Wednesday, April 29, 2009


There's a couple of interesting editorials out in from the Rockefeller University Press, which publishes the fine journals Journal of Cell Biology, Journal of Experimental Medicine, and one of my personal favs, Journal of General Physiology.

In the first, the Press's Executive Editor, Mike Rossner, discusses the practice of bundling large numbers of journals by the mega scientific publishers, and the effects on university libraries. Unsurprisingly, the current economic climate is affecting not just newspapers (do you hear that Boston Globe? the sound of inevitability), but will have big impacts on science publishing. And that doesn't even take into account moves towards Open Access. Check it out here.

Here's one very interesting tidbit from the editorial:
"The Rockefeller University library subscribes to bundles of online journals from several megapublishers. For one of the bundles, the top 10% of journals garner over 85% of the hits to the bundle from users at the University. Over 40% of the journals in the bundle had no hits at all from the University in 2008!"
In the second editorial, from the May issue of JGP, Editor Edward Pugh takes on one of my personal hobby horses: Supplementary Data. Now in principle there's nothing wrong with Supplementary data; it's just currently there seem to be few standards about how they should be dealt with, both in review and archiving. Pugh clearly sets out at least JGP's position on them:
"Several pressures now call for a review of policy on Supplemental Material. One pressure comes from the growing use of such material by other journals as an omnibus substitute for publishing scientific material. Increasingly, methods, theory, and even primary results are offloaded to supplements. As a community, we need to question such practices, asking whether they are dictated by the goals of science or by financial expediency, and inquire as to the short- and long-term consequences of such practices for science."
So go check that out too. Oh, and while you're there, check out a modest little paper by Blair, Kaczmarek and Clapham. All 14 figures of it that is!

Friday, April 24, 2009

Poll crashing vanguard for the science!

Ok, we all know internet polls are far from scientific, but if nothing else, they give an inkling of the organization behind the alternative positions.

In this case, there's a poll at the LA Times blogs (here), stemming from a recent pro-research rally helpd at UC in support of animal research. The results have tilted towards the anti research poll option, so for any of those folks out there who support the responsible use of animals in research, and realize that there can be little biomedical science without it, go and vote. And tell your labmates, friends, parents and grandparents to do the same.

And if you're interested in the things that impede meaningful debate about animal research, go check out Dr. Free-Ride's recent series on the topic!

Tuesday, April 14, 2009

Phew, so glad that is over!

I know there are many of you out there, sitting around, cooling your heels, and waiting with bated breath to learn how to actually measure a junction potential. And that post is coming. It's just not this post.

This post is the final end of a big sigh that wraps up last week's Week of Not Very Much Fun.

-First, I spent the weekend before last worrying about whether I had left my bag (complete with laptop) inside our daycare center or outside in the parking garage. The first being probably ok, the second not so much. It's amazing the complete and utter lack of recollection 5 months without >4 hours of continuous sleep will do to a brain. Luckily, the bag was saved by one of the day care folks. So I didn't loose my 4 year old laptop with its broken hinge, on which I'm writing this very post to you good readers.

-Second, I was all ready to spend last week working on a data presentation for the lab on Thursday (which is fairly involved, given the size of the lab and long stretches of time between turns), as well as a 25 minute talk for the Neurobiology Dept. on Friday. But, fate intervened, as we got our paper finally accepted (good!!), but the editors asked us to turn the final changes around in 2 days (ok, doable, but starting to cut things close).

-The final straw was the girl coming down with an ear infection. She needed a couple days off daycare, which my wife and I split. She improved so quickly after the ped visit, and thank FSM for antibiotics. That basically killed the possibility of the lab data club, but I was able to get the final manuscript changes done and the talk prepared. Of course, with even less sleep than usual. I think this led to one assessment of my talk, which was "Clear, but needed more enthusiasm." Fair enough, but we're almost at the breaking point here people.


No, not those guys on TV, though they do kick ass.

What I'm referring to are some myths we live by in the lab. One of cherished one among some people is that competition inside the lab improves productivity. That's complete bullcrap. Sure, there are lots of PIs whose management styles use it, but it's simply wrong. Apparently Candid Engineer's PI feels this way. Which sucks, even if it is all too common.

Unfortunately, what these jerky PIs ignore is the actual data that suggests that competition within groups hurts overall productivity. Teresa Amabile is a Harvard business school prof who has tracked the daily work of people in high tech, chemical, and consumer products industries, and the results run completely counter to many of the preconceived notions we have about creativity. An article in Fast Company discusses the 6 Myths of Creativity. All of them are good, but here's the money quote for this discussion:

5. Competition Beats Collaboration

There's a widespread belief, particularly in the finance and high-tech industries, that internal competition fosters innovation. In our surveys, we found that creativity takes a hit when people in a work group compete instead of collaborate. The most creative teams are those that have the confidence to share and debate ideas. But when people compete for recognition, they stop sharing information. And that's destructive because nobody in an organization has all of the information required to put all the pieces of the puzzle together.

I wonder how well this observation scales beyond individual lab groups to science as Science. How much competition is good, and when does it start to be detrimental? Certainly the last sentence here can be applied to Science.

Next, Bob Sutton is a Stanford B-school professor, who wrote a book called "The No Asshole Rule" (how great is that? Plus he has a kickass blog, which has been on the Googly Reader for some time). His recent post highlights another group's paper
...using quantitative analysis to uncover patterns across large numbers of studies -- in this case, 72 studies of nearly 5000 groups. The overall findings aren't a surprise, that groups that engage in more information sharing enjoy better performance, cohesion, knowledge integration, and satisfaction with decisions made
Now sure, these aren't academic lab groups, but as all the crankass PIs out there seems to insist on saying, academic science is the real world. So for any of you PI types who buy into this line of fallacious thinking, just stop. You're a scientist, go with the data.

And if not, then do us all a favor and wear a goddamn button that says, "I'm the Michael Vick of pitting my trainees against one another." Then we'll all be fairly forewarned.

Wednesday, April 1, 2009

What is a junction potential?

It's clear to me that a number of visitors to this humble blog arrive each day via a Googly search for the term "junction potential." I can only imagine that some must be fellow electrophysiologists, perhaps in their formative larval stages, searching for more information about this important topic. So, as a service to these folks, I thought a post or two about junction potentials, would be in order. First, what is a liquid junction potential? Then, How do you measure and correct for them?

So, what is a liquid junction potential? Sure, maybe you could look in some of the Electrophysiology Bibles. Or maybe you could even hit up an electrochemistry textbook. But it's 2009, and you've got two things on your side: Google, and me. So forget that, and allow me to regale you with the story of the liquid junction potential:

Long ago, in a galaxy far far away, there was a Gedanken experiment...
Figure 1: Set up of the Gedanken. No, it ain't to scale, though aspartate is bigger than potassium. Not shown is the impermeable wall separating the two solutions. Hey, it's my Gedanken thank you very much.

And in this Gedanken experiment there was a pipette filled with your typical pseudo-intracellular solution: You know the drill, high potassium (light blue), low calcium, and an anion species that's usually not chloride. This anion could be something like methanesulfonate, gluconate, or my own personal favorite, aspartate. The main thing to note is that all of these are bigger than chloride, and bigger than potassium. Thus, they have a lower mobility, meaning they don't diffuse as quickly as the accompanying cation.

Now, what happens when we stick this pipette into a bath solution that has your typical extracellular saline, made to mimic extracellular fluid (i.e., mostly sodium chloride)? Well, the chemical gradients favor the pipette constituents diffusing into the bath, and the bath constituents diffusing into the pipette. But remember, the aspartate is big, so it doesn't diffuse as quickly as any of the other ionic species. That slower diffusion of the anion leaves a net negative charge in the pipette. This charge separation across the junction between two solutions is THE LIQUID JUNCTION POTENTIAL!!!11!!!1!

Figure 2*: The Gedaken imposed barrier is removed, and ions are diffusing down their electrochemical gradients. The bigger, slower aspartate can't keep up relative to the smaller, faster potassium, sodium and chlorides. They get left behind in the pipette, generating an excess of negative charge.

Note that a liquid junction potential would also occur if the bath solution has cations and anions with significantly different mobilities. It just turns out that sodium and chloride have pretty similar mobilities, so that their contribution to the liquid junction potential is much smaller. But if you have N-methyl-d-glucamine (NMDG) as the main cation in your pipette solution, you'll have an excess of positive charge in the pipette solution, and a corresponding slightly positive junction potential.

Next up, how to measure the liquid junction potential.


*-Note that these figures were created using Inkscape, a very cool and usable opensource vector
graphics drawing program (a la Illustrator). Check it out, download it, play around with it!