Archive for: August, 2010

The ethics of data release

I was recently talking to a colleague who is in a field of genomics and we got on the topic of data release policies and I learned something interesting that I didn't know the sharing of genomic data: almost all major genomics centers are going to a zero-embargo data release policy. Essentially, once the sequencing is done and the annotation has been run, the data is on the web in a searchable and downloadable format.


How many other fields put their data directly on the web before those who produced it have the opportunity  to analyze it? Now, obviously no one is going to yank a genome paper right out from under the group working on it, but what about comparative studies? What about searching out specific genes for multi-gene phylogenetics? Where is the line for what is permissible to use before the genome is published? How much of a grace period do people get with data that has gone public, but that they* paid for?

It seems to me this is a very slippery slope because every genome paper has a different focus and it is no longer Glamour Mag worthy to just describe the genome of an organism. There has to be a hook and that hook is almost always related to the interesting biology of an organism or to resolution of a broader long-standing question based on the new data from the genome. However, these are the very things that people who are not part of the genome project would be interested in once the data are released.

The colleague I was talking to had the opinion that the (in her mind) small risks on someone scooping a major theme of the resulting paper were small compared to the benefit of the data to the community, fresh off the machine. However, she is a tenured prof with an impressive CV and a name that might scare off the vultures and I wondered whether she would have the same opinion if she was untenured.

Having my data pitched onto the internet the second I had it in my own hands would make me exceedingly nervous, even if my data were on the scale of a full genome. Stories of unscrupulous researchers more than willing to snap up any data they can find abound and I have seen blatant cases of it myself. Is the genomics community and anyone who can benefit from their data just that much more principled? Somehow I find that a hard sell. And how does one make a complaint about someone else publishing your* data if it is sitting in a public database?

I will be interested to see whether there are any high-profile dust-ups over this in the near future or whether a genome really is big enough for the whole community.

*Obviously we are talking about grant-funded projects, so the money is tax payer money not any one person's. Nevertheless, someone came up with the idea and got it funded, so there is some ownership there.

29 responses so far

Who do you work for?

Aug 12 2010 Published by under [Education&Careers]

I was recently discussing my first two years on this job with a colleague and mentioned my frustration in not having landed some Fed $$ just yet and how I could have approached the first year very differently. The colleague listened and basically told me that I'm doing fine and then added "No one thinks you are slacking, in fact many feel you are going above and beyond."

Wait, what? That doesn't even make sense. It would be one thing if everyone was like "Oh, do you really need another grant? I mean the three you have should keep you busy enough... and that chair your sitting on is actually made of money and accepted manuscripts!" But that isn't exactly the case.

It made me think. Am I setting too high a standard for myself? Is the department expecting too little? Then I realized that I don't actually care what my department's standards are, as long as I exceed them.

When it comes right down to it, what motivates me isn't checking the boxes that should lead to tenure, but rather proving myself to people in this order:

1. Myself. I have a bunch of ideas that I want to work on and to see funded and the desire to answer the questions I see as exciting are the reason I am doing this job instead of getting paid a lot more to do another job with my skills.

2. The colleagues in my field and especially the labs I have worked in. Every conference, every invited lecture, every month that goes by where we are not making  a big splash I can feel the people who know me waiting to see if I can deliver. Yeah, I was able to pump out a lot of papers as a postdoc, but now what? Can I launch my own program and make it successful? Luckily I feel like we are on the verge of making this happen.

3.  The people who hired me. No one wants to let down those who have given you an opportunity and turned down others who may have been similarly qualified. That new faculty smell wears off after a while and what lies beneath better not stink like bad cologne and BO.

If I can perform up the expectations of those groups, then I should be checking all the right boxes for tenure without setting out to do so explicitly. I know what I need to have on my CV by the time my fourth year review comes around, but I am not pushing to get those things done because of the specter if tenure, per se. I am also not particularly motivated by how my effort is viewed by those around me, since at some point the person who tries really hard and never gets over the hump is just that person who couldn't cut it. There is no A for effort here.

11 responses so far

A walk on the dark side

Aug 10 2010 Published by under [Education&Careers], Etc

Like almost any field mine has many sub-groups, not all of which play nicely together. There are dozens of reasons for the clustering and there doesn't tend to be a large amount of mixing over time. Perhaps the occasional one-off paper or collaboration, but they are few and far between.

As a trainee, I grew up on a certain side of the perverbial fence and continue to work with members of that group on a regular basis. For a variety of reasons, however, I can no longer be quite as active a member with that group and I have struck out on my own to a certain degree. As it were, this did not go unnoticed by others.

I should also mention that I am a fairly social person and have spent more that a few hours at conferences or pubs with a good number of the people in my field, regardless of their group allegiance. I rather like the discussions that occur between the groups, because it is extremely interesting to hear people lay out their arguments in a late-night discussion rather than in print after being sanitized by review. It's also a type of networking that I happen to be good at, for better or for worse.

Given the above, I guess it shouldn't have been that surprising a few months ago when I got a call from the head of a group I have had little 'official' interaction with i the past. I was invited to join a project that is in the early stages, but is quickly gaining steam. As things have moved forward, I now suddenly find myself involved in a least one major and a few minor publications as well as a grant application, which could greatly enhance some of my other efforts. Whereas this is a good thing for my personal advancement, I now clearly have a foot in different projects being driven by very different groups. While this isn't exactly a conflict of interest, it will be interesting to see how my new collaboration is viewed by those who I might consider to be my people.

It's a thorny issue that I am not sure how to navigate other than being completely honest with all parties about my collaborations and intentions. If I tread lightly, I am hoping to benefit from working in both circles without having either of them close me out. Hopefully I am not being naive as to how this will all play out.

15 responses so far

What I've done wrong

Aug 07 2010 Published by under [Education&Careers]

PiT has a good post about what to do as a junior faculty member once you get the keys to your lab, which I think it spot on. I won't belabor the points she brings up there because you can read it for ourself. Instead, I'll take this opportunity after 2 years on the job to reflect on what I screwed up.

Think of this as my "What I would tell two-years-ago-me if I had a time machine*" post.

The first thing I got wrong was deciding to strike out on my own and start an entirely new research program with little carry over from my previous work. Don't get me wrong, I really like the directions we have gone in the past two years, but this decision has killed me for funding. Coming from another country into the US system, I greatly misjudged the amount of "preliminary" data required for the proposals I was writing. It was my fault for not taking more time to understand the system, but I wasted a lot of time in the first year writing grant proposals that had no hope of getting funded, simply because I didn't have the data to back them up. If I had taken a ready-made project from my postdoc I could have used that to get things going while working up the other facets of the program.

Another consequence of this is a publication gap. I've had a few pubs out since starting this job, but nothing substantial that I can point to and say "look at all the cool shit I am doing!" This is not a good thing. It's not a killer, but I could have planned better.

The second thing I got wrong was not burning my start-up with a flame thrower. I have certainly blown through a ton of cash since starting, but for someone who didn't have enough preliminary data and has cash in hand, I didn't act fast enough. Eventually this message got into my head, but I should have been more focused on cranking out data on a large scale right off the bat than I was.

All in all,  I think these two points probably set my proposal getting back a year (hopefully not more...), and had I done more on either front I could have saved myself a lot of aggravation, but live and learn. So, if you are starting a new position right now I would strongly encourage you to think about the data you need to make a good proposal and spend whatever it takes as soon as possible to get those data in hand.

*Other than, ya know, the lottery number that week.

10 responses so far

Repost: The balance

Aug 05 2010 Published by under LifeTrajectories

Since there seems to be a tornado of "how do we pull this shit off" going around, I figured it might be a good time to 'me too' and repost this from only two months ago. I'm also trying to finish up the data for a talk  have to give tomorrow, so yeah, repost!

There has been quite the discussion recently about work / life balance and how it relates to gender issues. Things started with Isis' commentary on a ScienceCareers piece on balancing the chores with work, that was aimed specifically at women. After a bit of a scuffle, mostly on Isis's blog, Jim Austin had this to say at ScienceCareers. Despite the "special announcement" (which ends with the dismissive Thanks for your attention. You may go back to whatever you were doing.), I'm not sure Jim ever really heard Isis and Zuska's complaint that the implicit assumption in ALL of the ScienceCareer articles aimed at work / life balance was that the target audience was women and only women.

Based on the discussion, ScientistMother called out the men, and specifically Drug Monkey, to write more about how they deal with the balance between work and life. I think that's a fair thing to ask, because by not addressing this it appears is if it isn't a problem for us and I can assure you, at least in my case, that is not true.

Most of you will know that I am married and have a daughter who is just over two. While I am not in a two body academic relationship, my wife works close enough to where I do that we own one car. I mention this because it is critical to how our lives are scheduled. Basically, our hours are daycare's hours. We drop the Wee One off at 7:30 when it opens and we pick her up at the end of the day (though not when daycare closes), usually between 4:30 and 5:00. Those are my weekday in office hours, whether I like it or not because I have no other option to get home.

At first I found this difficult because I was used to working later in the day, but now I actually appreciate the restriction. Why? Because it means that no matter what I go home with my family and we play, eat dinner and have bath/bed time with our daughter together. I can go back to the office afterwards if I want, though more often than not I work in the evenings from home. But during the week we don't see the Wee One for that long each day and this schedule means that I see her all the time she is not in daycare. It means I have to be a bit more organized and that I have to get everything I can done during the day, but it also means that I spend more time with my daughter and, importantly, that the parenting burden is not skewed. For the same reasons, I try hard not to work much on weekends, but when I have to, I pick one day to get things done and spend the other day with my family or just with my daughter if my wife has to work.

As far as chores go, we have essentially reached a balance where the overall work is split evenly without both of us doing every task equally. I do more of the cooking and dish washing, whereas my wife does more laundry and yard work. We both clean the house when it needs it, which usually either happens in concentrated bursts or in fragmented pieces (just the bathroom gets done, or just the kitchen gets cleaned) during the Wee One's naps or after dinner. We take turns giving the Wee One a bath and putting her to bed. For the most part it works.

The tough part is travel. At the moment I travel more for work than my wife and that places an enormous burden on her during those times to single parent while I am away. For some reason, when I travel is also the time when random catastrophe strikes the household, making my time away that much more difficult on my family. There have even been times when my travel and changes around the house have caused anxiety in the Wee One, which was a bit scary. Travel times are stressful times and I've tried to make careful decisions about travel to get the most out of the time I am away. Sometimes it means missing a relevant meeting. It is what it is.

Kids are a lot of work. Relationships are a lot of work. Work is a lot of work. Everyone finds their balance and what makes the most sense in their relationship to get 26 hours worth of stuff done in 24 hours. There is no one right way to make it happen but allowing home duties fluctuate between us depending on each other's work burden at the time allows us to manage.

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Travel Notes

Aug 04 2010 Published by under Etc

I am on the road for the rest of the week, but thought I might check in with a couple of travel observations.

-In almost every mode of travel one sits facing the back of another seat. It doesn't matter if you're in the car, on a plane or riding the bus, you're not facing someone directly. Why have we decided that trains don't need to follow this tried and true tradition? Is there a more awkward way to travel that facing a complete stranger in a small confined space? How many things can you find to stare at to avert your gaze from the other person until it just gets weird? Not enough, as I found out today.

-It seems as though cab drivers come in two basic forms, your chatty variety and the silent one. I don't have a strong preference one way or another, except for the extreme chatter. The kind that only requires the occasional "uh-huh" to blather on about everything from their live philosophy to their hobbies. The dude driving me today got so into telling me how he thinks reincarnation works that he twice missed my hotel and I had him just drop me off near the building, by the loading dock, rather than have to circle the block again. If he had been a metered taxi I might of thought it was a ploy, but  this was pure verbal diarrhea.

-Why do they make hotel bathroom soap so hard to open? Usually your hands are wet by the time you realize you need to unwrap the soap and luckily they have encased it in smooth plastic shrink wrap that has no seams.

-There must be repressed issue I have when it comes to packing my toiletries. No matter how many times I check, I forget something. This time I have two tooth pastes (sorry honey) and no comb or floss. Considering that I badly need a haircut and I am a big fan of flossing*, one would think these would be easy to remember. But I brought soap! I guess in case I couldn't open the hotel soap.


*This started after one really bad trip to the dentist for a cleaning. I think at one point I was bleeding so badly that if the cleaning had been performed in an elevator, upon reaching our floor the people waiting in the lobby would have seen this.

8 responses so far

Repost: Your thesis means nothing, worry about the papers

Aug 03 2010 Published by under [Education&Careers]

Since this has topical relevance in my life right now, I thought I would repost this from October 19, 2009.

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.

16 responses so far

First defense and the talking jitters

Today was not only a big day because of the Scientopia launch, but also because I had my first student defend. This was a student who started with me a little less than two years ago and has done an excellent job getting things done at a time I needed it most. It's great that the student finished up and that a paper is almost ready to go, it is just odd losing one if the people who has been here since the beginning - but such is the nature of the beast.

One thing that the student asked me, which is a bit of a reoccurring theme, is how many talks did I have to give before I stopped getting nervous. I had to think about it, because whereas it has been a while since I got nervous before a talk, as a young and naive PLS I was a total fucking wreck before a talk. My knees used to shake during talks and even the anticipation made my digestion to bad, bad things.

So, I graphed it (this is science afterall):

Nervousness relative to talk experience.

I think for the first little while it doesn't seem like you are going to adjust. Every talk you are just as nervous as the one before and the only difference is you know how bad it is going to be. Somewhere after about 10 talks it starts to get better, but only marginally so (from eleventy to something in the normal range). Then there is a magical moment when you are no longer terrified the entire time you have to stand there and be the sole voice in the room. Once this happens there is a plateau where you still feel the nerves a bit before a talk and in the first minute or so, but you have the ability to crush those feelings once you start rolling. They persist, however, and can rear their ugly head if the environment changes substantially (really big talk, job talk). After that stage the bottom drops out and it pretty much becomes telling a story.

Maybe it takes a little longer for some and a little less for others, but the only way to deal with a fear of public speaking is to get up there and realize that there isn't that much to fear. Yes, we have all had that time we looked stupid standing in front of a crowd stammering out a circular answer to a question we barely understood, but to my knowledge, no deaths have been associated with such an experience. Often they become part of the War Story arsenal one can use to make others feel better (you think you looked like an ass? Let me tell you a little story...)

It's easy to look at people who seem to be natural speakers and think they left the womb that way, but I can assure you that at some point almost everyone has been terrified to stand up and present their work in front of crowd of like-minded individuals and everyone has a horror story. Rarely is new ground forged in this arena.

18 responses so far

Welcome, welcome

Aug 02 2010 Published by under Etc

Wow, so here we are. As you might imagine this little venture was in the works for a little while and special thanks really needs to be extended to Mark Chu-Carroll and Scicurious for making this all happen. Mark, in particular, has been the architect of this site and has done an amazing job getting 25ish bloggers organized and all moving in the same direction without any of us breaking Scientopia from the inside.

With that all said, I can imagine that many people reading over the next little bit will never have stumbled across my previous blog and have no idea who I am. Taking the lead of Dr. Becca, I think an introduction is in order.

I started my tenure track position in 2008, and like many junior faculty, it's been a sink or swim period in my life. For the most part I've been treading water so far. I've even learned a few things along the way.

You should also know that I am a super hero. I know this because while I am home I have the ability to ward off evil that quickly descends the second I leave town. Of course, I sometimes find ways to undermine even my own super powers, but the travel can be fodder for plenty of stories as well.

I also have a defective brain to mouth filter, that can sometimes get the better of me.

When I actually discuss science here, much of it is in the context of getting NSF funding and finding the best ways to approach their proposals. I have, however, started applying to NIH recently and will see where that goes. I'm heading to do an NSF panel this fall, which should be an interesting experience.

I'm adjusting to teaching undergrads in between submitting papers and proposals. This has been a challenge, but it's part of the job and something I got better at this year.

I also like to occasionally rant about anti-evolution wackos and the influence they can have on the country. Even the people working to promote evolution sometimes make we wonder.

Finally, I am excited about this new community that is forming here and hope to be able to engage readers in discussion as I continue doing the job I've always wanted to do. Since I started blogging I have been surprised at how useful it has been for me (I even wrote a five part post on the topic if you are bored 1, 2, 3, 4, 5) and hopefully my readers have benefited as much as I have. I'm looking forward to seeing what the future holds.

15 responses so far

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