Tuesday, November 25, 2008

Book amusement II

Earlier this year a book I edited was published. I had earlier posted about some amusing keywords listed on Amazon.com for it. This morning I checked on Amazon.com to see if anyone there had written a review of it. No one had. But what I did find there did give me yet another chuckle...

Now, if you buy this book directly from the publisher you'll pay ~$71. Amazon doesn't sell the book directly, but currently offers it via four resellers plus a used book seller. Here are the listed prices:

Reseller 1- $42.00
Reseller 2- $64.65
Reseller 3- $93.89
Reseller 4- $107.85

Almost a three-fold range!

Used book dealer- $112.22!!!!!! And yes, this is listed as a used copy... Perhaps one originally bought from International Books...

Wednesday, November 19, 2008

It's alive!!!!!

Yesterday I received a rather unexpected call - from my NSF program director. Apparently he's recommending that my recent proposal be funded! If you recall, this proposal is based on a new research program I was trying to raise from the ashes of my mid-tenure crisis. Apparently that new research program now has a life.

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Odyssey's new research program lurches into existence.
It's alive!

This certainly changes things over the next couple of months. Instead of working frantically to generate more preliminary data for a resubmission of the proposal, I get to look for a new postdoc.

And start up another new project.

'Cos my new research program needs...

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A bride!

Friday, November 14, 2008

Five things meme...

Gee, thanks JLK...

The 5 Things Meme

5 things I was doing 10 years ago:
1. Wondering if I should add experimental work to my research (I was a computational biologist).
2. Being totally besotted with my baby daughter.
3. Realizing the tenure clock ticks very, very quickly.
4. Enjoying being a first-time homeowner.
5. Celebrating the publication of my first paper as a tenure-track faculty (actually ten years ago this week!).

5 things on my to do list today:
1. Finish reviewing the all-too-large pile of travel grant applications on my desk.
2. Plan out how I'm going to squeeze in a protein expression and purification (that I'll be doing myself) in the next two or three weeks. My work has morphed over ten years from purely computational to almost purely experimental...
3. Spend time with my family.
4. Try to avoid spending an excessive amount of time reading blogs.
5. Go to bed at a decent hour.

5 snacks I love:
1. Apples.
2. Potato chips.
3. White chocolate chip-macademia nut cookies.
4. A freshly-baked cheese danish or walnut-jam scone or cinnamon doughnut from the bakery down the street (okay, so I cheated a little and squeezed three into one).
5. Beer (where I come from beer qualifies as a snack. And breakfast, lunch and dinner).

5 things I would do if I were a millionaire:
1. Put away a bunch for the kid's college tuitions.
2. Take a family vacation to Australia.
3. Take Mrs. Odyssey to Europe (sans kids).
4. Pay off the house.
5. Renovate the kitchen.

5 places I've lived:
1. Australia.
2. Pennsylvania.
3. North Carolina.
4. Missouri.
5. Maryland.

5 jobs I've had:
1. Selling car parts.
2. Chemistry lab demonstrator (like a TA).
3. Lead chemist at a phosphate fertilizer plant (thankfully only temporarily, although the town it is based in is one of the most beautiful locales I've ever seen).
4. Postdoctoral fellow.
5. Research Associate (this was the title the institution I was at used for postdocs who'd been around for too long).

5 people I'll tag:
Five people I don't know enough about (or want to know more about).
1. DocStymie.
2. JollyRgr (surprise we with things I don't know).
3. Professor in Training (if you can fit a meme in with everything else you've got going).
4. Bugger it. I'm stopping at three.

Wednesday, November 12, 2008

A week in the life of Dr. Odyssey

My last post was on having undergraduates do research. In the comments JLK asked:

Why be a professor at an MRU if you're not going to do your own research?

A simple question with a rather complex answer (or answers). The short answer is stuff happens. Read on for the more detailed answer.

I suspect the vast majority of us start our tenure-track positions at MRU's (Major Research University) fully intending to literally do our own research. Stand side-by-side with our trainees at the bench sweating over our own experiments. That was certainly my intent.

For the first few years it can be like that. But over time things change. We obtain new and more responsibilities. Grant writing. Publishing. Teaching. Committees. Reviewing (both manuscripts and grant proposals).

As we become more successful and better known the list grows. Study sections/review panels for grantmaking agencies. Traveling to give talks at other institutions. Meetings/conferences. Perhaps editorial duties at a journal. Service within scientific/professional societies. Even more grant writing. If you're lucky enough to gain "rockstar" professor status you can end up with even more of these responsibilities.

The time for actually doing our own research dwindles. I still manage to carve out some time to spend in the lab, but it's very limited. Instead we live vicariously through the efforts of the people in our groups. Instead of doing research we direct it. It's not that we don't want to do our own research. It's more that it's no longer in our job descriptions. By the time we hit mid-career (associate prof level - where I currently am) our job is to provide the environment, funding and intellectual background necessary for the research to occur.

Here is my week as an illustration (the current week, and just the weekdays). Note that my teaching load is very light compared to someone not in a College of Medicine.

Morning: I got in late (mid-morning) after taking one of my daughters to the dentist... I am an officer in a subgroup within a scientific society. I spent over an hour Monday morning dealing with subgroup business. This was followed by time spent in the lab helping an undergrad debug an experiment. I updated my blog while eating lunch.
Afternoon: More subgroup business. Finished preparing an exam I was administering in a 2nd year graduate student-level class Tuesday morning. Spent an hour working on a manuscript. Spent an hour with a student asking questions regarding the exam. Attended a seminar given by a candidate for an open faculty position. Talked to my lab tech about the protein prep she was working on.

Morning: Attended the chalk talk (future research presentation) given by faculty candidate. Proctored exam in grad-level class (we don't have TA's), met with the faculty candidate. Ate a sandwich before walking to other side of campus for...
Afternoon: Grad student committee meeting. Spent most of remainder of the day reviewing protocols submitted to the Institutional Biosafety Committee (IBC), of which I am a member. Talked to undergrad and lab tech about ongoing experiments.

Morning: Continued work on manuscript. Planned out project for a new high school intern about to join the lab. Wrote this blog entry. Will walk to other side of campus for...
Afternoon: IBC meeting. This will probably take at least two hours. At least they feed us... Hope to work some more on manuscript. Check with lab tech on results of a gel. Meet with new high school intern.

Morning: Start reviewing student travel award proposals for scientific society. Teach in 2nd year grad student course. Continue reviewing travel award proposals (there are 36 to do). Talk with undergrads in the lab about their projects.
Afternoon: Maybe spend two hours in the lab doing some research! Hopefully also work with lab tech learning new technique. Review more travel award proposals. Attend student seminar.

Morning: I try to spend Friday mornings working at home, mostly writing and reviewing. I'll try to get a manuscript review done and finish the travel award reviewing.
Afternoon: Meet with people in the lab. Attend weekly meeting held by a Center I'm part of. Get back to work on that manuscript.

Okay, so maybe I don't have 36 travel award proposals to review every week. I may have more manuscripts or grant proposals to review. Or other committee meetings. Or travel. And I haven't detailed any of the constant interruptions that occur during each day. You can see it's difficult to carve out big blocks of time to spend in the lab during the week.

Such is life.

I wouldn't trade it for anything.

Monday, November 10, 2008

Undergraduates in research

There are a couple of interesting discussions going on over at Isis's bright, shiny new home regarding how undergraduates should approach PI's they're interested in working with, and how said PI's interact with such undergrads.

I am a big proponent of having undergrads working on research projects. I like working with undergrads in the lab. They tend to be enthusiastic and willing to learn. I have pretty much always had one or more in my lab right from the time I started at Big State U. A number of them have been extraordinarily productive. During the almost 12 years I've been here I've published seven papers with undergrads listed as authors. Six of those have an undergrad as first author. Another, with an undergrad first author, should be submitted in the next couple of weeks. Some readers of my blog may recall that I am also PI on an NSF REU Site grant that pays for a bunch of students to come do research in the department each Summer.

Based on my experiences with these students I offer up the following:

For undergraduate students-

  • Choose the PI's you're thinking of approaching carefully. Just because they're working on something you think is cool doesn't mean they're a good choice. Do they seem approachable? Have they had/do they have undergrads in their lab? Do they have a large lab, which would increase the chance that you wouldn't have much interaction with the PI? Check out their website for a start.

  • Don't spam a bunch of PI's via email. Write each person you're interested in an individualized message. Indicate why you're interested specifically in them. Read up on the work they're doing. Every single undergrad who has ever worked with me scored a position because they had done their homework. And asked to talk to me.

  • Be honest about why you want to try your hand at research. We do know that many premeds want the experience to increase their odds of getting into med school. Personally I have no problem with that - I'm in a college of medicine after all. Some PI's don't want premeds in their labs for a variety of reasons, some quite good - if you're premed you probably don't want to be in those labs. Besides, if we know what you want out of the experience we are in a better position to help you get it.

  • A tepid reference letter for grad or med school from a "rockstar" professor won't help as much as an enthusiastic letter from a lesser known, more junior person. Tepid reference letters will often hurt your chances, not help.

  • Be enthusiastic and be prepared to work hard. And remember that the PI has many responsibilities and may not always be available when you want/need them.

  • Finally, keep in mind that many PI's at MRU's are not required to have undergrads in their labs. Paying tuition does not entitle you to a place in someones lab.

For PI's-

  • Undergrads are a lot of work. Even the really good ones. But they are, IMHO, worth the effort. Heck, I've got seven, almost eight, publications as a result of working with undergrads. And they're fun.

  • Don't take on an undergrad unless you're prepared to put in the work. You could assign them to a grad student or postdoc, but if you do, make sure you make some effort to stay involved in what they do. They came to work with you.

  • Having a trial period in which an undergrad does scut work (washing dishes etc.) is fine. Just don't make it too long. Using an undergrad as free scut labor makes you a jerk. If you're paying them to do scut work and have no intention of getting them involved in research, make sure they understand that before they start.

  • If an undergrad has earned authorship, give it to them. And put them in the right place in the authorship list. Bumping them out of a first authorship they've earned in order to give it to a grad student, postdoc or yourself makes you a serious ass wipe.

Undergrads can rock in the lab. If given the chance.

Saturday, November 08, 2008

Wednesday, November 05, 2008

Lab web site/wiki

In the comments to my earlier post on information management, Nat Blair wrote:

Here's another question though: what software do you use to store the tacit knowledge of the lab? Do you use a lab website to store some of that stuff? A lab wiki? Mostly just curious.

My answer at the time was that I wasn't using anything, but that I was considering implementing a wiki. There are a number of reasons why I hadn't implemented something. One was the draconian approach the administration here at Big State U. takes to any kind of web site created and maintained by faculty. A second was that implementing a wiki would require a substantial commitment of time on my part to get the software installed and running, plus an ongoing commitment to maintaining the software. I'm quite capable of doing this - I have a background in computational biology, although my lab is almost purely experiment-based now - but I'm not sure I can devote the time required. Nat's question did however spur me to spend some time looking for a simple solution. And I found one.

Google Sites.

There you can create a free web site with up to 100MB storage space. And, importantly, you can limit who can view and alter the site (e.g. upload or download stuff). Google (typically) provides a bunch of easy to use web-based tools for creating a site. So, with about two hours work I set up an intra-lab web site. I've uploaded many of our protocols and pdf's of some useful papers. There's a section including links to the web sites of the various vendors we commonly use. I've included a list gadget where any lab member can type in things that need to be ordered. Soon I hope to include a calendar gadget that will display everyone's schedules, including mine. It's a work in progress, but I think we're finally moving out of the dark ages with regard to lab information management.

Monday, November 03, 2008



How the hell did that get published?????? [Updated]

[DISCLAIMER: This post was prompted, in part, by recent posts over at Isis's temple and DrugMonkey's cage. One should not take the following as a comment on the paper under discussion there - I have not read it and it's way outside my area of expertise, so I'm not making any judgments about it whatsoever.]

All too often I find myself reading a peer-reviewed paper and wondering how on earth it managed to get by the reviewers and editor, and end up being published. In a reputable journal. I know many of my colleagues have the same experience.

I'm not necessarily talking about disagreeing with the interpretation of data. Rather, it's a matter of poorly executed, incorrect or missing experiments, lack of suitable controls, incorrect statistical analyses, egregious lack of, or incorrect, citation of other published work in the area, etc. In other words, truly bad papers.

How do these get published? I don't know, but I would like to offer a couple of suggestions based on my experiences on the editorial board of a mid-level journal. First up, let me state that I am a strong believer in the peer review process. I am also well aware that it has it's flaws. Secondly, a little background...

Here's how things are supposed to work at the Journal of Doodlewidgets. When a manuscript is submitted, the authors must supply the names of four potential reviewers plus suggest a member of the editorial board as someone suitable for handling the review process. The Editor then assigns the manuscript to an editorial board member (EBM), who may or may not be the one suggested by the authors. The EBM is then supposed to read the manuscript and decide if it's good enough to send out for review or whether it should be rejected without full review. Those manuscripts deemed good enough are then sent out for review. When the reviews are returned to the journal, the EBM makes a final decision (accept, reject, major or minor revisions) and the authors are informed. Many journals in my field have similar processes for handling submissions.

Here's where I see the system breaking down too often: at the EBM level on two counts.

1) As noted above, at the Journal of Doodlewidgets the EBM is supposed to read the manuscript and decide if it's good enough to send out for review. In other words, the EBM is supposed to perform a preliminary review of the manuscript. I suspect (know) this doesn't happen in many cases. There are those who join editorial boards just for the extra line on their CV's, and who can't be bothered with applying the required effort. It's not clear how to handle these people. The obvious answer is to boot them, but that's not so easy if the offending party is a Big Cheese. Journals like to have Big Cheese's on their boards for the cachet. And don't want the negative publicity that might occur if they boot a Big Cheese...

2) The bigger problem lies in the choice of reviewers. It's all too easy to send the manuscript out to two (or more) of the suggested reviewers. Problem is, those people are likely good friends of the authors. We all play that game. We suggest people we know who we think will review our manuscripts fairly. Or, in the case of a (hopefully) minority of authors, automatically favorably. In some cases, authors suggest ex-co-authors or collaborators. The corresponding author of a manuscript I handled recently listed as a suggested reviewer someone they were co-authors with on a manuscript in press! Needless to say that's just not on.

So, it's possible that a given manuscript receives reviews that are more positive than they should be, and the EBM (who hasn't bothered reading the manuscript) simply accepts them at face value. Or the EBM is good friend of one of the authors and over-rides a more negative review. Or, perhaps the manuscript is somewhat outside the EBM's area of expertise, in which case they assume the reviews from the suggested reviewers are legit. In the end, a substandard manuscript can end up being accepted...

Note that this is the opposite of the usual reviewing issue (reviewers being too harsh) often discussed on the blogosphere. And I'm ignoring the issues of lazy reviewers - a good EBM should pick up on those - or unqualified reviewers - which is the EBM's fault for using them.

It's not clear how to deal with this. If all EBM's were conscientious it wouldn't be much of an issue. But how do you ensure that the editorial board is stocked with only the good? I suspect Editors have some idea of who's dead wood, but since there are no good metrics for measuring EBM performance...

EBM's could ignore the list of suggested reviewers, but then what's the point of making authors go through that process? And most authors are probably making legitimate suggestions. You could simply scrap the idea of having a list of suggestions, but then it becomes a real crapshoot if you have a lazy or somewhat unqualified EBM handling your manuscript.

I don't know the best way to fix this, or even if it's as big an issue as I perceive it to be, but I do have three suggestions. The first is for EBM's to use at most only one of the suggested reviewers. Yes, that means making some EBM's work harder, but it's not that much effort. I know because this is what I do. My second suggestion is to require authors to submit a list of people who should be excluded from reviewing due to various conflicts of interest. By this I mean the kind of thing the NSF requires from people applying for a grant. A list of all co-authors and collaborators over the last four years. Plus postdoc and PhD mentors. Okay, so that's a bunch of work for the authors, but you do want that manuscript reviewed fairly, right? And you do want to see fewer crap manuscripts accepted, right? If you keep a running list, it's not that much work. Alternatively, suggesting inappropriate reviewers could be made grounds for immediate rejection, but that can be a difficult call for even the most conscientious EBM.

And finally, the EBM's name should be included in the paper. That alone should improve matters.

And thus endeth yet another long post.