work, I believe two main things must happen:

  1. Journals must be on board. If something is posted as a preprint, journals should still accept this work for peer review and potential publication. A preprint should also act somewhat as a “timestamp” so that the work cannot get scooped. And if it does, journals should still publish the work
  2. Funding agencies should accept that preprints count as legit indicators of scientific progress. Sure, it’s not peer reviewed, but this work should show scientific productivity. Sometimes it takes years for work to get published with nothing to show for it in the meantime. This is a nice way to overcome that hurdle.

It’s nice to see several senior scientists on board!

Scientists into criminals – update – Colombian researcher Diego Gomez faces 8 years in prison for sharing article #openaccess #YoComparto

deigomezCheck out the OpenScience article written by Diego Gomez, the Colombian master’s student who faces 4-8 years in prison for sharing an academic article over the internet with fellow researchers and students (a Master’s thesis).

I urge institutions that support research with public funds to encourage their recipients to publish their results in a way that assures equal access to information. Moreover, I call for researchers to back open access, in this way, we support the mitigation of inequality of science in our countries, we stay away from the illegality in the access to information, we can turn our research into an engine for development in our countries, and above all we will avoid that no other person like me, sees themselves involved in weary penal processes. Finally, I call to legislators and the managers of public policies, to cast their eye onto authors’ rights, because this situation can turn a scientist into a criminal.

If you missed it, here is the previous CauseScience post about Diego Gomez. Also, check out the Karisma Foundation and this Nature News blog post. Here is the link to Diego’s previously posted open letter. Diego can be found on twitter here –@diegogomezhoyos . Also sign this petition to promote open access worldwide.

Will Ebola spread to the USA in September? A new study suggests there is a small probability it could #science



NPR has a great summary and write up of a new study published in PLOS Currents: Outbreaks that calculated the likelihood of Ebola cases coming to the United States and other countries based on virtual airline traffic. The study concluded that within 3-6 weeks the ‘probability of international spread outside the African region is small, but not negligible.’

… the authors of a new analysis say many countries — including the U.S. — should gear up to recognize, isolate and treat imported cases of Ebola.

The probability of seeing at least one imported case of Ebola in the U.S. is as high as 18 percent by late September…

These predictions are based on the flow of airline passengers from West Africa and the difficulty of preventing an infected passenger from boarding a flight.

Luckily, the study looked at the probability of one case of Ebola spreading to these countries, not a more widespread outbreak. The authors of the study predict that any Ebola cases would be limited to small clusters of 1-3 people. If US hospitals are prepared, imported Ebola cases should be quite easily contained using isolation and proper infection control (which is the best measure to stop any spread of the ebola virus).