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?"