Cloth physics, genetics research

peterthomas introduced me to this interactive cloth physics demonstration via Twitter. It's awesome. Click it!

This is what I was hoping my bionerdary would reveal. Perhaps the rules of biology are very complex, but as you discover them useful patterns emerge, systems are revealed, and eventually you can actually do useful things.

I'm not quitting, but I think I've lost hope that genetics research will reveal itself in the useful way cloth physics does in my lifetime. Perhaps biology is too complex for my feeble mind. Perhaps it is too complex for the collective efforts of all of humanity to encapsulate effectively. Or perhaps, long after I'm dead, our children will pull up little "curing cancer" simulators on their computers and wonder what took us so long.

In any event, my desire to witness tangible progress arising from my daily/monthly work seems a poor fit for the current state of the art in mankind's attempts to grok biology via computers.

The daily poem from Writer's Almanac recently delivered what may be my very favorite poem of the Christmas season. As is the case so often, it's being aware of the commonplace and "ordinary" that so often brings epiphany, even in the parking lot of Wal-Mart:


Coming Out of Wal-Mart

by Mark DeFoe

The child, puny, paling toward albino,
hands fused on the handlebars of a new bike.
The man, a cut-out of the boy, gnome-like,
grizzled, knotted like a strange root,
guides him out, hand on the boy's shoulder.
They speak, but in language softer than hearing.

The boy steers the bike as if he steered
a soap bubble, a blown glass swan, a cloud.

On the walk they go still. Muzak covers them.
Sun crushes. The man is a tiny horse,
gentle at a fence. The boy's eyes are huge
as a fawn's.

He grips hard the orange and pink,
and purple and green striped handlebars,
smiling the fixed sweet smile of the sainted.


"Coming Out of Wal-Mart" by Mark DeFoe,
from The Green Chair. © Pringle Tree Press

Hidden Markov Models

Great quote from Cryptogenomicon:

David Lipman commented that the only thing that made HMMs interesting was their name - there’s something’s hidden, and a Russian is involved.

Read more about HMMs.

Not only is that hilarious, but his 95-page HMMER Users Guide includes such indispensable sections as "How to avoid reading this manual" and "How to avoid using this software (links to similar software)".

As scientists go, you gotta love this guy. :)

Warren in route to Antarctica!

My wife's father Warren has left our home sweet home in Nebraska, USA corn fields to fly to the other side of the globe and is currently steaming towards Antarctica. I drew a Google Map.

Today he's "at Sea" (that's all the official itinerary says for 9 of the 17 days of the cruise -laugh-). He has left the Auckland Islands, heading towards Macquarie Island.

First Snow

From my writer's desk at the second story window, I have a bird's eye view of the back yard and the season's first snow. It has come, as it so often does, quietly, blanketing the earth with a hush. The hum of traffic is muffled, the only sound a wind chime stirred by a breeze that also flutters the few remaining leaves that cling to maple and magnolia; the oak and ash are long since bare. The floor of the tree house is covered now in white, and the garden has only a few dark patches where leaves show through. Small drifts have formed on the roof of the garage, and occasional gusts cause it to swirl upward, then fall to the earth below. An occasional squirrel scampers across the yard, and earlier I saw one mourning dove on its usual perch a few feet away, but for the most part the wildlife seems to have taken shelter as if in protest of temperatures that have dipped into the thirties when yesterday they were in the fifties. I mowed the yard then, and had to remove my jacket; today only a few wheel marks show for my labors, and they are fast disappearing.

The blanket of quiet and snow has covered me with serenity. I sense that beneath the often-frantic pace of life there is a season calling me to quiet reflection as a balance to my usual frantic doing. And I'm reminded that the ingredients of peace are very basic: shelter, food, clothing. Today I have all these, plus the warming glow of raspberry tea and the quiet hum of a MacBook Pro. I'm a blessed man.

Feels good, makes no sense

I keep mulling over this chant from The Great Debaters that I watched last night.

Who is the judge?
The judge is God.
Why is he God?
Because he decides who wins or loses. Not my opponent.
Who is your opponent?
He does not exist.
Why does he not exist?
Because he is a mere dissenting voice of the truth I speak!

It feels powerful. Yet my brain can't help picking it apart, and it doesn't seem to fit in my head.

The judge is God? What is this God thing? How does that response answer or clarify anything?

God decides who wins or loses? Not my opponent? And not me? If God decides and God is all powerful then I'm just a puppet of God's whim, aren't I? So I don't control anything? Why are my actions and decisions important then?

My opponent does not exist, but he's a dissenting voice? But "a dissenting voice" would exist. As a voice. That dissents. Dissenting the truth I speak? On my debate team? Where someone decides on a coin flip which side of an argument I am to take? So the coin flip always lands on truth whenever it decides which side I am to take? What if I argue both sides? My opponents are always lying? Even when they take both sides?

Artsy stuff tends to do this to me. My emotional brain is fascinated by these shiny trinkets so it keeps picking them up, again and again, for reconsideration. But my analytical brain (which is dominant) can't make heads or tails out of those cryptic "answers".