Category Archives: Science

Science

Closed-Access Journals on the PR Offensive

I’ve talked in the past about the problem of access to journals. It varies drastically between institutions. Here at JHU, our access is pretty good. However, I’d say it was better, and certainly more convenient, at Washington University in St.Louis. But really, it shouldn’t matter what institution you’re affiliated with. Peer-reviewed research, and especially government funded peer-reviewed research, should be widely and freely available, from the internet, preferably in PDF format.

I’m not saying that anyone has to really give it away. Costs can be shifted around. However, for the sake of scientific review, collaboration, and progress, anyone should be able to access the papers. There’s already an extensive movement toward this standard. The Public Library of Science publishes several open-access journals, and carries out some advocacy of open-access publishing.

This, like the ability of bands to sell and promote their own music without the RIAA, is a threat to the traditional publishing industry. Nature recently published a brief article on the efforts of Elsevier, Wiley, and the American Chemical Society to counteract open-access promotion with their own PR. They’ve hired an expert on the PR-offensive to advise them in this effort. His advice allegedly includes tidbits like this:

The consultant advised them to focus on simple messages, such as “Public access equals government censorship”. He hinted that the publishers should attempt to equate traditional publishing models with peer review, and “paint a picture of what the world would look like without peer-reviewed articles”.

Do you see what’s going on here? Simple, but bald-faced lies, repeated often. Peer review is not at all limited to “traditional publishing models.” PLoS is a great counterexample. Also, public access is not government censorship, especially if taxpayer dollars paid for the research. I’d call that getting what you pay for. The argument is that,

“When any government or funding agency houses and disseminates for public consumption only the work it itself funds, that constitutes a form of selection and self-promotion of that entity’s interests.”

I mean, read that. Should a funding agency pay to disseminate everyone else’s work? Clearly these guys have hired an expert on crafting statements that seem reasonable but are actually quite deceptive and misleading. Based on the quotes from the involved publishers, they’re already drinking the kool-aid, or doing a good job of pretending to do so.

This issue has been covered and extensively discussed on Slashdot.

Best Practices: Number your references in scientific presentations

Have you ever watched an interesting scientific presentation? Usually, when a presenter shows a figure or mentions a published study, you’ll want to note the paper reference. However, these can be time consuming to write down, especially with names like Karagueuzian. (They’re usually given like “Karagueuzian and Chen 1999“)

There’s a simple solution to this problem. The academic publishing industry solved it a long time ago. Number your references. Even if you want to show the authors and years, you can just put a little number in parentheses, like (1) Karagueuzian and Chen 1999, (2) So and so et al…

But how will people use that? Post the key somewhere that people can find it, and mention it in the presentation. If you don’t have a convenient URL or link page to direct people to, you can always use TinyURL to make a short link that they can quickly write down. Or better, yet, post it on your blog.

Comments? Refinements? Would this help you? Would it drive you crazy?

Underlining and Mind-Mapping Read Papers Pays Off

When I read academic papers, I underline information I deem relevant, and later add that information to a mind map associated with the corresponding project. I’ve discussed this previously:

This worked fairly well once for my qualifying exam research at Tulane. However, that was a relatively small set of papers in a short period of time. For a project that’s been going on longer than I’m going to explicitly admit here, it’s not possible to keep as much organizational information in one’s head. I’ve been collecting and mapping reference papers for some time on this project, and I hoped that all that effort would pay off when it came time to write the introduction and discussion.

It’s paying off in spades!

Today I spent a few hours going down the list of important notes from papers I’ve mapped, and translating that into important points with reference markers (I.e. which paper to reference). It worked like a dream. I’m quite confident now that once I finish mapping the rest of the relevant papers, things will keep dropping into place.

There’s one important bit of feedback about mapping papers that I discovered in this process — don’t even bother mapping secondary information. That is, don’t bother mapping information that your paper cites from elsewhere. Just read and map the referenced paper. I pretty much quit underlining that stuff recently anyway.

Seeking Validation

Progress has continued smoothly on my class project. I’ve done one of the key validation steps in the project, and am just about ready to move on to the meat of the study.

What I did was to current-clamp the two different models, and compare this with the results of the exact same experiment in the paper that the models are taken from. Below, you can see the results:

Current Clamp Comparison

The top row contains snapshots of both types of model from the original paper. The bottom row shows my results for the same conditions. They’re essentially identical, although it’s hard to tell from the pictures in the original paper.

I still have a little more validation to do, but this is a pretty good sign.