Sometimes I listen to myself

I saw a talk this week, by John Fleck, science writer for the Albuquerque Journal. It was an interesting talk by all measures. Titled “Communicating Science: What the News Media Can Do, and What It Can’t”, I would have entitled it “Science Writing for General Audience Publication: How I do my job”.

Of most interest to me, was the discovery that, while trained in philosophy, this man was quite well versed or at the very least aware of what science really is, how it’s done, how to approach it, etc. Assuming he’s a representative sample of science writers, it made me realize that the divide between those who do science and those it impacts may not be in the news media (or the middle man, as I’d like to call it), but rather between those who write for news media and those who read it.

In developping (well, thinking about) the great idea I’ve been outlining on these pages, I’ve been thinking it should include tools for scientists to communicate (or at least to motivate scientists to communicate) outlying scientific ideas (to paraphrase a dicotomy Fleck used between the “core of a scientific subject” and the “outlying science in a field”) to the general public. In that sense, I’m suggesting we do exactly what I hinted at when asking Fleck a question after his talk. Cut the middle-man.

Traditionally, we have worked in a “proxyfied” way. I make science. I speak to a reporter. The reporter speaks to the people. If you’ve seen the movie “Office Space” (and if not, I highly recommend it), you might recognize one of it’s characters.

“I deal with the clients so the engineers don’t have too. I have people skills! What’s wrong with you people! Can’t you see that!”

I was happy to hear Fleck agree with me and encourage the audience to communicate directly to the public, blog,… I was concerned, although I did expect it, to hear him admit that, regarding communicating scientific developments to the general public,”It’s hard.”

All in all a good talk, although I would have like something a bit more confrontational. I would have liked Fleck to bring forward his vision for how we ought to bridge the divide between the world and the geeks. I like to think my idea could be it. (I often have visions of grandeur and live happily despite it.) We’ll see, although for that, I’ll need to find someone who’s much better at coding these things than I’ll ever be. Anyone interested? The job is open. Flexible hours, can work from home, you get an equal share of the company and no pay. Deal?

During my daily (who am I kidding, hourly) slashdot browsing, I came about this commentary regarding a new advocacy group lobbying for traditional commercial scientific journals.. The lobbying group is called Prism. They’re a Partnership for Rrsearch Integrity in Science and Medicine. The main point of interest on /. was about how this lobby group is all about getting copyright respected and yet puts up watermarked images from Getty on their website, suggesting they’re using unpaid images. I’m not so much interested in that detail, mainly since they seem to have corrected their website and have put up non-watermarked images. So either their web developer was stupid or didn’t have enough coffee that morning and picked the wrong file for the website or they saw what’s being said on the internet and quickly went to Getty, apologized, paid and went on their merry way. Either way,they are wrong in so many other ways, it’s funny even without the pictures!

I quote from their website, the issue of interest to Prism is to “protect the quality of scientific research”. This issue is of vital concern to “scientific, medical and other scholarly researchers who advance the cause of knowledge; the institutions that encourage and support them; the publishers who disseminate, archive and ensure the quality control of this research; and the physicians, clinicians, engineers and other intellectual pioneers who put knowledge into action.”

A nice listing of basically anyone involved in medical science, were it not for the simple problem that Prism was established by “The Executive Council of the Professional & Scholarly Publishing Division of the Association of American Publishers (AAP)” and doesn’t list anybody else as a member. You can list anyone you want, if you’re only comprised of “pay-for-access” scientific journals, then those are the interests you’re representing.

I really like how they describe themselves everywhere that they’re an advocacy group, a partnership, a coalition (of one group, sic!) and so on. Especially since they clearly state that their group’s role is to “educate policy makers and the American people about the risks posed by government intervention in scholarly publishing.” It sounds like lobbying, it looks like lobbying, it smells like lobbying. I’m going to commit myself and just say it. I think they’re a lobbying group. There, I said the evil word. 🙂

From the political-talk on their website, it seems that their interests are really aligned with mine. They want to “advocate sustainable business models to ensure continued investment and innovation in these essential contributors to scientific objectivity and integrity.”

Wow! How great! That’s exactly what I want to do! I want to start a website that innovates in how scientists distribute their scientific results, discuss them, rate them and how good/bad science is determined. I definitely want to innovate, since I want to propose an alternative to the current peer-review system! I also want good science (objective science done with integrity, sounds good) to prevail over bad science (data fudging, unethically paying women for parts of their body, you know, bad stuff). So why do they and I clash? Ah yes… I believe that scientists should keep the copyright of the articles they publish and not give it to the person who distributes it. It’s unfortunate that the entire leverage that scientific (commercial or traditional) journals have in terms of a business model is the copyright they get to the articles they distribute. Take that away and their business model crumbles. There are 4 interesting points on their main page (if you’re a lobbying group, you should put what you have most at heart right there in the front, right? Get people to “get it” right from the start), so let’s go through them one by one.

“What’s at risk?” they ask. Their answer is that we’re putting at risk the integrity of scientific research. “How?”, might you ask. Again, they’re quick to answer.

• “By undermining the peer review process by compromising the viabilty of non-profit and commercial journals that manage and fund it.”

Ok, that one is nice. There are numerous examples of research that went through peer-review. The classical peer-review. It came back with the holy seal of approval from “the community”, i.e. 3 experts (well, often times one of their graduate student) and one editor. The seal said “ACCEPTED”. No discussion after that, it goes through. Except the data was made up, it was generated by a random sentence generator program, made up by MIT undergrads or it was unethical research with fudged data, etc. There are even more scientists voicing their opinion, saying that peer-review is not so good. Great research gets rejected because someone feels it’s too much in contradiction of the accepted, current view. Nevermind that they could be right, they just clash too much with what’s accepted right now. Peer-review isn’t perfect, let’s not hold onto it to dear life, like it’s the only thing keeping modern science together.

• By “opening the door to scientific censorship in the form of selective additions to or omissions from the scientific record”.

Yeah, that’s a valid concern. Except I fail to see how commercial journals are playing a positive role there. You see, I see doctoring of reports in, like, the IPCC reports where the sponsoring agencies cut out stuff or add stuff. I’ve seen governmentally doctored reports. Except those reports haven’t gone through peer review! So this is a problem of how the government operates. Yes, we should tell the government that it can’t edit reports that come out of publicly funded research. Unfortunately for prism, it has nothing to do with commercial peer-reviewed journals.

• By “subjecting the scientific record to the uncertainty that comes wtih changing federal budget priorities and bureaucratic meddling with definitive versions”.

Let me tell you… I work at a national laboratory… if scientists aren’t being “subjected to the uncertainty that comes wtih changing federal budget priorities”… Seriously, it’s ugly. Congress hasn’t bothered telling us in the last 18 months what our priority should be. We could get shut down… Talk about uncertainties. What happens to all the reports we have that are unclassified and published on the lab web pages… Or maybe they mean to say that all open-access journals (ah yes, if you read on their webpage carefully, that’s really what they’re after! Open-access is bad!) are going to be funded by the government and that if the government stops funding them, they’re going to shut down the webpages? First of all, it’s not clear that all open-access journals are going to be 99.9% government funded and the answer is easy. Leave the copyright to the author! If my website closes, the author is free to distribute his work somewhere else! I reckon my website isn’t going to close though. 🙂

• By “introducing duplication and inefficiencies that will divert resources that would otherwise be dedicated to research”. [emphasis in the original text]

Right…. Inefficiencies… So let me get this straight. Two years to get a paper published, in 2007, with the accessibility of the internet, is efficient?!?! Seriously?! Okay, I’m being a bit extreme. What I’ve seen on average is 12 months. Still. A year! If you want to publish a paper today, you have to surrender your copyright (which means you have to ask for permission if you want to use a figure in a presentation), you’re giving them money (there are journals who make you pay to get the paper published and to get access to their material. You just try and get a color picture in there), they take 12-18 months to get your stuff published and they call themselves efficient?! Funny stuff.

Sorry José, but I’m going to keep working on my idea. I think I’ve got something here.

If you want a more detailed and more intelligent rebuttal of prism, go see here. Those arguments turn around “this lobbying effort is a PR stunt and their arguments are full of misinformation, half-truth, and fear-mongering.” I agree with everything that’s said. I go a step further, by saying that peer-review is broken (at least to a certain extent) and there’s a possibility to make something that’s more efficient. That part of my argument isn’t really needed to show that prism is no good, but I make it anyway. It’s my stick, you know?

If I’m going to be serious about this new way of disseminating science, it has to start now! I just saw on slashdot that a new science site, which they titled as “YouTube for Science” had started. It’s called SciVee. This is not exactly what I was thinking of (so I haven’t been scooped yet, pfiou!), but it has elements of what I’d like to see (so it’s dangerously close, bummer!). If I understand well, then SciVee allows you to upload a video (or just audio) of yourself talking about your paper and you can synchronize it with plots from your paper. This isn’t what I really had in mind, but it’s getting close. Their system has some limitations.

For starters, it’s looking at papers that have gone through the classical peer-review process. I’m aiming at something that, ultimately, can bypass the classical peer-review process. Conceptually, it would be easy to extend the SciVee service to include papers which haven’t gone through the peer-review process. You’re already uploading a video, it’s not much different to upload a paper. What’s harder then, is how do you determine what’s a good paper from a bad paper then? Their system is probably not really set-up for that. Plus they don’t have a review process and the standard “click here to make this paper (or SciVee as they call it) a favorite” is not good enough for scientific publications.

In the same vein as the previous comment, their uploading and reviewing process is linear. I believe there is a way to rate and comment on the videos of other users (from the explanation, it’s unclear whether you’re rating the video or the science, so would you rate low a bad video of bad science?), but it’s what I’d call a direct user input. You look at a video and you rate how much you think it’s worth. Let’s say, for the sake of the example, that it’s a 5 point scale. You would rate something 3/5 or 4/5. Any such system has several drawbacks. One is that you’re not always sure that users understand or at least share the same rating scale. 4/5 for me might be an outstanding paper with 5/5 being nobel prize material. 4/5 for you may be an average paper with 5/5 being anything between a really good paper and Nobel prize material. This makes such a scale less relevant. What I’d propose is to have a system whereby users can communicate with each other about the different papers available (or the SciVees as they call them). Papers are then rated based on how people interact with each other about those papers. If a paper gets lots of positive recommendations between users it gets rated higher. There also seems to be a system to comment on a particular SciVee. I don’t like comments as a main way of determining the value of a piece of work. I really don’t want to have to sift through 12 billion comments before I can decide whether the work was well done.

So far their system isn’t a community per say. Like I said, it’s linear. You upload, people download. Sometimes they comment and review. In their defense, they have a community aspect on the way. You can sign-up as a beta tester.

I should point out that I’m saying all of this as someone who hasn’t used the site as an author. One of the big drawbacks of the site right now is that you can only use it with papers in open access journals. The journals of PLoS are probably much much easier to use with this system. I don’t have papers in open access journals and more so not in PLoS journals. They do say that they’ll, at some point, accept getting abstracts from articles published in traditional journals (not open-access). So the expansion of their system relies on people publishing in open-access journals and with licensing options that permit re-using the material.

So like I said, it’s a good idea. It’s not completely MY good idea, but it’s a good idea. So whatever it is I want to do, I have to do it NOW! This definitely has the potential, with some added functions and maybe a complimentary service from someone else, to fill the niche I’m looking at. I still think by-passing the traditional peer-review system is the way to go. Not to abolish peer-review, but to change it drastically. The greatest hurdle of such a new service will be community acceptation. The traditional peer-review system has been used for a long time as a way to validate the worth of individual scientists. The community is probably not going to let go very quickly, so giving the right incentives to use the new system is going to be important.

There’s something that bugs me about journal papers. Something that bugs me deeply, to the point that I really dislike writing papers. Part of it is stems from my personnal interests. I’ve always liked to do puzzle. I like to collect different “mind patience games” (I know this in french as jeux de patience, the translation isn’t obvious to me). Solving these mind-benders always gives me great joy. In a sense, I think I approach science the same way. I like to reach “cute” milestones. They’re like little mind-benders. I don’t really like writing a paper telling people how I managed to get the peg outside of the wooden rings. Therein lies part of what bugs me about writing papers. Nonetheless, there is something else.

 I think part of what bugs me about writing papers, is three-folds:

1.  The rigid structure: You must write a paper in a particular tone. You must write a paper in a succession of sections that are always the same. You must use a general, non-descriptive, pompous title, like “Modelling of couch potato behavior using a stochastic TV model.” If you use a title with a question mark, like, “Do couch potatoes have different social rules?”, you are deemed a heretic. Don’t try to do this before you are 55 and have 25 years of experience in the field.
2. It has to fit within x pages: This is less true of journal papers than conference papers. Maybe this just has to do with the rigid strucure.
3. It takes 2 years to take a paper out: This is just ridiculous. Today, with the internet, there’s simply no reason for a paper to take this long to be published. Just absolutely none.

There are probably other things that bug me about journal papers. I just can’t think of them right now.