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!"