GMOs and pediatric cancer rates #GMOFAQ

There’s a post being highlighted by anti-GMO activists on Twitter that claims that cancer is now the leading cause of death among children in the US, that the rates of pediatric cancer are increasing and that this is because of GMOs. This is another egregious example of the willingness of anti-GMO campaigners to lie to the public in order to scare them and promote their agenda.

A simple look at data exposes the absurdity of their claims:

1) Cancer is not the leading cause of death among children in the United States

The Centers for Disease Control publishes annual statistics on the leading causes of death in the US broken down by age. These data show that malignant neoplasms are a serious problem – killing over 1,000 children under the age of 14 every year – making it the leading cause of disease-related death in children. But accidents remain the major cause of death by far.

One other thing to note from this table is the top 5 in any age group. This was not always the case, and is almost entirely the result of vaccination, another evil of modern science often highlighted by the same people who oppose GMOs.

2) Childhood cancer rates are not increasing

Another claim cited by the anti-GMO crowd is that childhood cancer rates are increasing at an “alarming rate”. Again, data says otherwise. Here is a report from the National Cancer looking at rates of childhood cancer from 1988 to 2008 that shows that they are virtually unchanged.

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3) There is no evidence that GMOs cause childhood cancer

If GMOs caused childhood cancer, you would expect there to be some difference in the rate of childhood cancer in the US after the introduction of GMOs into the US food supply in 1995. However the rate of childhood cancer has remained unchanged from its pre-1995 levels.

Childhood cancer is a horrible, horrible thing. We should do everything in our power to prevent and better treat it so that cancer, like infectious disease, disappears from statistics on childhood mortality. But it doesn’t do anyone any good to misrepresent the statistics in the name of a political agenda. So please anti-GMO campaigners, stop making stuff up, and stop using false statistics to try to scare people.

Posted in GMO | 4 Responses

I confess, I wrote the Arsenic DNA paper to expose flaws in peer-review at subscription based journals

In 2011, after having read several really bad papers in the journal Science, I decided to explore just how slipshod their peer-review process is. I knew that their business depends on publishing “sexy” papers. So I created a manuscript that claimed something extraordinary - that I’d discovered a species of bacteria that uses arsenic in its DNA instead of phosphorus. But I made the science so egregiously bad that no competent peer reviewer would accept it. The approach was deeply flawed – there were poor or absent controls in every figure. I used ludicrously elaborate experiments where simple ones would have done. And I failed to include a simple, obvious experiment that would have definitively shown that arsenic was really in the bacteria’s DNA. I then submitted the paper to Science, punching up the impact the work would have on our understanding of extraterrestrials and the origins of life on Earth in the cover letter. And what do you know? They accepted it!

My sting exposed the seedy underside of “subscription-based” scholarly publishing, where some journals routinely lower their standards – in this case by sending the paper to reviewers they knew would be sympathetic - in order to pump up their impact factor and increase subscription revenue. Maybe there are journals out there who do subscription-based publishing right – but my experience should serve as a warning to people thinking about submitting their work to Science and other journals like it. 

OK – this isn’t exactly what happened. I didn’t actually write the paper. Far more frighteningly, it was a real paper that contained all of the flaws described above that was actually accepted, and ultimately published, by Science.

I am dredging the arsenic DNA story up again, because today’s Science contains a story by reporter John Bohannon describing a “sting” he conducted into the peer review practices of open access journals. He created a deeply flawed paper about molecules from lichens that inhibit the growth of cancer cells, submitted it to 304 open access journals under assumed names, and recorded what happened. Of the 255 journals that rendered decisions, 157 accepted the paper, most with no discernible sign of having actually carried out peer review. (PLOS ONE, rejected the paper, and was one of the few to flag its ethical flaws).

The story is an interesting exploration of the ways peer review is, and isn’t, implemented in today’s biomedical publishing industry. Sadly, but predictably, Science spins this as a problem with open access. Here is their press release:

Spoof Paper Reveals the “Wild West” of Open-Access Publishing

A package of news stories related to this special issue of Science includes a detailed description of a sting operation — orchestrated by contributing news correspondent John Bohannon — that exposes the dark side of open-access publishing. Bohannon explains how he created a spoof scientific report, authored by made-up researchers from institutions that don’t actually exist, and submitted it to 304 peer-reviewed, open-access journals around the world. His hoax paper claimed that a particular molecule slowed the growth of cancer cells, and it was riddled with obvious errors and contradictions. Unfortunately, despite the paper’s flaws, more open-access journals accepted it for publication (157) than rejected it (98). In fact, only 36 of the journals solicited responded with substantive comments that recognized the report’s scientificproblems. (And, according to Bohannon, 16 of those journals eventually accepted the spoof paper despite their negative reviews.) The article reveals a “Wild West” landscape that’s emerging in academic publishing, where journals and their editorial staffs aren’t necessarily who or what they claim to be. With his sting operation, Bohannon exposes some of the unscrupulous journals that are clearly not based in the countries they claim, though he also identifies some journals that seem to be doing open-access right.

Although it comes as no surprise to anyone who is bombarded every day by solicitations from new “American” journals of such-and-such seeking papers and offering editorial positions to anyone with an email account, the formal exposure of hucksters out there looking to make a quick buck off of scientists’ desires to get their work published is valuable. It is unacceptable that there are publishers – several owned by big players in the subscription publishing world – who claim that they are carrying out peer review, and charging for it, but no doing it.

But it’s nuts to construe this as a problem unique to open access publishing, if for no other reason than the study, didn’t do the control of submitting the same paper to subscription-based publishers (UPDATE: The author, Bohannon emailed to say that, while his original intention was to look at all journals, practical constraints limited him to OA journals, and that Science played no role in this decision). We obviously don’t know what subscription journals would have done with this paper, but there is every reason to believe that a large number of them would also have accepted the paper (it has many features in common with the arsenic DNA paper afterall). Like OA journals, a lot of subscription-based journals have businesses based on accepting lots of papers with little regard to their importance or even validity. When Elsevier and other big commercial publishers pitch their “big deal”, the main thing they push is the number of papers they have in their collection. And one look at many of their journals shows that they also will accept almost anything.

None of this will stop anti-open access campaigners  (hello Scholarly Kitchen) from spinning this as a repudiation for enabling fraud. But the real story is that a fair number of journals who actually carried out peer review still accepted the paper, and the lesson people should take home from this story not that open access is bad, but that peer review is a joke. If a nakedly bogus paper is able to get through journals that actually peer reviewed it, think about how many legitimate, but deeply flawed, papers must also get through. Any scientist can quickly point to dozens of papers – including, and perhaps especially, in high impact journals – that are deeply, deeply flawed – the arsenic DNA story is one of many recent examples. As you probably know there has been a lot of smoke lately about the “reproducibility” problem in biomedical science, in which people have found that a majority of published papers report facts that turn out not to be true. This all adds up to showing that peer review simply doesn’t work.

And the real problem isn’t that some fly-by-night publishers hoping to make a quick buck aren’t even doing peer review (although that is a problem). While some fringe OA publishers are playing a short con, subscription publishers are seasoned grifters playing a long con. They fleece the research community of billions of dollars every year by convincing them of something manifestly false – that their journals and their “peer review” process are an essential part of science, and that we need them to filter out the good science – and the good scientists – from the bad. Like all good grifters playing the long con, they get us to believe they are doing something good for us – something we need. While they pocket our billions, with elegant sleight of hand, then get us to ignore the fact that crappy papers routinely get into high-profile journals simply because they deal with sexy topics.

But unlike the fly by night OA publishers who steal a little bit of money, the subscription publishers’ long con has far more serious consequences. Not only do they traffic in billions rather than thousands of dollars and denying the vast majority of people on Earth access to the findings of publicly funded research, the impact and glamour they sell us to make us willing participants in their grift has serious consequences. Every time they publish because it is sexy, and not because it is right, science is distorted. It distorts research. It distorts funding. And it often distorts public policy.

To suggest – as Science (though not Bohannon) are trying to do – that the problem with scientific publishing is that open access enables internet scamming is like saying that the problem with the international finance system is that it enables Nigerian wire transfer scams.

There are deep problems with science publishing. But the way to fix this is not to curtain open access publishing. It is to fix peer review.

First, and foremost, we need to get past the antiquated idea that the singular act of publication – or publication in a particular journal – should signal for all eternity that a paper is valid, let alone important. Even when people take peer review seriously, it is still just represents the views of 2 or 3 people at a fixed point in time. To invest the judgment of these people with so much meaning is nuts. And its far worse when the process is distorted – as it so often is – by the desire to publish sexy papers, or to publish more papers, or because the wrong reviewers were selected, or because they were just too busy to do a good job. If we had, instead, a system where the review process was transparent and persisted for the useful life of a work (as I’ve written about previously), none of the flaws exposed in Bohannon’s piece would matter.

Posted in open access, science | 144 Responses

NASA paywalls first papers arising from Curiosity rover, I am setting them free

The Mars Curiosity rover has been a huge boon for NASA – tapping into the public’s fascination with space exploration and the search for life on other planets. Its landing was watched live by millions of people, and interest in the photos and videos it is collecting is so great, that NASA has had to relocate its servers to deal with the capacity.

So what does NASA do to reward this outpouring of public interest (not to mention to $2.5 billion taxpayer dollars that made it possible)? They publish the first papers to arise from the project behind a Science magazine’s paywall:



There’s really no excuse for this. The people in charge of the rover project clearly know that the public are intensely interested in everything they do and find. So I find it completely unfathomable that they would forgo this opportunity to connect the public directly to their science. Shame on NASA.

This whole situation is even more absurd, because US copyright law explicitly says that all works of the federal government – of which these surely must be included – are not subject to copyright. So, in the interests of helping NASA and Science Magazine comply with US law, I am making copies of these papers freely available here:

Update: Copyright

For those interested in the issue of copyright in works of the US government, please see the following:

Section 105 of US Copyright Act, which states:

Copyright protection under this title is not available for any work of the United States Government, but the United States Government is not precluded from receiving and holding copyrights transferred to it by assignment, bequest, or otherwise.

House Report 94-1476 which details the reasoning behind this provision:

The effect of section 105 is intended to place all works of the United States Government, published or unpublished, in the public domain. This means that the individual Government official or employee who wrote the work could not secure copyright in it or restrain its dissemination by the Government or anyone else, but it also means that, as far as the copyright law is concerned, the Government could not restrain the employee or official from disseminating the work if he or she chooses to do so. The use of the term “work of the United States Government” does not mean that a work falling within the definition of that term is the property of the U.S. Government.

The only ambiguity in the case of these Curiosity papers is that not all of the authors are US Government employees, and thus the work is, I am told “co-owned” by the authors. I’m not sure what effect this has on the ability of Science magazine to assert copyright in the work, since, at best, they are doing so at the behest of only a subset of the authors. The law makes it clear that its intent is to direct the US government authors to place the work in the public domain, and that any agreement they enter into to restrict access to the work is invalid. This is why I view the practice of taking works authored (and funded) by the US government and placing them behind paywalls to be illegitimate.

Update 2: JPL has now posted the articles on their site 

As of today these articles are now available to download from the JPL website. I assume this was done in response to this post and the attention it received. (They were not there on the 26th when the press releases went out – I looked. And you can see from the PDFs that they weren’t downloaded from the Science website until the 27th.) Let’s hope that in the future that all NASA papers – and indeed the results of all government funded research – are made immediately freely available.

Posted in open access, science | 119 Responses

With its HeLa genome agreement, the NIH embraces a expansive definition of familial consent in genetics

I wrote before about the controversy involving the release earlier this year of a genome sequence of the HeLa cell line, which was taken without consent from Henrietta Lacks as she lay dying of ovarian cancer in 1950s Baltimore.

Now, the NIH has announced an agreement with Lacks’ descendants to obtain their consent for access to and use of the HeLa genome (the agreement applies only to NIH funded research, but the hope is that others will agree to it as well).

I think the NIH handled this reasonably well. There’s no way to go back and consent Henrietta Lacks, so one could reasonably argue that nobody should be allowed to use HeLa cells ever or generate and use information derived from their genome. But that seems like too harsh a judgment, especially given the pride the family takes in the use of Henrietta’s cells for research.

So I think it’s entirely reasonable, in this case, to give the family the right to consent for use of these cells, and to impose whatever restrictions on the use they see fit.

However, there are some issues raised by this case and this decision that warrant further discussion.

First, exactly when, and under what conditions, should someone’s heirs be able to consent on their behalf? It sounds like there was broad consensus from the Lacks family about how to handle this. But what if there hadn’t been? Does the consent right pass down strictly to one’s legal heirs? And maybe more relevant to existing use of clinical samples, many consent documents allow people donating samples to withdraw their consent in the future. Does that right also pass down to one’s heirs?

Second, and to me more importantly, is the issue I raised previously with respect to Rebecca Skloot’s op-ed on the topic. In both her piece, and in the editorial by Francis Collins and Kathy Hudson, there is mention of the need not just to make up for the lack of original consent, but to protect the genetic privacy of the Lacks family. The notion is that, because they are so publicly associated with HeLa cells, anything that is discovered about these cells will immediately be associated with members of the family. And with the decision announced today, the NIH is explicitly giving the Lacks family the right to veto uses of HeLa cells, not because Henrietta would not have consented to the use in 1951, but because they view it as an invasion of their privacy today.

This is indeed an issue, but it is a very different one than original consent. And unlike the original consent issue – which can be argued as applying narrowly to the HeLa case – the privacy issue applies to all genomic data, whether properly consented or not. Collins and Hudson talk about “de-identified” samples in their essay, ignoring the now abundant evidence that one can almost trivially deduce the donor of a clinical sample from a small amount of DNA sequence and the use of public databases of genetic information.

Thus, in the near future, any human genetic data out there will be subject to the same risk that the Lacks family now faces. We can’t set up a panel of family members for each of the tens of thousands of samples that will soon be out there. And even if we could, I don’t think we should. There is no sensible or even workable way to require familial consent for the use of someone’s genetic material.

We believe in the absolute right of individuals to make decisions about how samples obtained from them can be used. But the very nature of inheritance and genetics means that every decision they make by necessity affects other individuals – close relatives most acutely, but by no means exclusively. Figuring out how we deal with this is one of the major practical and philosophical challenges of the age of genetic information, and even though Collins and Hudson chose to punt this issue down the road in the name of comity with the Lacks family, it is an issue we are going to grapple with very soon.

And I am disturbed that the Director of the NIH has, in effect, embraced an extreme position on this issue – that families have the right to veto uses of someone else’s DNA.

Posted in genetics, HeLa | 5 Responses

Let’s not get too excited about the new UC open access policy

It was announced today that systemwide Academic Senate representing the 10 campuses of the University of California system had passed an “open access” policy.

The policy will work like this. Before assigning copyright to publishers, all UC faculty will grant the university a non-exclusive license to make the works freely available, provide the university with a copy of the work, and select a creative commons license under which is will be made freely available in UC’s eScholarship archive.

A lot of work went into passing this, and its backers – especially UCLA’s Chris Kielty – are to be commended for the cat herding process required to get it though UC’s faculty governance process.

I’m already seeing lots of people celebrating this step as a great advance for open access. But color me skeptical. This policy has a major, major hole – an optional faculty opt-out. This is there because enough faculty wanted the right to publish their works in ways that were incompatible with the policy that the policy would not have passed without the provision.

Unfortunately, this means that the policy is completely toothless. It provides a ready means for people to make their works available – which is great. And having the default be open is great. But nobody is compelled to do it in any meaningful way – therefore it is little more than a voluntary system.

More importantly, the opt-out provides journals with a way of ensuring that works published in their journals are not subject to the policy. At UCSF and MIT and other places, many large publishers, especially in biomedicine, are requiring that authors at institutions with policies like the UC policy opt-out of the system as a condition of publishing. At MIT, these publishers include AAAS, Nature, PNAS, Elsevier and many others.

We can expect more and more publishers to demand opt-outs as the number of institutions with open/public access policies grows. In the early days of such “green” open access, publishers were pretty open about allowing authors to post manuscript versions of their papers in university archives. They were open because there was no cost to them. Nobody was going to cancel a subscription because they could get a tiny fraction of the articles in a journal for free somewhere on the internet.

However, as more universities – especially big ones like UC – move towards institutional archiving policies, an increasing fraction of the papers published in subscription journals could end up in archives – which WOULD threaten their business models. So, of course (and as I and others predicted a decade ago), subscription publishers are now doing their best to prevent these articles from becoming available.

So long as the incentives in academia push people to publish in journals of high prestige, authors are going to do whatever the journal wants with respect to voluntary policies at their universities. And so, we’re really back to where we were before. Faculty can make their work freely available if they want to – and now have an extra way to do it. But if they don’t want to, they don’t have to.

The only way this is going to change is if universities create mandatory open access policies – with no opt-outs or exceptions. But this would likely require actions from university administrators who have, for decades, completely ignored this issue.

So don’t get me wrong. I’m happy the faculty senate at UC did something, and I think the eScholarship repository will likely become an important source of scholarly papers in many fields, and the use of CC licenses is great. And maybe the opt out will be eliminated as the policy is reviewed (I doubt it). But, because of the opt out, this is a largely symbolic gesture – a minor event in the history of open access, not the watershed event that some people are making it out to be.

Posted in open access, public access, University of California | 22 Responses

Those who deny access to history are condemned repeatedly

One of the most disappointing aspects of the push for open access to scholarly works has been the role of scholarly societies – who have, with precious few exceptions, emerged as staunch defenders of the status quo.

In the sciences – where most of the open access battles have been fought – anti-OA stances from societies have been driven by the desire to protect revenue streams from society-run journals. I had always hoped that the humanities – less corrupted by money as they are – would embrace openness in ways that science has been slow to do. Ahh for the naïveté of youth.

At my own institution – UC Berkeley – efforts to pass a fairly tepid “open access” policy were thwarted by humanities scholars who felt a requirement that faculty at public institution make their work publicly available represents some kind of assault on academic freedom. But that is nothing compared to an absurd statement released this week by the American Historical Association.

The gist of the AHA’s statement is this: they want universities that require their recently minted PhD’s to make copies of their theses freely available online to grant a special exemption to historians, allowing them to embargo access to their work for up to six years.

The ostensible reasons for this embargo request is to defend the ability of junior faculty to get their theses published in book form by a scholarly press – something they claim online access precludes. Here is their explanation:

By endorsing a policy that allows embargos, the AHA seeks to balance two central though at times competing ideals in our profession–on the one hand, the full and timely dissemination of new historical knowledge; and, on the other, the unfettered ability of young historians to revise their dissertations and obtain a publishing contract from a press.  We believe that the policy recommended here honors both of these ideals by withholding the dissertation from online public access, but only for a clearly stated, limited amount of time, and by encouraging other, more traditional forms of availability that would insure a hard copy of the dissertation remains accessible to scholars and all other interested parties.

They are basically arguing that, because of the tenure practices of universities, the history literature should remain imprisoned in print form – and that scholars without access to print copies should be denied timely access to this material - unless you think six years is timely.

What really galls me about this is that the AHA takes the way that academia works as a given. Yes, IF university presses refuse to publish books based on theses available online, and IF universities require such books for tenure, then young historians whose theses are made available online without an embargo are at a disadvantage. I’ve heard this from lots of young humanities scholars – and while I would dispute the extent to which it’s true, people really feel this way.

But shouldn’t the response to this sad situation by the leading organization representing academic historians – many of whom are in leadership positions at universities across the country – be to, you know, actually lead? Instead of a reactionary call for embargoes, they SHOULD have said something like this:

The way scholars in our field are evaluated is broken – so broken, in fact, that a young scholar in our field feels immense pressure to hide their work from public view for years so that they can cater to antiquated policies from our presses and our universities. The inability of our field to take full advantage of the internet as a means of dissemination should be a wakeup call for all of us in the field – and the AHA is committed to using our pull, and that of our members, to reform our presses and alter the rules for tenure at our institutions as rapidly as possible.

Shame on the AHA for being yet another scholarly society to let down the scholars they represent.

Posted in open access | 2 Responses

New Preprint: Uniform scaling of temperature dependent and species specific changes in timing of Drosophila development

We posted a new preprint from the lab on arXiv and would love your comments.

This work was born of our efforts to look at evolution of transcription factor binding in early embryos across Drosophila. When we started doing experiments comparing the three most commonly studied species, the model D. melanogasterD.pseudoobscura and D. virilis, we quickly ran in to issue: even though these species look superficially fairly similar, and develop in roughly the same way, they don’t really like to live at the same temperature, and even when they are grown in common conditions, they develop at different rates. So, for example, in order to collect an identical sample of stages from D. melanogater and the slower-developing D. virilis, you have to collect for different amounts of time- and we had no real idea of how this would affect the measurements we are making. And if you want to compare the tropical D. melanogaster to the cold-preferring D. pseudoobscura, you can either choose to collect at temperatures that neither prefers (21C) or grow them under different conditions, again with no clear understanding of how these differences affect our measurements.

So, a few years ago, a new postdoc in the lab (Steven Kuntz) decided to look at this question in more detail. He first developed methods to take time-lapse movies of developing embryos at carefully controlled temperatures, and then proceeded to characterize the development of 11 Drosophila species (all with fully-sequenced genomes) from different climates at eight temperatures ranging from 17.5C to 35C. He then developed a combination of manual and automated ways to identify 34 key developmental landmarks in each movie.

As was already well known, D. melanogaster development accelerates at higher temperatures taking around 2,000 minutes at 17.5C but just over 1,000 minutes at 32.5C.

Timing of D. melanogaster development at different temperatures

We observed similar overall trends for other species, with the other tropical species (D. simulansD. sechelliaD. erecta, D. yakubaD. ananassae and D. willistoni) showing similar patterns to D. melanogaster, while the temperature (D. virilis and D. mojavensis) and alpine (D. pseudoobscura and D. persimilis) were consistently slower even when grown at identical temperatures. The tropical species all started to show effects of high temperature (lower viability and slower development) at 32.5C, while the alpine species showed even greater effects at the cooler 30C.

Effects of temperature on development time for 11 Drosophila species


There’s a lot more in the paper about both of these issues, but the thing that I find really amazing, is that despite all of this variation in developmental timing both between species and at different temperatures, the relative timing of the 34 events we measured was virtually identical in all species and conditions. Indeed we find no statistically significant differences in the relative timing of any event between the initial cellularization of the blastoderm and hatching.

Proportional developmental time between species and at different temperatures


I find this almost perfect conservation of the relative timing of development across these diverse species and conditions stunning – and very much counter to what I expected – which was that different stages, which involve very different molecular and cellular processes, would be differentially affected by temperature, and that either selection or drift would have led to variation in relative timing between species. While there are lots of possibile explanations for this phenomena, the most straightforward is that developmental timing is controlled by some kind of master clock that scales with first-order kinetics with temperature, and which is the major target for interspecies differences in developmental timing. If true, this would be quite remarkable.

If you’ve gotten this far, you’re obviously reasonably interested in the topic. As I’ve written before, we are now posting all of our lab’s paper on arXiv prior to submitting them to a journal, and we invite you comments and criticism, with the hope that this kind of open peer review will not only make this paper better, but will serve as a model for the way we all should be communicating our work with our colleagues and interacting with them to discuss our work after it is published.

We’re going to try out PubPeer for comments on this paper. Please use this link to comment.

Posted in EisenLab, EisenLab preprints | 3 Responses

A CHORUS of boos: publishers offer their “solution” to public access

As expected, a coalition of subscription based journal publishers has responded to the White House’s mandate that federal agencies develop systems to make the research they fund available to public by offering to implement the system themselves.

This system, which they call CHORUS (for ClearingHouse for the Open Research of the United Status) would set up a site where people could search for federally funded articles, which they could then retrieve from the original publisher’s website. There is no official proposal, just a circulating set of principles along with a post at the publisher  blog The Scholarly Kitchen and a few news stories (1,2), so I’ll have to wait to comment on details. But I’ve seen enough to know that this would be a terrible, terrible idea – one I hope government agencies don’t buy in to.

The Association of American Publishers, who are behind this proposal, have been, and continue to be, the most vocal opponent of public access policies. They have been trying for years to roll back the NIH’s Public Access Policy and to defeat any and all efforts to launch new public access policies at the federal and state levels. And CHORUS does not reflect a change of heart on their part – just last month they filed a lengthy (and incredibly deceptive) brief opposing a bill in the California Assembly would provide public access to state funded research.

Putting the AAP in charge of implementing public access policies is thus the logical equivalent of passing a bill mandating background checks for firearms purchasing and putting the NRA in charge of developing and operating the database. They would have no interest in making the system any more than minimally functional. Indeed, given that the AAP clearly thinks that public access policies are bad for their businesses, they would have a strong incentive to make their implementation of a public access policy as difficult to use and as functionless as possible in order to drive down usage and make the policies appear to be a failure.

You can already see this effect at work  - the CHORUS document makes no mention of enabling, let alone encouraging, text mining of publicly funded research papers, even though the White House clearly  stated that these new policies must enable text mining as well as access to published papers. Subscription publishers have an awful track record in enabling reuse of their content, and nobody should be under any illusions that CHORUS will be any different.

The main argument the CHORUS publishers are making to funding agencies is that allowing them to implement a solution will save the agencies money, since they would not have to develop and maintain a system of their own, and would not have to pay to convert author manuscripts into a common, distributable format. But this is true only if you look at costs in the narrowest possible sense.

First, there is no need for any agency to develop their own system. The federal government already has PubMed Central – a highly functional, widely used and popular system. This system already does everything CHORUS is supposed to do, and offers seamless full-text searching (something not mentioned in the CHORUS text), as well as integration with numerous other databases at the National Library of Medicine. It would not be costless to expand PMC to handle papers from other agencies, and there would be some small costs associated with handling each submitted paper. However, these costs would be trivial compared to the costs of the funding the research in question, and would produce tremendous value for the public. What’s more, most of these costs would be eliminated if publishers agreed to deposit their final published version of the paper directly to PMC – something most have steadfastly refused to do.

But even if we stipulate that running their own public access systems would cost agencies some money, the idea that CHORUS is free is risible. There is a reason most subscription publishers have opposed public access policies – they are worried that, as more and more articles become freely available, that their negotiating position with libraries will be weakened and they will lose subscription revenues as a consequence. Since a large fraction of these subscription revenues (on the order of 10%, or around $1 billion/year ) come from the federal government through overhead payments to libraries, the federal government stands to save far, far, far more money in lower subscription expenditures than even the most gilded public access system could ever cost to develop and operate.

CHORUS is clearly an effort on the part of publishers to minimize the savings that will ultimately accrue to the federal government, other funders and universities from public access policies. If CHORUS is adopted, publishers will without a doubt try to fold the costs of creating and maintaining the system into their subscription/site license charges – the routinely ask libraries to pay for all of their “value added” services. Thus not only would potential savings never materialize, the government would end up paying the costs of CHORUS indirectly.

Publishers desperately want the federal agencies covered by the White House public access policy to view CHORUS as something new and different – the long awaited “constructive” response from publishers to public access mandates. But there is nothing new here. Publishers proposed this “link out” model when PMC was launched and when the NIH Public Access policy came into effect, and it was rejected both time. Publishers hate PMC not because it is expensive, or even because it leads to a (small) drop in their ad revenue. They hate it because it works, is popular and makes most people who use it realize that we don’t really need publishers to do all the things they insist only they can do.

CHORUS is little more than window dressing on the status quo – a proposal that would not only undermine the laudable goals of the White House policy, but would invariably cost the government money. Let’s all hope this CHORUS is silenced.



Posted in AAP, open access, politics, public access, science | 32 Responses

Apotheosis of cynicism and deceit from scholarly publishers

The Association of American Publishers, who lobby on behalf of most for-profit and society scholarly publishers, have long opposed moves to make the scientific literature more readily available to the public. But, as open access publishing has gained traction and funders increasingly demand free access to the work they fund, the AAP’s defense of the status quo has descended to new depths. Perhaps the most egregious is a letter sent last week to the California Assembly opposing AB609, which would provide the public with access to state funded research.

Here are their points:

State Universities Could be Faced with Open Access Publishing Charges Estimated at More Than $1 Million Annually

While AB 609 does not require authors to publish in author-funded open access journals, many journal publishers charge an article publishing fee to researchers to cover the cost to the publishers for making the journal articles freely available online. These costs could be substantial and are fundamentally unknowable, but the author of AB 609 has said that they may be similar to those in  the implementation of the U.S. National Institutes of Health (NIH) policy, upon which AB 609 has been modeled. In a congressional hearing on open access in 2008, the director of NIH indicated that the agency spends $100 million a year for page fees and open access charges. Therefore, one might estimate that California could spend $1.1 million each year on these charges, as California’s research budget is 1 % of that of NIH ($332 million vs. $30 billion). This rough estimate is likely an underestimate, as it only accounts for publishing charges and not for infrastructure, compliance, or the variation in open access charges.

Do you follow the publishers’ argument here?  Any time an author voluntarily chooses to publish in an open access journal, even if they are under no legislative mandate or pressure to do so, the publishers want those costs to count against any legislation that seeks to improve public access. This is pure balderdash.

And note how they compute this “cost”. They cite a quote from former NIH Director Elias Zerhouni who estimated that in 2008 the NIH spent $100 million on page fees and open access charges. But Zerhouni said this in 2008 as the NIH Public Access Policy was being introduced – thus these costs had were not in any way the result of the policy – they arose from authors choosing on their own how to publish their work.  And that $100 million includes page fees – charges leveed by subscription publishers on authors in addition to the subscription fees they charge libraries for access to their content. I know the open access industry very well, and revenues in 2008 were nowhere  near $100m for the whole industry, let alone from NIH authors. I’d bet, at most, total revenue was $20m, with max $10m from the NIH (and I’m sure this is an overestimate). So the vast majority of charges they are citing were actually payments in page charges to AAP publishers!

This is a completely preposterous and deceitful argument – one they undoubtedly know is wrong in both logic and detail – and demonstrates that they are willing to outright lie to achieve their legislative aims.

Savings to State Universities from Cancelled Journal Subscriptions Are Unlikely

There are no countervailing savings from the policies in AS 609 to offset the signifioant costs entailed. State universities would still need to maintain a large portion of their budgets for journal subscriptions, as students and researchers would oontinue to need to access research articles that are written by researchers from outside of California and not subject to the bill’s provisions, Where some smaller journals may be cancelled or go out of business, and others may change to an author-pays open access business model, there will be many that continue as subscription journals. In fact, some analysts have suggested that costs for subscriptions may actually increase, as publishers will still need to recoup their investments in publication from a smaller subscription base.

CA AB 609 Will Undermine Investments in the Peer Review Process that Ensures the Quality and Integrity of Scientific Research, Potentially Requiring California to Make Those Investments Itself

The peer review process ensures that research articles are rigorously reviewed by experts in specialized fields before they are published – in effect, the “checks and balances” of good science. Publishers invest in supporting the peer review process that vets the validity and significance of authors’ research findings by identifying appropriate reviewers, maintaining content management systems, providing enhanced digital coding and graphic design, disseminating the articles, enhancing the discoverability of article content and preserving the scholarly record. AB 609 would reduce publishers’ ability to continue those investments, and potentially transfer those costs to the California research budget.

So let’s put these two things together. The bill will not save California any money because libraries will not cancel any subscriptions, but will undermine publishers’ ability to carry out peer review because they will lose revenue from canceled subscriptions. Huh? They can not have it both ways. Either publisher revenues will drop OR California will save no money. These can not both be true at the same time.  Even if you buy their argument that the cancellation of subscriptions will undermine peer review, in order for this to happen, subscriptions would have to be cut, which would save California money.

I also love this ridiculous line:

AB 609 would reduce publishers’ ability to continue those investments, and potentially transfer those costs to the California research budget.

Note the complete logical fallacy contained in this one sentence. They are arguing that they need subscription revenue from California in order to invest in peer review, but if California cuts off these subscriptions then California is going to have to cover these costs themselves. So let me see if I get this. California is already paying for something, but if they stop paying for it, they’re going to have to pay for it themselves. My brain is going to explode.

There is no other explanation for this kind of lunacy other than the publishers think that they can kill this bill and others like it by making legislators think it will cost them money if it passes. But since this is manifestly false, they have to go through Olympic-level logical gymnastics in order to claim it is true. The publishers are lying, and they are clearly hoping that by lying in such a confusing way,  legislators – few of whom are familiar with the intricacies of scientific publishing – will believe what they’re being told.

CA AS 609 Will Negatively Impact California Jobs

California ranks second in the country for periodical and journal publishing jobs, employing approximately 17,000 people with a payroll of more than $250 million. By requiring surrender of their value-added, peer reviewed scientific journal articles within 12 months of publication, AS 609 will erode the financial sustainability of not-far-profit and commercial publishers, ultimately putting jobs at risk. Government mandates that make journal articles available free will likely have the same effect on the publishing industry as experienced by many newspapers when they chose to give their content away for free. Newspapers facing bankruptcy had to start charging for online access, as It Is unlikely that someone will subscribe to a newspaper (or journal) when they can obtain the articles for free online.

What a crock of shit. First of all, in order to make it sound like California jobs are at risk, the publishers lump journal publishing together with periodical publishing. I would hasten to bet that virtually all of the 17,000 jobs they cite are in the periodicals industry, and have absolutely nothing to do with scholarly publishing. In fact, there is relatively little activity in scholarly publishing in California – most journals are based in Boston, NY or Washington. And I suspect the biggest employer in the scholarly publishing industry is PLOS – who have >100 people working full time in their San Francisco office, as well as a larger pool of California-based freelancers and other contractors. Plus California is a hotbed for growth in open access publishing – including hot new startups like PeerJ.

And it is equally cynical to use the analogy of newspapers for the effect this bill would have on scholarly publishers. The AAP knows full well that unlike with newspapers, there is a perfectly viable alternative business model – open access – which PLOS, BMC and others have proven is both viable and profitable. They know that if subscriptions go away, scholarly publishing will not go away. But the obscene profits made by the AAP’s members will. And that is something they are willing to lie through their teeth to achieve.

AB 609 Is Unnecessary Because Publishers Are Devoted to Providing Access to Research and Invest in the Dissemination of Research in a Variety of Ways

Publishers provide access to published research articles through a variety of methods, including subscriptions, article rental and free-to-reader “open access” articles that are subsidized by author fees or sponsorships, Publishers have also voluntarily created programs that provide access to research literature for communities that have been previously underserved through outreach programs, such as patientlNFORM, the Emergency Access Initiative and Research4Life, as well as programs fOr” public libraries, journalists and high schools. Publishers have also worked with research funders, including government agencies and private foundations, for collaborative solutions to advance access to articles that report or analyze funded research. These collaborative, flexible partnerships are the rIght way to advance access while ensuring the sustainability of a well-functioning scholarly system. AS 609 takes us in an opposite direction and would contribute to fragmentation, duplication and dilution of efforts to build an infrastructure that is interoperable and efficient.

Yeah, that’s right. The AAP’s members are devoted to providing access to research. They are so devoted to it that they spent the first two pages of this letter arguing that providing access to the public would destroy their industry and take thousands of California jobs with them. The only reason that AAP members have done anything to make the literature available to anyone is that they know that their practices are deeply unpopular with the public, and so they create bogus access initiatives that they think will make them look like they’re trying. But this letter proves otherwise.

The only thing the AAP is devoted to is preserving the status quo – and lying to achieve their goal.

Posted in open access, politics, publishing, science, science and politics | Tagged , , , | 7 Responses

WTF? The University of California sides with publishers against the public

The University of California system spends nearly $40 million every year to buy access to academic journals, even though many of the articles are written, reviewed, and edited by UC professors. So you’d think the cash-strapped UC system would leap to back any effort to undermine the absurd science publishing system.

You’d think. But you’d be wrong.

Assemblymember Brian Nestande (R-Palm Desert) introduced a bill – The California Taxpayer Access to Publicly Funded Research Act (AB 609) – that would require recipients of state-funded research grants to make copies of their work freely available through the California State Library within six months of their initial publication.

Although I think that the six month embargo is unnecessary – there’s no reason not to make publicly funded works immediately freely available – I sent in a letter supporting the bill, as it establishes the state’s interest in ensuring public access to taxpayer funded research.

Hearings into the bill were scheduled for last week, but were delayed so that the bill could be modified in order to earn the support of the University of California – the flagship higher education system in the state, and the host of millions of dollars in state-funded research.

When I first heard this I was excited. “Finally,” I thought, “UC is stepping up to the plate and taking a strong stance in support of open access.” Then I read the letter UC had sent.

Adrian Diaz, the University of California’s Legislative Director, wrote that UC was “supportive of the legislation’s intent” but would only support it if the embargo period were extended to one year, and if its own grant programs were exempted from the bill’s requirements.

I was dumbfounded.

Here is Diaz’s rationale for extending the embargo:

The University recommends that the bill’s six month publication embargo period be amended to conform to federal public access policies. The National Institutes of Health (NIH) Public Access Policy and the recent public access policy direction to federal agencies from the Office of Science and Technology Policy (OSTP) both permit a twelve month embargo period for  published manuscripts. We believe that consistency between the different public access policies to which our researchers must comply will help avoid confusion and promote compliance with the law. A twelve month embargo period will also allow publishers, including small publishers and scholarly societies, to meet their needs for revenue while ensuring long-term public access to published research. UC believes that a twelve month embargo period will facilitate publication in leading scholarly journals, which may reject manuscripts for which the permissible embargo is only six months.

This is nothing short of insane.

When the White House issued its “public access” policy a few months ago, in which they directed Federal agencies to make works they fund available to the public within 12 months, I argued that open access supporters should not celebrate because this was going to establish a year long delay as the law of the land. And here is the first evidence that I was right.

But it is even more troubling that a university whose libraries are facing budget cuts every year while they try to keep up with the ever-increasing cost of journal subscriptions would cite publishers’ need for revenue as their guiding principle when judging policies related to scholarly publishing.

How can Diaz DEFEND this system?? A system in which universities fork over billions of dollars of public money every year in order to buy back access to papers researchers gave to publishers for free? A system that is bankrupting our libraries? A system that denies people access to research their tax dollars paid for?

What is wrong with the University? Is it so married to the status quo that it can not see that it is being immeasurably harmed by it? Is it so out of touch with its public mission that it reflexively sides with the establishment even when it means unambiguously thwarting a public good?

For decades universities have sat idly by doing nothing while the serials crisis loomed. They have been silent as immense change has come to scholarly publishing. And now, when they finally speak up, this is what they say?

THIS is why we can’t have nice things.


I sent the following letter to Mr. Diaz and other UC officials:

Adrian Diaz
Legislative Director
Office of State and Governmental Relations
1130 K Street, Suite 340
Sacramento, CA 95814

Dear Mr. Diaz,

I am writing in regards to your letter of April 12th sent to the Assembly Accountability and Administrative Review Committee regarding AB 609, The California Taxpayer Access to Publicly Funded Research Act.

Your letter expresses support for the legislation’s intent, but conditions UC support for the bill on a lengthening of the embargo period from six months to one year. I urge you to reconsider this position.

You write that a longer delay is necessary to “allow publishers to meet their needs for revenue”, yet this is true only for publishers that use a subscription-based business model that is outdated and no longer serves the interests of the research community or the public that funds it.

Journals that fund their operations through subscriptions have no choice but to restrict access to the content to subscribers. Thus the business model is fundamentally incompatible with what should be the goal of public research funders and public institutions of higher learning: to make the results of taxpayer funded research freely and immediately available to the public.

Fortunately, there is an alternative.

In 2001 I co-founded the Public Library of Science (PLOS), a San Francisco based non-profit publisher of scientific and medical journals that has pioneered “open access” – a business model in which the costs of publishing are covered by research funders, but the finished product immediately freely available. PLOS is a thriving company with a diverse portfolio in biology and medicine, including the world’s largest biomedical research journal, PLOS ONE, which will publish in excess of 25,000 articles in 2013.

PLOS’s success has led to an explosion of open access publishers, including several California startups, as well as new imprints from commercial publishers and scientific societies. And a few months ago the three largest private biomedical research funders in the world – the Howard Hughes Medical Institute in the US, the Wellcome Trust in the UK and the Max Planck Institute in Germany – collaborated to launch a high-profile open access journal called eLife.

In calling for the embargo period in AB 609 to be extended, the University of California is taking the position that subscription based publishing is in need of protection, even though there is a clear, California based alternative that would achieve the public access to taxpayer funded research you say you support.

Subscription based publishers – both commercial and non-profit – have long been thorns in the side of the UC library system, demanding ever increasing and unjustifiable fees – last year it was close to $40m – to provide faculty and students with access to publications that should and could have been made freely available. I urge you to speak with cash strapped librarians at any of the UC campuses – who every year are forced to cut subscriptions to important journals they are no longer able to afford – if subscription based publishers should be viewed as allies of the University of California in need of legislative protection.

The people of the state of California have every right to immediate free access to the results of taxpayer funded research, and the University of California should be urging the legislature to strengthen the public access provisions in AB 609.

I hope you will reconsider your position on this matter. I would be happy to discuss this issue with you or any of your staff.

Michael B. Eisen, Ph.D.
Associate Professor of Genetics, Genomics and Development
Investigator, Howard Hughes Medical Institute
Department of Molecular and Cell Biology
University of California, Berkeley

Posted in open access, politics | 31 Responses