Thursday, August 28, 2008

Let's make some stuff!

One of the things I really like about being a physiologist is that you get to make stuff, maybe something for your rig. So, you head down to the machine shop, and do your best impersonation of these guys:
Figure 1: Devastatingly handsome hosts of PBS' Router Workshop. Yes, that's correct, an entire show on the beauty you too can create with just a router and some weird ass bits. (Thanks to Isis, whose inclusion of figures I have totally ripped off - what's that saying about flattery?)

So, after agonizing over figures for what feels like countless hours, I was more than happy to help someone in the lab make a little extender thingy*, as a place to attach "sewer pipes*" for changing external solutions while patching. I don my trusty safety glasses (I love science and all, but I ain't losing a friggin eye for it), fire up the heavy artillery, and get covered in plexiglass dust! Good times indeed. The best part is, the result actually is better than my previous designs for extender thingies, and when compared to what someone else in the lab tried to deliver, it looks downright purty.

Figure 2: Nat's extender stands triumphant above a hideously maimed chunk of aluminum. Not that we're keeping score or anything.

Now, let's be clear here, I may be an anal retentive freak when it comes to figures and my recordings, but I am an utter mess when it comes to machining. I subscribe to the measure 6 times, cut 4, and still have the thing look like crap when you're done. All I care is that I make something that works, lasts long enough that I'm not continuously rebuilding it, and do it in a short amount of time. Remember, we're here to do physiology, not learn to be an expert machinist. Likewise with writing code and the like. Sure, it's gotta work and be maintainable, but it's a tool. Use it.).

* - Yes, we like to get technical here at junctionpotential.

Wednesday, August 27, 2008

I love making figures! I hate making figures!

I am deep in figure making and paper writing at the moment, which is why blogging, and the science book list, are languishing. But figure making is obviously is a good thing, and a much better place to be than, say, having no data to make figures. Still though, it's a difficult process for me, probably because I'm an anal retentive freak about figures, but also it's a challenging intellectual and creative act.

Figure 1: Nat's inspiration for figure making. (damn Phil Hartman was one funny dude)."This one's a little bigger than the rest, so we'll just discard that one. [pulls out another piece] And I don't think this little wrinkly one belongs in here. [pulls out another] And this ... well, I just don't like the look of that one at all. Alright, as a matter of fact, why don't we just start over and throw this out? [places bowl on counter]"

Good things about making figures:

As said above, it means you have data.

After 11 years of using Igor for data analysis and figure presentation, there are very few annoying questions like, "I want these symbols to stand off the x-axis, how do I do it?" Or, "why is there a limit in the number of columns I can have?" And since all my initial analysis there as well, there's no added importing data, etc.

It's rewarding to make something. Figure making is something where you can really bring out your creativity and where you can distinguish yourself. There's just something satisfying about seeing that figure, which distills the essence of your experiments, come together.

Bad things about making figures:

It hurts. Literally. Maybe my computer/desk set up isn't a paragon of ergonomic-osity, but it isn't so bad. Still, gimme a few days of dragging labels around to get them where I want them (as I said, anal retentive, see Fig. 1) brings out the repetitive stress injury like kegs of Busch bring out the new freshmen (who by the way, are descending upon Boston like locusts. What hell, I thought it wasn't much of a college town?).

It hurts. Like in the brain. The process of defining exactly what you want to convey in every figure panel, and then realizing that on paper is hard. For me it's a relentlessly iterative process, starting out with an idea in my mind's eye, which then undergoes radical alterations (Fig.1). Sure, this is what it's all about, but that doesn't make it easy. Ask an artist. You think their process is easy?

Sometimes it's hard to find all the appropriate expts for a given point you want to make. This is just partly my own organization problem, but sometimes I really wish you could easily add tags to your data files, and then use those for searching. But, prior to the arrival of offspring, this wasn't as much of an issue, since it fit pretty well up in my noggin, but a good couple of years of crap sleep has wrecked my memory. So now I need to keep much more explicit records for this. Which I'm getting much better at, but unfortunately doesn't apply retroactively.

Sometimes you realize you wish you had done certain experiments a little differently. Not so much that what you're thinking was wrong, but sometimes things like exact timing of solutions or voltage steps could be a little different, or some cells were recorded a little differently than others. This just makes talking about the figure painful. (Again, see Fig. 1).

The toner! The paper! I think I've printed 20 versions of this current figure I'm working on, and it's not even done. Well, what's a rich lab good for if not for profligate supply usage?

Ok, time to get back to the figures! I am interested to hear about others' figure making thoughts and feelings.

Monday, August 25, 2008

And we're back!

It was a great and truly relaxing vacation, but it had to end. That's ok though, cause I was getting antsy, needing my experiment fix.

So what did we do? Get up late, go to the beach every day, eat fried seafood and ice cream, and read.

I reread a bunch of Hille's book, the first part of Hume's Enquiry concerning human understanding, some Comte. Man I'm a geek!

I had a couple other ideas for the book list (I wrote em down somewheres here), and will add them before getting ready to propagate it!

Saturday, August 16, 2008

Vacation's all I ever wanted, vacation trying to get away

We're off to the Cape for a week, where we go to the beach every day so the boy can get crazy in the sand and water! And hopefully I'll get a lot of those in mentis experiments experiments completed.

But when I get back we can finish up the science book list and send it out! I updated the original post so check out the additions.

Friday, August 15, 2008

Our Igor, which art in RAM,
Hallowed be thy waves,
thy function compiled,
thy procedures be called,
In silico as it is in heaven.
Give us this day our daily our cell that so totally supports our hypothesis (and is figure quality to boot).
And forgive us our series resistance,
As we forgive them who couldn't tell a reversal potential from a junction potential,
And lead us not into Origin,
But deliver us from Excel.

Tuesday, August 12, 2008

The Rule Of Three

Does anyone else think there is a place for The Rule of Three in science? As in, for any of the main points of your work, give the reader (or listener) three items that support it. If you do that, then most likely the reader will buy into your line of reasoning. It's especially good if these points cover the most obvious and common objections.

After the first one, the reader thinks, "Hmm, ok, that's plausible."

After the second one, the reader thinks, "Yeah, they're probably onto something here."

And if the writer throws in one more, the reader thinks, "Alright, alright! I hear you! Enough already."

Give more than three, and you're risking pissing off the reader. Give less than that, and you're risking leaving some convinceable people unconvinced. (At this stage there's no need worrying overly much about those close-minded folks who will never change their minds).

[It's somewhat interesting to think about why adding more points, any single of which alone are not convincing, ends up makes the overall argument more persuasive. But I'll leave that for the epistemologists to worry about. Suffice it to say, most scientists are comfortable with terms like, "preponderance of the evidence" and "reasonable doubt" as standards for deciding when a certain thing is "known."]

*sigh* This is all brought on by revisiting some TRP channel literature, which is making me curse up and down, doing my best to channel my inner PhysioProf (though really, who am I kidding). Seriously people, if you're gonna string a bunch of experiments together, could you maybe, I dunno, try to convince me of one before you move onto the next? This is especially true if you're using a bunch of drugs of undefined specificity, which we all know are dirtier than my kid's diaper after a losing bout with the latest day-care GI bug.

Thursday, August 7, 2008

The Science Book Meme - let's start it! - UPDATED AGAIN!

After completing the "100 Books" meme recently, a number of folks (this blogger included) seemed to be annoyed at the dearth of science related books on the list. Well, rather than whining about it, let's start our own frickin meme. Take that you literary, fiction types!

Let's make a list of the "N* Science Books", populated with the most important/interesting/well known/seminal books in science, tag a bunch of people, and watch it spread through the blogosphere faster than an action potential travels down the squid giant axon.

Fire up some suggestions in the comments, discuss what belongs where, and let's see where this takes us. My thought was to leave off textbooks, and technical manuals, but if there's a consensus otherwise, then the mob rules!

Here's my initial list: (Updated to reflect additions by the excellent commenters - at least some people are reading!)

Origin of Species, Charles Darwin
The Structure of Scientific Revolutions, Thomas Kuhn
The Double Helix, James Watson
Rosalind Franklin and DNA - Anne Sayres
Nerve, Muscle and Synapse, Bernard Katz
Lives of a Cell, Lewis Thomas
Art of the Soluble, Peter Medawar (something else here perhaps?)
What is Life, Erwin Schrodinger
Random Walks in Biology, Howard Berg
Elbow Room - Dan Dennett
Godel, Escher, Bach - Douglas Hofstadter
Apprentice to Genius - Robert Kanigel
In search of memory - Eric Kandel
Neurobiology of Nociceptors - edited by Carlos Belmonte and Fernando Cervero
The Sexual Brain - Simon Levay
Advice for Young Investigators - Santiago Ramon y Cajal
King Solomon's Ring - Lorenz and Huxley
The Man Who Mistook His Wife for a Hat - Oliver Sacks
The Elegant Universe - Brian Greene
The Mismeasure of Man - Stephen Jay Gould
The Blind Watchmaker - Richard Dawkins
Genius - James Gleick
Surely You're Joking, Mr Feynman! by Richard Feynman
Brief History of Time, Stephen Hawking
Woman - Natalie Angier
Karl Popper - The Logic of Scientific Discovery
T-rex and the Crater of Doom - Walter Alvarez
An essay on the principle of population - Thomas Malthus
Astonishing Hypothesis - F. Crick
Witchdoctors and Psychiatrists - E. Fuller Torrey
The Eighth Day of Creation -
Horace Freeland Judson
Intuition- Allegra Goodman
The Billion-Dollar Molecule - Barry Werth
The Discoverers -
Daniel J. Boorstin
Natural Obsessions-
Natalie Angier and Lewis Thomas
The Genome War - James Shreeve
General Chemistry - Linus Pauling

Ok, that's what comes out of my brain without much prodding. What do other people have? Hopefully we'll get some coverage from non-neuro geeks.

*- I figure this will run its natural course like any good brainstorming session. Whatever number we get to, we get it. (Currently it's at 26; NO, 36! NO, 37!), but this list isn't set in stone; more can likely be added, and with sufficient agreement, removed if need be).