Hexanol Fermentation

Breed yeasts to produce hexanol, rather than ethanol

In conventional fermentation, yeasts turn sugars into ethanol. Ethanol, as everyone knows, is promising as an alternative fuel. The problem is that yeasts die at concentrations higher than about 10% ethanol by weight, and so the fermentation process can at best produce alcohol that is 90% water. Obviously, this “beer” cannot be burned as fuel, and the excess water must be removed somehow, by distillation or adsorbtion, which adds a significant energy cost to each unit alcohol produced. At the earth’s equator, solar energy can be relied upon to make up this energy cost. At the more extreme latitudes, that’s not necessarily the case.

Ethanol is not the only alcohol produced in fermentation. Higher alcohols such as butyl, amyl, isoamyl, and 1-hexyl are also produced, albeit in trace concentrations. As a fuel alcohol, 1-hexanol has a lot going for it compared to ethanol. Firstly, it’s much “greasier” than ethanol, having a thrice-longer hydrocarbon tail, and thus will handle and burn much more like the hydrocarbon fuels we’re already using. Second and most importantly, however, unlike ethanol, 1-hexanol is *not* infinitely soluble in water, meaning that at some concentration the fuel and the water will simply phase-separate. Now, instead of having to spend energy to dry the alcohol, you just tap it straight out of the bioreactor at burnable concentrations.

The only reason we’re not doing this already is that (known) yeasts don’t produce useful concentrations of 1-hexanol. But because they’re microorganisms and they reproduce rapidly and in huge numbers it’s not inconceivable that they could be bred to do so. What’s needed is a rapid, colorimetric, quantitative assay for hexanol concentration so that thousands of individual yeast cultures can be rapidly screened in high-throughput equipment like plate readers. Without such an assay, chromatography of some sort is required, slowing the process of screening down by many orders of magnitude. With the right indicator, though, it would be possible to screen yeast cultures almost as fast as they could be selected and grown. A rate of 10000 generations per year is entirely reasonable. Note that 10000 generations is approximately the same “distance” that separates homo sapiens from neanderthals.

The Passing of Two Trees

Yesterday I’m walking home from school and I look up to see some strange guy in a hard hat at the far end of the block waving at me with his arm. I look around for a minute and see that there’s some kind of construction going on and I realize he wants me to cross to the other side of the street. So I do. But it miffs me a bit, because I dislike it when anyone assumes authority over me that’s not clearly theirs.

As I get near my condo, at 2529 Rio Grande, I realize what’s going on: They’re knocking down trees, and not little ones either. Just inside the stone wall which is all that remains of the seedy block of furnished apartments that used to occupy the lot immediately north of my building, stood these two proud 40-ft. oak trees, just to either side of the main gate. I don’t know how old they might have been, but I bet they predated the complex that was demolished around them. The workers have to clear the sidewalks because the branches are large and heavy and overhang them to some extent.

Now, I don’t know if it was because I was already a bit grumpy with these guys, or solely because I was offended at the casual destruction of the beautiful old trees in my neighborhood, but I decided I was going to make a hard time for these workers, if possible, and in the best situation maybe stop them from killing the trees. I’m not such a radical (or maybe brave) person as to strap myself to one of the trunks, and it didn’t really look like there would be time to make it to the hardware store and buy chain and a padlock for that purpose before they were finished, anyway.

So I did the only thing I knew to do, which was call the city. I know Austin has fairly tough municipal regulations regarding the felling of trees inside the city limits. I thought maybe I could at least verify that they had a permit to cut down these trees and get them stopped or at least fined if they didn’t. The woman who answered the city information line was confused by my request at first: “There’s a tree you want to cut down?” she said. “No,” I explained, “I’m concerned that I’m witnessing the illegal felling of a protected tree.” There was a pause, and then she said, “Hold on, I’ll have to ask about that one.” So I get the hold muzak, which is an impossibly banal counterpoint to the scene of arboreal slaughter outside my window. While I’m waiting on hold, the destruction of the first tree is completed and the excavator starts filling in the hole left by the torn-out roots.

Eventually the woman returns to the phone, and it’s clear that she now understands and appreciates my situation. “You need to speak to the City Arborist,” she tells me, and gives his name (which I never figured out how to spell, and hence will not include here), and his number, which is 512-974-1876. “I’m sorry it took so long for me to figure that out,” she says. I tell her it’s OK, and she thanks me for calling. It’s obvious at this point that she’s on my side.

I call the Arborist and get his answering machine. The excavator is now rumbling toward the second tree. I leave a rambling message about who and where I am and how they sure are beautiful trees and I just wanna make sure the workers are within their legal rights cutting them down. I am conflicted. A large part of me wants to go down and confront the workers, but I realize that will only make them defensive and will not stop them from doing what they’re doing. I pace back and forth for awhile and figure the only thing to do is take pictures so I can make sure they get punished if it turns out they’re breaking the law. So I snap a frame or two and turn back to the computer to work.

There’s a loud CRACK a minute or two later and I go back to the window and see that the excavator has broken a large limb off the second tree. About then the phone rings, and it’s the arborist, who, to my pleasure, sounds concerned and gets right to the point: “Tell me what you’re seeing,” he says. And I do. As I’m talking, the excavator repositions itself and strikes downward into the tree’s crotch, splitting the trunk, and I realize that there’s no stopping them at this point. I tell the arborist as much. “But I took pictures,” I explain, “in case it turns out that what they’ve done is illegal.”

“Where are you again?” he asks. “West Campus,” I tell him. “Do you know the neighborhood?” He doesn’t. “Do you have an address?” Apparently he’s got a database of some sort that lists permit-holders. I don’t know the exact address, but I can extrapolate from mine and take a guess: “Try 2601.” A minute later he comes back and says, “Yes, there’s a permit to develop that property,” which I understand from his disappointed tone to mean that there’s nothing to be done. Apparently the rule in Austin is that private homeowners need a permit to fell any tree with a diameter of 19 inches or greater, but that developers have more flexibility. The arborist can’t tell me what the specific site plan calls for with respect to these particular trees, but he can tell me that there is a plan and it’s been approved, so in all likelihood these guys are acting in accordance with it and hence within the bounds of law. I thank him and he thanks me, and before we hang up he asks me to call again any time I’m suspicious of tree-related crime, because his office depends almost completely on concerned citizens/nosy neighbors like me to catch and prevent the illegal destruction of trees. I assure him that I will.

And that’s where the story peters out. I wanted to do something but I didn’t, basically, and although I got some sympathetic voices on the phone none of it changes the basic fact of the matter, which is that there are now two muddy holes in the ground where there were once two live, beautiful, healthy trees. And I stood to one side and watched as a man with a machine tore them up. Should I have tried, physically, to intervene? Should I have obeyed that impulse to chain myself to the trunk? I don’t know the spirit of a tree, but I know how hard it was to watch them be destroyed. It was like a crime was happening out on the street, in broad daylight, and everyone was just walking by indifferently. I didn’t want to be the apathetic one; I wanted to be the one who gave a shit. But I tried to be a civilized adult about the whole thing and now I regret it. Even if I hadn’t, ultimately, saved those particular trees, a show of strength might’ve brought some attention to the subject, might’ve made the developers or the city authorities or whoever think twice the next time they decided to hire out that kind of a dirty job. But in the end I was just like everyone else: Too busy with my own concerns to take hours out of my day to worry about something as simple as the killing of a tree.

The Abuse of Fire in Warfare

What follows is in response to an article on the use of white phosphorus (WP) by US marines during the siege of Fallujah that appeared in the North County Times.

As a chemist, I find the debate about WP as a “chemical weapon” sort of amusing. One might as well claim that we’re engaged in “chemical warfare” because the lead we use to make bullets is toxic.

It’s like that question they ask me sometimes at the post office: “Does your package contain any chemicals?” Well, OF COURSE IT DOES, because the universe is made of chemicals and if there’s any damn thing at all in the package, there’s chemicals in it. In that sense, any weapon that EXISTS is a “chemical weapon,” and the word becomes totally useless. The chemistry of WP is simply oxidation/combustion, which is the same chemistry that propels bullets and shells down gun barrels and causes fire in general, and the use of fire in warfare is as old as warfare itself. It just so happens that WP burns very hot and is self-igniting in air.

If “chemical weapons” is to remain a useable term, it’s best reserved for toxic compounds which are employed primarily to exploit their toxicology.

That being said, it seems likely to me that in the future, as war continues to be “humanized,” we will begin to see moral and eventually legal proscription of the use of burning as a means of offensive war. Destruction of uninhabited materiel or facilities is one thing, but the deliberate destruction of live human beings by combustion is pretty appalling. Think of the little Vietnamese napalm girl, or the fire-bombing of Dresden or Tokyo, or of the use of the flamethrower in trench warfare. Burning is agonizing, indiscriminate, and not terribly efficient versus shooting or blasting to bits. Burning is a frightening way to die (or, perhaps worse, to not die), and for this reason it is frequently employed as a psychological weapon.

I’m not necessarily advocating its regulation, because I think war is just nasty and efforts to “soften” it are hypocritical, but I can see it coming in the future anyway.

WoTD: "Catastrophize"

Essentially, to “catastrophize” is to overreact in a negative way to a setback, such as the one who is stood up for a date and becomes upset that he or she will never find love. Broadly, catastrophization is a habit of mind that’s commonly identified in the anxious and depressed. I don’t know enough to speculate about what causes the formation of such a habit, but I can admit to recognizing it in myself. I have often characterized my depression as “an inability to control negative thoughts,” and by these negative thoughts I essentially mean overwhelming catastrophization. When I’m depressed, even the smallest and most innocous event or impression can become symbolic of my total failure as a human being.

Recognizing the process as a habit, as something that can be lost or changed or replaced like any other habit, is itself very valuable to me. Even the simple fact that there exists a word to describe the phenomenon brings me considerable comfort–in the first place, it shows that I’m not alone in experiencing it, and in the second, well…everyone knows that to name a thing is to have power over it. The next time I begin to “catastrophize,” the word itself will occur to me, and in matching the sign to the signified I will be reminded that the catastrophe I perceive is in my head and not in the world. Maybe, in time, I’ll even be able to laugh about it, to find some humor in the extent to which I can blow things out of proportion, but of course there’s a fine line to be walked here. I can already hear myself thinking: “I’m catastrophizing again. It’s so like me to do that. No wonder I’m a such a TOTALLY WORTHLESS LOSER.”

As in learning to meditate, the trick to changing habits of mind like catastrophization is probably to avoid trying too hard. Instead of recognizing catastrophic thoughts and working really hard to stop, it’s probably better to just recognize those thoughts, release them, and then casually replace them with something else. Those three Rs could become a mantra: Recognize your negative habits, Release them in the moment, and Replace them with something more constructive. Perhaps there’s even a fourth R: Repeat the process until they change.

Maybe Not Too Little, But Probably Too Late

This week my father preserved for me a series of editorials from the Wall Street Journal by Charles Murray, of The Bell Curve fame, arguing his thesis for the reality of g, which he identifies as an inherent and inherited “intelligence factor” that differentiates the smart from the dumb. Distribution of g in the population follows a normal, or “bell,” curve, and he points up many of the oft-touted depressing statistics of U.S. public education and explains them–convincingly, in my view–in terms of the normal statistical distribution of intelligence in our population. He revives the spectre of the IQ score, and although he acknowledges quibbles about the accuracy of the tools used to measure it, he also advocates its phenomenological legitimacy. He deals summarily with Gardner’s multiple intelligences theory, citing relatively convincing evidence that g is a real phenomenon and can’t be wished away by egalitarian reformers. He recognizes how the notion of uneven distribution of g chafes agains our ideals of equality and the political difficulties attendant to making policy decisions based on a worldview which is in this sense elitist.

I see Murray as one of a small but growing vocal minority of intellectuals who are prepared to acknowledge that human beings are in most meaningful ways determined by their genes. As biology and neurobiology advance, we come to understand more and more how even very complex human behaviors can be predicted genetically. This is certainly not the first time in history that a deterministic elitist movement has surfaced, but it may well prove to be the first time that the unpleasant awareness of genetic determinism is answered by an ethical technical solution. Before long, it seems obvious to any scientifically-informed observer, biochemistry will allow human beings to achieve meaningful control of their genetic destinies, at which point a political battle will ensue between the forces that advocate non-intervention in genetic fate and those who recognize biochemical eugenics as an escape from determinism.

Brief meditation on human nature leads me to predict that the battle will be a short one. Voices in favor of accepting determinism–such as Murray, et. al.–run up against the ubiquitous phenomenological fact of choice: Whether it is real or not, human beings experience a process of decision making that causes them to behave as if they have some measure of control over their fates. Although most rational adults can be persuaded to admit, if pressured, that there are things in life over which they have no control, most of them would also prefer that it not be so. If offered a choice between the certainty of a brilliant and beautiful and happy child and the luck of the draw, which of us would leave it to fate?

Practical eugenetic technology is not with us now, and may well not materialize until twenty years hence. Even if it takes that long, however, it still seems likely that we will find ourselves living with a technology that can correct our genes before we find ourselves living in a political culture prepared to accept that they determine our fates. In that most probable case, Murray’s arguments, though convincing, come too late on the scene. Even if we begin now to implement the policy regime he advocates, it’s likely that by the time reforms come into place the biology on which they are founded will become subject to the same socioeconomic pressures which corrupt the system now. Western culture has lived in denial of biological determinism for decades now, and in resentment of it for millenia–are we going now to give in and accept it on the very eve of our liberation? Better now to begin preparing for that future culture of eugenetic control, to begin steering now toward’s Keillor’s Lake Wobegon, where all the children are above average, and away from Huxley’s Brave New World, where minds are manufactured to meet the demands of industry.

Another Fracking BSG Neologism

I propose the prefix “cylo-” to describe all matters pertaining to “cylon biology,” in other words that “cylo-” be used analogously to “bio-” to describe any subject pertaining to cylon biology rather than normal human biology. The show, after all, has established that cylon biology (“cylology,” under my new system), although generally indistinguishable from human biology at the macro-level, is chemically distinct. Which explains how Dr. Baltar can build a cylon detector and how cylons, though histologically identical to humans, can exhibit all the unique characteristics that they do, i.e. running for days without tiring, spinal bioluminescence, group consciousness, unusual RF susceptibility, etc. Thus “cylo-” can be assumed to denote that aspect of cylon physiology which is analogous to, but not identical with, human physiology.

Which gives us all kinds of great new words like “cylogenetic,” “cylochemistry,” “cylological,” “cylonic,” “cylosphere,” “cylome,” “cylophysics,” and my personal favorite, “cylohazard.”

In honor of this last term, I’ve made up a “cylohazard symbol,” which is derived from the analogous human biohazard symbol, differing in that it is based on a five-fold axis of radial symmetry, instead of a three-fold axis. This decision is in keeping with the established significance of the pentagon and the nested pentagon as a symbol of cylon hegemony in both the old and the new Battlestar Galactica series. Material which is infectious of cylons, such as samples of the “cylon plague” from Season 3, would rightly bear the cylohazard symbol, regardless of whether or not it was also infectious of humans. Material which is infectious of both species should properly bear both symbols.

Someday I might write a pseudoepistolary “ANSI standard” from the BSG universe describing the layout and appropriate use of the cylohazard symbol by itself or in conjunction with the biohazard, chemohazard, and or radiological hazard signs.

The Swerve Test

There is a road that begins, in my heart. with the general disdain I feel for most specimens of homo sapiens, and ends, in my spleen, with the blackest hate that one man can feel for another, the kind of hate most people, including myself, are fortunate enough never to experience, the kind reserved for a villain who has destroyed a loved one and witnessed by actions of murderous revenge. Arrayed along this road, like Burma-Shave ads on the highway to Abilene, are signposts, behaviors, that mark the boundaries between the states of disdain and dislike, dislike and loathing, loathing and hate.

It is somewhere around Wichita Falls, by my reckoning, that the countries of true hate begin. In mapping these infernal regions, I have found it useful to apply what I call “the sweve test,” which is really a pair of tests: Driving along, I mount a rise to discover the person of my enemy, standing in the road a short distance ahead, and put to myself the question, “Do I swerve to avoid him?” If the answer is yes, then he has not yet passed into the territory of loathing; if no, then the second test must be applied: Mounting a second rise, I discover the person of my enemy standing beside the road a short distance ahead, and put to myself the question, “Do I swerve to hit him?” If no, he is loathed; if yes, hated.

The swerve test has much to recommend it. First, it is accurate: In the best tradition of Skinner, it avoids murky subjectivity by addressing only behavior. While my own estimation of the extent of my distaste for a particular person may vary with the weather, the proximity of my next meal or the quality of my last, or whether or not I remembered to take my medication that morning, the volition to actually effect his destruction, either passively or actively, is much less mutable.

Second, the swerve test is precise: We may imagine the swerve as a kind of behavioristic quantum–the smallest act measurable as evidence of intent. Here is a heavy mass, moving with great speed, having tremendous inertia, and by a small motion of my hand I can deflect its course and thereby choose to spare or destroy my enemy. In the first test, I must expend this minimum effort to save him, and in the second, to destroy him. The two outcomes differ only by a quantum.

Third and finally, the results of the test are easy to interpet: At the end of the day, the subject of the swerve test, like Schrodinger’s cat, is either alive or dead.

Virtual Earth 2.0

I’m imagining a portable device that integrates a global-positioning system (GPS) receiver with a short range (say 25m) LIDAR (laser imaging detection and ranging) system that could be used to map the street-level topography of the earth–buildings, rooms, trees, streetsigns–as the user moves through it. I’m imagining a built-in-panoramic video camera that can be used to map textures onto all the surfaces. I’m imagining an internal hard-drive and/or cellular modem so that all this mapping information can be uploaded, sooner or later, to a central server that compiles location-mapping correlation data from multiple users to create an immersive 3D simulation of the real surface of the earth. I’m imagining stores and businesses and schools having sales, conducting meetings, and teaching classes at virtual locations inside the virtual earth at the same time they happen in the real earth, or even in lieu thereof. I’m imagining mappers competing to be the first to scan the inside of Kitum cave, or the top of Mt. Everest, or the basement of the Pentagon. I’m imagining that we’ll see it happen within 15 years. I’m imagining that the first people to make it work are going to be very, very rich.