18 March, 2010
Video Toaster
Audio quality is bad due to the room being boomy and the microphones on my camera being tiny. There ought to be Official Footage showing up soon that will likely sound much better.
I recommend listening to this on big speaker system with the EQ spiked for mids for maximum comprehensibility.
04 March, 2010
Post Ignite Talk
After the presentation, a bunch of people whose names I no longer remember shook my hand and told me that I'd given a great talk that was very interesting and many people shared their stories with me of how molecular biology has randomly affected their own lives. There were also a lot of people who knew about the Central Dogma, but had always viewed it as something to be memorized and had never considered biochemical pathways to be a form of useful, active information. Nonetheless, what people very specifically pointed out about my talk were my slides. I painted about half my slides by hand with soluble ink and watercolor. Here are many of them:
Translation.
Protein Folding.
Sonic hedgehog. It helps you tell your head from your ass.
Sonic Hedgehog talking to his buddies Smoothened and Patched.
Concentration gradient of Sonic Hedgehog helps Embryonic Pony determine anterior-posterior patterning.
Transcription. I chose to leave out semi-conservative replication to keep my talk focused.
Proteins have distinct functional motifs, like this one's tongue.
02 March, 2010
Bridge Cheese!
Right now I'm thinking it'd be lovely to move to Norway, somewhere up in Trollheim, and become a goatherder. Goats are nice, they'll eat pretty much anything you throw at them, and they even make milk and cheese (I believe you have to shake them to obtain the latter, though). The primary advantage of doing this in Norway instead of the Ozarks would be that I'd have no neighbors, and those that might be over the next mountain would be far too busy eating fish and enjoying socialized health care and education to care about me genetically engineering the goats.
I'd need 2 phenotypes, 1 with hooky fur and the other with loopy fur, but if I was successful, I'd have VELCRO GOATS!!! Not only could I harvest their wool for useful uses, but they've be velcro uses.
Now, what sort of uses would a velcro goat possibly have, you ask?
Well, for structural elements, of course. Specifically a bridge. A bridge over a fjord. Made out of velco goats. Sure, it'd be a loud bridge with all of the bleating and whatnot, and goats' eyes are damn creepy, but still, it would be a bridge made of goats over a fjord! Not only would it be biodegradable and able to consume the next Trollheimstadt's municipal recycling, but it would output bridge cheese!!!
Skäl!
28 February, 2010
Hedgehogs
And, because I'm

This is going down this coming Thursday, March 4th, at 7p. It'll be live-streamed, so I'll post a link as soon as I have one.
15 February, 2010
Microcluster Condensation in Immunological Synapses 1
In beginning the activation of the adaptive immune system, dendritic cells process and present sampled antigen in distinct molecules (MHC) that T-cells can recognize (via the TCR and CD4/8). Due to chunk recombination of V, D, and J regions of the TCR binding motifs and subsequent pre-programmed random mutagenesis* there is extremely high heterogeneity in the recognition cognates of the TCRs. So as dendritic cells (DCs) crawl through the thymus, lymph node, spleen, or other, they have many distinct antigens loaded into their surface display molecules, and every once in a while a TCR that has some binding affinity for that antigen will bind. What follows is the immunological synapse.
The immunological synapse starts out with the binding of the TCR and CD4/8 to the MHC, which nucleate the formation of the central supramolecular activation complex (cSMAC), when all of the TCR/MHC complexes from microclusters and merge into 1 more stable site. A lot of other things happen downstream of that, most of which are very interesting**, but what I find intriguing about this is: what sort of topology do the kinetics of microcluster condensation add up to?
All optimized networks have some sort of topology. This means the hierarchy of one node over another, because to have all nodes processing the same exact bandwidth is rather energetically inefficient. As such, there can be strictly hierarchical topologies like those found inside human corporations with management, there can be scale-free topologies in which hierarchy arises due to through-put optimization and is not strict (a good example of this is the server structure of the Internet), or others I don't know anything about yet.
Is microcluster condensation hierarchical or scale-free?
Unfortunately, it is extremely difficult to answer that question empirically because it happens so fast and because the cells involved are rather camera-shy unless given very exacting and munificent conditions. Therefore, this is more or less a thought experiment.
I posit that microcluster condensation is both hierarchical and scale-free, in turn; first, hierarchical and then, later, scale-free. Cook your noodle on that for a bit, and I'll explain my reasoning for why within the next few days.
*Not a contradiction of terms. The immune system allows for random mutagenesis of a restricted set of amino acids residues on T-cell receptors and B-cell receptors to greatly increase the range of possible binding motifs without great additional informational storage costs (DNA).
**E.g., I find the activation of such factors as NFAT, mTOR, et al to be interesting, but generally find the dynamics of histone deacetlyation to be rather dull.
13 February, 2010
Smokey Honey Chili
3kg ground beef
1 medium yellow onion, coarsely chopped
2 smallish yams, cut into ~5x10x7mm chunks
2 handfuls carrots, peeled and chopped like the yams above
1 large can tomatoes
1 can kidney beans
1 can black beans
4 cloves garlic, crushed
75ml whiskey
pinch lapsang souchong
25ml honey
spices
Directions:
1) Combine onion, garlic, yams, and carrots in large, deep saucepot.
2) Add generous dash of oil, salt, and black pepper.
3) Heat on high until onions are sweaty and garlic is nutty, then add whiskey and 10ml honey.
4) Stir in, continue stirring on high heat until most of alcohol smell is gone (we're after the colloidal flavors of the whiskey to caramelize them in suspension, not the ethanol itself).
5) Stir in ground beef until it is barely done.
6) Add in undrained can of diced tomatoes and tomato paste, stir.
7) Add drained cans of beans, stir.
8) Stir in remaining honey and lapsang souchong*.
9) Add generous cayenne pepper, ancho chili powder and Tabasco, moderate amount more of salt, black pepper, and file powder, and small amount of cloves and cardamom.
10) Reduce heat and let simmer, uncovered, until the protein leaking out of the beans begins to thicken the sauce to your desired consistency.
This was absolutely delicious, and it made enough to feed me for 2-3d. It was at once spicy and savory, but not sweet as one might expect from the ingredients because the low-weight sugars from the honey, cardamom and whiskey caramelized and added depth to the smoke of the lapsang souchong, ancho chili powder and cayenne. There was a faint hint of a mellow, orange sweet echo on the top of the palette, but this was largely obscured by the very well-complexed clay and blue flavors below it.
I set out in inventing this spice combination to get the mild tones of traditional chili while using sweet potatoes as the base. I succeeded on both accounts, I believe, and I really do recommend giving this one a try. I know I will be making it again sometime soon.
*Lapsang souchong is a Chinese tea that's much better at cooking than being drunk. It's a black tea that is dry-roasted over a fire of dry pine needles, and a hot cup of it tastes like literally drinking smoke. So I just added a very small amount this time to get the smokiness without resorting to liquid smoke. The tea leaves steep in the tomato juice, and they're completely edible.
08 February, 2010
Album
Toaster Sunshine - "Arc"
1. Oxidative Periphery
2. A Retrospective Abnegation of the Postmodernist Solipism
3. Swiftly Daftly Boom Boom Doom
4. Density Earache
5. Dishware Flossery
6. Additivity (Damitol)
7. Suburban Dirge
8. Erosion
9. Thermal Counterpart
10. Thunder Melted Your Words
11. Läpikuultava Syndan**
12. Aftermath
13. The Nineteen Shades of Concrete Unbeknownst to Sunlight
14. Saccharine Nocturne
15. Somewhere the Magic Happy
This is just a working title, and all the songs are in rough draft form. I think "Retrospective Abnegation of the Postmodernist" needs some more slices mixed in to make it more interesting (it was composed entirely out of about a dozen samples from Shostakovich and Bartoks' string quartets), "Suburban Dirge"'s violins need EQ tweaking, and I have noticed that there is a high pitched percussive artifact in "Thermal Counterpart" that needs to be found and dealt with. Also, something weird happened with "Saccharine Nocturne" upon conversion to an .mp3 that I'll have to track down.
Anyway, if you'd like to listen to the raw tracks in all their muddy glory, you can download a zipped version of the above album at: http://drop.io/ji4trez#. If you do so, please, by all means, criticize it as bluntly as you'd like.
*Notwithstanding the background music I tend to produce whenever there's a guitar handy, despite whatever else is going on around me.
**This translates to 'translucent heart'.
03 February, 2010
Passionate N00bity
Part of this is due to my dream of one day delivering a data talk in the form of a power ballad, but it's also due to confusion as to when I may break down the barrier of formality and ask a douchey question within the cloak of excited admiration? I recently saw a speaker present some really awesome new biotechnology she had developed in the course of her project and its applications. The tangibility of the data (real-time fluorescent tracking of cells in a living matrice by 2-photon microscopy; which basically meant actually seeing immunotyped immune cells crawling around and interacting with each other) was surreal and exhilarating, but when she talked about her methodologies I was left wanting. I don't want to out the speaker, so I cannot say exactly what my beef was, but it had to do with the algorithms by which she chose to quantify her data. I refrained from asking this question in the Q&A session because of the very civility I mention above, it just seemed like too rude a question to ask in such a polite intellectual subculture as an academic presentation. Of course, on the other hand, there was also the possibility that my question would have revealed my ignorant n00bity, and to be honest that also played a part in me not asking.
Nonetheless, when can we whup it up and get excited about the science all around us? Can I ever high-five or fist-bump a speaker when they've shown me something awesome or would doing so break down this fifth wall academic politeness has surrounded us with?
28 January, 2010
Old-School Anti-Woo
Nov. 20. 1905J. H. Todd
1212 Webster St.
San Francisco, Cal.Dear Sir,
Your letter is an insoluble puzzle to me. The handwriting is good and exhibits considerable character, and there are even traces of intelligence in what you say, yet the letter and the accompanying advertisements profess to be the work of the same hand. The person who wrote the advertisements is without doubt the most ignorant person now alive on the planet; also without doubt he is an idiot, an idiot of the 33rd degree, and scion of an ancestral procession of idiots stretching back to the Missing Link. It puzzles me to make out how the same hand could have constructed your letter and your advertisements. Puzzles fret me, puzzles annoy me, puzzles exasperate me; and always, for a moment, they arouse in me an unkind state of mind toward the person who has puzzled me. A few moments from now my resentment will have faded and passed and I shall probably even be praying for you; but while there is yet time I hasten to wish that you may take a dose of your own poison by mistake, and enter swiftly into the damnation which you and all other patent medicine assassins have so remorselessly earned and do so richly deserve.
Adieu, adieu, adieu!
Mark Twain
This was a response to an advertisement from a patent medicine salesman, apparently seeking endorsement. I hope to remember in the future to slam the proponents of alt-med woo with such grace and wit, for at the very least it is more elegantly entertaining. In the meantime, my respect for Mark Twain* has only increased.
*Sooooooo much better than Kierkegaard.
18 January, 2010
City of Loathing
I grew up in an area of the country where racism is everyday and accepted. African-Americans lived on Grand Blvd., Benton Park, Boonslick, Blanchette and in East St. Louis. Koreans lived down Manchester Blvd., Serbians lived through the worse ends of Kingshighway, Italians lived on The Hill, Irish lived in Dogtown, French lived in Soulard, Jewish people lived in Tower Grove and University City while Hispanics were practically invisible. Generic white people lived anywhere they damn well pleased, but were especially adamant in Florissant, Chesterfield, Hazelwood, Maryland Heights, Forest Park, and the Central West End. Saint Louis is a city of several million people that has been standing for more than 200y, and these divisions remain, perpetuated by infrastructure and class. The neighborhoods around the dying industrial zones just west of downtown are crumbling and so are the schools within them, and this just sets the stage for a cyclic repetition of the same social injustice. Meanwhile the office towers of Clayton feed the vibrant school discticts of Forest Park and the Central West End as well as luxury shopping villas like the Galleria.
But in all of this, it was the Page Avenue Extension project that most clearly illustrated the dystopic undercurrent of casual racism in the city. This project built another bridge west across the Missouri River, providing a direct line of transit from Page Avenue, which runs from downtown St. Louis all the way through to Maryland Heights, out to suburban St. Peters now. The largely white denizens of St. Peters nearly shat themselves in consternation, and the reason I kept overhearing was that now "black people could move in" and apparently would ruin everything. This highway project shaved about 30min of driving time off of getting from St. Peters to downtown, and I found it absolutely ridiculous to suppose that 30min by car would have effectively stopped African-Americans who wanted to move in from doing so. But that's what people were nonetheless afraid of.
And what disturbed me most about the whole thing was that the same people who had problems with the highway project were those who frequently also had tactical armories in the basements of their homes. That venal and irrational hatred, coupled with such easy access to powerful firearms, never sat well with me. This is the same city that sees the homes of interracial couples defaced with defamatory graffiti and witnessed the firebombing of the only Muslim mosque in the city with nary a murmur after 9/11. With Obama being elected, I would like to believe that racism has gone away, but I'm not so naive as that. Racism persists not because powerful people wish to keep oppressed minorities explicity repressed, but rather because those that have "made it" are desperately afraid of having to share their slice of pie with a strange group they perceive as not being of themselves.
Well, I cannot morally identify with those who cower in their suburban homes with semi-automatic assault rifles and hollow-tipped bullets in their basements for fear of simple progress. I reject their fear, I reject their hatred, and I condemn them for their prideful ignorance.
I left St. Louis in 2004. It had already left me much earlier.
*I can understand hunting guns and have no problems with them, but there is a massive difference between a single-shot hunting rifle and a semi-automatic tactical assault rifle loaded with bullets designed to inflict maximal harm.
