More on OA, mandates and Harnad-vs-Velterop

In a followup today, Jan Velterop makes the point that he knows Stevan Harnad is a strong supporter of peer review, but their disagreement in fact hinges on another aspect of that system:

…I know that Stevan is a very strong supporter of peer review and so am I. In a way, that is precisely the problem. Stevan wants peer review, but not to pay for the process of formal publishing in peer-reviewed journals. That, he argues, should be done by librarians. I wouldn’t dispute that, but according to him librarians should (or is it just will?) keep the subscription model going and in that way provide sustenance for the formal peer-reviewed journal system.

So in fact I misrepresented Jan’s argument somewhat; mea culpa. All parties agree that peer review is indispensable, and what we are disagreeing about is how to pay for it. Jan1 is (I think) emphasizing the connection between formal publishing and peer review. These two processes are not necessarily inseparable, but Jan’s argument has the advantage that the current peer review infrastructure is already in place, and we know it works. Stevan (again, on my reading) is arguing that we can achieve close to complete OA, at least of papers not currently in commercial archives, just by doing it using IRs — and then wait to see whether journal subscriptions decline. If they do, journals will simply have to adjust to what the market wants, offering their services as co-ordinators of peer review plus whatever else they find their customers will buy (nice pdf files, advertising, job markets, etc).
Suppose, by way of Gedankenexperiment, we wave a magic Harnadian wand: all researchers from this moment will archive postprints of all their papers; journals that strictly disallow this practice will be shunned. Not only that, but the bulk of archived literature will also be, at the wave of our wand, deposited in IRs by authors working through their own back catalogues. (Note that we have sidestepped the quality control quagmire inherent in posting preprints, with or without corrigenda, and completely ignored the Kitten Herding problem of getting researchers to do, well, anything.)
OK, now what? I simply cannot see university and other administrations continuing to pay journal subscription fees, so what are the journals (and the companies that run them) going to do? Not being a publisher or any kind of businessperson, I don’t know what they will actually do, but it seems to me that our magic wand has left them little recourse: lacking leverage, they will have to either go out of business or sell their remaining wares (including the co-ordination of peer review) for whatever the market will bear. A quick Google search on “serials crisis” reveals that, in many cases, the market will not likely bear what they are currently charging for subscriptions. Journals with significant cachet, like Nature or Science, will probably be able to charge a pretty penny, but smaller fish will have to either drop their rates or leave the pond. It’s the latter that worries me: if researchers force this scenario, they risk losing diversity within the peer review infrastructure. It’s also possible that, if significant numbers of journals close, their review boards will be effectively taken over by other organisations such as scholarly societies — it even seems likely to me that researchers will figure “why pay at all? we can run peer review for ourselves”. I don’t like that idea either; in fact, the more I think about it the less I like it. There is value in having a sizeable chunk of the peer review process co-ordinated by outsiders: commercial publishers respond to different incentives than researchers, and I think that independence is a useful hedge against, well, corruption.
Ideally, from an entirely selfish point of view as a researcher, every existing journal would simply lay off staff and move offices and so on until it could subsist on what it could charge authors for having their work reviewed (plus advertising etc as above). I simply do not know whether the transition would work that way.
So where does that leave governments that are considering mandating OA to publicly funded research? Should they mandate OA without specifying mechanism and risk the problems discussed above, or mandate OA through the existing journal system and risk handing publishers, some (in my opinion, many) of whom are decidedly unscrupulous, even more leverage? I still prefer the former option, because it seems much more likely to me that publishers would gleefully gouge if handed the opportunity than that a mandate which did not specify mechanism would precipitate Peer Review Doomsday as above. For one thing, though I ignored it for convenience above, the Kitten Herding problem is significant. Researchers are conservative in their view of structural change, and reluctant to spend much time on anything but their chosen research problems. Journals will likely control access to their archives for the forseeable future, so they will not lose all leverage at once, and researchers would much rather pay (what they see as) reasonable charges than have to deal with change. There are a number of different publishing models being tried out as alternatives to the subscription-based system. It seems to me that a mandate that doesn’t specify mechanism will make these experiments more pressing for publishers without forcing them into any immediate decision.
Two quick final points in reply to Jan:

If anybody has problems with the harnadian solution, it’s scholarly societies that publish journals.

I think this is because scholarly societies rely on journal income to fund other activities and are fretting over lost revenue, which tells me they do not think they could persuade their members to pay membership fees that would cover the loss. Perhaps, to be frank, we could afford to lose a few such societies.

It is just possible that there may be reasons why researchers are researchers and publishers publishers. Everybody can sow the seed to grow the wheat to grind the flour to bake the bread. Who, after all, needs farmers, millers and bakers?

Quite right, and I do not even want to be a farmer, miller, baker — or publisher. I am happy to buy my bread and my peer review, I just want to pay a fair price.
(It now occurs to me that part of the problem is that, although I strongly suspect I am being overcharged at the moment, I do not know what would be a fair price. I will think and write more about that, but this entry is too damn long already.)

1 I hope it will not seem overly familiar if I follow Jan’s lead and use first names, it sounds less combative and this is not a fight, it’s civil fucking discourse.

“Alms race”, hee hee. Funny, but not accurate.

(Attention Conservation Notice: this post assumes some familiarity with Open Access. I’ve included some background links but the essential introduction to OA is by Peter Suber: see his Open Access Overview and also the one-page version thereof.)
In his latest blog entry, Jan Velterop takes an entertaining but (I think) overstated swipe at Stevan Harnad for the latter’s postion on recent moves by publishers to get OA mandates to encompass the paid version, that is, where publishers offer OA on any manuscript in exchange for an extra fee. Harnad argues, if I read him right, that this amounts to a land grab by the publishers, since if their efforts were to succeed the governments in question would be mandating further payments to publishers, on top of the fees and subscriptions they already charge. Since authors can already self-archive, pace Velterop, this really is a kind of alms for the publishers. Velterop takes issue with what he sees as dismissal of the role of publishers in providing peer review and authentication:

Those with a ‘harnadian’ inclination should really not bother publishers at all with their articles. They should just ‘archive’ (read ‘publish’) them in some repository and move on. Shame the articles can’t be labelled as having been published in a peer-reviewed journal, which would make them more valuable and be noticed and taken seriously, but hey, everybody can see them and the publishers just haven’t been able to beg enough cash to publish them.

I think this is a mis-statement of Harnad’s postion in re: peer review. Neither he, nor any serious OA advocate that I know of, has ever indicated that they do not recognise the value in peer review. Harnad’s point, in the post in question, is not about peer review at all but about co-opting a government mandate to direct research funds into publisher’s pockets, when a free alternative is available.
That said, I think there’s more to mandatory OA to publicly funded research (of which, let me state up front, I am strongly in favour) than a simple choice between for-pay or free models. TANSTAAFL. Velterop:

Subscriptions, on the whole, currently sustain the journal system. But they have a downside. They do not, by definition, provide open access. So that’s why new publishing models have emerged that do.
Unfortunately, Stevan derisorily calls these new publishing models PPA, for ‘Paid Publisher-Archiving’. As if ‘archiving’ is what publishers do. Nobody pays a publisher for archiving and no publisher asks for payment for archiving. Publishers ask for payment for having an article peer-reviewed and formally published in a reputable journal.

Well, yes, but remember that researchers provide a good part of the value of peer review — the actual reviews! — to publishers for nothing. Publishers are therefore charging money for co-ordinating the review process and for “formal publishing”, which I take to include archiving and distribution. This is a legitimate charge for legitimate added value, but there is a limit to what the market will bear, particularly as costly print versions of journals move closer and closer to obsolescence. (I haven’t picked up a print journal in years, excepting only those old publications which have not yet been digitized.) At some point it could conceivably become attractive for researchers — perhaps through the NIH, or professional societies, for instance — to co-ordinate the review process themselves, construct a robust search architecture that encompasses the vast majority of institutional repositories and thumb their noses once and for all at the STM publishing industry. (Indeed, when it comes to constructing a global virtual archive, the Open Archives Initiative has done much of the heavy lifting already.) So, let the publishing companies beware. Researchers, if I know my tribe, don’t want the hassle (and we are talking about a mind-bendingly HUGE endeavour, if we are considering moving virtually ALL peer reviewing out of the current commercial infrastructure) — but if pushed far enough, they’ll act.
Harnad and other OA advocates make much of the fact that there is currently no evidence that OA reduces journal subscriptions. I think this may be somewhat disingenuous. Evidence drawn from physics/arxiv is of limited value in making predictions about the much larger and more lucrative (or, from a subscriber’s point of view, expensive) biomed field. Further, if the subscription model still has a much greater market share than any OA based model, it may not mean much if current subscription levels are not (yet) falling as OA grows. Harnad himself has written about the transition from the current system to universal OA:

An alternative outcome [to 100% self-archiving] is that when the refereed literature is accessible online for free, users will prefer the free version (as so many physicists already do). Journal revenues will then shrink and institutional savings grow, until journals eventually have to scale down to providing only the essentials (the quality-control service), with the rest (paper version, online PDF version, other ‘added values’) sold as options.

This is the outcome that strikes me as likely: who is going to subscribe to a journal whose contents can be had for free? I have been saying since the days of E-biomed that OA would mean a significant reduction in the size, both physical and financial, of the STM publishing industry. Don’t get me wrong, I shed no tears over the likely loss of a few companies and shrinkage of the rest; but the important question is how to maintain the integrity of the peer review and authentication system. Will journals (that is, the companies that publish them) simply accept the new order of things and quietly “downsize” until they provide basically just the quality control function? Harnad writes:

In none of these outcomes [see here] is peer-review itself compromised or put at risk; nor do authors have to give up, even temporarily, submitting to their established journals of choice.

Er, well, it may not be quite that simple. If I put my Doom&Gloom hat on, I can see a number of “established journals of choice” simply going out of business, leaving open the questions of what happens to their archives and, more importantly, how do we replace the resulting hole in the quality control infrastructure? We certainly do not want to allow a power vacuum into which will rush the remaining publishers, likely the biggest and some of the worst, gleefully wielding a new near-monopoly. Harnad writes:

Self-archiving could be done virtually overnight.

It could, but it won’t. Getting researchers to work together, even for their own good, is worse than herding kittens. We (the research community, and open access advocates in particular) are NOT going to wave a magical open-access wand and present the publishers with a fait accompli in which they must quietly acquiesce. Government mandates of OA to publicly funded research will go a long way towards forcing their hand, though — which, to return to the original point of this post, is why Velterop is mostly wrong and Harnad is mostly right: researchers should come out strongly against the attempt to have such mandates include what Harnad calls PPA.

We don’ need no stinkin’ ethics. Unless we do.

Dr Free-Ride has a good entry up about scientists and ethical behaviour. I have nothing to add to her basic point, which is that when ethics is seen as something imposed from outside, it is largely ignored; this idea will be entirely familiar to any researcher who has ever sat through the obligatory (!) ethics class or seminar or whatever their department requires.
Where I think Janet’s discussion is missing something is in how to deal with this issue (and to be fair, she was mostly pointing out the problem, not trying to solve it):

To get “buy-in” from the scientists, they need to see how ethics are intimately connected to the job they’re trying to get done. In other words, scientists need to understand how ethical conduct is essential to the project of doing science.

So OK, how exactly does that work? In a fairly straightforward sense, ethical conduct is demonstrably NOT essential to science or scientific progress. Science is being done now, often quite successfully (in terms of personal career advancement and, more importantly, in terms of real additions to the knowledge base), by unethical means. There is nothing about vivisection that makes it an inherently ineffective means of gathering information; many experiments that do not make it past IACUC would yield useful data. Further, if I successfully steal your ideas and publish them, I will have been doing science from the point of view of anyone (or anything, like the knowledge base itself) that doesn’t know or doesn’t care that I stole the ideas.
The trivial category here is unethical conduct like that of the Korean stem-cell team; this was dumb as well as wrong, because it produced bad data and was bound to be found out. The important category is unethical conduct that produces clean (useful, reproducible) data: what makes such conduct unethical, what aspect of its unethical nature makes it antithetical to doing science, and what is the mechanism of that opposition?
Within this category, we can distinguish between conduct that, if you get caught, will hamstring you within the scientific community (thieving) and conduct that, if you get caught, will cause the wider community to stop supporting you (vivisection). The key phrase here is “if you get caught”; that is, ethical judgement is community judgement. An individual cannot do much science without the scientific community; infrastructure needs alone make that clear. Neither, for even more obvious reasons, can the highly-specialized scientific community do anything without the support of the wider community. Unless you posit something like karma or divine retribution, I don’t think you can find an unethical behaviour that both produces clean data AND is in and of itself “anti-scientific”, that is, proof that ethical conduct is in and of itself essential to scientific progress — unless, that is, you take into account the reliance of scientific research on community support.
In other words: what is ethical conduct? Whatever the community decides is ethical conduct. Why is ethical conduct essential to the project of doing science? Because community support is essential to that project.
I have, of course, sidestepped the larger question of HOW the community — the scientific community, or society at large — decides what constitutes ethical conduct. It’s not true that vivisection is wrong only because if you get caught doing it your grant will be cut off (without anaesthesia, of course). Scientists are not just scientists, they are members of society at the same time. This is an enormous question, but a quick look at the scientific community will allow me to sketch my own view: why is it unethical for me to steal ideas? Because if everyone stole ideas, collaboration and other networks of trust would collapse. It’s far more efficient to act in good faith and initially to assume the same of others. The same holds true for the wider community: whatever benefit I derive from someone else’s disadvantage will eventually come back and bite me in the ass. On any but the short-term, immediate-future view, “do unto others as you would have them do unto you” is not a Divine Command but a sensible way to maximize one’s own preferences.

How to perpetuate the “arrogant scientist” stereotype.

In a comment on Janet Stemwedel’s blog entry concerning sexism on Slashdot, the increasingly ubiquitous PZ Myers wrote:

biology actually is a real science, unlike that code bashing the desk jockies (sic) do

I note that, without such code bashing, Myers would not have his bully pulpit from which to disparage other people’s professions and beliefs.
I’ll note further that real scientists do research. Try “Myers PZ” on PubMed some time: nothing since ’98, one paper since ’93. (He did stop sneering long enough to get a dinky little paper out of computer methodology, back in ’91.)
It makes me weep for my profession to think that this arrogant jerk is fast becoming one of its more public faces. It’s particularly galling to have him spout about what is or is not science, when he doesn’t do any.

Three must-read entries.

Blogging will continue to be a bit light around here as I’m actually doing some work, but here (in no particular order) are three articles you shouldn’t miss:
1. Rejecting Vaccine “Choice”

Focus on the Family’s position statement [PDF] – “Focus on the Family supports widespread (universal) availability of HPV vaccines but opposes mandatory HPV vaccinations for entry to public school.” – looks, at first glance, like a reasonable compromise.
But “choice” is a red herring. Focus on the Family has religious objections to the HPV vaccine? Religious exemptions to mandatory vaccines are already available in every state but West Virginia and Mississippi. (Anyone think that Focus on the Family would have trouble convincing the Mississippi or West Virginia state legislature to add in a religious exemption for the HPV vaccine? Me neither.) They will have the right to opt their daughters out of this health-, fertility-, and potentially life-saving vaccine, mandatory or not. What they’re really angling for is a way to deny it to other people’s daughters.
If it’s easy to opt out, why the battle over mandatory? Because mandatory = affordable. States cannot make a vaccine mandatory for school entry unless they are willing to provide it to those who cannot pay. And thus, through the CDC’s Vaccines For Children program, every state supplies children with required vaccines free of cost. But optional vaccines are a different story.

Dr Rivka is back and in fine form. I’ve elided her links and there’s more to the whole entry, so go read it.

2. The Federal Marriage Amendment and the New One Drop of Blood Rule

The Federal Marriage Amendment, like many of the proposed state laws and amendments, says “marriage in the United States shall consist only of the union of a man and a woman.” Simple, right? No. Sex, like race, turns out to be a lot more biologically complicated than it first appears.

Here’s a view of gay-vs-straight marriage that simply hadn’t ever occurred to me. Fascinating stuff from Dr Alice Dreger, a serious expert in the fascinating field of intersex identity. Do yourself a favour and read it. If you like that, you’ll also like her blog; check out the essays in the linked entry.
Obaddedvalue: I’ll make a small prediction. Just as homosexuality will eventually be normalized, that is, accepted as an ordinary part of the human condition, so too intersex will one day be seen as normal. We — humans — tend to react to physiologies and behaviours that stand at a significant distance from the mean by treating them as disorders, but if those conditions are not harmful we do eventually realise that and come to accept them. The “normal” part of the spectrum slowly expands, and it’s my hope and my belief that eventually nothing but true pathology will lie outside it.

3. Answering the AAP critique of FRPAA

The latest AAP/PSP critique of the latest US Public Access Bill (FRPAA) makes the same points (already rebutted two years ago) that they made in their prior critique of the NIH Public Access Proposal. […]
There is zero evidence that mandating self-archiving reduces subscription revenue….But even if self-archiving were ever to reduce subscription revenue, surely what is in the best interests of publishers’ current revenue streams should not over-ride what is in the best interests of research and of the public that funds it….
AAP provides no evidence of how making research findings accessible for free to would-be users who cannot afford access would “seriously jeopardize the integrity of the scientific publishing process.” AAP merely stipulate that it would….
[M]any researchers cannot afford access to much needed research, and the proof of this is the fact that when subscription access is supplemented by author self-archiving, research usage and impact increase dramatically….Researchers do not now have nearly as much access as they need, because no research institution can afford all or most of the journals in which the research appears. The demonstrated impact advantage of self-archived research is the direct evidence of the substantial access shortfall there is for research that is not self-archived….
[R]esearch is not funded, conducted and published in order to generate revenue for publishers, let alone in order to guarantee their current revenue streams and insulate them from any risk. […]
Surely it is not the business of American Association of Publishers to concern itself with the cost to tax payers of providing open access to government-funded research. But studies have indeed been done, across disciplines, and they have found that self-archived research has substantially higher research impact (25% – 250+%), and this translates into substantially higher return on the tax payers’ investment in research than what they are getting for their research money today….[I]t is a self-serving red herring for publishers (in reality fretting about their own current revenue streams) to portray this as a “tax payer” issue….

If you already know what AAP and FRPAA stand for, this one’s for you. Please consider writing your Senators to ask them to co-sponsor. If you have a blog or some other way to publicise the issue, please use it. If you don’t recognise the acronyms, I have all kinds of good intentions of writing introductions to open access/open science and why it is the last best hope of the free world, kind to puppies and good with ketchup — but, um, don’t hold your breath. I’m really busy.

I invoke *sneeze!* the *cough!* lazy web. *wheeze*

Ah, Selva is wondering about something that has also been puzzling me:

For the past few weeks I have been in sneezing hell. Everyday when I wake up, my phlegm factory wakes up with me and kicks into high gear producing copious amounts of that white jelly that dribbles out of my nose (disgusting? Imagine what I feel..It’s coming out of MY nose!) England has too many flowering plants. The damn pollen is killing me. Anyway, the question is: All the air borne irritants are present even while I sleep but I do not dribble when I sleep. Why? Why is that my nose runneth over only when am awaketh?

I, too, am afflicted with this yearly blight, this vile assault on my mucosae. Portland Anthophyta are trying to kill me; Satan has relocated his infernal Itch Factory to my nose.
On a bad (especially pollenaceous?) day, my nose and eyes begin to itch and run within moments of waking. Surely the offending gametes were present in the moments before I awoke: what part of the reaction requires consciousness? Conversely, what aspect of the sleep state prevents the physical manifestations of the allergic reaction? Now, sneezing being a reflex, it seems intuitively reasonable that it might be suppressed by sleep; although it seems less clear, itching might be a similar case1. I’m also aware that the sinuses can produce mucus in one’s sleep, as is anyone who’s ever had a cold or ‘flu. This is different: not only does the sneezing hold off while I’m asleep, but so does the snot. I sometimes wake with blocked sinuses, but never — unlike when I have a cold — with a runny nose. Once I’m awake, though, all bets are off and I have to make a run for the drug cabinet.
I have no idea what is going on, and would be most grateful if the lazy web could tell me. (A quick google reveals nothing of any use.)

1 Mechanism, of course, is a whole nother can of worms in both cases. Is there a neurologist in the house?

A very small personal tribute to Dr Anita Roberts

portrait of Anita Roberts from has lost one of its best: Anita Roberts died of gastric cancer on May 26 (thanks to Abel for the news, sad though it is). From the WaPo obituary:

Dr. Roberts, a Pittsburgh native, graduated from Oberlin College in Ohio and received a doctoral degree in biochemistry from the University of Wisconsin. She did postdoctoral work as a National Institutes of Health fellow at Wisconsin and Harvard Medical School before becoming staff chemist at Aerospace Research Applications Center in Bloomington, Ind. She then taught chemistry at Indiana University.
She joined the National Cancer Institute in 1976 and by 1990 rose to deputy chief of the Laboratory of Cell Regulation and Carcinogenesis, then its acting chief and, in 1995, to chief, a position she held until two years ago.

Dr Roberts also kept a personal journal of what she called her journey. Her last entry ends “Love to all of you, and no regrets”; we should all die so well.
In November of last year, having no idea that she was ill, I emailed Dr Roberts (cold; she had no idea who I was) to ask if she would send me some Smad3-knockout mouse embryo fibroblasts. For readers who are unfamiliar with gene knockouts, those are MEFs from a mouse strain in which the Smad3 gene has been deleted; this is a complex biological reagent which took many months to construct and formed a cornerstone of Dr Roberts’ work on TGF-beta signaling in cancer. Rather than ignore an ill-timed request from a complete nobody, Dr Roberts promptly forwarded my request on to a colleague who sent me the cells. I have been working with them for some months, and will now think of Dr Roberts every time I use them.
My thoughts are with her family and friends, whose loss is all the greater.

meme or trope or whatever; blogosphere motto

Steve Gimbel of Philosopher’s Playground is guest blogging at the excellent Lawyers, Guns and Money. His first post is calling bullshit on the admin response to Haditha, and well worth reading for that, but I want to draw attention to this (emphasis mine):

Acting in an ethically proper sense is a two step process. Step 1: determine what is the right thing to do in the situation. Step 2: do it. In most cases step 1 is trivially easy; it is step 2 — having the moral courage to stand up and do what is right, even when it is not expedient –that is most frequently the tricky one. […]
But there are a few questions for which step 1 is not only non-trivial, it is incredibly difficult. This is where you bring out philosophers to set the table by clarifying the issue and then everyone joins in to engage in the moral side of deliberative democracy or what I like to call “civil fucking discourse”: it’s civil in that it is an open-minded, good faith attempt to find truth, but it is not civil in that it is a knock-down, drag-out, intellectual cage match where all ideas are welcome in the ring regardless of where they sit on the political/religious/ideological spectrum.

“Civil fucking discourse”. I love it. I think the blogosphere has found its motto.