December 6th, 2012

a-links

[links] Link salad feels goofy today

Paul Krugman: Asimov's Foundation novels grounded my economicsThe fantastical tale offers a still-inspiring dream of a social science that could save civilisation.

Genomic InequalityTo successfully use a patient’s genetic makeup in a clinical setting, we must better understand the incredible diversity of human genomes.

Driving school for dogs in New Zealand — Because, uh. No. I got nothing. (Thanks to David Goldman.)

Oh-My-God particle — High energy physics on the hoof. (Via Daily Idioms, Annotated.)

Why The Universe Is Not a Computer After AllThe idea that our Universe is a giant cosmic computer pervades modern science. Now one physicists says this assumption is dangerously wrong.

New contender for oldest dinosaur — Warning, "facts" not valid for the reality-challenged and willfully ignorant.

Two meticulous maps showing the names and locations of every brothel, bar, casino and saloon that existed in the Levee District [of New York City? Chicago] between 1870 and 1905 — Because you know you wanted it. (Thanks to Lisa Costello.)

Wash. Issues Gay Marriage Licenses — A little bit of equality and justice for all. Know what's not happening? Traditional marriages aren't collapsing, God isn't taking vengeance on the United States, nor any of the other alarmist bullshit conservatives have trumpeted so hard as the inevitable costs of gay marriage. Just people who love each other getting married. Kind of nice to live in reality, isn't it?

Rove, Morris find themselves on Fox's bench — Huh. I thought being wrong was a consequence-free behavior for conservatives. Amazing. Admittedly, this is pretty minor, but it's an interesting signpost.

?otD: Are you smarter than you were yesterday?




12/6/2012
Writing time yesterday: 0.0 hours (chemo brain)
Hours slept: 9.0 hours (8.0 hours solid plus napping)
Body movement: 0.5 hours stationary bike ride
Weight: 217.4
Number of FEMA troops on my block teaching evolution to children and redistributing wealth: 0
Currently reading: The Hydrogen Sonata by Iain M. Banks

cancer_tumor

[cancer] In which we discover that I am in fact a mutant

My oncologist recently ordered a followup genetic assessment on some of my
existing tumor tissue. We did not discover any recently identified clinically significant mutations in my tumor tissue, but a specific rare mutation of unknown clinical significance was found. Specifically, the KRAS A146V mutation. As my oncologist said:
[I]t is unclear how or if this affects therapy. We were really looking for any other targetable mutations as listed and those were negative. We should stay the course.

More detail, per the pathology report, for those interested:
Gene Mutation Significance

KRAS A146V Only ~4% of KRAS mutations affect codon 146. Among 6 reported cases of colorectal cancer with mutations at this codon, none responded to treatment with an anti-EGFR antibody. A pre-clinical study of cancer cell lines harboring a similar mutation (A146T) showed that they were sensitive to a MEK inhibitor and resistant to an EGFR inhibitor. However, KRAS A146V was not evaluated in that study.


They tested a whole ton of gene complexes, which are just a bunch of alphanumeric soup to me. I will note the pathology report commented: "The screening consists of a multiplexed panel of 496 assays that can detect up to 643 different mutations known to occur in the genes listed above."

Living in the future is weird. Being this kind of sick in the future is weirder.

religion-belief_rev2

[religion|cancer] Discussing just how bad a Buddhist I would be

Yesterday whilst indulging in the diurnal ritual of my postprandial parboil (a warm baking soda bath which helps the Vectibix-induced skin condition and incidentally has the effect of profoundly exhausting me), Lisa Costello and I had a talk about what a terrible Buddhist I'd make. My observation was that in my extremely limited understanding of the practice, one of the keys of Buddhism was releasing the death-grip that most of us keep on our inner narrative and sense of self. Given that I pretty much define myself by my inner narrative, this strikes me as an improbable stepping stone on any path to enlightenment I might ever follow.

Somewhat to my surprise, Lisa disagreed with me.

We got into a long(ish) talk about how narrative relates to external reality, the nature of truth and what people tend to want to hold on to, mind-body dualism, and a few other related light conversational topics. As I've often said on this blog, I'm a relentless empiricist, firmly moored in the world of logos, who doesn't have any trouble acknowledging the value and power of mythos as a key component of human existence. Including my own personal version of mythos.

My sometimes ugly public quarrels with religion and the religious have entirely to do with people confusing their personal beliefs with some form of objective truth, and then projecting that confusion into the public square to the detriment of both themselves and the rest of society. When it comes to religion, I am a First Amendment absolutist. I will defend to the death your right to worship as you please (and equally my right to find your worship ridiculous); and I will defend to the death my right to be entirely free of the pleasures of your worship.

In the faith-holding sense, I don't believe in anything. The universe just is, evolution and thermodynamics don't require my spiritual assent to exist, any more than gravity or climate change or tomatoes do. That's not to say I'm some mindless, amoral spiritual void. My mythos is always aboil, bubbling over, as anyone who's ever read my fiction can probably attest. I just don't confuse the structures of my consciousness with the external reality of the world.

And cancer, like a morning hanging, has a way of focusing the mind. Cancer, at least my path of it, has seized my narrative, and will likely drive me for the rest of my life, whether to an early grave or to a long and thoughtful post-disease survivorship.

I would be a terrible Buddhist these days because the literalized metaphor of my suffering is written in scars across my body, in the daily convulsions of my stomach and my bowels, in the despair and fear and occasional triumph of my thoughts. I live in the valley of the shadow of death, and there is no one here to succor me except myself, and those whose hands reach back from the light beyond.

This suffering would make me a terrible Buddhist, because it keeps me too focused on my sense of self and my narrative in this world. But it might be making me a better human being. At least I love more thoughtfully and live more carefully than I used to. If I am coming to believe in anything in the faith-holding sense, it is that I have come to believe in my own death. Which is of course the least surprising aspect of life.

The narrative? She keeps changing.