Five More Thoughts - Even MORE Shtick Ed.

I always figured it a German sort of creole, but the spell-checker brings up "shtick" without the "c," and so who am I to argue? Eh spell-chequer wood knot lye two Mie. Whatever, the point is that the routine's still pretty much the same (wah wah wah wah, me me me me), and the alleged thoughts are too (perils of sarcasm, music inability, resentful foodie-ism, family follies, commuting--hating myself for doing it doesn't excuse constantly writing the same post). I'm going for more frivolity than last time, as I continue to avoid serious work, and to procrastinate a book review that requires an ounce or two of actual thinking. I don't even care what day of the week it is.

1. Not!
In age-old posts, I liked to speculate about language and culture. If Russian, say, is fabulously suited for sarcasm, Italian (by definition) for heated romance, then Yiddish is a great dialect for self-deprecating irony, or at least that is something years of consuming American humor has taught me. (I am not comfortable with this sort of generalization, but I needed a segue, you understand.) Even though life has any number of cruel built-in jokes, it's still not easy to go through it being only half-serious. Well, it does allow you to cut yourself a lot of slack when you make assertions, which is always handy in those cases when those assertions happen to be wrong, but unfortunately you can't ace living when all you ever go for is partial credit. But even if you must hedge constantly, it's better than being dead-ass wrong on everything without ever showing your work, right? I equivocate a lot, too. It drives me crazy, except when it doesn't.

The problem is that circumstances develop which require more confidence. When you sarcastically load every utterance with its own counterargument, savor every double entendre, then where does that leave you when you want to say something sincere, to someone you like or respect? I've been catching myself quipping all sorts of things that, if one were to fail to pick up the meaning I intend, then they'd be left with the exact opposite. "I like the dress, Sweetie. No, it's my honest opinion. No, really!" I don't always make good first impressions.

The fact that some people seem to understand what I mean, at the level I intend it, is a little unsettling. Either I'm a better communicator than I think I am, or one with fewer shades. Or else you're just as nuts as me.

2. I'm not dead yet.
When I was a kid, the Lego brand symbolized the quality sort of toy building bricks. Unlike the competitors that had been around forever--patriotically-themed frontier beams, the awful hub-and-spoke networks with the derogatory Romany name, or the metal screw-together bars that were vaguely Communist in their ugly, ill-fitting universality--the newfangled little snap-together plastic cuboids, with the bizarre product literature translated from the original Danish (and quickly-discarded pictorial instructions that were smart enough to avoid translation altogether), were awesome. The bricks were small enough, and fit together snugly enough that you could make anything out of them and have it stay together.

There were a small number of specialty pieces that could add angles, hinges, wheels, and a few other useful odds and ends--wings, 90^o headlights, cones, cylinders, windshields, and little dudes that achieved a sort of happy minimalist humanity--that could let a kid really innovate. I came to the age-appropriate scene when they were working at bifurcating their product lines to sucker in the completists. How I begged my mom and dad for the space-themed Legos (rockets, antennas, clear yellow blocks). My brother was big on the castle set (had some wall blocks, lances, Lego trees). It didn't take long before they all ended up in the big box. [I got a kick out of the "expert builder" Legos too, which ended up in a different box.]

The pre-made horses for the Lego knights were probably a bad sign, and over 25 years, the trend seems to have grown entirely out of hand. Best I can tell, each set is now comprised of approximately three highly specific, complex pieces that only nominally interact with pieces from other sets. I thought I saw a Bionicle thingie that didn't have any of the Lego buds on it at all. Might as well buy action figures.

In grad school, I bought Lego Racers (the video game), which, while having nothing to do with snap-together proto-engineering, somehow caught that spark of honest fun that some artist once caught on a smiling plastic yellow face. And virtual Lego has only been improving, by the looks of it. Lego Rock Band looks like tons of fun, somehow a little more pure than the block-less version of the game. Legos are dead, but the idea of Lego lives triumphantly on.

3. I'm dancing! I'm happeeee!
I've gone on about Rock Band, which is like a whole-family karaoke-full of fun. I like that we can do it together while I wait for the kids to warm up to the idea of participating in the jug band, and it's fun to pretend to drum, but of all the hobbies...

In my non-musical musical family, we're singers least of all. To be fair, my father (who is also the only one of us alive that can keep time) can produce credible, ear-pleasing, Garfunkular harmonies, but the rest of us possess voices that have been known to send dogs whimpering inside during the full moon. The local minister canceled Christmas in 1979 to keep my grandfather away from the hymnal. Yoko Ono once threw an egg at my mom. My poor daughters both adore singing, and enjoy chorus greatly, emote the notes innocently and without shame. My darling little girl (who I'd love to see get a shot at acting) has had a hard time landing prominent roles in the school productions because they're musicals. And yet I'm all for it--what can make you happier than singing, after all?

So getting a compliment for my voice was something entirely unexpected (and I'm sure my wife regrets it deeply). Granted, it was in comparison to two pre-pubescent girls trying to sing male parts, but I'm taking it. Evidently, I'm at least occasionally capable of hitting the same two notes that John Fogerty, Steve Perry, and Pete Townshend sing most of the time. Sweet.

(As I write this, Stephen Colbert is singing along with Elvis Costello, and faking it pretty well. Fucking talented people.)

4. Peer Pressure.
Colbert completely justifies anything else Comedy Central might ever do. I still haven't figured out what I like about Food Network (as I've often complained). Okay, I like to ogle the food, which they sometimes highlight between the personality parade. I also get a kick out of how they dub Japanese-accented English over Masaharu Morimoto's broken English. (Lou Ferrigno is somewhere flexing his muscles in sympathy.) I might enjoy Alton Brown's Mr. Wizard schtick if he weren't so damned smarmy about it.

And what's the alternative? Both times I've watched America's Test Kitchen, I've wanted to strangle that bespectacled know-it-all who tells me that everything I know about cooking is wrong. The presence of some interesting facts and explanations in there is that much more annoying, somehow. Maybe it's the presentation, like I'm being addressed as a ten-year-old. Any good material scientist knows the importance of morphology; any chemical engineer who's been around the block knows how touchy biochemical processes are to shepherd. I don't feel I need the level of condescension they offer.

Yesterday, I got schooled in the use of a potato ricer, which all the TV chefs have been playing with lately, and which I deeply suspect is a useless trendy gadget. Glasses-guy accented his shopping guide with an after-school vintage cartoon telling me the viscoelastic spuds I grew up with just. aren't. cool. Now, I always thought "creamy" was the goal, and my trick, such as it is, has always been to put plenty of fat and milk in there, as I whip the living crap out of them, mm-mmmm. I admit they're a little gluey. But why not? I associate "fluffy" with the under-processed (and slightly under-seasoned) taters that frequented my grandmother's table, and were preferred in eastern European households (data set of one). I admit they weren't my favorite. My mom also had a ricer at one time, long ago, that she used to turn leftovers into baby food. So I'm thinking, you're shitting me, right?

Of course I bought one. I'll report back.

5. I hate driving, have I ever mentioned that?
First we tried the local cooking shops, but the ricer required a trip to the nearest big megamall (helping to confirm the suspicion that it's a high-class, food-porn sort of gizmo), which, I'm sorry to say, isn't really that near. I hate everything about these places. I hate the crowd, the parking, the forced festivity, the canned indoor air, the designed inefficiency of moving around, the frenetic sense of holiday consumer pressures, the time crunch that prevents me from looking around at the rare item that's interesting (such as anything in the bookstore).

It's not even officially Hell Month yet, but there was no parking spots at the mall today. I'm happy to walk, but don't care to be stared down by looming blinkering fatasses on even the parking outskirts. Nor do I appreciate the dangerous pedestrians who scoot in front of my car to cross the street. When I stupidly jump out in front of moving traffic, I'm sure to make eye contact (what driver doesn't appreciate a thank-you wave for being forced to yield?) at least enough to avoid getting run over. It's a simple question of weight ratios, after all.

There's a special place in hell for the drivers of little cars that park deep in the slots, making them look empty, or better, let's damn the drivers of the street behemoths who block the view. The whole American consumer culture is overdue for a reimagining (which may not be voluntary when and if it comes), but I've got to tell you, in a lot of ways I'm more motivated by personal, and largely irrational annoyances.

[I need to go to bed. I'll clean up the English tomorrow, if so motivated.]

Review: Manhood for Amateurs, by Michael Chabon

Manhood for Amateurs is a collection of essays on fatherhood and masculinity from Michael Chabon. I'd come across it originally when August (he among the quiet friends) had quoted some select bits, and years later, I had the presence of mind to snatch it up from the bargain bin when I saw it there. It wasn't, as things turned out, the ideal time for me to read this book, although it's not because it failed speak to me easily. It did. It was great in its way. In fact, Chabon's humor is familiar, his self-effacement is similarly backhanded, and his values, while not quite identical, readily map to mine. I've gone so far as to write, not only on the same themes, but on some of the very same subjects as he does in this collection (Legos, for just one instance). Nope, my mild peckishness comes from a couple places: (1) Chabon's a zillion times a better writer than I am, and it's not a whole lot of fun reading a worlds-better version of your own schtick, which, I'll add, in Mike's case has also got him gainfully employed and all kinds of attention; and (2) I've been turning the corner a bit too often lately from ironic bemusement into a fairly devastating self-analysis.

I'll dwell on the second point a bit longer. Chabon often finds himself comically awkward and ineffectual, but let's not pretend he's not also charmed by this, that he doesn't likewise expect others to find it charming. He's managed to forgive his own faults, for the most part, or at least make peace with them, and he is generally a whole lot more sensitive to his younger self than I've been lately to mine. In one essay, he describes the failure of his first marriage, in the context of discovering the not-very-deep limits to his misery. Even his bitterness, as he tells it, comes with a certain ironic detachment. In one of the opening bits, he goes on about the low expectations and over-praising that fathers who pay minimal attention to their children tend to receive, and okay, it's a good bit, and true. It goes on to suck up, however, just a little bit, to the women who deal with these things as stoically as society expects them to, and while that doesn't seem so out of place in that essay, by that point, somewhere in there, I'm noticing that his family is successful and wealthy, his (current) marriage preternaturally respectful and sustaining, that he lives in an absurdly supportive liberal community (Berkeley CA), and the burdens placed historically on women aren't much shared by any of the group. Somewhere in there, and throughout the book, is the acceptance of male and female roles as they currently are. It's an unsettled and questioning acceptance to be sure, and it's happy how far they've evolved from his parents' day, but there you are.

Or maybe I can define this by contrast, citing an essay that really worked for me. A later one reveals his younger self as enamored with the role of a Henry James style affable cad, and how, while working with capable women, he was forced to identify and outgrow, with some chagrin, that brand of misogynistic little-shitness. We men often start out with all kinds of affirmation of that little-shit behavior, he observes, and indeed it's a bizarre sort of tragedy that learning how completely unwarranted it is, remains an optional exercise. That thought seemed to come from a more sincere place than remembering everything that dear old Mom went through. Or again, maybe it's just a reflection of where I'm at these days.

I wasn't in a mood to read a cautious celebration of nuclear fatherhood either (I don't feel like a failure at it, but I'm royally sick of the all the sitcom conventions that pervade our conceptions of the job) but lots of these thoughts got right to me. One of his early essays managed to win me by the second sentence: "Almost every day, at least one of my four children comes home with art... And almost every bit of it ends up in the trash." It seems to me that faking our way through fatherhood, uncomfortable with our own authority, is a nobler and more selfless struggle than trying to figure out girls, and I'm glad that Chabon is uncomfortable with the romance of it too. Here, his slightly childlike enjoyment of relationships and culture shines more brightly, and fits into place more snugly. With kids, a mild and jokey push against authority is just the level you want. (And I did think a lot of my own father while reading these sections).

And Chabon is funny in a comfortably self-mocking way. That goes on here in spades. He's got a sense of the bittersweet that I can't help but share. Thematically, it offers a powerful message that we always muddle by in an odd juxtaposition of youth and age, men and women, past and present, expectations and reality, memory and hope. It's never a wholly bad exercise to get yourself caught up in the heartbreaking beauty of now.

Information comes full circle

DNA--most of us think of it in some vague way as the stuff of life, some enormous string of data encoding every characteristic of the individual wrapped around it as some impossibly long Gödelian nightmare of a quarternary number. (The human genome is about 3 billion digits long, which allows on the order of 10^1800000000--almost two billion googol--unique codes.) It's that mystery stuff that is the blueprint for everything an organism is, from which proteins its cells express, to which organs it has and how many limbs, to its behavioral tendencies. The genome dictates how organisms process external information, which is to day that it influences everything the it does, whether it's at a high level, with brains (the human brain has about two orders of magnitude more neurons than a DNA strand has base pairs, but unlike natural DNA, they connect with one another nonlinearly) or at a low level, bending toward the sun, say. The organism's reaction to the outside world is part of its extended phenotype, and that response to the environment may include changing the environment, creating a cyclical relationship: the code creates external information that changes the environment, that the code must reinterpret. In the metaphysical extreme, the expression of DNA on an ecosystem level, or on an evolutionary level (over as many years as there are digits in the human genome) is a metastable means for the universe to dissipate energy into uselessness, information into meaninglessness. That sort of determinism doesn't lessen the burden on our freakish consciousness. In order to achieve that metastable species-wide state, or one of them, we still have to act, even if it's just the genes talking, and it's hard to tell where the story is going.

But at the bottom of that somewhat comprehensible tangle of life is a somewhat comprehensible tangle of sugars and phosphates. Actually, the molecule itself isn't quite so exotic as all that. The information capacity is vast, and many aspects of stringing it together remain mysterious, but it's held together according to some well-known chemical rules. It's composed of a phosphate/carbohydrate polymer chain with interacting base groups hanging off the side at regular intervals. Each of these bases is specific to only one other base, and for your single DNA strand to find a partner and make a double helix, then the whole sequence of bases has to correspond in the right order. A chain of bases will only stick to its complement (A and a in the figure), rejecting all others. Even a DNA strand of only ten base units can hold about a million different combinations, each of which has only one destined partner. If you're a chemist, that's as specific a reaction as exists, and it's where the fun with DNA begins.

[IMG]http://i219.photobucket.com/albums/cc74/Keifus/dnafigure1.gif[/IMG]

Over the last couple decades, artificial synthesis techniques have become good enough to manufacture short DNA strands (called oligonucleotieds) in a controllable way and in high quantity. That oligomer can capture a small and characteristic portion of a longer chain, and this specificity can be used to test for the presence of longer chains of interest. Oligonucleotides can be anchored (more chemistry), so that one end is permanently attached to a solid surface such as gold or glass. The sequence of the oligonucleotide is engineered to complement a small portion of a DNA strand of interest, for example from a known pathogen. An assay can be constructed to detect that target DNA. To do this, an solution which is thought to contain the molecule of interest (anaylyte) is passed over the immobilized DNA oligomer, which will grab the target sequence and anchor its whole strand to the surface. A second oligonucleotide solution, which is complementary to another portion of the target molecule is then passed over the surface. Instead of being anchored to a surface this second molecule pulls along a label at its end, which can be viewed with instrumentation. If the label is detected on the surface after being exposed to the analyte and the reporting molecule, then the test is positive. Chad Mirkin's group at Northwestern is using tiny metal particles as labels in this type of assay, which when properly treated are visible to the naked eye or can be measured electrically. The goal is to make spot tests for a variety of dangerous or important microorganisms.

[IMG]http://i219.photobucket.com/albums/cc74/Keifus/dnafigure2.gif[/IMG]

You can further manipulate oligonucleotides to make branched structures, as shown in the third figure. Here, the single strands are designed so that they complement only part of another strand. If you arrange the pattern just so (and if you have an army of grad students with brilliant lab skills), then you can make branched DNA structures. If you arrange the overlap of sequences just a little differently, then you can make branched structures with overhanging sticky ends, each of which will bind only to complementary sticky ends, much like in the assay experiment. The four-armed beastie in the lower figure will bind to itself, and should make a random sort of network (and will probably turn the mixture into a little vial of snot). You're not restricted to three or four arms, and you can have any variety of sticky ends. People have made closed shapes, three dimensional objects, and "tiles", which spontaneously form as each sticky end finds its own soulmate.

[IMG]http://i219.photobucket.com/albums/cc74/Keifus/dnafigure3.gif[/IMG]

Self-assembled DNA structures are pretty cool, but they aren't just laboratories curiousities. If a DNA code is used as a code, that is used by people to store information, then self-assembled DNA structures can be used to read it, pinning objects of known shape or with known labels onto a more complicated molecular scaffold, the sticky end of the known unit attracted to a piece of the code DNA.

You can go further than this and imagine branched DNA structures as a series of jigsaw tiles, such that each edge is attractive only to certain other edges. In this situation, the identity of a given tile depends on the identity of adjacent tiles. Given an initial soup of molecular Legos, or for a given "input" series that starts concatenating a pattern, tile structures can emerge such that a unique structures assemble from given inputs. Known inputs-->organization-->reproducible outputs. You've made a computer. It doesn't necessarily matter how that organization occurs, you may not even need to know what edges you have in the mix of tiles, but Wang's carpet has just done your thinking for you. Molecular computers using DNA have already been shown to solve known mathematical problems that are computationally intensive by conventional means. Can any pile of jelly hold a thought? I've got to go with yes, Stan.

I've been entertaining myself lately to think properties of the universe as purely informational. Entropy can be considered as the availability of alternate states of being for any datum you can name, and the second law of thermodynamics says that nature pushes for all states to eventually become interchangable, and therefore meaningless. It may be more accurate to say, however, that information is a property of universe. Information requires the existence of the stuff of nature configured a certain way--if information is encoded in atoms then the nuclear force and electrical forces control the arrangement of its components. If it's stored in the motion of the spheres, then it's masses arranging themselves gravitationally, if it's in molecules, the thoughts in your head, or the words on your screen, then dynamic patterns of electrical motion are holding your information. Human thoughts (and computers too) may in a broad sense be considered expressions of a few billion molecular codes, each a few billion spaces long. The human genome has reached an oddly recursive point where it can manipulate itself as well as its environment. Information comes full circle.

Some additional online references:

A DNA computer solves the travelig salesman problem (Scientific American article, also has some description of the DNA synthesis toolbox.)
DNA tile complexes (PNAS article)