Harold Varmus is one of the most high profile advocates of open access to biomedical research. As one of the cofounders of the Public Library of Science (PLoS), he has played an important role in making published results freely available to all. And he’s a Nobel Laureate, which ain’t too shaby either.

Varmus was interviewed by Ira Flatow for NPR’s Science Friday program about the NIH’s new policy requiring that research publications presenting results funded by the NIH be deposited in PubMed Central (the NIH’s free online archive of biomedical journal articles) within a year of publication. Before I get into the problems with Varmus’ interview, I’d like to highlight one important point Varmus made: the current NIH policy is a comprimise between the ideal open access solution and what pay-access publishers want. In the ideal situation, all papers published about publicly funded research would be made freely available at the moment of publication. There would be no moving wall before they can be freely obtained. But that would ruin the business model of the pay-access journals, who make a fair bit of their profit from both individual and institutional (i.e., university) subscriptions. If a big chunk of the articles in those journals were freely available, the journals would stand to lose many of their subscribers.

Despite making that point, Varmus struggled to point out the big differences between open access and pay-access journals. He was clear that the differences lie in the business models, but he did not present the details of those differences with the clarity required when speaking to the general public. First, he made it seem as if open access journals are the only ones that require a payment from the author in order to publish in those journals. Second, he failed to clearly point out that open access and peer review are orthogonal issues, despite a perfect opportunity to do so.

Varmus made the important point that open access and pay-access journal differ primarily in their business models, not in their approach toward publishing scientific results. However, he made it seem as if open access journals are the only ones who require authors to pay to publish. This is not the case, as pay-access journals also require authors to pay publication fees. Using a few journals from my field as examples, Genome Research charges $40 per page, Molecular Biology and Evolution charges $50 per page, Evolution charges $55 per page, and Genetics charges $65 per page. Those page charges may differ depending on whether you are a member of a society associated with the journal, and they often also charge additional fees for publishing color figures. Generally, a ten page article with one color figure will cost approximately $1000.

PLoS also charges authors to publish in its journals. For example, PLoS Biology charges $2750, PLoS Genetics charges $2100, and PLoS ONE charges $1250. These charges are fixed and do not depend on the length or contents of the article. Nucleic Acids Research, an open access journal published by Oxford University Press, charges $2670 to authors. Additionally, pay access journals often give authors an option to publish their paper with free access, for an additional cost. For Genome Research this cost is $2000.

As you can see, the publication charges for open access journals are often slightly more than those for pay-access journals. But it’s not as if one business model requires author payments and the other does not. Additionally, all journals I have encountered allow editors to waive publication costs if the author(s) cannot afford them. Some are more draconian in their presentation of those rules — see the page charge policy of MBE — but they all at least make that option available. This is true for both pay access and open access journals. Therefore, the primary difference in the business models between pay access and open access journals is not in the presence of author charges. There is a difference in the magnitude and application of those charges, but the primary difference is in whether the journal requires readers to pay to access the content.

What about Varmus’ defense of the peer review in open access journals? In this case, a caller phoned in to ask whether open access journals have the same peer review standards as pay-access journals (quite reminiscent of the whole PRISM affair). Varmus correctly pointed out that open access journals require the same scientific rigour as pay-access journals. However, he failed to hammer home the point that open access and peer review are completely orthogonal issues. That is, whether a journal offers open access to its content is independent of the nature of peer review the articles are put through. Conflating open access with peer review is a propaganda strategy of the anti-open access lobby, PRISM. I think Varmus wasted a great opportunity to make this explicitly clear.

In addition to discussing the NIH open access policy, open access business models, and peer review, Varmus also talked about publishing negative results. He pointed out the need for journals to make negative results available. This was somehow connected to Varmus plugging the new interactive features available in some PLoS journals — specifically, the ability of readers to comment on articles (a feature this is noticeably under-used), which I presume would allow readers to mention how their own negative results relate to the article.

The entire interview is available on the Science Friday website. Varmus did a good job, but he could have done much better. He needs practice in hammering home the primary talking points. Some of his message got muddled in his lack of a punchy delivery. I worry that the points may have been missed by those people not familiar with the details.