Some Like it Hot: Sick House Flies Purposely Induce a Fever

house fly

Fevers are thoroughly unpleasant and usually accompanied by other troublesome physical symptoms. Even so, they are often a good sign that our immune system is kicking in to help us “fight off” a nasty infection. Outside the world of endotherms (those of us that regulate our own body temperatures), some ectotherms—those that must seek heat to keep warm—also make use of fevers by finding a heat source to purposely induce them, a phenomenon known as a behavioral fever.

You might wonder why any creature, great or small, would choose to have a fever. One possible reason may be remarkably similar to the reason for fevers in humans: they help fight infections. If you weren’t aware of the massive insect-fungi war taking place right under our noses, the Cornell University Mushroom Blog says it all. In short, fungi have a terrible habit of infecting and killing all kinds of insects, and the insects’ best weapon of defense is to run to the warmest place possible. Make no mistake: the fever is not fun for the flies, and there are health risks and costs (like elevated metabolism and possible organ failure) the longer the fever is maintained. Nevertheless, it’s their best option.

In a recently published PLOS ONE paper, aptly titled “Discriminating Fever Behavior in House Flies, researchers at Penn State investigated this phenomenon further by testing whether house flies self-induced a behavioral fever in a dose-responsive manner to fungal infection. Fungus-infected flies were placed in boxes with temperature gradients (ranging from 77 to a balmy 102 degrees Fahrenheit), and their behavior was monitored throughout the course of the day.

Early in the morning, when the fungus had been actively growing all night, the flies hung out longer in the warmest parts of the box. As the flies’ increased body temperatures began to inhibit fungal growth, the flies would move to cooler areas; however, at night, the fungus would again begin to grow unabated, and the cycle would repeat. Interestingly, it was found that the higher the fungal dose, the higher the temperature of the induced fever. The researchers acknowledge that more work needs to be done, and other factors may contribute to the flies’ preference for heat. Nonetheless, this study underlines the importance and effectiveness of temperature regulation for suppressing infection in a surprising variety of species.

Citation: Anderson RD, Blanford S, Jenkins NE, Thomas MB (2013) Discriminating Fever Behavior in House Flies. PLoS ONE 8(4): e62269. doi:10.1371/journal.pone.0062269

Image Credit: Public domain

Free Webinar on “How to write Case Reports”


Research publication has become an integral part of medical career development and is key to ensuring best clinical practice. A case report is an important research publication type which can both improve medical understanding and directly facilitate best practice. Most case reports in the past have focused on rare or unusual diseases, but championed by Clinical Case Reports are now increasingly focused on important common events or procedures.
To discuss these issues and help you succeed in publishing your case report, we have invited Dr. Charles Young, the Editor-in-Chief of Clinical Case Reports, Vice president for Clinical Solutions at Wiley, and an Emergency Physician at St Thomas’ Hospital London, UK, to share with you his views and experience, and to answer your questions. 
Date: 29 May 2013 (Wed) 
Time: 6.30 – 7.30pm Singapore time/11.30am – 12.30pm UK time
Click here to check your local time.


#ignorantchemist Typographical amusement #ami2

We are doing well at reconstructing semantic material from PDFs (#AMI2) but the challenges we are thrown are considerable. Here’s today’s amusement:

#AMI2 can reconstruct most of this perfectly, but she doesn’t know what to do with a hyphenated-subscript. Nor do I, but I’m just an ignorant chemist. The publishing industry tells us that they need our money to produce beautiful easily readable typeset documents. So here’s an example of human readability from the same paper:

#AMI2 can read this, but can you? Wouldn’t it be easier to typeset it as equations? But that would take up an awful lot of space, and as we know journals have to reduce the space (I never understand why).

I have a plane journey so AMI and I can do some real hacking. We hope to release an alpha version RSN.

Harnad Follow-Up Comments to BIS Select Committee on Open Access

Follow-Up Comments to BIS OA Select Committee

Stevan Harnad


In the online era, the sole remaining barrier separating both the UK and the rest of the world from Open Access (OA) to their refereed research journal article output is keystrokes. It is important to bear this in mind in considering the following comments. Once global OA policy has seen to it that those keystrokes are being universally and systematically executed worldwide, not only OA itself, with all its resulting benefits for research productivity and progress, but all the other desiderata sought ? the end of Green OA embargoes, a transition to Gold OA publishing at a fair and sustainable price, CC-BY, text-mining, open data ? will follow as a natural matter of course.

But not if the keystroke barrier is not first surmounted, decisively and globally.

It is in the interests of surmounting this keystroke barrier to global OA that this summary strongly supports the institutional-repository immediate-deposit mandate proposed by HEFCE/REF to complement and reinforce the RCUK OA mandate.

Embargoes: About 60% of subscription journals (including most of the top journals in most fields) affirm their authors? right to provide immediate, un-embargoed Green Open Access (OA) to the peer-reviewed final draft of their articles by self-archiving them in their institutional repositories immediately upon acceptance for publication as well as making them OA immediately. The remaining 40% of journals impose an embargo of 6-12-24+ months on Green OA.

The optimal solution is for research funders and institutions to mandate that authors deposit the peer-reviewed final draft of all their articles in their institutional repositories immediately upon acceptance for publication, set access to the 60% of deposits that are un-embargoed as Open Access immediately, and set access to the other 40% as Closed Access during the embargo.

This means that for the 40% of the immediate-deposits that are embargoed, users web-wide will still have immediate access to the bibliographic metadata (author, title, journal, abstract) during the embargo, and individual users can request an individual copy for research purposes by clicking the repository?s ?request copy? Button; the author receives an immediate email and can then authorize emailing the requested eprint with one click.

This compromise is not OA but ?Almost-OA? and it can tide over user needs during any allowable embargo period ? as long as all the papers are systematically deposited immediately, not just the un-embargoed ones.

Regardless of whether the author publishes in a subscription journal or a Gold OA journal, regardless of whether the OA is immediate or embargoed, regardless of how long an OA embargo is allowed, OA mandates should require immediate deposit of all papers upon acceptance for publication.

This ensures that everything is deposited, as clocked by the date of the journal acceptance letter, that 60% is immediately Green OA, and that the remaining 40% can have ?Almost-OA? during the embargo.

This is a practical compromise that has already been tested and demonstrated to be effective. To insist instead on mandating immediate or almost-immediate Green OA (i.e., no or almost no embargo at all), needlessly risks non-compliance by authors, who will not give up their right to publish in their journal of choice simply because the journal embargoes Green OA. The right compromise is to mandate immediate deposit, and to tolerate embargoes for the time being. Once mandatory immediate deposit with 60% immediate-OA and 40% Almost-OA becomes universal, embargoes will shrink and disappear as a natural matter of course, under global pressure from the growth and benefits of OA. But everything must be immediately deposited first.

An immediate institutional-deposit mandate, as proposed by HEFCE/REF, will also recruit institutions to monitor and ensure timely compliance with the HEFCE mandate in order to be eligible for REF, thereby remedying the current defect in the RCUK OA mandate, which has compliance mechanisms for Gold OA compliance, but none for Green OA compliance.

Access Rights vs. Re-Use Rights (CC-BY): Online access to peer-reviewed research, free to all users, not just subscribers, is urgently needed in all fields of scholarly and scientific research. There exists no field of research publication in which access-denial is not a problem: for users, in terms of lost access to findings, for authors, in terms of lost user uptake and usage of their findings, and for the tax-paying public who fund the research, there is the lost return on their investment, in terms of lost research uptake, usage, applications, impact, productivity and progress.

Apart from the urgent and universal need for access to research findings, there are also further potential benefits from being able to re-use the texts of the articles in various ways: to text-mine and data-mine them by machine as well as to re-publish them in various new re-mixes or ?mashups.?

However, this further need for re-use rights, over and above online-access rights is neither urgent nor universal. In some fields, such as crystallography, certain journal-article re-use rights would indeed be very useful today; but in most fields the need for journal-article re-use rights is not pressing. Indeed many authors may not even want to allow it — especially in the humanities, where preserving text-integrity is particularly important, but also in other scholarly and scientific fields where authors are resistant to allowing re-mix and re-publication rights on their verbatim texts:

Note that all users that can access them are of course already free to re-use the findings (i.e., the content of the texts) of published articles (as long as author credit is provided through citation). But free online access already allows the re-use of findings. Text re-mixes and re-publication are another matter.

Moreover, there is an important negative interaction between re-use rights and publisher embargoes on Green OA: If Green OA did not just mean online-access rights, but also re-use and re-publication rights (e.g., CC-BY), then publishers would understandably be much more inclined to embargo Green OA: For if they authorized immediate re-publication rights, their own opportunity to recover their investment could be undercut by rival publishers free-riding on their content immediately upon publication! So subscription publisher embargoes on Green OA (now only 40%) would multiply and lengthen if re-use rights, over and above free online access, were mandated too.

The optimal OA policy is hence to mandate only free online access, and leave it up to the publisher and the author what further re-use rights they may wish to grant.

Once mandatory Green OA prevails universally, all this will change, and authors will be able to grant whatever rights they wish. But pre-emptive insistence on re-use rights today will only serve to further retard and constrain basic access-rights and provoke author resistance and noncompliance.

Author Choice and Journal Quality: One of the most fundamental rights of scholars and scientists is the right to choose whether, when and where to publish their findings. It is a great (and unnecessary) strategic mistake ? and will only generate author resistance and policy failure ? to try to force scientists and scholars to choose journals based on the journal?s economic model (subscription or Gold), licensing policy (CC-BY) or embargo length instead of the journal?s quality and suitability.

Journals earn quality track-records on the basis of the level of the peer-review standards that they maintain. Researchers ? as well as their institutions and funders ? want to meet the highest quality standards they can. And users rely on them to judge what work is of sufficient quality to risk investing their scarce time and resources into reading, using, and trying to apply and build upon. Unreliable and invalid research can retard productivity and progress just as surely as access-denial can.

The only requirement of an OA mandate should be immediate deposit of the final draft, with as short an embargo on OA as feasible, and as many re-use rights as the author can and wishes to allow. No restriction on journal choice, which should be based on journal quality-standards alone.

Gold OA and CC-BY should be left as options for authors to choose if and when they wish. They will grow naturally of their own accord once mandatory immediate-deposit becomes universal.

Pre-Emptive Unilateral Double-Payment by the UK: The UK publishes about 6% of the world?s annual research output. The majority of journals today are subscription journals. Hence the UK pays for about 6% of worldwide annual institutional journal subscriptions. Gold OA fees are additional expenditure, over and above what the UK spends on annual subscriptions, because institutional Gold OA fees are for providing OA to UK output (6%) whereas institutional subscriptions are for buying in access to incoming articles from other institutions, both in the UK (6%) ? and the rest of the world (94%). So institutional journal subscriptions cannot be cancelled until not only UK articles but the remaining 94% of published articles are made OA.

Suppose the UK decides unilaterally to pay Gold OA fees for all of its annual research output. That increases UK publication spending ? already stretched to the limit today — by 6%, to 106% of what it is today. Some of this extra UK expenditure (out of already scarce and overstretched research funds) will simply be extra payments to pure Gold OA publishers; some of it will be double-payments to hybrid subscription/Gold publishers. Both mean double-payment on the part of the UK (subscriptions + Gold); but hybrid Gold also means double-dipping on the part of hybrid Gold publishers.

Some hybrid Gold publishers have promised to give a subscription rebate proportional to their uptake of hybrid Gold. If all publishers offered hybrid Gold (as they can all do, easily and at no extra cost, in order to earn UK?s unilaterally mandated Gold subsidy) and all gave full rebates on subscriptions, that would mean that all subscribers worldwide would receive a 6% rebate on their subscriptions, thanks to the UK?s unilateral double-payment.

But for the UK, this would mean that the UK gets back in subscriptions only 6% of the 6% that the UK has double-paid for hybrid Gold OA (6% x 6% = 0.4% UK rebate), while the rest of the world gets a rebate of 94% of the 6% that the UK (alone) has unilaterally double-paid for hybrid Gold OA (6% x 94% = 5.6% rebate to the rest of the world).

In other words, unilateral UK hybrid Gold OA double-payments not only make UK output OA for the UK and the rest of the world, but, if rebated, they also subsidize the subscriptions of the rest of the world. (This is a classic ?Prisoner?s Dilemma,? in which it is to the rest of the world?s advantage to mandate cost-free Green, and at the same time cash in on the rebate from the UK?s unilateral Gold mandate.)

The optimal RCUK policy is hence to leave it up to authors whether they wish to pick and pay for the Gold OA option, but on no account require or prefer Gold, and particularly in the case of hybrid Gold OA.

(If publishers instead gave the full Gold OA rebate to the subscribing institution, that would be tantamount to letting all subscribing institutions publish Gold OA at no cost ? a ?subscription? deal that publishers are not likely to be in a big hurry to make, because if it scaled it would leave ?subscriptions? hanging from a skyhook! Even the premise that all hybrid Gold OA publishers would indeed faithfully refrain from double-dipping by giving a full rebate for the UK 6% Gold by reducing worldwide subscription costs by 6% is a very tenuous assumption.)

UK Leadership in OA: The UK was indeed the worldwide leader in OA from 2000-2012, thanks to the contributions of JISC, EPrints, and especially the 2004 Parliamentary Select Committee which first recommended that UK funders and institutions mandate Green OA. RCUK followed this UK Green OA recommendation and it has since been followed by 80 funders and over 200 institutions worldwide.

But this UK world leadership in OA ended in 2012 with the Finch Report and the resulting new RCUK policy of (1) restricting UK authors? journal choice, (2) downgrading Green OA, and (3) preferring and funding Gold OA and CC-BY, when what was really needed was only a (cost-free) upgrading of the RCUK compliance monitoring and assurance mechanism for Green OA.

Fortunately, HEFCE/REF has now proposed precisely the upgraded Green OA compliance mechanism that can once again earn back the UK?s worldwide leadership role in OA:

In order to be eligible for submission for REF 2020, all peer-reviewed journal articles must be deposited in the author?s institutional repository immediately upon publication (not retrospectively), regardless of whether they are published in a subscription journal or a Gold OA journal, regardless of whether their license is CC-BY, and regardless of whether OA to the immediate-deposit is immediate or embargoed.

Green OA Compliance Mechanism: The proposed HEFCE/REF immediate institutional-deposit mandate overcomes all the major obstacles and objections concerning author restrictions on journal choice, embargo lengths, sufficiency and disbursement of Gold OA funding, double payment, double-dipping, and (unavailable or unwanted) re-use rights:

All UK authors can publish in their journal of choice and no author is prevented from publishing for lack of Gold OA funds. Institutions are recruited to monitor and verify compliance with the immediate-deposit requirement for their own research output, ensuring that all deposits are made on or near the calendar date of acceptance for publication. Access is immediately Green OA (60%) or Almost-OA (40% during any allowable embargo period) (via the repository?s request a copy Button), thereby remedying the RCUK policy?s failure to provide a mechanism for ensuring Green OA compliance.

OA Benefits: The primary benefit of OA is that it ensures that no would-be user of the research is denied access for lack of subscription access.

As has been demonstrated in study after study, in every scholarly and scientific field: OA maximizes research downloads and citations, thereby maximizing research uptake, usage, applications, productivity and progress.

Gold OA Transitional Costs: The secondary benefit of OA is that it will eventually make publishing less costly. But for this to happen, Green OA must be universally mandated first. Pre-emptive double-payment (subscriptions plus Gold OA fees) by the UK, unilaterally, would just mean that the UK was paying even more than it is already paying for subscriptions, in order to make its own research output OA (Gold CC-BY). This is a highly counterproductive policy.

The UK should lead the way toward effectively mandated Green OA worldwide. Once Green OA is universal, institutional subscription cancellation pressure will force publishers to downsize and convert to Gold OA at a fair price, paid for out of institutional subscription cancellation windfall savings instead of double-paid, as with the unilateral pre-emptive Gold funding proposed by Finch/RCUK.

The worldwide network of Green OA repositories will take over the function of access-provision and archiving, unbundling the management of peer review to leave it as the sole remaining essential value still provided by peer-reviewed journal publishing and hence the sole remaining publishing cost. This ?Fair Gold” will cost a fraction of the current price per article, reckoned as 1/Nth of the worldwide subscription revenue of a subscription journal publishing N articles per year today. Hence Fair Gold will cost an order of magnitude less than the £500 – £5000+ asking-price for Gold OA today. (Please see the evidence of Swan & Houghton on the Green/Gold transition and the relative cost/benefits of Green and Gold OA, unilaterally vs. universally.)

Brief notes on points that arose during the Committee Hearing:

HEFCE/REF mandate proposal: The proposed HEFCE/REF institutional immediate-deposit mandate, if adopted, will completely remedy the flaws of the Finch/RCUK policy.

Embargoes and compromise: An interim compromise is needed on the problem of publisher embargoes on Green OA: The optimal compromise is not to insist on double-paying for immediate Gold CC-BY today, preemptively, unilaterally and needlessly, with all its perverse consequences, but instead to mandate immediate deposit of all articles independently of whatever allowable Green OA embargo length is agreed upon.

Journal Prestige & Price: A journal?s ?prestige? is based on its public track-record for quality. A journal?s quality depends on its peer-review standards. The higher the quality standards, the more rigorous and selective is the peer reviewing. The cost per accepted, published article of a highly selective, high-standard journal can be higher because the cost for the peer review of all the submitted and refereed articles that did not meet the journal?s quality standard must be factored into the price of every accepted article. With post-Green Fair-Gold not only is the cost of peer review unbundled from the cost of access-provision and archiving, but peer review can be provided on a ?no fault? basis, with each round of the peer-review service paid for, per paper submitted, irrespective of whether the outcome is acceptance, revision, or revision/resubmission and re-refereeing. This unbundling will re-distribute the cost of the peer review service equitably, so the no-fault peer review fee (1) discourages authors from making unrealistic submissions to journals whose quality standards their work is unlikely to meet, as in the days when peer-review was paid for by subscriptions and hence cost-free to the author, and (2) discourages journals from accepting substandard articles in order to earn more peer review revenues, because their revenue is based on peer review rather than acceptance, and their reputation depends on their track-record for quality.

Publishing costs as research costs: It has been repeatedly stated (particularly by the Wellcome Trust) that ?publishing costs are just a small part of research costs? (c. 1.5%), and hence that research funders should be prepared to pay them as such ? in the form of Gold OA fees. This sounds fine from the standpoint of a research funder like Wellcome, which need only fund research. But, as noted above, most publication costs today are paid in the form of institutional journal subscriptions. Wellcome does not pay the institutional journal subscriptions of its fundees? institutions: Those are paid by others, from other resources. Hence Wellcome payment of Gold OA fees (at today?s inflated asking-price, and often paid to hybrid subscription/Gold journals) is double-payment, but the double-payment is not by Wellcome. The UK government is ultimately paying for both journal subscriptions and RCUK Gold OA fees. Hence Wellcome?s motto that ?publishing costs are just a small part of research costs? cannot be applied to UK governmental funding until UK subscription costs no longer need to be paid and peer review costs have been unbundled and offered as Gold OA at a fair price. In other words, after global Green OA has prevailed globally.

Disproportionate publication costs for research-intensive institutions and countries: When publishing costs are paid by the institutions that provide the research (in the form of Gold OA fees) instead of by the institutions that consume the research (in the form of subscription fees), more research-intensive institutions pay more than less research intensive institutions do. But, as Houghton & Swan have shown, both will still pay substantially less than they are paying today in subscriptions, because the price of post-Green Fair-Gold publishing (freed from double-payment and downsized — by universal Green — to peer-review costs alone) will be so much lower than the current price of subscription publishing.

The cost of institutional repositories: Most institutions in the UK, EU and US already have institutional repositories (for a variety of institutional purposes, including OA). Their start-up costs were low, and have already been invested. Their annual maintenance costs (a server and some sysad time) are low, and part of existing institutional network infrastructure. The cost per paper deposited in an institutional repository is virtually zero, yet this represents the institution?s contribution to globally distributed access-provision and archiving. (Even for a global central repository like Arxiv, the price per paper is less than $7.) This is what will permit the current publication price per article ? paid in the form of worldwide institutional subscriptions ? to be reduced to just the price of peer review alone.

Finch on repositories: The Finch report, under the influence of publishers, suggested that Green OA is a failure in practise as well as inadequate in principle, so Finch accordingly recommended downgrading institutional repositories to the role of (1) data-archiving, (2) digital preservation, and (3) linking data to publishers? websites, where the articles reside. It should be evident now that this was a self-serving assessment on the part of publishers (as was Elsevier?s Alicia Wise?s plea during the BIS hearing not to have institutional repositories needlessly ?duplicate? access-providing and archiving functions that publishers already perform: ?Leave it to us!?). What institutional repositories need in order to successfully provide OA to journal articles is for funders and institutions to upgrade their Green OA mandates and compliance mechanisms to ensure immediate deposit of all articles, as proposed by HEFCE/REF (see above).

Publisher deposit: Publishers, in an effort to retain control over as much of the transition to OA as possible, have proposed to deposit papers (in institution-external repositories), on behalf of their authors, on publishers? terms and timetables. On no account should publishers be relied upon to ensure compliance with OA mandates: the mandates apply to researchers, not to publishers. Publishers are happy to comply when they are paid for Gold. But it is not in publishers? interests to comply with Green — nor are they required to do so. Authors are perfectly capable of doing the few keystrokes of self-archiving for themselves, at no cost. Once again, the optimal policy is HEFCE/REF?s, which proposes mandating immediate-deposit, by the author, in the author?s institutional repository, immediately upon publication. Institutions can then monitor and ensure timely compliance for their own institutional publication output, in their own institutional repository.

Complementary self-archiving mandates from funders and institutions: The RCUK/HEFCE/REF OA mandates can and should be complemented by institutional OA mandates, likewise requiring immediate-deposit, as well as designating institutional immediate-deposit as the sole mechanism for submitting published articles for institutional performance review. Belgium has provided the optimal integrated institution/funder model for this.

Patents, plagiarism: Both patents and plagiarism are red herrings, insofar as OA is concerned. OA concerns access to published articles. What authors wish to conceal, they do not publish, hence OA is moot. Plagiarism is possible with all published work, OA or non-OA. OA merely makes the words accessible to all users, not just subscribers. And inasmuch as copyright protects against plagiarism, it protects OA and non-OA work equally. Even CC-BY requires acknowledgement of authorship (that?s what the ?BY? refers to) (although in a ?mash-up,? the re-mix of words, even listing all authors, can be rather like crediting body-parts in a common grave); but for now, allowing CC-BY should be left entirely a matter of author choice.

Institutional vs. central repositories: All OAI-compliant repositories are interoperable, hence harvestable and hence searchable as if they were all one global archive. So it does not matter technically or functionally where articles are deposited, as long as they are deposited immediately (and made OA). But it matters a great deal strategically — for the effectiveness of mandates, for compliance verification, and to minimize author keystrokes, effort and hence resistance and resentment ? that mandates should require institutional deposit (and just once). Once, deposited, the metadata can be automatically exported to or harvested by other repositories, so they can be searched at a central-repository level for a discipline, nation, or globally.

?Evidence of harm?: Publishers often speak of repositories and Green OA self-archiving in terms of the presence or absence of ?harm.? But one must ask what ?harm? means in this context: Increased access, downloads and citations overall are certainly not evidence of harm — to research, researchers, their institutions, their funders, R&D businesses and the tax-paying public — quite the contrary, irrespective of whether the increase usage occurs at the publisher?s website or institutional repositories. Nor is it clear that if and when mandatory Green OA should eventually make subscriptions unsustainable — inducing cost-cutting and a transition to Gold OA at a fair price and without double-payment — that this should be counted as ?harm? rather than as yet another benefit of OA — to research, researchers, their institutions, their funders, R&D businesses and the tax-paying public — in the natural evolution of scientific and scholarly communication with technology (bringing not just universal research access, but lower publication cost), to which the publishing industry can and must and will adapt, rather than the reverse.

Embargoes and compromise: It has to be clearly understood that embargoes on providing Open Access to the author?s final draft are imposed by the publisher in order to protect and sustain subscription revenues and the subscription model. If the objective is a transition to sustainable Gold OA at a fair price, publisher OA embargoes are not in the interests of the research community. However, as a compromise, they can be tolerated, for the time being, as long as the HEFCE/REF immediate-deposit mandate proposal is adopted.

Redirecting funds: It is premature to speak of ?redirecting funds? from subscription payment to Gold OA payment. Journal subscriptions cannot be cancelled until the journal articles are accessible in another way. That other way is Green OA. Hence Green OA must be universally mandated first. The alternative is double-payment and double-dipping (see above).

Added value: The values added by publishers to the author?s un-refereed draft are: (1) peer-review, (2) copy-editing, (3) formatting & tagging, (4) print edition, (5) online PDF edition, (6) access-provision, (7) archiving. Once Green OA is universally mandated, (3) ? (7) become obsolete. It is not clear how much copy-editing (2) is still being done or needed. So the only remaining essential post-Green function of peer-reviewed journal publishing is the service of peer review (1). This is what can be paid for as Gold OA, at a fair, sustainable post-Green price.

Hybrid gold and embargo: One of the perverse effects of the Finch report?s recommendation to require authors to pick and pay for Gold OA if a journal offers it is to encourage subscription publishers to offer hybrid Gold as an option and to adopt and lengthen Green OA embargo periods beyond the allowable limit, so as to make sure that authors must pick and pay for Gold. This is why the Green option must always be allowed and embargo limits must not be draconian.

Open data vs article access: It is a misunderstanding as well as a strategic mistake to conflate open data and OA. The purpose of data is to be used. In general, the one who gathered the data must be allowed fair first data-mining rights. After that, it is reasonable for the funder to require that the data be made open for re-use. But articles are not data, and authors must be allowed to decide whether or not to allow their text to be re-used. (The findings and ideas can of course always be re-used, with acknowledgement; but that is not the same thing as re-using, re-mixing or re-publishing the verbatim text itself.)

Discipline differences: There may be discipline differences in the length of OA embargo needed to sustain subscriptions, but there are no discipline differences in the need for free online access to research for all would-be users, not just those who have subscription access.

?Reasonable access?: At the hearings it was asked ?what is ?reasonable? access?: it?s free online access to peer-reviewed research, immediately upon publication.

World Malaria Day 2013: Invest in the Future: Defeat Malaria


Since World Malaria Day was first instituted in 2007 by World Health Organization Member States, great progress has been made in malaria prevention, detection and treatment. Even so, over half a million people die each year from this disease, many of them children under five years old, with direct costs of the disease estimated to be in excess of $12 billion annually. Today, many countries worst affected by malaria transmission are on track to meet the 2015 World Health Assembly target of reducing incidence rates by more than 75% but continued research and support are vital to keeping this momentum.

Papers published recently in PLOS ONE highlight some of the work being done around the world to reach this goal and sustain the progress that has been made. A case study of Sri Lanka’s malaria program showed how better vector control and surveillance measures can substantially reduce malaria cases, and offers insight for the development of successful disease prevention campaigns in other countries.

In addition to control and detection measures, efforts to develop inexpensive treatments and efficient ways to produce vaccines continue to be important in the fight against malaria. Medicines derived from the extract of the Artemisia plant are widely used in malaria treatment, but in a paper published in PLOS ONE last year, researchers found using the whole Artemisia plant to be effective in malaria treatment in a mouse model. They propose that whole plant treatment may even offer a more efficient delivery mechanism, potentially having broad therapeutic power against many infectious agents and the ability to dramatically reduce treatment costs.

In another study, researchers from University of California, San Diego looked for a way to make safe and effective subunit vaccines less expensive to produce. They tested whether Plasmodium falciparum surface proteins 25 and 28, both powerful malaria transmission blocking vaccine candidates, could be produced on algal chloroplasts. Their work found algae a viable, cost-effective platform for producing malaria subunit vaccines, which could be a promising contribution in making these vaccines available to low-income countries.

These papers and many others support this year’s World Malaria Day theme to “Invest in the Future: Defeat Malaria.” As researchers continue to make strides towards the 2015 Millennium Development Goal to “have halted and begun to reverse the incidence of malaria,” you can read more PLOS ONE research on malaria here.



Abeyasinghe RR, Galappaththy GNL, Smith Gueye C, Kahn JG, Feachem RGA (2012) Malaria Control and Elimination in Sri Lanka: Documenting Progress and Success Factors in a Conflict Setting. PLoS ONE 7(8): e43162. doi:10.1371/journal.pone.0043162

Elfawal MA, Towler MJ, Reich NG, Golenbock D, Weathers PJ, et al. (2012) Dried Whole Plant Artemisia annua as an Antimalarial Therapy. PLoS ONE 7(12): e52746. doi:10.1371/journal.pone.0052746

Gregory JA, Li F, Tomosada LM, Cox CJ, Topol AB, et al. (2012) Algae-Produced Pfs25 Elicits Antibodies That Inhibit Malaria Transmission. PLoS ONE 7(5): e37179. doi:10.1371/journal.pone.0037179

Image: Anopheles by James Gathany for CDC

#openaccess: American Chemical Society charge additional 1000 USD for Creative Commons Licences

From the start of this month all RCUK-funded researchers will have to publish “Open Access”. Exactly what this means has been the subject of a messy set of polemics. But on the assumption that authors wish to publish under a CC-BY licence (effectively the only one compliant the with BOAI declaration – free to copy, use, re-use and redistribute) then are they able to?

I’ve taken a prominent journal – Journal of the American Chemical Society – in which I have previously published. Can I publish “Open Access” and comply with the RCUK requirements?

There’s a useful tool

Many publishers have been extremely poor at providing simple information for readers and authors. Often you have to chase round the buttons on the site (avoiding the (self-)advertising). Sometimes I get the impression that the publishers aren’t really trying to be helpful. Ross Mounce has done a great job on trying to winkle out licence and prices info and SHERPA have now done much of the grunt work in providing the right button to click. systematize this as well. So I can go straight to the key info:

What’s “Author Choice”? It’s ACS-specific and it’s some form of “Open Access” (according to the ACS). Many of these publisher-specific labels ( (Author|Reader|Free|Open)(Access|Choice|Article) have fuzzy words and fuzzy conditions.

But we have Creative Commons (and without CC we would be in an awful mess). CC provide a range of licences. ONLY CC-BY (CC0, and possibly CC-BY-SA) fit the BOAI definition of open access. Only CC-BY allows copying, re-use and redistribution.

Which, simply, is what Science is about.

Any restriction of access or re-use is anti-scientific.

It may be good business, but it harms science.

So it is possible to use a CC-BY licence when publishing with the ACS. But ONLY by paying an extra 1000 USD.

Does it COST this much to add a CC-BY licence?

Of course not. It shouldn’t cost anything (it’s a standard 50 characters on a page and a hyperlink).

It’s effectively a ransom from the publisher to raise extra revenue. The publishers can make up any set of charges they like. And the authors will either pay it or hide their publication behind an embargo-wall (say for 1-2 years).

Is this good for science? Of course not. It makes it harder to detect bad science. Humans and machines can validate or invalidate science if they are allowed to read the full text.

Very few publishers have earned respect during the evolution of Open Access. Most have been seen to value commerce above other considerations. There is no price pressure on OA.

And many “open access advocates” have actually welcomed non-CC-BY and embargoed green OA – which has led us to these huge APCs for BOAI Open Access.

To fight this we need strength from the funders and unanimity of purpose.

And we have this and it’s the primary redeeming feature in Open Access.

We need tools for uniform practice – what does a publisher offer? And we are getting them (kudos in UK to JISC, SHERPA, and Ross) and they are cutting through the fuzz.

We need tools for measuring author compliance. Because many authors simply don’t care about the funders requirements and will still publish in a completely closed manner so as to advance their careers and funding prospects. And we are getting them.

The organizations that have let us down are the Universities and their libraries. They don’t really care. They could have fought this battle 10 years ago instead of waiting for the funders to do it. They accept whatever prices the publishers charge for OA APCs and route tax-payer money or student fees to the publishers…

But that’s another blog post. Soon…

Update: The struggle continues… #ami2 would like alpha testers

A quick update. I’ve been spending most of my time on #ami2 which is now at raw alpha (see below). Other items of note include:

  • Mendeley is now owned by Elsevier. I shall blog this. If you care about Open scholarship you have to be seriously concerned.
  • Open Data Workshop (, ). Really exciting to see the concentration of interest. There was a pre-workshop evening run by OKFN – lightning talks (I gave a short one (3-4 mins) on #ami2 and the problems of scientific data. Many international visitors came.
  • Ross and Avril got married (@rmounce) – their 2nd or 3 weddings. Great occasion – thanks all.
  • Went to talk by Glyn Moody on Copyright.
  • Meeting by JISC/Cameron on tools to determine openness of livcences in scholpubs.
  • Opening of Materials centre at QMU (Martin Dove). CML continues to be valuable.
  • Good progress on CML dictionaries for compchem.
  • We keep fighting for “the right to read is the right to mine” at Brussels (Licences for Europe). Do university libraries care?? They’d rather buy things than fight.

Overall I worry seriously about Open Scholarship. The universities and their libraries don’t care and are giving it away and then buying it back. It’s getting worse not better. We should be fighting for our rights.

#ami2 is at raw alpha. That means that it can do useful stuff if you know what you are doing and know the limitations. We are not appealing for volunteers yet but if you want to be involved please let me know. You will need to be able to:

  • Run Maven and Java.
  • Use Bitbucket.
  • Get excited about really boring stuff (like errors in fonts, pagination etc.)
  • Sort problems yourself/communally.
  • Want to liberate information from PDFs.
  • Have a few minable papers (“Open” in some sense).
  • Be patient.
  • Respect copyright.

Currently there are no proper metrics but:

  • Ca. 1 sec per page
  • Useful compression for text-only (images can’t compress, of course).

Mail me or leave a message here or simply use Bitbucket ( ) and give feedback.

University College London signs up for Wiley Open Access Account


We are pleased to announce that University College London has signed up for a Wiley Open Access Account and now pays for their researchers to publish an open access article with Wiley. Authors affiliated with University College London can publish research articles in Wiley Open Access journals and/or OnlineOpen without directly paying any publication charges.

University College London becomes the latest funder to open a Wiley Open Access Account. Browse our growing list of institutions / funders who have an account or partnership with Wiley Open Access.

For further information, pricing and discounts please contact:

Tracing Our Footsteps: Archaeology in the Digital Age

pone.0060755 Geocon Bennett et al Figure 6

Human ancestors that walked the earth left few traces of their passage. Some of their footprints have lithified, or turned to stone, but some survive to this day, unlithified, in soft sediment such as silt. These fragile records of ancient footprints pose a sizable challenge to archaeologists today: how do you preserve the ephemeral? According to new research published in PLOS ONE, the answer may be to “record and digitally rescue” these footprint sites.

The authors explored two methods in this study: digital photogrammetry, where researchers strategically photograph an object in order to derive measurements; and optical laser scanning, where light is used to measure the object’s physical properties. To begin, the authors filled trays with mixtures of sand, cement, and plaster and instructed a participant to walk through these samples. Four wooden 1 cm cubes were then placed beside a select number of footprints and photographs were taken. A laser scanner was then used to measure the same footprints. This simple procedure was also replicated outside of the lab, at a beach in North West England.

In their results, they found that both methods offered similar levels of precision (though, the laser scanner was “slightly more accurate”) and that differences between the two were not statistically significant. These two methods are not, however, without their respective strengths and challenges. Photogrammetry can be an advantage in situations where records need to be taken quickly and inexpensively, as field work can be completing using a camera, tripod, and measuring equipment. This practice is, however, especially subject to human error. Additionally, the accuracy of the images – and consequently the measurements derived from the images – may be compromised by extreme lighting conditions and the depth of the footprint or impression. Alternately, laser scanning is more appropriate in conditions where a high degree of precision is required and footprints are more fragile (and thus unlikely to remain in an “optimal” condition). Laser scanners are, however, more expensive and require a large energy source. The authors advocate that both methods can, and should, be used in tandem to supplement each other.

These digital tools provide an innovative solution to preserving footprint records, especially in cases where traditional on-site, or off-site, preservation is impractical and costly. To learn more about this research and the merits and challenges of digital rescue archaeology, read the full text of the study here.


Image is Figure 6 of the manuscript.

Citation: Bennett MR, Falkingham P, Morse SA, Bates K, Crompton RH (2013) Preserving the Impossible: Conservation of Soft-Sediment Hominin Footprint Sites and Strategies for Three-Dimensional Digital Data Capture. PLoS ONE 8(4): e60755. doi:10.1371/journal.pone.0060755

Publicar en acceso abierto: 10 preguntas frecuentes

Presentación con motivo de la Semana del Acceso Abierto 2012.  A cargo de la Universidad Nacional de Rosario (Argentina) y CLACSO.

“Open access publishing: 10 frequent questions” presentation for the 2012 OA week, prepared by National University of Rosario in Argentina and CLACSO-Latin American Council on Social Sciences

Open access explained