Archive for: October, 2009

Why choose a lab?

Oct 21 2009 Published by under Uncategorized

As this semester rages on, we are drawing steadily closer to the time when grad school applications are due. Like many, I am trying to recruit students for next September and I started thinking about what makes a lab attractive to new students - in my case specifically, what makes a new lab attractive to students?

My experience was probably unusual and may not provide the best example. I was involved in research as an undergrad for a couple of years and realized that I wanted to go on and get a PhD. I asked my undergrad supervisor who he would recommend based on what he knew of the field and he gave me a list of names. I started there, made some contacts and arranged to speak to each one in person (which included some interesting road trips). I hit it off with one and the person had space in the lab and that was that.

For me, the strongest factor in my decision was the recommendation of my advisor. My personal interaction with potential grad mentors meant a lot, but the initial recommendation was really key to getting me started since the field I was joining is manageably small . I imagine, however, that most people don't go about choosing a lab in that way for a number of reasons, but how many students in their senior year know exactly what they want to go do and have the guidance to get there? If, for instance, a students likes biochemistry are they just applying to the top biochem programs that includes PIs in a field they think they want to pursue?

So, I would like to find out from you why you chose the lab you are in or got your degree from? Was it a good choice and would you do it differently now? Was it the subject or PI that got you interested? How much did suggestions from others influence you?

16 responses so far

NFL week 6: Snake in a bag addition

Oct 20 2009 Published by under Uncategorized

Brutal week for the NFL pool and brutal week for my eyes. We'll get to the pool in a minute, but there's something that's been haunting me since last night. Did anyone else watch the first half of the MNF game last night? Well, if you were tuned in with about 7 minutes left before halftime, you would have seen a tribute to the great QB and coach, Sid Luckman. Now I have nothing against the late Sid, but I have a bone to pick with ESPNs MNF producers.

Of all the footage of Sid available out there, rather than pick some football highlights or show ways in which his coaching ideas changed the game, the decided to pull out of the archives some instructional video from the 70s that Sid filmed for aspiring young QBs. At the opening of the clip we see Sid from behind, bent down as though receiving the ball from a center. The man is wearing white knee socks (literally), a t-shirt, foam-front-mesh-back trucker hat and a pair of loose gray cotton shorts, complete with vertical sweat line in the rear center. Whatever, the man is playing sports and people sweat, fine. BUT. Then he turns and does what seems like an 87-step drop back and the man has NO underwear on. Nothing under those loose cotton shorts. And for way too long he's running sideways facing the camera with his junk just flying around like an angry snake caught in a cotton bag. I swear, if that shit were in 3D I would have tried to save the cat from getting hit.

Damnit ESPN. I have a decent size HDTV and you throw that at me? WTF? Even the booth guys were trying to hold it together after the clip, with Gruden finally acknowledging the elephant in the room by asking Jaws if he had to wear those shorts to the tribute dinner. Did they not have underwear in the 70s? I'm pretty sure it was available. Was it made of wood chips or something, because that's the only excuse I can come up with. Was the producer just trying to mess with the booth guys or was it some nefarious plot to get 90% of the audience to rush to throw Commet in their eyes? Unfortunately, not even that gritty burning can make me unsee that footage.

As for the picks, basically most people did the equivalent of throwing soap in their eyes. Tom@microworld pulled off the win with 9 points, AA came in second with 8 and then there was a three-way tie for third between myself, PiT and CE with 7 points. It gets ugly after that, where a rash of 5s breaks out and there was no Benadryl to be found. The leader board remains largely unchanged. I'm steering the ship (45pts), with PiT as first mate (44pts) and Tom as the head chef (43pts). Alyssa is working as the quartermaster (41pts) and then there's a lot of people swabbing the decks (40-33pts). Cleaning the latrines in high seas is Tideliar (31pts).

Congratulations to Tom for this week and I hope the scars fade soon for those of you watching last night.

9 responses so far

Your thesis means nothing. Worry about the papers.

Oct 19 2009 Published by under Uncategorized

Whether it's tradition or a lack of well communicated expectations, grad students seem to be enormously focused on The Thesis. Students fixate on this document for months before writing it and then for weeks to months of actually writing it. I have to say, I've never quite understood that, because if you had to put odds on the people who will read your whole thesis it would look something like this:

2:1 Advisor
3:1 Committee/Examiners
10:1 Over-eager new student who takes on aspects of your project when you leave
1,000:1 You, after it's done.
100,000:1 Your parents
1238947692092y47nc783et687:1 Everyone else

When I got my thesis back from the binders, I opened it up and read the first sentence. In that sentence, I had a typo that made the word "three" into "tree". Seeing that, I promptly shut the thing and that was that. Never opened again.

The one caveat to this is if you never publish the papers. In that case, the community might find it and someone might crack it open, but probably not. But that's the point. Uncommunicated science might as well never have been done in the first place. Get the papers out. Don't focus on an arcane document that will gather dust for the next 50 years until the departmental office needs space and throws the old ones out. Write the papers, or at least write the chapters as papers so you can get them out quickly after the thesis. If you publish before you graduate, writing your thesis should be about as simple as slapping together a half-assed intro and conclusion (complete with typos that no one catches) and be done with it.

14 responses so far

Sorry about all the hamsters

Oct 16 2009 Published by under Uncategorized

I just had a web demo with a company that I am thinking of contracting for services. The demo was the type where you connect via a web portal and their technical staff can run you through their system by showing you their desktop. When the technician got on the phone with me and superimposed his desktop onto mine he closed a few windows to clean up his menu bar. For about five seconds or so, his email was up with a message open in the inbox. It contained a single line in large text.

Sorry about all the hamsters.

I didn't ask him about it, but don't think my mind wasn't wandering during his presentation, coming up with colorful scenarios after which one might receive such an email.

8 responses so far

Gone Fishing. Or whatever you want to believe

Oct 15 2009 Published by under Uncategorized

Like a few other young'uns out there, my To Do list is growing faster than I can actually DO anything. Recently, just being in my office is good for about 2 hours worth of random shit I don't want to do each day so I'm trying the hide out approach. Our new house has an actual office space nestled away in the finished basement. It's got everything I need, and importantly, one thing I don't - a phone. My cell phone doesn't even get reception down here and few people even have my home phone, mostly because I can't even remember the damn number. So today is for sitting with my laptop, unshowered with a pot of coffee brewing and just writing. Not emails, not evaluations or reports, not minutes of some meeting I was barely paying attention at, not a section of a grant that I won't even get money from. No. I'm writing stuff for me today. Come back tomorrow with your crap that you couldn't find someone else to do.

6 responses so far

NFL week 5: tiebreaker addition

Oct 13 2009 Published by under Uncategorized

For the second straight week, Candid Engineer has swiped a victory by winning the tie breaker, this time besting myself and Chall for the week win with 8 points. CE becomes the first person to win two weeks and did so in back-to-back fashion. This week the trophy stays put.

The leader board has not been shaken, but certainly stirred. PiT's system is showing some cracks with only 5 wins this week, but she remains in second place trailing me by only one point. In a possibly related development, last week I received an unmarked package filled with plastic farm animals making obscene gestures.

Only 4 points separates the top 8 players. Is this the week that there's a change at the top?

7 responses so far

Job link and education resources

Oct 12 2009 Published by under Uncategorized

I'm in an ugly stretch of vultures picking at the bony courpse of my time right now, so I'm posting two links that might be interesting to readers. The first is a job post that was sent to me from a friend and the second is a resource some might find useful for teaching.

Job Posting" Molecular Pharmacology at Purdue University

What someone in the department had to say about being a faculty member there:

"We REALLY REALLY want to reach out particularly to the women and minority scientist community to get diverse applicants The only real requirement (science-wise) we have for this position is that we need someone to pick up the torch for teaching pharmacology courses: the current course directors and lecturers on those topics are either getting tangled up in administrative positions or getting close to retirement. Other than that, we're hoping for some interesting, innovative biology-type stuff but keeping our minds open.

As monocultural as my department looks on paper, everyone here is really cool people, we have a great atmosphere and a very friendly, down-to-earth departmental community. People here TRULY COLLABORATE without fearing for their independence. I have been welcomed without hesitation into the group and feel very at home here, and our department head is really fantastic. In general people here are just straight-up folks. We have a formalized junior faculty mentorship program as well as an informal weekly lunch together that I have found totally invaluable to getting on my feet. Our tenure requirements are very rigorous, but everyone seems to be doing their best to help each other make it through (rather than trying to turf each other out). All in all, I think this is an excellent place to start a career and I couldn't be happier with my choice to join this department."

I also recently received this link to a blog for the 100 Best Open Source Apps for Educators. You may find some interesting new tools there.

No responses yet

New NSF stats

Oct 07 2009 Published by under Uncategorized

NSF just released their funding stats for 2008 (now that it's almost 2010) and throughout the document they make comparisons back to 2001. If you are applying to NSF anytime soon the document is worth looking over, but there are a few trends that jump out right away.

1) It should be no surprise to anyone that overall funding rates are down from 2001, but only by 6%. The total successful funding rate in 2008 was 25% for all PI's, with women being 27% successful and a rate of 25% for men. In a stat that hits close to home, "new" PIs only had a 19% success rate. In this case, "new" refers to any investigator who has not previously had an NSF grant as a PI (meaning that Doctoral Improvement grants and Postdoc fellowships don't count). I don't know whether this is due to experience or something more along the lines of the issues at NIH that Drugmonkey has been discussing, but it is certainly not receiving the kind of attention that the similar NIH phenomenon has been.

2) There is also a large disparity between NSF's Top 100 (the 100 most funded PhD-granting programs) and everyone else. Among researchers at a Top 100 university, the success rate was 27%, whereas it was 18% everywhere else. Obviously the confounding factor here is that one can argue that the people with the most successful or promising research will end up at a Top 100 university and also be more competitive for funding, but I thought it was an interesting observation.

3) The number of funded multi-investigator grants has increased marginally, but the number of funded single-investigator proposals has dropped by nearly 25% between 2001 and 2008. One might assume that the focus on collaborative research might push the multi-investigator grants up at the expense of individual grants, but this doesn't seem to be the case unless the number of PIs per grant has gone up from two to >2, but those data are not provided.

4) One thing that I found very surprising was the number of grants per PI. In the fiscal years 2006-08, 83% of PIs had one grant! That left 13% with two grants, 3% with three and 1% with four or more. As someone who has three very different projects that they are trying to get funded and has been talking with a colleague about a fourth, I'm not sure what to make of those numbers. If nothing else, it concerns me that reviewers might balk at a proposal just based on the number of grants held by a PI. Now, I'm not thinking that everything I am submitting will eventually get funded in the next year, but if these projects weren't fundable in my opinion, I wouldn't be wasting my time. Perhaps people who have served on a couple of panels (*cough* Odyssey? *cough*) might shed some light on the perception of when someone has "too much" funding.

5) Anyone on the postdoc market also won't be surprised to hear that whereas the number of senior personnel and grad students supported has gone up by 52% and 23%, respectively, the number of postdoc positions supported on grants has actually dropped by 10% since 2001! This stat sucks for a lot of reasons, but makes it clear where the squeeze is in terms of positions right now. Congrats, here's your PhD and your Dairy Queen visor!

6) Yet another stat that might be expected: it's getting harder to get grants on the first or even second try. The average number of times a proposal gets submitted before it gets funded is up from 1.8 to 2.2. Not a massive jump, but it reflects the fact that fewer grants are being funded on the first go and more are going back in for a third round.

7) Finally, good reviews are not what they used to be. The number of declined proposals that scored very well is up in a big way. In fact 1 in 4 proposals that receive an "Excellent" rating are not being funded. 57% of proposals that are rated between very good and excellent are declined and if your proposal falls in the range of good to very good, your chances of getting money are only 12.5%. So, even if your proposal is rated in the highest category there is still a 20% chance you will get back your reviews and scratch your head to figure out how the hell you are going to make improvement for the next round.

Take it for what it's worth, but it's data that you may be able to use.

8 responses so far

NFL Week 4: Brutal beat-down addition

Oct 06 2009 Published by under Uncategorized

Two things happen in week four that can make for ugly weeks in pools that pick against the spread. The first is that bye weeks come in and there are two fewer games to pick, so the scores look worse than the previous three weeks even if the success rate is the same. More importantly, however, is that Vegas has a couple of weeks of evidence to figure out which teams are actually good and which teams were just surrounded by hype. This usually translates to "better" lines, from the standpoint of Vegas, making it harder to pick against them. For the next 5 weeks, anyone who manages a double-digit win week will almost certainly prevail for the week.
Many of us were solidly thumped this week, with a slew of 5s and 6s on the board, but two people came oh, so close to double digits, with 9 wins. PiT continues her run of strong showing, clearly demonstrating that prior knowledge of football only clouds one's judgment when making picks and that an alternative system can do well (over at least 4 weeks). However, the tie breaker this week goes to Candid Engineer, who came back strong once she started paying attention to the spread. Congrats to CE!
Because our league drops the lowest score for each person, I was able to maintain the overall lead with 30 points. Odyssey and PiT are close behind with 29 each and there is a four-way tie for fourth place at 27 points, with Mad Hatter, Nat, Alyssa and Tom@microworld all battling it out. DGT sits alone with 26 points and CE, Chall, Tideliar and AA are tied up with 25. Driving the tiny Shriner car in the rear is Genomic Repairman with 24 points, but the spread from front to back is merely 6 points, which can be made up quickly.
Good luck to all next week and CE, come get your trophy.

8 responses so far

Disappearing data

Oct 05 2009 Published by under Uncategorized

No, we are not having trouble in the lab with data gone missing. What we are having issues with are data reported in glamour pubs that none of a gazillion authors on said paper can seem to locate. If you spent an entire section in your paper (where real estate is expensive) to talk about how you found a whole bunch of data points that you did not expect to find, isn't it a bit fishy that when someone writes you for those data that all of a sudden a game of email hot potato beaks out and the list of cc'd "people who probably have those data" starts to stretch longer and longer? This is not a paper from the last year and if the authors were following up on the outliers, they would have done so already. No, this just seems to be a case of vanishing data.

Damn Good Technician has previously discussed the lack of detail in methods section of glamour pubs and whether or not the caginess around some critical steps is a way to publish the bare minimum while maintaining a competitive advantage over anyone interested in the work, but this is different. In the paper, a big deal is made of the outliers, but less than 5% of those data are discussed specifically. That means that 95% of these interesting data points are never mentioned specifically, only alluded to as a group. Even in the supplementary data. How are people supposed to verify the interesting outliers if they are completely obscured? If it turns out that none of the authors can even produce the data in question, then what does that mean about the results? These data are critical and heavily-cited evidence for several theories. Shouldn't they be easily located? Surely we are not the first lab to inquire about them.

I am hoping that we see some resolution shortly, because if the authors can't provide the data in question I don't know what to do about it, only that it would be a major problem.

5 responses so far

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