Michael Eisen: ‘The Past, Present and Future of Scholarly Publishing

Very important manifesto – from PLOS co-founder Prof. Michael Eisen's lecture at the California Commonwealth Club:

…Universities are, in essence, giving an incredibly valuable product – the end result of an investment of more than a hundred billion dollars of public funds every year – to publishers for free, and then they are paying them an additional ten billion dollars a year to lock these papers away where almost nobody can access them.

It would be funny if it weren’t so tragically insane.

To appreciate just how bizarre this arrangement is, I like the following metaphor. Imagine you are an obstetrician setting up a new practice. Your colleagues all make their money by charging parents a fee for each baby they deliver. It’s a good living. But you have a better idea. In exchange for YOUR services you will demand that parents give every baby you deliver over to you for adoption, in return for which you agree to lease these babies back to their parents provided they pay your annual subscription fee.

Of course no sane parent would agree to these terms. But the scientific community has.

…So what would be better? The outlines of an ideal system are simple to spell out. There should be no journal hierarchy, only broad journals like PLOS ONE. When papers are submitted to these journals, they should be immediately made available for free online – clearly marked to indicate that they have not yet been reviewed, but there to be used by people in the field capable of deciding on their own if the work is sound and important.

The journal would then organize a different type of peer review, in which experts in the field were asked if the paper is technically sound – as we currently do at PLOS ONE – but also what kinds of scientists would find this paper interesting, and how important should it be to them. This assessment would then be attached to the paper – there for everyone to see and use as they saw fit, whether it be to find papers, assess the contributions of the authors, or whatever.

This simple process would capture all of the value in the current peer review system while shedding most of its flaws. It would get papers out fast to people most able to build on them, but would provide everyone else with a way to know which papers are relevant to them and a guide to their quality and import.

By replacing the current journal hierarchy with a structured classification of research areas and levels of interest, this new system would undermine the generally poisonous “winner take all” attitude associated with publication in Science, Nature and their ilk. And by devaluing assessment made at the time of publication, this new system would facilitate the development of a robust system of post publication peer review in which individuals or groups could submit their own assessments of papers at any point after they were published. Papers could be updated to respond to comments or to new information, and we would finally make the published scientific literature as dynamic as science itself. And it would all be there for anyone, anywhere to not just access, but participate in.

…If we all do this, them maybe the next time someone like Aaron Swartz comes along and tries to access every scientific paper every written, instead of finding the FBI, they’ll find a giant green button that says “Download Now”.

The lecture transcript.

 

Michael Eisen: 20 years of cowardice: the pathetic response of American universities to the crisis in scholarly publishing

I propose a simple solution. We should give the public access to the peer-reviewed scientific journals in which we publish our ideas and discoveries.Michael Eisen, December 22, 2005

The question inevitably asked is, “Who goes first?” Which major universities and which scholarly societies have the will, confidence, and financial resources to get the process started?

Our answer is simple and to the point. It is time for the presidents of the nation’s major research universities to fish or cut bait. Collectively, they have both opportunity and motive—and, in the Association of American Universities, they have an organization with the capacity to convene the necessary negotiations.Association of Research Librarians, March 1998

PLoS co-founder Michael Eisen has earned the right to call cowardice on the elite universities that have continued to allow the journal monopolies to maintain their out-date business model, and their extortion-level pricing. Other academics will sometimes write supporting open access, but overall their posture remains submissive. In this essay Michael is refreshingly clear and frank on why the serials crisis still exists, at least a decade after universities could have refused to pay the extortion:

When Harvard University says it can not afford something, people notice. So it was last month when a faculty committee examining the future of the university’s libraries declared that the continued growth of journal subscription fees was unsustainable, even for them. The accompanying calls for faculty action are being hailed as a major challenge to the traditional publishers of scholarly journals.

Would that it were so. Rather than being a watershed event in the movement to reform scholarly publishing, the tepidness of the committee’s recommendations, and the silence of the university’s administration, are just the latest manifestation of the toothless response of American universities to the “serials crisis” that has plagued libraries for decades.

Had the leaders major research universities attacked this issue head on when the deep economic flaws in system became apparent, or if they’d showed even an ounce of spine in the ensuing twenty or so years, the subscription-based model that is the root of the problem would have long ago been eliminated. The solutions have always been clear. Universities should have stopped paying for subscriptions, forcing publishers to adopt alternative economic models. And they should have started to reshape the criteria for hiring, promotion and tenure, so that current and aspiring faculty did not feel compelled to publish in journals that were bankrupting the system. But they did neither, choosing instead to let the problem fester. And even as cries from the library community intensify, our universities continue to shovel billions of dollars a year to publishers while they repeatedly fail to take the simple steps that could fix the problem overnight.

The roots of the serials crisis

Virtually all of the problems in scholarly publishing stem from the simple act, repeated millions of times a year, of a scholar signing over copyright in their work to the journal in which their work is to appear. When they do this they hand publishers a weapon that enables them to extract almost unlimited amounts of money from libraries at the same research institutions that produced the work in the first place.

The problem arises because research libraries are charged with obtaining for scholars at their institution access to the entire scholarly output of their colleagues. Not just the most important stuff. Not just the most interesting stuff. Not just the most affordable stuff. ALL OF IT. And publishers know this. So they raise prices on their existing journals. And they launch new titles. And then they raise their prices.

What can libraries do? They have to subscribe to these journals. Their clientele wants them – indeed, they need them to do their work. They can’t cancel their subscription to Journal X in favor of the cheaper Journal Y, because the contents of X are only available in X. Every publisher is a monopoly selling an essential commodity. No wonder things have gotten out of control.

And out of control they are. Expenditures on scholarly journals at American research libraries quadrupled from 1986 to 2005, increasing at over three times the rate of inflation. This despite a massive reduction in costs due to a major shift towards electronic dissemination. These rates of growth continue nearly unabated, even in a terrible economy. (For those interested in more details, I point you to SPARC, the Scholarly Publishing and Academic Resources Coalition, who tracks journal pricing and revenues).

The opportunity universities missed

Just as the serials crisis was hitting its stride in the mid-1990′s, fate handed universities an out – the internet. In the early 1990′s access to the scholarly literature almost always occurred via print journals. By the end of the decade, virtually all scholarly journals were publishing online.

This radical transformation in how scholarly works were disseminated should have been accompanied by a corresponding radical shift in the economics of journal publishing. But it barely made a dent. Publishers, who were now primarily shipping electrons instead of ink on paper, kept raising their subscription prices as if nothing had happened. And universities let them get away with it.

(…) The unholy alliance between journals and universities

The biggest obstacle to the rise of open access journals was (and to a large extent still is) the major role that journal titles play in how universities evaluate candidates for jobs and promotions. In most academic disciplines, careers are built by publishing papers in prestigious journals – those that are the most selective, and therefore have the most cache. Scholars rising through the ranks of graduate school, the job market, assistant professorships and tenure face a nearly contant barrage of messages telling them that they have to publish in the best journals if they want to succeed at the next step. Never mind that it is far less true than people believe. That people believe it is all that matters.

Almost everyone I know thinks that simply looking at journal titles is a stupid way to decide who is or is not a good researcher, and yet it remains. There are many reasons why this system persists, but the most important is that universities like it. Administrators love having something like an objective standard that can be applied to all of the candidates for a job, promotion, etc… that might allow them to compare not only candidates for one job to each other, but all candidates for any honor across the university. This is perhaps why no university that I know of has taken a forceful stand against the use of journal titles as a major factor in hiring and promotion decisions. And it is, I believe, a major reason why they are unwilling to cut off the flow of money to these journals.

It’s never too late

(…)

Read the whole essay for the solution. If Harvard is feeling squeezed by the extortion, then we may be reaching the tipping point.

Michael Eisen: How Bt corn and Roundup Ready soy work, and why they should not scare you

Michael Eisen addresses the second of his #GMOFAQ rebuttals:

Question 2) Maybe GMOs aren’t automatically bad, but isn’t it obvious that it’s dangerous to consume crops that produce their own pesticides and can tolerate high doses of herbicides?

Here’s a short fragment

The irony of Cry becoming a major bugaboo of the anti-GMO movement is that, until the gene that produces it was inserted into corn, it was the poster-child of a “natural” insecticide, preferred over chemical pesticides because of the potential for extreme host specificity and complete biodegradability. Bt spores were sprayed on crops for decades, and are still widely used to control pests by organic farmers. But the effectiveness of Bt as an insecticide is limited because it degrades in the matter of days – more rapidly when it rains. This led agricultural biotechnology companies to try and insert Cry genes directly into the plants, and there are now many varieties on the market, each targeting pests that are a particular problem for a given crop (some varieties of Bt corn, for example, targets the European corn borer).

Given what we know about Cry proteins, there is very little reason to be concerned about the safety of eating it. These are proteins that have evolved to kill insects – and not just insects in general, but very specific subsets of insects. And humans are not insects. Regulatory agencies in the US and Europe have consistently rejected claims that plants that produce their own Cry cause problems in either humans or farm animals.

Nonetheless, anti-GMO activists continually raise the spectre of “plants that make their own pesticide” as if this alone was sufficient reason to not only avoid them, but to ban them. Here is a banner running on the website of one of the organizations pushing the CA GMO-labeling initiative:

If you don’t know a lot about plants, I can see how this would seem threatening. But this picture and the anti-GMO campaign it accompanies are based on the flawed premise that ”normal” plants are pesticide free. This could not be farther from the truth. Almost since they first appeared on Earth, plants have had to reckon with a diverse array of animals determined to eat them. And this is a battle that continues today, as anyone who has tried to garden, or wandered through a forest, can attest. To fight off these pests, plants have evolved a dizzying array of defense mechanisms, including the production of a diverse arsenal of chemicals targeted at the insects and other pests that afflict them.

[snip]

I’m sure some people will say that we may have been eating insecticides all along, but we haven’t been eating Bt Cry protein and, under the “you never know” principle, should just avoid it. This would all be fine and good if there weren’t strong evidence supporting the value of Bt corn and soy in reducing pesticide use on farms and limiting collateral damage to insects that are in the vicinity of, but not eating, the relevant crop. As a panel of the US National Academies of Science reported in a 2010 study of GMOs:

The evidence shows that the planting of GE crops has largely resulted in less adverse or equivalent effects on the farm environment compared with the conventional non-GE systems that GE crops replaced. A key improvement has been the change to pesticide regimens that apply less pesticide or that use pesticides with lower toxicity to the environment but that have more consistent efficacy than conventional pesticide regimens used on non-GE versions of the crops.

To me, the demonization of Bt in anti-GMO rhetoric is a emblematic of everything that is wrong with the GMO debates. The producers of Bt crops have done a horrible job of explaining why plants expressing a single insecticidal protein should not – and do not – harm humans. And the anti-GMO advocates either have not bothered to understand the science behind their activity, or (worse) are cynically exploiting peoples’ fears of pesticides to promote their cause.

Michael Eisen: Transferring genes from one species to another is neither unnatural nor dangerous

Evolutionary biologist, PLoS co-founder, and UC Berkeley professor Michael Eisen is a resource for science-based commentary that you need to follow. Michael blogs at MichaelEisen.org, and is guaranteed to add value to your Twitter timeline at @mbeisen.

Michael caught my attention when we were prompted to update our understanding of GMO by the recent anti-GMO vandals’ attack on the wheat research being conducted by the U.K.’s famous Rothamsted Research.

The captioned post is Michael’s first delivery on his promise to address the nine myths/questions he has culled from the anti-science campaigners. Michael has tagged the topic as #GMOFAQ. Here is his personal nine-point assignment, which was introduced in his post titled “The anti-GMO campaign’s dangerous war on science“:

1) Isn’t transferring genes from one species to another is unnatural and intrinsically dangerous

2) The most widely consumed GM crops now produce their own herbicides and pesticides. Isn’t it obvious that it’s bad to eat these?

3) Why should I believe GM food is safe? Why should I trust the big companies that develop these crops? Didn’t it take years to realize PCBs, DDT, ‘good’ cholesterol, etc. were bad for us?

4) What about studies that show GM foods cause allergies, destroy organs and make mice sterile?

5) Why won’t GM crops will escape and contaminate non-GMO crops (and maybe the planet)

6) GM crops initially reduced spraying. But now we have resistant weeds&insects. Aren’t we on a ‘pesticide treadmill’?

7) Don’t GMOs destroy biodiversity?

8) Don’t GMOs undermine local agriculture in the developing world?

9) Aren’t Monsanto’s business practices enough to want to boycott GMOs?

Hopefully you have read enough to motivate you to plug yourself into a well-written stream of commentary – written for critical thinkers. His blog tagline is “a blog about genomes, DNA, evolution, open science, baseball and other important things”. We don’t care about the baseball, but are very keen on all the other topics. And you can see from the first paragraphs on #GMOFAQ Question 1) that you are in for a good ride:

Last week I wrote about the anti-science campaign being waged by opponents of the use of genetically modified organisms in agriculture. In that post, I promised to address a series of questions/fears about GMOs that seem to underly peoples’ objections to the technology. I’m not going to try to make this a comprehensive reference site about GMOs and the literature on their use and safety (I’m compiling some good general resources here.)

I want to say a few things about myself too. I am a molecular biologist with a background in infectious diseases, cancer genomics, developmental biology, classical genetics, evolution and ecology. I am not a plant biologist, but I understand the underlying technology and relevant areas of biology. I would put myself firmly in the “pro GMO” camp, but I have absolutely nothing material to gain from this position. My lab is supported by the Howard Hughes Medical Institute, the National Institutes of Health and the National Science Foundation. I am not currently, have never been in the past, and do not plan in the future, to receive any personal or laboratory support from any company that makes or otherwise has a vested interest in GMOs. My vested interest here is science, and what I write here, I write to defend it.

S0, without further ado:

Question 1) Isn’t transferring genes from one species to another unnatural and intrinsically dangerous

The most striking thing about the GMO debate is the extent to which it contrasts “unnatural” GMOs against “natural” traditional agriculture, and the way that anti-GMO campaigners equate “natural” with “safe and good”. I’ll deal with these in turn.

The problem with the unnatural/natural contrast is not that it’s a mischaracterization of GMOs – they are unnatural in the strict sense of not occurring in Nature – rather that it is a frighteningly naive view of traditional agriculture.

Far from being natural, the transformation of wild plants and animals into the foods we eat today is – by far – the single most dramatic experiment in genetic engineering the human species has undertaken. Few of the species we eat today look anything like their wild counterparts, the result of thousands of years of largely willful selective breeding to optimize these organisms for agriculture and human consumption. And, in the past few years, as we have begun to characterize the genetic makeup of crops and farm animals, we are getting a clear picture of the extent to which traditional agricultural practices have transformed their DNA.

With that motivation, do read the complete essay.