Friday, October 30, 2009


Protein folding patterns can be described by two rotational angles of the secondary structure: Φ (phi) and ψ (psi). There are eight theoretically allowed rotational angles for each of the two bonding angles, but only a few of these rotational angles will be allowed because of steric hindrance (stuff getting in the way). Hence, we have a Ramachandran plot of ψ v. Φ. The plot you see above has been rendered in 3D with % incidence forming the texture.

It's uncanny how you can take numbers from an extremely small system and create a 3D graph that looks a lot like a topo map. If our ideas were like bonding angles, I wonder if there isn't a comprehensive dimensional representation out there?

There are a couple of levels of potential.
1. Does geography influence the way we think? Does the natural landscape code for truth?
2. What if contradictory ideas (paradoxes) were really just helping to establish cognitive texture: just like "impermissible" bonding angles are still necessary to form the plot diagram...
3. Trying to establish the "truth" through systematic logic would take about as long or longer as taking a 100 residue protein (a pretty small protein) -- each with 10 conformational possibilities, and testing each conformational combination once every 1.0 × 10-13 seconds: it would take 1.0 × 1077 years. (See Levinthal's Paradox). Proteins like this fold in less than 5 seconds under physiologic conditions: therefore the enzymes and chaperones mediating this process must have some shortcuts. In order to arrive at a semblance of truth, we might have to accept some shortcuts through faith.


Monday, October 26, 2009

Before we leave...

Dear Family,

I love you.

I want to say it.

Mean it.

Monday, October 19, 2009


Mom is like the sunlight: true, clear, warm-bright. Mom is like a wind after listless sails, and a clear drink on dusty days.

Mom used to put me to bed every night. She would always say: "I love you hundreds of bushies" ... which being translated, means an extremely large quantity.

I remember waking up with so much energy that I had to run, jump, or wrestle. It was a joy to know that Mom fully approved of all of these exercises, especially outside. It was freedom, it was happiness. I'm sure it wasn't easy to let us go off on our crazy adventures: Mom did it anyways.

Mom makes the best bread I've ever had. The three of us grew up on simple, delicious, wholesome food that I hope to eat for the rest of my life. I was happy to find an ally in Mom when at around 4 or 5 years old I developed a liking for a supper of fruit and bread. This was a "fruitish" supper. And it's still my favorite.

Mom is incredibly adventurous. She showed me how to travel: how to be flexible, how to ask for help, how to pack light.

Mom was my tutor, driver / navigator to all those cello lessons, confidant, encourager, organizer, financial / academic adviser, nurse, cheerleader, waypoint, foundation, friend.

Mom gives so much. I'll never be able to repay the debt I owe. Mom, I love you with all of my heart.

Mom is like the sunlight.

Saturday, October 3, 2009


Timothy R. Howe , M.D. : I call him Dad.

This summer, Dad and I worked together to carry a load of gear from our campsite on Metallak island, across the lake, and up a short trail to where our cars were. Afterwards, as we canoed back to the island, I remembered how good it felt to have dad in the back of the canoe. Steady, strong, sure.

When I was little, Dad would sing me to sleep on restless nights. My favorite was Bill-Grogan's Goat, to which Dad added marvelous sound-effects. On hot nights, he would "fan" my covers up and down for a long time. When we were bad, Dad spanked us, but I don't remember a time when I got an undeserved punishment. When I stomped off to bed in a bad mood, Dad would come and rub my back and tell me how much he loved me. Believe me, despite many determined attempts to stay cranky, I never outlasted Dad.

Dad taught me how to ride a bike, how to paddle a canoe, how to ice-skate, how to build a fire, how to hike, how to make a bow and arrow, how to prepare for an adventure, how to ski-skate, how to make a debris hut, how to tie a bowline, how to make a basket, how to pray, how to smile when things get tough.

I went to the hospital (I called it the hostible) with Dad occasionally when I was little. It was fun to see all the nurses and patients cheer up as Dad rounded the corner. When our family went to Nepal for three months, I watched as Dad gave consultation, care, and compassion. The people of Huas valley loved and respected Dad; I'm certain they remember him.

I didn't understand how much I relied on Dad until I left home for Peru. Awash in a giddy fear that welled up out of my own insecurity, I read and re-read a carefully folded piece of paper Dad had handed to me on my way out the door. Nobody will ever understand how much that letter meant to me.

Then college, and another letter. Now I have a cell-phone, I call home whenever a trouble or a question faces me. I call Dad for over-the-phone diagnoses of my ills, solid advice, and substantial comfort.

I'm circling. I want to cut to the essence. It's the light in his eye. The rugged personality that exudes integrity and wholeness. The way Dad loves Mom and family. His deep relationship with God. It's the hand on your shoulder and the paddle in the back of the canoe; steady, strong, sure.