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° 02.08.30.fr | genetics for the computer scientist

The past week I've been reacquainting myself with the biology of genetics. Wednesday I finished reading Darwin's Radio (a "hard" sci-fi about genetics) and last night I watched Nova's Cracking the Code of Life. In trying to follow along I've also been reading HowStuffWorks' articles on DNA and Genetics. Of course, when trying to comprehend another field, I find it helps to map it to my own. So here are some metaphors, perhaps confused, for remembering how life works:

DNA
A sequence of four nucleotides {G, A, T, C}, paired together, that encode information for making proteins. Like a sequence of bits {0,1}, but instead of being base-2, I think it's base-4?
Chromosomee
A structure for storing DNA, the human genome is stored in 23 chromosomes which are densely clumped together DNA sequences. Like computer information stored on a number of platters within a hard disk.
Codon
Three base DNA base pairs. Like a byte which consists of 8 bits.
Gene
A section of DNA that encodes the definition for a protein that starts with a promoter and ends with a codon representing a stop. Like a network packet that has a start and end sequence.
RNA Polymerase
An agent responsible for reading the DNA (by unwinding it) and creating a message (mRNA) from it. Like a computer agent that transcribes local information and broadcasts it as a message on the network.
tRNA
Stores the amino acids necessary for building a protein. Like a graphics frame buffer stores textures that are used to compose an image.
Ribosome
An amazing enzyme that uses the information in the mRNA and the material in the tRNA to build a protein. Like a graphics card using instructions and textures to compose an image on the screen.

° 02.08.28.we | scandal

We can never know everything. We haven't the capacity nor time to give informed consideration to every important issue. So we rely upon labels and personalities to set the default values of our opinion. Generally, I'm sympathetic to the arguments of the ACLU and critical of those of the Federalist Society. I honor the lives of Gandhi and King, and despair over the likes of Kissenger and Cheney.

Personalities serve as a proxy to our conscience, and when an individual weakness is exposed, the fault transcends the individual and threatens the cause. This is unfair to the individual and their community: we all make mistakes and we never completely surrender our own conscience to another. But it's human nature to confuse the symbol for the thing.

Once, when I expressed my respect for Gandhi I was told, "he had sex with children." I've also seen this argument bandied about Muslim Pakistanis and hawkish Hindus: the Muslims want to attack Hindus, the Hindus want to discredit Gandhi's call to not kill Muslims.

When confronted with such an accusation we should give it consideration, but we should also not cast aside orthogonal virtues. Some say even Satan can quote Scripture and Jesus was not without sin. When, in a public figure practice does not follow principle I ask myself was the principle stated so as serve others, and was the practice uniformly condemned by the principle? For example, when Martin Luther King Jr. placed his life (both his family life and actual existence) in jeapordy when fighting for equality for all, he personally gained little but our respect. Nor did he claim a special exception for infidelity: he preached it was wrong and would not be able justify it as anything but.

A primary purpose of my writing is to capture the costly investment of my own consideration. Even for those topics I research, I'm bound to forget the particulars, and so it is with allegations about Gandhi. There is no claim that he ever had sex with anyone after his wife. His own personal goal, and not something he asked others to do, was to become a Brahmachari and to completely transcend libido and practice life long celibacy. To that end, both as a test and evidence of purity he encouraged a level of intimacy such as sleeping or bathing nude in the presence of women. He was scrupulously honest about this practice neither hiding it nor granting himself a special privilege. In fact, it is both of these things that prompted concern from his colleagues in a politicized atmosphere. Was his position naive or inappropriate? Probably. Hypocritical? No. Does it in anyway denigrate the principles of peace and compassion? Definitely not.

° 02.08.26.mo | bad hair day

Today I had a presentation at a web services forum and I thought my shaggy mohawk could do with a change. So yesterday I made sure to squeeze in a barber visit during a busy day. I didn't explain what I wanted well and, as happens with half of my last minute haircuts, this one looks dorky as all hell. (There's something about trying to make an effort that dooms me, Nora nailed it as the "sportcaster's hair cut".) Still, such experiences keep me humble, your ego can't get too big if you think you look silly.

° 02.08.23.fr | Dyna Magz

Dyna Magz In Michigan I was happy to find a new Magz kit: Dyna Magz! It has special "cuballs" that permit the joints to be stiff and consequently stronger. So for example, I was able to build this small suspending spinner! I'm also very pleased with the design I came up with to supend the spinner. Next step: a bigger spinner of course!

° 02.08.17.sa | the freaks on holiday

holland punks On Friday and Saturday we visited Nora's parents. One evening while walking through a park two punks ran up to say hi to Nora and me, when we were later asked what they wanted Nora responded, "the freaks know their own!"

I love the spirit and joy of live water: streams, sprinklers, oceans, pools, showers and slip-and-slides. So when I'm on holiday, I definitely want to go to swimming, which meant braving nearby Lake Michigan and its 53° water! I was surprised I was able to submerge briefly up to my shoulders, and that the cold was not shocking but a dull pain in my legs. We also visited an old-fashioned candy shop, drove about in a muscle car, and ate some of the best bread I've ever tasted.

wolf lake We then headed north and stopped at Wolf Lake. For the next 3 days we lounged about the Wolf Lake "resort" watching kids fight and play, we swam in the much more pleasant water during sun and storm and went tubing on a nearby river. I also embarrassed myself a bit with an overly smokey barbecue, and I finally let myself read Return of the Kings — which I'd been saving for a leisurely summer read. I was choked up at the end, as was the case for all three books.

wolf lakeCraving good vegetarian food, Nora suggested we drive to Ann Arbor. We had lunch at Zingerman's deli, saw Tadpole at the historic Mulligan Theater (the movie was preceded by a live organ performance; the organ lowered itself into the ground as the curtains rose), and ate a yummy dinner at Seva. The next day we ate lunch with a hippie, ("people call me Nature"), and drove to Grand Rapids where we splurged on a nicer hotel (the "resort" was $35 a day!), and went to Liquid Room, a gothic after-hours coffee-house/club. Friday morning, we relaxed in the hotel's pool and sauna, ate an Ethiopian lunch, and sadly ended our holiday enduring the hassle of airports.

° 02.08.07.we | not much

When "failed requests" for the present month start appearing in my web server logs, I suppose it's time to put up this month's page! (I'm flattered people are so eager they'll type this month's URI in manually, but if there's new content, you'll know!) However, while I have things to rant about, I've been preoccupied with my new camera and reorganizing photographs. For the past 16 months, I've had scripts that pretty much took care of generating my photo albums and such. I decided to go back and regenerate older archives as well; this required some improvements to the scripts and reorganization. Some links were broken in the process, so I've been watching the "failed referrers" to try to redirect queries for images to their new location. I didn't realize I had the top google image return for balloons until I deleted the ugly photo! I haven't bothered to restore the balloon image (google has already forgotten about it) but most of the links should be working now.

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