The Futile Cycle

There’s an interesting new web application from Nature publishing group called Connotea. It’s a free online citation/reference manager for scientists and physicians, and it seems to work very well indeed. It involves using a bookmarklet (i.e. a bit of JavaScript) to detect articles and add them to your library. Check it out; it’s pretty neat and well-made. There are videos explaining how it works. In a way, it feels like it’s trying to be a del.icio.us for the scientific world (del.icio.us is a social bookmarking site, where people can tag website bookmarks and browse other people’s bookmarks). It’s a cool experiment.

One of the things I like about Nature versus Science is how much Nature seems to be trying to embrace the new medium of the internet. Whereas Science is working to bash innovative publishing, Nature seems to be trying to explore the possibilities the internet has to offer. Maybe that’s because Nature is based in the UK, where a lot of experimentation has been done on internet media, particularly by the BBC, which has chosen to open its archives to the UK (i.e. taxpaying) public. As one of the heavy hitters of the scientific publishing world, Nature seems to be doing a great job in being open to new ideas, at least as far as a huge corporation with over 70 titles under its umbrella.

Time to get a few interesting links off of my list:

DNA Artistry: Pretty neat. These guys take your DNA and do a restriction enzyme digest, similar to what a forensic DNA test or a paternity test would do for looking at restriction fragment length polymorphism. They take that chopped up DNA, run it on a gel, photograph it, and send it back to you in a giant blowup. Nothing you couldn’t do in any biology lab, however.

A beatboxing flutist performs Inspector Gadget and the Super Mario Brothers Theme.

One reason I stick to Macintosh is that I rarely have to lose hours of my time online trying to figure out how to get hardware to work. I plug in, try things by following intuition, and then it almost always works. I don’t know any other company that understands this.

Take Logitech. It’s a strong brand name in the keyboard/mouse peripherals market, and yet its software sucks. Completely. I bought a wireless keyboard and mouse to use with both my MacBook and my PowerBook, since my PowerBook’s monitor is broken, making it a de-facto desktop computer by being tethered to an external monitor. Logitech touts one of the features of this set as having an easy-to-reach USB wireless receiver, for plug-’n'-play usability. Unfortunately, when I unplug the wireless receiver from one computer and plug it in again (either to the other computer or the same computer) Logitech’s software fails to recognize their own products. Thus, all the extra buttons on the keyboard don’t do anything, and ocassionally, the keyboard reverts to the “Windows” layout, where the Option and Command keys switch places.

I haven’t found a fix, other than uninstalling and reinstalling Logitech’s software each time I unplug and plug in the wireless receiver. This is not progress.

I wish more companies did their engineering like Apple, because although Steve Jobs’ minions aren’t perfect, they pay attention to details to make things work as seamlessly as possible. Most companies do not. Logitech, your brand represents shoddy design.

Perhaps I’m picky about my tolerance for useless or obscure scientific jargon, especially ones I feel have been redundantly coined, but I feel like I’m fairly lenient when it comes to accepting “-ome” words, like “genome”, “proteome”, “lipidome”, “secretome,” and so on. I even think that “interactome” and “allosterome” aren’t all that ridiculous. But “alpha-amino terminome”?? Seriously, at that point, you’re just making shit up.

Since one of my friends sent me an email about this Nature newsletter, I thought I’d get my opinion out about Open Access Publishing.

Firstly, I like the idea of it. Part of the optimism of science is about the free flow of information, for the betterment of all. Open access publishing, in a sense, utilizes the great infrastructure of the internet to provide a free peer-reviewed (i.e. non Wikipedia-style) repository of the latest and greatest research coming from academic labs. Since much of the research is funded by the government and taxpayer-money, it would be nice (though not a moral obligation) to open the publishing to the public. Open access also allows for more collaboration, a wider dispersal of knowledge, and a lower barrier of entry for smaller research units (like private researchers, small colleges, and other individuals). In all sorts of ways, open access publishing might be a good thing.

I wouldn’t, however, want to require that all published materials funded by the government get opened to the public. Just because something is paid for by taxpayers doesn’t mean that it has to be opened to be public. The point of spending taxpayer money is to fund things that would have a benefit to the public, something that under normal market situations wouldn’t occur. Thus, things like building highways, the police and fire-department, funding hospitals, funding innovation via patents, and funding basic-science research via grants. None of these have any guarantees that the public can use them directly, since all that is a moral necessity is that the public somehow benefits from their continued funding and existence. Thus, toll highways allow for better trade and transportation, even though some people might not be able to afford to use them. The public, by default, can’t just use patented products, even though they (technically) pay for it by giving the owners monopolies.

In addition, the main point I want to talk about is that I don’t know how sustainable Open Access Publishing is. Publishers have continuing costs every year, from server costs to print costs, and not all of that can adequately be covered by the publishing fees that are charged to every author. These one-time fees eventually run out for each article, so the best way to cover their costs would probably be through advertisements, but online advertising is a tricky and fickle business, and I don’t know how I’d feel about the possibility of a journal going belly-up based on the rapidly fluctuating online market. This isn’t a precise analysis of any finances, and this is all pure speculation, but it’s just something I’m worried about (since I do happen to like the model very much). I’d like it to succeed, but we’ll have to wait and see if they stick around after 10 to 20 years.

What I don’t like, however, is that the old model of publishing is attacking the new, as described in the Nature article. I really dislike the ACS, as their journal qualities are declining as of late, with too much bloat and not enough content, and this is just the final straw. I would never subscribe to an ACS journal, as they just aren’t very interesting. I don’t like Elsevier, either, because their websites suck, they facilitate arms trading, and now they’re involved in this mud-slinging.

The two models should compete on the open playing field. If Open Access is unsustainable, it’ll collapse, eventually, and go back to the traditional publishing method. If the Open Access umbrella succeeds, then too bad, publishers, go on to your next job. I don’t have any pity for those who can’t learn new skills or transition; that’s why you get paid less, because you’re less valuable to others. If you’re losing subscribers because of Open Access, then give people more value for their subscriptions. Bundle online access, utilize your huge archives. Maybe make your journals that much better edited, or more carefully selected. Write more interesting highlight articles. Solicit more review articles. If you’re losing money to the free, what it means is that your journal isn’t worth anything more than free, and that means you’re doing a terrible job.