So you want a piece of the NSF pie? Scope and budget.

Herein I continue my somewhat disorganized discussion of NSF funding...

Necessary disclaimers can be found here.

Okay, so now you've had a chance to study NSF's award statistics, it's time to think about the scope of an NSF proposal. Let's face it, a five year, four/five specific aim proposal probably isn't going to fly. Most proposals funded by the NSF appear to be for around three years and have a modest budget. Poke around here to see what the NSF has funded in your area recently to get a better idea of what you're dealing with.

The budget is all important here - it will define the scope of what you propose to do. Remember, those median annual award sizes are totals - direct plus indirect costs. Obviously if you are at an institution with a high F&A rate (say 90%), you're going to be able to ask for more than the median amounts. But don't get greedy - the NSF has limited funds. If your F&A rate is more modest (say around 50%), think in terms of the median amount. Figure out what the median direct rate would be - that's roughly what you'll have to work with (in practice, if you're funded, you're likely to take a modest budget cut, but don't worry about that too much). Let's say you're applying to the BIO directorate, MCB organization, Molecular Biophysics section (one of the more generous sections and the one I'm funded through), and have a F&A rate of 50%. The median direct costs (using the 2007 median annual award) are then:

Directs = $159,113/1.5 = $106,075

Basically $100k/year for three (maybe four) years in this example (remember - your mileage will vary). So the important question becomes what can you do with that? The answer will define the scope of your proposal.

What you can do with that amount of money is highly dependent upon the kind of work you do and the type of position you have. I'm in a college of medicine where each PI pays the stipend and benefits (but not tuition - yet) of their graduate students (no TA's). I might just be able to pay two students based on an award of $100/k per year if I'm very, very careful (i.e. miserly). Or one postdoc and part of a tech's salary. Etc. These considerations clearly limit the scope of what I can propose to do with an NSF grant. In the end I've found two specific aims are about all I can manage. If you're in a setting where TAships for grad students are plentiful, perhaps you can manage more.

Something to keep in mind while we're on the topic of the budget. The NSF will only allow you to pay two months of your salary per year from all sources of NSF funds you have access to. Recently there was a discussion at DrugMonkey's place about this. Let's take me as an example. I'm PI on an NSF research grant and on an NSF REU Site grant. If I get 0.5 months salary from the REU grant I can only take 1.5 months salary from the research grant. NSF doesn't appear to care how much of your salary comes from grants from other agencies.

One last thing while I'm thinking about it. Should you get an NSF award (congrats!), there are two types of research grant; Standard and Continuing. You have no say in which one you get. If you're awarded a Standard grant you're given all the money up front. If you get a Continuing grant you get one year's money at a time. Each new year is contingent on an annual report you have to submit (you have to put these in with Standard grants too). I've always had a Continuing grant and have never had an issue with obtaining the next year's money (I am quite diligent about putting in the required report). I've also never heard of anyone not getting their next year's money, but I suppose it's a possibility.

So you want a piece of the NSF pie? The NSF is NOT the NIH.

I've decided to put down some thoughts of mine regarding obtaining funding from the NSF. This will likely end up being a series of posts...

First, the necessary disclaimer: These are my opinions only, shaped by my experiences as an NSF-funded investigator (in a College of Medicine), a reviewer of NSF proposals, plus the experiences of some friends and collaborators. Your mileage will almost certainly vary.

Second, some background: I was awarded my first NSF grant in 2001. I renewed that in 2004 and have recently heard that my second renewal has been recommended for funding. I am also PI on an NSF REU Site grant. I have reviewed many NSF proposals, most from the BIO directorate and some from MPS, on an ad hoc basis. Finally, I sat on an NSF SBIR review panel for two years.


Now, let's get down to business here. If you're in the biological sciences, please repeat after me:

The NSF is NOT the NIH.

Keep repeating this until you are firmly convinced of the truth in that statement.

Now you would think that that's obvious, right? Apparently it isn't to about 25% of the applicants whose proposals I've reviewed for the BIO directorate...

Here are some, but not all, major differences:

1) Budget-

The projected FY 2009 NIH budget is $28.7 billion for R&D expenditures. The NSF? $4.5 billion for R&D. This is under the current Continuing Resolution. See the AAAS September R&D Update to see where I got these figures. These numbers have a very profound effect on many aspects of NSF funding versus NIH...


2) Mission-

The mission of the NIH is "science in pursuit of fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to extend healthy life and reduce the burdens of illness and disability."

The mission of the NSF "includes support for all fields of fundamental science and engineering, except for medical sciences." [Emphasis mine.]

The NIH funds biomedical research. The NSF funds all of the other sciences. Including social. Plus engineering. And mathematics. And the NSF mission includes a strong science education component (which I believe accounts for the disparity between the $6 billion total budget of the NSF versus the $4.5 billion it spends on R&D).

So, don't go proposing to solve cancer, or heart disease, or Alzheimer's in your NSF proposal. If you do I can pretty much guarantee it won't be funded. Basic biological science is fine (otherwise I wouldn't be funded), so there is some overlap between the NSF and NIH. But you need to be careful about how you sell your basic science to the NSF. Can't figure out how to sell your science without referring to the medical benefits of the research? Don't bother applying to the NSF.


3) Scope-

The scope (budget and period of funding) of an NSF proposal is very different to that of an NIH R01. The NSF keeps some interesting funding statistics. If you're considering applying to the NSF, go find the data for the last year or two for the directorate and organization (within the directorate) you are most likely going to send your proposal to. Study those numbers. Not the funding rates. The mean award duration and median annual award size. Your proposal needs to be in the same ballpark as those numbers (unless you're applying to a special program with special budget instructions). Sure, you can ask for more time and/or money, but you'd better do a very, very good job of justifying why you need more.

Oh yeah, one other thing. Those median annual award sizes? That's total. Direct plus indirect costs.


4) Proposals-

Aside from the fact that an NSF proposal is limited to 15 pages versus the (current) 25 page limit at NIH, there are other differences. I'm not going to go into great detail here. I'll probably cover some of that stuff in later posts. The main thing is to go study the NSF review criteria. And take them seriously. Intellectual Merit pretty much refers to the quality of the science proposed (and of the proposer). That Broader Impact stuff? Not something the NIH puts much weight on. The NSF, on the other hand, is very serious about it. I'm going to write a post devoted purely to Broader Impacts since this is where I've seen many proposals fail. Particularly those form new investigators.


5) Effect on tenure-

This is aimed at those of you in a College of Medicine. I got tenure based on my NSF funding. Here that's considered sufficient to satisfy the funding part of the tenure equation (assuming you've done very well on all other parts of the equation). That is not the case in all medical schools. There are Deans of medical schools who consider NSF money second class at best and will not approve tenure for someone with only NSF funding. Be sure you know what the ground rules are at your institution.

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...

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.


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...




A bride!

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.

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.

Monday-
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.

Tuesday-
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.

Wednesday-
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.

Thursday-
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.

Friday-
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.

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.

What a Whiny Poor Loser...

...Palin has turned out to be.

Good riddance.




At least for now.

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.

Vote

Please.

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.

Information management tools

The key to success as an academic scientist lies in successful management of two vital resources: time and information. Poor management of one or both of these will make success (as measured by the usual metrics of tenure, grants and publications) extremely difficult, if not impossible. I've been thinking about information management recently (I'll save time management for another post).

We live in the information age - ready access to the internet can easily lead to information overload, a debilitating condition that can lead directly to a lack of focus and an inability to act efficiently. This isn't the first time people have had to deal with information overload (or at least worried about it). James Burke notes in The Knowledge Web that the powers that be were concerned that the printing press would overload the citizens of the time with worthless knowledge (or more likely, knowledge the overlords would have preferred kept to themselves), so both church and state imposed strict censorship. Efforts to censor the internet have, so far, failed. In fact the internet has become such a ubiquitous part of our lives that I suspect any large-scale censorship efforts are doomed to fail.

So how to manage the vast amounts of information flooding our professional lives? Here I'm referring to external sources (i.e. not the flood of data from your lab). Buggered if I know a really good answer to that. I do know that the first step is to filter. Ruthlessly. The vast majority of the information flooding my academic life is useless, irrelevant and/or unimportant. Delete it. Block it. Just get rid of it. Otherwise you'll spend your days whacking useless moles.

Below I describe the tools and/or approaches I use to handle the bulk of the rest of the information. Your mileage may vary. I'd welcome comments from others describing other ways to handle this stuff. Note that I'm a Mac user, so some of the stuff I describe is Mac-centric.

Email
I find if I don't handle important emails within a day they tend to get ignored for too long. So I reply to the important stuff within a few hours when I can. Everything else is filed away or deleted. In some cases I've set up signatures I can use as a sort of form-letter reply, but I only use those for form-letter-style emails (e.g. the dozens of form-letter emails I get a week from people looking for a position in my lab).

And I make liberal use of Apple Mail's junk mail-learning feature.

I do tend to keep copies of most non-junk emails. I have set up numerous folders in Mail for this purpose. This has proven very useful at times when I've wanted to track down some piece of information I was sent some time ago.

iGoogle
I have a personalized home page I've set up with iGoogle. Right there on the front page I have gadgets for Google Reader, Google Calendar, Gmail Contacts, and gadgets I've created myself (a very easy process) for access to Big State U.'s web interface to email, links to my lab's homepage and various other links I use several times a day. My homepage also has a set of tabs linking to other personalized pages with gadgets for Google Docs and Google Notebook, various search engines (PubMed, Google Scholar etc.), the news, weather etc. etc. This is all very easy to set up and puts a whole bunch of stuff I use a lot all in one easy to access place. Furthermore, I can access it from any computer connected to the internet.

Google Reader
I love Google Reader. I have journal table of content feeds, grantmaking agency feeds, feeds from ISI's Web of Knowledge tracking citations to my published work, etc.* All in one place. Makes dealing with all that stuff really easy.

I just wish I could get my saved PubMed searches fed into Google Reader... Anyone know how to do that?

Calendars
Alright, so these are really time management tools, but they contain information too. I like iCal on the Mac. I have it synced with Google Calendar (via Busymac shareware - I'm too cheap to invest in MobileMe). This allows me to keep iCal on Macs at home and work all synced. And give me access to my calendars via my iGoogle home page. Any changes made to any of the calendars is automatically transmitted over the internet to the others. Cool.

Address Books
It's good to have the same address book on my Macs at work and home, my cell phone, and in Gmail Contacts. Good, but not as easy as I would like. My cell phone has Bluetooth, so that's not too bad. I did need a plugin to get it to play nice with Apple's iSync, but that was easy enough. Syncing the Mac Address book with Gmail Contacts isn't so easy (unless you have an iPhone or iPod Touch...). I use a little freeware program called A to G to help with this. Unfortunately any changes I make on either Mac or on Gmail Contacts isn't automatically transmitted to the others... Apparently this is being added to Busymac at some point. SpanningSync is another option for Mac users, but is a subscription service.

One day I'm getting me one of those newfangled iPhone gadgets...

Google Notebook
I've just started using this as a sort of glorified To Do device. I have notebooks with short-term plans for my various research projects, one for a new project I'm planning, one for non-research lab-related plans etc. The jury is still out on this one, but I like the idea of having ready access to this kind of stuff from where ever.

Bookmarks
You could keep track of bookmarks via Google, but I find that a little cumbersome. I use Firefox as my main browser and have downloaded an Add-In called Foxmarks. This syncs my bookmarks from Firefox on my Mac at work with that at home via the internet.

References
Back in the Dark Ages when I was a grad student I used to make photocopies of papers relevant to my research. This continued into my postdoc years. With the advent of PDF's I began printing them out. A lot of trees died. A lot. Early on as a postdoc I realized my ever-growing pile of papers was getting out of hand. So I hit on a system of labeling them before filing them away after reading. I started numbering them, starting at one. I'm now up to 2310 (I keep a note of where I am, and no, I haven't actually read all 2310 in detail, just most of them). That way I could file the papers numerically. At about the same time I started using EndNote. EndNote has a field called "Label" for each entry - that's where I put my numbers. So I can look up a paper in EndNote and find it in seconds in my files. In recent years I've tried to wean myself of the environmentally-unfriendly habit of printing out every paper I think I want to read. Instead I try to save and read the PDF on my computer. I rename each PDF with a number and enter it into EndNote with the number in the "Label" field. That way I can look it up and find it on my computer in seconds. And the Mac search feature, Spotlight, can be used to search via keywords etc. to dig up all papers related to a certain subject.


That's it for now. As I said above, I'd welcome comments from others describing other ways to handle this stuff.

Damn I'm getting into the habit of very long posts. Perhaps I should market them as a cure for insomnia...





* I like to know where my work has been cited. In part because it helps me keep track of the field, and in part because of vanity. :-)

Dear Graduate Student...

At Big State U. all graduate students have an advisory committee that generally consists of their mentor, two (sometimes three) other faculty from their department and one person from outside their department. Right now I'm the outside person on three such committees. Two years ago I was part of the qualifying exam for one of these students. I came very, very close to failing her at the time because she demonstrated an almost complete lack of knowledge regarding some of the methods she was using. I happen to know quite a bit about those techniques since I helped develop them. I believed at the time that that's why I was asked to be on this committee. Apparently not. The student was surprised to find out I knew something about these techniques... Anyway, I passed the student in the end because she seemed to have a pretty good grasp of the other aspects of her proposed research. I told the student I would be more than willing to help her understand and use the techniques in question. I have seen nothing of her since (she's in a different building on a different part of campus so there's very little chance of running into her).

Now here at Big State U. graduate students typically have a meeting once a year with their committee to keep the members updated on the student's progress. Students are also encouraged to talk to their committee members on a regular basis (although distressingly few do so). Last December I remembered that we should have probably had a meeting with this student by then, and emailed her asking her if she would be setting one up soon. She replied that she hadn't really thought about it, but that it might be a good idea... Nothing further happened.

In April she sent out an email to her committee asking when they would be available to meet. Now asking four faculty members when they're available without providing potential times never works. I and one of the other committee members both replied that it would be a good idea for the student to provide a list of potential times so committee members could then indicate which would work. She replied that this seemed like a good idea... Nothing further happened.

About ten days go (it's October now) I get this email from said graduate student:

Dear Dr. Odyssey,
I am beginning my job search and would like to use you as a reference.
Sincerely,
Graduate Student

Here is the ensuing email conversation that occurred:

Dear Graduate Student,
I am very surprised to hear that you are looking for a job. I assume that means you believe you will be graduating soon. I'm afraid that I cannot agree to act as a reference for you since I have no idea of how your research has been progressing. We have not had a committee meeting in two years and I have not seen you in that time.

I am also puzzled that you seem to believe you will be graduating soon. Typically the student needs the okay of their committee before starting to write their dissertation. I strongly suggest that you set up a meeting as soon as possible so that you can discuss this with your committee.
Sincerely,
Dr. Odyssey




Dear Dr. Odyssey,
I have not been able to set up a committee meeting over the last two years because I haven't been able to find a time when both I and Dr. Mentor's Other Graduate Student can have a meeting at the same time. Other Graduate Student has three committee members in common with me and we want to save them time by having a committee meeting together.

I will be starting to write my dissertation by the beginning of November and hope to set up my dissertation defense for February.

I will do my best to set up a meeting by the end of the year or early next year. You can decide then whether you will act as a reference for me.
Sincerely,
Graduate Student


Note: I am not on Other Graduate Student's committee. I strongly suspect the one person on that committee who is NOT on Graduate Student's committee is the outside person. It pretty much has to be.



Dear Graduate Student,
You really cannot have a committee meeting with Other Graduate Student. Each student needs to meet with their committee separately. I happened to run into one of your other committee members today and he has assured me that he does not want a joint meeting with Other Graduate Student.

Additionally, perhaps you did not quite understand my last email. Here at Big State U. you need your dissertation advisory committee to agree before you start writing your dissertation. Although this is generally a given, it cannot occur without a meeting of the committee. You need to set up a committee meeting as soon as possible.

Finally, I stand by my decision not to act as your reference. I have had no contact with you in two years and do not feel I could write a reasonable letter.
Dr. Odyssey




Dear Committee Members,
I am hoping to set up a meeting sometime in the next six weeks. When are you available?
Sincerely,
Graduate Student


Sigh... I sent her an extensive list of times I would be available.

About five days pass with no further emails from Graduate Student. Then, late yesterday:

Dear Dr. Odyssey,
I cannot set up a committee meeting at this time. The one member of Other Graduate Student's committee who is not on my committee is traveling and hasn't replied to our emails.
Sincerely,
Graduate Student


I haven't replied as yet... Obviously a call to Dr. Mentor is overdue. I strongly suspect that some of this is driven by Dr. Mentor, so it won't be a comfortable call.





Oh, and I do understand that I and the other committees members share some blame here. We have not been particularly aggressive in trying to get Graduate Student to organize meetings and I haven't made any efforts to meet one-on-one with her.

Notes from a small meeting

I'm back. Did you miss me?

Overall the meeting in the Armpit of the Midwest went very well (for me). I came away with a seminar invitation, ideas for a couple of cool experiments to do, and a bunch of good suggestions/ideas relating to my fledgling new research program. I also had a very informative and productive two hour lunch with Mega-Big Cheese (recent NAS inductee), Super Big Cheese and Former Postdoc Mentor (also a Super Big Cheese). To what extent I swayed the NSF review panel members who were there is an unknown of course. I've done what I can and now it's time to focus on getting stuff done for the resubmission should it be necessary...

Here are some observations from the meeting:

• When giving a 30 minute talk, it's probably not a good idea to spend 20 minutes introducing a subject that everyone in the audience has a good grasp of, 2 minutes on data and 8 on (over-reaching) conclusions... It would have been one thing if a graduate student had done this, but sadly it was a rather senior and well-known PI.
  
  
• If you're attending a highly-focused meeting on thingamabobs and present a poster on doozits (which aren't related to thingamabobs at all), don't be surprised if very few people show any interest. And don't spend the remainder of the meeting complaining loudly that very few people showed interest.
  
  
• If you're organizing a small meeting and want to have all of the talks loaded onto a single laptop, make the laptop available to speakers more than five minutes before each session starts. And use a PC (or at the very least warn all speakers in advance that you're going to use a Mac). I'm a Mac person, but even I recognize that, thanks to Micro$oft, Powerpoint slides made on a PC often don't work on a Mac, whereas the opposite usually (not always) works. It was very painful watching two inexperienced graduate student speakers struggling with screwed up slides that were prepared on a PC but didn't work on a Mac. And it wasn't their fault - they weren't given the time to look over their slides on the Mac prior to their talks.
  
  
• If you're organizing a small meeting, don't insist all talks are loaded onto one laptop. Get a switch.
  
  
• Just because you used to be a Big Cheese (no, you used to be one, but really aren't anymore - study sections have been telling you that for a decade, and rightly so) does not mean you get to ask off-topic questions after every talk.
  
  
• It's okay to canvass the powers that be to elect you organizer for next year's meeting. That's how it works. It's not okay, after being elected, to tell everyone that you didn't canvass. It's a small group. We're all aware of who does what. Now you look like a jackass.*
  
  
• Poster making is an art form. There's a lot of really bad art out there. Really bad.
  
  
• The right amount of beer + the right amount of wine = good science. Usually. Too much beer + too much wine + one graduate student = a messy job for the janitor.
  
  

* And before anyone leaps to the conclusion that this is sour grapes on my part, I organized this meeting a few years ago and am therefore not eligible to organize it again. That's how this one works.

The Armpit of the Midwest

Tomorrow I leave for a small, but extremely good, meeting being held just outside a small city I refer to as the Armpit of the Midwest. There are worse body parts you could name a city after, so clearly this isn't the worst place in the Midwest. But it's not great. Obviously I'm not going for the location. No, this is a very good small meeting that is not advertised, so it's kind of clubby, but is extremely rigorous. The most rigorous meeting I know of. The participants all tend to be good-natured, but present a poor or incorrect analysis, or inappropriate statistical analysis (or heaven forbid no statistical analysis!) and they will hand you your head on a platter. After having sliced, diced and julienned it. Followed by a quick puree. In the nicest possible way of course.

This is where I'm hoping to bolster the chances of my recently submitted NSF proposal. At least two of the review panel members will be there. I didn't get as much done as I had hoped - the central protein in my new research direction is a pain in the butt to make. I have managed to improve our expression and purification protocols to the point where we're getting a yield 3-4 times larger than at the time of grant submission. This was important because biophysical work can require a lot of material. And we've finished a couple of new experiments, but not the ones I had hoped to do. Oh well, I have what I have.

This is an important reason for attending meetings. Meetings are useful for improving the odds of getting funded. One could even view this as the main reason to attend a meeting. You should aim to impress the people who will/are reviewing your proposals. Your goals are to convince them that you're someone worth funding and, if you have a proposal pending, that you are making progress.

Hopefully I can do the above in the Armpit of the Midwest.

Two parties

Nope, not the political kind. A couple of weeks ago I was at a graduate student's oral qualifying exam. After we had all asked questions and it was clear that the the student had passed with flying colors, one of the other faculty asked the following question (accompanied with the qualifier that the student's answer's had no bearing on whether or not they passed):

You are going to hold two dinner parties. For the first you can invite any four scientists, living or dead. For the second, any four famous people who are/were not scientists, living or dead. Who would you invite and why?

I forget the student's precise answers, and for this post they're not important anyway. The first party was a test of the student's breadth of knowledge of science in general (including it's history). The second had to do with the student's knowledge of topics other than science. The faculty member wanted to stress the importance of knowing much more than just your own narrow little area of research.

I think I would invite the following (putting aside all potential communication issues):

Science soiree:

Josiah Willard Gibbs - he was the most under-appreciated theorist of his time. Perhaps ever.
James Clerk Maxwell - not just a famous theoretical physicist, but also a poet! Albeit not a great one... And a contemporary of Gibbs.
John Edsall - a protein chemist's physical chemist. I had the pleasure of meeting him once. A wonderful gentleman.
J. Robert Oppenheimer - someone who went from being the most influential scientist of his time to a victim of McCarthyism has got to be worth a dinner party. And he hiked around Corsica with John Edsall when they were both young.

Hmmm, obviously I have a thing for the physical sciences...


Celebrity carouse:
Ludwig von Beethoven - how he wrote his Ninth Symphony while deaf is something that has always fascinated me.
Picasso - no doubt he would keep the conversation interesting (and wine flowing).
Euripides - of the few authors of Greek tragedies whose work has survived, he is my favorite.
Charles Dickens - despite the best efforts of my high school English teachers, I really enjoy his books and their insight into Victorian England.



So, dear readers, who would you invite and why?

Five year plans

I had mentioned the use of a five year plan in a previous post describing my mid-tenure crisis. An anonymous commenter asked:

I was just curious about your 5 year plan...how detailed is it? For example, do you plan out the number of pubs per year? Do you plan out which/how many grant deadlines to target? (All Without knowing how the data will turn out!)

...which spurred this post.

I first came across the idea of a five year plan in Kathy Barker's At the Helm. I would recommend anyone about to start their own lab get a copy of this. I don't have my copy in front of me right now and I don't remember precisely what she says about five year plans (other than she recommends having one), so the following are my thoughts likely heavily tinged with hers.

Some opening points.

1) Not everyone will find this useful. Some/many people are quite good at managing their academic careers without something like this. I wish I were one of them.

2) This is something that needs to be referred to often and requires constant updating. Like your CV. You do update your CV regularly, don't you?

3) This is a medium- to long-term planning tool (i.e. six months up to five years). Anything short-term (less than six months) probably belongs in a calendar.


Why have a five year plan?

The simple answer is to get to where you want to be.

If you can't picture precisely where you want to be and what you want to be doing in five years, you need to figure out a) where and what, and b) how you're going to get there (i.e. a plan). Writing it down helps. If you can picture the where and what, you probably still need a plan.

Note that I used the word want above. No one can guarantee where you'll be and what you'll be doing. What is guaranteed is that you won't arrive at your destination without constantly thinking about how you'll get there.


What should be in it?

Anything that helps. But it must be obtainable. And somewhat specific ("get tenure", although obviously a great goal, isn't specific enough to be of any use). Entries must have definable target dates (which can be somewhat fuzzy, e.g. "late 2010"). What ends up in a five year plan is going to depend on where you are in your career and what the demands of your particular field are.

I use three (not mutually exclusive) categories for entries: Research, Career, and University.

Research
This includes anything research-related. Most of my entries involve funding. Be reasonable here. Yes, it would be nice to have:

Fall 2009: Get R01 for work on thingamajigs.

But being realistic, I would have:

Fall 2009: Submit R01 proposal for work on thingamajigs.

I also outline possible specific aims under a grant entry. These tend to change as the work evolves.

I also follow up with entries like:

Spring 2010: Resubmit R01 proposal for work on thingamajigs if necessary.

Something else I've included in my plan is a major equipment proposal for a time-resolved fluorimeter. This is something we don't have that would be very useful in my work. It would also be useful for others on my campus. So I have a set of goals with deadlines leading up to submitting such a proposal. One such goal was to organize a group of funded PI's who would benefit from this instrument. I've done that and that item has been deleted from my plan.

I do not include publishing research papers. I seriously doubt anyone can predict what research papers they will publish two, three, or more years from now. On the other hand, I would include plans for reviews and/or book chapters.

Career
Here I include anything to do with forwarding my career (other than the Research items above). Here I included getting myself on a Society committee (I was a little too enthusiastic with this and ended up on two...), some specific networking goals (I suck at networking...), volunteering for a foundation review panel, etc.

University
This category contains anything related to teaching and/or service within Big State U. For example, I recently became course director for an advanced graduate level course that had been stagnating for some years. I have goals for what I want the course to become and have entries in my five year plan dealing with each goal.

I also run a NSF-REU site and have specific goals for that outlined.



I do keep track of the goals I've met and those I haven't. As long as the former greatly outnumber the latter I figure I'm doing okay.

And that's it really. Nothing earth-shattering. Just a list of reasonable goals that help keep me on track.


Hmmm, the above sounds rather like an entry in a self-help book. Sorry about that.

Jon Stewart rocks!

Sarah Palin Gender Card

(Sent to me by RST.)

Sounds like science

Why is this thus? What is the reason for this thusness?
Artemus Ward, US humorist (1834 - 1867)

Mid-tenure crisis

I have a confession to make. About a year ago I had managed to put myself in a position that should be avoided at all costs. In regards to my research program, I had become...



complacent.



This is a bad, bad thing that no PI should ever do. I had been cruising along for about 7-8 years working away on a system, publishing a decent number of decent papers that garnered decent citations. Then about a year ago I was sitting on a bus going from Forsaken Conference Site in New England to the Boston airport. Sitting next to me was my good friend Rising Star Theoretician. RST turned to me and said, in more or less these words, "Your research program is going nowhere and you're in danger of becoming irrelevant." This was neither easy to hear, nor easy for RST to say. But he was right. Deep down I had known this for at least two years, but things were trundling along okay, so there was no immediate incentive to do anything about it. RST reminded me that there is always incentive to tend to the future of your research program. Having a future research program is the incentive.* I will always be in debt to RST for giving me a verbal kick in the pants.

I got lucky twice here. The first time was with RST's pep talk. The second time was a few months after that. I had just read a paper written by Benevolent Bioscientist, someone who had co-founded the field I was hoping to develop my new research program in. For reasons that are still unclear to me, BB had befriended me about a year previously and so I now knew him quite well. Anyway, the predictions he had made in this paper struck a chord. THIS was where I was headed. Or at least, some part of it. So I called BB to chat about his paper and the many opportunities it offered. BB told me I should work on protein X (one of the opportunities outlined in his paper). He said "I've been meaning to work on X for 10-15 years now and, to be honest, I don't think I'm ever going to get around to it. You should do it. Let me know how I can help." I knew protein X was important and I knew this was a generous offer. What I didn't quite grasp at the time was how important protein X is, and consequently how generous a gift this was. Protein X is a key player in not just one, not just two, but numerous disease states, including mental, cardiac and immune system disorders. And it's not understood at the molecular level. Protein X is an untapped goldmine that will lead to publications that are much more than "decent." And will lead me to NIH funding (I'm NSF-funded because of the nature of my previous work).

So here we are about a year after RST's pep talk. The old research program is (in hindsight predictably) rapidly dying. I have about one more decent publication I can squeeze out of that work. The all new research program based on protein X is still in its infancy, but it's growing stronger each day. Working on protein X has meant learning a whole new set of skills (I didn't train as a protein chemist), but fortunately I'm surrounded by colleagues who are willing to help. The timing is unfortunate (purely my own fault). I had to submit a renewal of my NSF grant in mid July. Obviously it had to be on protein X (there's plenty of basic science regarding X). It's not clear I had quite enough preliminary data (protein X is difficult to make because of its interesting properties), so I may be facing a funding gap for the first time.** But I'm having a blast in the lab. In fact, I'm more enthusiastic about my research than I have been in years. Staring from scratch again has been, and continues to be, hard. But I'm having fun.







* Have a written five year plan. It sounds dorky, but it works, and it should cover all aspects of your academic career. Read it and update it often. Never let your plan fall below the five year mark. If you can't see where your research might be five years from now, start developing a new research project with long term potential. Now.

** I'm working hard to avoid this. I will put in the two page update in the Fall, although I'm well aware those don't buy you much. More importantly I'll be presenting our data on protein X at a small meeting in early October. A number of the review panel members will be there, as will at least two of the people I suggested as reviewers (NSF does use reviewer suggestions - you'd be a fool not to provide some). With the exception of a much-needed two week vacation, since July I've been busting my guts making protein X and doing experiments. Come the end of September I will have the data. I hope.

I'm a such a geek...

Scientists for Better PCR

My favorite lines:

"PCR when you need to find out who your Daddy is... (Who's your Daddy.)"

Bad Science

I'm back from vacation. It's amazing what lying on a beach watching the waves can do for your mental health. Not to mention the restorative effects of good food and libations. I have colleagues who firmly believe that if you wish to be successful you cannot afford to take vacations. I counter with if you wish to stay sane and productive, how can you afford not to take vacations?

While enjoying the beach I managed to finish reading Gary Taubes' Bad Science: The Short Life and Weird Times of Cold Fusion which was published way back in 1993. Remember the whole cold fusion debacle? In 1989 Stan Pons and Martin Fleischmann of the University of Utah announced via a press conference that they had observed nuclear fusion at room temperature in what amounted to little more than a sophisticated test tube. Taubes, a science journalist who publishes in places like Science, wrote this book about the whole affair including the work of many groups who tried to replicate the cold fusion experiment. It's a fascinating read. I was absolutely astounded by the shear volume of bad science that resulted from the Pons and Fleischmann announcement. A surprisingly large number of scientists who should have known better claimed to have observed cold fusion in some form or another without having performed any controls. And furthermore, no one was able to reproduce the effect consistently. In many cases they couldn't reproduce their results at all... Cold fusion clearly was complete nonsense and perhaps even constituted fraud on the part of some of its proponents. I would recommend people read this book, especially science students. It is a wonderful description of how science should not be done.

At one point in his book Taubes ponders why scientists tend to react so violently to bad/fraudulent science. The answer is quite simple really. We all need to trust the results of other scientists. Science is built upon science. We have neither the time nor resources to replicate all the experiments that our own work is built upon. Sure, experiments that appear to point to amazing breakthroughs or are counter to current dogma will be replicated (or at least people will attempt to do so). But the vast majority of the data published by scientists is assumed to be good data. So we get really, really pissed off when it's not.




Perhaps surprisingly, perhaps not, the cold fusion field is still alive...

Vacation at the beach

See ya in two weeks!

In praise of small grants

Yesterday I was informed that I was awarded a small grant. It's only $35k/yr. for two years. Still, that's enough to pay for a pair of hands in the lab for two years. It's enough to get a new project up and running, and to generate the preliminary data needed for a large grant application. And it's enough to keep my lab afloat should my NSF renewal (submitted last week) not be funded first time through.

Many department chairs (and deans) in colleges of medicine tend to think it's NIH R01's or nothing. Maybe an NSF grant, but clearly that's 2nd class money. Small grants such as those given out by many foundations? Complete waste of time. This is a very short-sighted view and, when NIH funding rates are low as is currently the case, can be damaging. Fortunately my chair doesn't think that way. And of course neither do I. In fact my chair, despite having 3 R01's, still applies for the occasional small grant. He uses them to try out new projects/ideas.

Don't get me wrong. One can't, and shouldn't attempt to, run a research program funded solely by small grants. And you cannot, and shouldn't, be awarded tenure if that's all the funding you have (at least not in a research intensive science department). And deans tend to dislike them because they either don't pay indirect costs or pay a small percentage.

[For my non-science readers, indirect costs are funds taken from a grant to pay for infrastructure (ie electricity, phone service, buildings, maintenance etc.). Dean's like this money - the more they have, the more power they have. Hence their dislike of grants that don't provide such funds.]

Still, small grants are wonderful things. As I noted above, they're good for starting new projects, paying for an extra warm body, and, if necessary, bridging lapses in more major funding.

Cover your butt syndrome

I have a grant from the National Science Foundation, a Federal agency, to run a Research Experiences for Undergraduates (REU) site. Basically this lets me bring eight undergraduate students into the Department to do research for ten weeks during the Summer. The grant pays them a stipend and covers the cost of staying in the dorms for ten weeks. On Friday afternoon I had an interesting phone call from the University accounting office:

After introductions and various pleasantries...

Accounting drone: "We have a bill from University housing that they want to charge to your NSF REU grant. We need you to send us a written justification for paying for dorm housing on a grant. And we need it in the next hour or so - this is the last day we can pay this off the last financial year of the grant."

Me: "There's a specific budget line item for covering these costs. We justified that when we applied for the money. And it's a requirement of the NSF that we provide dorm housing."

Accounting drone: "We still need a justification for why you're paying for dorm housing on a grant."

Me: "This is a grant for training undergraduate students and requires us to provide dorm housing. I don't understand why you need a justification when we already had to provide that when we applied for the grant."

Accounting drone: "It's in case we're audited."

Me: "Audited by whom?"

Accounting drone: "The Federal government."

Me: "Let me get this straight, you need me to justify spending Federal grant money on dorm housing mandated by the Federal agency that provided the grant in case the Federal government decides to audit us because the University is afraid that such a Federal audit might get it into trouble if we didn't justify spending Federal dollars on Federally-mandated dorm housing?"

Accounting drone: "Yes."

Me: "I see..."



To her credit, this was not accounting drone's fault, and she did send me a copy of someone else's justification to copy from (there's more than one REU site on campus). But still...

Windows, windows, everywhere

This is kind of a scary read:

Top Ten Worst Uses for Windows.

Two posts in one day?

I just had to share this with anyone who hasn't seen it yet...

I never win anything

I have a much less than stellar record when it comes to winning things. Contests, lotteries, gambling of various sorts. It's not clear to me whether fate is conspiring against me or I'm just a living demonstration of the odds against winning those sorts of things...








But things can change. I just won a blue one of these! The 8GB version. Just for filling out a survey for a foundation that supports research into a particular disease. Happy, happy, joy, joy!

Book amusement

Here's some amusing tidbits regarding my book:

1) It's available on the publisher's web site for US$71.10. If you think that's expensive, check out Amazon.com. Amazon list it, but don't sell it. Instead they refer you to International Books who are selling it for US$183.93!!!!!!

2) On the Amazon page for my book it has the following section:

Suggested Tags from Similar Products

intelligent design (44)
delusional (27)
creationism (25)
apologetics (21)
evolution (19)
science (19)
religious fiction (15)
science fiction (10)
elitist (8)
unwise decision for cardiac health (1)

Okay, "delusional" and "science fiction" maybe I can deal with, but "intelligent design", "creationism", "religious fiction" and "unwise decision for cardiac health"?????

Das book

Published at last.

The book that is.

Woo hoo!

Home alone

Tomorrow morning the lovely L leaves for a four day visit to New Orleans with a girlfriend. I'm staying here with the kids.

It will be alright.

Really.

Honest.













Help?

An unfortunate headline?

Or at least a mildly amusing one.

http://news.bbc.co.uk/2/hi/science/nature/7390109.stm

Word of the day

stu·pid   (stōō'pĭd, styōō'-)
adj.   stu·pid·er, stu·pid·est
1. Slow to learn or understand; obtuse.
2. Tending to make poor decisions or careless mistakes.
3. Marked by a lack of intelligence or care; foolish or careless: a stupid mistake.
4. Dazed, stunned, or stupefied.
5. Pointless; worthless: a stupid job.

Example: This country wants to turn millions of tons of corn into greenhouse gas-creating fuel for cars while a large fraction of the world's population is starving.

Things that are sacred

India:



United States:



Interestingly, both emit noxious gases...

My thought for today

Ignorance is not bliss.
Ignorance leads only to pain and suffering.
True happiness comes only through knowledge and awareness.

So apt...

One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.
- Francis Crick.

Some blather to ponder

- Here's an interesting dichotomy:

I keep my work computer well organized. Everything is filed in appropriate folders, subfolders, sub-subfolders etc. Email is generally answered promptly and filed away. But my office... There are so many piles of paper it's hard to see any of the desktop. I have folders on the floor. Books and files on the window sill. It's a mess. How is it I can keep one part of my work life so tidy, but the other is a disaster area? Interestingly, in both cases I do know exactly where everything is. I never have to use the really cool search feature (Spotlight) on my Mac to find things, and I know not only which pile on my desk a particular paper is in, but also almost exactly where it is in the foot plus high pile. Usually within a half inch or so.

I'm going to devote at least 30 minutes a day for the next few weeks cleaning up my office (yes, it will take that long). That much clutter can't be good. Definitely bad feng shui.

- I updated my laptop to OS X 10.5.2 (Leopard) today. So far it seems to have worked without a hitch. It's worth updating for the built-in backup program Time Machine. Sure, there are a lot of backup programs out there. I've used a really good one called Carbon Copy Cloner for a couple of years. But somehow Apple managed to make backing up your computer cool. You have to see it.

- 'Cakes and her hubby, Barfless, gave me a book called "How to be a Genius" for Christmas. After having read it I understood why I haven't won that Nobel yet - you need to be a genius first. So, evil genius, or not-so-evil genius?

- JollyRgr and his L gave me Richard Dawkins' "The God Delusion". A must read. Really makes you think. Kind of made my head hurt. Dawkins does a great job of demonstrating what a crock "intelligent design" is.

- Lastly, M and J were watching "Chicken Run" yesterday when they came up with that famous old question: What came first, the chicken or the egg? After some debate amongst themselves. M decided chicken. J decided egg. It's so cool watching them grow up.

Did you know...

Einstein once said:

"Once you can accept the universe as matter expanding into nothing that is something, wearing stripes with plaid comes easy."

He (was) the man!

We're so vacuous

Why is it that people are more interested in this than this? How is it that our culture has become so completely mindless?

WHY DO SO FEW PEOPLE CARE?

Obama Baby!!

This is worth watching. My favorite part is the line comparing politicians to diapers...

The ouch! ouch! ouch! post

"To suffer both at once is - to say the least - unfortunate."


And this really brought tears to my eyes...

Future nominee for a Darwin Award

Apparently he's unrepentant...

An A for ingenuity, but...

...an F for intelligence.

Speaking of life and humor...

Courtesy of the lovely L, we have the best first wedding dance ever!

Believe it or not...

Awarded by my good friend DocStymie who has also won one.

According to The Shameless Lions Writing Circle, who originated the award, it is given for "blogs we love, can't live without, where we think the writing is good and powerful." I'm not quite sure how my little piece of the blogosphere qualifies, but I am very honored.

Apparently awardees are supposed to list "three things they believe are necessary to make writing good and powerful." I'm sure my three are far from unique and may perhaps even be considered cliched, but they are the three that top my list.


Good and powerful writing...

contains truth.

I'm a scientist. What I do is pursue truth, so perhaps I'm biased. But I do believe powerful writing contains truth. Truth isn't always welcome or pretty. We often hide it, or hide from it. But ultimately it cannot be denied.

is about life.

Life as we know it, life as it was, life as we hope it will be, or life as we hope it will never be. In some way, be it in small part or in whole, good and powerful writing is about life.

possesses humor.

Paraphrasing Blackadder, life without humor is like a broken pencil.


DocStymie inspired me to start a blog, in part because his writing embodies the three aspects of good and powerful I've listed. Thanks Doc.

*SNORT*

I just came across a scientific paper titled "Basic math in monkeys and college students." An appropriate comparison methinks.

It's a new year

And a Happy and Safe 2008 to All!

So what does 2008 hold in store for you? For me? Well, here's a partial list for my work:

1) I have a submitted paper I'm waiting to here back on. It may, or may not, need revisions. It probably will.

2) I have data for another two papers that I need to write.

3) I'm the new course director (ie in charge of) a graduate-level course that needs a complete overhaul.

4) I have a grant to write and submit.

5) I'm expecting the initial proofs for the book I edited soon. They'll need to be read carefully and all errors fixed.

6) I need to push along the new project to get it up and running.

7) I have to help organize the annual elections and dinner for the subgroup of the scientific society I foolishly got elected secretary/treasurer of.

Busy, busy, busy.

Did I mention that's the partial list just for January?

:-(

An Embuggerance

It's the last day of Hanukkah...

So put on your yamulkah!

New Look

What do you think?

Another gem from the BBC

Old fart?

You know this country could learn a few lessons from the BBC about what's newsworthy.

Only in America...

1. can a pizza get to your house faster than an ambulance.

2. are there handicap parking spaces in front of the skating rink.

3. do drugstores make sick people walk all the way to the back of the store to get their prescriptions, while healthy people can buy cigarettes at the front.

4. do people order double cheese burgers, extra large fries and a diet coke.

5. do banks leave the vault doors open, but chain pens to the counter.

6. do we leave cars worth thousands of dollars in the driveway and fill our garages with worthless junk.

7. do we use answering machines to screen calls and have call waiting so we don't miss calls from those people we didn't want to talk to in the first place.

8. do we buy hotdogs in packs of ten and buns in packs of eight.

9. do we use the word "politics" to describe the process so well. In Latin "poli" means "many", and tics are bloodsucking creatures.

10. do they have drive up ATM machines with Braille lettering.

Have a good weekend!

Just in case you were considering one of these...

Probably not a good idea.

Biomedical science consternation

Today I attended a seminar where the presenter, a fairly well-known, very well funded professor from another university talked about his work on a disease. Most of it consisted of describing animal models for this disease. Basically, that means genetically altering animals, in this case mice, the most common models, to show symptoms of a human disease. You then study the animal, comparing it to "non-diseased" animals, to try and learn something about the disease. It's a reasonably common approach and one that can be quite useful (but not one I use - I don't, and won't, work with animals). Anyway, the ideas behind this guys work were okay, but the actual experiments were shoddy. Full of holes. And yet he has three large grants from the NIH (the government agency that funds most biomedical research in the US). I commented on this to a colleague after the seminar. He agreed that the work was shoddy, but noted that "an animal model for a human disease is almost guaranteed funding nowadays." He's right. And it, really, really irks me. Why? Because shoddy science is pretty much worthless. The data and interpretations have a high likelihood of being wrong. And work done with animal models is very, very expensive. So much of this is wasted. At a time when funding rates (ie the number of grant proposals being funded) at the NIH are at almost historic lows. There are good young academic scientists not able to get funding and consequently being forced out of science. And yet shoddy science can get funded.

Sometimes the system really sucks.

And yet I wouldn't want to be doing anything else.

Sigh.

But....um....how?

http://news.bbc.co.uk/2/hi/uk_news/scotland/glasgow_and_west/7095134.stm

Am I going to become one of those bloggers?

You know, one who simply posts videos and stuff, but doesn't really say anything himself?

Maybe.



Still, this is worth watching.

Have a good weekend!

Somebody remind me...

...why this guy is counted as an ally!?!?!?!?!

Stuff

Random stuff in fact.

On the weekend we took the kids here. We went with several families we know. Loads of fun and highly recommended. My favorite slide was dubbed (by us) the "toilet bowl" (I think officially it's called the "Coyote Cannon"). You went down a steep tube that spat you out into a large bowl, which you proceeded to go around the sides of two or three times before being flushed down a hole in the middle, through a short tube into a pool. You can imagine why we named it the "toilet bowl".

Joke: A doctor is examining an old man. Making conversation, he asks the guy what he thinks of George W. The old man replies "He's a post turtle." Confused, the doctor asks the guy "What's a post turtle?". The old man replies "Have you ever driven down a country road and seen a turtle on top of a fence post? You know he didn't get up there himself, he doesn't belong there, he can't get anything done while he's up there, and you just want to help the poor dumb bastard get down."

I don't watch TV much, if at all, nowadays. I think I average no more than 30 minutes a week in front of the idiot box. Can't say I miss it.

Check out Apple's coming OS X upgrade called Leopard. Waaaaaaaaay cool. The "Time Machine" automated backup utility is worth the price of upgrading alone. Oh, I forgot, most of you use PC's. Sucks for you. :-)

Once again...

...the Nobel prize committees have overlooked me.
Sigh.

Signs of the times...

Silly signage
and
more silly signage.

I like the one featuring a wheelchair, with passenger, and a hungry crocodile.

An ISBN all of my own

Remember "The Book"? The one I'm editing, with chapters contributed by nine other groups (plus one from me)? After an effort akin to herding cats, I finally got all the chapters from the authors, eventually even in the right format (apparently scientists can't follow simple, clear instructions...). Now it's all at the publishers. They've announced the book on their website with publication due in the first quarter of 2008. And it has been assigned an ISBN! That makes it real, right?

Planes, trains, automobiles and... New York!

This last weekend (Labor Day weekend) the family went to New York City for a Bar Mitzvah (why else?). What a blast! I love visiting NYC, but couldn't live there. It's so alive. 24/7/365 alive. That's probably why I couldn't live there - too frenetic.

Anyway, we flew up to PA to spend a night with L's parents, then took the train to Penn Station in NYC. I highly, highly recommend this form of transportation. You get loads of room, comfy-ish seats, and you don't have to worry about cancelled flights or bad traffic. The kids loved it too. M has decided it's her favorite form of travel. Baby J loved being able to walk up and down the aisle (yes, he's now a toddler). I'm not sure all the other passengers appreciated his "visits" - one poor gentleman was asleep when baby J decided to scream right next to him - although some clearly did. Once in NYC it was a (thankfully) short taxi ride to the hotel. We didn't get to do much sightseeing given we arrived Saturday afternoon and left Monday afternoon (L and the girls did see an off-Broadway show - Gazillion Bubbles, or something like that), but we had fun.

Labor Day we went to the Bar Mitzvah. The party afterwards was everything you might imagine (and more) a NYC Bar Mitzvah would be like. Open bar (at 11:30am...), gourmet-quality food, and a DJ. We decided the DJ was on something - he was very hyped up. Early on I was watching the dance floor and saw a hussy-looking young women dancing with the Bar Mitzvah boy. She didn't look like one of the guests. In fact, my first thought was "THEY GOT HIM A STRIPPER?!?!?!?!?!?" Thankfully, no. She was one of the two dancers that came with the DJ. A little over the top and distasteful really. Especially given this was really a religious "coming of age" thing. Still, everyone had a good time. The kids loved it and the adults (L's family and I) laughed at it all. I think we'll talk about it for quite some time.

After the party it was a quick dash back to the hotel to get changed, a taxi ride to Penn Station and onto the train again. Another night at L's parents, and then flights home. An exhausting, but good trip.

Ironically, the Bar Mitzvah boy's mitzvah project was to promote efforts to combat global warming. Ironic because it will take the use of a lot of compact fluorescent bulbs, use of public transportation and/or carpooling, and much recycling to make up for the energy expended at the party...

Naaaaaahh... really??? Me???

Ganked from the Doc...

What Be Your Nerd Type? Your Result: Science/Math Nerd   (Absolute Insane Laughter as you pour toxic chemicals into a foaming tub of death!) Well, maybe you aren't this extreme, but you're in league with the crazy scientists/mathmeticians of today. Very few people have the talent of math and science is something takes a lot of brains as well. Thank whosever God you worship, or don't worship, so thank no deity whatsoever in your case, for you people! Most of us would have died off without your help.
Social Nerd
Literature Nerd
Drama Nerd
Gamer/Computer Nerd
Musician
Artistic Nerd
Anime Nerd
What Be Your Nerd Type? Quizzes for MySpace

Potpourri and other smelly stuff

I'm back. Did you even know I was gone?

I've just got back from a two week vacation. A week of it was at the beach, with the other week being taken up by a few days at the in-laws and traveling. I now feel more relaxed than I have done in a very long time. I guess I needed the break. Not doing any email during that time probably helped too.

Work was just a little tumultuous right before leaving for our vacation. I very nearly kicked one of the summer undergraduates out of the program. She had a family reunion to attend in California. When she was accepted into the program she asked if she could take a week off to go to that, plus see some friends. I told her a whole week out of a ten week program was too much. We compromised and agreed on four days. Well, she took a whole week anyway. I booted her, but after much begging on her part I relented and let her back in (I'm just a big old softy - but I did make her sweat). Around the same time I realized that my current research wasn't going anywhere and had no real future. A good friend, RP (Doc, you know who that is), had tried to gently tell me that at a conference earlier this year, but it took a few months for me to catch on. Perhaps he shouldn't have tried to sugarcoat it...

Anyway, you'd think realizing that my research program was reaching a dead end would be devastating. Perhaps it should be, but oddly enough I've found it energizing. There is a related area of research I've been looking to move into (intrinsically disordered proteins if you must know), and here's my big chance. I have a good hypothesis to work on, and I know how to test it. I have one model system that will be good for this. I just need to find another one, preferably two, so I can test the generality of the hypothesis. So over the next few months I'll be writing up the last two or three papers from my current research program while switching to the new one. That should keep me out of trouble for a while...

On an unrelated note, DocStymie put me on to an English band called The Maccabees. Check them out. They have the one album and it's called "Colour It In". If you have an English sense of humour you'll probably really enjoy "Latchmere". It's got a wave machine.


Okay, the sibs have each posted quiz questions. I guess it's my turn.

What's the difference between a duck?






Alright, alright, so it's an oldy... How about this one?


Who said "Never confuse efficiency with a liver complaint"? And in what movie?

Busy, busy, busy

It's been a busy month or two. I've been trying to get that book I'm editing finished so I can send it off to the publishers. I'm not sure I'll be doing another one any time soon... I'm also running a summer research program for eight undergraduate students, mostly from Appalachia (seven of the eight). That's been an enormous amount of work, but also a lot of fun. Mostly. Some highlights:

Welcome to the Big Smoke

On their second night in town the eight students decided to venture out to a local Mexican restaurant. They were seated next to a table with three flaming gay guys. Did I mention it was happy hour? Half price Margaritas? Make that three drunk flaming gay guys. Remember, these kids are almost all from small towns in a very impoverished part of the country. So these gay guys decide to make friends with the students. They even invited them to go watch the cross-dresser show the gay guys were appearing in. And one took a real shine to one of the male students (the female students thought this was the funniest thing they had ever experienced). A good time was had by all (except maybe the male student being hit on), and the gay guys paid for the students dinners...

We'll Send Then Home Better Than They Came (In More Ways Than One)

The students don't have a lot to do in the evenings, so they joined the campus athletics facility ($20 for the whole summer). They've become addicted to spinning classes given by this guy Patrick. Apparently Patrick could make a living as a motivational speaker - he pushes the students way past the point at which they thought they would collapse. They come in each morning exhausted from the class the night before, but they keep going back... And I'd bet that at least half these kids had never worked out before coming here.

Well That Was Awkward

The one bad part of this program so far (and hopefully the only one), came to a head last week. One of the faculty mentors was verbally abusing one of the students - the one working in his lab. This faculty member apparently has a history of being verbally abusive to the people in his lab. I had to pull the student out and put him in another lab (much to the student's relief). The really awkward part? This faculty member is very much senior to me. Thankfully, my chairman was ready to back me up if need be.

Fun, fun, fun.