Archive for: December, 2010

Scientific dissention: shouldn't we all be nice?

In case you've been living under a scientific rock, you might have heard about the Science article (PMID:21127214) reporting the discovery of a prokaryote that can incorporate arsenic into its DNA in place of phosphorus. Obviously this hit the press in a big way and was picked up by a shit ton of bloggers, who spread the word. Given that the science was done in a NASA lab, there was quite a bit discussed about the implications of this finding for life on other planets.

Then people started looking hard at the science. Rut-roh, Elroy.

One of the first and most vocal was blogger and UBC microbiologist Rosie Redfield, who jumped all over the paper. As Carl Zimmer reported at The Slate, many others agree with Rosie's assessment.

While I find the subject of the paper interesting and the debate more so, what really caught my attention was the scientific communities reaction to Rosie's critique.

Carl Zimmer contacted two of the authors of the paper about the apparent flaws in their study, and they circled the wagons:

"We cannot indiscriminately wade into a media forum for debate at this time," declared senior author Ronald Oremland of the U.S. Geological Survey. "If we are wrong, then other scientists should be motivated to reproduce our findings. If we are right (and I am strongly convinced that we are) our competitors will agree and help to advance our understanding of this phenomenon. I am eager for them to do so."

"Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated," wrote Felisa Wolfe-Simon of the NASA Astrobiology Institute. "The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner."

Wow. Really? Did I just slip into the 19th century by accident? Pass the watercress sandwich tray, please.

And what about the comments on Rosie's blog? While many were supportive, comment after comment after comment after comment after comment after comment after comment, hopped aboard the old "this isn't how scientific debate is done, this is unprofessional!" train. Choo-choo.

Dude. Fuck. Sigh.

This idea that science is somehow pure and fact-based alone, while being performed by scholars in tweed having "civil" conversations over tea makes me want to poke my eyes out with a rusty nail. Did Rosie's post relay her mistrust of the data and the motivation behind some of its gathering? Absolutely. But do her arguments against the data (and those brought up in the comment section) raise all sorts of red flags that we have seen from other cases the ended with a retraction of a high profile paper? Hell yes.

I don't know whether some of the fairly massive missteps in the data acquisition were a case of people being blinded by their own "discovery" or pushing out the answer they wanted, but there is no question that these data are premature, at best. However, both the paper itself and the way it has been presented at conferences, indicate very little of this preliminary vibe. Guess what? If you rush dodgey data out there and claim you have found a novel life form, you're going to hear it from the masses.

To my mind, this is a "good thing" and evidence that the speed of information transfer is working to make science better, not less professional.

27 responses so far

On the 12th month of Spandrel Shop, my blogger gave to me, a mindless sum-ar-yyyyy

Dec 07 2010 Published by under [Et Al]

Tis that time of year again. No, not the holidays. The 12 months of [insert your blog] meme. DM was the first to get it rolling, so let's play. I'm posting the first two lines of each post, mostly because I often start with a short sentence. Click the month names for the link.

Jan - I guess this is the post where I admit to being a little naive when I first stated this job. See, I didn’t do my PhD or a postdoc in the US, so applying to US funding agencies wasn’t something I had a chance to get involved in during my training.

Feb - Yesterday I was going through old folders on my computer and pretending to organize things when I found something I couldn’t place. I organize my “papers” folder by each manuscript and there was a subfolder that I couldn’t match with anything I had published.

Smarch - It’s been a long time since I had to take a test for a class, but I’m kinda reliving that experience today watching my students hover over the sheets of paper I have prepared for them this morning. I don’t think the test is hard, but we’ll see how they do.

April - Well, I think it’s time to make the official announcement on the blog. After all of the discussions how good postdoc life is and how teaching is sucking the life out of me I have decided to bail on this job and take a postdoc position in another country that I’ve always wanted to live in.

May - When I got my mail on Friday there was a letter from our research office. I had submitted a proposal for a small internal competition a while back to cover a grad student summer salary and a trip this summer and seeing the letter I knew that the decision was contained within.

June - Busy week, my friends. This week kicks off the summer travel schedule for me, which is going to be taking me out of town a lot.

July - I’ve done a decent amount of traveling in my life – certainly less than many, but I’ve hit some odd places. One thing it is easy to take for granted is the different styles and ways society has come up with to drop a deuce.

Aug - 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.

Sept - PiT has an excellent post up about the manuscript review process, which I thought might be worth following up with a post on grants. See, when I first sent proposals in I pictured a process during which my 15 pages of text was carefully read, considered over some time and probably looked over a second time for clarification and summation of key points. Hahahahahahhaahaha.

Oct - Having filled our previously advertised job in Seminar Napping, Employment University has a new position available immediately, entitled, Journal Club Killa.

Nov - One week remains in the Donors Choose campaign. That’s all.

Dec - This morning I was browsing through my favorite blogs and happen over the Cackle of Rad for a music post in which the delightful CoR assaults us with the band Pylon, who have apparently dragged up the ghost of the Cobain era Courtney Love to be their lead singer.

2 responses so far

Being the first pancake

Dec 06 2010 Published by under [Education&Careers]

The other day I received an email from a grad student that read as follows:

I'm a second year PhD track grad student, and my advisor is in his 3rd year of a TT position. As a request: I'd really like to hear your thoughts on what it's like to mentor PhD students for the first time. PhD students are an odd bunch, and It would be really nice to get a sense of what my TT prof is going through. I once heard a tenured prof talk about her first grad student, who dropped out after two years. She called him her "burnt pancake", because 'the first one never turns out right'. I don't really wanna be that pancake.

Fair enough, no one wants to be the guinea pig as someone else tries to figure out how all this works. At the same time, if the tenured prof from the email has (presumably) successfully mentored other students since (meaning that she isn't a tyrant or obstructionist), I would guess that it has far less to do with the advisor than it does the student. She may have been rationalizing the failure of her first student, but as the supervisor of a non-zero number of grad students I have found one thing very clearly: they are all completely different.

What I mean by this is simply that the process of mentoring a student who is interested in the work they are doing and intellectually up to the challenge is not all that hard. Yes, you learn a few things along the way that might head off some issues, but overall our job is to keep students on a productive path, get them resources and be a sounding board for ideas, problems and progress. Sticking to those points seems to work pretty damn well for most students.

I think more at issue here is the what the PI sees as failure is not necessarily what the students sees as the same thing. If a student leaves the lab (perceived as "failure" in most academic circles), it could be as much to do with the fact that they decided the life wasn't for them than anything else. They may have had a different opportunity or decided that they didn't like the path ahead. Maybe they had a long distance relationship that they didn't want to be long distance anymore. Who knows? But there is a good chance that they say leaving the lab as more of an opportunity than a failure, whereas the PI decided that she needed a do over because if she had more experience she could have kept that student interested in the amazing research she was doing. Obviously I don't know any of the back story, but I'm guessing that the student found something that was better for their life and the supervisor, unable to picture that possibility, decided that she must have messed up that student because she wasn't warmed up just yet.

I guess my advice to students of junior faculty is to focus on your project and pushing it forward. If your PI gives you the resources (physical and intellectual) to do something you enjoy, while still be available to help you when you need it, then I wouldn't worry too much about turning out like the first pancake out of the pan. If you like what you are doing and have a functional relationship with the boss*, there are not many ways in which "mentoring" can go horribly wrong just because the PI is supervising their first student. In fact, there are many ways in which being one of the first students in the lab can be a good thing, as long as your PI doesn't get crushed by the weight of getting funding (which can happen at any career stage, FWIW). Use your network of friends and your committee members if you think you need more perspectives than just that of your PI and be a little selfish about advancing your own career.

And if that means leaving a lab for a different opportunity, know that your move will only be seen as "failure" by the people you are leaving behind.

*Obviously, if your PI turns out to be a total douchecanoe, this is a whole other problem.

13 responses so far

The research proposal

Almost all graduate programs have some form of a research proposal that students have to write towards the beginning of their degree. Sometimes it doesn't happen until they are well into their research (which seems a bit counter productive) and some institutions make students write their proposal as early as possible. Either way, it is a fairly common requirement.

I have heard a lot of debate about the usefulness of this exercise, and although most people see value in having the student think about the approach they plan to take, there tend to be two extremes of PI involvement in the actual writing of this document.

On one hand, there are those who offer the student little help outside of comments once the document is nearly complete. The upside of this approach is that it forces the student into the literature and encourages more independent though at the formative stages of the work. Students also get practice writing a (sort of) scientific document, which may help some more than others. The downside, however, is that students typically take an enormous amount of time to create the document this way and the proposal rarely reflects the finished project once serendipity and actual data come into play.

The other extreme is allowing a student to use a grant proposal or lab manuscript as a template for their proposal, with the understanding that liberal "borrowing" of text and/or figures is expected. This approach drastically cuts the time required to produce the document, but may lead to the student spending far less time thinking about the work they plan to undertake and following the "lab plan" more closely with less of their own stamp on the project.

If the student's comprehensive or (less likely) qualifying exams are tied to the proposal document in any way, it could be argued that the first approach better prepares the student, but I can think of cases where this would also not be true.

So, blogoshphere, I am curious how you approach the research proposal, as a PI or as a student. What has been most effective for you and why?

22 responses so far

Anti-EMO sauce

Dec 02 2010 Published by under [Et Al]

Just so CoR doesn't think I'm listing to sing songy shit over here and to get that video Odyssey posted out of my head.

Bonus points for the strangest use of wine in a music video that I can recall.

3 responses so far

Music Warz!

Dec 02 2010 Published by under [Et Al]

This morning I was browsing through my favorite blogs and happen over the Cackle of Rad for a music post in which the delightful CoR assaults us with the band Pylon, who have apparently dragged up the ghost of the Cobain era Courtney Love to be their lead singer.

I'll counter with something a little easier on the morning palate, by a band whose new* album has been on constant repeat in my life for over a month.

*New in the US, it's been out in the UK for a bit.

7 responses so far

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