Archive for: December, 2011


Dec 30 2011 Published by under [Et Al]

Is there really any good reason to make post-vasectomy "sample" cups out of transparent plastic? The only thing worse might be a neon cup with the words "Caution! Semen Sample. Do Not Handle Without Gloves!" in bold on the side, but clear is a close second. As if it needs to be any more awkward to be carrying around your "sample", like the world's creepiest short-lived pet, you also need to walk into an office and place it on the counter as a display? How about an opaque cup with a colored sticker to put on the side, indicating the contents? What about just using the form that comes with it? I can't be the only one who has thought of this.

14 responses so far

Lab safety and who is responsible

Dec 28 2011 Published by under [Education&Careers]

In what is being viewed as a surprising move, felony charges were leveled against a UCLA professor and members of the UC administration as part of an investigation into the 2008 death of Sheharbano Sangji. The research assistant died after a lab accident left her with 2nd and 3rd degree burns over much of her body.

While a tragic accident, investigation found that several safety precautions were not taken that may have mitigated the damage. Not only were some of the experimental procedures in conflict with recommendations for handling the dangerous chemicals Sangji was working with, she was also not wearing a lab coat or eye protection. The legal action is largely being spurred by the fact that UCLA safety inspectors noted over a dozen safety infractions, including lack of personal protective clothing, only two months prior to the accident. Despite the warnings, no action was taken by the lab to correct the issues.

Obviously the level of risk is going to vary substantially from one lab to the next. A chemistry lab might be expected to contain more dangerous chemicals than an ecology lab, for instance. However, that doesn't mean that there should be variable levels of attention paid to safety. But the issue is always enforcement. Where does it come from? Who is ultimately responsible.

This was an active discussion on twitter (yes, I'm selling out that fast) this morning with @biochembelle, @Chemjobber and @piperjklemm. Chemjobber has already posted on the specifics of the case, but I am interested in discussing how we avoid this kind of failure in the lab.

Everyone has a story about their safety office indicating that they are either too militant or don't know their asses from their clipboards. Hell, I've even written about this topic. Yes, there may be cases when they dispense less than wise information, but when it comes to violations of the safety rules at your institution, PIs do so at their own risk. The UCLA case is making this point loud and clear.

As a PI I can attest that I will absolutely not catch every safety violation in my own lab. Why? because I spend more time in my office than in my lab, but at least two orders of magnitude and I haven't yet set up the webcam in there *puts on ToDo list*. So what can I do to make sure no one is mouth pipetting phenol at the bench with no pants on? Make it clear that I value safety by the following:

1) Assign one lab member (I don't have a tech) to stay on top of MSDSs, SOPs and waste, then check in with this person at lab meetings.

2) Point out any safety issues I do see when in the lab and bring it up at lab meeting.

3) Hold a meeting after our annual Safety and Risk seminar to make sure we are all on the same page and to discuss and changes.

4) Listen to anyone who has a concern. Ignoring a valid concern voiced by any lab member sends the message that you are not serious about lab safety or don't care about the safety of certain members.

5) Finally, the buck stops with the PI. As pointed out by @biochembelle, lateral or bottom up enforcement of safety rules is rarely effective. If you want you lab to take it seriously, the PI has to be the lab enforcer of safety. A senior lab member can be empowered to do this, but the PI needs to make it clear that it is important.

Or risk jail.

43 responses so far


Dec 22 2011 Published by under [Et Al]

Every now and again I run across a song I haven't listened to in years that just seems to fit the day. Too bad it's a crappy partial live video shot by someone right in from of the trombone...

3 responses so far

12 more months of Spandrel Shop

Dec 21 2011 Published by under [Et Al]

In further holiday wrap up news, I'm kicking in my contribution to the end-of-year summary meme. In a year that the lab landed NSF funding, we compared grad students to honey badgers, had a second daughter and then made sure there won't be a third, there has been a lot going on. Much like my previous years in this job, each new semester has brought new challenges and new understanding. Hopefully writing about much of it here has been useful to some. I know the discussion has been so for me.

The idea is to simply post the first sentence from the blog in each month. We've done this before, in 2010. Without further ado:

Jan - One song, two videos:

Feb - Way way back as a wee PLS in grad school, I can distinctly remember thinking that I would never be PI material because I couldn't imagine working as hard as my advisor.

March - "Fit". That term can be the bane of existence for those applying for faculty jobs (like the one Dr. Becca just got, go congratulate her!).

April - One of the things that has fascinated me about joining a collective has been getting all the personalities together in one place and trying to accomplish a single goal.

May - Osama Bin Laden is dead.

June - There can be a lot of gray areas in research, where decisions can be made that seem okay at the time, but in retrospect look pretty questionable.

July - Sometimes I am baffled by the search terms that get people here, other times I am just scared.

Aug - This second kid is going to be a challenge.

Sept - I will seriously post content shortly, but this week is all out as the specter of The New Year approacheth.

Oct - Tomorrow (or today, depending on when you read this), October 2nd, kicks off the ScienceBlogs campaign, which will run until Oct 22.

Nov - Having spent far too long on the student reviews of a manuscript for my class recently, there was one thing that really struck me.

Dec - My daughter turns four years old in a few months. How time has flown.

One response so far

Holiday delurking, take 2

Dec 20 2011 Published by under [Et Al]

The year and semester are winding down giving us a brief opportunity to take a breath. January NSF deadlines are looming and the spring semester is not far from rearing it's ugly head, but for now things are getting more quiet instead of less. It's a good time.

On top of everything that has happened this year both personally (new kid and no sleep) and professionally (new grant and more sleep), it's been an interesting blogging year as well. Scientopia has changed a bit and seems to be stabilizing after a few months of flying by the seat of our collective slacks. I've gotten to know some new-to-me bloggers better and even taken on twitter.

But once in a while I like to turn the conversation outward as much as possible and invite those who read but never comment to join in. I did this in 2009 and found it really interesting, so I'm trying again. For all those lurkers out there, your holiday gift to me can be saying hi and weighing in on what you might like to see from the blog in 2012 (12? really? crap). I would also be really interested to hear where (career-wise) you readers are at, since I have no idea whether I'm talking to a bunch of grad students or gray heads. I see a set of regular commenters often, but what would entice those of you who never comment to join in the conversation?

Take two minutes of your end of semester down time and delurk for the holidays!

35 responses so far

Repost: Parents in the workplace

Dec 19 2011 Published by under [Et Al]

It turns out the Weer One is not a great sleeper. Unlike her older sister, she has little interest in sleeping through the night from n early age. On Friday night, for example, she woke up every hour. Last night it was 1:00, 3:00 4:15 and 5:30. This morning I dropped the kids off at daycare and they had no heat, which needs to be fixed by 10:00 in order for the to stay open. Basically, this whole second kid thing is dominating us and we wander about like zombies. In honor of that and because I'm too tired to write something new, here is a repost from May 4, 2009.

If you are new to a workplace and interested in the lives of the people you work with, here a few tips to figure out who has young kids at home.
- We're the ones who come to work with smushed food or snot on our clothes without realizing it. Kids have an amazing ability to transfer these items to the one place you can't see on yourself, but everyone else can.
- We're the ones who come in on Monday looking more disheveled than Friday. Some weekends are far more tiring than weekdays.
- We're the ones who look like we were at a late night party or concert on a weeknight by the way we look some mornings. We weren't. More likely we were up much of the night because our kid is sick or just decided they would rather scream than sleep.
- We're the ones who have a cold 5x more than everyone else. Daycare is ground zero for every outbreak of every virus.
- We're the ones that are nodding off at 8:30 during dinner parties or evening departmental functions. When you are up at 5:30 am every day....
- We're the ones who will trap you in monologue conversation for 30 minutes if you ask us how are kids are. Want to see the pixelated pictures of my kid on my phone?
- We're also the ones with a constant source of amazement and amusement at home, no batteries required.

16 responses so far

2011 NSF Bio funding

Dec 16 2011 Published by under [Education&Careers]

Now that we are approaching the end of the year, NSF has doled out the money it is going to for 2011. It was a rough year in the Bio Directorate, with funding rates down pretty much across the board. The good news? This is the last year we will be seeing such low rates. The bad news? That is not because of increased funding from congress, but rather the new application structure. DEB and IOS have moved to a preproposal that will triage >2/3 of the proposals before the "full" proposal stage, and MCB has gone to an extended cycle. All three now place limits on the number of propsals a PI can be associated with in a given cycle. Whereas these changes are directed at reducing reviewer burden, the new numbers will be hard to compare to the ones over the last few years.

But where do things stand in 2011? Well, it depends on where you look. On NSF's funding rate page the numbers are higher than this graph found on the Bio Directorate home page, but they are in the same ball park.

The overall is reported around 15%, but if you look at just core programs the situation is a little more bleak. And in fact my own experience with a couple of panels in 2011 indicates that many were funding well below even these reported rates - closer to 7% in a DEB panel and 10% in an IOS one.

So how is the process going to change this? Well, the numbers will go up, but it's not clear hoow it will affect the types of proposals getting funded. Certainly there is going to be a large emphasis on The Sell for the preproposals. Whereas this is always an important aspect, PIs won't need to back it up with as much data in January as they would have previously. You'll need to put your money where your mouth is in August if you get the full proposal call, but by that time 2/3 of the competition will be gone. Additionally, the preproposal panel will be different than the those judging the full proposals.

Interesting times ahead.

2 responses so far

Tweeting a vasectomy

Dec 14 2011 Published by under [Life Trajectories], [Medicine&Pharma]

As should be clear by now, I was a bit busy yesterday afternoon having my vas deferens cut and cauterized. In an attempt to use my experience as a way to educate folks about the experience, I live tweeted the whole process, but since twitter is a fleeting medium, I thought I should summarize here as well.

Twitter reads from the bottom up in the images below, except in the "conversations" that read top down. Hey, I'm just the messenger.

My first appointment was about two weeks ago. The doctor briefly described the procedure and how he does it. I had specifically opted for the "no scalpel vasectomy" because the incision is small and recovery is supposed to be less. He told me that he had been doing the procedure for 16 years, which seemed like a decent amount of time to me. Then he told me to shave before my next appointment. After reading Abel's description of a dry shave, I was already ahead of the curve on this one. Having experienced the aftermath of the disposable razor quick shave after my tattoos, I knew that was not going to be a good thing.

But this is not an area I commonly shave and I was a bit worried about irritation. I didn't need razor burn to compound my post-op issues, so I thought about alternatives. CoR suggested waxing, but hell no. I decided to try Nair.

Having solved that problem, I was ready.

One thing I hate is being late. Seriously, I can't do it. The flip side to that, however, is that I often arrive too early for things. This happened yesterday when I got to the office 30 minutes before my appointment. Maybe not the best move when you're a little anxious about something.

I got called in about 5 minutes late and brought to the room, where I was unceremoniously given a paper sheet and told to undress. I assumed that the sheet was for covering me, but checked with the nurse to make sure. I didn't want her to come back in and be horrified that I was on a table covered by a glorified napkin when her intention was something entirely different. My assumption was correct.

With the doctor's blessing (although he said it was a first), I kept my phone with me for the procedure. The sheet was pulled aside and the nurse went to work on my member with a liberal dose of betadine. They slapped a grounding pad on my side for the cauterizing and off we went.

And then shit got real. Much like any procedure that is routine for the doctor, but not for the patient, it seemed like they got to work in a hurry. With the no scalpel procedure, they use an anesthetic "gun" instead of a needle for the local, which resembles an oversized stainless steel pen. The nurse fired it once so I knew what it would sound like and the noise was like a small cap gun. Braced for that, I was ready. The doctor said it would feel like being snapped with a rubber band, and that was basically the feeling.

After about 6 snaps on either side the doctor went to work, starting on the left. It was a very odd feeling, with some pulling that extended a bit up into my lower abdomen, but it wasn't painful. He finished up the left in a couple of minutes and then broke out the cauterizer.

Not even 4 minutes in and half done. No pain to this point either. In fact, there was very little pain throughout, even post-op. "Discomfort" is about the worst of it. Except...

At some point during the pulling and cutting on the right side they hit a patch that was not so numb. I think when my whole body jerked the doctor figured that out. However, I will say that it was more surprise and the reaction to "that sharp poke" I was nervously anticipating than actual pain. All additional local (and there was certainly some needed) was done by needle, but I never felt that at all. Then, back to work.

And as quickly as it started, it was over.

Laying on the tray were two 1cm section of vas, which the nurse placed in a jar for whatever reason. That might have been the strangest moment. I was given a bag with instructions and two "sample cups" and told to get dressed again. I did so gingerly, but only because I was concerned about pain, not because I was in any.

I was given a script for Oxy and an antibiotic, but haven't taken either. I settled on the couch with some ice and had a couple of beers, but that was it. I was getting around fine last night and even did the early morning feeding of the baby at 5:00am. After a shower and a bit more ice this morning I didn't see any reason not to go to work. Drop the Wee One off at daycare this morning and have been at my desk without incident.

The whole thing took about ten minutes. Yeah, it's a little nerve wracking and there is some discomfort, but there was almost no pain and I don't see any sign of complications at this point, nearly 24h post-op. I have no regrets and I would recommend the procedure to any guy thinking about it. I do not consider myself a tough guy by any stretch and the vasectomy was very straight-forward and easy.

I'm glad it's done, but I am more happy that we no longer (in a month or two) have to worry about an accidental pregnancy. I'm happy to have my wife get off The Pill, which she has taken for about half her life. I'm excited that I could do this for us and I encourage anyone who knows they are not going to have another child to sack up and get this done.

21 responses so far

The big day

Dec 13 2011 Published by under [Life Trajectories]

Heading to the doctor this afternoon armed with tight underwear and ice packs. All the gory details will be on twitter (@proflikesubst). Wish me luck.

5 responses so far


Dec 12 2011 Published by under [Education&Careers]

Routine is something that we're always told that kids need. They like predictability and to know what is going to happen. Routine keeps them feeling like there is some order and control of things. Certainly we have seen that first hand in how much the Wee One likes to know what each day will bring.

In some ways I'm stating to feel like the routine mindset is rubbing off on me as well. I can really get things rolling when I get in a schedule groove and can make time to do most things I need done. After living my life without a lot of routine, kids have forced me into a set schedule (and earlier bed time).

The last few weeks, however, have been anything but routine. I haven't had more than three days in the office for the last little while and those days are starting to be more and more jammed. It's also harder to get things rolling in this new fragmented space, so I waste more time when I can least afford it. This may be a good time to be less productive (is there a good time for this?) than other months, but it is a bit disorienting and harder to keep track of obligations.

Perhaps it is the time of year coupled with the fact that I am a little burnt from the semester, but I feel like I'm sliding backwards and losing track of some of those balls I can usually keep in the air.

2 responses so far

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