Below are the 13 most recent journal entries recorded in iamanangelchase's LiveJournal:

Wednesday, May 10th, 2006
3:35 am	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. Current Mood: pensive (Comment on this)
Monday, May 8th, 2006
6:09 pm	The Military-Industrial-Entertainment-Internet Dating Complex So Yahoo's just reconfigured the look of their home page. Which is fine. What's annoying me is that their hyper-brilliant pinpoint-accuracy laser-guided marketing software has noticed, somehow, that I was cruising their "personals" section, once, for a few minutes, several days ago. Now, as if they were a porn site that somehow managed to track down my e-mail address, I will never hear the end of it. Their software remembers my search parameters and sends me unsolicited daily e-mail "updates" of new potential matches. On top of that, instead of intresting economic and/or geopolitical news, the "featured headlines" on my version of the Yahoo home page have become articles like "Prenups," "20 Questions for When the Honeymoon is Over," and "Dating Red Flags." In a moment of weakness, I clicked on the banner for this last one, and was rewarded with this tripe, by one Michael Shnayerson who, besides being an editor at Vanity Fair has recently shat a book called "The Killers Within: The Deadly Rise of Drug-Resistant Bacteria." Now, as far as I can tell, being an editor at Vanity Fair does not qualify one as an authority on anything, except perhaps the purchasing habits of trendy rich assholes in New York. Not to worry, however: Before bestowing his ageless wisdom on dating dos and don'ts, Shnayerson establishes his ethos by boasting of "three decades of romantic misadventures." Now, throughout his article, Shnayerson assumes the tone of a respectable middle-aged man who's looking for a strong, healthy, lasting relationship and has somehow been consistenly star-crossed in his efforts to achieve same. He skirts the obvious question, however, which is: If you're such a catch, why have you been playing the field for 30 years? Of course, those who would question the author's right to make "objective" judgements about people should remember that he works in the fashion industry. For Vanity Fair, no less. Which is in New York. End of story. So those of you who were at a loss about where to go for dating advice after "Seinfeld" got cancelled, listen up: Dating Red Flags: The Dirty Dozen Chronic lateness Ketchup on eggs Rudeness to service personnel Scary divorce stories A deep attachment to disturbing pets Tendency to prefer "flings" Demon children Men who want to split the check on the first date People with strong emotions-either positive or negative-about their parents Bad sex Dirty underwear and/or socks An undercurrent of anger So, chronic lateness and rudeness to waitrons are certainly understandable complaints, as are "flinginess" (if misrepresented as steadfastness) and the bundling of terribly-behaved children into the package deal. But putting ketchup on the eggs? Liking wierd pets? Dirty socks? WTF? (Comment on this)
Thursday, May 4th, 2006
11:44 am	The Moussaoui Trial 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 always 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? Current Mood: annoyed (Comment on this)
Wednesday, April 26th, 2006
7:07 pm	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." Current Mood: grumpy Current Music: None (Comment on this)
Monday, April 3rd, 2006
6:36 pm	Garage Separations So it's an open secret that my initial interest in chemistry, 5 or more years ago, was spurred by psychedelic drugs. At the time, I was interested in them, and particularly interested in making them myself. My goal was not profit, but to experience personally some of the more exotic substances that were unlikely to be available on the black market. I have never considered selling, as I consider eventual legal trouble more or less inevitable once one begins supplying, to say nothing of the potential ethical problems associated with facilitating dependence and/or possibly creating an unsafe product. So I read a lot, back then, about how garage chemists worked to make illegal drugs "under the radar," as it were, and even though I never attempted any of it myself, I was always fascinated at the intellectual challenge of doing relatively sophisticated chemistry using crude materials and apparatus. The classic garage synth is the conversion of ephedrine or pseudoephedrine into methamphetamine, which structurally is a simply matter of removing the hydroxyl group at the alpha position. The chemistry is incredibly straightforward; the biggest problem is getting hold of the precursours. The common source for ephedrine and/or pseudoephedrine (which are equivalent precursors to methamphetamine, as they differ only in the stereochemistry of the hydroxy group which is removed) has traditionally been over-the-counter (OTC) medication such as Sudafed (TM). Ephedrine salt used to be available in "trucker speed" products such as "Mini-Thins" and in various "nutritional supplements" and diet pills, but a fairly recent decision by the FDA has banned the sale of ephedrine in any commercial pharmaceutical preparation, and there is no other appreciable legitimate use for it. So ChemHacks are left with Sudafed or generic equivalents thereof, and the essential problem in the illilcit manufacture of methamphetamine reduces to the separation of the precursor (pseudoephedrine) from the rest of the stuff in the pill itself. The problem is complemented by the manufacturer's positive efforts to make the active ingredient difficult to separate. So-called pill "denaturants" are present in essentially all OTC pseudoephedrine-containing products these days; these typically take the form of cellulose derivatives which make separation of the active ingredient by solvent extraction essentially impossible due to their tendency to polymerize and bind the active compound into a spongy mass of insoluble inactive crap. The way professional chemists separate complex mixtures (on a scale suitable for bulk preparation, rather than the very small scale needed for analysis) is column chromatography. There are many variants of column chromatography, but the most common laboratory benchtop method is so-called "flash" chromatography, in which solvent is pushed through the column by the pressure of compressed gas. Gravity-pressure chromatography is certainly possible, but it is mind-numbingly slow compared to vacuum- and/or pressure-assisted variants. As anyone who's ever done flash chromatography knows, it is at least as much art as science. With experience high-resolution separations become a matter of routine, but the required equipment is conspicuous and the necessary solvent volumes are expensive and inconvenient. Until recently, however, it seemed like the only way to go, and the part of my brain that is constantly turning these sorts of problems over was trying to think of ways to prepare a flash chromatography setup on a garage scale using only OTC, hardware-store type materials. Recently, however, I discovered that an alternative to flash chromatography does exist. It's called "dry column chromatography," and as far as I have been able to discern it is superior to flash chromatography in almost every way, except perhaps in the achievable resolution of the separation. For garage purposes, however, the affiliated pay-offs in terms of equipment accessibility and solvent costs are well worth it. No doubt some experience will be required to achieve repeatable and reliable separations, but experimentation is easily afforded when the operational cost is low. (Comment on this)
Monday, March 6th, 2006
9:17 am	Do-it-yourself supercritical fluid extraction 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 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. (1 Comment |Comment on this)
Sunday, January 15th, 2006
4:52 am	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. (1 Comment |Comment on this)
Thursday, January 12th, 2006
12:07 pm	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? (Comment on this)
Tuesday, January 3rd, 2006
3:06 pm	Back to What I Do Best - Part II 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. (Comment on this)
3:04 pm	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. (Comment on this)
Friday, December 30th, 2005
4:32 pm	The Walking Dead Vol. 4 - FAIR WARNING: MANY SPOILERS WITHIN So I've been reading this comic book, _The_Walking_Dead_, by Robert Kirkman, Charlie Adlard, and Cliff Rathburn. The geist of the narrative is the realistic dramatic depiction of the lives and loves of a group of survivors of a zombie apocalypse. It is gritty in its realism and generally (surprise) very depressing. The protagonist is white-boy small-town-hero cop Rick, who is shot in the line of duty, falls into a coma, and wakes up alone in the hospital a month after Z-day. He sets out for Atlanta, hoping against hope that his wife and child have survived and are in hiding there. Miraculously, he finds them, intact and in the care of his partner and best friend, among a group of survivors camped outside of the city awaiting government rescue. In his absence and based on the presumption of his death, Rick's partner has begun to move in on Rick's wife, and Rick's unexpected return initiates a power struggle between the two friends that culminates in the breakdown of the partner and, ultimately, in his death in a defensive shooting by Rick's young son. The remaining survivors take Rick as their leader and, realizing that no one is coming to rescue them, set out across the countryside in search of a safer place to live. They have several false starts and lose many of their party in heart-wrenching ways before happening upon a maximum-security prison, which they all recognize immediately as an ideal survivalist encampment, assuming they can clear the zombies out frist. In the process of doing so, they discover four surviving prisoners holed-up in the cafeteria: Dexter, a big scary black guy who killed his cheating girlfriend and her lover; Axel, a big scary white guy who looks a little like a Hell's Angels Santa Claus; a forgettable-by-design skinny black ex-junkie who is Dexter's punk lover; and, lastly, a wimpy bespectacled nonthreatening balding middle-age white guy who admits conviction for "tax fraud." The outsiders join forces with the prisoners and secure the rest of the prison for safe habitation. Things seem to be going well until one of our favorite female characters turns up decapitated. Immediately suspecting the convicted murderer, Rick and his party lock Dexter up again in his old cell. Two little girls are decaptiated and another woman mutilated before the killer is revealed, somewhat predictably, as the nonthreatening "tax" criminal. The murders raise an archetypal problem in survivalist fiction, viz. the re-establishment of law and order. Rick steps to the fore and, like Moses, declares the new law: "You kill, you die." The killer is thrown to the zombies outside the prison gate. Meanwhile, with the assistance of his lover, the embittered Dexter breaks out of his cell and into the heretofor-sealed-off "A block" of the prison, where he raids the armory. Brandishing a shotgun, he corners Rick and his party by the gate and demands: leave the prison or die. Unfortunately, Dexter and his lover forgot to close the A-block door behind them when they left, and the standoff is interrupted by the flood of hungry zombies they unwittingly released. The ensuing battle pits all the survivors--Dexter and his lover included--against the walking dead. During the course of the firefight, a zombie ambushes Dexter from behind and Rick--perhaps acting reflexively--shoots it in the brain, thus saving Dexter's life. Dexter glares at him and says "Don't mean shit. That don't change a fucking thing. Smart man woulda let it get me." Upon which Rick, after thinking it over for a second, calmly shoots Dexter through the head. Subsequently, he blames Dexter’s death on anonymous and accidental "friendly fire" during the pitched battle with the zombies. This decision on Rick's part, to kill Dexter in more-or-less cold blood, eventually precipitates a moral crisis amongst the survivors and, by proxy, amongst the book's real-world readership. As a result of it, Rick is demoted from his position as sole leader and a voting council of four men (on which Rick himself has a seat) installed in his place. Rick is not upset by the demotion, but is, rather, by the judgment against his character which devolves from his killing of Dexter. Which is really what I went through all of that to discuss. Although clearly in contradiction to Rick's rather simple-minded you-kill-you-die edict, my own emotional reaction to Rick's decision is that it was prudent, both from the point of view of personal self-defense and, especially, from the special position of authority and responsibility which is Rick's as designated leader of the group. Dexter's attitude, words, and actions clearly indicated that he regarded and would continue to regard Rick and his party as enemies, and that as soon as the immediate threat of zombie attack was met, his assault on Rick, Rick's family, and the group under Rick's protection would be renewed. Given the life-or-death consequences of expulsion from the prison, Rick's decision is clearly justified. His biggest mistake is trying to cover it up by blaming the killing on "friendly fire," which he justifies later by claiming he did not want so openly to contradict his own edict and thus potentially undermine the group's faith in him as a leader. This, of course, is the ultimate result anyway, but it might not have been--indeed, I would argue, it SHOULD not have been--if Rick had come clean about the killing at the time. His first and most fundamental mistake was to establish a homicide law with no provision for justified self-defense, which the killing of Dexter rather clearly constitutes. If the incident in which Dexter scorns Rick’s saving of his life had not taken place, the issue would not be so clear-cut. In shooting the zombie threatening Dexter, Rick has diverted his attention, his efforts, and his ammunition from the defense of himself and his allies. Things being as they are, he would have been perfectly justified in not doing so; even Dexter himself acknowledges this. That he does so in spite of their prevailing conflict is evidence of the goodness of his character—-he still hopes that Dexter’s relationship to the group can be repaired and, perhaps, believes that life in and of itself is worth saving. Dexter’s ingratitude at the gesture is infuriating in its vulgarity and its stupidity; smart man, we are tempted to chastise him, woulda kept his mouth shut. From a legalistic perspective, moreover, it provides all the evidence Rick needs that Dexter is a continued threat and should be eliminated as a matter of rational self-defense. This is the important point: Dexter’s statement is evidence of his ongoing hostile intent. So offensive is Dexter’s ingratitude, in fact, that in itself it might seem grounds for Rick’s action. It is tempting, along this line, to argue that Rick’s saving of Dexter’s life entitles him, for at least a short of period of time, to renege on that decision and end it. This is in keeping with the tradition, in many cultures, that a person whose life is saved by another is thereby indentured to that person, in a sense, and is obliged to serve his or her savior until death or the return of the favor. Consider the following twist on the situation: Dexter is in the act of staging a public suicide, with a gun to his own head, when the zombie attack breaks out. Rick then saves his life exactly as before, and Dexter responds, again ungratefully, weeping, “Shoulda let it get me, man. Shoulda let it get me.” Would Rick then be justified in killing him? Most folks, I think, would say “no.” Therefore we reject the notion of a special “license to kill” that devolves upon Rick on his saving of Drexel’s life, and likewise of the “aesthetic” argument that Drexel’s ingratitude itself justifies the homicide. But, given that the killing-as-told is clearly justifiable, why is Rick judged? Certainly he made mistakes, as mentioned above: He established an overly-simplistic law and then tried to cover up his own violation thereof. But overall his actions were entirely well-intentioned if not, perhaps, as well-thought-out as they might be. Rick is a cop, after all, not a lawyer or an intellectual. Why then does Tyreese, in particular, hold him to blame for Dexter’s killing? The answer, in keeping with the general direction that many of the book’s subplots are moving, is racism. Tyreese, a strong black man who, up to this point in the story, has been Rick’s best friend, made a brief living as a pro football player before Z-day. Although, by his own admission, he was not very good and did not last very long in the pro league, he made enough money during his brief stint to establish a comfortable middle-class living for himself and his daughter, who, in one of many tragic subplots, dies in a suicide pact with her white boyfriend early on in the story. Tyreese understands, in a way that Rick probably never can, the anger Dexter must’ve felt at being wrongly imprisoned for a crazy white man’s crimes, and surely he must wonder, if Dexter had been white, would Rick still have pulled the trigger? Dexter, as I’ve already hinted at, was (probably deliberately) drawn by the book’s authors as the prototypical white suburbanite’s nightmare nigger: physically powerful, none too bright, extremely angry, and prone to violence. Although Rick, unlike some of the book’s other characters, is not consciously racist, he is a white police officer from a small town in Georgia, and the other survivors-—who were probably not privy to the brief dialogue that precipitated the killing—-must surely wonder to what extent Rick’s subconscious fears might’ve motivated the shooting. Rick’s hypocrisy in the application of his own moral code, by which he himself should be killed for killing Dexter, also invites racist suspicions when compared to the treatment of the “tax criminal.” Although their crimes are not really comparable, the code that justified the execution of the murderer clearly justifies Rick’s own execution, and the fact that such reciprocation isn’t even briefly considered by any of the parties concerned seems to suggest that, while killing a white woman will get you thrown to the zombies, killing a black man elicits little more than a slap on the wrist. It’s somewhat of a manufactured crisis that can be dispelled with a bit of rational thinking, but as any reader of the book must understand, people, and these characters in particular, aren’t always rational people. Clearly, a storm of racial tension is coming in book 5. Whew. That was a lot of high-minded speculation over a comic book, but it felt good to do it. Although I was somewhat disappointed with the 4th and most recent volume of The Walking Dead, the fact that it elicited so much moral speculation on my part indicates that it’s still an effective and engaging story. My disappointment on finishing the 4th volume was really the disappointment of a junkie who, having waited three months to score, finds that he has not bought enough dope to satisfy his craving. The storyline of TWD is incredibly engrossing, and, because of the nature of the comics medium, it can be consumed orders of magnitude faster than it can be produced. Although it’s an ideal situation in terms of sales and marketing, it’s not really enjoyable, as a reader, to be constantly strung out. I have the option, of course, of buying the individual monthly issues instead of the bound quarterly volumes, but that is somewhat of an affront to my compulsive side, which wants my entire TWD collection to be in a consistent format. Maybe I’ll buy the monthly issues and then sell them back when the quarterly volumes come out, if I can find a place that will buy them from me. If you managed to stick with me through all that, all I can say is “Thanks.” :) If you feel inclined, you might do me (and yourself) a favor: go out and buy or borrow the series, read it for yourself, and let me know what you think. John Gardner has called fiction the art of “concrete philosophy;” if that’s so, then arguing about books and their meanings is one of the best things we can do to better ourselves as philosophers. (Comment on this)
Thursday, December 22nd, 2005
8:22 pm	Opting Out Christmas is a hard time to think about opting out of consumer society. Or maybe not. In one sense, it's hard because all around people are buying stuff and receiving gifts and generally wrapped up in the material posessions that make them happy. So envy, of both posessions and people, can make it hard. On the other hand, wanton commercialization around the holiday season has gotten so bad that even the most jaded yuppies probably notice it. So our moral and aesthetic judgements of the season's excesses can make it easier to consider alternatives. The most important thing I've done to "opt out" of the society of desire is stop watching television. On the one hand, this has improved my life because I do not, in general, suffer from cravings for the latest video games or movies or cars or books or other widgets. Also, I am freed from the paranoid atmosphere which television advertisers, journalists, and dramatists foster each for their respective purposes. The down side is that I also feel, at times, very alone, very excluded from the collective consciousness of the species which, let's face it, is centered squarely on the boob tube. The internet can help a lot in this latter regard; if I would use it more dilligently than I do now it would be relatively easy to substitute an online virtual community for the virtual community I lost when I turned away from TV. And the online community is superior to the television community in many ways. For one, it listens when I talk back to it. Another thing I've done to opt out of consumer society, deliberately or accidentally, is to surround myself with intelligent people who don't care overmuch about such things. Austin, TX, is a good place to be interested in nonconsensus reality, because despite the best efforts of the Starbuckses and Piers 1 of the world, Austin is still wierd. And austin will probably always be weird, to a greater or lesser extent, because of the concentration of educated intellectuals from all over the state at the University of Texas. The state and the school are some of the largest in the nation, and Austin tends to function as a refuge for bright young folks from the ignorant backwoods hellholes they were raised in. I would not go so far to say that rural life is inherently bad, but there's no question that people in big cities tend to be better educated and better paid. Austin, in particular, is often touted as the most educated city in the world on a per-capita basis. Even the cable guy's got an MA in something or other. And the most essential process of education is to make people tolerant of others' viewpoints. What's more, I'm situated close enough to the University where I work and learn that I don't have to use my car very often. In point of fact, it would be fairly easy for me to do without a car entirely in my present situation; groceries, entertainment, food, work, and education are all within a few blocks' walking distance of my front door. College campuses tend to be some of the greatest pedestrian communities in the world, and UT's, being so large and so old, is a fairly stellar example. I've got a friend who's been living in west campus for years without a car, caring for his sick mother, walking everywhere and working out of a small apartment priced for and targetted at the student market. The *dis*advantage of this location is that the real estate is expensive, and thus that the population tends to be wealthy rich-kid and frat-brother types. So from a keeping-up-with-the-neighbors perspective, it can be hard to adopt an openly anti-materialist lifestyle. Still, all and all, I'm not doing too badly. I make $1600 a month and it's more than enough for me; in fact I'm inadvertently saving up quite a bundle while I'm in school. By the time I graduate I will probably be able to put a down-payment on a house. What I need to be doing right now is paying more attention to my living space; it needs to be cleaned and redecorated to be really comfortable, and up to now I really haven't had the emotional energy or the time to do these things since, barring spending a lot of money, they entail a lot of work. Hopefully over the winter break I'll have time to get some of that done. So what did I resolve? First, to put more effort into developing and maintaining an on-line community that I can feel a part of as a TV-replacement. Second, to pay more attention to the upkeep of my pad, so that it's a pleasant place to be both by myself and with company. (1 Comment |Comment on this)
Wednesday, December 21st, 2005
10:51 am	Journal-keeping I've defiled so many virgin journals in my life; I can never commit. I can be pretty good about keeping a journal when my life's in the crapper, but as soon as things turn around (which writing itself tends to induce) I lose interest and go back to fiddling with LEGOs or something. And that's no way to maintain a relationship. Now, when I say "my life's in the crapper," what I really mean is "I'm depressed." From an objective point of view, my life is categorically *not* in the crapper. I have a beautiful girlfriend and a spacious condo within walking distance of the university where I am a successful graduate student in synthetic chemistry. I get along great with my happily-married-after-thirty-years parents and I see them once or twice a week. The stipend I get from the university is more than enough to live comfortably on. And yet my baseline happiness level is low; so low, in fact, that I am often tempted to the use of pseudolegal drugs to elevate my mood. It's a pervasive phenomenon, now and probably always in American (and possibly general human) society: The person who has all the secular trappings of a happy life and yet is still fairly *un*happy on a day-to-day basis. A lot of people--my parents, for instance--would tell me that what's missing in my life is spirituality, and to a point I think I'm inclined to agree. This is a touchy subject for me, however; my break with the Church of Christ as a teenager was acrimonious and I am still bitter about it. I believe the essential tenets of Christian dogma are irrational and readily corrupted to justify all kinds of horrific actions and attitudes. What's more, by the time it's watered down enough that I can stomach it, it's become as limp and flavorless as unitarianism. I personally think the whole enterprise should be scrapped and our attitudes reconfigured along the lines of the Dalai Lama's teachings, the gist of which, as I understand them, is: Compassion for the sufferings of others is the only lasting way to ease one's own, personal, suffering. This is a philosophical judo-throw in the spirit of Adam Smith--the selflessness of selfishness. The analogy to laissez-faire economics is not hard to make. "By serving one's own interest, one ultimately serves the communal interest." Some folks, I suppose, would be offended by that analogy. But I think it's accurate, to a point. The difference is that Smith's and the Dalai Lama's arguments are opposed in their causalities: Smith starts by asking "What makes for a happy society?" and answers "Selfish people"; the Dalai Lama starts by asking "What makes for a happy person?" and answers "Selfless concern for society." This is a vast simplification of both arguments, of course, and it may not be possible to draw any really meaningful conclusions from it. We should not, for instance, give in to the superficial temptation to say that capitalism is thus incompatible with personal happiness as the Dalai Lama sees it. Or should we? There's no doubt whatsoever that consumer society is bad for personal happiness, or at least that a philosophy which is grounded too strongly in materialism is bad for personal happiness. And it seems clear that when the monetary powers-that-be pursue their own rational self-interest in the spirit of Smith what results is a consumer society filled with advertisements and meaningless schlock to be bought and sold. And to make such a large market for so much stuff that people really don't need one has to generate a culture of consumption in which people feel inadequate without late models cars, appliances, homes, etc. Desire, the Buddhists say, is the origin of suffering. Thus, isn't a culture that feeds on material desire really a culture that feeds on human suffering? I think just maybe it is. So how do I opt out? Therein lies the rub. (Comment on this)