Good parts of Genomics

Well, despite what I said recently about hating genomics, the last week or two have actually been pretty cool, ever since we gave up on becoming programmers (which is kind of sad, because I think it would be useful to know a bit of programming).

Anyway, we have been talking about Next Generation sequencing, which is the technology that is in use right now to sequence genomes. It is light years ahead of what was in use just a decade ago in the Human Genome Project in terms of time required, quality of data, etc. As we have been talking about this, Dr. Udall keeps correcting himself and reminding us that the correct term is Second Generation, not Next Generation, because there is already a Next Next Generation (Third) on the horizon, and they don't want to confuse people.

Of course, with the constant reminders that Third Generation was coming, one day we asked what it was. It blew my mind. Now, I recognize that most people who read this blog are not Sam (in fact, I'm pretty sure only one of you is Sam), so I don't think everybody will be as interested in this as we nerds are. That said, it is pretty awesome.

Pacific Biosciences has technology in development that they claim will be able to sequence a human genome in "minutes" for under $100. (click the link and go to "demo" at the bottom for a cool video). This will be available in 2010. So, the original human genome took about 10 years to complete, and now 10 more years later we think we will have it in under an hour. Science is just incredible.

More band names

Well, it has been a bounteous few weeks in my classes, with lots of new band names.

First, we got a couple of good immature, teen-punk bands. "Vigorous Gas Producers" and (one of my true favorites) "The Sausage Disease." We followed those up with "Swabbing With Sputum" and "Mexican Goat Cheese," both of which I think would fit in a similar, but ever-so-slightly more mature, group. Maybe in the range of Green Day instead of Blink 182.

We got a couple of good one-word names like "Invader" and "Shanker," and even a rockabilly-esque "Greased Watermelon." There was a crazy-but-adorable Japanese-pop "Fuzzy Test Tubes" (which is what Dr. Robison calls mice). And for good measure, one more Death Metal bands "One Time Kill."

I think, though, that my favorite thing to come from all this wasn't a band name at all. The best had to be a low-budget horror movie called "Return to the Dark Zone." It makes me wonder what the first Dark Zone was about. And why anybody would want to return there. And whether or not Bruce Campbell was in it.

Frustrated rant

Well, today I need somewhere to complain, and I figured, where better than the internet? That's where everybody else does it, right?

I am in a genomics class at BYU, and it is frustrating. Very frustrating. Just in case you don't know what genomics is, here is a brief summary (and those of you who do know what it is, you should realize that I am sacrificing some accuracy for the sake of simplicity).

Genomics is the study of all the DNA in an organism, or its genome. Genomes contain huge amounts of data. Seriously huge. Imagine trying to publish the genome in a book. If you typed A, T, C, and G (the four types of data in DNA- think 1's and 0's for computers) in 12pt. font with one inch margins, your book of one human genome would be just over a million pages long. So, lots of data. To help search all this data, we use computer programs, and often scientists have to write their own.

Now we get to my complaining (the part I'm sure you've all been waiting for). In my genomics class, we are supposed to learn some basics of PERL, a computer programming language. After spending two days in the computer lab, I have learned how to log in, how to move a file from someone else's folder to mine, and how to run that file. We also learned how to look at the code for that file, but what we see looks like this:

#!/usr/bin/perl
print "ARGV=",@ARGV, "\n";
print "ARGV[0]=",$ARGV[0], "\n";
print "ARGV[1]=",$ARGV[1], "\n";
open(DNAFILE, $ARGV[0]) or die "cant open $ARGV[0]: $!";
while() {
print "line $_\n";
$str = $_;
print "string is $str\n";

So, it's not super-helpful.

Today they asked us to write a program, scavenging the bits of code we needed from other, already functional programs. To me, this sounded like giving me a bunch of sentences in Chinese and saying, "Now, using any words you need from those sentences, write a novel." I had no idea even of where to start an assignment like that. So I, being a very hard working, problem solving kind of guy, sat and stared at my screen for several minutes.

Close to the end of the time limit, the teachers saw that there were two groups in the class: those who were getting computer science degrees (who had finished the assignment in a few minutes and were bored) and those who were completely lost and had given up. The teachers got frustrated with our lack of trying, and we got frustrated with their lack of explaining, and everybody left the class in a bad mood.

The sad part of the story is that there's no satisfying conclusion. I'm still frustrated about it. If anybody out there happens to know a good PERL programming guide, let me know. Or if anybody wants to copy and paste Chinese characters into a novel, that would probably be fun, too.

Retraction

If you have not watched tonight's Heroes, DO NOT READ THIS POST.

I just wanted to be among the first nerds to post this, since I finished watching Heroes a few minutes ago. I hereby replace their B+ with an F-. They killed Ando, dangit. You can't kill Ando. He's the best part of the show.

If they want their B+ back, they'd better make Ando's death somebody's dream...or have Hiro travel back in time...or something.

Media review

I'm going to take a page from the book of John and do a quick runover of the books and movies that have entertained me lately.

Hot Fuzz- A
When I heard that it was a comedy/cop movie/action flick, I was thinking it would be like Naked Gun. I was pleasantly surprised. The action was funny, but not so over-the-top silly that it was not enjoyable as action.
I watched an edited version (it is rated R), and the people I watched with had seen the original release. They said it was missing some of their favorite jokes, but I thought it was just fine edited. Some movies seem to lose a lot in the editing process (like Gladiator), but this one was more along the Blues Brothers lines, where I was left completely satisfied with an edit.

Fight Club- D+
This movie I give a mercy D+ because there were a few enjoyable parts. The best of those is the very end. Those few good parts did not, however, manage to redeem the movie. The acting is pretty good, but not great. The plot was interesting, but when they finally revealed the huge surprise, it wasn't that satisfying. And the girl looks too much like Jonny Depp for me to think she's attractive. All in all, not a great movie.

Heroes- B+
Season three is so far not the abysmal failure that season two was, but it still just doesn't have the magic that season one had. I watch the new episodes, but I don't need them in the same way that I needed to keep watching season one. The jury is still out on the promicin shots, but I think they're kind of lame. In fact, the whole plot of season three seems a lot like The 4400. I really enjoyed The 4400, but I am not sure I want to see it redone by Heroes. I give it a B+ out of good faith, because they seem to be heading in the right direction (i.e., away from the flying dork and towards Nice Sylar).

And some books for good measure...
Finding Darwin's God- B
This was an all-around good book. It was written by Kenneth Miller, a devout Catholic and a scientist, and the basic premise is that it is OK to believe in both science and religion. I think that every person who wants to study a physical science and keep their faith should read it. To quote a small part of what he says,

From time to time I have to struggle to explain to my students, and even my colleagues, not only why Darwinian evolution does not preculde the existence of God, but how remarkably consistent evolution is with ... even the most traditional of Western religions.

So, it's a good book. I could keep quoting the parts of it that I liked, but I will spare you.

Mistborn: The Final Empire- A
If I could give this book something higher than an A, I would. It is the best nerd book I have read in a long time. It's like if The Lord of the Rings and Sneakers had a baby. Magic, intrigue, fighting, a great heist, and lots of other great stuff. Brandon Sanderson really pulled it off with this one.

Dune- C-
Maybe I had had it built up too much, or maybe it just wasn't my style, but I really thought Dune was boring. It was like the Leviticus of SciFi. It just didn't keep me interested. I'd say more specifically, but it was a few months ago, and not too memorable, so I'll leave it at that.

Well, that's enough for today. I may continue this thread some other time.

Science boring...interest fading

I am in an immunology class here at BYU, and it can be super-boring. Not all the time, but sometimes it is a struggle to pay attention. One day I noticed that things on Dr. Robison's Powerpoints sounded a lot like death metal band names. Things like "Suicide Program" and "Death Domain."

Once I noticed this, the names started popping out at me all over in that class. Names like "Syphilis Test." The names weren't limited to just death metal, although those are the best ones. Today we talked about "Himalayan Fantasy," which my friend Brad says sounds to him like psychedelic rock, and "Ultrasonic Nozzle" which would probably be some sort of indie-folk-pop.

The moral of the story? Maybe scientists aren't as boring and nerdy as they want us to think...