New and Exciting in PLoS this week

Monday – time to check out PLoS Biology, PLoS Medicine and PLoS Neglected Tropical Diseases, as well as, of course, PLoS ONE.
As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Equity for Open-Access Journal Publishing by Stuart M. Shieber:

Scholars write articles to be read–the more access to their articles the better–so one might think that the open-access approach to publishing, in which articles are freely available online to all without interposition of an access fee, would be an attractive competitor to traditional subscription-based journal publishing.
But open-access journal publishing is currently at a systematic disadvantage relative to the traditional model.
I propose a simple, cost-effective remedy to this inequity that would put open-access publishing on a path to become a sustainable, efficient system, allowing the two journal publishing systems to compete on a more level playing field. The issue is important, first, because academic institutions shouldn’t perpetuate barriers to an open-access business model on principle and, second, because the subscription-fee business model has manifested systemic dysfunctionalities in practice. After describing the problem with the subscription-fee model, I turn to the proposal for providing equity for open-access journal publishing–the open-access compact.

Prolonged Grief Disorder: A Problem for the Past, the Present, and the Future:

In systematically, and to me at least, persuasively establishing prolonged grief disorder (PGD) as a uniquely identifiable illness that requires specific treatments, Holly Prigerson and colleagues have separated PGD from normal grief and from other forms of pathologic grief responses [2]. Is it useful to include it in the DSM (Diagnostic and Statistical Manual of Mental Disorders)? I believe it is for several reasons. First, treatment for PGD is effective and substantially different from treatment for other forms of psychiatric illnesses that can be triggered by or arise with grief and loss.

The Validation and Assessment of Machine Learning: A Game of Prediction from High-Dimensional Data:

In applied statistics, tools from machine learning are popular for analyzing complex and high-dimensional data. However, few theoretical results are available that could guide to the appropriate machine learning tool in a new application. Initial development of an overall strategy thus often implies that multiple methods are tested and compared on the same set of data. This is particularly difficult in situations that are prone to over-fitting where the number of subjects is low compared to the number of potential predictors. The article presents a game which provides some grounds for conducting a fair model comparison. Each player selects a modeling strategy for predicting individual response from potential predictors. A strictly proper scoring rule, bootstrap cross-validation, and a set of rules are used to make the results obtained with different strategies comparable. To illustrate the ideas, the game is applied to data from the Nugenob Study where the aim is to predict the fat oxidation capacity based on conventional factors and high-dimensional metabolomics data. Three players have chosen to use support vector machines, LASSO, and random forests, respectively.

One response to “New and Exciting in PLoS this week

    What follows is a critique of the “Compact for Open-Access Equity.” The Compact states:
    “We the undersigned universities recognize the crucial value of the services provided by scholarly publishers, the desirability of open access to the scholarly literature, and the need for a stable source of funding for publishers who choose to provide open access to their journals’ contents. Those universities and funding agencies receiving the benefits of publisher services should recognize their collective and individual responsibility for that funding, and this recognition should be ongoing and public so that publishers can rely on it as a condition for their continuing operation.
    “Therefore, each of the undersigned universities commits to the timely establishment of durable mechanisms for underwriting reasonable publication charges for articles written by its faculty and published in fee-based open-access journals and for which other institutions would not be expected to provide funds. We encourage other universities and research funding agencies to join us in this commitment, to provide a sufficient and sustainable funding basis for open-access publication of the scholarly literature.” /signed/

    My critique is based on points that I have already made many times before, unheeded. All I can do is echo them yet again (and hope!):
    Regardless of the size of the current asking price (“reasonable” or unreasonable), it is an enormous strategic mistake for a university or research funder to commit to pre-emptive payment of Open Access (OA) journal (“Gold OA“) publishing fees today — until and unless the university or funder has first mandated OA self-archiving (“Green OA“) for all of its own published journal article output (irrespective of whether the article happens to be published in an OA or a non-OA journal).
    There are so far five signatories to the “Compact for Open-Access Equity.” Two of them have mandated Green OA (Harvard and MIT) and three have not (Cornell, Dartmouth, Berkeley). Many non-mandating universities have also been committing to the the pre-emptive SCOAP3 consortium.
    If Harvard‘s and MIT‘s example of first mandating Green OA is followed, and hence Green OA mandates grow globally ahead of Gold OA commitments, then there’s no harm done.
    But if it is instead pre-emptive commitments to fund Gold OA that grow, at the expense of mandates to provide Green OA, then the worldwide research community will yet again have shot itself in the foot insofar as universal OA — so long within its reach, so urgent, and yet still not grasped — is concerned.
    The fundamental problem is not that of needlessly overpaying for Gold OA by paying prematurely and pre-emptively and at an arbitrarily inflated asking price (although that is indeed a problem too).
    The fundamental problem is that focussing on a commitment to pay pre-emptively for Gold OA today gives institutions the false sense that they are thereby doing what needs to be done in order to provide OA for their own research output, whereas this is very far from the truth:
    No institution can or will pay for Gold OA publication of all (or even most) its research output because
    (1) not all (or even most) journals offer Gold OA today,
    (2) not all (or even most) Gold OA journals’ asking price is reasonable or affordable today, and
    (3) most of the money to pay for Gold OA is still tied up in institutional journal subscriptions today.

    But most important of all is the fact that
    (4) OA can be provided for all of an institution’s research output today by mandating Green OA self-archiving, which moots (1) – (3).
    (1) – (4) jointly comprise the reason pre-emptive Gold OA payment is not at all what is needed today. What is needed is OA itself, and that is what Green OA provides, regardless of journal funding model (subscription or Gold OA).
    Once Green OA has been mandated universally and is being universally provided by institutions, journals will eventually adapt, under subscription cancellation pressure, downsizing to provide peer review alone and converting to Gold OA to cover costs. Meanwhile, institutions’ own windfall subscription cancellation savings will be more than enough to pay journals for Gold OA publication at this much-reduced price.
    But none of that can happen today, through pre-emptive payment for Gold OA. And meanwhile research progress and impact keep being lost, needlessly, because institutions are focusing on funding Gold OA when what they urgently need to do is mandate Green OA.
    Once an institution has mandated Green OA, it no longer matters (for OA) what it elects to do with its spare cash. It is only if an institution elects to focus on spending its cash to pay for Gold OA instead of mandating Green OA that an institution does both its research and its pocketbook a double disservice, needlessly.
    The creation of high-quality, self-sustaining Gold OA journals such as the PLoS and BMC journals was historically important and timely as a proof-of-principle that peer-reviewed journal publication is viable even if universal Green OA eventually makes subscriptions unsustainable. But what is urgently needed now is not more money to pay for Gold OA but more mandates to provide Green OA, hence OA itself.
    Finding money to pay pre-emptively for Gold OA while subscriptions still prevail and OA itself does not is an extremely counterproductive strategy, if access to refereed research — rather than publishing reform — is the real raison d’être of the Open Access movement (as it certainly is and always has been for me).
    Gold OA is not the end, but merely one of the means (and by far not the fastest or surest means) of providing universal OA. Full speed ahead with (mandating) Green OA; publishing will adapt naturally as the time comes.
    Harnad, S. (1991) Post-Gutenberg Galaxy: The Fourth Revolution in the Means of Production of Knowledge. Public-Access Computer Systems Review 2 (1): 39 – 53
    Harnad, S. (1995) Universal FTP Archives for Esoteric Science and Scholarship: A Subversive Proposal. In: Ann Okerson & James O’Donnell (Eds.) Scholarly Journals at the Crossroads; A Subversive Proposal for Electronic Publishing. Washington, DC., Association of Research Libraries, June 1995.
    Harnad, S. (1999) Free at Last: The Future of Peer-Reviewed Journals. D-Lib Magazine 5(12) December 1999
    Harnad, S., Carr, L., Brody, T. & Oppenheim, C. (2003) Mandated online RAE CVs Linked to University Eprint Archives. Ariadne 35.
    Harnad, S., Brody, T., Vallieres, F., Carr, L., Hitchcock, S., Gingras, Y, Oppenheim, C., Stamerjohanns, H., & Hilf, E. (2004) The Access/Impact Problem and the Green and Gold Roads to Open Access. Serials Review 30. Shorter version: The green and the gold roads to Open Access. Nature Web Focus.
    Harnad, S. (2006) Opening Access by Overcoming Zeno’s Paralysis, in Jacobs, N., Eds. Open Access: Key Strategic, Technical and Economic Aspects. Chandos.
    Harnad, S. (2007) The Green Road to Open Access: A Leveraged Transition. In: Anna Gacs. The Culture of Periodicals from the Perspective of the Electronic Age. L’Harmattan. 99-106.
    Harnad, S. (2009) The PostGutenberg Open Access Journal. In: Cope, B. & Phillips, A (Eds.) The Future of the Academic Journal. Chandos.