Category Archives: Science

Is it immoral to hide your research behind a paywall?

Mike Taylor’s followup post, which has also attracted lots of excellent comments. Here’s a sample

As noted a few days ago, I recently had an article published on the Guardian site entitled Hiding your research behind a paywall is immoral. The reaction to that article was fascinating, exhilarating and distressing in fairly equal parts. Fascinating because it generated a fertile stream of 156 comments, most of them substantial. Exhilarating because of some very positive responses. And distressing because some people who I like and respect absolutely hated it.

Those people’s main objections were nicely summed up by a response piece by Chris Chambers, published a few days later on the same site: Those who publish research behind paywalls are victims not perpetrators. It’s a good, measured article, and I highly recommend it — not least because it’s apparent that while Chris thinks my tactics are all off, he makes it clear that he shares the goal of universal open access and further significant reform in scholarly communications.

So I’d like to clarify a couple of points that I didn’t make clearly enough in the original articles (but which I addressed in two separate comments on Chris’s article); and then I want to throw the floor open to see if we can hack through the more difficult issues that it raises.

A clarification

Chris wrote:

Do scientists who follow accepted publishing practices deserve to be labelled ‘immoral’, as Taylor claims?

The intention of my original article was not to say that the individuals who allow their work to go behind paywalls are immoral people, but that the act it itself immoral. If that feels like a fine distinction, it’s not. For a variety of pragmatic reasons, essentially moral people commit immortal acts all the time. At the trivial end of the scale, something as insignificant as not bothering to sort the recycling; at the other end, while no-one would claim dropping atomic bombs on civilian populations is an essentially moral act, many people would accept that in the context of WWII, the Hiroshima and Nagasaki bombs were justified or even necessary. (And please: no-one cite this as ‘Mike says publishing behind a paywall is exactly like nuking civilians’!)

So my goal in the original piece was not to castigate individuals as immoral people, but to push us all into deliberately thinking through the moral implications of our publication choices — decisions that all too many scientists still make without thought for the accessibility or otherwise of their work. I stand by my original assertion that it’s immoral to accept public funding to do research, then hide the fruits of that research from the public that paid for it. But that doesn’t mean that I am ‘labelling’ anyone. My apologies if that distinction wasn’t clear.

To summarise the intent of my article: the decision of where to publish is a moral one. Please, all you moral people out there, make a moral choice.

The curse of  journal prestige

And so we come to the vexed subject of journal rank. First of all, it’s encouraging to see that most people seem to agree at least that the effects of journal rank are A Bad Thing — that judging scientists by what journals they have published in is at best corner cutting, if not outright dereliction. This is not controversial any more, if it ever was: the ridiculous experience of PLOS Medicine as they  negotiated (yes, negotiated) their initial impact factor tells you all you need to know about such metrics.

As Chris wrote in his article:

In many (if not most) fields, the journals in which we publish are judged to be an indicator of professional quality. [...] Science is bad at being scientific: the actual quality takes second place to the perception of quality, which is so strong that journal rank creates its own biosphere.

The problem here seem to be one of wrenching an entire community out of a delusion at once. Because the things I hear over and over again are: 1. ‘Of course, I personally would never judge a paper by what journal it’s in, or judge a scientist by what journals her papers are in’. And 2. ‘I need to get my papers in glamourous journals so that people will judge me well’. Everyone is worried about being judged by the very criterion that they insist they would never judge by.

I don’t pretend to have a solution to this absurd circle. Well, I do: we should all just stop it. But I don’t have a strategy for reaching that solution. One thing that is infuriating to see is that even when the REF and the Wellcome Trust so very explicitly say ‘We don’t care what journal your work is in’, researchers continue to disbelieve them. I would love to hear constructive thoughts on what can be done about this.

Read the whole thing and the comments, where Michael Eisen closes the circle with this:

Can somebody please call snopes.com? Everybody here is do sure that you have to have a Science, Nature or Cell paper to get a fellowship/job/tenure because “somebody told them so”. So scientific of y’all. How about somebody look at some actual data? I have. I will post more details on my blog when I get a moment, but the basic things I have found are:

1) I looked at new hires in the top 10 biology departments in the US. All had recent assistant professor hires who had not published Science, Nature or Cell papers prior to getting their jobs. A fair number of new hires published their postdoctoral work in OA journals.

2) I looked at recent awardees of several major postdoctoral fellowship programs, and again, while there were certainly many people with SNC papers, in all cases there were exceptions.

3) I looked at two prominent young investigator awards, and, surprise surprise, there were a fair number of awardees without glamour mag publications (including one whose work was published in PLoS ONE).

So let’s cut out the “somebody told me” crap. Whether people said it or not, it’s simply not true. Is there a correlation between getting jobs and fellowships and SNC publications? Yes. Of course. Because, first of all, everybody believes it’s essential and works hard to get their papers there. And the same basic criteria for cutting edge science are used by the editors of these journals as are used in hiring/fellowship decisions. So there would be a correlation even if there were no causal relationship.

Do I think it helps to have glamour mag publications if all else is equal? Yes. It probably does a little.

Peter Kareiva: Myth-busting scientist pushes greens past reliance on ‘horror stories’

Stewart Brand has “green creds” with most of the environmentalists that we know. Since Stewart posted a Google+ note on a longish E&E profile on Peter Kareiva I thought I should have a look. I’ve mostly read Kareiva’s essays and lectures, but haven’t looked much at his history. If you have been flustered by Kareiva’s criticisms of the old-school Sierra Club/FOE types, you are not likely to find this profile comforting. I think is that Kareiva is spot on – e.g., his Breakthrough joint paper Conservation in the Anthropocene- Beyond Solitude and Fragility. See what you think…

Peer-reviewed and truth are not synonyms

Russ Roberts interviews Brian Nosek in this Econtalk podcast: Nosek on Truth, Science, and Academic Incentives. I learned quite a bit about flaws in the academic incentive structure, and how challenging it is to make structural changes in the publishing pipeline that will impact on the quality of papers (and the research).

Brian Nosek of the University of Virginia talks with EconTalk host Russ Roberts about how incentives in academic life create a tension between truth-seeking and professional advancement. Nosek argues that these incentives create a subconscious bias toward making research decisions in favor of novel results that may not be true, particularly in empirical and experimental work in the social sciences. In the second half of the conversation, Nosek details some practical innovations occurring in the field of psychology, to replicate established results and to publicize unpublished results that are not sufficiently exciting to merit publication but that nevertheless advance understanding and knowledge. These include the Open Science Framework and PsychFileDrawer.

Does new information slow down your life?

Very interesting! Thanks to Tyler Cowen for this

From William Reville, here is a speculation:

Finally, here is a ‘guaranteed’ way to lengthen your life. Childhood holidays seem to last forever, but as you grow older time seems to accelerate. ‘Time’ is related to how much information you are taking in – information stretches time. A child’s day from 9am to 3.30pm is like a 20-hour day for an adult. Children experience many new things every day and time passes slowly, but as people get older they have fewer new experiences and time is less stretched by information. So, you can ‘lengthen’ your life by minimising routine and making sure your life is full of new active experiences – travel to new places, take on new interests, and spend more time living in the preset.

Most of the short article considers why ‘the return journey’ often seems to run by much faster.

This is based on the book Making Time by Steve Taylor, interviewed by BBC here [Youtube].

Memory and the Cybermind

We have all become a great cybermind. As long as we are connected to our machines through talk and keystrokes, we can all be part of the biggest, smartest mind ever. It is only when we are trapped for a moment without our Internet link that we return to our own humble little personal minds, tumbling back to earth from our flotation devices in the cloud. — Daniel M. Wegner

Harvard psychology professor Daniel M. Wegner wrote a delightful essay for the NYT Sunday Review. Daniel is talking about us!

THE line that separates my mind from the Internet is getting blurry. This has been happening ever since I realized how often it feels as though I know something just because I can find it with Google. Technically, of course, I don’t know it. But when there’s a smartphone or iPad in reach, I know everything the Internet knows. Or at least, that’s how it feels.

(…)

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.

Naïve theories are suppressed by scientific theories but not supplanted by them

We read a fair bit of current science most days, then are a bit shaken by our lack of progress in educating the broad population. This New Yorker piece looks at some of the work attempting to account for our failure:

Last week, Gallup announced the results of their latest survey on Americans and evolution. The numbers were a stark blow to high-school science teachers everywhere: forty-six per cent of adults said they believed that “God created humans in their present form within the last 10,000 years.” Only fifteen per cent agreed with the statement that humans had evolved without the guidance of a divine power.

What’s most remarkable about these numbers is their stability: these percentages have remained virtually unchanged since Gallup began asking the question, thirty years ago. In 1982, forty-four per cent of Americans held strictly creationist views, a statistically insignificant difference from 2012. Furthermore, the percentage of Americans that believe in biological evolution has only increased by four percentage points over the last twenty years.

Such poll data raises questions: Why are some scientific ideas hard to believe in? What makes the human mind so resistant to certain kinds of facts, even when these facts are buttressed by vast amounts of evidence?

A new study in Cognition, led by Andrew Shtulman at Occidental College, helps explain the stubbornness of our ignorance. As Shtulman notes, people are not blank slates, eager to assimilate the latest experiments into their world view. Rather, we come equipped with all sorts of naïve intuitions about the world, many of which are untrue. For instance, people naturally believe that heat is a kind of substance, and that the sun revolves around the earth. And then there’s the irony of evolution: our views about our own development don’t seem to be evolving.

This means that science education is not simply a matter of learning new theories. Rather, it also requires that students unlearn their instincts, shedding false beliefs the way a snake sheds its old skin.

Read the whole thing.

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.

False Positive Science

This science policy post by Roger Pielke Jr. is a gem. You’ll want to keep these principles in mind whenever you read new research press releases (much of the science reporting you read in the media is regurgitated press releases). Here’s an excerpt:

(…) The problem of “false positive science” is of course not limited to the discipline of psychology or even the social sciences. Simmons et al. provide several excellent empirical examples of how ambiguity in the research process leads to false positives and offer some advice for how the research community might begin to deal with the problem.

Writing at The Chronicle of Higher Education, Geoffrey Pullam says that a gullible and compliant media makes things worse:

Compounding this problem with psychological science is the pathetic state of science reporting: the problem of how unacceptably easy it is to publish total fictions about science, and falsely claim relevance to real everyday life.

Pullam provides a nice example of the dynamics discussed here in the recent case of the so-called “QWERTY effect” which is also dissected here. On this blog I’ve occasionally pointed to silly science and silly reporting, as well as good science and good reporting — which on any given topic is all mixed up together.

When prominent members of the media take on an activist bent, the challenge is further compounded. Of course, members of the media are not alone in their activism through science. The combination of ambiguity, researcher interest in a significant result and research as a tool of activism makes sorting through the thicket of knowledge a challenge in the best of cases, and sometimes just impossible.

The practical conclusion to draw from Simmons et al. is that much of what we think we know based on conventional statistical studies published in the academic literature stands a good chance of just not being so — certainly more than the 5% threshold used as a threshold for significance. Absent solid research, we simply can’t distinguish empirically between false and true positives, meaning that we apply other criteria, like political expediency. Knowing what to know turns out to be quite a challenge.