Wednesday, October 26, 2011

Feast of the Open Access Week: PLoS Won

By Michael Eisen | it is NOT junk)

When Pat Brown, Harold Varmus and I started the Public Library of Science (PLoS) 10 years ago with the goal of making the scientific and medical literature a universally freely available resource, most people in the science publishing industry dismissed us as naive idealists who didn't understand that publishing is a business that has to make money, or derided us as dangerous radicals hellbent on destroying them.

So it has given me considerable pleasure to watch, over the past year or so, as one traditional publisher after another has responded to the smashing success of PLoS One by launching direct ripoffs that seek to capitalize on the business model we have established.

For those of you who don't know, PLoS One, launched in 2006, does things a bit differently than most scientific journals. Every paper submitted to the journal is peer reviewed, but the reviewers and editors consider only the technical merits of the paper in deciding whether or not it should be published – they do not attempt (as virtually all other journals do) to gauge the potential significance or sexiness of the paper. The result is a simple and objective peer review process that gets papers published quickly and, because it is an open access journal, in a place where it is accessible for anyone to find and read. To cover the costs of running the journal and handling the paper, authors of accepted papers pay a fee (currently $1,350 – he money comes from their research grants or institutions, not from their own pockets, and any authors who say they can not pay are granted waivers).

And apparently authors love PLoS One, because they are sending us lots of paper. The journal published 6,700 articles in 2010 and will publish around 12,000 in 2011. This has clearly caught the attention of lots of established publishers, as the past year has seen the launch of a series of PLoS One clones, including:

joining already existing offerings from open access publishers BioMed Central, Hindawi and others.

This is, in many ways, exactly what we hoped would happen. In 2001 most publishers lacked both the foresight to see how publishing could better serve the research community, and the incentive to bother figuring it out. Now, PLoS One's volume, and the threat it poses to their existing journals, provides the motivation, and PLoS One's financial success (it is profitable) serves as an inspiration. Our goal was always to see that papers were published in open access journals. If they were PLoS journals – great. But if they were from other publishers – that's great too.

And here, there is a bit of a rub. PLoS and BMC established the standard for open access publishing by adopting the Creative Commons Attribution License (CC-BY), which allows for unrestricted reuse and redistribution subject only to the constraint that the original authors and source be cited. Several of the new journals follow our lead and use CC-BY, including G3, Open Biology and SAGE Open. I fully endorse what these publishers are doing, and have already published one paper in G3.

The others have not been so enlightened, using exclusively (or in one case optionally) licenses that restrict commercial reuse or the generation of derivitive works.

CC-BY-NC – BMJ Open

CC-NC-SA – mBio, Biology Open

CC-BY-NC-ND – Scientific Reports

CC-BY or CC-BY-NC-ND – Cell Reports

This is a very misguided decision on the part of these publishers. The rules governing reuse of content matter a lot if we are ever going to start making more effective use of the published scientific literature. The non-commercial licenses employed by BMJ, Nature, ASM, Company of Biologists, Cell Press and Nature all – rather absurdly – prevent PLoS from reusing their content in tools we are developing to help researchers organize literature in their fields and make the contents of papers they care about more useful. I hope this is a short-lived mistake and that, following Netflix, they realize the error of their ways and switch to a CC-BY license (in the meantime, I urge people who care about open access to continue supporting only those journals that use the CC-BY license).

There is, obviously, still a long way to go before we achieve our original goal of making every paper immediately freely available. Buit it's hard not to see events of the last year as anything but a major victory for PLoS and open access.

Happy Open Access Week!

[UPDATE: I want to clarify that Cell Reports does not view itself as a PLoS One clone, as it will be rejecting papers on the basis of impact/importance. I also want to commend them for offering the CC-BY license to authors, although I think that many will naively choose the NC version].

Friday, September 30, 2011

PLoSONE: Global Conservation Priorities for Marine Turtles

Wallace BP, DiMatteo AD, Bolten AB, Chaloupka MY, Hutchinson BJ, et al. (2011) Global Conservation Priorities for Marine Turtles. PLoS ONE 6(9): e24510 - Read full article here for free

Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs), and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts) we developed a "conservation priorities portfolio" system using categories of paired risk and threats scores for all RMUs (n = 58). We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority-setting for widespread, long-lived taxa. Image coutesy: WWF. Read full article here for free

Tuesday, September 6, 2011

Hot in PLoS ONE: Do Facial Expressions Develop before Birth?

Citation: Reissland N, Francis B, Mason J, Lincoln K (2011) Do Facial Expressions Develop before Birth? PLoS ONE 6(8): e24081. doi:10.1371/journal.pone.0024081

Background

Fetal facial development is essential not only for postnatal bonding between parents and child, but also theoretically for the study of the origins of affect. However, how such movements become coordinated is poorly understood. 4-D ultrasound visualisation allows an objective coding of fetal facial movements.

Methodology/Findings

Based on research using facial muscle movements to code recognisable facial expressions in adults and adapted for infants, we defined two distinct fetal facial movements, namely "cry-face-gestalt" and "laughter- gestalt," both made up of up to 7 distinct facial movements. In this conceptual study, two healthy fetuses were then scanned at different gestational ages in the second and third trimester. We observed that the number and complexity of simultaneous movements increased with gestational age. Thus, between 24 and 35 weeks the mean number of co-occurrences of 3 or more facial movements increased from 7% to 69%. Recognisable facial expressions were also observed to develop. Between 24 and 35 weeks the number of co-occurrences of 3 or more movements making up a "cry-face gestalt" facial movement increased from 0% to 42%. Similarly the number of co-occurrences of 3 or more facial movements combining to a "laughter-face gestalt" increased from 0% to 35%. These changes over age were all highly significant.

Significance

This research provides the first evidence of developmental progression from individual unrelated facial movements toward fetal facial gestalts. We propose that there is considerable potential of this method for assessing fetal development: Subsequent discrimination of normal and abnormal fetal facial development might identify health problems in utero.