Wednesday, August 30, 2006

The Writing Process: A Test of Will

Well, I'm still buried deep in the "writing process." Last week, my advisor and I bumped the manuscript back and forth a few times and then on Friday he dropped a major bomb on me. The 9 page (single-spaced) document was now 4.5 pages! Over half of the introduction was gone and the first and last sentence of most paragraphs were deleted.

We talked about it for about an hour and he pointed out a few things that he still wanted me to work on. I spent most of the weekend angry about what was happening and realized that the editing process ultimately comes down to a test of will. I can argue and argue for the way I want it to be. My advisor can do the same. Ultimately, one of us has to back down or we both have to bend. I'm not sure why, but my experience has been that bending doesn't work. It's like the paper ends up sounding to wishy-washy because you never come straight out and say what you want to say. After a couple of days of thinking about it, I decided to just let my advisor have his way. I decided that it would be better to get the paper done and published (even if it isn't exactly how I want it) than to continue through this torture of editing and re-editing with him.

So, on Monday, I took my poor, hacked up paper and made the changes that we discussed last week. I sent it back to him and within 10 minutes he came over to my desk (after all, it just doesn't take very long to read 4 pages) to tell me that the paper is choppy and it's like we've taken 3 steps backward. Well, why do you think it's choppy? BECAUSE YOU DELETED THE FIRST AND LAST SENTENCE OF NEARLY EVERY PARAGRAPH!!!

Well, things seem like they're going from bad to worse when he next says to me, " We need to make this even shorter. Let's get it down to three pages." So, my 9 pages are now three pages and my 6 figures are now 3 figures. Is this progress?

We're planning on contacting some journals this week to see if they're interested in it. If we can finally get this thing out there, I'll be happy to just have it behind me. I need to get on with my postdoc/job search and I've been waiting to get this off my plate first. I don't think I can wait any longer, though, if I'm still going to defend in March.

Wednesday, August 23, 2006

Guinea Pig

I spent an hour and a half this morning as someone else's model organism. A grad student in the computer science department is working on a fancy-shmancy 3-D imaging system that doctors might use someday.

So, I got to spend 90 minutes with box strapped to the side of my head and funny sunglasses on. I stared into the display (which gave a composite image from two separate displays) and then I had to do things in 3-D like make the angle betwen two rods equal 90 degrees, or change the length of one rod to be the same length as the other rod (all in 3-D, with the rods at random orientations).

As the test was proceeding, I have to admit that I was starting to get test anxiety. I had no idea how I was doing--no feedback from the computer or the administrator at all. I started to slow down to be more precise. I thought about how I hate having sloppy data in my own work, so I shouldn't screw this grad student over by giving her sloppy data.

Then, I looked at my watch and realized that it was taking much longer than I thought it would. So, I started to fly through the puzzles, only to be slowed back down by my fears that I would do poorly and the administrator would be disappointed. Really, it was amazing how much I was worried about doing worse than average for this study. I realize now that this is the same stress that kept me competitive in high school. You don't want to look dumb in front your peers. You don't want to be "below average."

Well, when it was all over, the adminstrator let me take a glance at my results. Turns out I did second best of all the subjects so far. That sounds about right (after all, I wasn't valedictorian in high school either).

So, being a guinea pig wasn't that bad in the end.

Monday, August 21, 2006

A Coincidence Yields a Pentel Energel

Last Sunday, I had a friend tell me that I had to give Pentel Energels a try. He was confident that it was the best pen out there. So, on Monday, I started googling for other people's opinions on the pen, and I found this review. Since the blogger was offering a free one, I figured I'd take him up on his offer. While I'm no pen expert, here are my impressions of my new Pentel Energel 0.7 mm Needle Tip Retractable pen (that's a mouthful):
  • Clicking mechanism: In this post 9/11 era, everyone has a heightened awareness of what is going on around them, especially when travelling. I fear that if I clicked this pen open or shut in an airplane that the people around me would think I was cocking a handgun. Part of the reason for all the racket when its clicked open or closed is that the pen is engineered with a mechanism to automatically retract the point when the clip is pulled on (thus preventing you from putting your "loaded" pen in your shirt pocket). I've seen this feature on other pens and mechanical pencils, but it was never quite as loud as this pen is.
  • Pocket protecting mechanism: As described above, this mechanism is to prevent you from ruining your shirts. I think it is more accurate to say that it will limit the damage, but it won't completely save you. From my own testing (luckily I'm wearing a darker dress shirt today), the open pen makes its way most of the way down my pocket before the safety mechanism retracts the point. With a white shirt, I'm sure that the marks that could be left behind would show through.
  • Ergonomics: The barrel is just a little bit wider than most pens I use. It's got a rubber grip that provides no cushioning, just grip.
  • Writing quality: The ink flows smoothly. Line width and weight varies according to how fast the pen is moving, but for normal writing the ink delivery is consistent. The tip operates smoothly.
  • Ink quality: Since I work in a lab, I was interested in how quickly the ink dries and how it would stand up to the 2 most common chemicals in the lab: water and ethanol. I was actually shocked by how quickly the ink dries. I would say it is dry within a second of hitting the paper. I was unable to smear it with either water or ethanol, so it would make for a great lab pen.
  • Moleskine writing: I tested the pen out in my moleskine as well. I still haven't found the right pen for moleskine writing. Most of them bleed through (or at least show through too much). This pen wrote nicely in the notebook, but showed through just like the others. Maybe I should just find a notebook with thicker paper than keep trying to find a pen that won't show through so much.
Overall, it's a very nice pen. 0.7 mm is a bit wider than I prefer, but there are 0.5 mm Energels out there that I'll have to compare with this one.

Tuesday, August 15, 2006

Body and Mind: Staying Fit in Grad School

I spent the first year of grad school sitting at the bench, sitting at my desk reading articles, sitting on the bus to/from campus, and then sitting around at night watching television. While I don't think I put on too many pounds, I knew that my energy level was falling from lack of activity.

Luckily, I eventually found another grad student to play racquetball with and for the next three years we played twice a week. I also got into some pick-up basketball games, so I got close to achieving my goal of exercising 3-4 times a week. Now, I recognize that racquetball isn't the most demanding sport (the court is only so big and the ball can only go so far), but it was better than nothing.

With the birth of my son, I found that my racquetball schedule just wasn't going to work out any longer. I went about 6 months without any exercise before I had my 30th birthday and resolved to get into a regular exercise routine.

Despite not going running since high school, I decided to take up running since I thought it would likely give me the most bang for my buck and it is more convenient than swimming or cycling (given my circumstances). So, I started out with a 0.5 mile loop on the day after my 30th birthday. I came home completely out of breath and convinced that I was doomed. After a couple of days off, I gave it another shot and had the same results. It took another couple of tries before I was able to come home not in serious pain and distress.

So, I stepped it up to 1 mile, and then 1.5, then 2, and 2.5, and so forth. Once I got up to 3 miles, I started driving to a few different places near my house for a change in scenery (that 0.5 mile loop was beginning to look way too familiar). While I hit a few snags along the way (shin splints and back problems), I was up to about 5 or 6 miles by the end of the year. Except for times when I'm sick or travelling, I've been pretty good about getting in 3 runs each week of 4-7 miles each.

Now what has this done for my graduate school experience? One thing is that there have been many days I've walked around the lab in pain. Of course, it's a good pain because I know it's coming from well exercised muscles.

I've found that running has been good for clearing my mind. I don't typically run with music or any other distractions. I focus on the scenery and my breathing. It's a time for meditation. Occasionally, I think about science when I run, but mostly it's a time for me to escape.

Running has helped me maintain higher energy levels. Grad school isn't usually very physically demanding, but keeping your energy up is important (you don't want to fall asleep at your desk). On the rare days when I plan a "marathon" experiment (like timepoints every 15 minutes for 8 hours), I appreciate that my body has learned to endure through my running.

So, while I've talked up running, I would suggest that each grad student pick a physical activity to engage in 3 or 4 times a week to stay in shape. It can be as easy as taking a 30 minute walk at lunchtime. If it's too hot at lunchtime, you can get off the bus at a stop on the opposite side of campus and make a 20 minute walk part of your daily commute. This is definitely a case where something is better than nothing. Pick something that you'll enjoy and/or that the people around you are into. It will make it that much easier to stick with for the long term.

Monday, August 14, 2006

Body and Mind: Maintaining Good Health in Grad School

After fighting off my second cold in the last three weeks, I felt it would be appropriate to post a few thoughts about maintaining good health in grad school (not that I'm a great example of this right now). It's pretty obvious that if you feel like crap physically, you're not going to be at your best mentally. Since you need to keep your "A" game on in grad school, it's important to take care of your body. You don't want to have to suffer at the bench with a runny nose and sore throat, or endure hours at the computer with a headache and nagging cough if you can help it. Even worse, if you're TAing, then you might find yourself having to lead discussion sections/recitations while sick. There isn't really anything worse than that--well, actually there is one thing. Giving a talk while sick is the worst of the worst. On top of feeling the normal pre-talk jitters, you feel like absolute crap. You have to stand in front of a group of people, project your voice, and hope that you don't pass out mid-sentence.

The last time I gave a talk while sick I was honest about it and asked the audience's patience if my voice was hoarse. I even asked them to quietly leave the room without disturbing me if I happened to collapse while speaking so that at least I could get an uninterupted nap. At the end of that talk, some jerk asked me a detailed question about the statistical analysis of my data. In a not-so-professional moment, I simply told him that my head really hurt and to take a little pity on me and not expect an answer from me on that particular day.

So, anyway, here are my top tips for staying well in grad school. You've probably learned most of these things as undergrads, but at the very least I can remind you of the basics:
  1. Sleep. Sleep well and sleep often. Most people I know who are consistently sick operate on less than 5 hours of sleep each night. I average between 7.5 and 8 hours each night and it allows me to make it through the day with no stimulants (I'm one of the few grad students who can get by without coffee or colas). In addition to keeping you healthy, sleep is great for refreshing your mind and coming up with new ideas. Many famous inventors used short naps as a tool to get new ideas. In my own experience, I've dreamt about my work many times and I've even had a few of these dreams yield real-life working solutions to the questions that had me stumped. I know that 8 hours seems like a huge chunk of the 24 hours you get each day, but I don't think there is any single better use of it than sleeping. Guard it, protect it, and it will do you well.
  2. Nutrition. When I was a kid, they taught us about the 4 food groups. Now, they teach the food pyramid (I think). Personally, I don't worry too much about these programs and instead follow two simple rules: eat variety, and take it easy on fatty foods. I eat fruits and vegetables every day. I eat meat (usually poultry) about every other day. I suffer a weakness for sweets and ice cream, but mostly I try to eat a balance of starches, dairy, proteins, fruits and vegetables.
  3. Vitamins. I don't have any solid proof that they do anything good for me, but I consider them as insurance for the times when I'm less diligent about eating properly.
  4. Germs. An ounce of prevention is worth a pound of cure, right? If you can keep the germs away then you won't have to worry about getting sick at all. So, what does this mean to you? Wash your hands often (especially after taking public transportation or using a public computer or a common piece of lab equipment). In my lab, we use microscopes a lot. I've seen people sneeze while on the scope and not even wash their hands before putting their hands back on the scope. Needless to say, I used a Kimwipe+EtOH on the scope before I next used it. Also, if you're sick and you can afford to stay home (your advisor is understanding and you don't have anything pressing going on) then stay home! Don't bring your germs into the lab and make everyone else sick. You're not going to make friends by getting the whole lab sick.
  5. Exercise. I'm going to be writing a separate post on this a little later, but for now I'll just say that you've got make time in your schedule for exercise at least 3 or 4 times a week. The benefits of exercise are both physical and mental.
So, I hope that this post finds you feeling well and that you can use this information to help stay healthy while in grad school!

Tuesday, August 08, 2006

Back to (Grad) School Roundup

In the coming weeks, our department as well as many others across the country will be welcoming their new grad students (a couple overachievers have even already been here for a few weeks). Here's some recommended reading for grad school newbies:

In the begininning...
Joining the lab--the big talk
Grad School Advice -- Year One
Grad School Advice -- Year Two
Grad School Advice -- Year Three
Grad School Advice -- Year Four
Summers in Grad School

And here is one resource I wish I would have discovered 5 years ago: Networking on the Network by UCLA's Phil Agre.

Thursday, August 03, 2006

Paper Writing

You do research so you can publish. If you publish, you prosper. That's the accepted way it works in academia.

So, writing should feel like a "reward" after all those months at the bench, right?

Unfortunately, writing can be the hardest part of grad school. First, it takes so much more time than you'd ever expect. Second, it requires going through many, many, many edits as you get input from your advisor, labmates, and anyone else you care to share your drafts with.

On top of the writing, you have to make figures. Sometimes, this can be fun, but if the journal is particular about things then you can find yourself (again) spending way more time on it than you'd have ever expected.

Right now I'm writing up a paper based on research that has been going on for a couple of years. It's hard to believe it's taken this long for these results to be ready for publication. This project was one of those unusual ones where you see the hot result on the first day and then you spend the next two years sorting out a bunch of the details and trying to work up some other data to support/strengthen the initial findings. So, after two years of trying to bulk up this story, we've finally decided to write it up and see what the reviewers think about it.

My last paper went through about 50 revisions over the course of about 6 months before it was submitted. With this one, I'm on version 2 now, but I expect it to get to 10 (at least) before submission for publication. My boss and I have to engage in the longest rally in the history of manuscript tennis before he'll give it the green light. What it comes down to in the end is who's willing to finally give up and just give in. We try to wear each other down until we get our way on each point. When one of us gives in, we send it along to everyone else in the lab and get their input.

After hearing back from everyone in the lab, we have to go through it all again and see how it looks in it's final form. Then, it's off to the reviewers so we can start our battle with them...