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.

Aaaarrrrggghhh!!!!!

Here's one from the little bro...

My pirate name is:

Dirty Tom Rackham

You're the pirate everyone else wants to throw in the ocean -- not to get rid of you, you understand; just to get rid of the smell. You have the good fortune of having a good name, since Rackham (pronounced RACKem, not rack-ham) is one of the coolest sounding surnames for a pirate. Arr!

Get your own pirate name from piratequiz.com.
part of the fidius.org network

Eight things

I read this over at the Doc's place and have tagged myself.

Here are the rules:
Each player lists 8 facts/habits about themselves. The rules of the game are posted at the beginning before those facts/habits are listed. At the end of the post, the player then tags 8 people and posts their names, then goes to their blogs and leaves them a comment, letting them know that they have been tagged and asking them to read your blog.

1. I walk the two miles to work each day. And back. I'd like to be able to claim I do it for the exercise, or to help save the environment, but I don't. I do it because I enjoy it.

2. I went to high school with a guy who was an Olympic gold medal-winning swimmer. He was a jerk. JollyRgr can confirm that.

3. I saw Inxs play in a pub long before they recorded their first album.

4. I have colleagues I don't respect. Sure they're good scientists, or at least they do all the things that supposedly make you a good scientist. But they treat the people in their labs, and the administrative people in the department, like dirt. For that I can't respect them.

5. I spent five years learning to play the cello. I haven't as much as touched one since high school.

6. My first paper as a postdoc, the one that really launched my career, almost didn't get published. After collecting all the data, writing the paper, sending it out to the journal, and receiving positive reviews that guaranteed it would be published (in a fairly high profile journal no less), I found a bug in the computer program I had written to generate the data. A big bug. A really bad big bug. I got lucky. We were going to withdraw the paper, but the editor handling it put it on hold instead until we could figure out if and how things changed. Luckily for me, the data changed just a little, and the conclusions not at all. I got published and here I am.

7. I find it almost impossible to resist a fresh (still warm!) cinnamon donut. Or a frosty cold beer. Unless it's mass-produced swill masquerading as beer.

8. Despite the facts that I'm a faculty member in a biochemistry department, I teach biochemistry, and I do biochemical research, I have never taken a biochemistry course. Or even one in biology. Not even in high school. The academic system can be very strange sometimes.

So there you go. I must say it's quite difficult to come up with eight things. Or at least it was for me. Of course now I'll post this and immediately think of eight different, more interesting things... C'est la vie.

Well duh!

They needed "experts" to figure this out?????

Tee hee

One day, three boys were walking over a bridge when they heard a guy yelling for help. It was President Bush. He was drowning, and the three boys rescued him. He thanked them dearly and promised them whatever they wanted as a reward.
The first boy wanted $10,000, so Bush gave him the money. The second boy wanted a Ferrari, so Bush gave the boy a Ferrari.

The third boy wanted a wheelchair, Bush said, “Why do you want one of those, son, you're not handicapped.” The boy replied, “I will be when my dad finds out whose life I saved.”

The BBC and sports on the web

The BBC sports web site does a masterful job of providing an over-by-over description of international cricket matches. They even manage to capture the uniquely dry wit of the British sports commentators. The web site also has live coverage of European football (soccer) matches. But I think they've gone a little too far with their live coverage... Now they're providing live coverage of World Snooker 2007! Snooker is a very clever and difficult game, far more so than pool. I even used to watch it every now and then televised on "Pot Black" back in Australia. But it makes for the most incredibly boring web coverage...

Truer words never spoken...

...than the conclusion of this little gem.

Mac's vs. PC's

Making a forest

I'm putting together this book. You may recall I've blogged about this enterprise in the past. It's nearing completion (and none too soon!). There are now four outstanding chapters. One of the authors hasn't answered a single email from me this year, so I've written him off. Two others promise their chapters are on the way. One of them told me today that I would have his by Wednesday (tomorrow). We'll see.

The fourth chapter? That would be mine. Hey, I'm the editor of the book, I can set my own rules, right? Just because everyone else was supposed to get their chapters done by mid-February doesn't mean I had to. As it was, almost none of them got their's to me on time.

So I've been busy writing my chapter. It's supposed to be a review of my research on unfolded protein states. Basically a summary of my current body of work, linking it all together and placing it into perspective with respect to everyone else's work. I'll be damned if it doesn't all make a lot of sense and hang together. My work that is. It's almost as if I had carefully plotted out the direction of my work over the past decade. I didn't. Research doesn't work that way. Research evolves. It goes where it goes, not where you try to make it go. I've been so busy planting trees (working on various research problems) that I hadn't noticed that I've managed to make a forest. It's pretty cool. At least I think so.

Once I've finished this chapter I think I'll add a stream to my forest. And maybe a lake.

Word of the post:

foofaraw \FOO-fuh-raw\
-noun

1. Excessive or flashy ornamentation or decoration.
2. A fuss over a matter of little importance.


Today's trivia question:

In our initial trivia frenzy we established the Beatles made five movies, each of which had an album associated with it. Which of those albums was the last to be released in England? Bonus points if you can tell me which year.

Creativity, genius and toilet repair

Interesting juxtaposition in yesterday's newspaper here. On the front page was a big article about the deplorable state of the studio art teaching building here at Big State U. Apparently the building itself is considered ideal for studio art in that it has loads of space and abundant natural light. Problem is, the building is in such bad shape it's close to condemnation. There is not ventilation system (studio arts often require use of noxious chemicals and/or produces significant amounts of dust), no air-conditioning (the temperature inside can exceed 100F in the Summer), most windows won't open, the electrical wiring is out of code and insufficient to power all the equipment in the building, the internal stairs are in danger of collapse and the plumbing bursts on a regular basis leading to flooding. Renovation estimates run from $30 million upwards. The administration here at Big State U. are in hot pursuit of the state government-mandated Top 20 status and have decided that science and technology should be the focus. So there are no plans to properly fix the studio art building.

In the same newspaper there was a very cool column (also featured here in the LA Times) written by Walter Isaacson, author of the Einstein biography "Einstein: His Life and Universe". In this column Isaacson makes the point that genius is a combination of smarts, rebelliousness and creativity. Creativity. That makes a lot of sense to me. Many of the best scientists I know have a very creative side. My good friend DocStymie springs to mind. A great scientist who happens to also be a musician with the great American novel inside of him (have you started writing it yet Doc?). Other scientists I know paint, sing, play muscial instruments, write and/or lose themselves in fantasy-based computer games. Creativity is key to good science.

So, Big State U., you want to be Top 20? I think perhaps you should fix the studio art building. Pronto.


Now, dear readers, on to toilet repair. Go on, admit it, that's the real reason you're bothering to read this, isn't it. You just want to hear all about my exploits with the poo pipeage. So, in our kids playroom downstairs there's this water stain on the ceiling. It's more or less below the upstairs porcelain throne. It's been there for a while and is slowly getting worse. I recently (Friday night) read an article in a home improvement magazine that pointed out that slow leaks like this one can cause extensive damage to the flooring and joists if left unrepaired. I decided maybe it was time to do something. My first step was to do some internet research. This confirmed what I thought might be the case - the most likely cause of the leak was the wax ring that seals the bottom of the toilet to the waste pipe. This seal is compressed by the weight of the toilet, plus user, forming a tight waterproof ring around the pipe. If however, it wasn't installed correctly, the bolts holding the toilet to the flange that connects to the waste pipe were tightened too much or were too loose, and/or the toilet could rock, this wax seal could develop a leak. Replacing the wax ring is, in principle, very straightforward. Most difficult step appeared to be putting the toilet back with a new ring attached. This has to be done by lining up the two small bolt holes over the bolts in the floor while keeping the toilet fairly level. Step two was to talk to a friend who is something of a home handyman. My main question was could I do this by myself. His answer was maybe, but you're better off with help. So he ended up spending much of the afternoon helping me. Pulling out the toilet was very easy (I remembered to empty all the water first!). That revealed that the old wax ring was in pretty bad shape. That wasn't the worst of it though. Whoever had installed the wax ring had overtightened the bolts holding the toilet down. This had caused the flange to bend and separate from the waste pipe, bending and putting a small hole in the pipe in the process (the likely cause of the leak). The subfloor looked fine though, which is good because that would be a very major repair job (although my friend claims we could handle it over a couple of weekends).

By the way, this isn't as yucky as it might sound. You flush a lot of clean water down that waste pipe, so it's actually pretty clean looking. Thomas Crapper was a clever man. I bet he had a creative side.

Anyway, we ended up having to cut and file the top of the waste pipe to get it level again. We then installed a replacement flange (thank goodness I had help from someone with a clue), and a new wax ring. All in all a very satisfying three hours work. Now we just have to wait a couple of weeks for the ceiling below to properly dry out before I dig out the damaged plaster, patch and seal it. Then we'll have to wait a few more weeks to be absolutely sure there isn't still a slow leak. My friend and I are pretty confident we fixed it though.

Yes, I did wash up. Thoroughly. Several times.


Word of the post:

jux·ta·po·si·tion [juhk-stuh-puh-zish-uhn]
–noun

1. an act or instance of placing close together or side by side, esp. for comparison or contrast.
2. the state of being close together or side by side.
[Origin: 1655–65; < F < L juxtā side by side + F position position]

—Related forms
jux·ta·po·si·tion·al, adjective

For an example, read the above post again.


And now for a music trivia question:

What was Nancy's real name in Rocky Racoon by the Beatles?
(Yes, I'm still on my Beatles kick.)

Sweet Loretta Fat, she thought she was a cleaner, but she was a frying pan.

I'm currently suffering from blog block. It's not that I can't think of things to write. It's that I can't think of things to write when I have the time to sit and write. Bit of a bummer really. Especially when my blog is approaching 3000 hits.

So here's some randomness...

Thanks to my little brother, I now have all of the Beatles' albums. They all fit on my 2G iPod nano. With lots of room to spare.

I was listening to Beatles tunes while following the Australia-England one day cricket match on Sunday. Fittingly, the song "Help!" came on half way through England's innings. It didn't help them.

"'I dig a pygmie' by Charles Hortree and the Deaf Aids" is the opening line to which album? (Little brother you're not eligible to answer.)

Who played lead guitar on "While My Guitar Gently Weeps"? I know the answer. Do you?

Twenty years ago I was a graduate (postgraduate) student. My research involved long computer simulations. I used the university mainframe. It filled a large room and had disk drives that looked like oversized washing machines. My current PDA fits in my pocket. It is faster and has more memory than that mainframe.

And finally, do any of you know someone who owns a Zune? I've seen them in stores, but never one out in the wild.


Word of the post:

magniloquent \mag-NIL-uh-kwent\
-adjective

Lofty or grandiose in speech or expression; using a high-flown style of discourse; bombastic.

Of applications and white supremacy

Regular readers (both of you) might recall that I'm heading up a program to have a bunch of undergraduates do research in our department over the summer. Last Friday was the deadline for applications. Here are some interesting tidbits from that process:

We received about 60 applications. Not bad at all. I am told by people with similar programs that next year we will receive up to 300! We got the grant money to run this program in mid-February which is when most programs have their deadlines. Many students would have already arranged something for the summer before we got going this year. I'm not sure I can handle 300 applications...

Of the 60 applications we have about 10 that consist only of one or two letters of recommendation. No application form, transcript etc. as required. What's with that? It takes a lot of time and effort to write a letter of recommendation. I think it's disgusting that so many students would ask faculty to write such letters and then not even bother to apply. Okay, one or two applications might have got lost in the mail, but 10?

Apparently some foreign students are blind to the stipulation that applicants be US citizens or permanent residents (a requirement of the NSF who is funding this program). Despite this being in big bold red letters on the home page of our web site. And stated in at least two other places on the web site. And on the application forms. I haven't counted those students in the 60 apllications.

One young lady from Romania emailed me to see if she was eligible. When I replied that she was not, she promptly invited me to be her "friend" on Facebox (apparently a Romanian version of the very popular US Facebook). I haven't replied to that, or the following three invitations... She's on my junkmail list.

Here's a copy of an email I received late Thursday night (keep in mind the deadline was Friday)-
"I was thinking of applying to the program but I thought the deadline was later than tomorrow until I just saw on the website. I can send in all required application materials by tomorrow except for the recommendations. I have told my professors they can have another week to send their recommendations. I hope that's okay." [Emphasis mine]

My reply-
"No, it's not okay."

Finally on applications, while I was typing this I received three express mail envelopes with more application materials and a phone call from some student's mother who wants to hand deliver an application... Oy.



And white supremacy? DocStymie, this is one you'll really like:

Rep. Charlie Rangle, D-N.Y. (remember he's black) when asked on public TV what he thought about the President, replied, "Well, I really think that he shatters the myth of white supremacy once and for all".



Word of the post:

sang-froid \sang-FRWAH\
-noun;

Freedom from agitation or excitement of mind; coolness in trying circumstances; calmness.

Example: It takes remarkable level of sang-froid to catch a Matthew Hayden six with one hand while not spilling the beer held in the other. (See here, although I'm afraid it will be lost on Americans.)

For JollyRgr

I'm posting this here because stoopid LiveJournal isn't letting me post comments on DocStymie's blog...

The good Doc had blogged about a recent paper that appeared in the (new) scientific journal PloS Biology. This concerned modeling all the proteins in the yeast proteome.

The recently-shaved JollyRgr had asked:
"yeast proteome something like human genome in general concept????

Am I on the right path???"

So here's the answer...

Kinda sorta. The genome is the set of blueprints (genes) for making the various components of a living organism. Think DNA = genome. Each gene encodes a component. Proteins make up many, probably most, of those components. The proteome is the set of all proteins in an organism. So the genome encodes the proteome, plus more. Yeast, like humans and all other living organisms, has a genome and associated proteome. We use yeast as a model organism because it's genome, and proteome, has many of the same components as the human versions.

So there you go.

I'm back...

Actually have been for almost a week. Too much life happening here.

Anyway, the trip was good. The Kaddo Borawni was superb, as was the Lamb Lawand... Hmmmm, goooood!

Not much to say other than point out Vista has turned out to be, well, a typical Microsoft product as demonstrated here and here. Is anyone surprised?

In all fairness, Apple is not without it's issues. DocStymie, you may want to be aware of this one.

Finally, it's World Cup time! Cricket that is. Ireland tied Zimbabwe. How cool is that?

Instead of a word of the post, here's little quote from the online commentary of the England-New Zealand match from the BBC:

"Whoosh - almost a disastrous run-out as KP calls for an insane single. Vettori hurls the ball at McCullum with Vaughan half a pitch short, only for the 'keeper to fail to gather the ball. Massive let-off.

In reply to those of you asking for more info on the gaggle (this in reference to an earlier comment about a group of young women)- specifically, how many are international class - I say two things: firstly, that that sort of sexist badinage has no place on the BBC, and secondly, about half of them."

I love the English commentators...

It's that time of year again

Time for me to go hang out with 5000 other geeks. Yes, it's scientific meeting time. Time for bad talks, overwhelming numbers of people, too much coffee, beer and good science. This year it's in Baltimore. I'll also get to go to one of my all time favorite restaurants - the Helmand. Maybe more than once.

Sorry you won't be there DocStymie. You'll be missed. I'll have some Kaddo Borawni for you.

After Baltimore I have to spend a couple of days at a workshop at the National Science Foundation in Washington, DC. It'll be a long trip (for me) - Friday to Friday. I hate being away from the family that long. The meeting will be good, but not being with the lovely L and the kids will suck.

No word of the post tonight. I'm too knackered.

Irony

I believe I used this as a word of the post before, but this is too good an example to pass up...

Word of the post:

i·ro·ny
n. pl. i·ro·nies

The use of words to express something different from and often opposite to their literal meaning.
An expression or utterance marked by a deliberate contrast between apparent and intended meaning.
A literary style employing such contrasts for humorous or rhetorical effect.
Incongruity between what might be expected and what actually occurs: "Hyde noted the irony of Ireland's copying the nation she most hated" (Richard Kain).
An occurrence, result, or circumstance notable for such incongruity.
Dramatic irony.
Socratic irony.

Example: See here.

Detective iTunes?

Who would have thought a music player/library program could detect fraud?




Word of the post:

bloviate \BLOH-vee-ayt\
-intransitive verb

To speak or write at length in a pompous or boastful manner.

Example: I have never bloviated in my blog. Never. Honest.

Thinking quotes

Our University publishes a research magazine about every quarter. Generally it's not very interesting, at least to me. However, on the last page they tend to have a series of quotes. These quotes are related to one another in some way. The current issue has a series of quotes regarding thinking. I thought some were worth sharing:

"The important thing in science is not so much to obtain new facts as to discover new ways of thinking about them."
- Sir William Bragg

This is more true than many non-scientists might think. My postdoctoral advisor was very fond of saying "If you want to find a really good research project, just open a textbook and find a passage that starts with 'It is well known that...' There's your research project." My own work involves expanding upon observations first made over forty-five years ago!

"A great many people think they are thinking when they are really rearranging their prejudices."
- William James

"A conclusion is the place where you got tired of thinking."
- Harold Fricklestein

"Today, if you are not confused, you are not thinking clearly."
- Irene Peter

Talk about a great excuse for my constant state of confusion...



Finally, here's one for the current occupant of the White House and his cronies:

"All war is a symptom of man's failure as a thinking animal."
- John Steinbeck


Word of the post:

ob·strep·er·ous [uhb-strep-er-uhs]
–adjective

1. resisting control or restraint in a difficult manner; unruly.
2. noisy, clamorous, or boisterous: obstreperous children.

No example. I just like the way obstreperous sounds.

Yesterday was a good day

We heard from the National Science Foundation that a proposal I had submitted last August is funded. This is to run a summer undergraduate research program. We're going to host eight undergrads in our labs and give them research projects to do. Pretty cool. My chairman is very happy about it. He told me so. Twice. Of course now the real work begins...

Being a typical government agency, the NSF has given us funding right at about the time we should be finishing our recruiting for the summer. So we have to recruit very quickly. Oh yeah, we're also supposed to have a detailed website for our program by yesterday, or even earlier. So I'm busier than a one-legged man in a bum kicking contest.

And the NSF is requiring me to attend a workshop in DC in March... Fortunately this starts the day after a meeting I'm attending in Baltimore ends. So I've extended my trip. I'm not terribly happy about being out of town so long, but that's the way it is.

Word of the post:

kvetch \KVECH\

adjective:
1. To complain habitually.

noun:
1. A complaint.
2. A habitual complainer.

Example: One of our less successful faculty has become a kvetch. It's very irritating. Not that I'm kvetching.

For DocStymie and P

This shouldn't happen.
I'm sorry Doc.
Odyssey


Mi Shebeirach

Lyrics by Debbie Friedman and D'rora Setel

Mi shebeirach avoteinu
M'kor habracha l'imoteinu

May the source of strength who blessed the ones before us,
Help us find the courage to make our lives a blessing
And let us say: Amen.

Mi shebeirach imoteinu
M'kor habracha l'avoteinu

Bless those in need of healing with refuah sh'leimah
The renewal of body, the renewal of spirit
And let us say: Amen.

Happy Australia Day!!!!

May the snaggers be hot,
the stubbies ice cold,
the fireworks bonza,
and all yobbos stuck at home crook.




Word of the post:

egg-nishner
Strine

A device for cooling.

Example: Geez it's bloody hot mate! Pass a bloody stubbie and turn up the egg-nishner.

A Happy New Year to One and All!

And what better way to start the New Year than pondering the fates of those who saw fit to remove themselves from the gene pool.




Word of the post:

ev·o·lu·tion [ev-uh-loo-shuhn or, especially Brit., ee-vuh-]

-noun

1. any process of formation or growth; development: the evolution of a language; the evolution of the airplane.
2. a product of such development; something evolved: The exploration of space is the evolution of decades of research.
3. Biology. change in the gene pool of a population from generation to generation by such processes as mutation, natural selection, and genetic drift.
4. a process of gradual, peaceful, progressive change or development, as in social or economic structure or institutions.
5. a motion incomplete in itself, but combining with coordinated motions to produce a single action, as in a machine.
6. a pattern formed by or as if by a series of movements: the evolutions of a figure skater.
7. an evolving or giving off of gas, heat, etc.
8. Mathematics. the extraction of a root from a quantity. Compare involution (def. 8).
9. a movement or one of a series of movements of troops, ships, etc., as for disposition in order of battle or in line on parade.
10. any similar movement, esp. in close order drill.

'Tis the season

'Tis the season when the local newspaper receives multiple letters complaining about the "War on Christmas".
There isn't one.
'Tis the season when saying "Happy Holidays!" is construed to be a slight against Christianity.
It isn't.
'Tis the season when politicians preach good will towards all men.
They don't mean it.
'Tis the season when rampant consumerism goes way beyond "rampant".
Not what it should be about.
'Tis the season when homeless people freeze to death unnoticed.
Remember them?
'Tis the season when genocide goes unchecked while the first world turns the other way.
Darfur.
'Tis the season when many of us eat more in a day than many others have for a week.
Do you really need a third helping? Do I?

But despite all this,
'Tis the season where I wish one and all

PEACE


And that is the word of the day. No definition required.

Thoughts on thinking

Ever think about the form in which you think? I have been lately. As I type this I'm thinking in words, more or less. But I also sometimes think in pictures, both static and moving. Or mixtures of words and pictures. Although I haven't talked to people about this, I suspect this is true for many people. But those aren't the only forms in which I think...

When I think about my science, my research, I think in molecules. Spinning, writhing, twisting, tumbling molecules. Amino acids, peptides and proteins. Water and ions. Atoms bonded to one another, interacting with bangs, thumps and bright colorful sparks. Molecules dancing around one another, twisting in knots. Crashing into one another. Sticking to each other like tiny fragments of velcro, or being flung apart by rainbow sheets of repulsive energy.

I see a weird and wonderful world in my head that cannot be seen using existing technology. This of course can be a bit of a problem for me. I can "see" in my head how some of the systems I work on behave, but I don't have the tools in the laboratory required to measure what I see. This can be frustrating. Of course what I see in my head could be wrong. But I don't think it can be completely wrong. My molecule thoughts have their basis in what I've found during my research, what I've read, and from talking to fellow scientists. I think my molecule thoughts are more right than wrong. But I can't prove it.

There are many scientists who would respond to my admission by deriding it as pure fantasy, nonsense, or the product of a disturbed mind (which it may well be). Not, I'd wager, those whom I admire, whose work has, and continues to have, profound influence upon mine. They might think in molecules. Or they might not. It doesn't matter. They would understand.



So there you have it. I'm weirder than you thought, if that's possible. Accept it, move on, and tell me, in what forms do you think?



Word of the post:

pre·sen·ti·ment
-noun

A sense that something is about to occur; a premonition.

Unsolicited advice

Don't eat beans before a plane ride.




Word of the post:

im·prov·i·dent [im-prov-i-duhnt]
–adjective

1. not provident; lacking foresight; incautious; unwary.
2. neglecting to provide for future needs.


Example: See story linked above.

Yes, yes, I know...

...it's been a long time between posts. It's not that I have nothing to say. There's just so much to choose from; Darfur, Microsoft's Zune, Iraq, the Ashes series in Australia, the perennial blather topic of Bush, Docstymie's discovery that he is one degree of separation from J. Robert Oppenheimer, Father of the Atomic Bomb (which means I'm also one degree of separation from him, and we're both two degrees of separation from Edward Teller, and probably no more than three from Albert Einstein)... No, it's not a lack of subjects. It's a lack of time. So, dear readers, I present you with this gem from Norway, land of smoked salmon and tax-free strippers.


Word of the post:

ineluctable \in-ih-LUCK-tuh-buhl-adjective

Impossible to avoid or evade; inevitable.

Example: “Those war plans rested on a belief in the ineluctable superiority of the offense over the defense” (Jack Beatty).