Wednesday, December 31, 2008

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.

Monday, December 29, 2008

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

Sunday, December 14, 2008

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.

Tuesday, December 9, 2008

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.

Thursday, December 4, 2008

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".

Wednesday, November 19, 2008

Space junk

Reading about space junk this morning because an astronaut lost a briefcase-sized tool bag yesterday.

Great reader comment from waldo:

They demoted Pluto from the list of planets because it hadn't
cleaned up it's orbit. If this littering keeps up we'll have to demote earth too.

Wednesday, November 12, 2008


Received this pic in an advert from today.

This images totally resonates with me. This is exactly what a typical Omaha Chess Club meeting looks like. And the hot pump-wearing chess groupies are always clamoring to ride in the carts when we all go out chess shopping before and after every meeting. Sneaky chess paparazzi must have been hiding in the bushes since we didn't issue any press cards last month.

Tuesday, November 11, 2008

Jealous much?

In case you didn't know, I married a hottie: The Nexus Team

Scroll right to the Andrias. :)

Saturday, November 8, 2008

Undead source code

I wrote a little web tool in 2000 while Justin Hopkins was interning with me. I used it for a couple months, then forgot about it. Then, suddenly:

On Jan 14, 2005, at 2:47 PM, Wayne & Susie Griswold wrote:
> Jay, where's my friend the Optimal Bitmask Thingy?
> I can't live without it and the link doesn't work anymore!

-laugh- Someone uses that? I fixed the link.

Then I forgot about it again.

On Nov 6, 2008, at 5:46 PM, Wayne & Susie Griswold wrote:
> Jay, it's been a few years, but when I went looking for my
> favorite bitmask tool, the Optimal Bitmask Thingy, it was
> gone!!! Can you make the link work again? Please?

-laugh- Raised from the dead again:

Jay's IP Optimum Bitmask Thingy

Justin and Josh might get a kick out of the fact that this tool
refuses to die, 9 years later. :)

Enjoy. :)

Why don't municipalities SAVE, then spend?

To: planetmoney(at)npr(dot)org

Hi guys. I love the Planet Money podcast. Maybe you can help me understand this.

It seems so simple. Yet I never hear anyone talk about it.

David(?), near the end of the Wisconsin/Ireland/Germany podcast:
"There is a tragedy here too. Over the last 30 years there have been a series of financial innovations that have just been plain good. They have allowed city governments, local governments to get money more cheaply."

Every year a million finance professionals invent new, complex ways to enrich themselves without actually producing anything. Every such web will eventually collapse under the weight of collective greed.


So why don't cities and individuals SAVE money, THEN spend it?

Why don't we all do this?

I hope you can help me understand. :)


Jay Hannah
Omaha, NE

Friday, November 7, 2008

Dream job? Pass.

I don't understand me.

17 months after starting my part-time adventures in genetics research (showing up at the medical center 3 days a week), I am now trying to find someone else with my skill set to take this job on, full time. I'm not leaving, but apparently I don't really want this gig full time either.

I think it's the money. Plus the current lack of some big, computationally extensive pipeline for me to wrestle every day and be the expert on. I like knowing big balls of code inside and out, and having people need me for high powered data nerd ninja action. Plus the lack of other people like me sitting here. Lack of coworkers is depressing.

Or maybe it's just the money.

YOU are rich

How do so many Christians take so much of the Bible seriously and ignore this one?

It is easier for a camel to go through the eye of a needle, than for a rich man to enter into the kingdom of God. (Matthew 19:24)

If you're going to believe the Bible it seems to me that perhaps women will be fine, but if you're male and have Internet access (rich!), then you're in trouble.


Thursday, October 30, 2008

Entering the Bloggersphere

It is said that once you expand your world you cannot return to the self you were before crossing over. So it is for me with "blogging". It reminds me of my pet grandmice as they are placed carefully into their exercise ball. As they move forward, taking what must seem to them normal steps, that colorful little sphere careens forward at incredible speed. In a flash they are propelled across the room. Unless good fortune heads the projectile down the hallway (certainly the vermin have no control of it), the outcome is .....Yikes! Who put that wall in my path?
Ok. I'm in the bloggersphere. Taking the first step now.....

Friday, October 24, 2008

The Restless Tide

Through the years I’ve often read poems and sung songs about the ocean’s “restless tide,” but until we stayed overnight at Maine’s Little River Lighthouse its meaning never really connected. That reality began to soak in as our little boat ferried us to the island at high tide, our guides explaining that the dock would be high and dry during low tide. We were told that the water level here varies as much as 28 feet between the tides, and this twice a day!

From the moment we set foot in the boat until we disembarked a day later we were surrounded by the ocean’s ebb and flow, an incessant surround sound somehow both soothing and unsettling—soothing in its rhythmic regularity, unsettling in its chaotic churning.

For an Iowa farm boy like me the constant spew of foam and spray had no parallel; even the wind was more buffet than breeze. I began to think about how different must be the life outlook of an Iowa farmer and a Maine fisherman. What would it be like to cast your net upon the restless sea rather than plow straight furrows in terra firma? How would it differ to rely on a daily catch rather than a single autumn harvest? And does it take more courage to gamble daily on the vagaries of the ocean, or to risk it all on one big jackpot?

I’m thinking that for hardiness and courage the edge likely goes to the Mainian, although for sweat and grit the Iowa farmer comes right alongside. Either of them, in comparison to a city-dweller, is to be envied for a living connection with land or sea, and the courage to embrace a love that both gives and takes away.

Noah's Ark

Buzz Carver has been on the ocean since childhood, and has spent the last twenty years as a full-time lobsterman off the coast of central Maine. Last Tuesday night he took four of us Midwesterners out to sea so we could get some sense of the vocation that claims him and his father before him. He only ran a dozen or so lobster traps for our benefit, rather than the 250 he might haul in a routine work day. But it was enough to get a pretty good sense of what he does all day long, year-round.

It’s a pretty basic routine: boat out to any one of his more than 700 lobster traps, marked by a bright pink-over-yellow buoy. Snag the rope with a hooked gaff, lashing it to a hydraulic winch to bring it alongside. Haul the metal trap aboard and remove the lobsters inside (measuring each one carefully, tossing back males that are too small and females designated for breeding). Empty the mesh bag that holds the old bait and replace it with new salted herring. Then throw the trap back overboard and head for the next one.

It used to be they stopped lobstering in the winter, but now the catch goes on year-round. The difference in the colder months is that Buzz travels to more distant sites, up to thirty miles from his bayside home. It’s hard and sometimes dangerous work, but as his boat cuts through the water, throwing plumes of foam from the prow, as he pulls alongside a rocky isle to point out a family of seals, as the seagulls circle overhead and the sun begins to set in crimson colors…Well, this is obviously a man who has found an enviable merger of vocation and avocation.

Never mind that the price paid by Canadian-controlled processing plants plummeted this week from $4 a pound to $2, that acts of trap vandalism and pilfering are on the increase, that it costs $100 to purchase each trap and the accompanying gear, that state and federal fishing regulations are often inconsistent and inept.

Buzz is a Maine lobsterman, and hopes to always be. And his son, Noah? Suffice to say that when Buzz was finally able to buy his first new boat a year ago he didn’t name it for his wife Suzanne, as customary. Instead, painted on the stern is a scripture passage from Genesis, and in larger letters the name of his craft: Noah’s Ark.

A year in the life?

-ponder- I guess this "Integration Candidates" page I just made is sort of a list of possibly general use tools I've worked on over the last year... : BioCMS (RT username: guest, password: guest)

Wednesday, October 15, 2008

Shrink, episode 1.5.1

I've come up with a new theory about the dynamics of my motivation system.

As long as I can remember I've had a bordering-on-maniacal obsession with efficiency in my work. Computer programming is a great way to try to fill this hole: everything is off or on, black or white, efficiency gains can all be measured objectively and quantitatively (this program runs 26.4% faster than this other program). My work (lines of source code) is easily presented to other people, proving that I performed difficult labor. Tangible gains can by proven on a daily basis.

I need a plan. I need a direction. I need structure. I need to attack problems. I need to see myself progressing. I need to prove to myself, and anyone else who cares, that I am succeeding. Every day.

In science most substantive things take months or years. It's hard to prove that you're making substantive progress daily, weekly, even monthly. It often (to me) feels like floundering around hopelessly, grasping with overly educated guesses at various straws while blathering incessantly1.

My new theory goes something like this: My pattern of mental self abuse2 has taught me that if I can't prove that I made tangible progress today, then I haven't, and I'm a slacker. This feedback system declares the vast majority of academia a monumental waste of time. School is massively inefficient because it attempts to broadly prepare you for future challenges, many of which may never happen.

So the feedback loop in my head, every day in chemistry, goes something like this: "Why am I attempting to memorize factoid number 700? I'm never going to use this, and I've already forgotten most of the factoids so far. Why are you sitting here? You suck at this." My mental defenses kick in, saying "but I'm good at programming. I can prove it. Look at my paychecks! Look at my source code!"

Hopefully this spring semester I can break that feedback loop and be OK with investing, in a massively inefficient manner, "in myself." By knowing and forgetting more chemistry. And math. To get the degree. Which may be good to have. Someday.

Because this week I realized some of it does stick. Listening to a JCVI genius present 4 hours of material this week, he threw out some key words I never would have loosely understood without that semester of chemistry. 5 months later I do remember the gist of a few nuggets of what I learned through that book I can't help hating. (I'll just keep telling myself that 5% sticks and that's OK. -laugh-)

So, through constant meditation and daily affirmations maybe I can survive getting this degree. In the year 2014 Zach will be out of high school and maybe I can try out a "dream job" w/ JCVI or NCBI or something...

I guess we'll find out. :)

1. Hyperbole. But you get the gist.
2. My shrink rated me a 10 on a 10 scale. That surprised me. :)

Thursday, September 25, 2008

Shady Characters

Here's one of my very favorite picture of the beloved and I, snapped by brother Lynn as we adjusted an umbrella during the Michigan graduation fete last spring...a candid moment of togetherness.

Pedal On!

After several years of cycling I finally signed on for an organized ride. I'm hooked! It was great having a new route, all mapped out, with stops for snacks and lunch, plus a whole mob of other enthusiasts to chat up as we stood in line at the porta-potty. By the end of the day we'd pedaled 49.5 miles, and my biking buddies were urging me to consider riding the MS 160 next years. I just may do it...the immediate goal being a 61-mile ride in my 61st year.

Bulbs, Bulbs, and More Bulbs

Some five years ago my friend Sam Rose gave me 150 or so day lilies; recently I dug them up to give them some growing space. How incredible the increase! I still had my 150 plants, but also mailed a boxful to Sam in Arizona and to Brother John in Nebraska, plus gave a wheelbarrow full to friends Bud and Mark. Mother Nature, thou art one prolific lady!

Monarch Reveries

For several years I've been on the lookout for a caterpillar of the monarch butterfly, with no success. I've even allowed milkweeds to grow in our fence row--the host plant around which the monarch life cycle revolves. Still no caterpillars (except for the plastic one my jokester neighbor planted). Then a few weeks ago as I was digging up the day lily bed there it was, the zebra-striped green-white-and-yellow crawler remembered from my childhood, when the Hannah boys grew them by the score. Fantastic! I transplanted it to the milkweed, where it began at once eating voraciously, just as I remembered. Then two days later it disappeared. I thought a bird must have eaten it, since usually they form their cocoon right on the milkweed. Bummer. Then a day or so later I happened to glance to the side as I was going up the back steps and there he was, our caterpillar, suspended upside-down, curled up in the beginning of a new life stage. Within two days the familiar gold-rimmed pale-green cocoon formed, and in my daily comings and goings I watched for signs of hatching out, only to come home one evening to find that my friend had taken flight. I didn't get to see him on the wing, but my imagination soared as I thought of his long journey to winter in Mexico. All of which has brought me to a new item on my Bucket List, joining the migration to see the wintering site firsthand. I've seen small monarch clusters in Iowa and in Michigan; how amazing it would be to see entire mountainsides robed in flutters of orange and black!

Guns, or Butter?

We shared in a United Nations peace vigil last Sunday. A display by the American Friends Service Committee (the Quakers) illustrated the cost in human life exacted by the war in Iraq—142 pairs of combat boots, each one representing a soldier from Missouri or Kansas killed in the war to date. A few pairs of civilian shoes were interspersed with the boots, representative of the hundreds of thousands of Iraqis who have likely died in the war (but whose deaths we don’t tally, being only collateral damage).

And then there’s the financial cost of the war. Pointing out that one day of the Iraqi war costs $720 million, a series of banners fluttered the message that we could have instead done any of the following:
• Provided a $1,700 health insurance policy for 423,529 children
• Granted 4-year scholarships of $20,000 to 34,904 state university students
• Hired 12,478 elementary school teachers at $57,000 each
• Provide renewable electricity for 1,274,336 homes at $565 each
• Offered Head Start to 95,364 kids ay $7,550 per kid
• Built homes for 6,482 families at $111,000 each
• Provided free school lunches for 1,153,846 kids at $624 per year
• Built 84 new elementary schools at $8.5 million each
• Offered healthcare to 163,525 people at $4,400 per year

In just nine days of Iraq war expenditures we could do ALL of the above. Imagine what could be done with five years of war expenditures! Surely a trillion dollars should have bought us more than it has. (Unless you’re Shell Oil, who this week opened the first Western-owned oil company office in Iraq since 1972, when the nation’s oil supplies were nationalized. Now there’s a great investment!)

Decades ago President Eisenhower lamented that each bomb built is at the expense of needed social services, and in his 1961 farewell address to the nation he sounded a prophetic note of caution, saying "In the councils of government, we must guard against the acquisition of unwarranted influence, whether sought or unsought, by the military industrial complex. The potential for the disastrous rise of misplaced power exists and will persist. We must never let the weight of this combination endanger our liberties or democratic processes. We should take nothing for granted. Only an alert and knowledgeable citizenry can compel the proper meshing of the huge industrial and military machinery of defense with our peaceful methods and goals, so that security and liberty may prosper together."

Evidence that this counsel went unheeded is reflected in the words of Martin Luther King, Jr., speaking six years later about the Vietnam War and the spirit of militarism, saying “A nation that continues year after year to spend more money on military defense than on programs of social uplift is approaching spiritual death.”

Ask not for whom the bell tolls…

Wednesday, September 24, 2008

Improve your vision today! Remove your glasses!

Hopped on the motorcycle this morning in heavy fog. Odometer: 7777. After about 3 seconds I couldn't see through my visor. Visor up. After 3 more seconds I couldn't see through my glasses. Glasses off.

Shitty vision + heavy fog + your body IS the crumple zone? Bad Idea.

Either I've never pulled that trick before, or I've forgotten. Eyelids are the best windshield wipers ever. Next time I'll bring contacts or Lasik eye surgery with me. :)

Monday, September 22, 2008

Windows Is Shutting Down

Windows is Shutting Down

by Clive James

Windows is shutting down, and grammar are
On their last leg. So what am we to do?
A letter of complaint go just so far,
Proving the only one in step are you.

Better, perhaps, to simply let it goes.
A sentence have to be screwed pretty bad
Before they gets to where you doesnt knows
The meaning what it must be meant to had.

The meteor have hit. Extinction spread,
But evolution do not stop for that.
A mutant languages rise from the dead
And all them rules is suddenly old hat.

Too bad for we, us what has had so long
The best seat from the only game in town.
But there it am, and whom can say its wrong?
Those are the break. Windows is shutting down.

"Windows Is Shutting Down" by Clive James from Opal Sunset: Selected poems, 1958–2008. © W.W. Norton & Company, 2008.

Friday, September 19, 2008

Shrink, episode 1.3

New theory: I have a tape recorder in the back of my head playing my personal mix tape of Greatest Hits of Verbal Self Abuse. I think I constructed this system in high school when I started running 3 miles, 3 nights a week to lose weight to date girls. It motivated the hell out of me. I beat myself mercilessly with a wide array of creative self loathing. By any objective measure, my physical transformation was a great success. Unfortunately I never felt good about any gains I made because I was too busy hating the way I looked, and by extension hating myself, no matter what.

Over the last 18 years I don't think I've consciously recognized that the tape recorder is still back there. Still looping. Now I'm practicing recognizing it. And hitting the off button.

Maybe I can make a new tape. It will have some positive things to say about me. :)

Wednesday, September 17, 2008

Law and the Long War

A great book I'm reading: Law and the Long War: The Future of Justice in the Age of Terror. His excellent intro lays out the gulf between the two major opposing perspectives on the Bush administration's actions, and argues for middle ground. So far I'm on the human rights side of the argument and not in the middle ground at all, but I just started the book, so maybe he'll convince me.

Maybe Erin and Pete can find some middle ground too? :)

Saturday, September 13, 2008

Shrink, episode 1.2.2

Huh, nope. I found a counter-example, and my example from earlier is working fine now. Maybe the crazy is sleeping. :)

Shrink, episode 1.2.1

Fascinating. I am unable to attach any positivity with emotional weight to my own actions. The clinician in my head finds this curious and intriguing. My emotional brain finds these attempts at physical therapy very painful. The clinician watches, enthralled by all the baseless, hyperbolic drama. It wonders why we choose to torture the poor creature.

Friday, September 12, 2008

Shrink, episode 1.2

I offered my self diagnosis: (1) I have pinned my self esteem on my work for so long that now that my "career path" seems to be sending me through Chemistry (really bad) and Calculus (maybe won't be so bad?) my self worth is taking serious body blows. (2) While politicians have no sense of shame, or can ever point out any mistakes they have ever made, I have the opposite problem. I can tell you 3 things I screwed during my morning commute today.

Sue introduced me to cognitive behavioral therapy and Dr. David Burns 10 forms of twisted thinking. I definitely need work on "3. Mental filter", and "4. Discounting the positive". I'm going to keep a log of my crazy and see what I come up with. :)

Friday, September 5, 2008

Grassius debugus

Helped a guy at Grassius use -link and Bio/Graphics/ link_pattern() today. Yay me! :)

Sunday, August 31, 2008

Run on the bank. In reverse.

I got an email from Kiva today saying that they've made a systems change so that I get Kiva credit back not when a loan has been fully repaid, but every time Kiva receives partial payment back from the field partner. So, suddenly I had a bunch of Kiva credit I wasn't expecting until next year.

Cool! So I hopped out to to grab me some more loans, to find that only 3 loans were available to fund. Usually there are hundreds. And those 3 were actually funded already (Kiva is a little laggy about updating loan statuses). So apparently this systems change has suddenly freed up hundreds of thousands of dollars in donor's money, causing a flood of new loan purchases, to the point where they've run out of people to loan money to!

As Jane Sladen said: "kind of like trying to buy Elton John tickets on line - click before they're gone!!"

So here I am with Kiva credit and nobody to loan money to. What a terrific problem to have! This bump is a little weird but I'm sure after a few days the newly improved cash flow of donors will enable Kiva to give more loans, faster overall.

(Hopefully nobody decides to pull their money out instead of waiting patiently for loan opportunities. I'm sure Kiva will soon catch up with the total capacity of their donor pool.)

Saturday, August 23, 2008

Watch your spelling, nerd boy

pixilated -adjective
1. slightly eccentric or mentally disordered.
2. amusingly whimsical, prankish, silly, or the like.
[Origin: 1840–50, Americanism; pix(ie) + (tit)illated]

pixelated -adjective
1. pertaining to a printed image which has been digitized; visible as a pattern of pixels; also written pixellated

We aren't in 1850 any more, Toto.

Midwest tour

My Geocaching travelbug U. S. Navy (2 of 4) has been making the rounds since April 2006.

Sunday, August 10, 2008

The Dark Knight

Sometimes the movie lives up to the hype, and in my view The Dark Knight is one of those. I find Batman's voice a bit unreal, and the two-face dude (DA Harvey Dent) is totally over the top, but that, I suppose, is understandable since it is, after all, based on a comic. What I did find believable was the dual nature of shadow and light found even in our heroes--a conundrum well expressed in the movie's title. Harvey particularly shows how a "good guy" can go over to "the dark side." This seemed completely believable. Actually Batman himself seems so principled that at times I had a hard time relating to him. In the scene where Batman has a clear opportunity to run down The Joker with his Batmobile but instead swerves and wrecks the vehicle...well, as much as I consider myself nonviolent I think in a case of "him or me" I would have chosen him, the maestro of chaos. Wouldn't you owe it to the public, really? But on the other hand, I sure wouldn't want to return to the days of the vigilante and every man wearing the law on his hip. Ah, yes: paradox again.

Friday, August 8, 2008

Blinded by the white

Wow. What is Lucky wearing? Perhaps all his TVs have drawn him into The Matrix? Or maybe he's been hanging out with Vin Diesel?

Wednesday, August 6, 2008

Lock-in, or Lock-out?

Even after 39 years of marriage, and five years of dating preceding it, there remain variances of perception between my beloved and me that crop up unexpectedly, like the stones heaved up by frost each spring in fields that last fall were clear. They're common things, usually, which makes them all the more unexpected when stumbled upon. The latest came to focus as I was locking the back door as I left for a bike ride. "Oh, don't lock me IN," Sharon said. "I'm not," I replied, "I'm locking others OUT."

The incident was amusing on one hand, and disconcerting on the other. My intent was to take what I considered reasonable security precautions as I left, making it less likely that an intruder might enter the home. What I did for Sharon's protection, however, was received as over protection. She chooses in this, and a number of other matters, to live in what she views as trust rather than fear. Well and good. But the rub comes when my natural tendencies toward security conflict with her desires for risk-taking. If I leave the door unlocked, even at her request, I do so with a nagging sense that I'm not being responsible in my care for her. Part of this is probably selfish: I wouldn't want to live with the guilt in the unlikely event that something happened. But part of it is simply an expression of who I am, and the way I convey care or concern.

I'm reminded of a book title that asks, "Do I Have to Give Up Me to Be Loved by You?" The answer, it seems to me, is "Yes, but..." Yes, I choose to change my behavior often in accommodation to the needs and wishes of my companion, as she does for me. Why else be married, if we both just want to live unto ourselves? Our differences are as vital as our likenesses in our marriage covenant, perhaps more so in creating growth. This is just the nature of relationships, which means allowing the other to have effect upon your life. BUT if I give up too much of my self to be in relationship with another, then I'm not really being true to myself, or offering to the other the gift of my uniqueness.

My beloved and I have bumped into this paradox repeatedly throughout the years, so much so that we have posted on our bedroom dresser this passage from Leviticus 19:34-- "The alien who resides with you shall be to you as the citizen among you; you shall love the alien as yourself."

Seeing Through Glass, Darkly

How are we ever going to really “go green” here in the US without an integrated approach to conservation and the environment? A case in point: last year it was possible in Independence to recycle glass containers, either by paying the trash hauler or by taking it to a recycling center. Today you can do neither. Why? The official explanation is that is no longer “economically viable” to recycle glass, since its major ingredient—sand—is so readily and inexpensively available.

I think of that explanation with distress every time I now throw away glass after several decades of trying faithfully to “reduce, re-use, and recycle.” It seems so obviously short-sighted to consider only the cost of glass manufacture when determining “economic viability.” What about the cost of hauling the stuff to a landfill, maintaining the landfill, and creating new landfills? Oh, that.

Well, if you throw in all THAT expense just maybe it might be a viable option. But industry doesn’t look much beyond the bottom dollar for their investors, and government doesn’t look much beyond re-election by the taxpayers, and neither looks much beyond the press of immediate issues, so who cares all that much about a few tons of glass bottles?

Years from now, when people are mining our landfills to reclaim the treasured resources we’ve squandered, what will they think of us? Surely seeing all our discards, not the least of which will be glass, they’ll view us as fools and wastrels.

Warts and All

Our bath house at Morris Park has two seemingly permanent occupants. Nearly every time I open the door and turn on the light I’ve learned to look in the corner for Tom and Tess—a pair of toads who seem to find the dark and the damp, crawling with insects, an ideal home.

The names were Sharon’s doing. Although I’ve long respected toads for their role in gobbling up insects harmful to the garden, I’ve never before been on a first-name basis.

Observing them, it’s difficult for me to see the infatuation children’s writers seem to have for these lumpy creatures. They seem to do very little other than sit around waiting for lunch to crawl by, and if you pick them up they pee on you. Hardly adorable traits. Nor do they seem particularly wise as sometimes depicted in children’s books; this particular pair seems barely able to keep from being squished in the door as it opens and closes.

Maybe I just haven’t had a sufficiently long-term association out of which new perceptions might arise. Karen Stark, who came over for campfire foil meal tonight, says she once had a toad that seemed to enjoy being petted—even turning over on its back to be stroked on the stomach! They’re not like frogs at all, she hastened to assure us.

So I guess tomorrow I’ll quit with the tip-toe, hands-off approach and see if I can form a more lasting relationship. Maybe I can at least quash the persistent urban legend that humans give you warts.

Postscript: This morning only Tess remained in the bath house, squatting in the center of the shower drain. Tom apparently was off hunting and gathering, as all good males are wont to do. By afternoon, Tess had also departed, which I take to mean that my twice-daily intrusions may have led them to choose a less-frequented neighborhood. Ah, the challenges of inter-species dialogue!

Fawn Memories

One more step and I’d have literally stumbled upon it. While dutifully cutting brush in the middle of an Iowa field, eyes scanning for the next nuisance weed, I glanced down just in time to stop mid-stride. Curled into a tan-and-white ball, hidden in the knee-high grass, was a lone fawn, lying completely still. The mother would have fled long ago, seeing my approach, but had obviously left strict instructions (or was it simply instinct?) not to move under any circumstances. I too froze, not wanting to harm or startle the young one, then spent fifteen minutes or so just taking it all in—a spotted marvel I felt privileged to have seen. When Sharon arrived on the scene I called her over, then went to the car to get a camera. Through all this the fawn remained frozen without the slightest twitch, other than the occasional blink of an eye lid. In the end we backed off to leave her in peace, and for ourselves felt a deep sense of peace as well.

Wednesday, July 30, 2008

Sons of Anarchy, Esq.

I just saw a promo of a new TV show about bikers/gangs called "Sons of Anarchy." In the ad, a bad-ass lookin' biker dude looks with disdain at the dork in the truck next to his bike at a stop light and says "we're all free men, protected by The Constitution."

Perhaps he doesn't understand the definition of the word "anarchy?" I'm pretty sure citing legal documents is the last thing an anarchist is supposed to do when arguing his political/ethical world views.

Thursday, July 24, 2008

Out of Africa?

One of our tickets* is about cheek swabbing people to find out where their ancestors came from. This Wikipedia page is awesome: Human mitochondrial DNA haplogroup.

* RT#356 username guest, password guest.

Tuesday, July 22, 2008

Beauty everywhere

Last night playing Ghost Recon 2 my medic got stuck in a wall (bug) so I shot him in the head so he'd fall backwards, then patched him up. Problem solved.

This morning on my motorcycle I was following a large maple tree on a truck. At a stoplight I got the chance to hide in the foliage and touch the pretty leaves from the comfort of my bike. (Hard to sniff anything in the full face helmet though.)

Arrived at work and some gal is bitching that her stylist did her highlights wrong again.

My Walden Pond. July 22, 2008.

Monday, July 21, 2008

Way too funny. And then me.

IRC can be crazy funny. I didn't know about that site until I got quoted in it (still pending moderation).

Fingers crossed!

Delicious ethnicity

I am deeply offended that Fu Newmanchu has replaced his totally awesome bottling (left) with the boring corporate pit of despair on the right. The dressing, which I've been buying for months, is far less tasty now.


Monday, July 7, 2008

DistractoBot 9000

As if sitting in 12 IRC channels wasn't enough I'm in Twitter now too. It's yet another ADD wet dream.

But why?

/me slaps himself as his off-the-clock lunch break stretches towards a half hour...

Somehow I'm getting exposed to a lot of iPhone rants today. Politically correct and incorrect alike.

Friday, June 20, 2008

Paparazzi all over me

I never even took my camera out of my bag, yet I somehow I have over 700 photos and growing of the YAPC::NA 2008 conference.

Amazing. :)

Saturday, June 14, 2008

Gusty flying

Ryan invited me to check out his planes, so I packed my pair of hounds and he flew two of his electric Styrofoam planes briefly in gusty 8am winds. We then checked out the Western Flyers R/C field. Very cool. Heading back again a week from Tuesday to check it out when there's a bunch of people.

Friday, June 13, 2008

Doggie Ghost in the Machine

Sammie passed away a few months ago, but you can still see him in Google Street View.

Poker, YAPC::NA 2008 in Chicago

We've had 2 poker nights in a row. A good time was had by all. :)

My lightning talk for Yet Another Perl Conference in Chicago next week was approved. So now I just need to write up a talk and fill 5 minutes without fainting. :)

Wednesday, June 11, 2008

Google Street View

Well, we're official. Our house is visible in Google Street View now. No, they didn't drive right past our house for some reason, but you can see it, dead ahead, on the north end of 162nd street.

Crazy kids and their toys...

(This is all funded by business advertising revenue and real estate agents, right?)

Heck, while you're at it, check out: my parents house, the med center DRC tower from the north and south (see the construction cranes in the background?); ConAgra; the Omni Hotels reservation center (you can barely see it), corporate office and Dallas Mandalay; the Luxor casino...

Friday, June 6, 2008

waskely wabbit

Perhaps someday I'll stop ssh hopping for a living and get a clue. #poe tried to help me today: 1, 2, 3, 4 (<@perigrin> on a mac look for SSHKeychain).

Thursday, June 5, 2008

Amateur game addict

I'm haven't dumped dozens of hours into a game in years, but I just blew ~10 hours and lots of sleep on this one: Desktop Tower Defense. Super addicting, and waaay too easy to get started. :) After a hundred attempts I finally beat hard mode tonight, with a score of 6589 and only 4 lives lost. Phew! Now I never have to play this game again!

I wrote the CLAB well converter today. It's pretty cool. :)

I presented the ChemChains sandbox at the Omaha Dynamic Language Users Group on Tuesday. What could possibly be more fun than boolean networks?

Monday, June 2, 2008


So I'm walking to work, listening to the NPR Podcast Spies For Hire with author Tim Shorrock... Did I hear this correctly?

70% of our intelligence spending is outsourced? Ok. And people often leave government agencies to work for private firms, and then end up back in the same agency. But now they're a contractor and getting paid 2 - 3 times their former salary... But the nice thing about having contractors doing government work is that if they have a drinking problem you fire them. With a "lifetime employee" it's not that easy...

So, let me get this straight. 70% of my tax money is being spent on contractors. Who are often the same people doing the same job but I'm paying them 2 - 3 times as much money? And the benefit I am getting with all that extra cash is that no one has to fire an unproductive government worker? Who, what, thinks they're entitled to a lifetime of employment with or without productivity?

I've got an idea -- FIRE THE BASTARDS. We've become so hamstrung by our own human resources hand-holding and team-building bullshit that we're spending 70% of our budget over-paying for the same work to get done by the same people? 70% of $60B being paid 2 times as much is $21B a year wasted because we don't want to get rid of people that don't perform?

Ok, I just massively oversimplified a complex problem. But 70% of our budget on contractors?! For reasons anywhere close to that one? Really? Are we that stupid?

Yee gods.

Thursday, May 29, 2008

Sunday, May 18, 2008

Karate choptastic

Wow. Ever seen a karate chop of a brick in super slow motion? Not only is his hand like jello at impact, you can see a WAVE in the BRICK!

Friday, May 16, 2008

IRC on the bus

Wow. rjbs spends 2 hours commuting on the bus twice a day, but at least he's online the entire time thanks to his Franklin CDU-680 EVDO and $70/month in Sprint fees...

Crazy kids and their new fangled gadgets. :)

Wednesday, May 14, 2008

:( Spammers suck

The spam wars rage on. I am angry.

-tirade redacted-

Glyph::dna, Kiva props

My ISP went "poof," so I made an ungraceful migration to a new one. Between that and my lappie hard drive dying it's been a tough month in the personal computing front. :)

I added how to add a DNA track to the BioPerl wiki. BioPerl is so cool. :)

It's been a month since we made our first loans on, and now our first round of re-payments have arrived! mwoohahaha! Oh, and did you know about Kivafriends and Kivapedia?

Sunday, May 11, 2008


The second-story window in front of my writer's table looks out at a silver maple that has been putting on quite a show. In recent weeks thousands of whirligigs have formed, grown, and turned turned from green to brown. Now they are ready to try their helicopter wings. Though calm prevails in the late afternoon as I write, the wind has been up the past few days and with each gust a fleet of earth-bound kamikazes has been launched. Some of them, in brief defiance of destiny, have caught an updraft and captured my attention for their odds-defying ascent. By contrast, some never catch the wind but fall straight down in a graceless headlong plunge. But the majority describe a rhythmic circular glide pattern as they wend their way earthward. It's an amazing sight, with the ground below, and for yards around, covered with seedlings. From the ranks of thousands, some few will take root and themselves parent seedlings in turn as the cycle of life repeats once more. Since it's all about propagation, I guess you could say the whole event is sexy, just like spring.
Our Logophiles writers group has been meeting monthly for the past five years, and has recently begun "assigning" writing topics. I chose a thought from Rainer Maria Rilke's observation that "to write rhythmic prose one must go deep into oneself and find the anonymous and multiple rhythm of blood." Which prompted the following poem about the writing life:

Shooting Up

Pity the poor literary junky,

high on myth-and-metaphor,

brain seized upon by the


of a well-turned phrase,

a just-so sentence,

heart racing to

scratch out a simple line of truth

in that fleeting instant

when writer’s ink

dilates the pupils and

guides the trembling hand.

Tomorrow the crash.

Friday, May 2, 2008

Yay! I *is* smart!

Sweetness. I'm starting to understand this bioinformatics stuff enough to submit patches to minor problems in the work of Harvard grad students. :)

Evidence this week: Corrected arrows in (1) Denaturation, another PCR glitch.

(Last semester I found a few glitches in professor's slides and even two in my textbook. Yee ha. -grin- ... Come to think of it, there was a typo in my Chem answers book this semester too. That one made me scream. -frown-)

Sunday, April 27, 2008


How very much of my life I have rushed through, unobservant and unaware! I was hiking a few weeks ago, stopped to catch my breath, and in doing so found myself in the friendly watch care of a gnarly tree limb that for all the world looked like a mythical sea urchin, or dragon, or something of that ilk. How long had it been there, watching hikers come and go? Had anyone ever seen it there? Will anyone ever see it again? I felt oddly chosen by a strange confluence of events: having misplaced my camera, rushed back to the truck to get it, then traversed a second time the trail on which I had earlier bypassed this forest sentry. Had I not become winded on my second traverse, had I not happened to glance back the way I came, had the lighting been even slightly different, odds are I would have missed the whimsy altogether. I’m grateful…and, hopefully, more aware of the need to be more aware. It’s as the poet says, “The world lacks not wonders, but wonder.” I wonder how much I’ve already missed in the daily rush of life?

Brothering in Illinois

The wind blew, the rain descended, and the earth shook, but the Brother Escapade continued undeterred. In our second annual April outing, Brother John & I followed up last year’s Arkansas exploration with a tour through southern Illinois. It seemed like an odd choice, but friend Bill Crisman recommended the area highly, having grown up near the swamp there. Swamp? Yes! Our whole preconception of Illinois as agricultural flatland underwent a radical shift as we trudged through not only a huge swamp of Louisiana ilk, but also rolling hills and sheer rock cliffs the likes of Arkansas.

The cypress trees in the swamp were most amazing—massive upthrusts jutting out of the dark water, reaching a hundred feet or so to the first limbs, all upheld amazingly by a root system of flying buttresses (an interlacing web of gnarly roots, much of them above water.) We were there one day at sunset and experienced a profound silence, broken only by the calls of Canadian geese and the hammering of woodpeckers against old growth timber. As we left the site we were treated to a rare sighting of a pileated woodpecker, whose extraordinary size accounted for the deep drumming sound we’d heard echoing in the swamp.

Midway through our stay an earthquake measuring 5.2 shook our area. We learned that the epicenter was only about fifteen miles away, but the 4:30 AM tremors awakened neither John nor I from our slumbers, even though it awoke Sharon back home, 250 miles distant, as our house swayed and rattled. It was a far cry from the New Madrid quakes of 1811 and 1812 that leveled entire forests in the area and caused the Mississippi River to flow backward for several days. We probably wouldn’t have slept through that one, although we were both pretty beat from a 20-mile bike ride the day before.

We managed to savor not one, but two, GREAT barecue places: Mac’s in Cairo (thanks for the recommend, Bill!) and The Seventeenth Street Bar in some little town I’ll have to locate again on a map. We also stood beneath the state’s record cherry bark oak tree (GARGANTUAN!), visited Superman’s hometown (Metropolis), saw Fort Massack, and just generally spent five days wandering about seeing what we might see—a lot like our childhood adventures to the woods in days of yore. I think our language needs a new action verb: brothering!

Poem: "To The Virgins, To Make Much Of Time" by Robert Herrick. Public domain.

To The Virgins, To Make Much Of Time

Gather ye Rose-buds while ye may,
Old Time is still a flying:
And this same flower that smiles today,
Tomorrow will be dying.

The glorious Lamp of Heaven, the Sun,
The higher he's a getting;
The sooner will his Race be run,
And nearer he's to Setting.

That Age is best, which is the first,
When Youth and Blood are warmer;
But being spent, the worse, and worst
Times, still succeed the former.

Then be not coy, but use your time;
And while ye may, goe marry:
For having lost but once your prime,
You may for ever tarry.

Thursday, April 17, 2008

Need another RAM upgrade for my melon

What I tried to learn this evening: Paraphyletic vs. monophyletic groups in phylogenetics. Oh. And I should learn trig again.

Sunday, April 13, 2008

Emitting Good Vibes

Dad's ordination is... NOW!

Good vibes!! Good vibes!!

Here's hoping you and your calling are maximally joined. :)

14 microloans before breakfast

Wow. I'm a big fan of They make it super-easy to loan money (in amounts as small as $25) to needy entrepreneurs world-wide, with a 99% return rate. We stuck some of our "getting almost no interest from the bank anyway" savings into Kiva, and made 14 micro-loans around the world, all in less than an hour.

Check out our lender profile. :)

Talk about saving the world. I wish I had written that software. :)

Abraham, Martin, & John

Last week was the fortieth anniversary of the assassination of Martin Luther King, Jr., during which I again heard excerpts from King's final sermon, delivered impromptu in support of a sanitation worker's strike in Memphis, Tennessee. To paraphrase his remarks, "I fear no man tonight. I would prefer a long life, but length of years is not the ultimate concern. Though I may not get there with you, I have seen the Promised Land!" One can only wonder what might have been the happy result had King been able to pursue his growing vision not only of an integrated US but of a world where ALL (both oppressed and oppressor) were "free at last."

I was reminded of a 60s song about Abraham, Martin, and John, with its references to Lincoln, MLK, and JFK, concluding "it seems the good they die young." One could surely add Jesus to that list, and Gandhi, and so many others, both women and men. Of course any such list would need to avoid sentimentality--the "good" are not without human foibles. But the greater truth is that such souls show the unitive potential of our race.

So what is it about our ken that so often causes us to snuff out the bright lights that could illuminate the future's path? Fear and greed are two commonalities evident in these early deaths. Who was fearful of, who stood to lose from, the abolition of slavery, the end of the Vietnam War, the freeing of India from colonial rule, a Poor People's March on Washington, the abolition of Temple rituals? The answer is caught up in Walter Wink's phrase, "the powers and principalities of this world."

The testimony of Abraham, Martin, and John is that these powers and principalities may have their moment in the sun, but ultimately the universe "bends toward justice" in a great reversal where the greatest shall be least and the last shall be first. Thank you, brothers, for your faith-filled witness. You give sanitation workers and the likes of us renewed hope. May we have the courage to pick up the fallen torch and carry it forward.

Past Observances

Sharon and I presided at the memorial service yesterday of a woman whose wedding ceremony I performed nearly 29 years ago. The odd thing is that I don't recall anything about that earlier occasion, even after seeing a wedding album that includes my photo and a signed letter I sent the couple at their request following the ceremony with references from sources I had used in my remarks. I was pastor of the Englewood congregation at the time, and 1979 was the year we accepted full-time church appointment, so shortly after we moved to Canada and were gone from Independence some 17 years. This may help explain my lapse of memory, and subsequent contacts have only been once or twice going to their home to offer prayer, but it's still most peculiar to stumble upon a record of my past as though I were an outsider rather than a participant. I hope this is not an early symptom of Alzheimer's, surely one of the cruelest of diseases for both that person in their confusion and their loved ones as they increasingly become strangers. I remember the "long farewell" of several parishioners in Sioux City, IA with this illness and I shudder to think any of my loved ones would be similarly burdened. I tend to think this particular void in my memory bank may be more an expression of my general inattention to life as I have filled it to overflowing with busy-ness and over-commitment. I hope to more fully experience those things I am blessed to encounter in the future and live more intentionally rather than frantically.

Saturday, April 12, 2008

A Voice from the Past

Listening to the voice of my father-in-law, recorded more than fifteen years ago, I remember why I miss him so. He was a man without guile, having no need or desire to impress a single soul. He had a ready laugh for the human condition, beginning with his own. He had a genuine curiosity about life, with little need to defend his views or ideas (with the exception of an occasional close-minded Baptist preacher, whom he engaged in bouts of scripture wresting until they wearied of the sport and came around no more). He was genuinely content with the simple joys of life, having no need for sophisticated entertainment or consumption. He was down-to-earth, genuinely in love with the mystery and wonders of creation. He had a zest for life, without fear of death. So many of these things which define what I consider fulfillment, so easily seen in his life, elude me altogether, or are grasped only with much difficulty. I wish I could talk with him more to learn how he came by these traits I so admire.

Model T in the mud

Transcript of file 1 is complete.

Saturday, April 5, 2008

Earl C. Humphrey oral history

I received digital copies of all 6 tapes yesterday, and have started a transcript. It's amazing to hear my grandparents voices again after so many years.

Wednesday, April 2, 2008

A tutorial to last a hundred lifetimes

Criminey. This "tutorial" on would take many lifetimes to master. It covers just about everything I've ever heard of (and more) in the overlap between biology and computers.

Sunday, March 30, 2008

A Great Letting Go

A few months back Sharon & I were camping in Iowa and early one brisk fall morning had the following experience:

A Great Letting Go

There was no wind,
no motion or sound, that early morning after
the first killing frost,
all frozen in place but one--
a persimmon tree,
the day before heavy-laden
with rounded leaves
of yellow and green,
hastening now to drop its burden
before the morning light
revealed its work undone,
shuddering imperceptibly
in a great letting go,
a flutter and a rustle,
hinting of great forces unseen,
laying one last colored shroud
on a season turning now
to brown and gray.
By noon her work was done.

JBHannah 11/7/07

Friday, March 28, 2008

drag-n-drop database design

WWW SQL Designer is way too cool. 2.0 was released today.

This tool allows you to draw and create database schemas (E-R diagrams) directly in browser, without the need for any external programs (flash). You only need JavaScript enabled.

Wednesday, March 26, 2008

Nerdy music

Jonathan Coulton's music is awesome. "Code Monkey" and "Re: Your Brains" are simply great. The inappropriate for all ages "First of May" is another favorite of mine. :)

On the nerd front, it's all Creative Commons licensed, so I peer-to-peer'd a bunch of his .mp3's, donated $10 by buying a monkey on his site, and will donate more as I listen to more of his music. I predict he'll make more money from me than he ever would have just selling traditional albums.

Friday, March 21, 2008

Audio heirlooms

I'm going to give these fine folks a shot at converting our 6 Earl C. Humphrey audio cassettes into digital media. They have noise reduction techniques that hopefully far surpass what I would be able to do on my own. I'm looking forward to hearing that voice again after 8 years...

The tapes are pushing 20 years old. They should be OK. Knock on wood.

The plan is to then launch transcript pages on my wiki that the fam can help transcribe, edit for spelling corrections, flushing out hard-to-hear regions/words, etc., and link to various resources around the 'net.

This should be cool.

Thursday, March 20, 2008

Don't read this

Super-geeky and offensive, completely inappropriate for all ages and all audiences humor that no one should ever read:

still laughing

Wednesday, March 19, 2008

Eagle Sightings

For forty years since marrying and moving to Independence, MO, I’ve been routinely making the five-hour drive from there to hometown Mt. Pleasant, Iowa.: north up Interstate 35 about halfway, then east on US 34 for the remainder of the five-hour trip. I well know the towns, the hills, and the scenery in all four seasons. But in those scores of drives I saw something this trip I’d never seen before: bald eagles.

The first was perched in a tree near the Ottumwa packing plant along the Des Moines River. I slowed and almost stopped to take a picture, but couldn’t find a safe pull off or turn around. I continued on reluctantly, yet grateful for even the brief one-time sighting.

It’s my habit when making this trip to while away the miles watching along the roadside for hawks--usually, red-tails, which have grown greatly in number through the years. I’d seen at least a dozen in the course of the afternoon, so I wasn’t surprised as I continued along to spot another one in a huge cottonweed tree alongside the road. But wait! That’s no red-tail. That’s another bald eagle!

Almost as though on auto pilot, this time my truck crossed over the highway rumble bars to a stop. The sound of tires on concrete disturbed the eagle, who took flight. So large, so regal! I was feeling good just to have seen one so close when he reeled, and, unexpectedly, landed again in a treetop not quite as near the road but still within clear view. My truck crept forward a couple hundred feet and came to a cautious stop. I opened the door and eased my way out, camera in hand, looking through the view finder. Not bad. I snapped a few shots, then realized there was a tree branch disrupting the composition, so I moved toward the rear and steadied my telephoto against the truck bed, hoping against hope that I wouldn’t spook the quarry. Ok, now, look to the right a little bit…that’s it…hold it…hold it…Snap! That should be a good one, I was thinking as the eagle lifted off once more, this time to disappear over the horizon.

I mention all this because there are some who even yet don’t seem to understand the significance of a species going extinct. Such was the path of the bald eagle until a few decades ago. Today they’re plentiful enough to have their names removed from the endangered list, but only due to the diligence of a lot of very devoted environmentalists and many responsive legislators.

It could be argued that I had driven that highway dozens of times and never seen a bald eagle, so what had I really lost? You don’t miss what you never had, right? The answer to that question came only through an unexpected encounter that in an earlier day would have been routine. To me it was a thrill to see what for the most part has been only a photo in a bird book. There was a connection there that’s hard to describe: something to do with it being the American national bird, I’m sure, but something beyond that as well—the soaring sense of freedom, the grace and beauty, the sense of sharing this planet with so many wondrous creatures.

Yes, I’d driven that road many a time. But until that very day I never knew what I was missing. I’m so grateful we’ve at least begun to preserve the wildness that connects with something deep within.

Friday, March 7, 2008

Spongebob Rectal Thermometer

I'm a big fan of Spongebob, butt... was this really necessary? Have all other merchandising opportunities been saturated?

the youth of today

full email thread

OBrien, TG wrote:
> Sadly, I no longer wonder about the youth of today;
> my assumptions were proven.

Those damn kids.

I'm 32. Can I join the grumpy old men club yet? :)

I'm back in chemistry after 15 years, and I'm not too different from the other students straight out of high school when the subject matter being crammed down my throat is of no interest to me.

When our interests are being served (rare) we're typically happily and similarly engaged, the 15 year age gap not making much difference.

Of course outside of class our lives are drastically different.


Tuesday, March 4, 2008

Cool wallpapers

InterfaceLIFT has really cool free wallpapers, even for dual monitors and what-not.

Sunday, March 2, 2008

A Building Recognition

We dedicated a new Habitat home a few days ago. Sometimes in the midst of the rather drawn out process of hammering one of these homes together you lose sight of what it's really all about. But when Marilyn, tears streaming down her face, describes living in a homeless shelter five years ago and now having the very first home of her own for herself and her two daughters...Well, it's one of those moments when you feel that you've truly received more than you've given, and your joy, as the Bible says, is full. Standing shoulder-to-shoulder with this community of all colors and ages and backgrounds, even if you can't call them by name, you suddenly recognize, Hey, I know you: You're my brother or sister! So good to see you here!

Saturday, March 1, 2008

Virtual Reality (Or Pseudo?)

"Virtual reality." The term has been around long enough to have made the dictionary: "the generation by computer software of an image or environment that appears real to the senses." (The Oxford Dictionary)

I'm increasingly grateful that my own childhood years pre-dated virtual reality. Instead, I had what, at the risk of redundancy but for the sake of emphasis, might be called "actual reality." The images and environments I have in my memory are not just the appearance of reality, but reality itself--watching a cocoon twitch violently and finally break open to reveal a shrink-wrapped butterfly that oh so slowly unfolded; biting into a sun-warmed tomato, red juice gooshing down neck and stomach; climbing a young sapling to the very top, then riding it backwards to the ground; hearing the shrill call of cicadas, mingled with the low barumph of bullfrogs in a rhythmic symphony; being battered by the wind in early spring, numb fingers sending home-made box kites aloft until they nearly disappeared from sight.

The wonder of these moments is so real to me even decades later that I can still see and taste and smell and hear and feel their touch as though they were here-and-now. So when Louis Armstrong sings "What A Wonderful World" I find myself without fail singing along with him the closing exclamation,"Oh, yeah!"

It deeply saddens me that so many of "the computer generation" seem to prefer virtual reality over reality itself, which I can only liken to keeping the wrapper and throwing away the chocolate bar. How could any computer role-playing game compare to the suspense of night-time hide-and-seek, or playing "soldiers" with home-made weapons, or charging each other full-tilt as knights armed with horseweed stalks? How could even the best nature documentary compare to actually experiencing the Northern Lights, or the Milky Way? How could even theatre surround sound capture the marvel of a click beetle arching its back, then snapping itself into the air for a perfect acrobatic flip?

I could go on and on, but I suppose it would be futile. Reality is like a good joke: sometimes you just don't get it unless you were there.

The Itch to Scratch

I discovered an interesting thing about myself during a recent 3-day, 1600-mile road trip: if I don't get a bit of solitude and do a bit of writing every day or so, I get cranky. I suppose it may be similar to what runners experience, where at a certain level of conditioning the daily rush of endorphins becomes so addictive that a day missed is a day lost. I'm not quite at that stage, but I learned that the itch to scratch out a few lines each day can only be relieved by rubbing up against keyboard or pen, even if ever so briefly...Ah, there it is--that contented bliss, like a sow raking her hide against a hedge post. Life is good. : )

Friday, February 29, 2008

News, or History?

“The only thing new in the world is the history you don’t know.” Whether or not Harry S Truman actually said it, the actor who portrayed him on President’s Day at the Truman Library offered that pithy one-liner during a “White House press conference.” The whole morning was one of hands-on history, including samples of home-baked cookies from “Presidential Cookies” cook book, and a host of intriguing interactive displays. (It was my best Presidents Day ever, making me think I may add the presidential libraries to our Encouter-All-the-National-Parks-of-the-US-and-Canada itinerary.)

But those few words attributed to Truman (along with a dozen fresh-baked cookies and a cookbook for Mom) were my major “take away,” summarizing what I’ve of late increasingly realized.

(I wonder if Truman knew that the writer of Ecclesiastes said it much earlier: there’s nothing new under the sun. Probably so. From early childhood he was an avid reader, particularly of history and great lives.)

Somehow whenever I find a good historical book or documentary it still astounds me to discover, You know, those folks hundreds or thousands of years ago were pretty much like me. They pondered the same mysteries, exhibited the same emotions, strove for the same goals, suffered the same disappointments.

It’s also pretty amazing to discover that much of the technology we pride ourselves on in our “modern” world actually has root in discoveries hundreds or thousands of years ago—possibly even including flight, surgery, war machines and other marvels we consider inventions of our own day. Who knew? …Only those who read their history. Ever hear of DaVinci?

While this realization is, on one hand, rather comforting (the past is perhaps not all that foreign to the present, and those who lived it weren’t all that foreign to me), it is also rather disconcerting. I’ve witnessed the great truth of the adage, “Those who ignore their history are doomed to repeat it.” For instance, the invasion of Iraq has so many similarities to the invasion of Viet Nam just forty years earlier that you have to marvel how anyone could have been so ill-informed as to think we would be greeted as “liberators.” I guess they only read the history books about France’s warm welcome of the Allied soldiers, not the history of the Middle East, where one occupier after another has had to admit defeat, century upon century.

Truth be told, I doubt that Commander-in-Chief Bush had much knowledge of either event. The expression that from the outset of his presidency seemed to best characterize him was “singularly incurious”—the exact opposite of President Truman. By contrast, Bush seemed to be almost proud of being a non-reader. Little wonder, then, that he missed Martin Luther King’s sermon, “Beyond Vietnam,” which, with a few very minor adjustments, was a prophetic cautionary tale about repeating our error of the past. Truman was right, and bears repeating: “The only thing new in the world is the history you don’t know.”

Thursday, February 28, 2008


         PNAS     PNAS              PNAS

Am I the only one distracted by PNAS being written all over the place? PNAS

PNAS        PNAS               PNAS

Whoah. This is way too cool.

Jim Rogers, Ph.D totally freaked me out yesterday with his presentation. Staggeringly cool. Abstract below. (Reading abstracts is boring, but trust me: this presentation was off da hook for programmer wanna-be bionerds. -grin-)

Is this exactly up my alley? Perhaps this will finally motivate me to learn C? :)

Emergent Information Processing in Biochemical Networks:
New Results and Challenges for Understanding Cells

As our understanding of biochemical pathway structures increases, it is clear that these pathways form networks of astonishing complexity. This creates an immediate challenge in trying to make sense of the enormous amount of data that studies of these systems generate. The field of bioinformatics has arisen in recent years to meet this challenge, and has been very successful in helping laboratory biochemists interpret their vast data, allowing them to understand the complex structures of the chemical networks they study. However, even when these chemical network structures are worked out, it is often times still not clear how these structures actually function or why they are so complex. This has led to the need for another level of quantitative analysis of biochemical systems. In this talk, results of such a study will be presented that show that some of these cellular networks have emergent information processing ability. In addition, there will be a general discussion of the future of biochemical analysis and the important role that computer scientists may have in the process of understanding basic cell biology and disease.

Ooo! You can read online here: Emergent decision-making in biological signal transduction networks

Wednesday, February 27, 2008


Anyone seen my father? His daily blog entry is now 17 days overdue... :)

-poke-, -poke-

Weekly bioinformatics meeting

Here's a whirlwind tour of my 10:45 meeting this morning and the Wikipedia pages I cruised while trying to follow along.

MCBIOS 2008, "a regional iSCB conference," presented by OKBIOS: tandem repeats, variable number tandem repeats, protein structure prediction, and glycobiology.

Thursday, February 21, 2008

Oh, crap! I have to get ready!

My wife works at home. Last week I was sitting in her office on the family Mac reading email when she panicked because she was going to be late for work.

8:51 - "Oh crap! I have to get ready!"
8:52-8:56 - Commute to bathroom, get ready, commute back to the office.
8:57 - Succesfully arrived at work with 3 minutes to spare.

-laugh- What a sweet deal.

Why am I spending an hour in the car every day?

Ah, Chemistry. I love you.

You have rules. Thousands of them. Good for you. You have exceptions to those rules. Thousands of them. Way to go.

Ag is silver. Sure. Why wouldn't it be? And it's electron configuration is [Kr] 5s1 4d10, not [Kr] 5s2 4d9. Of course! Rules are for breaking, right? Absolutely. Hell, you keep good company, silver! Half of Period 5 breaks the rules. What's the point in having rules if you're just going to follow them? You incorrigible little imp, you! :)

Chemistry, you're a cheeky monkey and I love you.

P.S. Fuck off.

Tuesday, February 19, 2008

Data diving for diseases

If you squint you may see breast cancer hiding in this picture. If you spot it please send me an email. In the meantime, we'll keep kicking out these heat maps of gene expression data from microarrays.

Only perl can parse Perl

I got thrown into yet another new-to-me ball of Perl today and thought it would be really cool if I could kick out a GraphViz graph of all the subroutine calls, like Alan Ferrency attempted back in 2000: Looks like nobody has really pulled this off and sent it to CPAN? #perl-help sent me to PPI which cites Randal's famous line: "the only thing that can parse Perl is perl"!

Bummer... If only I had unlimited free time I could probably get close-enough? I'll email Alan and see if it's moved since 2000. :)

Eric Maki inspired me in Issue 4.1 (Winter 2007) of The Perl Review. But his is Perl op codes, not Perl 5 subroutine calls... -ponder-

Wednesday, February 13, 2008


Actually gamed a little tonight while the computer was updating itself. Beat another dungeon in The Legend of Zelda: Phantom Hourglass on Zach's Nintendo DS.

Monday, February 11, 2008

Roadtrip to Lincoln bionerdiary, Crash

( aviary, only with biology and nerds. get it?)

Heading to Lincoln on Friday to meet a professor there and get a feel for his secret high-profile cutting edge research... I hope he's designing four-assed monkies.

My Netflix movie was Crash. Started off pretty disgusting, and I feared I was in for a non-stop racial stereotype fest. After surviving the first few sequences, the interweaving of the character development started to show, and the rest of the movie was terrific. Hopefully these shocking examples of bigotry are rare indeed in 2008. We have evolved, haven't we?

Crash was as intense as Mr. Brooks, a movie stunning it its power and the raw evil of its characters. Mr. Brooks is an excellent movie. And no one should see it.

Both films tap deep into the shock receptors of our reptile brains. Seems a strange way to make a living. Not at all how I earn a buck, staring at a computer screen all day pushing bits and bytes around inside some servers...

Sunday, February 10, 2008

Truly A Good Death

Death is not always the enemy, but sometimes a friend. Sharon and I presided yesterday over one such interment and memorial service. Evelyn Barwise: 90 years old, beloved of her familiy and friends, still living in her home ater 60 years, hoping against hope that she would not have to move into assisted living. Her wish was granted last Tuesday as she died quietly in her home, with no heroics or drama, just as she would have wished. The interment at Oak Ridge with the immediae family was a time to reflect on "ashes to ashes, dust to dust," and the passing of life's seasons during a time of winter, with spring but a few weeks away. At the memorial service grand-daughter Alissa read her essay about the meaning of "Gramms' " life, and surely no finer tribute was more beautifully expressed. Other glimpses of this outstanding lady were caught up in selections she had made of music, verse, and scripture, most memorable the words of Victor Hugo read in closing: "Be like the bird who, halting in his flight on a limb too slight, feels it give way beneath him, yet sings, knowing he hath wings."

Thursday, February 7, 2008

2nd dream job "offer" today

Not quite two years into my bio* adventure, I've had my second bite of possible full time employment in my dream field, where I can Make A Difference.

Oh, but the money... That beautiful, seductive mistress that has treated me so well over the last 8 years...

I just can't seem to break free and accept my dream job -- making less than half of what I made merely one year ago... Step back to my 1998 salary after rubbing elbows with the execs and a billionaire?

Are these my dream jobs? Am I a money addict? Does the smaller paycheck overshadow the careers that had me so lovestuck mere months ago?

My job / life satisfaction algorithms are causing me much guilt, confusion, and frustration.

At least this time it's me torturing me, not The Man and The System... :) This hamster needs to pick a treadmill.