Thursday, July 29, 2010

Good olden tyme science (now with Squid Axon videos!)

Isis posted an awesome video of physiologist John Severinghaus discussing his work on altitude, while working on White Mountain Research Station. Very interesting, and from this neurogeek's perspective, a part of physiology that I know little about.

It got me thinking about the great old experiments in my own subfield of ion channels and electrical excitability. I'm a big fan of going back and actually, you know, reading the foundational literature in the field. That's just me, I don't expect everyone to love it, but I always wonder at how clearly those greats viewed things, and how much their work shapes the later development of the field (especially with regards to what questions are considered important).

For electrophysiology, this leads to One Prep, One Prep to Rule Them All:


As most biologists likely learned at some point in school, the squid giant axon provided the system that Alan Hodgkin and Andrew Huxley used to analyze the basis of the action potential. Nowadays though, I'd gather there aren't many electrophysiologists who have actually seen the axon or it's beautiful action potential in real life. I know I haven't.

Luckily, we have our own kick ass old science videos. Back in the 1970s, J.B. Gilpin-Brown at the Marine Biological Laboratory in Plymouth, England, filmed a movie called "The Squid and its Giant Nerve Fiber". Now, the entire work has sadly been lost, but there are some parts which have been saved. These videos are available at the Bio 300 course site taught at Smith College, and they include J.Z. Young dissecting out the giant nerve (which he was the first to describe). If you're interested in this kind of stuff, I highly recommend you go check them out (Quicktime needed).

My favorite video is the one aboutvoltage clamping the squid axon. Here are some stills I captured from it:

Figure 1:The squid axon action potential. A thing of beauty, no doubt. Complete with hot oscilloscope action (yeah, that ain't digital!). Note the afterhyperpolarization.

Figure 2: Here, Alan Hodgkin, Nobel Laureate, prepares to ACTUALLY DO AN EXPERIMENT ZOMG!!! He's picking up the axon and getting ready to insert the electrode. I know, sorry, it's an old white d00de, wearing a vest and tie ferchrissakes. But I'll admit that I love his papers.

Figure 3: A family of voltage step currents, showing the early inward sodium current followed by the delayed outward potassium currents (responsible for the membrane depolarization and repolarization, respectively). IT'S EXACTLY LIKE THE DAMNED TEXTBOOKS! Hell, I think it might be the textbook figure. Note the slight deviation in the voltage clamp (pesky series resistance; now that's a post for another day), and the potassium tail currents.

Phew, ok, sorry to get all hot and bothered. Beautiful currents will do that to me. Now I need to get to my own electrophysiology. But these are awesome. Anybody got any more old science videos to share? I love this stuff.

Belatedly, and memely, yours

Earlier this month the "Who are you, what are you doing and why do you keep looking at me!!??!" meme came back with a vengeance worse than the West Nile virus fears in Eastern Massachusetts. I saw it on Drugmonkey, wherein I cringed at my old age.

Two years ago, Ed Yong at his Not Exactly Rocket Science blog (currently living here) posted this question to his readers, asking them why they come to the blog. From there it spread to various other science blogs.

Since my own return to blogging, I thought I'd ask my readers out there why they follow these ramblings, and what brings them here. What posts do you find most interesting. I'm especially interested in hearing from any lurkers out there. Besides, DM tagged people, and who am I to ignore that?

Wednesday, July 28, 2010

It starts early

The Patriarchy that is.

The other day my 4 1/2 year old son told his mother the following:

boy: "But you can't be a doctor, you're a girl, and girls aren't doctors. They're nurses. Only boys can be doctors."

Which is of course odd, because not only is his mother very much a doctor, but so are the vast majority of mothers of the kids we hang out with (as well as a large majority of the mothers at his daycare). And he had no problem saying that Daddy is a scientist, and "does science."

It's also a big odd, because when my wife was admitted to the hospital before our second kid arrived, he referred to all the nurses and doctors as "doctors" - male or female. Even though he knew what a nurse was, as his aunt is one.

So what was it that turned the tide, and sent him to the DarkPatriarchy side?

A buncha stupid flashcards at school that show a doctor as a man, and a nurse as a woman. WTF?!?

Of course his parents reacted in the way all good generally socially progressive types would: His mother gave the daycare folks a stern talking to, while his father beat him.

Case closed!

Seriously though, how much of this can we counteract in his little brain? We're just going to have to teach him to see it as well.

(Disclaimer - if you need a disclaimer to inform you which part of this post not to take literally, you really oughta move along elsewhere.)

Tuesday, July 27, 2010

juniorprof's #painresearchmatters campaign

In case any of you readers out there missed juniorprof's roaring back into the science blogosphere, I thought I'd take a moment to highlight his campaign to improve the awareness of pain and pain research, in all its facets, from the toll it takes on those who suffer from it, to current and new therapies, to new basic science. If you have a story to add to the discussion, from whatever perspective, head over to his blog to contribute. Or check out his Twitter feed if you're into that sorta thing.

From a neuroscience standpoint, I can attest to the fact that although pain is an incredibly interesting topic, it isn't up there front and center with the Big Questions of Neuroscience. Off the top of your head, how many Nobel prizes have been awarded for pain related research? I got nothing (OTOH, there's a number of ion channel and synapse related prizes I can name). During out intro to neuroscience course in grad school, I think we had one, count 'em ONE, guest lecture about pain. Try and guess how many we had about synapses, or the visual cortex? Nothing against those systems; I love them too, and some of my best friends are synaptic physiologists. It just serves to illuminate the priorities of the field.

Come to think of it, this is reflected in my own bias as well. See, during grad school I did research on nociceptors, those ornery little neurons that convey signals about injury to the central nervous system. And yet, I never did call myself a "pain researcher," nor do I know think back on that as "pain research." Why is that?

I'll admit that some of that it to prevent being labeled as "too applied" or "too disease oriented" in my research question. I liked to believe my research had broader applicability to questions of excitability and action potential electrogenesis, so I shied away from it. Now that I think about it, that personal bias is counterproductive when it extends throughout the community. I'd hazard a guess that you probably know the feeling, that applied research is somehow lesser, or done by "those clinical people (and we all know how good they are, knowwhatImeannudgenudge, aren't we great, high fives) leads to a situation like juniorprof tweeted yesterday:

"Pain #1 reason people seek medical attention but pain rsrch less than 1% of NIH budget"
(reference for that here)

That's just crazy. Crazy crazy crazy. It makes me regret how I characterized both my research and myself as a scientist.

So I'll say it loud, and say it proud, I was, and still am (for about ~35% of my time depending on which project I'm currently focusing on and don't even get me started about that last grad school paper but don't forget I had two kids so cut me some slack) a PAIN RESEARCHER!

I think in the near future I'll write up a few posts on nociceptor excitability and ion channels. Thanks for the inspiration juniorprof!

Friday, July 23, 2010

You know what else sucks?


But I'm guessing all you on Wordpress already know that.

Somehow the block quotes in the previous post are screwing up the text color. Any ideas?

Citation Classics -

Bill Hooker over at the LifeScientists feed at FriendFeed posted a link to a collection of “Citation Classic” articles, which were short reflections written by authors years after publishing a paper that were highly cited. Many of these are available for downloads as pdfs, and I find them endlessly fascinating. Sure, many of the highly cited papers are reviews, and reflections on “What I did this summer - Sat in my office and wrote a review that my secretary typed up” aren’t terribly interesting. But by and large, those about experimental papers are cool.

Sometimes these reflections really bring home how much the practice of science has changed over time. Bernhard Frankenhauser describes his paper with Alan Hodgkin on the effect of calcium on squid axon excitability (i.e., surface charge screening effects):

“The exciting [Ed. Wait, Bernie, you forgot to tell us whether that was an unintended pun or not!] and exhausting three-month period of experimental work was followed by two years of struggle with the analysis of the measurements and with the manuscript.” [EMPHASIS ADDED]

Not too much worrying about getting scooped I see. Seriously though, how the hell did this work? I always find that halfway through the analysis and initial drafts, I need to go back and do a few more experiments, either because the initial ones weren’t quite good enough (“crap, we really needed to wait 3 minutes after agonist removal to have full recovery, not the 2.5 we used”), or to follow up and extend the observations.

But they also show that somethings haven’t changed: And that means griping about Nature editors. As John Foreman puts it (writing about his paper with Mongar and Gomperts on calcium and secretion):

“Our experiments were written up and sent to Nature. The referees’ reports were both favourable and enthusiastic, but the editorial staff of Nature was not quite so keen. It took quite a lot of pushing, as I recall, to convince them to publish the paper. In the end, of course, the relented and now, with the hindsight of the Science Citation Index, I guess they are content that we fought for what we considered to be the right place to publish this manuscript.”

HAHAHAHA, take that you bastards! Are you happy with the 550 citations you got in the 14 years since we published what you thought was boring crap? How do you like your impact factor now, eh? (Foreman wrote the above in 1987; Web of Science presently reports 615 cites).

So go check em out, and lemme hear what your favorites are.
For the electrophysiology/excitability geeks out there, here’s a few worth your time::

-Hodgkin and Huxley on their 1952 paper presenting the model of action potential. I’ve cited this, have you?
-Eccles on “how my book that was cited on 9 pages of some recent other book was published right in time for me to get my Nobel”
-Toshio Narahashi on “how I brought a vial of TTX into the US and boy I’m glad there wasn’t a TSA back then”
-Denis Noble and Dick Tsien’s on cardiac pacemaker currents. (this one’s interesting because they themselves called the current a K+ current, though they were upfront in saying the reversal potential was actually off for a strongly K+ selective pore. As we now know, HCN channels are permeable to both K+ and Na+. See, sometimes it’s ok to report observations that you’re not quite sure what to do with. Somebody else will come up with an answer.

Thursday, July 22, 2010

Calcium imaging sucks...

...unless you’re interested in calcium. If you’re using it as a proxy for channel activation then it sucks.

There’s a tendency among those of us who study calcium permeable channels to use fluorescence imaging of Ca sensitive dyes as a way to assess channel activity. And sure, the degree of channel activation will determine the resulting fluorescence signal, and generally speaking more activation will lead to more signal. Plus it’s just easy to do: in a day you can try a huge range of manipulations, you’ll get hundreds of cells as a result (making those statistics sure seem impressively significant). Compare that with a good day of patch clamp where 10s of cells is a GREAT day. I get it. I’ve been tempted by that dark side as well.

Still, frankly, it sucks. There are so many uncontrolled and/or untested variables present in your typical Ca imaging run that if you’re making dose-response curves, or inhibition curves, or whatever, then really, you’re deluding yourself if you think you’re only looking at the channel. And don’t even get me started on those people who treat a given delta ratio as equivalent over the whole range of ratios. GRRR.

In that case, it’s time to suck it up and do the electrophysiology. Yeah, it’s hard, it’s slow, blah blah waa waa whatever. If you want to characterize a channel, do electrophysiology. If you want to see how that channel affects intracellular [Ca2+], do imaging. But then really, WTF are you doing overexpressing that channel in some poor cell line, sitting in the incubator, just minding it’s own business?

Wednesday, July 21, 2010

Did I really just do that?

I put a happy face emoticon in the comment line after stopping an acquisition run.


Of course, this was a cell that I left in the middle to go to CVS and pick up some stuff. It was still happy when I got back, holding current not more than 1 pA different. By that point though, I start to get the willies using any results. Too long whole-cell and weird stuff happens.

Come to think of it though, I bet if you trawled through my lab notebook, you'd find some "WTF" in there as well. Probably some much worse language to.

So, how many of you out there do the same?