Don’t make fun of grad students

‘Tis Better to Give

Both my birthday and the holiday season are coming up soon, so I’ve updated my wishlist. (link in the sidebar). In addition to asking for books and video games this year, I thought I’d try something a little different. I’m asking you to help some underprivileged kids learn science.

Donors Choose is a site where teachers in low-income areas and underfunded schools submit proposals for what they’d like to do in their classroom. Today, I set up a challenge, and picked a few science-related projects that I liked.

Now I’m asking you to help by donating to one of these projects. I set a goal of 200 dollars, which is pretty modest. So skip your grande lattes for a week, click on the link below and donate 10 or 15 bucks to a pretty darn good cause. It’s heartbreaking to see how little most of these classrooms are asking for, and easy to see how many children’s lives can be affected by such a small amount of money.

And in case you needed more reason to donate, here’s my blurb from the challenge page:

In an era of increasing politicization and misrepresentation of science, it’s more important than ever to teach children about how the scientific method works. Science teachers are on the front lines of this culture war, and it’s important that they have the resources that they need.

Solutions like this are no substitute for adequate school funding, but we can’t wait around for that kind of education reform. Doing so would mean losing a whole generation of scientists. The potential to change the world is in these children’s minds. Let’s give these kids and their teachers the support that they deserve.

The Trouble with Wikis

There’s been the usual buzz this year about replacing your notebook with a wiki for taking notes in class. Frankly, the buzz is bullshit. Wikis will never catch on as notebook replacements for a couple of reasons:

1) Mathematical symbols are a pain in the ass to represent in wikis. By the time you get the appropriate symbols and formatting in, you’re three equations behind the professor.

2) Assuming you don’t have a fancy-pants tablet PC, there’s no way to copy diagrams off of the board. I suppose you could use a digicam or something if you were really dedicated, but syncing all the pictures up with the appropriate pages of the wiki would be a pain.

3) Formatting is a pain in the ass to do in a wiki. When I’m taking notes, and there’s a REALLY important point, I might write it larger, underline it three times, or put a big star next to it. How do I do that quickly in a wiki? How do I connect concepts with an arrow, or write notes in the margins?

In my experience, wikis and other electronic note-taking tools have far too many disadvantages to make them viable alternatives to paper and a pencil. Sure, having a searchable archive of all my collegiate notes sounds great in principle, but ask yourself: How often do students really reference their notes from years ago, or even from the previous semester? (hint: it’s pretty close to never)

Wikis are great for doing some things, but note taking is not one of them.

Cancer Genome Mapping

Our lab got some good press today, as one of our cancer genome mapping grants was officially announced. The goal is to use next-generation sequencing methods to quickly and cheaply identify structural variation in cancer genomes. This isn’t my primary project, but as always, the whole lab will be providing some peripheral support of the project.

Story in the Houston Chronicle and on the BCM webpage.

Is a PhD for you?

I ran across a great response to this question today:

Is it worth it for me to get a PhD if I don’t intend to hold a job that would require one and my only reason for wanting one is so I know lots of stuff?

Some excerpts from the best response (a few comments down):

Absolutely not. I don’t know what you plan to get a PhD in, but at least for my program you don’t burn 7 years of your life doing extremely difficult and complicated work for long hours with little pay if you are not planning to use it.

In the end a PhD is only school for a year or two. After that it is a job. A difficult, time-consuming, high-pressure job with little pay and a time limit.

There’s more:

It is not a place to be unless you are absolutely, 100% sure it is what you need for the life you want to live. It is not something that a sane person does for fun, and certainly not what someone does for no reason.

I enjoy it, I really do. But I know it is what I need to live the life I want, the life I have wanted since before I can even remember. And I am sacrificing a huge amount to do it. I do not know a single PhD student who is not certain that this is what they need for the career they have chosen. Those that were not certain are no longer in the program. And there are plenty who have developed doubts since entering.

He’s on a roll:

If your goal is to have fun it is even worse. You will be sacrificing a lot of potential pay you could be earning while working a normal job. When you get out you will have to compete with younger people who are more up-to-date on the latest material (since you would have spent the last several years focusing on an extremely narrow and probably esoteric topic to the exclusion of all else). It has serious costs that will hurt you unless you specifically plan your career path to take advantage of it.

These are the kinds of facts that everyone should know before they enter a serious PhD program. It’s not extended college, it’s not a lot of fun some days, and it certainly doesn’t make financial sense.

That said, most days I wouldn’t want to be doing anything else with my life.

The Cost of College

A look at how unreasonable college costs have become, from Inside Higher Ed

In 1974, a year of attendance at the University of Oregon (the flagship university in my state) cost what a student working minimum wage could earn working 27 hours a week, year-round. That is a lot of work for a full-time student during the school year, but was not impossible and could be offset by more work hours in the summer.

By 2004, a full-time student would have to work 46 hours a week to pay for the same attendance. That is essentially impossible, cannot be sufficiently offset by summer earnings and is the fundamental gap that policy makers either don’t understand or choose to ignore because it is too depressing and can’t be fixed.

I’m not sure that I agree with the author’s proposed solutions, but the article contains several more good illustrative examples of how unaffordable college is becoming for those in the middel and lower classes.

via Uncertain Principles

Drinking from the Firehose

From the always accurate PhD Comics

Collegiate Culture

Tonight, I took a little trip down memory lane and read some of the old posts on my college fraternity’s message board. As I remembered old friends and acquaintances, I was struck by how different my social circle is now than it was in college. In college, I hung out with a few science majors, but I had even more friends who studied the arts, literature, history, and politics. Thanks mostly to my involvement in Phi Sigma Pi, I was surrounded by one of the brightest and most diverse groups of people that I’ve every had the privilege to know.

Things are a bit different now. My friends are every bit as intelligent, but they’re also almost entirely from the graduate school at BCM, which is anything but a diverse institution. Don’t get me wrong, it’s a great place to do science, but it’s a research institution, not a college campus. It’s very much a monoculture of highly rational and highly focused individuals. People are here to focus their time and energies on research in one very specific subdiscipline, and as a result, they tend to experience tunnel-vision.

After 18 months of immersion in this culture, I sometimes feel like I’m losing my ability to zoom out and see the world through from different angles. I miss talking philosophy over lunch and then catching a crazy play in the evening. I miss walking through the art gallery while arguing about the inherent flaws in communism. Mainly, I miss talking with people who provided an alternative perspective to my own, and thus complimented my talents. That circle of friends was really a place where our whole was greater than the sum of our parts.

I try to fill these holes by reading on diverse topics and hitting up the occasional jazz concert or art show, but doesn’t even come close to replacing the ubiquitous diversity that you find on liberal arts campus. I’m beginning to realize that I took much of my time in undergrad for granted, and beginning to understand how fortunate I was.

All bemoaning aside, this really has two effects on me. The first is that it makes me realize that I need to work harder to seek out more diverse events and people here in Houston. The second is that it really strengthens my desire to get back on a small campus, in a teaching role this time. Tier I research schools are great for funding and great for research, but I need more than this culture can offer.

Today’s schedule

1:00 pm: Face off with my quals committee in what promises to be a gruesome battle to the death.

6:00 pm: pick up the girl at the airport

8:00 pm: either celebrate my victory or drown my sorrows

2:00 am: Crash. Hard.

UPDATE: I passed. Life is good.

Missing out

College student graduates from UVa in one year

From the comments at MeFi:

Good for this guy and everything, but to me it’s like having a filet mignon speed-eating contest. He missed the point.

Yarrrrrrr!

Chris: you should work the fact that it’s International Talk Like a Pirate day into Journal club
Chris: I’m thinking - do the whole talk in pirate-ese
Ian: arr, that be a good idea
Chris: double bonus points for using the words “bacteriorhodopsin” and “mizzen-mast” in the same sentence

Ian: ninjas or pirates?
Chris: though both rank high on the awesome-scale, pirates are vastly superior in every way
Ian: only ninjas have the real, ultimate power

As seen in an AIM profile

I am ready to meet my qualifying exam committee, but whether they are ready for the great ordeal of meeting me is another question.

– Winston Churchill, slightly adapted by Mike

Implosion

Pictures and Video of the implosion that happened across the street from BCM this morning.

The angle the pictures were taken from is just about the same as I would have had from my office. From the view and the caption, he was probably an office or two over.

Science Triumvirate

Some science humor, a great article on certainty and Science, and a solid reminder that Science is a means, not an ends.

Ruminations

I’ve always been someone who’s prided myself on my intelligence, and I’ve always been ahead of the class. From the time when I read a book to my preschool class, all the way through my undergraduate degrees, I’ve always felt that I was one of the smartest people in the room.

Here, in graduate school, I’ve reached a level where this no longer holds true. In fact, in many situations, I feel like I’m wearing the dunce cap.

At least once a day, I’m exposed to parts of biology that I knew absolutely nothing about. Sometimes I even learn about whole fields of research whose existence I couldn’t even have dreamed up. While this is sometimes cool, it’s also pretty overwhelming.

It certainly doesn’t help that during rotations, I’m starting from scratch every two months. Due to the variety of labs I’ve been through, it’s a constant barrage of new pathways, new techniques, and a new alphabet soup of acronyms and vocabulary that are unique to every field. For first years, ‘drinking from the firehose’ is an apt analogy.

At its best, grad school is exciting and invigorating. I’m around so many people who are at the top of their field, publishing groundbreaking research, and working towards noble goals. At its worst, it’s disheartening and frustrating. Listening to the best researchers in their fields can make you realize how very far you have to go.

At this point, I’m more than ready to join a lab. I’m tired of classes, tired of rotations, tired of seminars over things I’ll never research. I need to start making real progress toward something, no matter how distant and amorphous that dissertation may be.

That’s what grad school is all about. We’re not here to become the world’s leading expert in biology, we’re here to carve out a small niche for ourselves, whether that be in calcium channel function in mammals, or application of novel bioinformatics algorithms to the human genome. We’re here to pick one thing, and research it until we become an expert in our tiny corner of science.

I guess what I’m trying to say is that I’m ready to begin.

PhD Comics

I stumbled across this site the other day and it’s got some pretty good takes on lives of graduate students. Many of these jokes aren’t funny to anyone who hasn’t experienced the wonderful world of graduate school. To those of us slaving away for crap pay and the far-off promise of a degree, they’re funny because they’re true.

Some of my favorites:

• Don’t ask…
• Vacation
• The Author List
• Deciphering Academese
• Addressing Reviewer Comments
• It’s all Binary

The first comic deals with something I learned quickly.: Never ask someone when they’re graduating. We live in a world where your graduation date isn’t based on set requirements, but upon the whims of your advisor and committee. You’re not done until they say you’re done, and in the worst case, that can be quite a while.

This is why choosing a good mentor is important, and why I’m semi-freaking out about my decision.

Update

It’s been almost a month since I went on hiatus, and I feel like an update is in order.

First of all, the big news: I graduated last week! Now that I have my degrees in Biology and Computer Science from Truman State University, I’ll be entering a PhD program at the end of July (see earlier posts).

Graduation was a bittersweet time for me. As I was out at the bars on the Friday night prior, it occurred to me several times that the conversation I was having was almost certainly the last time I would ever speak to that person again. Sure, I’ll keep in touch with close friends, but I’m really going to miss those casual acquaintances - the ones at the edge of my social circle, who seemed like fascinating individuals. I don’t know how many times I bumped into these people at the bars and exchanged pleasantries, without ever really getting to know them as well as I’d have liked to. Sigh - c’est la vie, I suppose…

Prior to moving to Houston, I’ve got some traveling planned. Here’s a rough itinerary:

• May 19th: Daytona Beach, FL for a week of relaxation with friends and bros.
• May 27th: Back to Kirksville for Dick’s wedding with Heather
• May 29th: Lake of the Ozarks for my family’s Memorial Day fish fry
• June 3rd: Kansas City with Mike for Christian and Miranda’s wedding
• June 7th: Houston with my mom and Heather to search for apartments (and to have some fun, if we find one quickly enough)

After that whirlwind tour, I’ll be back at home in St. Louis for another month and a half, working at CompUSA and trying to sort through my life, which is currently packed up in cardboard boxes in my parent’s garage.

Since I’ll be away so much in the next few weeks, I’m going to keep the blog on hiatus for now, and return in mid-June with a lot of pictures, and more of my usual rants on OSS, media, culture, technology, politics, and anything else that tickles my fancy.

I hope all is well in your life, and as I said before, feel free to drop me an email if you’d like to chat - chris at (this domain name) dot com

News Briefs

• I’ve been accepted into the computational biology program at Baylor College of Medicine, and will be moving to Downtown Houston next fall.
• The actual name of the program is “Structural and Computational
  Biology and Molecular Biophysics”, but that’s way too long, so in casual conversation, I’ll continue to call it ‘computational biology’. (Most people look rather confused even at that).
• My spring break trip was great, and I promise pictures and details, as soon as I finish writing the second half of this XML parser in Lisp. (yes, that’s about as fun as it sounds…)
• My wearing of an Omaha Royals hat should not be misconstrued as support for the Kansas City Royals. I won’t say that I hate the KC Royals. It’s really more of a pity thing. No city should have to root for a team that sucks that much.
• School is… well… crappy right now. I don’t enjoy any of my classes, as they’re the ones that I put off until the end for a reason. Thankfully, nice weather has hit K-ville, and it’s brightened my mood considerably. It’s amazing what a little soccer or frisbee with friends will do for your disposition.

Calculus II

Hours I spent in Calc II class this semester: roughly 75
Hours I spent on Calc II homework/studying: roughly 150
Things I remember after only 9 days out of school: 2

1) Pendulum clocks swing in cycloidal arcs, so the distance travelled by the pendulum dosen’t matter. A well designed one always takes 1 second to swing from one endpoint to the other.

2) If you graph the curve of 1/x on the interval from 1 to infinity, it stretches infinitely far to the left and approaches, but never reaches zero as the line goes to infinity. This is basic calc 1:

If this line is rotated around the x-axis, you get a horn-shaped solid of revolution. This is also nothing new.

Through integration, we can find the volume of this integral (and it is exactly 2*Pi). This means that the volume of this surface is finite, but the surface area is infinite, since the line 1/x stretches infinitely far.

Put in real world terms, you could easily fill the shape up with the right amount of paint, but you could never produce enough paint to cover it’s surface.

Things like this are why I don’t believe in the religion of math.

Repost From Last Year

Exams are here
So let’s all cheer
Hooray for the holiday season

If you lose all your friends
and your relationship ends
At least you ll have a reason.

(I’m on hiatus for another week or so.)