Biophysical Society Bulletin | November 2018

Publications

Publications

Open Access in Biophysical Journal As with many journals, papers in Biophysical Journal (BJ) are not freely available until 12 months after publication. This policy protects the journals’ subscriptions. For the Biophysical Society, subscription income is vital to the royalty payment that the Society receives from Cell Press, and constitutes a significant portion of the Society’s revenue (27% of Society income). This historic “reader pays” model of restricted access to publications has been challenged as elitist and contrary to the spirit of the global scientific enterprise. Indeed, several funding agencies demand that manuscripts resulting from their grants to investigators be published as open access (OA), that is, no embargo on free access. Govern- ment funding agencies in several countries are also insisting that papers from their citizen scientists are published in open access journals. As a result, most journals now provide an alternative model for sharing papers, which is the hybrid open access mod- el. For publication as OA, authors might pay a flat fee that includes page charges, figures, and open access; alternatively, authors might pay an open access fee in addition to page charges and or other publications costs such as color charges. For Biophysical Journal , authors who want their papers to have open access now pay $1,800(US) in addition to page and color charges. For reference, an average 10-page article with OA now costs an author $2450. Currently, about 10 percent of all BJ authors select OA, but due to requirements from outside agencies, we expect this percentage to increase. The Biophysical Society opted to move from publishing BJ independently to publishing it under the Cell Press aegis in 2009. The Society has benefited from Cell Press associa- tion through its larger global presence and publicity, as well as lower publication costs. The Society maintains complete control of the editorial content and editorial process, and its editors are all appointed by BPS. Revenues from BJ accrue to our Society. This background is important to appreciate the new open access structure that will affect BJ on 1 January, 2019: BJ will increase open access fees to $2,500, with a commensurate reduction in page charges of up to $700 for these articles. Will all journals become exclusively open access? Most scien- tific publishers say that is the future (see next article). There are financial consequences for any journal moving toward this model. The most obvious is the loss of subscription revenue. Although access to Biophysical Journal is a benefit of BPS membership, libraries and institutions are major subscribers

Know the Editor Tom Perkins

to the Journal. This 2019 increase in open access fees is a responsible move in preparing for this inevitable shift to open access at some point in the future. When you decide where to publish, please consider that Bio- physical Journal is our Society journal. It is not for profit. It will only flourish if you support it with your papers. — Kathleen B. Hall , Chair of Publications Committee Plan S – The Push for Open Access by 2020 On September 4, 2018, 11 European national research fund- ing organizations announced the launch of “Plan S,” an initia- tive that stipulates “scientific publications that result from research funded by public grants provided by participating national and European research councils and funding bodies, must be published in compliant open access journals or on compliant open access platforms.” The target date is January 1, 2020, for this initiative to take effect. Publishers and open access supporters met with staff at the Office of Science and Technology Policy recently as the Trump Administration is considering changes to the federal open access policy for publicly funded research. According to the 10 principles of Plan S, the hybrid model of publishing is not compliant with the Plan. This will impact Biophysical Journal as well as many other society and com- mercial journals. While publishers ponder the implications of Plan S, one of the immediate impacts will be that researchers will be severely restricted in where they can submit their work for publication (one estimate is over 85% of existing journals). Among the other principles outlined by Coalition S are two that have raised a lot of questions and eyebrows: • When open access fees are applied, their funding is stan- dardized and capped (across Europe) [Note, the amount of the cap has yet to be determined]. • The funders will ensure jointly the establishment of ro- bust criteria and requirements for the services that com- pliant high-quality open access journals and open access platforms must provide [no word on how far this will go with funders dictating publishing practices to journals]. The full list of 10 principles is available at https:/www.scien- ceeurope.org/coalition-s/. One proposal that has been put forward in response to the capping of open access fees (also called article processing charges or APCs) is to institute submission fees. APCs apply only to accepted/published manuscripts, which pay for the evaluation of all other submitted manuscripts, accepted or not. APCs for hybrid journals will only increase without off- setting subscription fees. Submission fees, applied across all

manuscripts shifts the model to where one is paying for peer review, bringing “peer review in line with lots of other services that cost money regardless of whether you succeed or fail, such as professional exams...” Of course submission fees would be unpopular with authors, and other proposals are sure to surface. In the meantime, publishers are looking for ways to publish high-quality jour- nals without charging excessive APCs. In Search of…Content In the realm of scholarly publishing, only about 45% of people use searching to find articles; 55% of the time articles are found via related articles, emails, alerts, and other non-search discovery techniques, according to a recent report by Renew Publishing Consultants How Readers Discover Content in Schol- arly Publications: Trends in Reader Behavior from 2005 to 2018. In this large-scale survey of 10,977 readers of scholarly pub- lications, when asked “When you need to do a search for arti- cles on a specific subject, where on the web do you start that search?” the leading answer was a bibliographic database (abstracting or indexing service, such as Pub Med), followed by an academic search engine, such as Google scholar or Mic- rosoft Academic Search. The third most popular method was a general search engine (e.g., Google). While abstracting and indexing services are a primary dis- covery source for the academic and medical sectors, aca- demic researchers rate academic search engines as the most important discovery resource when searching for journal articles. Only the academic sector uses Google Scholar more than Google. In China, Google Scholar is the dominant search engine for finding journal articles, although Baidu is growing in popularity. To learn more, see the full report at http:/ renewpublishing- consultants.com/wp-content/uploads/2018/08/How-Read- ers-Discover-Content-2018-Published-180903.pdf From the Blog CRISPR: Facts, Myths, and How to Engage the Public BPS member Kelsey Bettridge, Johns Hopkins Universi- ty School of Medicine, writes about the public dialogue surrounding CRISPR and offers advice on how to talk to non-scientists about the facts and misconceptions about the technology. https:/www.biophysics.org/blog/ crispr-facts-myths-and-how-to-engage-the-public biophysics.org/blog

University of Colorado, Boulder Editor, Molecular Machines, Motors and Nanoscale Biophysics

Tom Perkins

What are you currently working on that excites you? I am excited about the diversity of new scientific projects our lab is pursuing, ranging from model globular proteins and RNA pseudoknots to membrane proteins and human beta cardiac myosin. This diversity is enabled by a series of recent improvements in atomic-force-microscopy (AFM) based force spectroscopy (e.g., force stability, temporal resolution, and efficient, site-specific anchoring of biomolecules to coverslips and AFM tips). These improvements allow for a broader range of systems to be studied by AFM and do so more rapidly and with higher precision. The exciting intellectual challenge is to determine the biophysically interesting questions to ask in these diverse areas of force spectroscopy and then try to provide a nuanced presentation of our results to each com- munity. What has been your biggest “aha” moment in science? My biggest “aha” moment was when I was a graduate student in Steve Chu ’s lab. The scientific question was: Do entangled polymers exhibit a special tube-like motion called reptation, as proposed by Pierre de Gennes? Some polymer physicists loved the idea; others thought it was nonsense. In the early 1990s, a few groups were just starting to succeed at visualizing the dynamics of individual DNA molecules in an optical microscope via fluorescence. The conundrum vis-à-vis reptation was how to visualize one DNA molecule entangled in a mesh of other identical but unstained DNA molecules. Then came the “aha” moment. I was reading the original paper detailing YOYO, a newly developed dye for staining DNA. Most of the paper described YOYO’s synthesis and pho- tophysical properties. To me, the key sentence stated that when YOYO-stained DNA was mixed with unstained DNA, the YOYO molecules didn’t dissociate, but rather stayed bound to the original molecule. We now had the key reagent, and my labmate Doug Smith and I went on to experimentally confirm the fundamental assumption of reptation. To this day, our success reminds me of the importance of reading the details in the primary literature.

November 2018

November 2018

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