Biocurious

/ a biophysics blog

University libraries, budgets, and open access

Posted 27 November 2008 by PhilipJ under &

I’ve been playing with numbers in my head based on the statistics from my home institution – the University of Toronto – relative to publications, the real cost of open access publishing, and the U of T library’s annual budget for journal subscriptions.

It turns out that U of T is listed as an institution on some 6470 publications per year (averaged during 2000-2004, data from Thomson Scientific), and as of 2005-2006, the U of T libraries (spread over a couple of campuses) have a periodicals budget of just over $10 million per year (see section 7, “LIBRARY ACQUISITIONS COMMITMENTS” in the 2005-2006 budget). For the rest of this article, let’s assume the American and Canadian dollars are roughly equal in value (which was the case until a couple of months ago).

At present, that $10 million a year largely goes to closed-access publishing houses (not just the Elseviers and Macmillans of the world, but also the much-loved not-for-profit societies which publish journals as well). This gives the university students, faculty, and staff access to the literature both on campus and off, via the internet. While this in principle works well, journal subscription costs have been skyrocketing, and university library budgets have not been able to keep up (and I surmise things will only get worse with the hit to university endowments recently). The breadth of subscriptions will surely fall in the coming years.

What, then, if the university decided to embrace the open access movement entirely? This is obviously a pie-in-the-sky idea, but bear with me, as the result is interesting.

Subscription costs would obviously be nil for an open access journal: we are all free to access the content of an open access journal via the internet, with no restrictions on who can read the content. In contrast, the author would pay to publish the article. This is perhaps the biggest resistance from scientists (and I’m sure the situation would be similar in the arts, or law, or what have you) to the open access movement, many feeling they don’t have enough funding for students or experimental equipment as is, and couldn’t possibly afford to pay to publish as well. I can appreciate this argument, though some progress is being made as you can specifically request funding to cover open access publication charges from some of the granting agencies.

(Also, let’s be honest, the current situation of paying for page charges and to have colour figures means the author is already paying to publish, and sometimes non-trivial amounts.)

The funding supplied to the library for journal subscriptions could instead go towards paying for the publishing costs in open access journals. Using the PLoS journals as our benchmark, premium quality publications would cost around $2500/article (the current fee to publish in PLoS Biology or PLoS Medicine), while the bread-and-butter publication costs are maybe closer to those of PLoS ONE — $1300/article.

Let us imagine that 10% of the publications coming out of U of T are of the premium variety, while 90% are your more run of the mill papers, and that there are open access journals in which to publish them. Using the current costs from the Public Library of Science, 650 premium papers would run around $1.6 million dollars, while the 5850 “bread-and-butter” papers would cost an additional $7.6 million each year. This is already less than the 2005-2006 periodicals budget of slightly over $10 million!

Let’s further assume that the economies of scale would kick in if universities around the world decided to embrace this philosophy. This should lead to an overall lowering of the publication costs, all the while bringing access to academic literature to everyone with an internet connection. It is also easy to imagine the costs being even lower, as the collaborative nature of academic work means many papers now have authors from multiple institutions, all of whom could share in the cost of publishing. (Determining the rules for who-pays-what would be tricky, but should be doable.)

There are probably some key issues I’m missing here (the most obvious one which I’ve even mentioned is that we need open access journals to publish in!), and my idea is prefaced on the assumption that universities are the significant driving force in the academic literature game, but I think the take-home message is reasonably clear, at least using the University of Toronto numbers: we could already afford going entirely open access.

I certainly wouldn’t feel bad if Elsevier and their ilk went out of business given the exorbitant increase in subscription costs and the non-obvious reasoning why, and I’m sure the societies could come to embrace the open access movement, which would bring the majority of high quality journals into the fold.

So, what’s the hold up?

Update — Peter Suber’s commentary (showing my conservative estimate of how much it would cost is potentially much higher than would be the case) is well worth a read.

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PZ Myers: "Science is not Important"

Posted 22 November 2008 by Andre under &

This Wednesday evening I went to see PZ Myers talk about science blogging at a the Kelly Writers House here on campus. It was a nice place for a talk and PZ was entertaining and interesting. But he did say one thing that I’ve heard from quite a few scientists that always bothers me.

He was discussing how professionally written press releases are often a source of frustration for scientists because they emphasize the wrong points or overreach when discussing the significance. That’s often true, and at some point hearing that every bit of incremental progress could help cure cancer is numbing. His advice to press release writers is to replace “important” with “beautiful” because that’s usually the real story. He doesn’t study zebrafish development because it’s important but because it’s beautiful. That’s a big part of the day-to-day motivation for me and I think for most scientists, but it’s only part of the story. Science is important, and all those seemingly incremental results are important the same way each brick in a building is important.

How far down the road of “science shares more with art than engineering” do you want to go? Our society supports the arts because they provide beauty and insight and enrich our lives. We support science because it is inspiring and lets us reach beyond ourselves to see and understand things that didn’t seem possible and because it provides tangible advances that improve the quality of our lives. Those benefits are worth a lot to people. The National Endowment for the Arts has a budget of around $150 million. The National Science Foundation has a budget of around $6000 million. The response to Sarah Palin’s imbecilic attack on fruit fly research would not have been half as effective if it had been only that fruit flies make beautiful experiments possible.

I wouldn’t have the chance to do science for the sake of beauty if it wasn’t also important and scientists and press release writers shouldn’t be afraid of saying that.

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Micropipettes and the shakes

Posted 8 November 2008 by PhilipJ under

Dr./Mrs. Jekyll/Hyde has been teaching a new laboratory tech the tricks of the trade (or, as it turns out, some basic algebra), and in one of the posts mentioned something that we often don’t think about in science education but is critically important when you’re actually in a lab: having good hands.

This is important for a variety of reasons: pipetting solutions, filling the wells of a gel before running electrophoresis experiments, or even simpler things like not stabbing yourself with a needle or not dropping expensive samples. The shakes can be the difference between having to do experiments only once and wasting an entire week repeating them, with questionable results each time.

Not drinking coffee is, for me at least, not an option. Thankfully, my Ph.D. work involves very little that explicitly requires extremely good hands (mind you, pipetting solutions in a dark room under dim red lights* is annoying no matter how good your hands are…). I was not so lucky for my Master’s work, where, you may recall, I dealt with micropipettes.

Making the micropipettes was annoying for consistency reasons, but actually getting a micropipette into a flow chamber was the real fun part. Our flow chambers looked like this:

flow chamber

Brown tubing, having an outer diameter of ~160 microns, and an inner diameter about half that, was squished between melted Nescofilm between two No.1 coverslips, and was the means of inserting micropipettes into the active flow area.

pipette tipThe micropipettes, shown on the right, were tapered to ~1 micron at the very tip (the polystyrene bead held by suction at the tip is 2 microns in diameter), and for practical reasons were usually 3-5 cm long. They were connected to a length of thin tubing so as to allow for easy connection to a syringe, and the whole contraption was mounted on an aluminum clamp, with a separate clamp specifically to hold the micropipette in place.

As I mentioned above, I drink a lot of coffee, and while I don’t have a serious case of the shakes, I don’t have a particularly steady hand. Despite this, I would insert the micropipettes into the brown tubing by hand. We had a 20x optical microscope with two-dimensional motion on the microscope stage. I would mount the flow chamber to the stage, centre everything such that it was all in focus, bring a micropipette tip into the field of view by hand, and, once also focussed, try to move the stage so that the pipette tip ended up in the brown tubing.

This would (obviously) often result in disaster, as any time the tip of the pipette would touch the brown tubing it would be ruined, no matter how incidental the contact. For a while I was keeping a log of successful tips to ruined ones in my lab book, and the ratio got so depressing I had to stop. By the end of my Master’s though, despite my regular multiple cups per day, I had developed a couple of tricks to raise
the success rate. The most useful of which was to introduce water into the system.

Flushing the flow chamber with water would produce a large (under the microscope, anyway) bead at the opening aperture of the brown tubing, which, after Kimwiping it away, would leave a slight meniscus of water right at the entrance. When the tip of a micropipette was nearing the entrance to the brown tubing, the pressure difference in the pipette tip would result in rapid suction of water from the meniscus into the pipette. With much practice, rapidly moving the stage once observing water in the pipette led to, near the end anyway, maybe as high as a 50% success rate in getting tips into chambers.

While my Ph.D. work has it’s own series of issues (this week’s: overlap two 200 femtosecond pulses focused into a ~100 micron diameter area. Spatially is simple, temporally, less so), I am very happy I don’t have to do anything like that anymore. I think I’ll have another espresso to celebrate!

* I’m working on the most-obviously-photoactive protein you can imagine. Take a guess which!

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Molecule of the Month: Mechanosensitive Channels

Posted 6 November 2008 by PhilipJ under

Mechanosensitive Channels

We are remarkably resistant to changes in our surrounding environment. Our bulky bodies allow us to weather extremes of heat and cold, and our skin protects us if we go for a swim in fresh water or salty water. If things get too uncomfortable, we can always get up and walk away, finding a warmer or cooler or drier place. Bacteria don’t have as many options. They are tiny and they are immersed in water, so changes in the environment can pose life-threatening challenges. For instance, if it rains they may be suddenly surrounded by fresh water. This is dangerous because the water seeps into the cell through osmosis and increases the pressure inside. At other times, the bacterium may be shifted suddenly to salty conditions, which pulls water out and dehydrates the cell. Bacteria have methods for resisting these changes, so they can keep a steady, comfortable osmotic pressure inside.

Bacteria control their internal pressure by changing the concentration of molecules inside. If they are placed in salty conditions, they resist dehydration by transporting ions into the cell and by synthesizing more small molecules. However, if they are placed in pure water, they must reduce their inner concentration of ions and small molecules. In that case, they use mechanosensitive channels that open and allow small molecules to leak out. For instance, in laboratory tests, cells that are placed in fresh water rapidly lose more than 95% of small molecules like amino acids, sugars, and potassium ions. However, they keep their proteins or ribosomes safely inside, so they recover quickly and can start up protein synthesis minutes after the conditions return to normal.

Find out more here at the PDB.

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Molecule of the Month: Poly(A) Polymerase

Posted 9 October 2008 by PhilipJ under

poly(a) polymerase

Most of the RNA found in our cells is built using our DNA genome as a template. In special cases, however, our cells also build RNA strands without a template. For instance, the end of (almost) every messenger RNA strand is composed of a long string of repeated adenosine nucleotides. These long poly(A) tails are not encoded in the genome. Instead, they are added after RNA polymerase finishes its normal process of transcription. After RNA polymerase releases the RNA strand, other enzymes add the finishing touches, editing out introns, adding a cap to the front end, and building the long poly(A) tail at the other end.

A complex of over a dozen enzymes oversees the creation of a poly(A) tail on messenger RNA molecules. Several special sequences at the end of the RNA recruit this complex to the proper place. Then the RNA strand is cleaved, and about 250 adenosine nucleotides are added to the new end. The enzyme poly(A) polymerase, PDB entry 1fa0 from yeast, shown here, is responsible for the creation of the poly(A) tail. With the help of two magnesium ions, it binds to the messenger RNA and adds adenosine nucleotides one at a time to the end of the strand.

More from the PDB here.

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Cosmic Variance Donors Choose Challenge

Posted 2 October 2008 by Andre under

It’s been a while, and what better way to end my blog leave than by promoting a good cause? There’s an organization called Donors Choose that connects potential philanthropists like you directly with classrooms in need of resources. One of the nice things about it is that you get to contribute directly to a particular project that you find worthwhile. Your money will go exactly where you want it to go. Last year I donated a small amount to a project and in return I got a collection of letters from the students that benefited. It was incredibly touching to get such heartfelt letters, especially when considering that the request had been for something quite simple: an overhead projector.

Of course, this also represents a great opportunity for some friendly competition. You see, the people at ScienceBlogs have done this for a couple of years, but now Sean at Cosmic Variance has initiated his own challenge and all he wants to do is “crush the folks at ScienceBlogs.” Non-ScienceBorg science bloggers, unite!

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