2006-12-25

Restlessness...

for 48 hours or so, now. Nothing fascinates me; the greatest curiosity I can achieve is a kind of abstract Orwellian intellectuality: We're all doomed, and I can express the sentiment with excellent prose. I find myself straining to visualize a blueprint or a mechanical drawing of some revolutionary object which is just barely beyond my powers. I have fantasies of inventing bold new weapons, based on heretofor unknown principles of science, by an act of profoundly original innovation, of the type which only naive laymen and children are really capable: A new route, perhaps, to a fusion bomb, without the use of a fission primary--a garage-scale process unlocking megatons, realized secretly by Einstein, hinted at by Oppenheimer, and ruthlessly suppressed by history. The hardware store thermonuclear bomb. A manipulation of plywood and foam rubber that creates momentary access to new dimensions. Necronomignosis. When it finally comes to me I will have relief, and the world will tremble.

2006-12-24

A Spartacus Moment

This holiday season found me stretched out in front of the giant TV at my parents' house watching Stanley Kubrick's first movie Spartacus, a fictionalization of the Third Servile War of 73 BC with Kirk Douglas in the eponymous lead, on cable one evening. As I drifted in and out of consciousness, I was reminded of the last time I saw the movie, which was 17 years ago, at Westwood Junior High, in my Freshman Latin class. I cannot for the life of me remember the teacher's name, but although I disliked her at the time, looking back as an adult I recall her as a patient and diligent instructor.

We watched the movie, Spartacus, in her class, including the famous climactic scene in which the defeated slave army refuses to identify their leader to the conquering Romans in exchange for leniency and, as a consequence, is crucified en masse along the Appian Way.

Some days later, Ms. What's-Her-Name was conjugating verbs on the chalkboard, with her back to the class, while my friend Lee, who sat beside and slightly ahead of me, was practicing spinning, tossing, and juggling his pen a la David Letterman. The pen slipped out of his control and flew toward the chalkboard, impacting just beside the teacher and falling into the chalk-tray. She picked the pen up, turned slowly, and presented it to the class.

"Who threw this?" she asked quietly.

There was a long pause, pregnant at least with triplets. Lee squirmed in his seat.

"I'm Spartacus!" I cried, suddenly.

A wicked grin spread across Lee's face. A second later, he echoed, "I'm Spartacus!"

"I'm Spartacus!" called an unknown voice from the back of the room.

And then the whole class joined in: "I'm Spartacus! I'm Spartacus! I'm Spartacus!"

She was beaten, and she knew it. Her anger melted into an amusement she tried, unsuccessfully, to conceal from us, and class went on with a wonderful feeling of light good humor.

It is one of my fondest memories from that otherwise-traumatic period of my life.

2006-12-23

My Favorite Ceiling Fan Design


I like the no-BS minimalism of the 3-bladed unit. It lacks ridiculous brass details, does not use materials in a superficial way, and achieves a cool modern look without the ridiculous "modern" price tag. You can buy one of these for as little as $25 online.

Devilnition Definition

In honor of Ambrose Bierce's subversive lexicon The Devil's Dictionary, I hereby coin the word "devilnition" as follows:

devilnition - n. a verbal definition, in the style of a dictionary entry, which imparts a subversive, ironic, or humorous meaning to the defined word, e.g. "Scientist - An intellectual who distracts himself from depressing contemplation of insoluble philosophical problems by meticulous attention to inconsequential physical ones."

In Case You Ever Wondered...




...this is what a nerve-gas bomb looks like. These pictures, taken from an eBay auction, are three views of an aluminum cluster bomb submunition, of U.S. manufacture, intended to contain and disperse Sarin nerve gas. The U.S. no longer openly manufactures or maintains a nerve gas arsenal (and is actively engaged in the destruction of existing stockpiles). This object antedates the modern policy, which was established, I believe, in 1975. The seller assured it clean and safe to handle. It sold for $163.00.


Spray Paint Can Design Gaffe


The little lip at the top of the spray can and the little indentation in which the nozzle is set catch paint from the spray. On extended spraying, it pools there and begins to slosh out and drip onto the floor. If the top of the spray can were a smooth curve without this lip and indentation, the can would work much better.

Obligated to Configurate - How Ironical



So, it turns out, at least according to www.dictionary.com, that "configurate" actually is a word, but its meaning is essentially indistinguishable from "configure," and it costs one more syllable and two more letters. William Safire could probably give a name to this phenomenon, but it's notable also in the cases of "obligated" versus "obliged" (where the savings is a more impressive 2 syllables for 2 letters), and in that of "ironical" versus "ironic" (again 2 and 1).

2006-12-17

Tempur-Pedic Assvertising


As much as I love my Tempur-Pedic pillow, and as much as I pine for one of their full-size memory foam mattresses, I can't help but make fun of the fact that theirs is surely the only successful international corporate logotype to predominantly feature an ass-crack.

2006-12-11

A Postmodern Primer in Orwellian Prose

Several years ago I undertook to update George Orwell's classic maxims of clear prose, from his 1946 essay Politics and the English Language, to better reflect modern sensibilities.

1. Never use a metaphor, simile, or figure of speech which has been run into the ground.

2. Never employ a polysyllabic construction where a monosyllabic construction will suffice.

3. If it is possible to cut a word out, always be sure to cut that word right out of there.

4. The passive is never to be used when the active is possible.

5. Never use patois, neologisms, or argot if you can think of everyday English equivalents.

6. Any of these heuristics should be disregarded, if, in the course of putting them through their paces, respectively, one is impelled to commit unpardonable stylistic faux pas.

Rudolph the Sh*t-Faced Reindeer

You know Dasher and Dancer and Prancer and Vixen,
Comet and Cupid and Donner and Blitzen.
But do you recall
The most tragic reindeer of all?

Rudolph the sh*t-faced reindeer (Reindeer)
Had a very ruddy nose. (Like a crabapple!)
And if you ever saw it, (saw it)
You would say his drinking shows. (Like Bukowski!)

All of the other reindeer (reindeer)
Call him names behind his back, (Like degenerate!)
So Rudolph the sh*t-faced reindeer, (reindeer)
Crawls inside a fifth of Jack. (As in Daniels!)

Then one hazy Christmas morn,
Santa intervened: (Oh, no, no)
"Rudolph, you have wrecked your life:
You crashed my sleigh and it killed your wife."

Now the reindeer take turns driving (driving)
Rudolph every other day (Even Saturdays!)
To meetings of a 12-step program (Al-Anon!)
At the local YMCA. (Like where Daddy goes!)

2006-12-04

The 4-Course Submarine Sandwich

The original idea of the sandwich was to produce a meal which could be consumed tidily without utensils, perhaps while engaged in some other activity. But why sacrifice quality? Why not take the original concept to its logical conclusion and put a 4-course meal on a sandwich? Exploit the spatially linear form of a submarine sandwich to mimic the temporally linear form of a multi-course meal. The sandwich becomes biased along its length, with one end clearly indicated as the starting end, which contains ingredients evocative of a soup course. As you eat along the sandwich, the soup ingredients give way to salad, and then to meat, and finally to dessert. Obviously, planning the dishes to compliment one another is important here, even moreso than in a traditional multi-course meal.

2006-12-01

Freezing Water by Fast Hydrostatic Decompression

It's my understanding that freezing water fast enough to prevent crystallization and its negative effects on biological systems is a classical probem in cryobiology and cryonics. A more mundane application is food preservation, where flash-freezing has demonstrable advantages over slow freezing.

It makes sense that water is slow to freeze, because it has such large thermal mass. In a body of water of any appreciable size, the time it takes to conduct heat away from the central regions to the periphery is significant. There are inherent limits to the speed at which heat can be conducted out of a body of water. Freezing water by lowering its temperature is, obviously, limited by the speed at which you can move heat away, and the larger the body of water the slower that speed becomes.

But there's another way to freeze water. Consider the phase diagram for water here. The line from point M to point O represents the boundary between liquid and solid phases, and is either the freezing line or the melting line depending on which side you start from. Water is fairly unique among materials in that this line has a negative slope; among other things, this is an expanation for why ice is less dense than liquid water. For my purpose, please notice that at higher pressures the freezing point of water is lower than at ambient and lower pressures.

I propose to freeze water by first compressing it, so that its freezing point is lowered. Then it is cooled to a temperature below its freezing point at normal pressure. Because the elevated pressure will keep it in liquid form, it does not matter how fast the temperature is lowered, because the phase transition will be held off. Then, once it's cooled to, say, -5C, you rapidly release the hydrostatic pressure and the liquid, now under ambient conditions and well below its freezing point, should solidify very rapidly. Unlike temperature, the hydrostatic pressure of a liquid can be varied essentially instantaneously throughout its volume.

I read now here that this technique is actually in use to freeze food products. I haven't yet discovered if it has been applied to cryobiological problems, however. It's generally referred to as "Pressure Shift Freezing."

2006-11-29

Schlegel Diagrams


These beautiful Lewis structures are essentially 2-dimensional projections of Buckminsterfullerene (C60)--buckyballs flattened out. They represent the same molecule, but from different perspectives, one centered on a hexagonal face and one on a pentagonal face. I just think they're pretty. Might even make nice tattoo motifs, if one were inclined towards ultra-dorky chemistry tattoos. There are other Schlegel diagrams representing the higher fullerenes, but they are not so pretty as these, IMO.

2006-11-27

Fluorohydrofullerenes?

Even educated non-scientists know about fullerenes, the novel allotropes of elemental carbon resembling soccer balls or geodesic domes. C60, a spherical structure containing 60 carbon atoms, is the archetype. Each carbon atom in a classical fullerene is sp2 hybridized, meaning essentially that it is bound to three other atoms arranged more-or-less in a plane with it. A carbon atom is said to be "saturated" if it has four bonds (sp3 hybridization), and any carbon with less than four--like those in fullerene structures--is said to be "unsaturated" because it could, at least in terms of classical valence bond theory, accept at least one more bond. These are the same "saturated" and "unsaturated" that gives us the terms "saturated fat" and "unsaturated fat." The chemistry to take an unsaturated carbon to a saturated one is rudimentary and is practiced every day on vast industrial scales.

So I'm driving along the other day and it occurs to me that fullerenes are unsaturated--they're just carbon. Could we dump them in a reactor with hydrogen and a metal catalyst, just like we do with the vegetable oil that ends up in your oreo cookie filling, and produce the saturated hydrocarbon equivalents of fullerenes? Hydrofullerenes? So I went to the library and, per Hirsch and Brettreich's excellent book Fullerenes, found out that the short answer is "Yes, but not exhaustively." While partially-hydrogenated fullerenes like C60H36 can be produced and are relatively stable, exhaustive hydrogenation has not been achieved and is probably impossible, at least under practical conditions. This is believed to be a consequence of steric crowding on the exterior of the carbon shell; the more positively-charged protons you stick on to it, after a point, the less stable it gets.

The next-most intuitive question, at least for me, is "How about fluoridation?" The realization that flourine atoms can be treated analogously to hydrogen atoms in hydrocarbon chemistry gave us Teflon and the whole modern field of fluorocarbon chemistry. So if we can't make perhydrofullerenes, how about their perfluoro analogs? A sort of "Teflon sphere" idea? Turns out, again per Hirsch and Brettreich, that the answer is "No." Again, while partially-fluorinated fullerenes can be and have been produced, perfluorination turns out to be unfavorable for reasons which are analogous to those which disfavor perhydrogenation. The only difference is a sign change: While the surface of perhydrofullerene is too positively charged to be stable under practical conditions, the surface of perfluorofullerene is too negatively charged to be stable under practical conditions.

So my hare-brained idea is this: Try to fully saturate C60 using a "hetero-fluoro-hydro" strategy, so that the complimentary positive and negative partial charges of protons and fluorine atoms on the sphere's surface stabilize the structure. You could either hydrogenate and then fluoridate, or fluoridate and then hydrogenate. My intuition favors the latter, because while it's known that fluorine will displace hydrogen, the opposite reaction does not occur, to my knowledge.

I'm not an expert in the field by any means but I've done some rudimentary literature searches using phrases like "hydrofluorofullerene," "fluorohydrofullere," etc. and not found any precedent.

As to benefit, who knows? My readings to date indicate that fully saturated fullerenes of any type have been produced only in trace quantities, if at all. It would be a significant achievement to produce saturated fullerene in significant yield. Then you study its properties and start to think applications. If nothing else, being the first to make lots of saturated C60 could be good for one's scientific career.

The point has been made that the fullerenes and fullerene type structures are highly stable. They are even more stable, in fact, than carbon in its adamantane geometry (i.e. diamond), because the sp2 hybridization of the carbon atoms in fullerenes allows for an enormous amount of resonance stabilization when the double bond electrons delocalize through the enormous pi-system. (Which is what makes them conductive.) This is something I glossed over earlier in discussing the energy costs of saturating fullerenes, when I only mentioned steric repulsion at the surface. If you saturate a fullerene, you're also breaking a very large resonance stabilization. This is why, as some have suggested, it appears to be feasible to exhaustively perfluoridate diamond surfaces--adamantane carbon is sp3. But it is not safe to assume that because diamond can be perfluoridated, so can fullerenes, again because diamond is not resonance stabilized and fullerenes are.

The hetero-fluoro-hydro strategy I propose might offset the steric costs of saturation with complimentary electrostatic interactions on the surface, but I don't think it'll help much with the resonance-breaking problem. However, because the studies I've seen suggest that it's really not too hard to at least partially saturate C60, my intuition is that the steric problem is much more significant than the resonance-breaking problem. After all, the first double bond should be the hardest to break, because it will have the most extended resonance and hence the most stabilization. And since they've already made it to C60H36 by conventional hydrogenation techniques, it follows that sterics are the limiting factor, not resonance.

Peroxidation appears to be a workable strategy, c.f. Chemical Physics Letters 384 (2004) 283-287. Tsukuda and co-workers demonstrate convincingly that they can produce C60On with n <= 30 by corona discharge ionization. Again, it hasn't been done in quantity, but Hirsch and Brettreich seem to think it could be. The paper includes a really cool figure showing C60O30. I would also note that traditional "wet" metal catalytic epoxidation has been tried many ways, and they can't seem to get more than 6 oxygen atoms installed.

2006-11-25

An Amarillo Armadillo


Maybe the folks who live in Amarillo, Texas, aren't really so proud of the fact that their city means "yellow" in Spanish. If I were on the city council, however, I think I'd want to embrace the fact, and move to make Arty here the city mascot.

On rumination, however, it occurs to me that there are at least three reasons why such a move is unlikely. I've already mentioned one, which is the association of yellow with cowardice. The second reason, as has been pointed out to me elsewhere, is that an animal that curls into a ball or runs away when threatened only worsens the implications. Finally, there's the fact that public admission of the Spanish origin of the city's name is likely to be unpopular given the present political climate in Texas--especially rural Texas--regarding Mexican influence in American culture.

2006-11-24

GPOV

My girlfriend, like so many of the really smart people I know, is something of an insomniac. It's understood between us that she is free to use my computer, watch my TV, eat out of my kitchen, read my books, and generally make herself at home during her sleepless small hours at my condominium. Often I find endearing bits of evidence of her vigils during the daylight hours--a DVD left in the player, a book out of place, an empty cracker box in the kitchen trash. Last week I woke up one morning and found that she'd left Google Earth open on my desktop. The search queue immediately caught my attention, as the top three entries were "Auschwitz," "Buchenwald," and "Dachau." I had to ask her about this later.
"Why," I put to her, "were you looking at satellite pictures of concentration camps in the middle of the night?"
"Oh," she replied, with complete nonchalance. "I wanted to see what they looked like from God's point of view."

2006-11-20

On The Possibility of a "Heat Pill"

It was suggested on halfbakery.com that a pill could be created that would generate a comfortable heat in a person's gut. These are my thoughts on the subject.

The first problem is going to be finding a reaction that is sufficiently exothermic that the amount of stuff we can pack into a pill will give off the necessary heat. Obviously, the reaction should have no toxic or gaseous products. We might call this the "thermodynamic" part of the problem.

To give an idea of how much heat we need, let's adopt drinking a cup of hot tea as a model system. An 8 oz cup of hot tea at a "comfortable drinking temperature" of 65C contains 8 oz = 237 mL of water at 65 C - 37 C = 28 C above body temperature. The heat required to elevate 237 mL of water by 28 C is (237mL)(28C)(1 cal/CmL) = 6636 calories, or about 7 Kcal.

Dry calcium chloride (CaCl2) gives off about 18 Kcal/mol when dissolved in water. Dividing the required heat by the heat of solution of CaCl2 gives us (7 Kcal)/(18 Kcal/mol) = 0.39 moles of CaCl2 that we must dissolve to give off 7 Kcal. Unfortunately, the molar mass of CaCl2 is 111 g/mol, so 0.39 moles of it weighs 43 grams! With a density for CaCl2 of 2.15 g/mL, we're left with 20 mL of dry salt that we must consume. Even though the solution products are the harmless and physiologically ubiquitous ions Ca2+ and Cl-, the consumption of this much salt is bound to produce a strongly hypertonic solution in the gut, which will almost certainly cause dehydration and diahhrea.

A better candidate is calcium oxide (CaO), also known as quicklime. Although the hydration of calcium oxide is slightly less exothermic than that of calcium chloride at 15.5 Kcal/mol, it also has a significantly lower molar mass of 55 g/mol, meaning we can pack more reactivity into the same mass. It has higher density, too. What's more, besides heat, hydration of calcium oxide produces calcium hydroxide (CaOH2), a medium-strong base that will react exothermically with bile acid (HCl) to give off even more heat, water, and *hydrolyzed* calcium chloride (i.e. we're not going to get any more heat out of CaCl2 at this point).

Assuming that the biggest horse-pill we can swallow is 3 mL, multiplying by CaO's density of 3.35 g/mL gives us about 10g of CaO that we can reasonably ingest in a single pill. 10g CaO is 0.18 moles, so the hydration step alone should produce (0.18 moles)(15.5 Kcal/mol) = 2.8 Kcal. What's more, each mole of Ca(OH)2 is 2-normal in hydroxide, so we end up with 0.36 moles of base. Acid neutralization of hydroxide liberates 13.7 Kcal/mol as a rule, so we can expect an additional (0.36 mol)(13.7 Kcal/mol) = 4.9 Kcal from the acid-base chemistry. Summing contributions from hydration and neutralization of CaO gives us 2.8 Kcal + 4.9 Kcal = 7.7 Kcal given off by our 10g quicklime pill. From a strictly thermodynamic point of view, we could actually afford to make our horse-pill a bit smaller. Incidentally, the hydration of quicklime is, I believe, the same reaction that is used to heat MREs.

So it looks like we've solved the first part of the problem. We've found a reaction with the necessary energy density that is without toxic or gaseous byproducts. We're still basically eating a salt pill and have to contend with the expected consequences of that, but we haven't produced any particular substance that's going to poison us. The problem now is one of kinetics, i.e. it has to do with how fast things happen. The hydration and neutralization of quicklime in the stomach are going to happen lickety-split fast, and so we're essentially going to get all 7 Kcal dumped into the gut over the course of a few seconds. This will probably produce sufficient local heating to generate steam. What we need is a sustained release (SR) formulation for our pill that will prevent all of it from reacting at once.

More insight can be had from our model system. Although I've never tried it myself, my guess is that, while 65C may be a comfortable "sipping" temperature for hot tea, a person who took a whole cup at that temperature and slammed it down his or her throat all at once, which is approximately the same effect our pill would have, wouldn't be very happy or very comfortable. This, of course, is not how people drink hot beverages. It takes minutes to drink a cup of hot tea, during which time it probably cools considerably. To get a realistic idea of how much heat we actually absorb from a cup of hot tea, and how long it takes us to do it, it would be necessary to measure the temperature time-course of a real cup of tea as it is being consumed and integrate to get the area under the curve. This would not be a difficult experiment. Once we knew the absolute heat absorbed from a real hot beverage, we could adjust the absolute energy goal for our pill accordingly. More importantly, once we knew how long it takes to comfortably drink that beverage, we'd know the time-course over which our pill was expected to give off its energy. This information, in turn, would determine the composition of our SR formulation.

SR formulation entails a slowly-dissolving matrix which releases the active ingredient into the gut at a measured rate. This matrix, unfortunately, is going to add mass and volume to an already ungainly pill. Because we don't need a particularly long-lasting SR formulation, however, it's probably possible to keep the volume gain as low as 100%, i.e. we can probably safely assume that SR formulation will no more than double the volume of the pill. If we then half our target heat, so that one pill equals about half-a-cup of tea, we've both solved the pill-size problem and provided a more versatile dosing system: One pill for light warmth, two for full strength, and three for extra strength.

This is an interesting inquiry both because it is fairly easy to model and because it suggests a couple of simple experiments. The first, mentioned above, involves measuring the real heat absorbed by a real body from a real cup of hot tea, and the second, readily implied, is to pack 10g of quicklime into one or more gelcaps, dump them in an unstirred container of 0.1N HCl, and see what happens to the temperature and other observables.

2006-11-14

He of Pants Unsuitable

Several years ago I designed a couple of chess sets, and among the feedback I received there was an e-mail from a gentleman named Ray, who also made chess sets and had, in fact, won some awards for his "themed" chess sets, which included a set made from various makes and sizes of fire hydrants. Ray was an interesting guy; during the course of our correspondence, I learned that he was about 50, that he lived with or near his mother, and that he'd served in Vietnam. He was single, and one of the last times I heard from him he'd taken off around the world to meet a Russian mail-order bride he'd been conversing with via e-mail. He got as far as Paris, as I recall, before chickening out. He sent a long group e-mail to myself and others of his friends describing the journey in lavish and sometimes eccentric detail. As an example of the latter, I recall a confrontation he described between himself and an airline employee at the Denver airport in which he was told that his "pants were not suitable for flying." His e-mail did not include a description of the pants in question, leaving the nature of their unsuitability for us to imagine. The incident is described in passing, as Ray's experience of the Denver airport was simply in passing, but I found the phrase evocative and it has since become one of my favorite idioms: "His pants are not suitable for flying" has, in my mind, approximately the same meaning as "his elevator does not go all the way to the top" and "he's one card short of a full deck." I say "approximately" because, while the latter expressions clearly imply lunacy characteried by deficiency, of one sort or another, "his pants are not suitable for flying" seems to lack this perjorative connotation. One whose pants are not suitable for flying is crazy in an entirely benign way; as long as there are responsible personnel to remind him to change them before boarding an aircraft, no harm can come of him.

A Subtle Kindness

I knew I liked Dr. M_______ the second week I was in the Chemistry department. I was riding the elevator up from the basement. It stopped at the ground floor and a college-age male with some kind of neurodegenerative disease rolled onto the elevator in his wheelchair, together with a woman who was obviously there to assist him. The doors closed, and at the next floor Dr. M_______ got on. The kid in the wheelchair was parked right in front of the buttons. Without missing a beat, and with a slightly impatient tone, Dr. M_______ says "Five, please." "Sure," the kid replies amiably, and reaches out a trembling, scrawny arm and, with some difficulty, presses the button for five. Nobody said anything for the rest of the ride up, but you could feel both the kid and his assistant, who might've been a sister, flush with gratitude. Most people, in that situation, they look at the kid and feel like they can't ask anything of him, so maybe they nod politely and smile awkwardly while they reach around him to press the button for themselves. Dr. M_______ saw, in the second between the time the elevator doors opened and the time he stepped on, how rarely this kid would find himself in a situation--ANY situation--in which HE could be the one helping out, instead of the one asking for help. He saw an opportunity to make the kid feel like a normal person, and he took it, without being patronizing, without trying to politely tippy-toe around the glaring fact of the kid's handicap, and without second-guessing himself. He saw all that, and he did it, and he never once let on that he knew what he was doing. But he did, and everybody on that elevator knew he did, and every one of us, including me, had a brief glimpse of authentic human kindness. From that moment on I knew he was someone I wanted to know better.

2006-11-13

Memphis, Tennessee

Recorded in 1959 and released as the B-side of "Back in the USA," Chuck Berry's song "Memphis, Tennessee" was not an immediate hit in the US, but would creep as high as #6 on the British pop charts in 1960(?). Although diametrically opposed in tone, the song's story foreshadows Berry's 1965 hit "Promised Land" (covered by Elvis in 1973) with its protagonist negotiating a cross-country long-distance phone call with the operator. In "Promised Land," the narrator's tone is jubilant and triumphant, but in "Memphis, Tennessee" it is somber and morose. "Memphis" is the story of a young man returning a long-distance call to a girl named "Marie," who lives in Memphis, "on the south side/high up on a ridge/just a half-a-mile from the Mississippi bridge," with whom the narrator had been emotionally involved, and subsequently separated "because her Mom did not agree." The songs plays with listeners' expectations; based on the typical content of pop songs from that era, most people automatically assume that the narrator is a young man, just starting out in the world, who remembers Marie as an early sweetheart, perhaps from his teenage years, with whom he was forced to part because of her mother's disapproval. The last line of the song, however, turns our expectations on their heads:

"Marie is only six years old. Information, please: try to put me through to her in Memphis, Tennessee."

The song so effectively misleads us that this line commonly horrifies first-time listeners--he was involved with a six-year-old girl? On repeated listening, however, we realize that the idea of a romantic or sexual involvement between the narrator and Marie is never stated, and come to understand that Marie is not the narrator's former sweetheart, but his child. The "Mom" mentioned in the lyrics is not a tyrannical mother-in-law figure, but the narrator's ex-wife, who "tore apart our happy home in Memphis, Tennessee" not by meddling, but by divorcing the narrator and maintaining custody of their daughter, Marie. And so in one line the song gains a tremendous gravity, transmogrifying from an adolescent paen to puppy love (which is what most other pop songs of the era actually were) into a much more serious lament of a much more mature situation. A young man (and he must be young, for how else could his sweetheart's *mother* effectively exert control over their relationship?) who loses a sweetheart is consolable--he has a long life ahead of him and should be able to find another. An older man who has missed the formative early years of his daughter's life due to an acrimonious divorce is not so quick to find solace, and his is a situation that most grown men, regardless of age, could at least relate to (if not actually identify with.)

Coming as it did in 1959, this one key line in this one particular song anticipated, in its affect, the metamorphosis of Rock 'n' Roll itself from children's music to adult fare, a process which would not be well underway until the advent of Cream in the late '60s. That the song was released as a B-side and did not find widespread acceptance until covered by Lonnie Mack in 1963 is perhaps, at least in part, due to the anachronism of its theme. Rock 'n' Roll audiences were younger, then, and not ready for the emotional weight of a subject as serious as divorce and the pangs of fatherhood. With its incestuous blurring of the line between mother and lover, the song, of course, is ripe fodder for Freudian analysis, and especially given the pedophiliac tone of some of Berry's other songs (e.g. "Sweet Little Sixteen") and the sex scandals that rocked his career ("C'mon, baby, just let me pee on you!") the way is clearly open for disappointing moralistic interpretations of "Memphis, Tennessee." Such tawdry readings miss the more profound meanings of the song and of its position in cultural space.

2006-10-16

The Sweet Science

It has been theorized that part of the appeal of boxing is grounded in the homoerotic tension that seems to underly so many hypermasculine behaviors: Two hypervirile men enter the ring and pound on each other until one of them literally cannot continue. Then, if it's been a good fight (i.e. if Tyson wasn't involved), they hug each other and cry like sobbing sisters. That's the real pay-off, getting to show their soft sides and have them appreciated by the world without having to seem like a pair of sissies. All that's required is that they nearly beat each other to death first.

Science has an analogous process. From the very beginnings of scientific education, the objective nature of the discipline--the non-self-ness--is emphasized to all students. The style of written science (the passive voice) is deliberately chosen to eliminate personhood, and is often explained with words to the effect of, "we don't care WHO made the measurement, just that it was made and was such-and-so." For this reason, scientists can be notoriously bad at giving credit where credit is due. It's not that they're all glory-grabbing assholes who want to steal others' work; just that they've spent their adult lives steeped in a culture that doesn't care who made the measurement, only that it was made and that it was such-and-so.

But sometimes, after a long and illustrious career that includes the luck and determination to be associated with a major discovery, an individual scientist achieves the crowning glory of a Nobel prize. At this point--and the culture of science is very clear about this--he or she is suddenly allowed to be a human being again. I have before me a commemorative article in Chemical & Engineering news ("C&E," as it's known in the trades), published as a cover story on the occassion of the one-year anniversary of Nobel laureate Richard Smalley's death. Pp. 14-15 include a gray topbar spread cleverly titled "HUMAN ELEMENT" which, without excusing itself, describes Richard Smalley the person, in emotional terms. Because he spent his life negating his personhood through science, on the occasion of his apotheosis and death it is appropriate that his personhood be emphasized. This is the rational scientist community's chance to revel in the emotions that we spend most of the rest of our time trying to supress, eliminate, and control for.

Maybe science is for man-vs-world what boxing is for man-vs-man; a kind of ultimate theatre of conflict. As in any conflict, premiums are placed on strength, willpower, and determination--on denial of the "baser" urges that lead us to sleep until noon and massage our data and and give up if the math gets too hard. It's as if we acknowledge the certain pathological quality that one needs to achieve greatness as a scientist. We recognize it and acknowledge that it must have great personal costs, but because it is of such great value to society it is nonetheless condoned and encouraged in the young.

2006-09-26

Auspicious File Extensions

I got to wondering whether anyone had been bold enough to adopt .GOD for some proprietary file format. Turns out, according to the folks over at filext.com, there was once an Australian outfit called "Games on Demand" that used .godd to denote something called an "Arena Partial Downloaded Game" file, which is not so very exciting. Note that they opt for the four-letter extension with the extra terminal "D" to avoid potential blasphemy. Games on Demand is apparently no more, so maybe they paid the price anyway. The last few lines of Revelation tend to suggest that the Almighty is pretty touchy about his IP.

Which got me thinking about other provocative three-letter homonyms that might make amusing file extensions. SEX, for instance, has more than one usage: Alpha Software uses it to denote something called an "Alpha five set index," and there's at least one report that some Urban Chaos game files use the carnal extension.

.EAT, interestingly, appears to be unexploited. So, too, .DUG, .LOW, and .YAK. It's kind of an amusing game to brainstorm applications that might use such extensions...

2006-05-10

A Scientist Watches the Evening News

I do not really believe in a cabal of conspirators sitting around a table beneath an eye-and-pyramid in a basement in Geneva any more than Descartes really believed that an Evil Genius had his brain trapped in a jar, but I think Descartes had the right idea in positing this paranoia as the only basis for a truly rational epistemology. We do not assume the worst is true, but we exercise maximum skepticism by imagining the worst and asking, "How do we know it isn't true?" The idea, for instance, that 9/11 was really the work of powerful behind-the-scenes forces who wanted to effect certain changes in the American political system and/or the world economy, and not demonic terrorists, deserves to be examined rationally. Although my personal belief is that things happened more-or-less as the mainstream media has presented them to us, I see that belief as irrelevant to the question of knowledge. I don't know what really happened on 9/11 any more than you do, and it is almost certain that neither of us ever will. We are wise, then, to withhold judgement idefinitely, and especially to avoid making important decisions based on judgements we might otherwise be tempted to make. Politicians are not citizens in a court of law and should be presumed guilty until proven innocent, for the same reasons that a man who stands to lose his life or his freedom as punishment for a crime should benefit from the opposite presumption, and that is, that it is better to err on the side of caution. For me, for now (and probably forever), 9/11 was a tragedy on par with an earthquake, a hurricane, or a tsunami: Certainly we would prefer that it never happened, but there is no one to blame for it but God.

2006-05-04

The Moussaoui Verdict

So I'm completely in a tither about the outcome of the Moussaoui trial. I am on the one hand pleased that they decided not to execute him, and on the other fairly vexed that the whole country--even the judge who sentenced him--seems to regard this as some kind of failure. I'm apalled by the fact that people across the nation seem to be comforting themselves with the thought that he's going to spend the rest of his life in supermax custody, which is by many accounts a fate worse than death. There were jeers in one editorial to the effect of "he'll rot in a cell before he burns in Hell." Shame on all of us.

To cap it off, there have been noises about how he's going to be denied even the 5 monthly non-contact visits afforded to other prisoners in this most extreme manifestation of solitary confinement, although I really don't see how they're going to get that one by the ACLU. The sentencing judge wagged her finger at him and said he would never get to speak publicly again, but that seems incredibly naive to me as I really doubt they're going to be able to hold him completely incommunicado, in which case lines from his letters and/or interviews will (probably sooner rather than later) find their way into various "true crime" and other exploitative books, copies of which will probably end up in the Library of Congress for indefinite historical preservation on the federal dollar. I would also point out to the scolding judge that, although most people in the English-speaking world today know Moussaoui's name, very few of those same people could produce hers if they were offered money to do so.

I really wish the media had paid more attention to exactly what crimes he was convicted of, rather than focusing almost exclusively on the outrageous things he said and did in the courtroom. The impression I get is that he was mostly convicted of vocally supporting Osama bin Laden, the 9/11 attacks, and Islamic jihad in general which, as distasteful as it may be to most of us, is not a crime. Considering that he was actually in federal custody as the 9/11 attacks took place, it would seem that the worst they could possibly get him on would be conspiracy, and although there's a long legal tradition of taking conspiracy very seriously I have had a problem with it since law school. Conspiracy is a charge that's relatively difficult to prove beyond a reasonable doubt (especially when, as in this case, the defendent wants you to believe he was involved) and relatively easy to trump up with courtroom theatrics and propaganda (again, much easier when the accused does his best to help you out). Although the federal prosecutors have produced long lists of Moussaoui's alleged crimes and he was obviously found guilty on some particular charge, we all know, deep down, that his was mostly a show trial. 9/11 happened, the people most directly responsible for it died in the act, Osama bin Laden slipped through our fingers, and the Iraq war proved to be about something else altogether: SOMEBODY STILL OWES US AN EYE! So it's politically expedient to barbecue this guy who's obliquely connected and who, guess what, wants to be a martyr anyway, so why don't we give him his chance?

Well, they had to try somebody for it, right?

Right?

2006-04-26

Resident Evil 4

In 1983, when I was but a tot of eight, a new videogame appeared at the arcade ("Tilt," it was called) in the local shopping mall. This was in the days of the Atari 2600, when the arcade experience was still emphatically superior to that of home-console players. The new game, "Dragon's Lair," offered a radically different approach than other games on the market at the time, which were almost entirely sprite-based. The stand-up cabinet housed an early laserdisc player, and the game featured full-motion animated video, giving it a look which was light years ahead of its competitors like "Centipede" and "Defender." In today's terminology, "Dragons Lair" was all "cut scenes." Gameplay was miserably poor, however: It amounted to moving the joystick in a particular direction at a particular time in the video, thus affecting the "action" of the game and determining which video clip would play next. As in a choose-your-own adventure book, making the wrong choice would lead to death. UNLIKE a choose-your-own-adventure book, there were no instructions; you had to guess, based on what was happening onscreen, which direction to move the joystick and exactly when. The superior graphics (which even now is often the standard by which all videogames are judged, rather than playability) justified its 50-cents-a-game pricetag when ALL the other games were just a quarter. In fact, now that I think about it "Dragon's Lair," may well be the first 50-cent arcade game I ever saw. I played it once or twice but quickly recognized it as a rip-off. Choose-your-own adventure videos, thankfully, did *not* take off in the market, and "Dragon's Lair" was relegated to the domain of historical curiosity.

Until today! The dunderheads at Capcom have included the concept in the latest installment of their highly-successful Resident Evil franchise. On the whole, RE 4 is a pretty good game. The atmosphere is appropriately 'orrifying throughout. Also, the game looks spectacular - better than any other console game I've seen - and the playability of the shoot-em-up stuff is not bad at all. The environment has some good "actions" built into it, which can induce some impressively cinematic spontaneous gameplay. Now, instead of just blasting everything in sight when the "zombies" attack, you can run into an empty building, push a dresser in front of the door, run upstairs, and knock down the ladder that the zombies are using to climb up and get you *while they're climbing.* Then you can toss a grenade down on them and watch the parts splatter. The PlayStation 2 version of the game even supports progressive-scan video, so if you have the right connectors and a good display you can enjoy all this action in high resolution. The various weapons available to the male lead, Leon, are satisfyingly powerful and effective, and there's plenty of the oh-my-god-I-can't-believe-this-new-gun excitement. Plus, once you've played the game all the way through you can go back and play parts of it again as a different (female) character with different weapons and moves, which is a hallmark of the RE series and a clever way to recycle all those environments the designers put so much thought into.

But it's a long way from perfect. The storyline and dialogue are *feeble* to say the least, and although the angry villagers and other beasties that attack you throughout the game aren't technically zombies (they're hosts of mind-controlling parasites), you tend to end up thinking of them as such anyway. It's easy to identify the game's various cultural influences: the parasites look exactly like facehuggers from the "Alien" movies, and the beseiged-in-a-farmhouse-by-zombies motif of the early chapters is clearly evocative of "Night of the Living Dead." The girl, Ashley, whom you're supposedly rescuing and who follows you around all the time, falls in and out of the clutches of the bad guys so many times you rapidly stop caring. The random scruffy vagabond "merchants" that inexplicably inhabit the enemy compound to sell you state-of-the-art weaponry (but no ammunition) during slow spots in the game stretch the credibility of the storyline well past the breaking point (to say nothing of the random "shooting ranges" that you can practice at from time to time). None of the puzzles are in the least bit difficult. The bosses, while requiring a good balance of arcade and puzzle-solving skills, are entirely predictable. If I have to watch one more "nightmarish transformation" of a humanoid badguy into some kind of polytentacled arachnid whose only weak spot is its eyes, I'm going to laugh myself silly.

But the absolute worst part of the game are the random choose-your-own-adventure cut scenes. Those habituated to "resting" during video game cut scenes are in for a rude shock: RE 4 demands that you *closely* watch the action of the cut scenes, because every so often you're faced with a "Press B quick or die!" scenario. No matter how carefully you play during the shoot-'em-up portions of the game, these *BOO!* scenes are almost certain to take you by surprise, the first time, and flush all your hard work down the drain. They're easy to clear when you know when and where they're coming, of course, so including them just seems like a mean way to randomly kill the player his or her first time through the game. It's almost as if somebody at Capcom got annoyed with the thought of people not watching their (insipid) cut scenes, and therefore designed them with built-in pop quizzes. The final jet-ski chase out of the exploding cavern is a particularly annoying instance of this. It's easier to kill the final boss than it is to successfully navigate the caverns on the jet-ski without being killed, which of course breaks the tempo of the game's final moments in a very frustrating way.

Still, I enjoyed RE4 enough to play it all the way through, at least the first time. Faced with the prospect of starting over as the female character, I find myself less than enthusiastic, although I'll probably play the new chapters through anyway so I can see all of her available weapons, which promise to be much cooler than Leon's, at which point my opinion of the game may have to be revised somewhat. I'll let you know. But until then, RE4 gets an emphatic "eh."

2006-03-06

Do-It-Yourself Supercritical Fluid Extraction (DIY SFE)

So I've been fascinated with supercritical fluid extraction ever since the idea was first mentioned by Dr . VandenBout in my general chemistry class some four years ago. For the uninitiated, a supercritical fluid is a substance heated and compressed above its so-called "critical point," which is a coordinate on the pressure-temperature plane above and to the right of which the distinction between liquid and gas becomes meaningless. Theoretically, any substance can be made into a supercritical fluid, but of course some substances have more accessible supercritical domains than others. Carbon dioxide, for example, is the most commonly-used and -studied supercritical fluid because its critical pressure and temperature are accessible with relatively inexpensive apparatus.

The neat thing about supercritical fluids is that their capacity to solvate particular organic molecules can be tuned very selectively by precise adjustments of temperature and pressure. So they make useful solvents for industrial processes. In the case of CO2, an added "green" benefit is that the supercritical solvent is entirely benign, environmentally. Ever since I first learned about supercritical fluid extraction, I've been interested in the possibility of constructing a "garage-scale" supercritical fluid reactor. After doing some light reading on the subject in my old instrumental analysis book, I realized that, if a suitable pressure vessel could be found, performing supercritical fluid extraction of, say, natural products or pharmaceuticals could be readily conducted by the average shmoe in his garage using widely available materials. It is not even necessary to purchase or rent a high-pressure CO2 cylinder, as grocery-store dry ice can serve as the CO2 source, and can be conveniently measured out in the solid phase by weight or even volume. Simple calculations using the ideal gas equation give particular volumes and weights of dry ice to achieve particular pressures at particular temperatures. The dry ice is simply loaded into the pressure vessel, along with the material to be extracted, before sealing. The spreadsheet below gives all necessary physical constants and the results for an 8-quart pressure vessel:

DIY SCF Calculations
PV = nRT

SCP(CO2): 100 bar / 98.69233 atm / 1450.377 psi

SCT(CO2): 40 C / 313.15 K

Ves.Vol.: 8 qt / 7.570824 L

R 8.21E-02 L atm mol-1 K-1

MW(CO2): 44.01 g/mol

d(CO2[s]): 1.6 g cm-3

n=PV/RT

n = 29.08 mol => 1279.7 g => 799.8 mL

The big problem turns out to be the pressure vessel. My first thought was that a high-end kitchen pressure cooker might do the trick. NOT SO. A "high pressure" in the world of pressure cooking is 15 psi overpressure, which is about 2 atm. To access the supercritical fluid domain for CO2 requires nearly 50 times that pressure. A pressure cooker would explode (messily) long before the necessary pressure could be achieved. What's more, that pressure needs to be dynamically maintained. To recover solutes by supercritical fluid extraction, the SCF itself is slowly bled from the reactor and bubbled through an appropriate solvent, e.g. methanol. The CO2 blows off into the atmosphere and the goodies remain behind in solution. The reactor, however, needs to be designed to maintain constant pressure during this slow bleeding of the SCF. On a garage scale, this might be achieved by steadily elevating the vessel's temperature to compensate for bubbled-off SCF, but what effects the temperature ramp may have on substrate solubility are unknown to me. In "professional" SCF reactors, constant pressure is maintained by employing a syringe-type pressure mechanism in which reactor volume is continuously decreased during the extraction. Even if the "temperature ramp" method proposed above proved workable, the development of a useful garage-scale technique would still await the discovery or invention of a suitably accessible pressure vessel.

2006-01-15

Despair

Perhaps 15 minutes ago I awoke from another dream featuring characters and scenes from my adolescence. I was wandering around in the upstairs rooms I enjoyed as a teenager in our house in Richardson, TX, and my longtime-schoolmate Joel Efrussy was there. I was explaining to him in an expert tone my theory of the causal link between certain types of coat-hangers and various disease-states--some types of coathangers could cause anemia, for instance. My tone was sardonical, and Joel understood it to be sardonical, but both of us winked at the joke and played along, he nodding and grunting appreciatively, and I gesturing and expounding dramatically. During the discourse I wandered back and forth between my sitting room and my bathroom, changing clothes, and I definitely remember that at one point I was talking to him with my pants around my ankles, wearing only boxers besides. I was at ease in this condition, but he was not. Before he left he regarded me with concern and asked if I were abusing cocaine, and I assured him that I had not taken cocaine in a very long time. After he left it seemed like a lie, and I had to reassure myself again that, no, I was not abusing cocaine.

Which is the last thing I remember before awaking, again myself at 30. In the foggy transition state that is more waking than sleeping but not very clearly either, I was assailed by a sense of nostalgia for friends and associates from high school--Joel, Lindsey Grayson, Melissa Henry. I could not, at the time, remember Melissa's name, but I did remember catching mononucleosis by kissing her, which led eventually to my two-years-long bout with tonsilitis and associated health problems, and which I mark as the beginning of the depression which characterized most of my 20s and the origin of my taste for prescription painkillers. I began then to think of my mother, and of the fact that, at thirty, I am still the focus of her irrational anxiety, when it materializes, and of the responsibility that devolves upon me in that position. I had again the thought, which assails me in times of despair, that I was living only to protect my mother from the pain of my death, and that--somewhat shamefully I write it--once she were gone I would at last be free to die. Then the mounting pressure of despair was upon me, and I felt panic swell as I lay there in the darkness in the bed with my beloved, and in that moment even she I questioned, and some effort was required not to begin crying.

And I was reminded of a scene from Roman Polanski's film "The Tenant," in which the protagonist, played by Polanski himself, witnesses a similar emotional breakdown in a woman in a cafe who is, to him, essentially a total stranger. She is so far gone that she does not care whether she weeps publicly or not. After looking uncomfortable for a moment, he rises to the occassion, grips her by the arm, and says with appropriate concern, "You must not give in to despair." The sense of the scene (the mise-en-scene, maybe?), however, is that it's a hopeless effort and he is rather naive to try to help her. Still, I was comforted by the memory of the line--"You must not give in to despair"--and I think that is because it both offers practical advice to the desparate and, in its succinctness, in its familiarity, in its ethos, it suggests a commonality of experience which is the best balm for profound suffering: The sense that one is not alone in one's unhappiness. We all know the experience of despair. It is utterly common to the human condition, and the sin is not in feeling it, but in giving up in the face of it. There *is*, of course, a certain reward that comes to those who do give in to despair, but it is a bitter peace, and it is characterized by the kind of eagerness for death that culminates in suicide. Acceptance of death, of course, is a fundamental spiritual milestone, but I do not believe at present that total abnegation of hope is the correct route thereunto.

Which leads me to consider the sensation of despair: What is it? The adjective that first comes to mind, when I free-associate the word "despair," is "overwhelming," and I think if we were to examine the average English sentence containing the word "despair," very often the word "overwhelming" would appear nearby. Despair overwhelms us, in the sense that we feel powerless or hopeless before it. That, indeed, is the essence of despair--the obliteration of hope beneath a crushing wave of guilt, sadness, and anxiety. These emotions are the triple threat of depression: The afflicted person is guilty about the past, sad about the present, and anxious about the future. All three temporal faculties--memory, perception, and imagination--are colored by darkness. This taxonomy is interesting to me, in that, like all taxonomies, it suggests a systematic approach to the problem: To manage despair, we need healthy ways of responding to the past we remember, to the present we perceive, and to the future we imagine.Now, as I write, both the act of writing and the physiochemical transition from sleeping to waking have relieved me--the despair I felt on awakening has evaporated almost completely and I can see the potential of the day. This is a transformation I have to undergo almost every day of my life. Usually on waking (in the morning, at least), I am more or less miserable, and the temptation to retreat back into sleep, rather than face the uphill climb into consciousness, is strong, which is why I frequently sleep so late. If I am somehow obliged to be awake, I will eventually overcome my inertia and find my happy place again, but very often it takes an hour or two to get there. I have a hard time with afternoons, as well. My best times are the dusk-hours from 6 to midnight; this is the time that the earth seems most beautiful to me. This type of daily mood-cycle, again, is characteristic of the clinically depressed, although, like most of the qualities of that disease, almost everyone experiences it to a lesser extent. Thus we have "morning people" and "night people." This observation itself suggests a strategy: I should try to schedule my activities so that I can sleep during the times of day which are most unpleasant to me.

And that's what all this is about, ultimately: strategies. I was terribly afraid when I began this journal that it would be nothing more than an exercise in adolescent "whine-tasting"--a chance for me to come out and pray openly on the streetcorner like the Pharisees. BUt that's not what it is: It's about examining my emotions so I can find intelligent ways of coping with them. Did I make any progress today? I think so. Recognizing that I'm a night person and planning my days accordingly--that is, chiefly to avoid obligations in the afternoon--is a good one. Another useful trick is recognizing the difficulty of mornings for me and trying to plan to ease them: going to bed early, taking measures to ensure comfortable sleep, and doing something I enjoy first thing are all useful strategies in this regard. Also, the breakdown of phenomena into memory/perception/imagination is also a useful starting point--I should begin collecting positive mediations for each mode. I already have one: the guided mindfulness regime promulgated by Jon Kabat-Zinn is exactly a meditative exercise for improving the present. That may be the best place to begin.

2006-01-12

Salutaridine Synthase

Today I met with Dr. Marvin Hackert, a specialist in protein crystallization at the University of Texas at Austin, to discuss my plans to isolate and crystallize an enzyme critical in the biosynthesis of morphine, which I imagine as a step on the way to developing a synthetic or semi-synthetic catalytic preparation for use in the manufacture of morphine. The enzyme, salutaradine synthase, has not previously been crystallized and the purpose of doing so would be to determine its 3D structure, particularly at and around the active site.

My notes from the meeting suggest a two-sided approach to the problem, which might be called top-down and bottom-up. The top-down approach is theoretical; it begins with the enzyme's gene sequence, or that of an isoform, and would approximate the 3D structure by computerized "fitting" of the primary sequence derived from the genome to the known structure of an analogous protein, if one can be found. Although inexact, this approach has the virtue of being inexpensive. It could give useful insight into the structure of the active site and, hence, to the mechanism of catalysis, thus paving the way for the development of an entirely synthetic catalytic system. The program to perform the "morphing" operation in which the sequence is extrapolated to a structure by analogy to a known protein is called SWISS-PDB, and is freely available through the internet.

On the practical side, the approach would be to isolate and purify the enzyme from a homogenous biological sample, crystallize it, and attempt to regenerate its catalytic activity in vitro. It would appear that the 1995 Amann, et. al, paper includes an assay that depends on the catalytic activity of the enzyme to track it through the isolation and purification process. This is something of a revelation, as my previous understanding was that the enzyme was inert apart from its associated cell membrane and that it had not been regenerated in vitro. It's a good sign because it indicates that such regeneration is possible and, moreover, routine enough to be used as an assay. Even if I fail ultimately to determine empirically the protein's structure, development of a reusable catalyst derived from the biological matrix could provide publishable and patentable results. Although this secondary goal does not require elucidation of the enzyme's structure, the effort to crystallize the protein is wasted in the absence of sequence data, because ultimate structural determination depends on both an x-ray diffraction pattern and knowledge of the primary structure.

First questions:

1. What parts of the poppy genome have been sequenced?

2. Is there compelling evidence of the existence of salutaradine synthases in man?

3. Are the seminal investigators still working on this problem and are they willing to talk?

4. How much protein should I reasonably expect to need for the crystallization project?

2006-01-03

A Light-Sensitive Chemical Fuse

My second idea is more trivial and probably doesn't have useful applications--or at least, not any that could not be done more safely and reliably by electronic or electromechanical systems. Briefly, it is a light-sensitive chemical fuse for explosives, and is inspired by the chemical-time-delay fuses used by Allied amphibious saboteurs during the Second World War to set off "Limpet" magnetic mines below the waterlines of enemy ships in port. This fuse, the operation and history of which are explained in great detail on pp. 98-99 of Dorling-Kindersley's "The Ultimate Spy Book," used a mixture of water and acetone to dissolve a celluloid disk restraining a spring-loaded firing pin; when the disk dissolved, the pin was released to mechanically initiate the primer charge. The concentration of acetone in the water-acetone mixture determined the rate of dissolution of the celluloid and, hence, the delay before firing. Fuses were equipped with interchangeable glass ampoules containing various concentrations of acetone and water which had been calibrated to produce various delays ranging from several days to a few hours and identified by color-coding the ampoule glass. An orange ampoule, for instance, produced a delay of 6 to 9 hours, depending on the ambient temperature. The fuses were armed by turning a screw which crushed the ampoule, spilling its contents onto the celluloid disk and beginning the process of dissolution.

My own idea works along the same general principle, but uses a different chemical system to release the firing pin in response to daylight. The charge is placed during the nighttime hours and is armed by removing a cap covering the transparent reaction chamber. When the sun rises, the light enters the exposed reaction chamber and initiates a radical chain-reaction between liquid bromine and a suitable alkane, producing the corresponding haloalkane and, most importantly, hydrobromic acid. The acid dissolves a thin metal disk restraining the firing pin and thus initiates mechanical detonation as in the Limpet mine. Because the reaction is a chain process, the presence of even a small amount of radical initiator, such as that produced by heat-induced homolytic decomposition of molecular bromine, could ultimately cause premature release of the pin. Such an eventuality would render the fuse useless and would be dangerous to the operator. Thus the system must be stabilized by the addition of a few percent of a radical inhibitor such as TEMPO (2,2,6,6-tetramethylpiperidinoxyl). This would prevent "substoichiometric" exposure to light and/or heat from initiating the reaction.

"Tuning" the system to produce the proper combination of substrate alkane, reactant concentrations, and disk metal and thickness would be the object of some applied research. The design criteria are that the system be shelf-stable, heat-resistant, shock-resistant, economical, and fast-acting under the appropriate conditions.

Certainly there are electronic systems already in existence that could serve analogously as a photofuse. Thus some advantage must accrue to the use of an all-chemical system to justify the development expense. The chemical system proposed is fairly straightforward and is derived from a basic reaction found in any respectable sophomore organic chemistry text. For this reason, such a device is relatively obvious and may already have been developed, patented, manufactured, and/or used. Likewise, there may be a more esoteric photosensitive reaction that could be better made to serve the same purpose. I'd have to peruse the patent and academic literature to determine these questions, and given that no compelling demand for the chemicomechanical switch seems to exist, such researches are probably not worth the effort. Lastly, I would point out that, although the device I propose has been described hereinbefore as a fuse for detonating explosives, it could in fact be applied to any single-use photoswitching application; one simply would substitute the firing pin with a spring-loaded electrical switch or mechanical linkage that would activate whatever mechanism.

Back to What I Do Best

Today I put personal, philosohical, and aesthetic/literary speculation aside for a moment to concentrate on my preferred activity, which is invention. And by that I mean invention in the Thomas Edison sense. My friend Billy once told me that he could see me making a living as an old-school bowtie wearing "inventor," and many of my lifescripts involve coming up with some clever new product or process and starting up a company to exploit it commercially. Today I have two ideas that came to me while reviewing my sophomore organic chemistry text in preparation for the Spring qualifying exam in the UT O-chem division.

The first is a computerized reaction-predicting expert system incorporating a large neural-net architecture and trained using the CAS reaction database. One of the foremost marketable skills of an accomplished chemist is his or her ability to make better guesses than most folk about what will happen chemically when particular substances are combined under particular conditions. This ability accrues from long years of experience performing and studying chemical reactions and by the judicious application of analogic reasoning. A neural net is a computer system which imitates in a data structure the connectivity of animal neurons in a brain, and has been proven and applied to be useful--just like a human brain--in many complex pattern-recognition problems. At UT, for example, departmental chemists are working on developing an artificial chemical analysis system that imitates the human system of taste, mostly in that it uses a neural net and must be trained, like a real brain, to recognize certain chemical species by their "flavor." Basically, a large number of colorimetric chemical probes are combined into a single raster image, with each pixel representing the colorimetric response of a particular probe. The neural net "looks" at the complex picture that results and, during the training process, learns to associate particular patterns with particular analytes; subsequently it is able to identify solutions containing the same or similar analytes. Research is ongoing to develop the resolution of the system to a manportable "electronic tongue" that could be used to qualitatively identify all kinds of chemical mixtures in real-world applications. An interesting result of the neural-net pattern recognition process is that IT DOES NOT MATTER EXACTLY WHAT EACH CHEMICAL PROBE IS RESPONDING TO, only that there are a lot of them and that they respond in different ways. Thus the designers, builders, and operators never need to know if the color changes are happening as a result of pH or hydrophobic interactions or enzymatic complexing or any other conceivable chemical process--as long as there are a sufficient number of independently-responding probe channels the resulting patterns can still be diagnostic of particular analytes.

I propose to use the same technology to predict what will happen in a chemical system containing particular substances under particular conditions. The user inputs the chemical species present and the reaction conditions--including pressure and temperature ramps--and the system makes qualitative and quantitative predictions as to the outcome. It does this not by simulation or by theory-based calculations, but by pure neural-net-based pattern recognition based on extensive training from a database of known reactions. Since the introduction of computerized information storage and retrieval in chemistry, the Chemical Abstracts Service (CAS) has been assembling a large electronic database of experimentally-proven reactions; today this database contains tens of millions of known reactions including products, conditions, and yields, all already stored in an electronic format designed to be machine-parsable. So the software I propose would simply build an enormous virtual neural-net on a computer's hard disk (as large and complex a net as can be reasonably constructed given the presen state of the computational art), and then would automatically parse the entire CAS reaction database and use it to train the neural net. Subsequently the system's predictions would be tested against the outcome of real chemical reactions which were not part of the training set. Whether initially successful or not, the system could be designed to automatically familiarize itself with new reactions as the CAS reaction database was updated. Sooner or later in the course of technological history, depending on the rate of development of computational power and on the rate of accumulation of chemical knowledge in the CAS database, the system *will* begin to make practically useful predictions. My own intuition is that both contributing factors are already sufficiently advanced to allow useful predictions to be made given the present-day condition of technology, but of course only actual development and testing of the system will tell for certain. In fact, I would be surprised if such a system is not already in development/operation. If anyone who reads this knows of such an effort, I would love to hear about it.