Tuesday, December 30, 2008

Life seems to be approaching a new steady-state of normalcy. I suppose adding a new member to the family, especially under difficult circumstances, will do that to you. But as with many stressful, tiring, and anxiety provoking events (grad school, post-doc, residency, arrival of the first child), these are times that show we have more inner wherewithal than we expected. Of course, that's not to say that there aren't a lot of ups and downs!

Let me just note that this experience of the second child is so different than that of the first. We're different as parents obviously, having so much more confidence. I'm not examining the baby every few seconds thinking, "OMG, is she breathing????" Also, this baby might be a little more chillun than the first, though of late she has certainly found her "voice". Then there's the consideration that we have another short person who needs attention, and is determined to retain his 6:30-7 AM wake up time. *rubs bleary eyes*

Still, although the amount of work is greater, it's kinda more of the same. In that way, it's so different than the complete sea change that occurred when we brought the first one home. Cause sheesh, we made some goofy rookie mistakes. So, if you're expecting, let me give you some advice. Set up your changing table early. Because no baby wants to be experience the touch of a cold leather sofa minutes after arriving home! And bring extra clothes to the first pediatrician appointment..and, aw, there's plenty more *blushes*

Other than all the work at home, and the work at lab, I'm trying to carve out a little time to blog. There are a whole host of things as post material that are on my mind.

Monday, December 22, 2008

Movie mania memes!

This is just too fun of a meme to pass up. I don't consider myself a huge movie fan, but let's see how this shakes out.

(x) Rocky Horror Picture Show
(x) Grease
(x) Pirates of the Caribbean
(x) Pirates of the Caribbean 2: Dead Man's Chest
( ) Boondock Saints
(x) Fight Club
( ) Starsky and Hutch
(x) Neverending Story
(x) Blazing Saddles
(x) Universal Soldier
( ) Lemony Snicket: A Series Of Unfortunate Events
( ) Along Came Polly
( ) Joe Dirt
(x) KING KONG [The 1976 Jeff Bridges, Jessica Lange version, not the original or Peter Jackson one]
Total so far: 9

( ) A Cinderella Story
(x) The Terminal [I hate Tom Hanks. Well, let me qualify that. I hate post "Big" Tom Hanks.]
( ) The Lizzie McGuire Movie
( ) Passport to Paris
(x) Dumb & Dumber
( ) Dumber & Dumberer
( ) Final Destination
( ) Final Destination 2
( ) Final Destination 3
(x) Halloween
( ) The Ring
( ) The Ring 2
( ) Surviving -MAS
( ) Flubber (orignal only)
Total so far: 12

( ) Harold & Kumar Go To White Castle
( ) Practical Magic
( ) Chicago
( ) Ghost Ship
( ) From Hell
( ) Hellboy
( ) Secret Window
( ) I Am Sam
( ) The Whole Nine Yards
( ) The Whole Ten Yards
Total so far: 12

( ) The Day After Tomorrow
(x) Child's Play
( ) Seed of Chucky
( ) Bride of Chucky
(x) Ten Things I Hate About You
( ) Just Married
( ) Gothika
(x) Nightmare on Elm Street
(x) Sixteen Candles [One of the best in the John Hughes, suburban teenage white kid flicks]
(x) Remember the Titans
( ) Coach Carter
( ) The Grudge
( ) The Grudge 2
(x) The Mask
( ) Son Of The Mask
Total so far: 18

(x) Bad Boys
( ) Bad Boys 2
( ) Joy Ride
( ) Lucky Number Sleven
(x) Ocean's Eleven
(x) Ocean's Twelve
(x) Bourne Identity
(x) Bourne Supremacy
( ) Lone Star
( ) Bedazzled (original only)
(x) Predator I
(x) Predator II
( ) The Fog
( ) Ice Age
( ) Ice Age 2: The Meltdown
( ) Curious George
Total so far: 25

(x) Independence Day
(x) Cujo
( ) A Bronx Tale
( ) Darkness Falls
(x) Christine
(x) ET
( ) Children of the Corn
( ) My Bosses Daughter
(x) Maid in Manhattan
( ) War of the Worlds
( ) Rush Hour
( ) Rush Hour 2
Total so far: 30

( ) Best Bet
(x) How to Lose a Guy in 10 Days
( ) She's All That
( ) Calendar Girls
(x) Sideways
( ) Mars Attacks
( ) Event Horizon
( ) Ever After
(x) Wizard of Oz
(x) Forrest Gump
( ) Big Trouble in Little China
(x) The Terminator
(x) The Terminator 2
( ) The Terminator 3
Total so far: 36

( ) X-Men
( ) X2
( ) X-3
(x) Spider-Man
(x) Spider-Man 2
( ) Sky High
( ) Jeepers Creepers
( ) Jeepers Creepers 2
(x) Catch Me If You Can
(x) The Little Mermaid (With a happy ending? Are you kidding me?)
( ) Freaky Friday (original only)
( ) Reign of Fire
( ) The Skulls
( ) Cruel Intentions
( ) Cruel Intentions 2
( ) The Hot Chick
(x) Shrek
(x) Shrek 2
Total so far: 42

( ) Swimfan
( ) Miracle on 34th street
(x) Old School
( ) The Notebook
( ) K-Pax [Did anyone see this garbage?]
( ) Kippendorf's Tribe
( ) A Walk to Remember
( ) Ice Castles
( ) Boogeyman
(x) The 40-year-old-virgin
Total so far: 44

(x) Lord of the Rings Fellowship of the Ring
(x) Lord of the Rings The Two Towers
(x) Lord of the Rings Return Of the King
(x) Indiana Jones and the Raiders of the Lost Ark
(x) Indiana Jones and the Temple of Doom
(x) Indiana Jones and the Last Crusade
Total so far: 50

( ) Baseketball
( ) Hostel
( ) Waiting for Guffman
( ) House of 1000 Corpses
( ) Devils Rejects
(x) Elf
(x) Highlander
( ) Mothman Prophecies
( ) American History
( ) Three
Total so Far: 52

( ) The Jacket
( ) Kung Fu Hustle
( ) Shaolin Soccer
( ) Night Watch
(x) Monsters Inc.
(x) Titanic
(x) Monty Python and the Holy Grail
( ) Shaun Of the Dead
( ) Willard
Total so far: 55

( ) High Tension
( ) Club Dread
( ) Hulk
( ) Dawn of the Dead
( ) Hook
( ) Chronicle Of Narnia The Lion the Witch and the Wardrobe
( ) 28 days later
( ) Orgazmo
( ) Phantasm
( ) Waterworld
Total so far: 55

( ) Kill Bill vol 1 [It's on my list of things I'd like to see, but really, with two kids watching movies is kinda low on the priority list]
( ) Kill Bill vol 2
( ) Mortal Kombat
( ) Wolf Creek
( ) Kingdom of Heaven
( ) the Hills Have Eyes
( ) I Spit on Your Grave aka the Day of the Woman
( ) The Last House on the Left
(x) Re-Animator
(x) Army of Darkness
Total so far: 57

(x) Star Wars Ep. I The Phantom Menace [F.U. JarJar]
( ) Star Wars Ep. II Attack of the Clones
( ) Star Wars Ep. III Revenge of the Sith
(x) Star Wars Ep. IV A New Hope
(x) Star Wars Ep. V The Empire Strikes Back [I agree with Dante, this is the best]
(x) Star Wars Ep. VI Return of the Jedi
( ) Ewoks Caravan Of Courage
( ) Ewoks The Battle For Endor
Total so far: 61

(x) The Matrix
(x) The Matrix Reloaded
(x) The Matrix Revolutions
( ) Animatrix
( ) Evil Dead
(x) Evil Dead 2
( ) Team America: World Police
( ) Red Dragon
(x) Silence of the Lambs
( ) Hannibal
Total so far: 66

( ) Battle Royale
( ) Battle Royale 2
( ) Brazil
( ) Contact
( ) Cube
(x) Dr. Strangelove [Peter Sellers's greatness and James Earl Jones's first role.]
( ) Enlightenment Guaranteed
( ) Four Rooms
(x) Memento
( ) Pi
( ) Requiem for a Dream
(x) Pulp Fiction
(x) Reservoir Dogs
( ) Run Lola Run
( ) Russian Ark
( ) Serenity
( ) Sin City
( ) Snatch
( ) Spider
(x) The Sixth Sense
( ) The Village
( ) Waking Life
( ) Zatoichi
( ) Ikiru
( ) The Seven Samurai
( ) Brick
( ) Akira
Total so far: 71

Phew, that was actually pretty easy to do. It's also useful for fleshing out the NetFlix queue.

As for tagging folks, I tag anyone who's actually reading and actually wants to do this!

Saturday, November 29, 2008


Our baby was born today at 9:07 AM.

She's awesome. Doing great right now, breathing on her own, and just amazing her parents by how beautiful and wonderful she is.

Older brother has opted to reserve judgment, but the presents his little sister "brought" him are an excellent start. A right whale, an orca, and a crocodile for our budding naturalist.

Thursday, November 27, 2008

Happy Thanksgivings and Birthdays

Happy Thanksgiving to everyone out there. Hopefully you're getting to spend it with your loved ones.

As for me, I'll be meeting my new daughter today. After some prematurely broken membranes, it's time to bring this little girl into the world. She's early, at only 34 weeks, but in the grand scheme of things, that mean she'll very likely do great.

And the benefit is now we have an easy name choice. Cornucopia Blair anyone?

Tuesday, November 11, 2008

Discussion of blog policies

If anyone has comments, thoughts, discussion on the newly posted blog policies, please feel free to do so here.

Blog privacy policy


In the spirit of keeping the debate as open and honest as possible, I will give my commenters with significant leeway when making comments. Anonymous comments are ok, as is some level of profanity (let's keep it R-rated at most).

Spam is not ok. Offending comments will be deleted without warning.

There are some guidelines: If a person's attacks on another become unduly personal or threatening, then you will be warned. After sufficient warning if the behavior does not change, you will be banned.

Private emails:

Anything you send me via email I will keep private, unless you specifically agree otherwise.

Real life interactions:

If you know me in real life, I will not discuss any real life interactions here without your explicit prior consent. Of course, at times real life occurrences will suggest topics I want to explore more fully on this blog. In that case, my approach will be to broaden the scope of the discussion to remove any possibility of attributing specific things to specific people.

Personal data:

I will never intentionally divulge personal information to any other party. Period.

So, if you use a pseudonym, I will not seek out your real life identity. If I do come to learn your real life identity, I will never propagate it to others.

There is only one exception to this rule:

If I suspect a person of participating in illegal activities, then I will turn over any and all information to the proper legal authorities.

I have installed a site counter on this blog, but only for the purposes of seeing how many people come to visit, and to see what sites are linking here. I will not release any IP information.

Changes to this policy:

Seeing as no policy can foresee all eventualities, changes to this policy are possible. When such a case arises, I will discuss it openly to make people aware of the change. Note that the new policy will not be considered to apply retroactively.

Monday, November 10, 2008

Paper sections, hunh, what are they good for?

Phew, it took a helluva lotta time, but the twin attention grabbers of finishing/submitting our manuscript and then the U.S. election have finally subsided. And that's good, because I was going crazy, first obsessing over the details of the paper, and then the daily election polls.

Working on the paper made me realize that I am simply crazy about some things. Like, I'll argue six ways from Sunday against abbreviations, which any sane person would just let go of. And that there are some aspects of a paper that I will work for hours upon end to reach some personal Platonic ideal, whereas there are others that I couldn't care less about. That made me think more about the goals and importance each section in a paper (e.g. Abstract, Intro, etc.). Coincidentally, today Female Science Professor posted about Introductions.

It made me wonder how other people rank the importance of paper sections. For me, I would put it as follows:

  • Figures. It's the data stupid! Figures have to look good, and embody the points you want to make. I love it when a good figure whallops me with its significance. I'll admit that this is damn hard, and I can't be sure my own figures always meet this criterion. And, it's not simply the visual design of the figure; it's also a combination of experimental design, clarity of the data themselves, and the placement within the flow of the argument. This is perhaps obviously the part I spend the most time and effort on.
  • Abstract. I put this here, even though typically the amount of time and effort spent writing the abstract isn't terribly large. But it's so important IMO for two reasons: first, it's indexed in PubMed, so beyond the keywords, this is a place to put terms you think your target audience will be searching. Second, it's a place to put the one or two take home messages that you want the reader to come away with. Something short and sweet that will stay identified with your paper, perhaps a nice number indicating the size of your effect.
  • Results. Speaking as a reader, I may not always fully read this section, but if and when I do turn to it to evaluate one of your experimental findings, it'd better be super clear. Usually I want to know why. Why did you actually do this experiment? Sure, it might be obvious to the authors, but it's not always to the reader. So tell me. Throw me a frickin bone once in awhile. Then tell me what you think the results mean. Don't leave the interpretation to the methods.
  • Materials and Methods. Again, these are required to really evaluate the experimental findings. And by the gods, if you use a method but mention it solely by referencing one of your old papers, then you're likely to lose me. It's ok to reference yourself there, but at least give me a brief sentence to describe what you're doing.
  • Discussion. Try and tell me where your stuff fits in with the previous literature, and extend what you think it might mean. Suggest new experiments.
  • Introduction. Turns out I differ from FSP here. I like a nice short and sweet introduction, with just the barest essentials. But I wonder if this is a disciplinary dependent effect: there are so many reviews published in biosciences now, that it's easy to reference those as a stand in for any more detailed consideration in a single given paper. Is that the case in physics?
Actually, this list make perfect sense to me. I have always considered myself very datacentric person, in that data has the highest priority over theories, models, frameworks, whatnot. And, this list matches the order of sections when I read papers, and the importance I give to each. For example, if I'm pressed for time, I might not read the Intro or Discussion at all, or maybe just read the first sentence of each paragraph.

Still though, maybe other people have different lists, and if so, perhaps my papers are failing them? So let's hear it readers!

Friday, November 7, 2008

Excuse me , but what plasticware did you use for these experiments?

Checking my daily feeds in Reader this morning, I came across this little nugget in Science:

"Bioactive contaminants leach from disposable laboratory plasticware" by G. Reid McDonald and colleagues. From the abstract we get the money quote:
We demonstrate that these manufacturing agents leach from laboratory plasticware into a standard aqueous buffer, dimethyl sulfoxide, and methanol and can have profound effects on proteins and thus on results from bioassays of protein function.
Now, I honestly haven't gone and read the entire short paper, but it immediately brought to mind an example of something similar known for some time in the ion channel field:

"A light stabilizer (Tinuvin 770) that elutes from polypropylene plastic tubes is a potent L-type Ca(2+)-channel blocker" by Glossmann and colleagues. With wonderfull Teutonic thoroughness these folks found a component in polypropylene tubes that can leach out and block calcium channels. Having done my thesis with a guy who knows a little about calcium channels, this was a finding that was well known in the lab. Inevitably a new postdoc or student would order a case of polypropylene tubes that would end up donated to some molecular biologists posthaste. Polypropylene: good for centrifuging, autoclaving, and holding phenol solutions. Not so good for making your recording solutions. Instead we used polystyrene.

But I get the sense it isn't something appreciated that widely in the field. So, this is my attempt to serve you all, increasing awareness of the pernicious effects of these components on your recordings. A modest contribution, to be sure.

And if you're having trouble making people remember it in your labs, here's something to chant while marching through the hallways. It's already trite and overused, so why not?

"What do we want?"


"When do we want it?"


Thursday, October 30, 2008


I can haz been tagged? Yes, apparently. And since there are those among you who believe I never respond to memes, here goes the 6 random things that you never really cared to know about Nat. Gripping reading, truly. Hopefully you all don't have grants or papers to finish, because you might just be spending all day today reading and pondering these 6 little pieces. First, the rules:

1. Link to the person who tagged you. River Tam! but I think someone else did too! Not sure who though.

2. Post the rules on your blog.

3. Write six random things about yourself.

4. Tag six people at the end of your post and link to them.

5. Let each person know they’ve been tagged and leave a comment on their blog.

6. Let the tagger know when your entry is up.

So here goes!

1) I'm an obligate left sided person. Writing, eating, kicking a ball, hell even my left eye (R.I.P.) has higher acuity. The right side is only good for sleeping on, and mousing, or using a manipulator for electrophysiology. In fact, I find it hard to do the last two with my left hand. Years of training apparently can overcome the natural preference I suppose.

2) I have a family nickname, that nobody else calls me: Bugs. In fact, when my family refers to me by my name, it feels weird.

3) I started grad school at Stanford. During the whole interviewing process, I never thought that I'd end up there, but I was interested to see the department I applied to and also to see California. Yet when I visited, I could really get the sense that it was a special department, and came away convinced that it was the right place for me. And it was great. But the whole residency match process didn't want to cooperate, so when my soon to be wife matched to do her residency in Boston, I immediately started the process of trying to find a place in Boston to which I could come. We had already lived apart for nearly 2 years, and there was no way I wanted to let that continue. Actually in the end, it all worked out for the best. The only thing I miss about California is the weather.

4) When I was a little kid, whenever someone would ask me what I wanted to be when I grew up, I answered zoologist. And though I'm not really a zoologist, I am a biologist. So that's pretty close.

5) When I entered college, had no intention of majoring in biology. I thought I'd do something like economics or study languages or something. In fact, as a second year I took a series of non-major biology courses to fulfill the Core requirements. But it turned out I enjoyed them so much that I completely switched over, and never once looked back.

6) I had to retake a driver's test in 2005 after 11 years of not having a driver's license. I had (stupidly it turned out) let mine lapse after I went to college and my parents moved to England. During that time I was living in Chicago so it wasn't much of an issue as public transportation was fine. Of course it stunk in California, which it turns out it not made for pedestrians. But after a few years driving around Boston, I'm back to being the mediocre driver I always was!

Okay, I won't tag anyone, but if you're reading, feel free to join in and blame me!

Wednesday, October 15, 2008

5 Year Plans

On Monday we got a flat tire on one of our cars, which luckily happened in a parking lot while the boy was sleeping. I put the spare on without waking him up, but the tire place didn't have the exact tire in stock. So while waiting for it to arrive from their warehouse, yesterday I went to Starbuck's to help force myself to edit the paper with the final changes. There I sat, getting high on caffeine.

I took a quick break from red pen action, and sat down to start something that Odyssey over at Pondering Blather suggested some time ago, which was to make a 5 year plan. This has been frankly somewhat daunting, but really I found it pretty helpful. It has made me prioritize what I want to do, by thinking explicitly about my broader goals.

Sure, this is blatantly obvious, and I have done broadly similar things before, but never quite kept up on it. Nor had I made it so explicit, but with greater experience, I feel more comfortable filling out the details. Previously I was also hesitant to formulate a plan like this because I hate the idea of forcing scientific projects into definite time frames, for fear of adding some unconcious bias to the thought process. First though, a lot of what goes on this isn't necessarily about experiments, but other related goals. And it's all fungible anyway, since no one can predict how things will turn out. One reason, you know, why we do experiments.

Besides, there are ways to keep yourself honest and keep yourself open to seeing unexpected things in your data, while still being able to evaluate how much progress has been made and what tasks remain. In the past I think I was able to get away with just sorta going with the flow, but now that I have more family responsibilities and helluva lot less time, this approach no longer works.

I definitely recommend taking Odessey's advice in this case, so go fill out your own 5 year plan. Ok, now I'll get back to plotting world domination *ahem*, I mean advancing human knowledge, while at the same time fighting my inner organization-productivity nerd lust to implement it all in Liquid Planner.

Monday, October 6, 2008

Well this one goes to eleven - NOW NEW AND IMPROVED!

Seeing as I'm still deep in the paper production time, I've been thinking a lot about whether there is an optimal number of figures, and if so, what that number might be. Then Dr. Jekyll + Mrs. Hyde got the ball rolling in wondering why seven figures seems to be the norm. Also, we've probably all heard the anecdote that as the number of figures in a paper increases, the number of people who read it decrease.

I think that the number of figures per se is not terribly meaningful. Unless there are journal dependent requirements (think GlamourMagz), then a paper should have as many figures as are needed to tell the story. If that's 5 figures, good. If that's 15 figures, so be it.

But what's important to me is that each figure contains a coherent point*, conveys that point as succinctly as possible, while still reflecting the reality of the result.

What really gets all up in my grill is when people cram panels into a set number of figures, while blending the points together. That's one way to fit into an external figure limit, while increasing the amount of data presented. I think it fails because it dilutes the take home message from each figure. Also, it destroys any visuo-cognitive impact a figure has. When I look at a figure, I want to be able to see that message almost immediately, and preferably without referring to the legend. When I have to go through each of A-J panels, that ain't gonna happen.

So as a little test, I quickly went through 15 pdfs that were in my "PapersToSummarize" folder, and looked at the total number of figures, as well as the total number of panels in each figure. What struck me was that regardless of the total number of figures, the total number of panels was actually not that different. Now, this is a completely non-random sample, and reflects mostly electrophysiology related papers, with only a smattering of GlamourMagz, but let's look:

Table 1:

Ok, so the median number of figures was 7, perhaps reflecting DrJ+MrsH's impression that 7 is heaven. But also, it's pretty clear that regardless of total number of figures, right about 29-35 panels (overall avg was 32 panels). So those people who don't read a paper with too many figures (if they even exist) are deluding themselves in thinking that really means anything. See, here's a graph to prove it (and they say there's no science on science blogs. There's goddamn regression line in there. You call that no science?):

See, there ya go. Papers with more figures have more panels, but the slope is only ~2 panels/figure. Also, extrapolating to zero figures gives us the predicted absolute minimum panels for a zero figure paper, ~20. Anyway though, the correlation is crap here, with R-squared 0.21.

After doing this, I decided to check back on my papers from my thesis lab, since as those were two author papers, I did the lion's share in planning the figures and their layouts (I'll include the albatross around my neck, one manuscript that will, will see the light of day, even if I have to drown a couple hundred crewmen to publish it; it'll make for a kick ass song though):

11 figures, 27 panels, for 2.5 panel/fig.
11 figs, 27 panels, 2.5
10 figs, 29 panels, 2.9
And the number of panels ranged from 1-5. Pretty consistent.

So readers, tell me: What is your ideal number of figures?

*by point here i mean someting like a quantum of scientific result. Yeah, I just made it up, but maybe other people intuitively understand it.

Thursday, October 2, 2008

Horse, get over here! Cause I'm getting back on ya.

Ok, it's been way, way too long since I last posted, but now I'm back.

For those of you out there who've hardly been able to contain yourselves in my absence, here's a real quick update:

The SGP Calcium and Disease meeting was great. It was one of the first small meetings I had ever been to, and though I am definitely a fan of one of the biggest of the big scientific meetings, namely the SfN meeting, I can see the benefits of a small meeting. Especially as just randomly chatting and conversing with new people is not one of my strengths, the forced interactions in a small meeting really facilitate that (more discussion on optimal meeting size was had over at DM's tree). So I was able to meet and chat with people ranging from other postdocs, to new faculty, to some bigwigs. At this stage, that's important for me. I'll be making it a point to try to go to more of these small meetings.

Overall my talk went well, but it occurred to me that while it was a good post-doc talk, clearly it was not job talk level. Now that criterion can't be the sole guide for what I'm doing science wise, but it has to enter the equation at some point. That I've at times willfully ignored this fact in the past is clear, to my own detriment. But I'm working on altering my approach to a lot of things, while still working within my own set of values. I'm currently in the midst of a lot of self evaluation, which I'll likely post more about later.

The other reasons for light blogging include the work on our paper, which is nearly complete, as well as a combination of moving spaces within the lab (which everyone thought was crazy, to my utter amusement), and the wife's semi-annual hospital service time, which kept mommy at work longer than usual.

But all of those things are done or in the home stretch. So in the immortal words of Optimus Prime, "LET'S ROLL!"

Wednesday, September 3, 2008

At the SGP Calcium Signalling and Disease conference

As I referred to in my earlier post, I'll be heading to the Society of General Physiologists' conference on Calcium Signaling and Disease down in Woods Hole, starting tonight and running through Saturday. I'll be giving a short talk about the work I've been doing on TRPC5, and the meeting overall looks to be quite interesting. If any of you folks out there are attending the meeting, swing by and introduce yourself, and we'll celebrate with the appropriate libation, and talk some science!

Dear Brain Thingy in My Head

Dear neurons residing in my skull,

I realize I've been working you hard recently, to write up this paper and get ready for the SGP meeting. And you've responded in force, and we've been in the flow for what seems like forever, so much so that it's been nearly effortless. Finally it seems like we've got a solid toe-hold on this wonderful, amazing, and beautiful TRPC5 channel that has messed with us for so long (stupid, annoying, crap TRPC5 channel that it is - I know, it's a love-hate relationship). The secrets of the connections between intracellular and extracellular calcium and voltage won't remain hidden forever. But might I make one request?*

At 1:30 AM, I think it'd be best if we all were sleeping, and not thinking about shifting G-V curves. Cause you need your slow-wave sleep and we all end up feeling it when 5:30 rolls around. Just sayin.

*Still though, given the choice between this state and just about any alternative, I'll stick with dreaming of currents.

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).

Thursday, July 31, 2008

Genealogies, of the academic variety

Neurotree is a really cool website that aims to create and store the training relationships between neuroscientists. From it, I learned that on one side of my family, the Bean side, I am 6 steps from Charles Sherrington (below, from Wikimedia), the English physiologist who coined the term "nociceptor" (yup, I actually read his book The Integrative Action of the Nervous System, where he used that term. How come that wasn't on the damn book list meme, eh?). Sherrington shared the 1932 Nobel with Lord Adrian for their work on neuronal physiology, and trained three Nobelists as well: Eccles, Granit and Florey.

The other half of my tree, the Clapham side (hmm, I am Bean-Clapham spawn! Something about that makes me chuckle. In an uncomfortable way), brings me to a distinct group of physiologists, with Erwin Neher (gulp, another Laureate), up to Haldan Keffer Hartline (another Laureate) , who himself trained with Werner Heisenberg!. Wow, I didn't know that! For those of you keeping score at home, that's another Laureate, this time in Physics.

Great; now I can fail to live up to my academic parents' expectations, as well as my real life ones! :) Ok, my real parents always said they'd be happy with whatever I chose to do. Hopefully my academic parents agree!

The other cool thing about Neurotree is the cluster analysis of neuroscientists, which reflects the relatedness of the various subdisciplines within neuroscience. Having some way of tracking the changes in this through time would be pretty cool. I wonder if you had the information about how those clusters changed through time, would you be able to pinpoint the early papers and workers who led this shift? They are real pioneers of new clusters. Could you also tie that into people's published works? I wonder how those papers that signal the birth of a new cluster would rate on the citation analysis metrics some people are so worried about?

Now anyone can browse the tree, so go check it out. If you're a neuroscientist and haven't been added, then go make an account and fill in some details.

Wednesday, July 30, 2008

The Book Meme

Alrighty, let's not get all serious and stuff in here, with the science and whatnot. Let's do a meme! It's 2008, memes are the new worm, and juniorprof tagged me with the 100 book meme. Here's the list below, with completed reads in bold and partial reads in italics.

1 Pride and Prejudice - Jane Austen
2 The Lord of the Rings - JRR Tolkien
3 Jane Eyre - Charlotte Bronte
4 Harry Potter series - JK Rowling
5 To Kill a Mockingbird - Harper Lee
6 The Bible -
7 Wuthering Heights - Emily Bronte
8 Nineteen Eighty-Four - George Orwell
9 His Dark Materials - Philip Pullman
10 Great Expectations - Charles Dickens
11 Little Women - Louisa M Alcott
12 Tess of the D’Urbervilles - Thomas Hardy
13 Catch 22 - Joseph Heller
14 Complete Works of Shakespeare -
15 Rebecca - Daphne Du Maurier
16 The Hobbit - JRR Tolkien
17 Birdsong - Sebastian Faulks
18 Catcher in the Rye - JD Salinger
19 The Time Traveller’s Wife - Audrey Niffenegger
20 Middlemarch - George Eliot
21 Gone With The Wind - Margaret Mitchell
22 The Great Gatsby - F Scott Fitzgerald
23 Bleak House - Charles Dickens
24 War and Peace - Leo Tolstoy
25 The Hitch Hiker’s Guide to the Galaxy - Douglas Adams
26 Brideshead Revisited - Evelyn Waugh
27 Crime and Punishment - Fyodor Dostoyevsky
28 Grapes of Wrath - John Steinbeck
29 Alice in Wonderland - Lewis Carroll
30 The Wind in the Willows - Kenneth Grahame
31 Anna Karenina - Leo Tolstoy
32 David Copperfield - Charles Dickens
33 Chronicles of Narnia - CS Lewis
34 Emma - Jane Austen
35 Persuasion - Jane Austen
36 The Lion, The Witch and The Wardrobe - CS Lewis
37 The Kite Runner - Khaled Hosseini
38 Captain Corelli’s Mandolin - Louis De Bernieres - They made a book out of that crap Nick Cage movie? Who knew?
39 Memoirs of a Geisha - Arthur Golden
40 Winnie the Pooh - AA Milne
41 Animal Farm - George Orwell
42 The Da Vinci Code - Dan Brown
43 One Hundred Years of Solitude - Gabriel Garcia Marquez
44 A Prayer for Owen Meany - John Irving
45 The Woman in White - Wilkie Collins
46 Anne of Green Gables - LM Montgomery
47 Far From The Madding Crowd - Thomas Hardy
48 The Handmaid’s Tale - Margaret Atwood
49 Lord of the Flies - William Golding
50 Atonement - Ian McEwan
51 Life of Pi - Yann Martel. Well, the wife read it. Does that count?
52 Dune - Frank Herbert - Yeah, I read the trilogy. Multiple times. It's still sorta whack though.
53 Cold Comfort Farm - Stella Gibbons
54 Sense and Sensibility - Jane Austen - What is UP with the Jane Austen on this list?
55 A Suitable Boy - Vikram Seth
56 The Shadow of the Wind - Carlos Ruiz Zafon
57 A Tale Of Two Cities - Charles Dickens - And the Dickens. What the hell?
58 Brave New World - Aldous Huxley
59 The Curious Incident of the Dog in the Night-time - Mark Haddon
60 Love In The Time Of Cholera - Gabriel Garcia Marquez
61 Of Mice and Men - John Steinbeck
62 Lolita - Vladimir Nabokov
63 The Secret History - Donna Tartt
64 The Lovely Bones - Alice Sebold
65 Count of Monte Cristo - Alexandre Dumas
66 On The Road - Jack Kerouac
67 Jude the Obscure - Thomas Hardy
68 Bridget Jones’s Diary - Helen Fielding
69 Midnight’s Children - Salman Rushdie
70 Moby Dick - Herman Melville
71 Oliver Twist - Charles Dickens - Listen, whoever wrote this list, 19th century British novels are not my thing. You've proved it, ok. Are you happy now?
72 Dracula - Bram Stoker
73 The Secret Garden - Frances Hodgson Burnett
74 Notes From A Small Island - Bill Bryson
75 Ulysses - James Joyce - I'll take The Dubliners or Portrait…please.
76 The Bell Jar - Sylvia Plath
77 Swallows and Amazons - Arthur Ransome
78 Germinal - Emile Zola
79 Vanity Fair - William Makepeace Thackeray
80 Possession - AS Byatt
81 A Christmas Carol - Charles Dickens - I sat through Scrooged.
82 Cloud Atlas - David Mitchell
83 The Color Purple - Alice Walker
84 The Remains of the Day - Kazuo Ishiguro
85 Madame Bovary - Gustave Flaubert
86 A Fine Balance - Rohinton Mistry
87 Charlotte’s Web - EB White - I find "Elements of Style" to have a much better plotline
88 The Five People You Meet In Heaven - Mitch Albom
89 Adventures of Sherlock Holmes - Sir Arthur Conan Doyle
90 The Faraway Tree Collection
91 Heart of Darkness - Joseph Conrad
92 The Little Prince - Antoine De Saint-Exupery
93 The Wasp Factory - Iain Banks
94 Watership Down - Richard Adams - Somehow couldn't get into it. Watched the cartoon on TV with my dad though.
95 A Confederacy of Dunces - John Kennedy Toole
96 A Town Like Alice - Nevil Shute
97 The Three Musketeers - Alexandre Dumas
98 Hamlet - William Shakespeare
99 Charlie and the Chocolate Factory - Roald Dahl And James and the Giant Peach and The Twits and have read some of his non kid stuff.
100 Les Miserables - Victor Hugo

Wow, 13 completed reads, and 7 partial reads. 20 per cent! Still, this proves two things. Nat doesn't read fiction. Which I freely admit. I am much more of a non-fiction creature. Secondly, overwrought and needlessly wordy 19th century fiction sucks. What a waste of time!

There are actually very few books on this list I haven't read that I actually wish I had. I count only 1984 and One Hundred Years of Solitude on that list. If you got an argument as to why any of the others is a must read, with which I should edify myself, let me hear it.

I won't tag anyone, but if you're reading this, feel free to put your own up, in the comments here if you have nowhere else to put it.

Tuesday, July 15, 2008

David Linden starts as Editor in Chief of Journal of Neurophysiology

Linden is professor of neuroscience at Johns Hopkins, and an electrophysiologist to boot! He replaces Eve Marder (Brandeis) another electrophysiologist (we izz in ur science, recording ur currentz!), as the Editor-in-Chief.

In his opening editorial, he says some things I like to hear. Here's a snippet:

I've always greatly admired the scientific ethos of the Journal of Neurophysiology. Reading the Journal reminds me of what I like best about science. I like that it publishes full-length reports, which are still being cited 20 or 30 years on. I like that each paper can stand on its own, without 10 supplemental online figures...I like that the Journal of Neurophysiology has been guided solely by publishing excellent and interesting science, regardless of perceived "sexiness" or "impact factor."
Hoo-ray! I like the sentiments, that's easy to see. Turns out Linden is actually a pretty funny guy, who has a blog, The Accidental Blog, where I found a link to a podcast of neuroscientists, Neuroscientists Talk Shop. Sounds interesting, and it's getting loaded onto the MP3 player as we speak. Yay, more geek talk!

Course, I haven't published in J. Neurophys. But it's always been on my watch list.

Friday, July 11, 2008

Dreaming of heaven...of the electrophysiologist's type

I've often said that in electrophysiologist's heaven, there's no series resistance, and you have an infinite number of solutions in a special magic fridge/shelf, containing every possible permutation of divalents, weird anions, or whatever.

Cause dealing with the lack of those two things is a series pain in the ass.


Thursday, July 10, 2008

What are the 'bibles' of your field?

Dr. Jekyll & Mrs. Hyde had a quick post on about how she doesn't read too many science books anymore (she's a postdoc), leading to the question of what's the point of a book length treatment when the science is always progressing? That's a good question, so go over there and comment on what you think is the proper role for science books.

But it's obvious that there are some books which most scientists in a given field own, and have read, and have incorporated into their thought process.

You know, the bibles of the field.

They're the books that everyone has on their shelf, the ones you spent your book money on as a grad student, the ones you point younger scientists to when they have a question, the ones you just know in your gut will have the answer once you peruse the table of contents. Some are methodological bibles, some are conceptual bibles, and some blend the two.

For electrophysiology, I can immediately think of three main bibles. They are, in no particular order:

"Ion(ic) channels of Excitable Membranes", by Bertil Hille, currently in its third edition. If it's a question about some fundamental basic property relating to ion channel function, or you want a good overview of the squid action potential, then this is the place to start. Still a favorite, though I have to say I prefer the 1992 2nd edition, for the tactile sensation of its cover, it's wonderfully incorrect title, as well as its modest overall size. The third edition sadly fails each of these criteria.

"Single-Channel Recording", 2nd edition, edited by Erwin Neher and Bert Sakmann. Maybe you've heard of them, having won the Nobel in 1991 for their development and use of the patch clamp technique. The book is largely covers methodological questions, though it's title is a misnomer; it covers a lot more than just single channel recording.

"The Axon Guide" edited by Rivka Sherman-Gold. Published by Axon Instruments (now owned by Molecular Devices), it covers a lot of basic material as well as more detailed questions in an accessible, easy manner. It was out of print for some time, and then Axon made it freely available in pdf form. You can download it from the Overlord Master Molecular Devices here. Everybody I train in patch clamp gets this, and I quiz em about it. I especially like its treatment of filters and digitization, two topics which many young biologists haven't heard much about. And series resistance. Oh the series resistance. That my friends is a post in itself.

So, what are the bibles of your field?

Yeah yeah, Maniatis, ok whatever. What else ya got? Cause that's bor-ing!

Wednesday, July 9, 2008

Wednesday quick hits

When blogging has been nonexistent for years, is it fair to say that recent blogging has been "light"? Still, things have been quite busy around here lately, mostly as we work to firm up the shape of a manuscript looking at the regulation of TRPC5 channels (Hmm...seems like a post describing TRP channels more generally is in order - put it in the hopper, which is already bursting at the seams). But in between bouts of analyzing current amplitudes and looking for series resistance errors (pine away you molecular and cell biologists, but remember, you made your choice, wrong as it was), I have been following some interesting science related blog posts and whatnot.

Yaroslav Nikolaev posted an interesting picture of scientific progress. Not sure I agree that the real bottleneck is always assessment stage but check it out. Hmm, it seems I should list 'epistemology' as a hobby in my social networking personae. Whoa, geek overload coming!

The Amazon Kindle looks pretty cool, anyone out there using it? Because I'm in the process of totally phasing out paper printouts of journals (which is going pretty well), so maybe I could expand the scope even further.

Sigh, research misconduct is such a downer. How prevalent is it really, and in what ways is the current architecture of science promote it?

What online reference managers are people out there using? I've been using Connotea, but have also checked out CiteULike a little bit. And I've tried Zotero as well, but it was SLOW. None of these have really grabbed me, so does anyone have a killer app they want to suggest? And no, please don't mention Papers. We're non Mac type in Junction Potential land.

AutoHotKey is an awesome little free app that let's you easily make shortcuts, etc. I don't think I could live without it now.

It's been a few weeks, but my brother and I hit the Iron Maiden show they played in Massachusetts at the Comcast center. Yeah, it was as awesome as it sounds. And yeah, I can hear the jealousy out there.

Wednesday, July 2, 2008

Conceptual and experimental innovators in science and Galenson's creative types

I just read the Wired article "What Kind of Genius are You?" by Daniel H. Pink from 2006 about University of Chicago economist David Galenson's then recently published book "Old Masters and Young Geniuses: The Two Life Cycles of Artistic Creativity". It's a tad old, and I have lost the source of the link, but it's definitely worth reading, and I just had to write a blog post about it.

Reading the article, I felt intellectually buffeted by the force of Galenson's hypothesis and its apparent explanatory power, similar to the way I felt the first time I read Kuhn's "The Structure of Scientific Revolutions." Galenson's idea arises from studies of artists' lifetime production (well, he is a economist) and is this: there are two essential types of creative artists, the "conceptual" innovators" and the "experimental innovators". The conceptual innovators make dramatic leaps in their fields, often doing so at early ages after which their production declines. The second type, "experimental innovators" instead often take much longer to develop their most significant output, spending a long time developing and experimenting with techniques. Conceptual innovators seem to 'know' where they're going and where they want to take the field, whereas experimental innovators don't, and evolve bit by bit, letting the work develop and seeing where it takes them:

Picasso and Cézanne represent radically different approaches to creation. Picasso thought through his works carefully before he put brush to paper. Like most conceptualists, he figured out in advance what he was trying to create. The underlying idea was what mattered; the rest was mere execution. The hallmark of conceptualists is certainty. They know what they want. And they know when they’ve created it. Cézanne was different. He rarely preconceived a work. He figured out what he was painting by actually painting it. “Picasso signed virtually everything he ever did immediately,” Galenson says. “Cézanne signed less than 10 percent.”

Experimentalists never know when their work is finished. As one critic wrote of Cézanne, the realization of his goal “was an asymptote toward which he was forever approaching without ever quite reaching.” (p.2).
Now, I immediately starting thinking about how this might apply to different scientists. I am convinced that there are many parallels between how artists work and how scientists work. That's not suprising, as both are intensely creative human endeavors, and probably many scientists would agree. Could this be another region where there are significant parallels between artists and scientists?

I say yes, but exactly how meaningful these categories are remain to be examined (and is rife with all the difficulties of measuring the output of scientists). But I definitely think there are conceptual and experimental innovator types among scientists, at times manifested in their approach to questions. There are those who are good at coming up with new hypotheses and models when the hard data to make any of those connections is weak or even non-existant. This might lead to a lot of negative experiments, but if you can do it right and you hit on something new, then significant progress can be made. In fact this led me back to Kuhn, regarding those scientists who develop the new paradigm must buy into it before there is significant data to show it's better than the current (think Copernicus pushing the heliocentric model of the solar system before it performed better than the Ptolemaic model-it took ~80 years and Kepler to make the heliocentric model perform better).

But the other approach is to take a subject of interest, and just start doing experiments, and try and let the results 'talk' to you, leading you to the next experiment. At some point, if you're lucky and perceptive, you have a decent shot of seeing something that isn't expected, and is the first step in the path towards a significant advance forward.

I'll be the first to admit that I am firmly in the second camp, and am an avowed experimentalist (hard to call myself an innovator). For just about all the projects I've worked on, I've decided on a particular subject or subfield, and then started to do experiments.

In my view, both of the approaches are valid and useful, and in principle I don't think either has an inherent greater probability of leading to something "new." I sometimes wonder though whether the slow approach, might produce something in the end which is perceived as being less shocking simply by virtue of the fact that all of the preceding experiments made the final result likely, or even inevitable. With the conceptual innovator, it's more obvious when "before" and "after" occurred. In that case, is the conceptual approach more likely to garner the attention needed for publication in a high profile journal? This might be taking things too far, but I suspect there is something to it.

Of course, the dichotomy between the two types isn't anywhere near complete. Conceptualists aren't making up things willy-nilly, totally disregarding all that has come before. And experimentalists must have some sort of model, however implicit, or else how would they choose among the infinite number of possible experiments. Galenson himself has said there are certainly people who straddle the extremes. Yet there are strong tendencies, and I wonder how far the concept can be extended to scientists.

So, my small and somewhat reticent readers: Are you a conceptual or an experimental innovator?

Thursday, June 26, 2008

I won't surrender my idealism

There's a thought provoking discussion going on among some of the heavier weight science bloggers which has so many subthreads running through it that it's hard to summarize. So it's prolly best to go check out the posts over at DrugMonkey (here) and YoungFemaleScientist (here)

It's a back and forth that goes back a number of posts, with a lot of commenting. Essentially I think it boils down to this: YFS is a postdoc who thinks the system of science is in many ways fundamentally unfair, and as such needs changing. Physioprof and DrugMonkey are faculty members who aim to describe the system as it is, to help postdocs succeed in that system (which they readily grant it flawed, yet over which they feel they have limited ability to change).

Overall both make good points, but I take issue with some of the things that PhysioProf says in his latest post.

The money quote:

"In a winner-take-all system like this, there will always be people who do not succeed through no fault of their own. People who are smart, talented, dedicated, hard-working, articulate, persuasive, and who do all the right things sometimes still fail. This is the nature of a winner-take-all system: there is an intrinsic randomness that influences to some extent who succeeds and who fails. It is the same in professional sports, law, medicine, performing arts, entertainment, comedy, business, entrepreneurialism, journalism, engineering, and most other professional career enterprises.

Many of us may not like this situation, but this is how things currently work. Academic science is not a fucking Care Bears tea party, and wishing that it were is not going to make it so."

I have two big issues with this. First, there's no consideration for how well the current system of science might work to improve, or hinder, the quality of the end product: knowledge. Might it be that the system as is exists produces worse science than a different system? The fact that the essential randomness of the system might lead people to lose faith in the justice of the entire process. And when they do that, they start behaving badly. Dr. Free-Ride has it right, so check out her post.

If it is the case that the system is worse than it was (or might be), don't you have some obligation to change it? DrugMonkey does say in the comments that his blogging is one way of changing things, and that he also does his best to nudge things towards a better course in his real life working as a scientist. That's good, but it leaves me to wonder why the vitriol towards YFS, who is doing the SAME thing, in her way.

Secondly, I hate the way that PhysioProf impugns people who might want to change the system with the dismissive reference to a "CareBear tea party." I read it as saying to anyone who is an idealist about science qua science, or who feels that some current practices pervert what we see as a noble a pursuit worth dedicating one's life to, is hopeless naive. To that I say, fine, and can I get another helping of naivete?

Because I won't surrender my idealism for the project of Science. If that means I "fail" in the end, well, I will have my head held high when that time comes. I would rather live with the failure than to abandon my principles.

Tuesday, June 24, 2008

The Messy Phase of a Scientific Problem

-juniorprof started an interesting discussion about whether to be a producer or consumer of the literature. I started to write a comment in response, but it sorta ballooned up, went off on a bit of a tangent, and so I moved it here. Be sure to check out his post there (and his blog in general, it's a good one).

Overall, I find the message behind the dictum of the famous neuroscientist that juniorprof relates, which is to "be a producer not a consumer [of the scientific literature]" to be kinda ambiguous; of course all scientists need to have some engagement with the body of work they're involved in, and of course it can be easy for some folks to be too wrapped up in the literature to the detriment of their own creativity and experimental production. As juniorprof added in the comments, with which I agree, it's best to start a new project by going through the literature, and then after that to let your experiments guide you.

As part of his post juniorprof also warned against getting too wrapped up into the minutiae of details that can at times overcome a particular subfield (the state of which can be diagnosed by the presence of negative results against this or that hypothesis). I like that too in principle, but I can think of a couple examples where it took the field several years and a lot of negative experiments to converge on a better understanding of a process, and in so doing helped to reveal a more broadly interesting and relevant results.

Cases in point are the signalling mechanism that causes M current inhibition by receptor activation, and whether long-term potentiation (LTP) occurs as a result of changes in pre- or postsynaptic properties. It took a long time before it became generally agreed that PIP2 depletion inhibits M channels, or that postsynaptic glutamate receptor insertion underlies many forms of LTP, and I can think of lots of experiments with negative results done to assess the multiple alternatives. Sure, in isolation any one of those results isn't terribly informative, unlike a good positive result would have been; yet in the aggregate they reflect the shared knowledge of the field which had to be accounted for in the final scheme. And I would argue that only the existence of these negative results enabled the final positive result. (Still though, if you do have a negative result, stick it somewhere where you also have some amount of positive results and appreciable march towards the final answer. And by the gods do NOT highlight the negative result in the title. GAH!).

Also, the final papers which cemented the current understandings of these processes were published by people who were actively researching these questions throughout the messy period when lots of negative results and back and forth papers were being produced. So, I find it unlikely that any single researcher could sit out the ugly phase, work on something else, and then "swoop back" in and make a strong positive situation). Instead, I think that only by those people actively involved and invested in the line of inquiry were likely to have the ability to make the final connections and apply them to their question.

Now, I'll grant first that spending time on expts in the "dirty" phase isn't glamorous, and might be a hard sell to funding and promotion folks. I'm more thinking about how this process plays out for science per se (naive and unwise, I understand). Secondly, you have to make sure your initial process has some level of importance before you decide to commit to it. In this way it helped that M current (as an example of ion channel modulation more generally) and changes in synaptic strength such as LTP were intrinsically important questions. These two also had the lucky effect that their answers became important in and of themselves, as examples of PIP2 modulation of ion channels and activity dependent insertion of ion channels, respectively. Maybe it's not lucky though, since you should probably assume that a question which takes that long to settle is likely to generate an answer that is pretty novel when all is said and done.

So where does that leave us? Hmm, my main dictum is, "Do good science".

Thursday, June 19, 2008

Well, at least it wasn't a terribly offbase decision...

You Should Get a PhD in Science (like chemistry, math, or engineering)

You're both smart and innovative when it comes to ideas.

Maybe you'll find a cure for cancer - or develop the latest underground drug.

Ok then, so I chose correctly, and I certainly did enjoy getting the Ph.D. (as well as generally enjoying my time now). Though it might also explain why the whole current situation in science feels so...psychically disturbing at times.

Friday, June 13, 2008

Do citations in supplementary data not count in ISI?

I came across something troubling today in the supplementary information that accompanied a paper I was going over. Now I have a lot of misgivings about the whole concept of supplementary data, yet I hadn't realized this one until now.

That is, in the Thomson ISI database, citations made in supplementary data are not counted in the "Times Cited" count. That's worrying to me, because one of the most prevalent ways for people who are not experts in a given field (or subfield, or subsubfield...) to assess the influence of a scientist or paper is to use the number of citations the paper garners. For example, these citation counts are used to create the impact factor to rank journals (and at times erroneously to rank individual papers), and the Hirsch, or h-, index used to evaluate scientist output.

Meaning, if these citations are not included in ISI, then for all intents and purposes they do not exist.

So now, not only can supplementary info be used as a dumping ground for your inconclusive or crappy data, but you can also stick references to your competitors in there and shaft them their citations.

But hey, at least you've got your plausible deniability!

Anyone else troubled by this? Anyone else have opinions on supplementary data?

Thursday, June 12, 2008

Some open access goodness from the Clapham lab

Recently, my colleagues in the lab have published open access papers describing their work on various TRP channels.

One, headed up by Sebastian Brauchi (a former postdoc in the lab, who now has his own lab in Chile) and Grigory Krapivinsky, describes the role of TRPM7 on cholinergic vesicle fusion. It was published as open access in PNAS. Download it here.

The second describes work by Stephanie Stotz and colleagues on the sensory transduction mechanisms elicted by the chemical citral (a component of lemongrass). They found multiple effects of citral on a number of TRP channels expressed in sensory neurons, and published their work in PLoSOne. Get it here.

Yay for open access! Actually though, my advisor David always self-archives all of his publications, and they're available at the lab website here.

Wait! You're a postdoc, blogging under your own name? Are you insane?

Heh, I know, it does seem a little kooky at times.

Am I worried that my current advisor, or future colleagues (wherever they may be) will look askance at the idea of spending time blogging? I'd be lying if I said I was completely at ease with it, but I always come back to convincing myself of the personal utility of blogging. What do I mean by that?

Well, I plan on focusing primarily on blogging about science related topics, whether it be my own research, commenting on other research in my fields, and in thinking about issues related to science at large. This won't be a blog where I discuss my personal life, or complain about coworkers or things like that. There are definitely places for those kinds of blogs, but this isn't one of them. There won't be a hard firewall between the personal and professional, but there won't be LOLcat links (beyond that one, promise).

Instead, I see this as a way to more fully explore and think about issues that are already kicking around in my head. Stuff that my brain is chewing over, and will not let go. So while it may seem that this blog is going to take up a lot of time (and it may) but it might just let me offload some of that congitive processing time, refine its use, and free up resources for more obviously pertinent tasks. And this is one reason why I decided to do my blogging under my real name. That will force me to think a little more about my writing. Also, I didn't want to worry about my anonymous blog becoming 'outed' at some point, and risk hurting people I had written about. Better to prevent that temptation from doing that in the first place (but I certainly don't fault anyone for being anonymous. Sometimes a little spleen needs to be vented, and somethings in science are all messed up, and talking about that helps us all. A great example is YoungFemaleScientist).

And there will prolly be more indirect, and more distant in time, benefits of the blogging, related to becoming part of the broader science blogging community. That community is just a tip of the iceberg in the burgeoning Science2.0 movement (though I hesistate to call it a 'movement', that implies too much of a top down approach - it's more organic and distributed). I've got another post in the brain to discuss some aspects of Science2.0, but it seems obvious, and I'm convinced, that the increases in communication and interaction enabled by the spectrum of Web2.0 technologies can only help improve science and will improve the research and recognition of those involved. If I can get some 'early adopter' advantage, well, at this point I'll take whatever I can get! See, there is a selfish benefit to it all, which is a good way to motivate people to do things that also benefit the group at large.

Thursday, June 5, 2008

The Very First Post

Well, everything has a beginning, and so it is with this blog. Today, appropriately enough on Harvard's commencement day, I begin my foray into blogging. It's been some time coming, and I've wrestled with whether I should even get into this in the first place, and if I did take the plunge, what I hoped to accomplish.

Having no particularly clear answers to those questions, I just decided to take the plunge, and let the blog evolve towards whatever state the forces involved dictate. Consider it a beta version if you wish.

Of course I do have things I want to talk about, thoughts to share, and conversations I hope to start. Many of them will likely involve neuroscience, my academic field, which at least in terms of cellular neurophysiology seems poorly represented in blogspace (I couldn't use the term blogosphere here; to me that connotes some cloud of more politically interested blogs, carrying on discussions between themselves. I have no interest in becoming a part of that). I think it's clear that blogs will emerge as an important medium to enhance communication among scientists, and that's something of which I want to be a part. As a place for less formal communication about science, blogs appear ideally suited; I just wish there were more researchers doing it.

Beyond that, I've always taken a keen interest in "Science" and the big issues that surround it: the ethics of science, the practice of science, and how we can organize science to produce the best ultimate outcome, which in my view is the production of information that informs and improves humanity. I don't claim to be anything more than an interested layperson in these areas, but I can bring a "view from the trenches."

Lastly, why "The Junction Potential" for a blog title? There are a couple of reasons. First, it's an electrophysiology thing. As every young electrophysiologist learns, there is a junction potential between your pipette solution and the external solution, arising from the different ion mobilities. This affects the actual voltage you're applying to the cell membrane, and needs to be correctly measured or calculated, and then offset. In terms of electrophysiology, the junction potential isn't always paid a lot of attention, nor it is usually a big deal if you don't account for it initially (you can always correct it after the fact). That's a perfect analogy for this blog I'd wager.

The second reason is perhaps more profound. I have become convinced recently that many aspects of Web2.0, be they social networking/bookmarking tools, folksonomies, wikis, and blogs, will profoundly change the practice of science (this is by no means an original conclusion of course). They have the potential to drastically increase the junctions scientists make with their subjects and with their colleagues (yes, I know, groan). Besides, I needed to call it something.