Scientific Meanderings

Grad school has swallowed me whole, lately. I've had a lot of interesting observations and musings I've wanted to jot down here, but I keep forgetting or putting it off. Let's get a few of these out there:

• So, what do you do for a living?

In one of my classes, we learned of a study where researchers wanted to see whether or not gonorrhea undergoes selective mutations during an infection. How did they test this? They infected volunteers with the freaking thing and sequenced the bug at various times during the infection.

I'm not sure I can put a dollar value on what it would take to willingly get infected with an STD, regardless of whether antibiotics will treat it. I'm having enough trouble getting a date these days without something like that mucking it all up.

• The Pertussis Scare

Today we talked a lot about bordetella pertussis, the bacteria behind whooping cough. The disease is typically included in a cocktail vaccine, including diptheria and tetanus as well. I found it interesting that, for a period of time starting a few decades ago, Europe ceased to include pertussis in the mix due to some fears of deaths that may have been related to the vaccine. It turned out that they weren't, but there was enough public fear and bad PR floating around that it was only recently that Europe began vaccinating for pertussis again. As you would expect, there's been a lot of whooping cough in Europe in the meantime.

Given everything I hear about Europe's reactions to new vaccines, drugs, and genetically modified crops (especially GM crops), this doesn't really surprise me. It makes me wonder: We hear so much about how the US is so scientifically illiterate, how we're these religious nuts who want to drag scientific progress back to the dark ages and revert medicine to the time when leeches were considered the hot new thing. Why is it, then, that our more "enlightened" cousins across the pond always seem to be so eager to break out the pitchforks and torches when a new drug weighs the same as a duck?

• Where's it all coming from?

In a related anecdote, while talking about pertussis it was shown that pertussis infections have been ticking upward for the last 20-30 years, with a noticeable spike during the 90s. There is apparently some debate over whether this is an actual increase in cases or just better reporting of cases. The argument being that, with vastly improved technologies for diagnosis, we're just finding the infections more readily than in the past.

We didn't discuss it in class, but I can't help but wonder if it isn't related to illegal immigration. It's not news to anyone who's been paying attention that a lot of the people coming here illegally don't get vaccinated from anything themselves, resulting in upticks in diseases only rarely seen in the US. Several of the studies cited to us about the spread of the disease were centered in California, which isn't exactly a model of immigration law enforcement.

I really don't have much to add to that. Curiosity, but not much else.

Health care not a right

I saw this post over at National Review's The Corner, and it rang true with me, largely because I've had this argument dozens of times before.

The idea that we have a right to health care is quite dangerous. All rights we've enshrined heretofore were things that could only be taken away from you; life, liberty, etc. Health care, like any other good or service, is something that can only be given.

If we enshrine a right to something that must be given to us, it creates an ever-dreaded slippery slope. At what point do the rights stop? and who gets to decide?

Celebrity

I've said for a while now that I think Obama's popularity is driven by a "cult of personality," or perhaps a "cult of celebrity." Either way, I tend to think that there's a lot more at work behind this than people thinking his policies are super-duper.

The response I tend to get from liberals to this range from, "Nu-uh," to, "You're just jealous 'cause you lost." Perhaps. Then again, when I see stuff like this, I can't help but feel vidicated. I'll include a screencap in case it goes away.

Pelosi and the Pope

Not a news story per se, but I enjoy this National Review post discussing Nancy Pelosi's recent visit to the Vatican. The short version is that the Pope gave her (and by extension, all pro-choice Catholic politicians) a dressing down for supporting abortion.

While it's no secret that I disagree with Catholic theology (one of these days we'll finish a conversation, Ryan) on everything that separates them from Protestants, I appreciate that the Pope doesn't pull any punches on this issue. In the structure of the Catholic church, there is no room for "disagreement" on issues like this. If you're going to claim the church as your own, you have some requirements to meet. I think that the broader Christian church is the same in principle, though there's obviously no central power structure for enforcement. Not that we've seen any pro-choice Catholic politicians excommunicated recently.

I must disagree with the author of this on one point, however. He states that politicians like Pelosi are where they are because they're poorly catechized, getting their teachings from high-brow Catholic intellectuals who don't want to deal with "embarrassing" teachings. I can't give them this much leeway. The teachings of the Catholic church are accessible enough that there should be no mystery on what it really teaches. For crying out loud, Pelosi just got it from the horse's mouth (so to speak). If she suddenly changes course and becomes a pro-life politician, I'll offer up a heartfelt apology, but I doubt she, nor any other pro-choice Catholic politician, is going to change anytime soon. These people hold onto their religious affiliation, I suspect, out of political expediency, even necessity, rather than any heartfelt conviction. Perhaps it's the cultural identity that they desire instead. Either way, there is no other explanation for people who claim a title while denying its most important or relevant teachings.

Who will police the police?

Coast Guard?

Okay, enough Simpsons references. This is an interesting story. It seems that a cop in Iowa emailed a bunch of mugshots (the article leaves us to guess who they were sent to) of people wearing Obama shirts. Apparently he remarked on the quality of Obama's fanbase and it was not well received. He was suspended for 30 days and will be undergoing "DPS training." Whatever that is.

On the surface, this looks like an unseemly quashing of free speech. The officer sent the email on his own time from his own computer. However, the article seems to imply that the officer broke some sort of departmental policy in doing this. Perhaps the mugshots he made public were not quite ready to be made public? We're left to guess.

Still, can you imagine if such an event had happened during the Bush administration? I'm not sure we'd be hearing the end of it.

Pandora's Cell

Developmental biology is a Pandora's Box of scientific mysteries. We understand a lot of things about how indeterminate lumps of matter know to become a thumb or a finger, the spine or the lungs, or any number of other things. For all that we know, however, there's an almost endless list of things we don't know or don't understand. Especially when it comes to humans, since the methods that would be used to study them are almost universally considered unethical, even to people who don't think twice about harvesting embryos for stem cells.

So, when I read about experiments like this, where scientists try to make human/animal hybrid embryos, I start to wonder how we get scientists so devoid of morals or ethics.

My best guess as to why this fails is probably genetic incompatibility with the transcription factors. Transcription factors are the proteins which latch onto your DNA and signal for other proteins to be made. They're usually pretty picky about where they will bind, and even slight changes in either the TF or the DNA it binds can be fatal. More than likely, the TFs in the animal cell just aren't good enough to keep things going.

My only other guess would be that they're attempting to turn on genes which turn off at development. Cells turn these genes off (and work very hard to keep them off) because letting them run rampant leads to all kinds of problems. Cancer is usually the most obvious result, but I'm sure it's not the only one.

I'm really not complaining about the failure. The monsters who do these sorts of things ought to have their degrees stripped away.

They all need better games

My cousin (who needs to update his freaking blog sometime) passed along this article entitled, "The Wii needs better games now."

While I don't usually trust people in the mainstream media to write about such matters, I can't disagree with the premise of the article. The Wii is suffering from a drought of good content. Sure, there's fun stuff to download on Wii Ware, but the last full game I bought was Mario Kart, and that was almost a year ago. When I go to the stores, the shelves are full, but full of what? Crappy movie or TV tie-ins, animal sims, pet sims, "girl" games, silly sport games . . . it's like a wasteland of entertainment. Nintendo's own products are considered the best, but the last thing they produced was Wii Music, a product I doubt will light the world on fire. My DS suffers from the same problem.

Still, I can't merely fault the Wii for this. Most other consoles are also under the curse of a lack of creativity. It's a field full of sport franchises, endless sequels, and remakes of games that didn't need them. Where are the games with memorable characters and good writing?

If you're a Wii owner, what have you bought in the last year that you liked, or what are you looking forward to?

The Beginning of Wisdom

There's something very odd about being in a lab where you don't really know any of the experimental techniques. I'm starting to suspect the following is true in most areas of life, but current circumstances have brought it to mind.

When you're ignorant of something, is it better to find the information on your own, or to go to an expert and seek their assistance? When is one path better than the other?

This is not usually easy to determine. Experiments which are commonly done in the lab can be tricky. Sometimes when I need a ubiquitous reagent or piece of plasticware, someone will be happy to point it out to me. Other times I'll be told to, "Just go look for it." Sometimes I'm confused about the exact nature of the protocol, since my tutorial involved very general outlines. If I ask someone about, say, precise volumes or concentrations or reagents to add, sometimes I'm told what I seek. Sometimes I'm told to just go "find a protocol on Google." Other times I'm given such a run-around it's silly. "Hm . . . I don't remember. Why don't you go ask that guy?" It's even better when I get to the end of the chain, usually three or four people down the line, and they question the experiment in the first place. "Why would you run that? It won't work and won't show you what you want to do? Here's a different three-day experiment you need to run instead."

Perhaps there is no set answer, but I find that I have a difficult time knowing when to take one path or the other. I suppose figuring out the difference is a large part of success in this field.

Making Bad Professors

I've written before about all the joys of being a TA. One of the things I never covered was how being a TA is very poor training towards taking over a classroom. This article from the Pope Center discusses the problems of taking graduate students and chucking them into a classroom with little to no formal training.

I can certainly speak to this from my own experiences. Since I've mainly taught chemistry, my experience has largely been teaching labs. UMSL gave me the opportunity to throw in discussion sessions as well. Typically, the lead-up to any of this at the start of the semester was anything from a day to a week of seminars about being a TA. Some of it plain common sense and some of it just policy. I found much of it to be unhelpful, but like I said, a lot of it is common sense.

I saw a lot of foreign grad students sent to lead classes or discussion groups who had very poor english. That should never happen. You are handicapping their students by giving them a second hurdle to overcome (aside from understanding the material).

If I had to give my own thoughts to improving the situation for science TAs, this is what I might say:

• Public speaking classes

These should be optional but available. Not everyone is comfortable or competant at speaking in front of others. Tossing these people into a teaching position doesn't help anybody. If the person isn't meeting a certain level of english proficiency, don't let them get out of this, either.

• Allow time to test the labs

This is a big one. Most lab TAs will have no idea how the lab is supposed to go until they see their first section go through it. This can lead to TAs not knowing how to answer certain questions or knowing that the results are poor until too late in the session.

The easy solution to this would be to bank time for the TAs to all do each experiment before teaching it. This way they know the equipment, they know the reagents, and they know what each stage of the experiment looks like.

• Give the TAs real authority

This one is truly necessary for discussion sessions. I had a very talkative, very unruly group for my discussion sessions. The students showed up for the graded quiz, and didn't really care to participate in anything else we were to do there. In one lab, a student started swearing at me when she failed to follow the directions and had to repeat the experiment.

In every case, I really had no recourse. I'm not allowed to deduct points at any stage for behavioral problems. I was only allowed to report to the professor about the problem and let them handle it. It usually meant a warning to start, then an "official" warning in the form of a hearing with a disciplinary panel. Too much run around for a very slow pay off.

The point is, the power lies in the hands of either the students or the professor. The TAs are simply middle men with no ability to keep students in line short of having campus police haul a disruptive trouble maker out of class. That's not helpful to anyone.

• Give them a chance to lecture

The thrust of the Pope Center article was that TAs in these settings aren't being given proper preparation to become a decent professor. This is a big problem for science TAs, who may not ever be in front of a classroom until they get their PhD and a teaching position. An easy remedy would be to allow the TA(s) to teach at least part of a lecture sometime during the semester. It gives them experience, and the professor could easily observe and give corrective guidance.

I realize that's not a feasible option for courses with 300 students and 20 TAs, but the option could at least be offered to those TAs. Nobody learns to drive by first pulling onto the interstate during rush hour or going into a downtown metropolis. Why should teaching be any different?

No, it's not a lie

Despite the fact that I'm forecasting political grumpiness for the next 4-8 years (unless something really stupid happens), this is still pretty darn funny.

Long term savings?

This was just a little thought experiment, so try not to take this too seriously. I saw someone quote some numbers recently to the effect that a Prius gets ~46 mpg, while a comparably sized standard vehicle gets 31 mpg. The price difference between these vehicles was said to be $7000.

So, I thought to myself . . . how long do you have to drive that Prius to make up the price difference?

Feel free to check my math, but here's the formula I used:

ΔE * G * M = Δ$

Where ΔE is the difference in fuel efficiency of the vehicles, G is the cost of gasoline, and M is the number of miles you have to drive to make up Δ$, the difference in cost between the two vehicles. Efficiency, in this case, has to be put in gallons per mile to work out properly.

Anyhow, I estimate that if gasoline were running $4/gal. again, you'd have to drive that Prius for 175k miles to make up that $7k price difference.

That's not a good number, especially because it only gets higher when gasoline is cheaper. This also doesn't take into account any differences in maintenance costs, since I have no idea what that might be. Unless you're driving that car a lot, it's going to take a very long time to make up the price difference on gasoline costs, and it's entirely possible that by the time you've driven the car that much, vehicles at least as efficient (if not more) will be similarly priced as the non-hybrid.

I only bring this up because I heard on the radio this morning that part of Obama's plans for reducing government cost is to make all government buildings more energy efficient. I don't know what goes into such measures, but I'm betting it will be expensive. The question is, however, what's the return on investment? Or more precisely, how long will that building have to stand before that investment is returned?

If it's anything like our Prius example above, it could be decades before that cost is made up, which seems like the intent is more to pander to environmental groups than offer any substantive benefit to the tax payer. Perhaps I'm just being cynical, but I haven't heard anybody challenging him on this one yet.

Press A to Jump

One of my favorite new shows to be made in the last few years was Big Bang Theory. If you haven't seen this show yet on CBS, you really ought to. The show centers around four friends who work at a California university; two are theoretical physicists, one is an engineer for the space program, and the other is an astrophysicist. The show is a constant barrage of geek culture, and it is both hilarious and sad, in the sense that I see myself in way too many of the jokes.

Because the show is such a tribute to geeky interests, the writers seem to make an effort to get things as accurately as possible (within trademark limitations, I imagine). However, they made a mistake that every movie and television show (ever) makes. In one episode, the guys sit around and play Halo. Since there's not a lot of action to see on screen when you show people playing video games, writers tend to have their actors play the game in a absurdly over-the-top manner. People will stand up for no reason, they'll mash buttons both rapidly and randomly, in an attempt to communicate to us that, yes, they're playing a game.

Someday, I want a television show to give us a bit of credit and trust that, when we see the character holding the controller and staring at the television, we know they're playing video games.

The comic comes from Digital Unrest, so do give them some traffic so I don't feel too guilty about posting this.

Select Difficulty

While I was home for the holidays, I had the good opportunity to fire up my old NES. Between that, and two recent discussions on video game difficulty, and I thought I had some good blog fodder.

Shamus points out in his video that a lot of "hardcore" players, or at least those of us with a modicum of skill, grew up learning to play on the old NES. We had a lifetime of scaling difficulty, both in game quality and control scheme complexity, to get to where we are, so people who are just joining the party are right to feel overwhelmed by the mess that is modern video gaming.

There's something to be said about the part pertaining to new players. There's a reason games like Bejeweled and Chuzzle are so popular. While there was a time that you would sooner admit to being a chronic bed-wetter before telling girls you played video games, these days it's really easy to convince women to play a game of Wii Sports, Mario Party, Mario Kart, Rock Band, etc.

Still, I find the former more interesting. I think there's a lot of nostalgia that goes into saying, "Video games in the NES era were perfect! We learned to game in a beautiful harmony!"

I think it's many of those older games which paved the way for today's games, which feature crushing difficulty and what Shamus likes to call "Do it again, stupid" (DIAS) syndrome. DIAS is the state where the game presents you with a challenge with little room for error. When you fail, you have to repeat the challenge over and over until you get it right. Sometimes failure sends you back to an earlier point in the game, which leads to a frustrating situation where you might have to play the same 10-20 minutes of a game over and over because of one part you can't get past.

Here's a few examples from the games I picked up this past week:

• Super Mario Bros. 3

This game is considered one of the best games for the NES, even one of the best ever made. While the game is quite fun, I would argue that most people only ever beat it by "cheating" with the Warp Whistles, which no casual player would have known about. Playing the game normally takes something on the order of 6-8 hours, and there's no save function. Many of the levels contain puzzles which would be nearly impossible to solve without access to game guides. Others feature situations requiring such lightning fast reflexes and time-critical moves that only someone well-versed in the genre is going to tackle it. The point being, this is a hard game.

• Teenage Mutant Ninja Turtles

If you were eight years old and played this game, it was like a slap in the face. I'll post this link, with a warning for foul language. You controlled the turtles one at a time, going through levels to rescue Splinter from Shredder. Sounds like fun for someone who watched the cartoon every day, right? Except the game was filled with labrynthine levels, rare health pickups or power-ups, and swarms of enemies too big to avoid and too strong to kill quickly. Since you could freely switch between the turtles, you technically had four lives. However, some of the turtles had attacks which were nearly useless. You could "rescue" a turtle who lost all his health, but figuring out where those locations are was a feat in itself. Very few people who played this game ever made it to the end, and even fewer managed to topple Shredder when it happened.

• Mega Man

Okay, I remember this game fondly as well, but I never finished it in my youth. Once again, the complexity of some of the jumping puzzles, as well as the difficulty of the enemies, made it nearly impossible for an unskilled player. Most levels featured a robot which was difficult to avoid and stole half your health if it touched you. Some of the bosses were only within reach of most players (including me) due to a cheat involving the pause button, a feature removed in future installments of the game.

So, a lot of the older games are difficult. So what? My point is that there are games of crushing difficulty from every era. We may remember those games fondly in retrospect, but most of us put them down in frustration at one point or another. We kept up with the hobby because of the games that were within reach of our skill level. Those games can still be good today, and I think it's worth keeping in mind the things which made those games good when looking at the newer games. A game can be easy enough for new players without simplifying it too much. Sure, games like Nintendogs convinced a lot of people to buy a DS, but they can still be challenged by, and enjoy, games like Phoenix Wright.

Not that anyone's asking my opinion on game design theory. I can dream, can't I?

Oh, and no discussion of difficult video games of the past would be complete without pointing you to the Angry Video Game Nerd (again, be wary - he uses lots of foul language).

A retrospective on December 31

Most years, at the start of the new year, I tend to think about where I'm heading, what I want to accomplish, and how I want my life to change in the twelve months to come. Given how much of my life is up in the air for 2009, my thoughts have been drawn more to previous years and what my perspectives were at the time.

On Dec. 31, 2008, I was playing cards with my cousin and his wife. I'm in Maryland studying immunology and wondering where my studies will take me in the next few years, when I'll ever find a girlfriend, and whether I'll be home before next Christmas for any reason besides my sister's graduation.

On Dec. 31, 2007, I was in Chicago, celebrating with college buddies at a party which was sparsely attended due to a foot of fresh snow. I was excited about having just earned my MS and incredibly confused as to where I would end up for my PhD work.

On Dec. 31, 2006, I was with my cousin and his wife, again, but this was a party, so there were many others as well. I was working my my MS, still sore about having left Northwestern, and trying to figure out if I'd ever get over my ex-girlfriend.

On Dec. 31, 2005, I was in Evanston, at a party with Northwestern people. My girlfriend was visiting at the time, so she was there as well. I was spending quite a bit of time then wondering whether I would make it at Northwestern and hoping that the classes would not be as crushingly difficult as I feared they would be. I'd also just started doing research with my new PI, and I was very hopeful about where it was heading.

I could go further back, but I find the retrospective helpful. It's interesting what things we're worried about at various times in our lives and how those thing change over the course of just a year. One year doesn't seem like that much time, but when I look back at prior New Year's eves, it seems like an eternity.

I don't know what the coming year holds for me, but I'll wish all of you the best for the next twelve months.