Do open-access electronic journals really help science?

The latest fad in the scientific publishing world is open access e-journals. In my field, for example, the Optical Society of America’s Optics Express has become one of the most popular journals, despite being only a decade old. The journal is basically a peer-reviewed website; people submit self-produced papers in either Word or LaTeX form, and those that are accepted are made directly available in PDF form on the website for free download. In theory, this democratizes access to the scientific literature, and increases the distribution of knowledge, but it comes at a cost.

In order save money, the OSA foregoes the cost of typeset articles produced by a professional editor. The optics literature is now awash with papers produced in Microsoft Word. Much of it has the production value of a junion high book report, except with more equations. Word was never meant for mathematical typesetting (and frankly it’s not worthy of anything published) and the results are abysmal and amateurish. Even though it doesn’t technically affect the content, we should take some pride in the presentation of our work. At best, poorly produced papers are inefficient to read, and at worst, they contribute a subtle psychology that says that sloppy work is acceptable and that what we do is not worth the effort to present well.

[Update: The lack of typesetting in Optics Express helps keep the publication charges around $1000 for most articles. As pointed out PlausibleAccuracy below, not all OA journals are author typeset. For example, the Public Library of Science has beautifully produced articles. However, they charge more than twice what the OSA charges to publish.]

In any case, this brings us to the most problematic issue: The way most open-access journals work is by charging an arm and a leg to the authors for publication. Not only does this limit the people who can publish to those with sufficient funding, it also puts the journal in a position of conflicted interest. As professional societies struggle financially, they are under pressure to accept more papers to bring in cash. With open-access, they make money by accepting papers. With closed journals, they make money by producing good journals.

As I understand it, Optics Express is actually a profit center for the OSA. They cannot possibly be objective about peer review when each rejection costs them thousands of dollars. In the end, editors have a lot of power; I recently reviewed a paper for a ultrashort pulse measurement technique that would not work for the majority of cases one would encounter in practice. I pointed this out, and recommended the article be significantly redone. Next month, I found it in Optics Express, virtually unchanged.

So, we’ve democratized the consumption of information at the expense of the democratization of its production. Do you want the best ideas to be published, or the widest distribution of marginal content? I’d argue that society is best served by making sure the best ideas are published, even if it means having to charge for access to those ideas.

While ensuring that people in developing nations are not denied access to information for want of money sounds noble, should we not also be worried about bad science being published for want of money by the publisher, or good science not being published for want of money by the scientist? In fact, perhaps we shouldn’t even be all that concerned that somebody who can’t afford a $25 journal article is not be able to read about a $250,000 laser system. I know that’s harsh, but there is a certain logic to it: if you can’t afford the journal article, you probably can’t do much with the knowledge.

I do agree with the principle of free access, but only if it’s done with integrity. Ideally, journals should be handled by foundations, with publication and distribution paid for by an endowment to be used only for that purpose. At the very least, there should be no overt financial incentives or disincentives to publication for either party. The primary concern should be the quality of the publications, not the political correctness of its distribution.

Maybe there are dumb questions…

I’ve been wondering about the following: When somebody says “think about the color blue” you cannot help but have an image of blue (or something blue) pop into your visual cortex no matter how hard you try otherwise. Moreover, the thought apparently triggers rather similar neural patterns to those excited if you were actually seeing it. But if somebody says “think about raising your right arm” your arm does not shoot up. If motion is caused by the brain, initiated by thought, and my thoughts are not entirely in my control, why is it that I am nonetheless in total control of my physical movement? There must be some pretty interesting machinery to insulate our normally chaotic thoughts from our motor control system so that we’re not constantly smacking people whenever our subconscious mind wants to.

Saudi Oil and the US dollar

Last week the dollar began to recover in value as the Bush administration finally started making serious noise about a strong dollar policy. Now, right on the heels of that display, the Saudis finally agree to up production.

Both events were a bit long in coming, at least relative to the reasons stated by each party. The Bush administration claimed it was (finally) worried that imports would become too expensive if the dollar were allowed to continue its slide. They didn’t seem concerned the past several years as the dollar slowly dropped a third in value. After all, it was their policies that caused it. Similarly, the Saudis have been fighting production increases all the way as oil has quadrupled in value. But now $140 is the magic number where they start to care?

It leads one to think maybe the two capitulations are connected. After all, high oil prices hurt America. A devalued dollar hurts the Saudis, as oil is priced in dollars. Priced in Euros, for example, the Saudis aren’t raking it in as much as it would seem. Given how much they trade with Europe, the dollar’s fall has offset a lot of the increase in the price of oil, especially given that they probably have a lot of production costs that are priced in other currencies, squeezing them from both directions. So, we prop up the dollar to help them, they increase production to help us. Given the connection between the Bushes and the Saudis, maybe the two governments finally addressing these longstanding problems at the same time is not a coincidence. Nor, perhaps, is it a coincidence that this coincidence happens during a presidential campaign.

REALbasic: Cross-platform that really doesn’t work

It sounds too good to be true. Write once, run everywhere. (Where did we hear that promise before?) Alas, it is. I’ve been working with REALbasic for about a year, now, and my conclusion is that it’s not ready. Given that they have been working on it since 1996, I suspect it never will be. As a language, it’s amateurish. Threads are not native, and are actually cooperative as opposed to preemptive. Kind of like the Mac back in the 1980s. Worse, threads hand over control not at regular intervals, but at each iteration of a loop. Who came up with that horrendous kludge? It’s hard to believe they have the gall to actually release a version of their software dubbed “Professional.”

But being merely amateurish wouldn’t be enough to warrant a blog post. I’m warning people off of this piece because it’s so buggy as to be almost unusable. I’ve had problems with bugs in their semaphore class not actually protecting resources from all threads. (Apparently they really have a problem with this thread thing.) Most problematically, however, the IDE itself is highly unstable. Sometimes, under Linux, it gets confused and when you hit “delete” in an editor window, it actually think you want to delete the whole method, not just the current character. That’s obviously a problem, especially if you don’t catch what it just did, and accidentally hit save. Restarting fixes this. Right now, whenever I set a breakpoint, it crashes with a segfault upon reaching the breakpoint. Running without the breakpoint works fine. Clearly, they need more work.

Maybe in another ten years they’ll be ready, but for now I suggest anybody considering REALbasic learn a real language instead. BASIC can potentially be a great language, but in the hands of these guys, it’s open mike night.

For the love of all that is holy, stay the hell away from OpenOffice

Twice now I’ve had it hopelessly corrupt a file on me. (What is it they say about “fool me twice, shame on me?”) Saving isn’t enough with this ungodly piece of shit. You need to run ten minute backups of the file you’re working on so that OpenOffice can’t kill it. The latest accomplishment of this pig astounds me: I opened a document and had OO open up a second window, so I could edit one part while looking at another. At some point, I close the window in which I was editing. Poof, the changes I made in that window were erased. You probably think I accidentally deleted something, right? Nope. Going back through the undo history, my changes just weren’t there. Things I’d done before the changes that were lost were undoable, so something fishy clearly happened. You also probably think I stupidly opened two windows using two different instantiations of OO, so that one overwrote the other. I didn’t; I used the “New Window” function. I suspect there is some bug with how OpenOffice handles two windows on the same document.

If this stupid blog does one thing useful, it will be to save just one person from using the complete waste of space that is OpenOffice. I can’t tell you how much I’d be willing to pay for Microsoft Office if I could go back in time and use it instead of OO, but I can tell you it’s a lot more than Microsoft charges for Office. What’s really embarrassing is that using a “community developed” version of office software is exactly the kind of stupid, false economy for which I railed against desktop linux.

Poem for the day

Didn’t see that coming, did you? I think this one is especially appropriate for the time, as well as needed balance to the last post:

O look, look in the mirror,
O look in your distress;
Life remains a blessing
Although you cannot bless.

O stand, stand in the window
As the tears scald and start.
You shall love your crooked neighbor
With your crooked heart.

(W.H. Auden)