Science publishing has a Zika problem

Zika virusScience publishing has a problem. I agree with Nobel Laureate Randy Schekman, who wrote that prestigious science journals like Cell, Nature, and Science – which he calls ‘luxury journals’ – are damaging science.  The succession of articles on Zika virus nicely illustrates this problem.

The big three in science publishing – Science, Nature, and Cell – have published many papers on Zika virus since the beginning of 2016. Many of these have had a turnaround time of a week or two – the time between when the papers were submitted, and when they were published online. A rapid turnaround time is unusual, and not compatible with proper peer review of the work. Indeed, many of the papers have been clearly rushed into print, and lack proper controls and clear explanations of what has been done.

The recent publication in Cell Host & Microbe of a description of an infectious DNA clone of Zika virus is a perfect illustration of the problem with luxury journals. Infectious DNA clones of viral genomes are nothing new – the first were described the late 1970s and 1980s. They are important reagents, allowing manipulation of the viral genome to study replication and pathogenesis. But publishing a reagent has never been enough to get into a high profile journal.

As a postdoctoral fellow with David Baltimore in 1981, I was fortunate to publish the first report of an infectious DNA clone of an animal virus – poliovirus – in Science (At the time there were no luxury journals. Years later Nobel Laureate Paul Berg asked why we chose to publish in such a lowly journal). A few years later, I submitted a paper to the Journal of Virology describing the construction of an infectious DNA clone of a different serotype of poliovirus which had the unique ability to infect mice. The paper was rejected because, I was told, it didn’t contain any new results.

The first infectious DNA clone of a calicivirus – the family that includes noroviruses, agents of human gastroenteritis – was published in 1995 in Virology. The senior author told me the paper was rejected from the Journal of Virology because an infectious clone is ‘just a tool’.

The Journal of Virology is a solid journal that publishes many important articles in the field. But no one would mistake it as a luxury journal.

Some infectious DNA clones of viruses have been published in prominent journals – for example, Ebolavirus and influenza virus in Science (2000 and 2001). Zika virus is a flavivirus, and the first infectious DNA of a member of this virus family was for yellow fever virus, published 27 years ago in PNAS. Subsequently there have been many reports of infectious DNA clones of other flaviviruses, notably, West Nile virus, published in Virology in 2001. This virus, which entered the United States, gained quite a bit of attention in the press.

Technically, there is nothing novel about making an infectious DNA clone of Zika virus. It is an important reagent, just as infectious DNA clones are important for the study of all viruses. But the paper reports no experimental results using the Zika virus infectious DNA that advance the field. In my opinion, the infectious DNA clone of Zika virus should not have been published in a high profile journal.

Clearly the paper was published because Zika virus is hot and it will garner the journal a great deal of publicity, a consideration that should not determine whether an article should be published or not. It is the science that should drive publication – and the luxury journals have lost track of this fact.

Schekman points out that the reputations of luxury journals reputations as the “epitome of quality” is only “partly warranted”: they don’t always publish outstanding work, and they are not the only journals to publish great science. He feels that they “aggressively curate their brands, in ways more conducive to selling subscriptions than to stimulating the most important research”. They are driven by impact factor, which Schekman and others, including myself, think is wrong. Highly cited papers are not necessarily correct; they might be “eye-catching, provocative or wrong”. He says that editors accept papers that will ‘make waves’ and therefore influence, inappropriately, the direction of science. He favors open-access journals that are edited by scientists, and so do I.

In my view there are two main forces that have corrupted science publishing. The first is one that Schekman notes: that these journals are in the business of selling subscriptions. The Cell and Nature journals are owned by for-profit publishing companies. This situation is problematic because the drive for profit is not necessarily compatible with the need to publish high quality science. Editors know that controversial or prominent (e.g., Zika) papers will drive advertising revenue, but this should not even be a consideration when deciding what to publish. The publication of scientific data should not be a for profit enterprise. Unfortunately, Science magazine, which is published by the non-profit AAAS, seems to be driven by the same corrupting influences.

A second problem is that decisions at the luxury journals are typically not made by working scientists, but by full-time editors. A professional editor cannot possibly know the field as well as a working scientist, who spends his or her days in the trenches of science: designing experiments, interpreting data, guiding students and postdoctoral fellows, reviewing manuscripts, writing grants, going to meetings, and much more. The result is that the working scientist is fully immersed in science every day, all year, and is in the best position to know what work is significant, advances the field, and should be considered for publication.

These two factors control what kinds of papers are published. The luxury journals want high-impact papers that are of broad interest. But the problem is that it’s not always clear exactly where a paper fits in. Many of us have had the experience of submitting a paper to Cell, Science, or Nature, only to be told ‘it’s not of sufficient interest’. But the real reason is that the paper won’t sell advertising, or subscriptions; or perhaps the editor who made the decision simply doesn’t sufficiently understand the field.

A paper on an infectious Zika virus DNA clone will help Cell Host & Microbe get more advertising. A year ago, the journal would not even have reviewed the paper.

It’s no secret that publishing controls our scientific careers. Decisions about important things like hiring, promotion, tenure, and grant funding revolve around what you have published and where. I’ve been on many tenure or grant review committees, and it’s common to count the number of Cell, Nature, and Science publications as a metric of quality. The same occurs when examining job candidates for professorial positions.

In other words, the luxury journals are controlling the careers of scientists. Journals motivated by profit, run by professional editors who are not scientists, are deciding who is hired, promoted, tenured, and who gets grant money.

Unfortunately it is a system that scientists have created and nurtured until it has become an absurd and untenable situation, and it has to change. The PLoS journals and eLife are helping to do that, but what is also needed is to diminish the importance of the luxury journals to the careers of scientists. That is a much harder goal to achieve, as all my colleagues who are sending their Zika virus papers to luxury journals, will admit.

TWiV 385: Failure

TWiVStuart Firestein, Columbia University neuroscientist and author of the book Ignorance, returns to TWiV for a chat about his latest work, Failure. This book is all about how experiments that don’t work, or provide the wrong conclusions, are essential for the progress of science.

You can find TWiV #385 at, or listen below.

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Scientists: Engage the public!

Science and technology play important roles in the nature and quality of our lives, so it is not surprising that as a society, we are increasingly challenged by problems that have a scientific component. Individual decisions about vaccines, regional choices about water availability, or global agreements about climate change all require that science have a voice during the decision-making process. The microbial sciences touch upon such a wide range of issues that scientists in those fields are particularly relevant to these discussions. If scientists do not participate in these dialogues, then others will fill the void and the information may not be accurate or science based. Scientists must communicate about science with public audiences in order for members of the public to make informed decisions about the complex issues that face us in our technologically advanced society.

Read the remainder of this article at mBio

TWiV 352: Science art with Michele Banks

On episode #352 of the science show This Week in Virology, Vincent meets up with Michele Banks in Washington, DC to discuss her career as a creator of science-themed art.

You can find TWiV #352 at

Be curious

During my visit to the University of Vermont today I had lunch with seven talented Microbiology Ph.D. students. One of them asked me what was an important quality to have for achieving success in science. I said without hesitation, ‘Be curious’.

It’s the answer I always give. Being curious is the first step to being a scientist, and it’s the quality you must always have to be a successful scientist. If you are not curious about the world around you and how it works, do something else.

Which is why I find this statement by Aaron Swartz extremely moving:

When I was a kid, I thought a lot about what made me different from the other kids. I don’t think I was smarter than them and I certainly wasn’t more talented. And I definitely can’t claim I was a harder worker — I’ve never worked particularly hard, I’ve always just tried doing things I find fun. Instead, what I concluded was that I was more curious — but not because I had been born that way. If you watch little kids, they are intensely curious, always exploring and trying to figure out how things work. The problem is that school drives all that curiosity out. Instead of letting you explore things for yourself, it tells you that you have to read these particular books and answer these particular questions. And if you try to do something else instead, you’ll get in trouble. Very few people’s curiosity can survive that. But, due to some accident, mine did. I kept being curious and just followed my curiosity.

(from Dave Winer)

If Swartz is right – and I suspect he is, at least in part – then by driving curiosity out of kids, we are destroying future scientists. Except for the rare few who keep on following their curiosity.

This Isn’t the Petition Response You’re Looking For

Death star 1Yesterday I noted the petition to ban intelligence involvement in public health campaigns. While exploring We the People I found another interesting petition, this one to secure resources and funding to build a Death Star by 2016. Because it garnered over 34,000 signatures, it was noted by the White House and received a response from Paul Shawcross, Chief of the Science and Space Branch at the White House Office of Management and Budget:

The Administration shares your desire for job creation and a strong national defense, but a Death Star isn’t on the horizon.

Among other reasons for not building a Death Star, Shawcross noted:

Why would we spend countless taxpayer dollars on a Death Star with a fundamental flaw that can be exploited by a one-man starship?

But the real reason for posting this interesting item on virology blog is that Shawcross brings it back to science:

We are living in the future! Enjoy it. Or better yet, help build it by pursuing a career in a science, technology, engineering or math-related field. The President has held the first-ever White House science fairs and Astronomy Night on the South Lawn because he knows these domains are critical to our country’s future, and to ensuring the United States continues leading the world in doing big things.

If you do pursue a career in a science, technology, engineering or math-related field, the Force will be with us! Remember, the Death Star’s power to destroy a planet, or even a whole star system, is insignificant next to the power of the Force.

It’s a thoughtful and amusing response from Shawcross. Please read it.

The gender bias of science faculty

If you were a science professor, and you received two equally strong applications for the position of  laboratory manager, one from a female, one from a male, which one would you pick? The answer might surprise you.

It is well known that women are underrepresented in many fields of science. Whether or not this disparity is a result of gender bias by science faculty has not been investigated. To answer this question, a randomized, double-blind study was conducted in which science faculty from research universities were asked to rate the application of a male or female student for a laboratory manager position. Identical applications were sent to all participants in the study, except that half (n=63) received materials from a male student, John, and the others (n=64) received materials from a female student, Jennifer. The faculty were then asked to rate the student’s competence and hireability, and the amount of salary and mentoring that they would offer.

The results clearly show that the faculty felt that the female applicant was less competent than the male student, and offered Jennifer less career mentoring and less starting salary than John. Faculty gender, scientific field, age, and tenure status did not affect this bias. The data indicate that the female applicant was less likely to be hired because she was considered less competent than the male applicant.

What might be the reason for the subtle gender bias observed in this study? The authors suggest that it is due to a belief that women are less competent in science than men:

The fact that faculty members’ bias was independent of their gender, scientific discipline, age, and tenure status suggests that it is likely unintentional, generated from widespread cultural stereotypes rather than a conscious intention to harm women.

I found the difference in mentoring offered the male versus female applicants most disturbing. An understanding and supportive mentor is an important component required for a successful career in science. Lack of encouragment and positive judgements may cause women to leave academic science before they reach university positions.

How can this subtle bias be eliminated? The authors suggest educating faculty and students about the existence and impact of bias within academia, an approach that has reduced racial bias among students.

We need more scientists in the US – one million over the next ten years, according to a 2012 report from the President’s Council of Advisors on Science and Technology. Achieving this important goal is jeopardized by faculty gender bias.

We discussed this work with Jo Handelsman, senior author on this gender bias paper, on episode #48 of the science show This Week in Microbiology. You can find TWiM #48 at

TWiV Special: Ignorance with Stuart Firestein

On a special episode of the science show This Week in Virology, Vincent and Stuart Firestein, author of Ignorance, discuss why ignorance – all of what we don’t know, and even what we don’t know we don’t know – is the driving force of science.

You can find this TWiV Special at

TWiV 184: Reforming science

On episode #184 of the science show This Week in Virology, Vincent, Rich, and Alan consider how to reform the scientific enterprise to make it more effective and robust.

You can find TWiV #184 at

How to read a scientific paper

On episode #169 of This Week in Virology we had a good discussion about how to read a scientific paper. Many individuals have asked about making this into a separate audio file, so here it is.

Click the arrow above to play, or right-click this link to download our thoughts on how to read a scientific paper (22 MB .mp3, 30 minutes).

Transcript of this discussion (pdf).

Epidemiologist Michael Walsh has shared a PowerPoint presentation on this topic (482 KB PowerPoint file).