You are Elsevier: time to overcome our fears and kill subscription journals

Having spent a decade fighting the scientific publishing establishment, the last few weeks have been kind of fun. Elsevier, the Dutch publishing conglomerate that has long served as the poster child for all that is wrong with the industry, has come under withering criticism for pushing legislation that would prevent the US government from making the results of taxpayer funded research available to the public.

Scores of scientists (myself included) have slammed the hypocrisy of the bill. Prominent publishers, fearing a backlash against Elsevier’s overreach, have come out in favor of government public access policies. Even the editors of The Lancet, one of Elsevier’s prized possessions, called the bill a “damaging threat to science“.

But amidst all this richly deserved opprobrium, we must not forget that Elsevier are in a position to behave so poorly because we let them. Publishers control the paywalls that restrict access to the scientific literature. But individual researchers control the fate of their own papers. And the only reason a paywall ever stands between anyone and a paper they want to read is because its authors chose to put it there.

The scientific community could decide tomorrow to eliminate restrictions on access to the research literature. But, because of a complex stew of narrow self-interest, vanity, laziness and tradition, the majority of scientists continue to feed the beast – unwilling to act on their own to change a system they know is wrong.

I love how Kevin Zelnio puts it:

Scientists’ idealism is honorable, and genuinely heartfelt. Few other groups of people really do want the change the world in such a positive, progressive manner. Yet, in a twist of irony, few other groups who prize evidence and free thought systematically follow dogmatic traditions that are directly in conflict with their idealistic world view. Why are some of the smartest people in the country allowing publishing companies to fleece them, their institutions and libraries, the federal government and the american taxpayers of their money?

And last week, mathematicians Tim Gowers and Tyler Neylon launched a new effort to get researchers to exercise their collective power to make scientific publishing better serve their and the public’s interest by organizing a boycott of Elsevier journals which has (at this writing) around 3,000 signatures (including mine).

The boycott isn’t perfect. I wish they hadn’t focused exclusively on Elsevier – they are hardly the only bad actors in the field. And it’s crucial that the focus be on papers. Nobody views turning town invitations to review to be a big sacrifice – and publishers will just find someone else. Same thing with editors. But papers are their lifeblood. Cut off the supply, they will have no choice but to alter their publishing practices. But even as it is written now, if this kind of collective action actually worked, it would have a huge impact. So the question is, will it?

We do have a historical precedent. In late 2000 my postdoctoral mentor Pat Brown, frustrated with the refusal of most publishers to participate in the newly launched PubMed Central, began circulating a letter in which scientists pledged to exclusively publish in, review for and serve as editors of journals that placed their contents in PMC with no more than a 6 month delay. The letter quickly received a list of prominent signatures, including many Nobel Prize winners, leading us to go public with a new site to gather public support for building an “online public library of science” (from whence the name PLoS derives).

Within a year 30,o00 people had signed the letter. But, when push came to shove, few followed through on their pledge. Publishers did not respond to the call from their constituency, leaving only a handful of journals in PMC  and the nascent open access options from BioMed Central to choose from. Pat and I and a handful of the strongest OA supporters kept our promise, but most did not.

It was very disappointing. We had the opportunity in front of us to change things for the better, and we let it slip through our fingers. Pat and I spent much of the next year attempting to cajole, guilt and embarrass our colleagues into sending their papers to OA or PMC journals. But it wasn’t working. We always got some variant on the same refrain:

I didn’t build the system, and I’d change it if I could, but if {I/my postdoc/my graduate student} want to get a {job/grant/tenure/postdoc} our papers needs to be published in {insert name of high-profile subscription journal}

Nevermind that this widely and deeply held belief – that success in science requires publishing in high impact journals – is incorrect. When push came to shove, most signers of the open letter abandoned this effort to fix a broken system, and continued sending their papers to non-OA, non-PMC journals.

But there are very good reasons to believe that things are different now, and that we can succeed with a new organized effort to deny publishers that are not serving our interests the papers on which they depend. The most obvious and important difference is that the landscape of open access publishing has changed dramatically since the original PLoS boycott. Indeed it was its failure – or more precisely the excuses colleagues gave us about why they weren’t participating – that led Pat, Harold Varmus and I to refocus PLoS as a publisher.

PLoS had many goals, but chief among them was the desire to give authors open access options where they would be confortable sending all of their papers. While PLoS Biology and PLoS Medicine haven’t succeeded in displacing the glamour mags Science, Nature, The New England Journal and The Lancet, they provide viable high impact open access alternatives, our community journals have become very prominent in the communities they represent, and PLoS ONE is now the biggest biomedical research journal in the world. BioMed Central is also thriving, and a wide range of new open access publishers and journals have come online in the past few years. And eLife, a joint open access project from HHMI, Wellcome Trust and the Max Planck Society will launch later this year.

Thus, people joining in the new boycott have no excuses not to follow through. There are plenty of viable OA options and it is simply unacceptable for any scientist who decries Elsevier’s actions and believes that the subscription based model is no longer serving science to send a single additional paper to journals that do not provide full OA to every paper they publish. So, come on people! If we do this now, paywalls will crumble, and we all be better off. So, come on! Let’s do it!

[UPDATE: I changed the original title of this post from “You are Elsevier: Publisher boycotts then and now”  to more accurately reflect my point].

Posted in open access, PLoS, publishing, science | Comments closed

Nature’s shiny sounding copout on open access

Nature has an editorial in this week’s issue on broader issues surround access to the scientific literature.

Several people have sent it to me with some variation on “Wow, Nature is saying good things about open access”. I was skeptical, given that Nature has a long history of occasionally saying the right things about open access one day, but then editorializing against it or running news pieces with a strong negative slant the next. There are things to like here. The piece does reaffirm Nature’s opposition to the Research Works Act – indeed, they dismiss it as an inconsequential distraction. And it expresses a useful sentiment:

In short, the literature is becoming ever more multifaceted, and intermediaries will be needed to supply added value and usability. It is hard to imagine such a primary literature and all of those seeking to add genuine value to it thriving when its key results are behind subscription firewalls.

But it follows this up with the bromide publishers have trotted out for a decade:

But a vision for open access in which all results — text, data, grey literature and so on — are immediately available in their published versions requires the costs of that added value to be paid for.

This is such an incredibly disingenuous and patronizing thing to say. The scientific community is well aware of this – spending on the order of $5 billion a year of public money to support biomedical research journals – with Nature receiving a healthy chunk of it. And, as Nature is well aware, one of the main reasons governments have not shifted this money from wasteful subscriptions that provide access to a limited number of people is that most publishers have failed to offer such to option, and have opposed any move towards government support of real open access. And yet, Nature – arguably the most powerful publisher in the biomedical sciences – denies any agency, placing responsibility squarely on the government’s shoulders:

Above all, they need to find the money to make the vision viable. Only then will the open research literature truly come to fruition, and only then will those wishing to provide added value be able to invest confidently in doing so.

But what do you think publishers would say if the government did what I have long argued they should – announce tomorrow that they will no longer fund journal subscriptions and will shift all of the money they currently spend on them to support open access publishing. I am sure publishers would start shrieking about how terrible it was for the government to intrude in the free market, like Nature does in this piece:

The only way that can happen is for governments to recognize the complexities of this terrain, and the damage that can be done to the providers of added value and to research itself as a result of poorly considered prohibitions or compulsions.

This is what annoys me most. It reinforces what is the biggest hypocrisy pushed by publishers – that governments have to spend billions of dollars to support the services they provide, but have no right to specify the terms under which publishers should operate. This “give us the money, but don’t tell us what to do” sentiment is exactly the same as that spewed by Elsevier in the Research Works Act.

Nature has always been very savvy about changes that are coming in scientific publishing. They clearly understand the issues, and – with projects like Digital Science – are trying to position themselves to capitalize on this future. But if Nature had any guts at all, and if they really believe that the future can not be realized “when its key results are behind subscription firewalls”, they wouldn’t dispense the kind of copouts we find here. Instead, they would lay out – and embrace – a clear plan for governments and other research funders to embrace real open access.

Posted in intellectual property, open access, PLoS, publishing, science | Comments closed

Plagiarist or Puppet? US Rep. Carolyn Maloney’s reprehensible defense of Elsevier’s Research Works Act

There has been lots of activity this week surrounding the “Research Works Act“, a bill introduced in the US House of Representatives that seeks to end the NIH’s Public Access Policy. Despite the flurry of attention to the bill, its authors – Reps Carolyn Maloney (D-NY) and Darrell Issa (R-CA) have remained silent (save a brief twitter exchange between Issa and Tim O’Reilly).

That changed today when a letter from Rep. Maloney defending the bill was published on the blog of Harvard researcher Alex Kentis (she was responding to his expression of opposition to the bill). Maloney writes:

Dear Dr. Kentsis:

Thank you for taking the time to contact me about your opposition to HR 3699. As someone who represents thousands of researchers, research institutions, and publishers, and a strong advocate who helped double NIH funding, I appreciate the opportunity to respond.

First, I think it’s important to point out that this bill does NOT impact research reports and raw data generated by government-funded research. This information would still be available at no cost to the public. Reports that suggest that these NIH funded research papers (prior to peer review) will not be available for free are wrong. Authors still retain the ability to share data, reports, and other forms of research findings derived from the taxpayer-funded research. However, once a publisher has worked on a manuscript, spent private funds to improve it and has peer-reviewed it, under this bill, the government would not be able to take that work-product and disseminate it for free. The information, the manuscript, and the data can be made available for free before they receive any private investment.

The purpose of HR 3699 is to support the continued investment and innovation by private-sector publishers in scientific, technical, medical and scholarly journal articles and to advance the public interest in the important peer-review publishing system that helps ensure the quality and integrity of scientific research.

The importance of peer review cannot be overstated. It is the system by which experts give informed comments on papers in highly specialized fields of science. It is essential to providing independent, informed, objective assessments to maintain the quality of scientific articles and ensure that science develops independently of ideological and political interests. Because peer review happens and fixes problems prior to publication, we never hear about the false or erroneous research that would otherwise make it into journal articles.

Moreover, the publishing industry has invested in providing public access to scientific journal articles. Patients can get free access to information on new research through various publisher programs including PatientINFORM. Anyone can go into research libraries for free access to the articles in which publishers have invested substantially to ensure their high quality.

Two-thirds of the access to PubMed central is from non-US users. In effect, current law is giving our overseas scientific competitors in China and elsewhere important information for free. We are already losing scientists due to a reduction in funding for federal research. This policy now sends our value-added research papers overseas at no cost.

Finally, as people continue to struggle during these difficult economic times, it is important to be mindful of the impact of various industries on job creation and retention. New York State is home to more than 300 publishers that employ more than 12,000 New Yorkers, many of whom live in or around New York City in my district. New York City scientific publishers represent a significant subset of the total, and more than 20 are located in Manhattan, publishing thousands of scientific journals and employing thousands of New Yorkers. This bill saves American jobs. No industry could survive a model whereby they invest private dollars and are then required to give it to the federal government to disseminate the final product for free.

Once again, I appreciate your taking the time to contact me.

Sincerely,
CAROLYN B. MALONEY
Member of Congress

I will point why I think her letter is ignorant, ill-informed, deceptive, patronizing, jingoistic and generally vile an a separate post. But first I want to point out something else that struck me about the letter.

Last Thursday, I wrote a post here speculating on the link between Rep. Maloney’s support for the bill and the large number of contributions she has received from senior American executives of the Dutch publishing conglomerate Elsevier. My post got some good play, and obviously came to attention of people at Elsevier, because shortly after it was posted comments began to appear from Tom Reller, Vice President for Global Corporate Relations at Elsevier (I know this is really him from communications we’ve had via email).

Although I disagree with virtually everything Reller said (here is my response to his post), and find many of his points to be factually inaccurate, I’ll give him credit for remaining engaged in the discussion and defending his point of view. I read his comments closely and considered them carefully. Thus, they were still fresh in my mind when I read Rep. Maloney’s letter today. And let’s just say that it was hard not to detect a certain, umm, “similarity”, between the comments he posted as part of an ongoing dialog on my blog last week, and those sent out today by Rep. Maloney.

So that you can make your own judgment, I’ll repost his first set of comments here for your examination:

Elsevier, along with other commercial and non-profit publishers do indeed support the Research Works Act and commend Congressman Issa and Congresswoman Maloney for co-sponsoring this important legislation. You ask why Congresswoman Maloney co-sponsored this legislation? Simple. New York is one of the country’s leading publishing states with more than 300 publishers that employ more than 12,000 New Yorkers, many who live or work in or around New York City. Elsevier and many other publishers have offices located in Congresswoman Maloney’s district. We support her because she has been a strong supporter of this important industry, our employees and good public policy. And we believe the Research Works Act is good public policy.

For starters, the Research Works Act would only apply to journal articles where the private sector has provided a value-added contribution in the creation of these information products. The bill specifically excludes research reports and the raw data generated by government-funded research. Authors still retain the ability to share data, reports, and other forms of research findings derived from the taxpayer funded research, including their submitted manuscripts.

But while the government may fund the research, it does not fund the peer review process, editing, or publication of these private-sector information products. Elsevier and other commercial and non-profit publishers invest hundreds of millions of dollars each year in managing the publication of journal articles. Government mandates that require private-sector information products to be made freely available undermine the industry’s ability to recoup these investments.

The publishing industry has invested significantly in providing public access to scientific journal articles. Patients can get free access to information on new research through various publisher programs including PatientINFORM. This program is provided in partnership with major heath organizations including the American Cancer Society, American Heart Association, and the American Diabetes Association. In addition, many publishers offer a low-cost (between $1 and $4) access through DeepDyve and other similar view-only services. Free access to journal articles is also provided through research libraries throughout the country. Publishers have also partnered with the United Nations to create Research4Life which provides free access to medical and agricultural institutions and practitioners in the developing countries. Millions of articles are downloaded each year as part of this program.

We’re very proud of what Elsevier has done throughout the years to expand access in sustainable ways, improve the research experience and enhance knowledge and discovery. And there are millions of researchers and other information professionals who value that contribution as well.

Now, I’m no expert on analyzing text (ok, I am, but that’s neither here nor there), but COME ON. Several sections Rep Maloney’s letter are sentences long copies of Reller’s comments , and the overall content and style are all but identical. These were clearly written by the same person.

Of course I don’t exactly how it came to be that a member of the US Congress was sending out emails defending a bill that were apparently written by the same person who was defending the same bill a week earlier on my blog verifiably identified as the head PR person for a company who would be a major beneficiary of said bill, and whose senior executives from all across the country just happened to have made lot of recent donations to said member of Congress. I’m sure it’s all just a coincidence.

Yeah, right. The comments on my blog were clearly Reller – his writing was natural and engaged directly with what other people were saying, so I’m sure he wasn’t just spouting prepared text. There are only two viable explanations for how essentially the same text ended up in Maloney’s letter. Either she copied it from my blog without citing its source (a clear violation of the Creative Commons Attribution license that governs all content on the site), or, Reller wrote the letter, either directly, or indirectly by preparing text that Maloney’s office could use to defend the bill. So Rep. Maloney a plagiarist or an Elsevier puppet.

Look, I’m not naive. I know this is the way our government works. Some monied special interest wants the shape the law to their liking, so they essentially buy a member of Congress by donating money to them and having their top executives do so as well. What they get for their money is access, a pliant ear, and the submission of legislation crafted to advance the narrow interests of the donor, often at the expense of the members own constituents and the broader public interest, and, in this case, in direct conflict with many issues the legislator has fought for in her career. Since the member of Congress doesn’t really care about the issue, or understand what the bill actually does, the donor provides their PR spin for them to use in defending it. Sometimes the bills don’t pass. But often they do. That’s how we end up with a government whose actions are often so wildly out of line with the public good.

So, given the history of their campaign contributions to Rep Maloney, I’m not really surprised to find that Elsevier’s fingers would be all over this bill and Rep Maloney’s defense of it.

We (my colleagues at PLoS and many others) have spent over a decade fighting to secure public access to publicly funded research. We finally start to make some progress – imperfect as the NIH Public Access Policy is, it is an important step in the right direction. And what happens? A member of Congress who faces no threat of defeat in the upcoming election disgracefully sells out the public good in exchange for some measly campaign contributions, and then doesn’t even have the decency to defend her actions with her own thoughts and words.

Posted in intellectual property, open access, PLoS, politics, science, science and politics | Comments closed

Protect public access to taxpayer funded research

I have an op-ed out today in the New York Times prompted by a new effort by publishers to restrict public access to the results of publicly-funded scientific research. If you’re as incensed by this as I am, you have several important opportunities to weigh in.

Help protect the NIH’s Public Access Policy in Congress

If you live in the US, write to your representative and urge them to oppose the awful Research Works Act (HR 3699), especially if they sit on the Committee on Oversight and Government Reform.

Urge scientific societies and university presses to quit the Association of American Publishers

It isn’t all that surprising that big commercial publishers like Elsevier would support the Research Works Act in an effort to maintain a system of scientific publishing has been incredibly lucrative for them.

But it is disheartening to see just how many scientific societies and university presses are members of the Association of American Publishers that has gleefully backed this bill (and likely played a role in writing it).

Many societies who are members of AAP have taken important steps towards open access in recent years. My own society, the Genetic Society of America, for example, launched its own open access journal in 2011. If you are a member of one of these forward thinking societies, you should demand that your membership dues no longer support efforts to roll back open access, and pressure the society to quit the AAP.

Unfortunately, many other societies (the AAAS, publisher of Science, and the American Physiological Society, and the Ecological Society of America come to mind) have sacrificed their principles in the name of profits from their journals, and have expressed opposition to the NIH Public Access Policy. If you are a member of one of these societies you should quit until they remember that they exist to serve the interests of the scientific community and public, not to oppose them.

Comment (by January 12th!) on the White House Office of Science and Technology Policy’s request for information on public access

The America COMPETES Reauthorization Act of 2010 contains language authorizing the OSTP to develop policies that assure widespread public access to and long-term stewardship of the results of federally funded unclassified research. Many publishers and others have already weighed in offering various bad ideas that would undermine, rather than advance, public access. The more scientists, students, teachers, caregivers and other members of the public who weigh in on the side of advancing open access, rather than retreating from it, the better.

Posted in open access, PLoS, politics, science, science and politics | Comments closed

Our scientific societies need to quit the Association of American Publishers

By coming out in favor of the odious Research Works Act, which would end the NIH’s Public Access Policy, the American Association of Publishers has proven, once again, that it is eager to place its narrow interests ahead of those of the scientific community and public.

It should come as now surprise that publishing behemoths like Elsevier would back such a reactionary piece of legislation. But it should infuriate members of the scientific community to know that most of their scientific societies are backing this repeal effort through their membership in the AAP.

The AAP has a long history of opposing efforts to provide access to the scientific and medical literature. And, with the latest action, there can no longer be any doubt that this organization is hellbent on thwarting beneficial change in scholarly publishing.

In contrast to the actions of the AAP, some of the scientific societies who are members of AAP were early proponents of PubMed Central, and many others have, in recent years, taken important and meaningful steps towards open access. This puts them at clear odds with the actions of the AAP.

I urge all of my colleagues to join me in calling for the societies that represent our interests to denounce the Research Works Act (HR-3699) and to suspend or withdraw their support for the AAP until it recognizes the importants of public access to scientific research and immediately ceases to oppose efforts to provide it.

Please contact your societies directly and express your dismay at their support for HR-3699.

These societies are members through FASEB:

  • The American Physiological Society (APS)
  • American Society for Biochemistry and Molecular Biology (ASBMB)
  • American Society for Pharmacology and Experimental Therapeutics (ASPET)
  • American Society for Investigative Pathology (ASIP)
  • American Society for Nutrition (ASN)
  • The American Association of Immunologists (AAI)
  • American Association of Anatomists (AAA)
  • The Protein Society
  • Society for Developmental Biology (SDB)
  • American Peptide Society (APEPS)
  • Association of Biomolecular Resource Facilities (ABRF)
  • The American Society for Bone and Mineral Research (ASBMR)
  • American Society for Clinical Investigation (ASCI)
  • Society for the Study of Reproduction (SSR)
  • Teratology Society
  • The Endocrine Society
  • The American Society of Human Genetics (ASHG)
  • Environmental Mutagen Society (EMS)
  • International Society for Computational Biology (ISCB)
  • American College of Sports Medicine (ACSM)
  • Biomedical Engineering Society (BMES)
  • Genetics Society of America (GSA)
  • American Federation for Medical Research (AFMR)
  • The Histochemical Society (HCS)
  • Society for Pediatric Research (SPR)
  • Society for Glycobiology (SfG)

And many others are direct members of the AAP. A partial list includes (a full list is here):

  • AAAS
  • American Academy of Pediatrics
  • American Anthropological Association
  • American Association for the Advancement of Science
  • American Association of Cancer Research
  • American Chemical Society
  • American Geophysical Union
  • American Institute of Physics
  • American Mathematical Society
  • American Medical Association
  • American Nurses Association
  • The American Physiological Society
  • American Psychological Association
  • American Society of Clinical Oncology
  • Association for Computing Machinery (ACM)
  • Federation of American Societies for Experimental Biology (FASEB)
  • The Feminist Press
  • Highwire Press – Stanford University
  • Journal of Rehabilitation and Development (JRRD)
  • JSTOR
  • Massachusetts Medical Society
  • National Academy Press
  • Nature America
  • New England Journal of Medicine
  • Oncology Nursing Society
  • The Optical Society

Their actions on this matter are egregious and they need to know we disapprove.

 

Posted in intellectual property, open access, PLoS, politics, science, science and politics | Comments closed

Elsevier-funded NY Congresswoman Carolyn Maloney Wants to Deny Americans Access to Taxpayer Funded Research

In 2008, under bipartisan pressure from Congress to ensure that all Americans would be able to access the results of taxpayer-funded biomedical research, the US National Institutes of Health instituted a Public Access Policy:

The NIH Public Access Policy ensures that the public has access to the published results of NIH funded research. It requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to the digital archive PubMed Central upon acceptance for publication.  To help advance science and improve human health, the Policy requires that these papers are accessible to the public on PubMed Central no later than 12 months after publication.

The policy has provided access for physicians and their patients, teachers and their students, policymakers and the public to hundreds of thousands of taxpayer-funded studies that would otherwise have been locked behind expensive publisher paywalls, accessible only to a small fraction of researchers at elite and wealthy universities.

The policy has been popular – especially among disease and patient advocacy groups fighting to empower the people they represent to make wise healthcare decision, and teachers educating the next generation of researchers and caregivers.

But the policy has been quite unpopular with a powerful publishing cartels that are hellbent on denying US taxpayers access to and benefits from research they paid to produce. This industry already makes generous profits charging universities and hospitals for access to the biomedical research journals they publish. But unsatisfied with feeding at the public trough only once (the vast majority of the estimated $10 billion dollar revenue of biomedical publishers already comes from public funds), they are seeking to squeeze cancer patients and high school students for an additional $25 every time they want to read about the latest work of America’s scientists.

Unable to convince the NIH to support their schemes, the powerful publishing lobby group – the Association of American Publishers – has sought Congressional relief. In 2009, the AAP induced Michigan Rep John Conyers to introduce the “Fair Copyright in Research Works Act” which would have ended the NIH Public Access Policy before it even got off the ground. Fortunately, that bill never left committee.

But they are back at it. A new AAP backed bill – the “Research Works Act” – was just introduced by Reps Carolyn Maloney (D-NY) and Darrell Issa (R-CA). Its text is simple and odious:

    No Federal agency may adopt, implement, maintain, continue, or otherwise engage in any policy, program, or other activity that:
    (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher of such work; or
    (2) requires that any actual or prospective author, or the employer of such an actual or prospective author, assent to network dissemination of a private-sector research work.

This bill would not only end the NIH’s Public Access Policy, but it would forbid any effort on the part of any agency to ensure taxpayer access to work funded by the federal government.

Why, you might ask, would Carolyn Maloney, representing a liberal Democratic district in New York City that is home to many research institutions, sponsor such a reactionary piece of legislation that benefits a group of wealthy publishers at the expense of the American public? Hmm. Wouldn’t happen to have anything to do with the fact that she’s the biggest recipient of campaign contributions from the publishing industry, would it?

According to MapLight, which tracks political contributions, Dutch publisher Elsevier and its senior executives made 31 contributions to members of the House in 2011, of which 12 went to Representative Maloney. This includes contributions from 11 senior executives or partners, only one of whom is a resident of her district.

It is inexcusable that a simple idea – that no American should be denied access to biomedical research their tax dollars paid to produce – could be scuttled by a greedy publisher who bought access to a member of Congress.

So I urge you to call/write/email/tweet Representative Maloney today, and tell her you support taxpayer access to biomedical research results. Ask her why she wants cancer patients to pay Elsevier $25 to access articles they’ve already paid for. And demand that she withdraw H.R. 3699.

Representative Maloney:

Twitter: @RepMaloney @CarolynBMaloney

Phone: 202-225-7944

FAX: 202-225-4709

Email: Use this form

 

——————-

UPDATE

Several people have commented that the language of the bill I quoted refers to “private sector work”, thinking that this means it does not refer to work funded by the US Government. This term is defined in the bill as:

The term `private-sector research work’ means an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the United States Government (as defined in section 101 of title 17, United States Code), describing or interpreting research funded in whole or in part by a Federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing. Such term does not include progress reports or raw data outputs routinely required to be created for and submitted directly to a funding agency in the course of research.

They are using intentionally misleading language to distinguish works funded by the government but carried out by a non-governmental agency as “private sector research”. Thus, under this bill, works funded by the NIH but carried at a University would be “private sector research”.

This language is in there because the US Copyright Act specifically denies copyright protection to works carried out by federal agencies, and the authors of this bill did not want it to be seen as amending Copyright Act, something that would have ensured its defeat.

Posted in intellectual property, open access, politics, publishing, science, science and politics | Comments closed

Stop the presses! H5N1 Frankenflu is going to kill us all!

I have watched the escalating hysteria about recent NIH-funded experiments to humanize H5N1 influenze (aka bird flu) with a mixture of amusement, horror and confusion. The amusement is born of the predictable hysteria that always infuses media coverage of research on lethal virus. The horror comes from the largely unchallenged move to censor publication of the experiments. The confusion comes from my own somewhat mixed feelings about the value of the experiments and their public health threat. I should add that this is an issue I know a lot about, as I did my graduate work on the evolution of human influenza viruses.

To quickly summarize the issues at hand, we all remember the brief panic that ensued a few years back when a largish number of people in Asia died from H5N1 infections, leading to runs on face masks and stocks of ineffective anti-influenza drugs. H5N1’s moment in the sun passed once it was realized that, while the virus was very lethal, it had an extremely low rate of human-to-human transmission, meaning that a global epidemic was not imminent.

Nonetheless, the high rate of mortality in otherwise healthy individual brought back fears of the 1918 H1N1 pandemic which is estimated to have killed as many as 40 million people worldwide (including my great grandfather). And, while the currently dominant H5N1 is a crappy human virus, we all know that flu evolves very rapidly and thus the prospect of a highly transmissible H5N1 emerging in the future warrants serious concern.

With this backdrop, researchers at the University of Wisconsin and at the Erasmus Medical Center in the Netherlands independently carried out experiments in which they selected for variants of H5N1 that could be transmitted through the air from ferret to ferret (which are the choice model species for studying influenza in humans). In the work at Erasmus, carried out by Ron Fouchier and colleges, a total of five changes in two of the virus’s eight RNA chromosomes were sufficient to create what appears from its laboratory properties at least to be a potentially devastating human pathogen.

Like any scientist, Fouchier prepared a manuscript describing what were sure to be high profile results, and submitted them to the journal Science. The Wisconsin group (about whose results we know a lot less) submitted their paper to Nature. While under review, both papers were apparently forwarded to the US National Science Advisory Board for Biosecurity, a panel that develops “policies addressing life sciences research that yield information or technologies with the potential to be misused to threaten public health or national security”.

Earlier this week the NSABB issues its findings:

Following its review, the NSABB decided to recommend that HHS ask the authors of the reports and the editors of the journals that were considering publishing the reports to make changes in the manuscripts. Due to the importance of the findings to the public health and research communities, the NSABB recommended that the general conclusions highlighting the novel outcome be published, but that the manuscripts not include the methodological and other details that could enable replication of the experiments by those who would seek to do harm.

Although the recommendations are technically non-binding, Science has agreed to implement them with regards to the Fouchier paper.

My first instinct was that this represents a typical overreaction to scientific research on a dangerous pathogen, and that the small marginal reduction in the risk of misuse this censorship would accomplish does not justify the potentially stifling impact the spectre of censorship would have on future research on human pathogens and on any potential “dual use” technology.

After thinking about this for a while, my overall views are unchanged. But I will admit that the issues here are more complex than I would like them to be.

Issue 1: Is the risk real? Although it is impossible to know how this virus would affect humans, its behavior in ferrets establishes a non-trivial possibility that the evolved Rotterdam virus could cause a lethal global pandemic. Assuming that it is, it remains unclear whether the bigger risk comes from the physical virus Fouchier created escaping or being intentionally released from the lab, or from someone with bad intentions recreating the virus from published information and releasing it.

It’s of course impossible to know for sure, but I am much more afraid of the actual viruses sitting in Rotterdam. It is widely believed that the H1N1 viruses that have been circulating since 1978 were accidentally released from a Russian biological warfare research station. If the virus is as bad as is feared, a single fuckup in its handling could have disastrous consequences. And if I were a terrorist hellbent on obtaining the virus, steal it would seem like a far easier course than recreating it from a Science paper.

I’m also skeptical that the terrorists we fear getting their hands on this virus would think of flu as their biological weapon  of choice, because, once released, it would be virtually impossible to contain its spread across the globe. And its likely that people in the developed countries they would target would be the least adversely affected, as they are best prepared to treat people who are infected and to develop and distribute vaccines and anti-viral medications.

Furthermore, if someone wanted to develop such a virus as a weapon, and had the skills to actually do it, they would also presumably have enough knowledge to have independently concluded that they could create their own lethal virus by passaging it through a secondary host like pigs or ferrets. This is hardly a secret – it’s the most widely accepted model for the natural movement of viruses from birds to man. And even if they hadn’t thought of it, enough’s been said in the press already to allow them to recreate these experiments without reading about them in a journal.

But, all that aside, I acknowledge that publishing details of these experiments entails some degree of risk. Which brings me to:

Issue 2: Is the knowledge produced by these experiments valuable? Here’s where things get complicated for me, because truth be told, I think these were really stupid experiments that have little practical value. The ostensible reason for carrying out and publishing these experiments is that they tell us important things about what a human transmissible H5N1 virus will look like, allowing us to better detect and prepare for a future pandemic.

I think this is very wrongheaded, and exhibits an almost willful ignorance of the ways that viruses in general, and flu in particular, evolve. RNA viruses like flu have very high mutation rates, and sample an astonishing diversity of variant sequences even in the course of infecting a single individual. The best demonstration of this is the rapidity with which drug-resistant strains emerge whenever any of the available anti-influenza drugs are used. It is because of the rapid emergence of resistance that use of these drugs is largely restricted to managing outbreaks in places with highly susceptible individuals, like nursing homes.

Sequence analysis in the last few years suggests that the virus can readily sample many alternative paths to avoid immune surveillance (the chief selective pressure it experiences during any outbreak). And it is highly likely that there are many paths the virus could follow to make it infectious in humans. Thus the fact that Fouchier has identified one such path, likely tells us very little about what a naturally occurring human H5N1 virus might look like. Indeed, the ease with which multiple groups selected strains with the right properties to spread among humans strongly suggests that there are multiple paths to achieve this end. If we assume there is only one way to have created such a virus – as would be required to give this work great practical significance –  it is highly unlikely that it would have emerged in a small ferret colony, even with the viruses high mutation rate. So I think Fouchier’s own results suggest that there are many ways in which H5N1 could acquire the ability to infect the human population. That he found one of them is interesting, but not all that useful.

This is not to say that I think the experiment is completely flawed. One of the guiding principles of research should be doing experiments that could potentially yield surprising results – and this could have been such an experiment (and it may actually have been – I can’t tell without reading the papers). But I am sympathetic to the notion that, given the risks of the experiments themselves, if not the data they produce, perhaps these experiments just should not have been done. There are lots of experiments to be done in the world, and I don’t think it’s the worst thing in the world to think about the risks in choosing which ones to pursue. That said, I am unwilling to say what many of my colleagues have argued – that these are unambiguously worthless experiments whose pursuit was completely reckless.

And, in any case, it doesn’t matter, since these experiments were already done. That, we can not take back. So we return to the question of whether the results should be published. The more I think about this, the less I think this particular experiment and virus is really the issue. If we ignore the larger issues, I conclude that the risks from publishing the full details of the experiment are small, but so are the gains. And I’m not downplaying the risks of the virus here, just the marginal risks of publishing a paper describing it. I simply think it’s very unlikely that in this case information in a paper would be the key missing ingredient to enable to deployment of an H5N1 weapon. But I’m also not going to argue that our ability to fight off a future H5N1 pandemic would be hopeless crippled by suppressing these results.

But this issue is not just about this paper – indeed my feeling that publication is not really all that significant makes the larger issues involved more significant. The spectre of censorship is a huge risk to science – it has the real potential to discourage people from working on dangerous pathogens – precisely the kinds of things we want people TO work on. And it can similarly discourage people from pursuing risky lines of research if they fear they may take them to censorable subjects.

Furthermore, if there is really something to fear in science, it is not experiments like the ones Fouchier carried out. Rather it is enabling basic technologies that are the most dangerous. Terrorists make massive use of the internet, for example. We probably have a lot more to fear from terrorists hanging out on Twitter than we do from those scouring the methods section of Science (if they can even find the relevant information in the 223 pages of supplementary material). Should the development of the internet have been stopped if this future threat had been foreseen? And, if details of Fouchier’s experiments were used by terrorist molecular biologists to remake his virus, they would almost certainly make use of DNA synthesis technology. Should we have banned its publication and dissemination? I don’t think these are idle questions, because the logic that led to censoring the Fouchier paper is the same.

But the thing that really really annoys me about this whole debate, is the disproportionate attention paid to mitigating the risks of these experiments compared to the far greater risks that surround us. It seems insane for a government to spend so much time wringing its hands about publishing the results of a few potentially dangerous experiments, when it does things every day that entail a far, far greater risk to its peoples’ health and well being. For example, we continue to ship massive amounts of arms to sketchy “allies” across the globe, many of which are destined to end up in the hands of terrorists, who would have a far easier time using them against us than they would any H5N1 virus. And we have done little to address the sorry state of our public health infrastructure – something that is an indispensable part of our response to major pathogen outbreaks, whether of natural origin or otherwise. And let’s not even talk about our stubborn refusal to deal with global warming…

I’m not saying that the fact we do nothing about ongoing major problems means we should ignore smaller or less likely ones. But I remain uneasy that the quick censorship trigger being pulled here with the easy acquiescence of most of the scientific community augurs future restrictions on science that will do real harm to one of the few things with the potential to protect us from deadly viruses and the other real and imagined perils of our future.

Posted in bioethics, evolution, politics, publishing, science, science and politics | Comments closed

Does the UC patent amendment provide an opportunity for mischief?

About a month ago, I received an email with the subject “PLEASE SIGN NOW: UC Patent Amendment”. Being quite interested in issues of intellectual property in academia (as I will explain below, I think all IP arising from publicly funded work should be in the public domain) the combination of such insistent language along with the word “patent” caught my attention, and so I read the message, which read:

When you first joined the University of California, you signed a Patent Acknowledgment or Agreement (depending on when you joined UC) as a condition of employment or your ability to use UC research resources and facilities. Because of recent court decisions in the case Stanford v. Roche, it is necessary for you to sign an amendment to that document.

This amendment clarifies the original intent of the Patent Acknowledgment or Agreement you signed: to assign to the University rights to inventions and patents you may conceive or develop while employed by UC, using UC research facilities and/or resources, or using gift, grant or contract funds received through the University.

This is not a change in the Patent Policy; it is simply an amendment that clarifies the existing Acknowledgment or Agreement in light of the court decisions.

Your electronic signature on the Patent Acknowledgment/Agreement Amendment available here will ensure that the University is able to fulfill its intellectual property obligations to research sponsors, industrial partners, the federal government and others.

Several things about this email really pissed me off. First, nowhere in the email or on the page where we were supposed to sign the amendment could one find the actual text of the amendment! Whenever anyone asks me to sign something without actually seeing what I’m being asked to sign, I get a bit suspicious. I had to go to the FAQ to find the actual text of the amendment. Dodgy and weird.

But more importantly, I was astonished by their claim that this is not a change in patent policy. Where does the university’s “patent policy” reside if not in the previous excessively legalistic patent agreement I was forced to sign when I joined the university? And if courts interpret this document as meaning one thing, then that is what the university’s patent policy is. I understand that they didn’t mean it to mean that, and that they don’t want it to stay that way, but surely by asking compelling me to sign an amendment to a legal document in response to a Supreme Court decision, they are changing the university’s policy. And their claims to the contrary of totally deceitful.

Given my general hatred of IP in academia, and the exceptionally sleazy way this was all handled, my initial reaction was to simply say “NO FUCKING WAY” and refuse to sign. But, well, it turns out that I might be legally obliged to sign this thing (or, more precisely, UC says I am legally obliged to sign, but I am skeptical of this and am seeking a legal opinion), and I don’t really like to needlessly disobey the law

This got me thinking about an alterative, subversive way of exploiting this situation to further my ends. The Supreme Court case that led UC to amend their patent agreement – Roche v. Stanford – was complicated, but the relevant part rested on the justices deciding that a Stanford employee saying he “shall assign” intellectual property developed in the course of this employment at the university to Stanford was trumped by his having said he “hereby assigns” that same intellectual property to Roche.

I haven’t read the whole case, and I probably wouldn’t get the nuance even if I did, but it’s this distinction between “shall assign” and “hereby assign” that has sent the university IP people into a tizzy, as is clear from the amended text:

I acknowledge my obligation to assign, and do hereby assign, inventions and patents that I conceive or develop 1) within the course and scope of my University employment while employed by the University, 2) during the course of my utilization of any University research facilities or 3) through any connection with my use of gift, grant, or contract research funds received through the University.

As explained in the FAQ, the words, “and do hereby assign” were added to “provide a present assignment of invention and patent rights to UC, addressing the problem created by the Supreme Court decision”.

So… if the problem with the current patent agreement that I am currently operating under is that doesn’t provide a present assignment of invention rights to UC, and if the Supreme Court has found that present assignments trumps the obligation to assign in the future contained in the current UC patent agreement, then what would happen if – before I signed the new UC amendment (which I am told I have until February 29, 2012 to d0) – I made some kind of statement that “I hereby assign and inventions and patents I conceive as part of my employment with the University of California to the public domain”? I’m no lawyer, but the Supreme Court seems to have said this trumps my current agreement with UC, and, if I did that first, it seems like it might trump any future agreement I signed with UC – thereby accomplishing what is my ultimate goal – to make sure that any intellectual property I develop while working for a public university carrying out publicly funded research should be in the public domain – free for anyone to use as they see fit.

One final thought – I’m not even really sure how much this applies to me. Although I am a UC faculty, I am also an Investigator with HHMI, who during the term of my funding are my official employers. As such, I assume my primary IP obligations are the HHMI and not UC. I have not received any information from HHMI suggesting that its patent agreements require amendment.

Some other links about this UC Patent Amendment:

Posted in intellectual property, open access, science, science and politics | Comments closed

TNR IS A LIE: Stephen Glass’s anagramic FU

CNN.com is fronting a story about Stephen Glass, the former reporter editor at The New Republic who was famously exposed in 1998 as a serial fabulist and became the subject of a Hollywood movie.

I had read the article – “Hack Heaven” –  that ultimately got him caught. It told of a teenaged computer whiz kid who was getting big bucks from a computer company whose system he had broken in to to tell them how he did it:

Ian Restil, a 15-year-old computer hacker who looks like an even more adolescent version of Bill Gates, is throwing a tantrum. “I want more money. I want a Miata. I want a trip to Disney World. I want X-Man comic book number one. I want a lifetime subscription to Playboy, and throw in Penthouse. Show me the money! Show me the money!”

I’m not sure why, but I have a habit when I’m reading of rearranging names and words in my head to make anagrams. Mostly it’s just a background process, but this time I stopped, noticing that the main character’s name – IAN RESTIL – was an anagram for TNR IS A LIE (TNR is the widely-used acronym for The New Republic).

I bring this up now because I’m still amazed that, in all the press and movies and so forth about Glass, nobody has pointed out that not only was he making up stories out of whole cloth, he was encoding messages confessing his crimes and giving his employers and editors the finger. (I wrote the the editors about this at the time, but I can see why they didn’t want to mention it.)

I’ve passingly looked at other Glass pieces to see if this was a common practice of his, but haven’t found anything else. But I think the more interesting thing is how serial liars often are like this. They initially make up a few things in a story that is mostly true. When they get away with it, they keep upping the ante – eventually making stories up completely. But once you’re completely fabricating things, the only way you can escalate is by taunting the people who you have been fooling all along.

And, while we’re on the topic of Glass, does anyone else find it amusing that he is having so much trouble being allowed to be a lawyer. Seems like the kind of guy you might want to represent you if you were on the wrong side of the law…

 

Posted in misc stuff | Comments closed

When a photo caption says it all

This is from a kind of silly article in the NYT about how people are generating too much DNA sequence data and we can’t really deal with the deluge. They get lots of smart people (many of whom are my friends) to talk about this problem – but I think they’re making a mountain out of a molehill. Other fields (anything involving the capture of lots of images – like cell biology or astronomy) are swimming in far bigger seas of data, and don’t make a big deal out of it in the NYT. But, whatever, a bit of harmless whining never hurt anyone.

I just thought it was particularly funny that an article that I felt just didn’t get it would be capped by a photo that demonstrated that they didn’t get it – that is not a picture of “some cells”, but rather a picture of an Illumina sequencing flow cell, which is only, you know, the whole subject of the article.

UPDATE: My friend Lior Pachter expressed my sentiments about the article perfectly on FB:

A compressed genome can be stored in a few Mb of data, something like the size of a decent quality photo taken with a new cell phone. For perspective I think that we are currently taking about 1/3 trillion photos per year. The fact that the data is currently being stored in its redundant raw format is either gross stupidity or purposeful scamming by charlatans trying to make a quick buck selling disks, its hard to tell which. Frankly, unless the animal is endangered, shouldn’t we just go back and sequence it in 3 years for the price of a USB key? Why is all this crappy Illumina sequence filled with errors being stored in the first place? It is true there are significant and interesting and challenging computational problems related to high-throughput sequencing, but they have to do with coupling relevant and statistically sound analyses with interesting biological experiments.

Posted in misc stuff, science | Comments closed