Sorry, world.

This blog just isn't going to happen. There's too much going on in life to spend more time in front of my computer! Check back in six months--I may yet have a change of heart. Until then, adieu.

Lab protocols in haiku, part 1

What if all the protocols I work off of and write were in haiku? Maybe they'd look something like this:

subclone dna
transfect into hela cells
measure fluorescence

It would make them that much easier to remember. And I'd be that much more distracted.

R

Apartment move

I finally moved apartments, something I've been looking forward to for a long time. The current state of my kitchen:

About normal, really.

I thought this picture an interesting reflection of my life:

Wallet: home made in 3rd grade
Coffee cup: because a strong cup of coffee on a saturday makes the world a better place.

Demitasse: because American coffee is good, but Italian is even better.

Candles: for my aesthetic sensibilities
RC car: because (not diminishing those aesthetic sensibilities) yes, this is a bachelor pad.
Pile of garbage: my backpack was long overdue for a cleanout.
Toolbox: containing the basic necessities for putting together Ikea furniture. And, of course, duct tape.
Socks: so I can wear my flops to work, and my lab shoes at work.
Duster: for the annual cleaning.
Coffee table: $10 from another grad student.

Accidental insight

I enjoy the suggestions Google makes for me as I type in the search box. Normally they're helpful, sometimes they're entertaining, and sometimes (assuming the suggestion algorithm is based on query frequency), they provide some insight into the "average internet user." If news and YouTube comments were reflective of the average person, the average person would be an idiot. Google queries are more accurate, but I'm yet sure just how much. Start typing "people without," and these are the top suggestions:

- belly buttons
- health insurance
- emotions
- fingerprints
- a conscience
- friends
- eyebrows
- arms legs

Numbers, part 2

- If you spend $1.50 a day on coffee, that'll add up to $25,000 over 50 years.
- If you sneeze once a day, that adds up to about 30,000 sneezes over a lifetime.
- If you spend 10 minutes a day reading blogs, that adds up to some 200+ days over a lifetime that you could have spent doing something more interesting.

Hm.

A day in the life

7:30: alarm goes off
7:35: alarm goes off
7:40: alarm goes off. get up. check weather, news, email.
7:45: bathroom and dress. avoid shaving (possible). avoid clothes (not possible).
7:55: breakfast while making lunch and coffee
7:15: pack up. brush teeth. feed Shark (beta fish). go to car. go back to apartment to get whatever i forgot. go back to car.
7:20: tune ipod. usually a podcast from ROCKHARBOR or Mars Hill Church. "redemptive commuting."
7:50: arrive at cubicle sweet cubicle. check email. plan day.
8:00-6:00: work. about 1/3 research work in cubicle, 1/3 lab work, 1/3 class work. eat lunch while working, but take multiple shorter breaks. research work centers around journal articles. lab work involves subcloning plasmids and growing bacteria and tumor cells (both ironically difficult to keep alive). class work involves facebook, gchat, xkcd, and the occasional textbook.
8:30: coffee
9:00: snack
10:00: meet with advisor. realize i did everything wrong. consider quitting PhD.
11:00: lunch 1
12:00-1:00: hold office hours. encourage nervous students. terrorize overly confident students. try to sound like I know what I'm talking about ("well, that problem is so simple, why don't we try this other one..."). get free food and coffee in exchange for homework answers.
1:30: coffee
2:30: lunch 2
3:30: falling asleep. go for a walk. get coffee. turn on Pandora.
4:00: snack
5:00: plan how I'm going to get a great idea to save the world, start a company, get bought out by J&J, and retire to the south of France.
6:00: realize I can save a day if I transfect some cells now.
7:00: go home. hungry. get dinner. check email.
9:00: talk to girlfriend.
11:00: shower. prayer. read McCollough's 1776. glad i don't live in the 18th century. sleep.
1:00am: wake up to neighbors. again. 1:30: back to sleep.

Comments

Allow me to indulge in what may be intense irony:

Comments below YouTube videos and CNN.com can provide some of the most astonishing insights into peoples' minds. And not usually in a good way. Consider these comments below a result CNN article on the Lawrence Livermore nuclear fusion lab:

- Why do "scientists" insist on trying to find new ways to destroy the world?
- I thought fusion was drink and fission was something you did with a pole and bait down at the creek.
- YAY!!!! a new place to cook my meat loaf! cmon guys, its called common sense.
- Didn't these guys watch Spiderman I. Dr. Octopus did the very same thing and it didn't work out so well for him...Do these guys really think that Spiderman will save them when this thing causes the end of the world...when will it be done again...oh yeah, end of 2012 when the Mayan Calnder ends!!!
- What a waste of time. You can't create a star without an immense amount of mass.
- We could use your mom. Gravity problem solved!

The list goes on. Simultaneously funny, sad, and aggravating. Mostly sad.

For more, see http://xkcd.com/202/.

Numbers

- Most cells are microscopic, yet most human cells have over 3,000,000,000 base pairs (in the right order) packed inside them.

- The average human body has trillions of red blood cells (1,000,000,000,000), and produced 2,000,000 new ones per second.

- e. coli can replicate themselves every 20 minutes. One bacterium can thus yield eight in one hour, or, in theory, 4 thousand billion billion bacteria in a day.

Biology is awesome.

Tissue engineering

It's what I want to do. And no, it has nothing to do with Kleenex. I am not getting a PhD so that I can spend my life engineering new ways to make blowing your nose more pleasurable. The goal of tissue engineering is to re-create biology tissues for replacement and repair of damaged ones. The closer you can get to the real thing, the better. For all the brilliant minds devoting their efforts to engineering, we can't do better than nature. We keep trying, and we can't do it. So instead, we take our inspiration from nature. It's called biomimetic engineering. It's good stuff.

In the meantime, I'm studying molecular biomechanics. Mechanical engineering on the teeny-tiny scale. Micro-meters and nano-neutons. The forces on cell nuclei and embryonic tissue. That kind of thing.

That's all I've got for now. Thanks for reading.

Winter in pictures

Last time I posted pictures, it was of leaves changing color. That was a long time ago. This also happened to be my first winter; these pictures are for anyone who doesn't live in a ridiculous climate like that of Pittsburgh.

Snow is cold and wet and inconvenient and completely awesome. My next ambition is to make snow sculptures a la Calvin and Hobbes.

Blog 2.0

Dear readers,

I'm restarting my blog with the purposes of 1) informing, 2) educating, and 3) entertaining. It's not intended as 1) a rant, 2) a procrastination tool, or 3) replacement for real interpersonal communication. That's the plan, anyway. Possible topics include:

- Where the wild things are: my experiences as an undergraduate

- Heiku: when eighteen syllables is one too many

- Graduate school and goldfish

- Pyramids built by slaves: an analogy for academic research

- Sex(AI) before cleavage, and other oddities of bioengineering

Enjoy!

Richard

Terminology

Last week in Engineering Cell Biology we learned about ligands in mammalian signaling pathways called Desert Hedgehog, Indian Hedgehog, and, of course, Sonic Hedgehog.

This week while programming I learned that when working with an empty matrix, text objects have no children.

What's next?

Two experiences

The Twilight Zone: getting to campus by 7:00 or 7:30 and being the only one around. Going into my office area and seeing only empty cubicles. An earily timeless.

Hell: I went to the fitness center at my apartment complex and, like the office, was the only one there. Except at the fitness center, the tv was on and tuned to a sports talkshow with the volume up and the remote NOWHERE to be found. I could feel my brain cells dying.

Life update

My apologies, faithful readers, for the lack of posts. Graduate school, it turns out, is not all fun and games. I suddenly find myself lacking in free time, sleep, and a social life. At the moment I'm frustrated because it is a GORGEOUS fall day outside, and I'm inside pecking away at this computer.

If you've time to burn, you can see a bit of what I live in at these sites:
- The Dahl Lab
- The Davidson Lab
- PhD Comics

Snapshot

Determination or desperation?

Saturday morning. Left the office last night at 7PM--the wild friday night of a graduate student. Started work at 8 this morning. At 11, still enjoying coffee and pajamas. Programming a model of bidirectional microtubule motion due to dynamic transitions of mutated Ncd molecular motors. Mmmm...

An observation

Science fiction and, more specifically, Hollywood, has a theme of the world becoming more mechanical. More specifically, of biology becoming more mechanical. The Matrix, Star Trek, the Terminator series, and others all have this theme. I myself joked that I'd invent the Borg for my PhD research. 

But the theme is false to reality. In fact, the opposite is more true. Rather than biology moving towards machinery, machinery is becoming more biological. Computer interfaces better reflect the traits of the user. Medical solutions are less mechanical/surgical and more therapeutic. Electronic communication includes text, sound, and images. 

This is a profoundly good trend because it keeps people closer to their humanity. And it will only get stronger. The mechanical things that are visible in everyday life will continue to become less and less apparent. 

And now I need to stop "philosophizing" and get back to work (or perhaps this is my real work?...).

Thursday's weather forecast

Busy, with a chance of snow.

SNOW!!!!!!!!!!!!!!!!!

This is October. I'm used to October being hot, dry, and windy. Not snowy. Snow is the cotton balls on fancy Christmas decorations, not a reality. Snow is the stuff in movies that apparently is cold, because people wear coats when in it. Snow is necessary for a snow cone on a hot fall day in California. But surely it can't be real.

I'm excited, can you tell?

Journal analogies

Cell :: NYT
Nature :: CNN
Science :: USA Today (pie charts!)
Journal of Cell Biology :: Washington Post
Tissue Engineering :: Pittsburgh Post-Gazette

The google home page today is...

...BRILLIANT. I will be geeking out about it all day!

Life update

My thanks, faithful readers, for visiting this blogs. In the blogosphere, "never have so many said so little with so much," so I am particularly grateful you choose to come here. I attached a hit counter and found this site gets 10-15 hits a day. Enough to make me excited.

- Yesterday, I was in someone else's house/apartment for the first time in two months. That's moving to a new city for you.
- Yesterday, I met the wonderful group of people, the kind you meet and immediately know you should spend time around them.
- Yesterday, I saw for the first time in my life trees in the countryside changing colors.
- Yesterday, I was assigned an advisor (and today, a cubicle). My life as a graduate student begins to take form.
- Yesterday, I had an incredible conversation with an incredible friend, as we sought to understand an incredible God.

Yesterday was a good day.