John Petrie’s LifeBlag

My brother told me about the web page Symphony of Science, where its proprietor, John Boswell, mixes the voices of famous scientists (e.g., Carl Sagan, Michio Kaku, Richard Feynman) with an autotuner and puts them over R & B–style music. You should check it out.

I have seasons 1–5 of South Park on DVD, and I don’t ever plan on buying any more because every episode is available for free 24/7 at its official website, southparkstudios.com. I know there is abundant evidence that giving something away for free actually increases its sales, but I at least understand the basis of where the RIAA is coming from. I won’t pay a penny for South Park as long as it is available on demand for free.

One of the worst things Amazon.com has ever done is lump the reviews and ratings of the DVD version and the Blu-ray version of every single movie together, so that you can’t tell whether someone’s review and star-rating refers to the DVD version or the Blu-ray version, unless they state they’re reviewing the Blu-ray version specifically. What idiot thought of that? I can’t imagine the level of stupidity required to approve of that idea at multiple levels of management in the Amazon company hierarchy. It is inconvenient, counterintuitive, and simply inaccurate because the two different products are, um, different products!

So, it turns out my TV is a hell of a lot sweeter than I had ever thought. It is a Samsung SlimFit high-definition television. It is capable of displaying 720p and 1080i video. It’s only 30 inches diagonally, and it’s a cathode ray tube TV, so it isn’t as awesome as the larger TV I’m going to buy next summer, but, hey, that means it has a higher pixel density. I found this out because Kathy got me a Blu-ray player for Christmas, and I hooked it up to an HDMI port in the back of my TV (hmm, that should have made it obvious to me that it was an HDTV, but it never occurred to me), and it plays Blu-ray movies in very nice quality. I tried out my new Blu-rays of Star Trek: First Contact and Harry Potter and the Goblet of Fire, and I’m pretty sure they looked as awesome as they could on a 30″ TV. Maybe a new LCD (or plasma, if they existed at 30 inches) would show an improvement over my 3-year-old TV, but the Wikipedia articles on plasma displays and LCD screens indicate that, other things being equal, CRT produces the best picture in terms of color accuracy, sharpness, and blur. (The problem is, other things aren’t ever equal, not anymore.) However, CRT picture quality fades a lot sooner than the flat-panel displays, so I’m sure mine doesn’t look as good as it used to in high-definition. Those two movies looked really awesome, though; you could tell the source and the display were both high-definition.

I began to suspect that my TV was capable of playing video at some level of high definition (either 720 or 1080 vertical resolution) the night before I discovered it for sure, as I was reading my TV’s manual for probably the second time. I don’t remember reading a lot of it when I got it in August 2006. I think I was reading it to determine if it might be possible for me to use my TV’s remote control for both the TV and the Blu-ray player (both Samsung). I know it’s possible to use the Blu-ray player’s remote to control the TV, but I don’t think it’s possible to change the picture’s aspect ratio/zoom with the Blu-ray remote, and I’ll need this for watching regular TV content that is widescreen because I don’t have high-definition cable, so most things are 4:3, so I have to zoom in on a widescreen program to avoid having black bars on the sides and top and bottom. It might be possible, but first I’ll need to figure out how to navigate my TV’s menus with the Blu-ray controller; all it can do so far is power-off, power-on, and change the volume, channel, and input source.

Well, fuck you, you fucking Redditors! I submitted this article from the Daily Mash (Britain’s Onion), about how Santa hates ginger kids, to Reddit, thinking at least a few of them would get a kick out of it, especially since it is reminiscent of a glorious South Park episode. But, no, I went to check on it a day or two later and saw that it had a score of 0, meaning one more person down-voted it than up-voted it (it starts with a score of 1 upvote—yours—so its vote-score at a given time is the number of other upvotes minus the number of downvotes, plus 1). Probably one loser down-voted it and no one else liked it enough to vote. That person was probably a red-headed abomination himself, goddamned ginger motherfucker, I’d like to bash his face in…

You know what’s stupid? That old saying (I guess it qualifies as an “old saying” now) that if a million monkeys banged away at a million typewriters, they would eventually reproduce the complete works of Shakespeare. Obviously you could fill in any other writing(s) and it would remain equally true, i.e., not at all. It would literally never happen because the universe would end before it happened. Oh, it isn’t a metaphysical impossibility, but it is a physical one.

Let me give you some background. I recall reading this article from the BBC News about the futility of the WEP wireless encryption protocol and the superiority of WPA. One of the network security experts they interviewed said something that blew my mind. Do you know how long it would take the best computer-hacking (password-guessing) programs to guess a 20-character password by brute force? (On average.) What would you guess? I assume it could only contain letters and numerals. So that’s 36 possible characters, times 20 places, and computers can try an awful lot of them per second. Would it take weeks? Years? Decades?

This guy said that on average, it would take longer than the entire history of the universe to guess a 20-character password by brute force. Fourteen billion years! Wow! This is verified by the all-knowing God Himself.

A computer that could perform a billion billion computations per second would require 10¹³ years to guess a 128-character phrase, which is 1,000 times longer than the age of the universe. A 256-character password would require 3×10⁵¹ years.

No one has any way of even guessing how long the universe will last. It could be 3×10⁵¹⁵¹ years. If it lasts that long, it probably will have died in ice many eons before, killed by the Second Law of Thermodynamics. It doesn’t matter. That old saying about monkeys on typewriters has no relevance to the actual universe. Not just monkeys, humans, the Earth, and the solar system, but the entire universe itself could not last long enough for it to happen. You could make it a trillion trillion monkeys, who can type as fast as Lieutenant Commander Data can read, and they would never come even remotely close to producing a single page of any Shakespeare play.

In my searches related to the aforementioned 3D puzzles, I came across some puzzle vendor and enthusiast sites, one of which contained the text of this New York Times article about the stomachion, a children’s game that seemed to be the subject of a manuscript Archimedes wrote 2200 years ago. From what I can tell, this is almost universally believed to be the oldest known example of a puzzle. This website points out that the stomachion is the same type of puzzle as the more familiar tangrams, which most of us did at some point in our youths.

The fascinating thing about Archimedes’ investigations of the stomachion was not that he wrote a treatise on how to play a children’s game, but rather that he founded the discipline of combinatorics by trying to figure out how many different ways the strips of paper in the stomachion could be arranged to form a square. As Gina Kolata wrote in her New York Times article, which focuses on the efforts at restoring and interpreting the manuscript as much as on its contents:

…a historian of mathematics at Stanford, sifting through ancient parchment overwritten by monks and nearly ruined by mold, appears to have solved the mystery of what the treatise was about. In the process, he has opened a surprising new window on the work of the genius best remembered (perhaps apocryphally) for his cry of “Eureka!”…

The Stomachion, concludes the historian, Dr. Reviel Netz, was far ahead of its time: a treatise on combinatorics, a field that did not come into its own until the rise of computer science.

The goal of combinatorics is to determine how many ways a given problem can be solved. And finding the number of ways that the problem posed in the Stomachion (pronounced sto-MOCK-yon) can be solved is so difficult that when Dr. Netz asked a team of four combinatorics experts to do it, it took them six weeks.
[...]
The diagram involved 14 pieces, and the word “multitude” seemed to be associated with it. Mr. Heiberg and those who followed him thought this meant that you could get many figures [of animals, plants, household objects, etc.] by rearranging the pieces.

“This is part of the reason people didn’t see what it was about,” Dr. Netz said. …[T]he old interpretation seemed trivial, hardly worth Archimedes’ time.

As he examined the manuscript pages, piecing together their text, he realized that what Archimedes was really asking seemed to be, “How many ways can you put the pieces together to make a square?” That question, Dr. Netz said, “has mathematical meaning.”

Archimedes was truly an amazing person. I use that word with the fullest extent of its meaning. It is difficult to understand, much less appreciate, how extraordinary and seemingly superhuman his mind was. I put him in a class with Da Vinci and Einstein and no one else who ever lived (that we know of). His founding of the field of combinatorics only adds to my already reverential and awestruck feelings towards him.

Gigagalaxy Zoom

Because the universe is awesome and beautiful. (HT: Dark Roasted Blend.)

An intriguing video summarizing the first chapter of Rob Boynton’s book Imagining the Tenth Dimension. I think it is based on some of the ideas (well, his ideas) of string theory, and it reminds me a little bit of Michio Kaku’s books.

Chemistry is cool:

Check out Michael Bach’s amazing and expansive collection of optical illusions. Some of them will undoubtedly be familiar to you from your youth, and you’ve probably also seen a couple of the more sophisticated ones on computers more recently. But they’re all fascinating and worth perusing for an hour or two. He introduces his site thusly:

“Optical illusion” sounds pejorative, as if exposing a malfunction of the visual system. Rather, I view these phenomena as bringing out particular good adaptations of our visual system to standard viewing situations. These adaptations are hard-wired in our brains, and thus under some artificial manipulations can cause inappropriate interpretations of the visual scene. As Purkinje put it: “Illusions of the senses tell us the truth about perception.”

You can click on his first one and then keep clicking “Next” to browse through all of his illusions, or you can keep returning to his list to pick and choose which ones to visit. I recommend the former method. If you’re short on time, or lazy, or impatient, I’ll tell you my three favorite: the lilac chaser, the spiral aftereffect, and my favorite optical illusion of all time, Ted Adelson’s checker-shadow illusion.

So claims one Christopher McDougall in a new book, Born To Run. The book was largely inspired by his discovrery of the Tarahumara indians of Mexico, a reclusive tribe populated by the greatest long-distance runners in the world. Read Random House’s description of the book, which should entice anyone interested in running or even physical fitness to at least consider buying it:

Full of incredible characters, amazing athletic achievements, cutting-edge science, and, most of all, pure inspiration, Born to Run is an epic adventure that began with one simple question: Why does my foot hurt? In search of an answer, Christopher McDougall sets off to find a tribe of the world’s greatest distance runners and learn their secrets, and in the process shows us that everything we thought we knew about running is wrong.

Isolated by the most savage terrain in North America, the reclusive Tarahumara Indians of Mexico’s deadly Copper Canyons are custodians of a lost art. For centuries they have practiced techniques that allow them to run hundreds of miles without rest and chase down anything from a deer to an Olympic marathoner while enjoying every mile of it. Their superhuman talent is matched by uncanny health and serenity, leaving the Tarahumara immune to the diseases and strife that plague modern existence. With the help of Caballo Blanco, a mysterious loner who lives among the tribe, the author was able not only to uncover the secrets of the Tarahumara but also to find his own inner ultra-athlete, as he trained for the challenge of a lifetime: a fifty-mile race through the heart of Tarahumara country pitting the tribe against an odd band of Americans, including a star ultramarathoner, a beautiful young surfer, and a barefoot wonder.

With a sharp wit and wild exuberance, McDougall takes us from the high-tech science labs at Harvard to the sun-baked valleys and freezing peaks across North America, where ever-growing numbers of ultrarunners are pushing their bodies to the limit, and, finally, to the climactic race in the Copper Canyons. Born to Run is that rare book that will not only engage your mind but inspire your body when you realize that the secret to happiness is right at your feet, and that you, indeed all of us, were born to run.

What I found even more fascinating was this excerpt from Born To Run, which appeared as an article in the UK’s Daily Mail. You might as well read it on the Daily Mail’s site, but I’ll paste it here for posterity in case gets taken offline in the future (not that I won’t have my own hard copy by then):
(continue reading…)

I am not good at science and I don’t really like it that much. I think the latter is the cause of the former, but maybe it’s the other way around. It requires way too much time and emotional investment for paltry results and slow progress. It requires that you care about the most insignificant, minute things as if they affect anyone’s life outside of yours. You have to be satisfied with a success ratio of 10%. Everyone gives this advice to grad students: The 10% (or less) of the time you succeed has to ignite you and carry you through the 90% of the time things don’t work. It doesn’t, for me. I don’t like the physical act of doing the work, period. I don’t like having to attend to the minutiae of cell culture and other things on the weekend, which usually ends up disrupting other plans that I hoped to fulfill, as if I were a normal person in a normal profession.

When I look at the post-docs in my lab, I realize: I don’t want their life. Both grad students and post-docs are expected to work almost every day and sacrifice their free time to produce the occasional, small piece of data. To succeed in science, you have to be obsessed with it. I’m not being hyperbolic to make a point. Many people say you have to eat, sleep, and breathe science, to be thinking about it all the time and always coming up with new ideas and new connections—while you’re exercising, eating, sleeping, commuting, relaxing, whatever—in order to come up with the right experiments and to be passionate about them.

I guess I’m just not. I don’t have that obsession. I wasn’t that good at lab work in my undergraduate lab, and maybe I didn’t care enough to instill in myself the right habits and right attitudes to start being successful and working efficiently and making as much progress as I could each day. I also have bad lab hands. Some people can do things just right and produce lots of good, clean, tight data fast; I can’t. This isn’t a motivational issue, it’s just a matter of skill. I wasn’t born with a lot of it and I haven’t gone to enough effort to develop it, I guess.

I had my second thesis committee meeting on March 17, and it was easily the worst one I have ever even heard about. At this meeting, my mentor and my committee told me in no uncertain terms that if I don’t produce a substantial amount of good data and demonstrate more thorough, careful, Ph.D.-level execution of my experiments, they would kick me out of grad school. I’m pretty sure that’s what my mentor wants to do anyway, regardless of whether I improve or whether I want it or not. He says a Ph.D. advisor and a thesis committee would be doing a disservice to a student to let him languish in an unsuccessful thesis for years and never be productive, so he thinks it is for my own good. He could be right, but getting a master’s degree after a dishonorable discharge from a Ph.D. program in the middle of the Second Great Depression has a low probability of helping anyone, in the short term. It is in my short-term and long-term best interest to earn a Ph.D. and put those letters after my name and bring that appearance of prestige to any job I apply for; going into something non-lab-related after receiving a consolation master’s from your Ph.D. program probably looks worse than leaving science right after college and never gaining the experience of grad school to begin with.

I have heard about other people’s committee meetings, and I’ve never even heard about a bad one, much less two bad ones in a row or one that was this bad. My lab mate had his first committee meeting during my first full year in the lab, and he was very nervous about it because he didn’t really realize how formal it was and how much effort he needed to put into it until a week or two before it, but it turned out great and he said he got a lot of good advice and positive feedback. He said he was interrupted at least once per slide with questions, suggestions, different interpretations, etc. It was definitely a two-way discussion, not him presenting his experimental aims and his data to a stiff, judgmental crowd. And this is someone who often joked, when he had to present his data to our lab, that he had to gussy up his PowerPoint slides to camouflage his lack of data. He wasn’t the most productive, and he had a family so he didn’t even work as many hours as I do. But his committee meetings all went great, to the extent that they let him receive his Ph.D. after only four years of graduate school so he could enroll in dental school. He chose a good profession.

At least one or two other people told me about their first committee meetings, before I had mine, and they said they went great and their committee was positive about this or that, and they got good suggestions for what to focus on in the upcoming months and how to do it and so forth.

My first committee meeting did not live up to my expectations, based on the experiences of my friends. My committee seemed unimpressed and skeptical of my progress, my productivity, my knowledge, my results, and generally everything. They only interrupted me a few times during the entire presentation. Not nearly once per slide. I think they were just unimpressed with my intellectual progress in designing interesting experiments and my technical progress in getting the data. I hadn’t done enough, and what I had done, I didn’t do well enough.

My second committee meeting ended up a little worse, but I knew what to expect. My mentor had already dropped the “master’s” word in a one-on-one meeting with me the previous week. He had repeated a bit of valuable advice he received from some professor in college; in fact, he said it was just about the most valuable thing he learned in college: You can put forth 150% as much effort as your peers for a while, and stay competitive in something you aren’t naturally talented in for a while by sheer force of will and effort, but you can’t keep that up forever. It wears you down and eventually you will lose to the people who are naturally gifted at that profession anyway. Sometimes even more important than picking something you love is picking something you’re good at, and I’m not good at lab work. He said this to me. I already knew it. I already knew I wanted to take my Ph.D. and go somewhere off the beaten path with it. Anywhere but a wet-bench lab. I know I cannot stake my future professional success on my ability to produce data at the bench.

My committee basically agrees. Before thesis committee meetings start, the student leaves the room while his mentor talks about his progress and abilities and strengths and weaknesses and so forth, I don’t know what they talked about for 20 minutes, but it wasn’t good and it was longer than most of those discussions last, I can tell you that much. He probably told them basically what he told me the week before: He thinks I don’t put enough time and effort into things and I shouldn’t even be a scientist. Perhaps effort is a problem, but time isn’t. I spend a lot of time in lab and I always do the things I think I need to do in a given day, a given week. Despite never, ever wanting to, I always go into lab on the weekends, usually both Saturday and Sunday, to take care of my cells or my westerns or my bacterial cultures and make sure no neglect befalls them during the weekend. It’s true, I don’t usually do any real experiments on weekends or drive any project forward—I just maintain my cells or do what’s necessary to keep things from dying or overgrowing or take time-points of RNA or stimulate my cells at the right time or whatever—but I don’t think any more should be expected of me and I don’t think this makes me a bad student or a bad scientist.

I am in the middle of my fourth year of grad school. A four-year master’s would be worse than a two-year master’s from a Ph.D. program, and that’s the main reason I want to work really hard for the next four months and stay in this Ph.D. program until I graduate, not get dishonorably discharged with a consolation master’s. I want to as hard as ever to get that Ph.D. so that I’ll be in a better position to promptly leave research!

I chose Genetics as my major at the University of Georgia at the time I filled out my application, and I never changed it. I wanted to discover the genes that underlie human diseases and/or develop therapies to cure the humans suffering from them. Then when I got into my more advanced biology classes and into the lab, I realized there are very few monogenic diseases left to determine the causes of anymore (my future mentor Francis Collins had taken care of that!). As a scientist, you study basic biological systems—a gene, or its protein product, or a particular cellular process or pathway—that you expect to improve our understanding of the natural world, our own physiology, or future medical treatments. This didn’t affect my vision of life as a scientist or change my mind about what I wanted to do, but when I look back on it I really didn’t like undergraduate research very much. This was largely because I wasn’t good at it. Maybe the lab itself didn’t quite inspire me to develop into an expert experimentalist or to devote whatever time and effort and willpower were necessary to get good data fast, but the deficiency ultimately was with me.

My intellectual passion has always been political-economic theory, and I realized this in college. I thought basic biomedical research could develop into a passion of equal or nearly equal ardor, especially when I got better at it and I could make a living doing it. I reasoned that I should choose something with promising career prospects and learn to love, or at least like, it, rather than confining myself to a field I loved and slowly grow miserable in it as I struggled to make a living. Now I see I will be unable to make a living in the “safer” career field! And I don’t want to!

Part of me says I should listen to what Red Forman would tell me: “It isn’t supposed to be fun. That’s why they call it work. Dumbass.” Everything worth doing is hard, many other jobs (including some I’d like to have) consist of slow progress, incremental steps, etc. Many people, and many of my scientist peers, would rather be enjoying life than working in the lab, but the difference is they are kind of good at it, and their 10% success rate can get them through the all-too-frequent failures. You have to be passionate about the subject and about doing the day-to-day tasks that comprise your job. Either I am less passionate about them, or I don’t listen to Red’s advice as much as they do and just suck it up and do it, or I am less submissive to the idea of being a slave to science all my life—maybe I have higher standards about how much I should enjoy my work and my life, and how much my work should contribute to human society to satisfy me.

Either way, I’m going through a hell of a time in my professional and personal life because of too much self-doubt, too little free time, too much stress to succeed with too little ability to do so, and too few job prospects for a libertarian failed scientist in the Second Great Depression.

Whether I leave a few months or a couple years from now, I’ve decided I must switch gears to find my calling and pursue it with all my heart. I think this has to be in the field of political economy and public policy analysis. Obviously I love it enough (what I know of it) to devote my professional life to it—that’s what I want to do in my free time, instead of lab or a lot of other things. I’ve decided I need to find a way to make my passion into my calling, not try to make my current career choice into a passion to sustain me.