Molecular Theology

Monday, June 09, 2008

So long

I'm putting this blog officially on hiatus. Unofficially, it's been there much longer -- any blog where you're aiming for once post a month, but the interval between posts grows larger than that, is already nearly dead. If I'd ever developed even one reader, well, thanks for your interest. This blog may return at some point, but don't hold your breath.

Monday, February 25, 2008

Frostiana

Robert Frost wrote a fair bit about stars, science, and religion. We sang a setting of his "Choose something like a star" on Sunday, so I've been reading a bit of him, which I haven't done since high school. Here's one:


Skeptic

Far star that tickles for me my sensitive plate
And fries a couple of ebon atoms white,
I don't believe I believe a thing you state.
I put no faith in the seeming facts of light.

I don't believe I believe you're the last in space,
I don't believe you're anywhere near the last,
I don't believe what makes you red in the face
Is after explosion going away so fast.

The universe may or may not be very immense.
As a matter of fact there are times when I am apt
To feel it close in tight against my sense
Like a caul in which I was born and am still wrapped.



There's much of Frost which I don't like, or disagree with, but I love that final image: the warm, close, embracing universe. He's not using it very positively here, it's suffocating, but so intimate, like hiding under the covers.

Sunday, December 23, 2007

Happy Solstice

Monday, July 23, 2007

In my heart

I wrote a note for Fox Jr.'s cardiac surgeon this morning, letting him know that the arrhythmia came back. It was a disappointment to us, and will be to him: it means that the procedure to fix it hadn't worked after all, and it was back. Darn.

It came back Saturday night, and we ended up in Emergency after midnight. Summer Saturday night in a Northern boom town, Emergency is a busy and bloody place. A bald man with not one but two black eyes walking out, dismissed. Another man, sitting and waiting, holding a cloth to his bleeding hand, his girlfriend patiently waiting with him. Coming in behind me, two young men, one helping another, the other stooped, in a white undershirt and gold chains, all dripping with blood from his head. "Can we get some stitches for my friend here? He's still bleeding..." You need to talk to the Triage nurse, right here. The nurse sat him down, cheerily asking, "so what happened?" "Well, I was just sitting on the sidewalk, chillin'..." I never heard what happened after the chillin'. The EMT next to me told me that her job is thwarting natural selection.

Fox Jr. didn't have to wait. Heart stuff is funny: even if you're acting fine, if you have no pulse, or your pulse is too rapid or irregular for the basic machines to measure, you go right in. I guess if your heart doesn't work for even a few minutes, you're dead, so we take heart stuff seriously. And by convention, we call you dead if your heart doesn't beat for even a few seconds. That happened to Fox Jr. once, in ER late some previous night. He hadn't converted spontaneously, so they administered adenosine. A short sharp pulse of drug, plunged straight into a vein, rapidly followed with a pulse of saline, to drive it straight into his heart. His heart stopped beating, the ECG lines went flat, and he was dead. This will feel funny, they'd warned him. Yeah, I'll bet it did. It restarted within a couple of seconds, a slowed irregular beat or two, then a normal rhythm, carefully traced out on the ECG chart. He'd been rebooted.

A common experience when having your heart stopped is "an impending feeling of doom". I've heard that phrase before, it's also been reported for people experiencing severe transfusion reactions. The scientist in me wonders about the nature of the doom receptor, or the doom sensation pathway. Where is it? What are the triggers? At what levels are the signals processed? However it works, it would seem to be accurate.

My sister-in-law saw a guy die recently. She's thinking of going into medicine, and somehow scored an OR visit. It was an open-heart surgery, a triple-bypass. They hooked him to a heart-lung machine, and stopped his heart. No pulse, flat line, beeee... He was now dead. Then the anesthesiologist went to lunch: her job was to keep his heart going, and that wasn't needed while it was stopped. She came back before it was time to restart it. All was very relaxed and routine, with the most excitement coming from the surgical nurse, explaining all the different kinds of specialized retractors.

The circulation of the blood was discovered by Harvey. It's so fundamental, the heart and its connection to life, it's hard to understand how people thought about themselves before the heart of Harvey. Where was the seat of life? What was that thing in the middle of the chest? Was it still the seat of emotions? As an undergrad, I read an English lit monograph called the Heart of Harvey. I didn't understand it then, but it's still on my shelf. I should read it again someday, and look for clues about what's in my heart, and the hearts of the people I love.

Thursday, June 28, 2007

A milestone in synthetic biology

Today Craig Venter's group published the first "booting" of a bacterial genome. It's a major step towards creation of totally artificial living organisms. Conventional genetic engineering merely fools around with the natural slightly, throwing gum into the gears of life. Synthetic biology is about completely novel design and creation. Design is tough, but we can start with natural sequences. DNA synthesis is no big deal, though assembling megabase sequences is not so easy. The final step, taking raw DNA and booting it, like booting a computer from a sequence of bits, has been thought an obstacle. Now it's been done.


The full report appears in Science, with an accompanying news item.

So why is this theology? Well, we are made of molecules. And the ability to control those molecules, and create new life forms, in ways entirely unlike nature... it's not playing God, it's being God.

A hamster funeral

The family hamster died last week. We knew it was coming, a long-expected transition. He'd had a full, long life, as hamsters go. A day or so before, he was acting sick, with wet fur. Some internet research, and hushed parental conferences, and we decided that no, we wouldn't take him to the vet, but we would try to clean him up and make him comfortable. He looked perkier the next day, but the morning after that, he was stiff and motionless.

Our cat died some months ago. He'd gotten sick, went to the vet, and never came back. The daughter was heartbroken, because she'd never gotten the chance to see the body, say goodbye. So my wife made sure that I knew how important the hamster was, and how important it was that it be handled well. And then she left, with me alone in the house, with a sleeping five-year-old and a dead hamster. And a funeral to arrange.

I put on a solemn face, and went to wake her up. The hamster died last night, I told her, first thing. She woke up smoothly and calmly. She was unfazed. I think we went to the kitchen to talk about it. I don't think we ate. She wanted to know where his body was. Right there in the cage, we hadn't moved him. She wanted to see him early, I think. I remember mentioning that we had to figure out what to do with him. I suggested that she pick flowers from the garden. Flower petals, she decided. Good idea. I went to look for a box, and found one. It was nice, a gold colored box that had a bit of a pedestal inside to house a piece of consumer electronics. She wanted to carry him downstairs to put him in the box. She arranged the flower petals around him. He looked sweet and sad, and very very dead.

We said words. She a simple goodbye, for me, a sentence or so about a good life, and how he was much loved. We closed the box.

And then there was the question of what to do with the box. In our culture, it's traditional to bury the dead. But not only did I not particularly want to reserve some part of the garden for a hamster corpse, we have dogs, and the dogs love to dig. Very little would disturb the sanctity of a burial more than being dug up and carried around the yard.

So I talked about how we are made of the molecules of the earth, and how we go back to the earth. Our city has, in addition to a competent recycling program, a lovely composting program, where the entire municipal household waste stream ends up in a large composter and ends up as fertilizer. So I suggested that we return the hamster to the earth through the city's composter and the fields, recycling the molecules and returning them to the earth to become new life.

She thought about this. I admit was a bit nervous, I didn't want her to think I was disrespecting the hamster or the occasion, didn't want her to think that I was suggesting that we just throw away a beloved family pet. She made a decision, I breathed a mental sigh of relief, as she picked up the box holding Puzzle Panda, and solemnly but firmly placed him in the recycling bin.

Now I'd really screwed up, and could see only disaster ahead. She may be only five, but she's not fond of being wrong. I contemplated doing nothing, and letting the minimum wage workers at the recycling sorting center deal with the corpse of a dead hamster rolling across their sorting belts. Or trying to secretly move the box later. But I chose to interrupt fast, and said hesitantly that the recycle was for cans and glass and plastic, not composting, so...

She picked it up and placed it in the kitchen garbage. Sigh of relief. So long, Puzzle Panda. It'll be all of us, one way or another, someday.

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Monday, May 28, 2007

Stupid biochem question...

On a large scale, life is a nonequilibrium phenomenon, driven by a free energy flux coming from the sun. On a smaller scale, it's chemical: we eat stuff, and burn it, oxidize it, and exhale the CO2. So you can also see life as a flow of redox potential, or so says the book in front of me. But are these different? Different language for the same thing, or separable concepts? Is this flow of redox potential just the form that the energy flow takes, or are they (even sometimes) distinct?

I really care. I'm not saying "energy flow" to be merely mystical or evocative (though it is that), but because it matters, both philosophically and professionally.

Damn. So much learning, so little knowledge. Or maybe I'm just stupid.

Faux cowboy poem

Across the west white hills I saw
three horses
one black, one gray, one dun
they were ridden by no one
they walked real slow, heads bowed
down towards the setting sun

Sunday, May 06, 2007

So long, Art

I wrote not long ago of a friend, seriously ill, but in recovery. Or so I wrote. And hoped. But it was not to be: he died last week. No flowers, said the obit, just donations to the Liver Foundation. Damn it, I thought you were going to make it. I thought you were going to be okay. I thought you were going to come back. But no.

None of us are getting out of here alive, though, as another friend said. It's just a question of how and when. And what you do before you go.