Tuesday, September 29, 2009

Words aren't always enough

As I was scanning through the ToC alert for last week's edition of
Nature, I saw a correspondence entitled "A communication wipeout by gabbling presenters", in which Dongwook Ko of Charles Darwin University in Australia writes:
I have noticed a trend among speakers at scientific conferences to speed up their oral presentations so that they can compress as much information as possible into their allocated time slots.Talking so fast can create a problem for those in the audience whose native language is not the one being used by the speaker — almost invariably English on today's stage.
I would say that 'talking so fast' actually makes if difficult for many in the audience, even if they are native English speakers. At least, it does for me. I am not an android. I cannot process a gig of data in 5 ┬Ás. And I cannot follow you--or the story--if you're blowing through four slides a minute.

Put another way:
More data ≠ better talk

The best speakers present appropriate background and clear, concise data in a well-organized manner. They also know how to keep to time, for the most part, such that they don't have to choose between flying through 10 slides in the last 4 minutes or running 15 minutes over time. Neither is a good option because you're going to lose some folks either way. Speaking clearly and at nice, consistent pace doesn't guarantee a good talk, but at least it gives your data and your story a chance to prove its worth.

-ome out

To whomever originally came up with the idea of sticking the suffix "-ome" on a term to describe the entire collection of said term (and "-omics" to describe the characterization of the collection of said term)...

Did you ever stop to consider the consequences of this action?!?!

I'm thinking 'genome' is the first example of this phenomenon. That was fine. I was even ok with 'proteome'. But it has gotten completely out of hand. Now we have: lipidome, glycome, glycoproteome, allergenome, peptidomes, secretome, transcriptome, metabolomes, phenomes...

And today's addition to the -omes from PNAS: the surfaceome, to describe the transmembrane proteins expressed at the cell surface.

Really? It was catchy and sexy the first few times, but now not so much.

Now if you'll excuse me, I'm going to see what's happening with the bloggome...

Sunday, September 27, 2009

Turning the tables

I admit it. I was spoiled in grad school and the first eight months of my postdoc. Paramed is a fantastic guy. Owing to his bizarre (even by academic science standards) work schedule, he always had a lot of free time during the week--sometimes too much free time that drove him a little crazy, but that's not really the point.

Because Paramed was only working two days a week and
I was working six, he took care of many of the domestic duties: laundry, cooking, cleaning, sometimes even grocery shopping. On a few occasions when I had to work really late, he would bring me dinner at work. While I was in the midst of preparing for my defense, I sent him off to a strange city, by himself, to find us a place to live.

Now the tables have turned. Paramed is still working his two days a week, but now he has class three days as well. So what "free" time he has is spent reading and studying. This is actually really great because we had agreed early in our marriage that once I was done with grad school, he would have his chance. Oddly, we seem to be spending more time together actually talking (as opposed to sitting in silence while staring at the TV): Paramed actually tells me about his days now. He's excited about what he's learning and shares it with me, which sometimes leads to heated philosophical discussions, something we've not engaged in on a regular basis for a while. And I get to tell him how what he's learning in class is applied in real-life research. Plus his college is just a few
blocks from where I work, so we walk together (both from and to home) on most of the days he has class, which gives us more time to talk.
Of course, this means he doesn't have the time to be the domestic king he once was--and it's my turn to take more responsibility. We are still trying to achieve equilibrium. Currently things are not ridiculously busy in the lab, and I've been able to leave the lab around the same time consistently. (I have a sneaking suspicion that this will change in the next few weeks, but I'll just have to figure out a way to make it work.) My evenings are now filled with meal prep and tutoring (which accounts for the recent sporadicity of my blog posts). To be honest, Saturdays have typically been work-in-the-lab and veg-out-at-home days, and I'm not quite ready to relinquish that. So Sundays are being filled with balancing the checkbook, paying bills, grocery
shopping, cleaning, planning, etc. This kind of sucks because when Monday rolls around, I feel like I've already put in a day's work, even though the week just started.

I'm glad to be able to do for Paramed what he did for me for the past few years. It's just a matter of establishing a new balance and not becoming overwhelmed by the immense changes in our lives now. Now back to calculating that equilibrium constant.

How to get your advisor interested in publishing

Wait for an upcoming grant submission deadline. Amazing how motivating this can be for a PI.

I've mentioned previously that I've been trying to get my last manuscripts from Bear's lab submitted. After my defense (almost a year ago now), there was no move to submit. Six months ago there was no sense of urgency. Then this summer he's suddenly interested. Submitting papers that he's been clinging to for five years. Getting after me to send him a polished, revised draft. Turns out his R01 is up for renewal again in the spring.

I guess this is one situation in which a trainee should be grateful for the competitive funding environment.

Now if only I can pitch the last manuscript's discussion in a way that (a) is supported by the data, (b) does not require outlandishly complex models, and (c) makes Bear happy... then all will be well and I may at last be done with my graduate work.

Saturday, September 26, 2009

You must bring us a shrubbery!

Hello again, blogophytes.

You may have noted that my posts are more sporadic these days than they were a few months ago. Life is keeping me busy, and of late, I seem to only find enough time to write on the weekends.

I'm even working tonight. I have the dubious duty of writing (my first) protocol amendment. Do not mistake me--I understand the purpose and the importance of IACUC protocols and amendments. But some things seem so repetitive. I'm asked to specify changes and how it improves the project. Then I'm asked to provide the reason and justification for the changes. Then I'm asked to detail the changes. Subsequently, for certain categories of changes, I am again asked to specify and justify. And (almost) finally, a shrubbery--or in this case, flowchart.

Why do I have the feeling that after submitting the paperwork I will be asked to cut down a tree with a haddock?

Sunday, September 20, 2009

No, really, I am

Over a month ago, I was commenting--OK, OK, whining--about how ridiculously busy I was and then had a 2-page research proposal to write in one week to compete for a training grant at BRI.

Based on the timeline supplied by the grant admin, I had anticipated hearing a decision a couple of weeks ago. I hadn't, so I assumed that I hadn't gotten it.

Then a few days ago, I received an email of congratulations--I'm on the training grant.

My reaction: Woo hoo (i.e. slight enthusiasm). This provides a buffer period, during which my salary is paid (taking a little pressure off Guru) and giving me some critical time to gather crucial preliminary data for fellowship proposals. This is absolutely necessary as (1) there are two components of my project, which we think are connected but have no evidence for at this time, and (2) I want to propose in vivo experiments, but we have no prelim data for this aim--Guru's lab does a lot of in vivo work but not with regard to the mechanism/pathways I'm studying. So even though I have funding for the next year, I have an enormous burden of data to generate in the next 2 to 6 months (corresponding to submission deadlines). And my first experiment since the lab's move was kind of a bust--not because I didn't see what I had hoped, but mainly because of technical issues. I mean, is it too much to ask for antibodies that detect what the company claims without picking up 30 nonspecific bands?

Anyway Guru congratulated me earlier in the week while I was in the midst of preparing for an experiment, so I didn't have much to say.

He subsequently announced at lab meeting that I had gotten this fellowship, which evidently is pretty competitive. I sat quietly, probably with reddened cheeks and likely looking uncomfortable--because I generally don't like being the center of attention even when it's of the positive variety.

Later Guru approached me and commented that I didn't seem very excited about this fellowship. I was caught off guard. I assured him that I was excited, but I had just had a lot of other things going on. I'm not sure he was convinced.

There are many factors contributing to the lack of visible excitement:
  • At PSU, getting on a training grant of this sort wasn't exactly difficult. The grant's director said, hey, we've got x spots open. Your PI said, I want to put student A on it. You wrote a brief paragraph for grant records. And that was that. I'm simply not accustomed to an institutional training grant being a competitive award.
  • I haven't felt great this week. Hell, I haven't felt great for a long time. And when I feel like crap, I don't get overly excited about much of anything.
  • I really have had a lot going on, both in and out of the lab. So for me, it was one of those hey-that's-cool-now-let's-get-back-to-work moments.
  • I have a bit of a complex when it comes to being made the center of a group's attention based on my achievements. (And yes, putting it in writing in that manner does make me realize how bizarre it sounds.)
After Guru's comment, I felt kind of bad about my lack of outward reaction/enthusiasm. I feel that I should explain myself. I don't want him doubting my commitment to his lab or this project because I am excited about the possibilities.


P.S. - I really have missed blogging over the past few weeks... as you might guess by the appearance of three posts in less than 24 hours. Thanks for staying with me :)

They Might Be Giants... and Big Geeks

This could be one of the geekiest, coolest, funniest things I've seen for a while. (Hey, I don't get out much.)

They Might Be Giants have put out a new album, "Here Comes Science" (which I learned about courtesy of Eastern Blot). Yes, they wrote it for kids... and maybe I have the emotional maturity of a four year old sometimes because I think the videos are fantastic!

About half of the videos from the album are posted on YouTube... or you can buy the album and videos from iTunes. For your Sunday morning pleasure (I listed my favorite one last):

Saturday, September 19, 2009

Learning without teaching

Last weekend I got together with former member of Bear's lab (we'll call him Forte) who was in town for a meeting. Forte was a senior grad student in the lab when I joined, and he taught me a lot about the techniques used in our lab, the system we were studying, and the politics of the lab. He finished up a little less than a year after I joined. It had been a couple of years since I'd seen Forte or talked with him much, sometime before I finished my dissertation.

Part of our recent conversation revolved around the education we received at PSU and what we learned from Bear. At one point, Forte commented that when he left grad school, he thought he didn't get a great education there--sure, he learned stuff, he got his Ph.D., but it just didn't seem like much... until he went somewhere else and realized the breadth and depth of his training compared with colleagues from other institutions. We also talked about the similar experiences we had as we left PSU: We were pissed with Bear. We were so ready to be gone. We questioned what we had learned from him. We just wanted to get out manuscripts out and get on with our lives. Then, a few months after we left, we realized that we had actually learned a lot from him and why he did some of the things that pissed us off so much.

Trainees (myself included) become very upset when there is a lack (sometimes perceived, sometimes real) of formal, structured mentoring. Our PIs becomes enamored with the newest shiny object or cool project or sexy data, and we feel ignored and neglected. Sometimes we're just left completely alone for weeks or months at a time. Our PIs only communicate to get slides or figures or data or whatever for a talk or grant or paper. As a trainee, you essentially have two options: (A) Decide that your PI is out of touch, that he doesn't know what he's doing, and ignore everything he does... or view it only as the antithesis of what should be done. (B) Realize that he's been pretty damned successful up to this point and start paying attention.

I chose option B. That's not to say I didn't do my share of bitching and commiserating with fellow grad students. But I also paid attention to how Bear ran things. When he made suggestions or recommendations, I listened. By doing this (I realized after some time, distance, and reflection), I learned some incredibly important things from Bear. I learned how to write manuscripts, how to put together a clear, concise presentation of data. I learned a lot about grants--writing, submission, review processes. I learned that I should keep up to date with what's being published, not just in my field of study but in other fields as well, and with what's going on in science policy and funding. And a hell of a lot more. But in the end, the most important things I learned from Bear... he never actually taught me. He showed me, even if he didn't know I was watching.

Sunday, September 13, 2009

Alive-at least for today

Has it really been 2 weeks since a last posted? Did I get caught in a time warp?

Oh how I have missed blogging--both the reading and the writing portions. Unfortunately many evenings I've been completely wiped out from pure exhaustion, migraines, respiratory issues or some combination of the three. The other evenings I have either been sick of looking at a computer screen or busy. To be honest, I should be working on other things right now, but I don't have the patience or brain power to do anything serious. I have accumulated many unrelated--and possibly some incoherent--thoughts, which I have decided to share in traditional RBOC style. Deal with it.
  • We gave up our HD cable and DVR today. At least I get to keep a few of my guilty TV pleasures with basic.
  • I have arrived at the conclusion that Paramed either works for (a) power-tripping dickheads or (b) incompetent assholes.
  • Starting experiments after a move kind of sucks. Because (a) you don't know where anything is, (b) there is little to no logic in the initial unpacking, (c) many things are out because we didn't want to order them just before the move, and (d) it always takes time to get momentum going.
  • There are definitely some upshots to moving: I can see a tree from my window. I've already met more people. I have access to more equipment.
  • My engagement ring was stolen after I mistakenly left it somewhere I shouldn't have. At least they left my wedding band. Fortunately (?) I freaked out more than Paramed.
  • I cringe every time I get an email from Bear these days because it is inevitably about a manuscript. I have my Ph.D. I am so ready to be done with grad school.
  • I had a great time catching up with a former colleague from grad school, talking science, family, and utter gossip.
  • You know how you reach those points where things are so crazy that you say, "If I can get through the next week/month/year, things should calm down." Does that ever actually happen?