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Below are the 17 most recent journal entries recorded in Brian Johnson's LiveJournal:

    Thursday, July 14th, 2011
    10:06 am
    Notes on nutrition and metabolism
    I wrote this in June 2003, two months before defending my thesis. I was doubtlessly procrastinating writing up my theorems and proofs. It's my notes on some document or web page that explains glucose and fat metabolism, and it's just as true 8 years later. There's more to the story of how to improve your health with diet, of course, but the open-loop regulation of fat storage and metabolism via blood glucose levels is very important to understand, and explains much of our country's current "obesity epidemic".

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    Thursday, July 1st, 2010
    11:30 pm
    Hanford tour highlights
    Hanford was the site of the first large scale nuclear reactors in the world, with the first one, the "B" Reactor, going online ("critical") in September 1944. The purpose of these reactors was not to generate power, but to transmute Uranium into Plutonium for the war, and later the cold war, effort. Heat was a waste product; the maximum rate of transmutation was limited by how fast heat could be safely removed from the reactor cores, so each reactor had equipment to pump tens of thousands of gallons of water from the Columbia river through the core per minute. Water entered the front of the core at about 40-50 degrees F, and exited the back of the core one second later at almost boiling. Nearly a dozen such reactors were operated at power levels on the order of 250 MW each, all dumping their waste heat into the environment, for decades. It's mind boggling to me how much energy was wasted just to produce Plutonium.

    Despite being built in less than a year, with construction proceeding directly off of concept diagrams, the Hanford reactors held up surprisingly well over time. There were no serious reactor accidents in the entire history of the site, and no reactor workers were exposed to life-threatening radiation. Engineers had the foresight to build the reactors with several safety systems, including giant fans that constantly blew air from the manned areas, towards the reactor core, and out of the unmanned areas of the building; a set of boron control rods suspended above the reactor which could be dropped into the core in the event of an accident; and an ingenious mechanical/hydraulic system to shut down the reactors in the event of an electrical power failure. They would never pass safety review today, of course, but they were far more sophisticated than comparable-era British and Russian reactors for Plutonium production.

    We got out of the bus at the "B" Reactor, the first to be built, and spent about an hour inside the reactor building learning about its history. The bulk of the presentation was held on the main floor, directly in front of the decommissioned reactor core. There is, of course, no more spent fuel inside the reactor; but the graphite blocks, cooling pipes, and concrete shielding are all originals, and the interior of the reactor core remains moderately radioactive. (The remaining structures in the core have been carefully sealed off to prevent any contamination of the surrounding structure.) It was quite surreal to consider that I was standing no more than 50 feet from the inside of a decommissioned nuclear reactor core. There were plenty of vintage-era signs and placards with safety info, as well as several closed doors with "dosimiter required beyond this point" warnings. Incidentally, most (all?) of the Plutonium used in the Trinity test and the Fat Man bomb were produced in the "B" Reactor. By the end of the war, production had ramped up to the point where Hanford was producing enough fissile material for about one bomb per month.

    The Hanford reactor fleet continued to be used through a good portion of the cold war, dutifully generating irradiated fuel rods at a predictable rate. The irradiated rods were stored under water at the originating reactor for about three months, to let the shorter-lived fission products decay, then loaded onto a train and taken (with half a dozen empty cars between the shipping container and the locomotive, to protect the engineer from radiation) a few miles away to one of several generations of Plutonium separation plants. These structures are also still standing, and are among the most radiologically polluted structures in North America. At them, the fuel rods were dissolved in nitric acid, then separated into Plutonium, unspent Uranium, and fission products. All of this work had to be done with manipulator arms and television cameras, to avoid irradiating workers with fatal doses of radiation.

    The separation process is (sort of) detailed on wikipedia (search for "PUREX"), and all I can say is that it's a chemical nightmare. Much of the heavily contaminated equipment from these processing plants was later buried at various locations on site, but a few pieces were too heavily contaminated for even that -- instead, they were pushed down a dead-end underground railway siding, to be dealt with "later" after the radioactivity had decayed. I wonder when "later" will be.

    At many points in the separation process, radioactive waste liquids were produced, which were stored on site in underground tanks; many of the original tanks have leaked, and their cleanup has turned into the most challenging cleanup task at the entire Hanford site: the contents of the tanks have to be removed with robotic equipment, the recovered material vitrified, the emptied tanks filled with grout or cement, the contaminated soil and water cleaned up, and the empty tanks covered over with layers of protective material. What a mess. The necessary water treatment plant, which will remove chemical contamination from groundwater pumped up from recovery wells, is under construction and will be finished in late 2011. (Radiological contamination generally was trapped by soil under the tanks and never reached groundwater -- the main groundwater contaminants are carbon tetrachloride and hexavalent chromium.) The (enormous) waste vitrification plant is half complete and scheduled to go online in 2019, assuming a relatively constant budget -- as we learned, inconsistent budgeting is a frequent theme at the Hanford site.

    Hanford also hosts the decommissioned Plutonium finishing plant, where extracted Pu was purified and reduced to pure metallic puck-shaped discs, but we saw and learned little about this structure; apparently, it had stored a large stockpile of finished Plutonium until 2009, which was only recently sent offsite to a storage facility called WIPP in New Mexico the Savannah River facility.

    The Hanford site is also home to a stupefyingly large quantity of low level waste, mostly contaminated soil and machinery. This is all being consolidated in one location near the middle of the site, to limit the ability of water and erosion to release the (very dilute) toxic chemicals and radiological material. The pit for this material is enormous, and currently measures 1 mile long by 1/5 mile wide by hundreds of feet deep. It is about half full and is in a continuous state of construction and expansion. We got to step out of the bus at the edge of this pit while their practices and procedures were explained to us; it is, without a doubt, the largest man-made hole in the ground that I have ever seen. The trucks and bulldozers operating in it literally looked like toys from our vantage point.

    We also got to see where old nuclear submarine power cores go after they are defueled and decommissioned. There's a big pit at Hanford with about 100 of these large cylindrical devices. They can't fill in the pit, because the cores contain lead, and it's not legal to bury lead, but they are there for long term storage nonetheless.
    Sunday, May 17th, 2009
    11:51 pm
    IRIX makemovie .mv file?
    I have an A/V project from my college days that I'd love to turn into a DVD image so that I can watch it. The audio's in an AIFF file -- not much problem there -- but the video is in the IRIX "makemovie" format with a .mv extension. I know it's NTSC and interlaced because I made it :) but I have no idea how best to play or convert such a file these days.

    Dear Internet, can you solve my problem?
    Tuesday, February 10th, 2009
    8:17 am
    Gravity Probe B status
    General relativity, the theory of gravity, is hard to test, because we don't live near any strong gravitational fields. "Strong" means something like the gravity of a black hole; Earth's gravity is really weak by comparison. Successful tests have taken two different routes: either find a place in the universe where gravity is strong, and infer what you can about it via indirect observation; or, make do with the weak gravity of the Earth, and compensate by building a really accurate experiment. Two such tests have been undertaken using man-made spacecraft operating in the local space near the Earth.

    The first test was relatively easy. The second one was arguably the hardest experiment ever done in space, and the results are still being analyzed.

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    Sunday, October 19th, 2008
    10:16 pm
    The world is not magic
    Sean Carroll of Cosmic Variance wrote this post three years ago. It is of fundamental importance.

    Caroline, after making a good-faith effort to understand the distinction between quarks and leptons, pleasantly but firmly demanded to know “What is the practical use of all this? What can we actually do with it? Why is it worth spending time on it?”

    My line on these questions is that there isn’t necessarily any practical application (although there may be spinoffs); we do it as part of a quest to understand how the world works. I was trying to explain this, with less than complete success. But then Caroline’s younger sister ... leaned across the table and said “Because the world is not magic. This is what I always taught my kids, and it’s what everyone should understand.”

    The world is not magic. The world follows patterns, obeys unbreakable rules. We never reach a point, in exploring our universe, where we reach an ineffable mystery and must give up on rational explanation; our world is comprehensible, it makes sense. I can’t imagine saying it better.

    I am able to think and make this post because Hydrogen is fusing into Helium in the core of the sun, keeping its third planet warm and providing electrochemical energy to a wide variety of vastly complex molecular machines that inhabit it; because billions of years of competition have evolved molecular machines that are just barely capable of intelligent thought and action; and because the last five hundred years of experience have taught those intelligent machines that knowledge and understanding come from applying the scientific method. Every link in this chain is worth understanding in exquisite detail, because it betrays the other point of Sean's post.

    Of course, there are different connotations to the word “magical.” One refers to inscrutable mystery, but another refers simply to a feeling of wonder or delight. And our world is full of that kind of magic. ... The very fact that our world is comprehensible should fill us with wonder and delight. The world is not magic — and that’s the most magical thing about it.
    Tuesday, September 23rd, 2008
    1:08 pm
    A side of the subprime mess I wasn't completely aware of
    AIG failed not because it bought mortgages or mortgage-backed securities, but rather because it wrote policies, called "credit default swaps", to insure others against the risk of default in mortgage-backed securities. Literally, one of these policies says that the insurer would pay an amount (e.g. $1000) to a creditor if a particular counterparty of that creditor defaulted on a particular loan. The creditor paid the insurance company a modest premium (e.g. $1 a month) for this coverage. AIG evidently wrote tons of these policies, insuring all kinds of parties against being defaulted on.

    Over the last 10-15 years, these insurance policies have turned into a tradable financial instrument that got passed around all over the place, including being traded to non-insurance company owners who couldn't possibly pay the claim if there ever was a default. This introduced some danger that these insurance policies were actually worthless, depending on who the insurer side of the policy had been traded to. Sometimes, instead of trading the policies, various parties would arrange for additional insurance policies that offset (hedged) their risk, effectively "passing the buck" to someone else. In some cases a creditor couldn't even figure out who would ultimately be on the hook in case of default because of the complex chains and webs of such insurance policies. As long as everyone makes sure everyone else is solvent and has sufficient collateral for whatever obligations they are carrying, as is the case for instruments like stock options or commodity futures, these arrangements work -- but that wasn't the case with credit default swaps.

    Even worse, there is systemic risk in this kind of a scheme. The danger is that defaults on mortgages are not sporadic, random, independent events, but rather tend to follow a pattern. If one homeowner defaults, it's more likely that other homeowners are defaulting at the exact same time. So defaults come in waves; each wave can be small or large, but because credit crises tend to escalate, we expect to see large waves of default with some significant frequency. In this particular case, the variable-rate mortgages that were available to homeowners with poor credit ratings provided a trigger for a very large wave of default if and when (a) housing prices stopped appreciating, and (b) the economy went into recession.

    Warren Buffett saw this coming 5 years ago and directed Berkshire Hathaway to completely get out of the credit default swap business. This article has more detail.
    Wednesday, April 30th, 2008
    7:31 pm
    A Capella Math Humor
    This is a perfect example of what happens when math grad students have too much free time on their hands.

    Current Mood: amused
    Saturday, November 17th, 2007
    1:40 am
    Science on the witness stand
    It's unusual for expert scientists to be called upon to give a full and complete explanation of an entire branch of human knowledge which is understandable by and intended for a non-expert. This is exactly what happened in the Dover intelligent design court case. Plaintiffs' strategy was to invite a series of scientists into the courtroom to explain science to the presiding judge. Over the course of three weeks, the courtroom turned into a college-level science classroom, team taught from the witness stand by a biology textbook author, a paleontologist, a geneticist, and an assortment of experts on selected topics. These expert witnesses explained the theory of evolution, the mechanism of natural selection, and how these theories are supported by the modern study of genetics.

    The story is in this week's NOVA, Judgement Day: Intelligent Design on Trial.

    For the non-experts who attended the trial, one of the most significant experiences was in learning just how much knowledge science had uncovered. The forefronts of human knowledge aren't usually exposed to the average person, and many of the trial attendees found themselves literally amazed at the detailed understanding of the natural world that our experts have built up over the decades. Biologists don't just have an explanation of how species come into existence; they have whole stories to tell. One of the witnesses has spent much of his entire life studying the bacterial flagellum, and was able to answer questions about its structure and function, and its relationship with other bacterial cell structures, in exquisite detail.

    I wish scientists would come out of their laboratories more often to tell the stories they've unearthed. Most people, I think, are uninterested in science because it hasn't been presented to them in an interesting and compelling way. Maybe, instead of starting with the boring basics and losing people for good before seventh grade, we ought to be telling the most compelling and amazing stories we can find. Then maybe the students will ask "How do we know that?" instead of being told to ask.
    Wednesday, October 31st, 2007
    11:28 pm
    Tuesday, October 30th, 2007
    11:07 pm
    They found me!
    Back in 1989, in the summer between my seventh and eighth grade years, I started playing a roguelike game called Moria. It was the first such computer game I had ever discovered, and I loved it. I played for hours on end on the University of Minnesota's 8-processor Encore Multimax mainframe, which I was able to access through an account graciously provided by the UMTYMP program. My family was driven bonkers by the sheer number of hours I monopolized our phone line with my 2400 baud modem, but I could have cared less. I just wanted to defeat the Balrog! Eventually, sometime between 1991 and 1993, I succeeded. The game was a horrible grind towards the end; like many winning Moria characters, my Ranger was held back at the end by a long and exhausting search for Boots of Speed.

    In June 1994, I lost access to my U of Minnesota UNIX account, but I had managed to get an early version of Debian Linux running on my shiny new 486 PC. At some point, thinking that I might want to play the game once more, I downloaded the Moria source code, typed make, and was dismayed to see screen after screen of compile errors. After a bit of experimenting, I determined that some very minor changes to some #ifdef lines enabled Moria to compile on Linux, so I sent a patch to the maintainers adding "GNU/Linux support".

    I never played Moria again after that, being much too busy with my frosh year at Harvey Mudd College to have time for a dungeon grind alone in my dorm room. Later in college, I returned to roguelike games, but it was Nethack that attracted my attention, not Moria.

    Nonetheless, my Moria Linux patch was incorporated into the main Moria source tree, and my name was added to a list of some 26 contributors to the source code. But Moria is unfortunately not free software; the source code license allows you to download, compile, and play the game, to modify the source code, and to give away the source code for free -- but not to provide the source code to someone in exchange for money. Consequently, Moria is not available as part of any Linux distribution, nor are any of its descendants, most notably Angband, free either. And that's where things have stood for many, many years.

    Recently, a brave developer named Ben Asselstine sought to remedy this licensing issue. Turning copyrighted non-free source code into free, open source software is not easy. Basically the only way to proceed is to contact all of the original copyright holders, and get each and every one of them to agree to relicense their code under a free, open source license. The older the software, the more difficult it becomes to track down and contact all of the original copyright holders. Ben's Moria relicensing saga is described nicely in Freeing an old game. But, to make a long story short:

    We still lack [the consent of] one final contributor who is especially hard to find because he has a common name. If anyone reading this article knows a “Brian Johnson” who likes to do computer programming and was old enough to add “GNU/Linux support” to Moria in 1992 [sic], please have him contact me.

    Earlier today, Ben finally succeeded in contacting the right Brian Johnson. And with my consent, Moria will finally become free software.

    Current Mood: touched
    Sunday, August 26th, 2007
    12:22 am
    Overheard in Union Square
    Guy, speaking to his girlfriend: "There's a lot of men over there. Men can't think, so if you get too many of them together, it's a problem."

    Current Mood: amused
    Thursday, October 12th, 2006
    1:51 pm
    Another Cassini photo
    I know I've already posted a few, but this one just looks *so awesome*! The sun is eclipsed by Saturn.

    Monday, September 25th, 2006
    12:57 pm
    Saturday, July 1st, 2006
    2:56 am
    A Different Point of View

    Image credit: NASA/JPL/SSI
    Wednesday, April 19th, 2006
    6:13 pm
    Something Big and Far Away
    This is one of the most awesome photos I've ever seen. Care to guess what you're seeing here? (Explanation in comments.)

    Wednesday, December 21st, 2005
    12:53 am
    A Need for Speed
    (NASA News Release) NASA is in the final stage of preparations for the launch of its New Horizons spacecraft, destined to lift off for Pluto in January 2006. If all goes well, New Horizons will blast off January 17, 2006 atop an Atlas V rocket; the launch window extends until February 14, 2006. The spacecraft will make a gravity slingshot past Jupiter in 2007, and arrive at Pluto as early as mid-2015.

    The compact, 1,050-pound piano-sized probe will launch aboard an Atlas V expendable launch vehicle, followed by a boost from a kick-stage solid propellant motor. New Horizons will be the fastest spacecraft ever launched, reaching lunar orbit distance in just nine hours and passing Jupiter 13 months later.

    Edit: As of March 2011, five years after launch, New Horizons is as far away from the Sun as Uranus.
    Sunday, January 9th, 2005
    4:42 am
    Excellent BBC Article
    Krakatoa: The first modern tsunami

    "The same geological suture line that caused the recent Sumatran earthquake was responsible for Krakatoa, and the effects, tragic and disastrous, were uncannily similar and world-affecting.

    First came an ear-splitting bang.

    It was the loudest sound ever made since mankind started noting such things.

    The police chief over on Rodriguez Island heard it clearly, like a cannonade of naval gunfire, but he was 4,776km away."

    Current Mood: intrigued