Thursday, January 26, 2006

Tips for Purchasing a Llama

The Science Creative Quarterly offers up some tips for purchasing a guard llama. Apparently, this is a legitimate concern, as the author cites five related articles (although I'm not sure if they are real publications, and I'm not ambitious enough to find out for myself). Among the concerns is overqualification (yes, llamas come with different skill sets):

There is nothing worse than an overqualified llama. For instance a llama, trained in the delicate arts of diplomacy, will become depressed and distant if it is only given the task of guarding your ’86 Chevy Cavalier from any would-be vandal. Consequently, it will probably let its guard down and you will be left with a llama with very low self-esteem and an antennae-less ’86 Chevy Cavalier with the words “Wash me” scrawled onto the dirt caked rear windshield.

There's the Onion and Sports Pickle; SCQ may be our equivalent source of science humor.

Wednesday, January 25, 2006

Republican Fear Factor

In this week's cartoon, Tom Tomorrow introduces us to Fear Factor, neo-con style. Among the things Republicans are scared of:

  • They're terrified that their wives could get an abortion without their permission.
  • They're terrified that their religious beliefs might be undermined by secular society.
  • They're terrified that heterosexuality itself will be undermined by gay marriage.

It seems obvious to me that these are irrational fears, but it's not obvious to a large portion of this country. These fears manifest themselves in bigotry and oppression of others. Women are denied the right to any abortion regardless of the conditions. Certain religious beliefs (or religion in general) are endorsed by government, and in situations in which everyone is given fair treatment they claim oppression. A loving couple is denied the right to marry because they don't fit what a small minority has deemed the appropriate union (in my opinion, marriage as an institution should not receive government endorsement, but I'm a bit jaded).

A little background on where I stand on abortion: I think that any first trimester abortion should be allowed regardless of the conditions. There should be no restrictions, and they should be easily accessible. Anything after the first trimester should require the woman to show adverse health risks associated with pregnancy. She should not need to jump through loops to show she is at risk, and these abortions should also be easily accessible. I think I stand in the mainstream on this issue.

The last two Republican fears aren’t so easy to mock. One of them is the fear of terrorists. Terrorism is a legitimate concern, although the threat of terrorisms is often blown out of proportion and used to manipulate the general public. The comic isn’t mocking our fear of terrorism, but how the neo-cons use it for their own benefit. They take advantage of the average American's fear that terrorist will blow up their suburban neighborhood. They then use that fear to strip us of civil liberties in the name of anti-terrorism.

As opposed the first three examples (abortion, religion, and gays), it’s not so much the fear of terrorism that is the problem, but the response to that fear. It’s exaggerated and aimed in the wrong direction. We see the same thing in the final fear: “BIRD FLU”. As Tara so nicely pointed out, there may be a rational fear of a pandemic. The paradox is, if immunologists treat it properly (by vaccinating the public and preventing the virus from entering the country), then it appears that all of their work was for not because there was no epidemic. If they fail to act, then the disease may spread and they look like buffoons for not acting. Either way, they lose (there is the possibility that they do not respond and the disease does not spread, in which case they come out on top).

What concern me most are the rational fears to which the administration provides an inadequate response. Abortion, secularism, and gay marriage are important issues, but not nearly as significant as a bungled response to terrorism and pandemic. Of course, if we can’t adequately respond to regular old influence, what makes us think that the response to bird flu will be any better? Maybe it will be used as a scare tactic with no substantive strategy planned in response (see the government’s response to terrorism).

Tuesday, January 24, 2006

50 People Who Suck

The BEAST give us the 50 Moast Loathsome People in America. Of note to Clash, Culture, and Science:

46. Bruce Chapman

Charges: Founder of the misnamed “Discovery Institute.” Despite its pioneering title, Chapman’s organization seeks to make one of the world’s oldest, dumbest ideas the prevailing ideology. Seems to believe a petition signed by 400 PhDs and professors is convincing proof of Intelligent Design’s widespread acceptance. A lazy dissembler, he blames the lack of actual research and peer-reviewed articles on ID on academic “blackballing.” Right, ‘cause Galileo had it easy. Chapman’s sole trailblazing achievement in the field of academic inquiry has been in proving scientists can be even smugger-when driven by theology.

Exhibit A: Held high-level positions under Reagan and Bush, Sr. Is not a scientist.

Sentence: Infested and colonized by scabies mites: eyeless, brainless parasites unique to humans—perfect evolved to afflict us. Succumbing to the maddening itch, Chapman skins himself alive.

40. Tom Cruise

Charges: Criminal narcissism. After mega-lawyer Bert Fields threatened to sue The BEAST over Cruise’s inclusion in last year’s Loathsome List, we responded by giving him the editorial finger, and bracing ourselves for the legal spanking of our lives. Instead, the episode seemed to trigger a cascading ego crisis, culminating in a rapid and irrecoverable image downgrade from exalted idol to ridiculous buffoon. From his laughable claim of psychological expertise to his worst acting performance ever—as a man in love—Cruise simply cracked up on camera in 2005, and a public hitherto willing to overlook his obsessively inauthentic personality and comical religious affiliation had finally had enough. Cruise is a perfect example of a person who is simultaneously in love with and completely unfamiliar with himself, living in perpetual fear of self-actualization, and asserting a legal right to live free of criticism. A guy who can do whatever the hell he wants, yet chooses to devote his life to maintaining the public perception that he is somebody else.

Exhibit A: “I care man, I care. I care about you. I care about your children. I care about these people here in this room. Every one of you. And I...I mean it. That is not just some words to me. That is a promise.” Seriously, can’t even act like a human being.

Sentence: A lifetime of forced, joyless sex with famously beautiful women, only to have his colossal gay porn library posthumously bequeathed to the Smithsonian by bitter, unloved offspring.

39. Dr. David Hager

Charges: A Bush appointee to the FDA who was the key figure in its rejection of emergency oral contraceptive Plan B as an over the counter drug, which Hager bragged was the second time in fifty years the FDA has ruled against the overwhelming approval of its own advisory committee. The author of books like Stress and the Woman’s Body and As Jesus Cared for Women, Hager repeatedly sodomized his ex-wife for years against her will, alternately apologizing for or denying it when confronted by her, offering excuses like “You asked me to do that” and “Oh, I didn’t mean to have anal sex with you; I can’t feel the difference,” she told The Nation. Seems a bit fishy, a supposed authority on women’s health who can’t detect such a significant distinction with his most sensitive instrument.

Exhibit A: “My official comment is that I decline to comment.”

Sentence: A three-day group ramming by the multi-dildoed Oregon chapter of NOW, after which Hager will walk with a pronounced limp, never to regain control of his sphincter, and discover himself to be inexplicably pregnant.

37. Donovan McNabb

Charges: Played so poorly that his demoralized and alienated teammates yearned for the return of ego-vampire Terrell Owens. A chocolate commodity so inoffensive he makes Hershey bars look militant. Responded indignantly to loopy criticism from the head of the Philly NAACP, but laughed off Rush Limbaugh’s racist broadsides. Choked in the fourth quarter of Super Bowl; this year he enjoyed the worst fourth quarter passer rating in the league. Made over $11,000,000 in 2004.

Exhibit A: Logged only significant playing time this season with his mom in soup commercials.

Sentence: Peon at a Campbell’s Soup cannery in China. Flogged routinely for underperformance.

33. Johnny Damon

Charges: Any baseball player with highlights in his hair should be faced with the same penalty system applied to those using performance-enhancing steroids. It’s ruining the game. And if a ball player is going to grow a beard, it should be a Charlie Manson/Thurman Munson scraggle of bushy whiskers, not a neatly manicured and softly conditioned frame for your pretty face. The only thing that got Damon to step into line and quit hair-farming was a 52 million dollar check from the New York Yankees. Boston prayed for the multi-bladed Gillette that officially made him a Yankee to slip while gliding over his Adam’s apple and spill his lifeblood into the bathroom sink.

Exhibit A: Going from the Red Sox to the Yankees is like fucking the guy that murdered your husband.

Sentence: Killed by barrage of hurled D cell batteries when he takes the field at Fenway next season.

16. R Kelly

Charges: As if videotaping himself urinating on an underage girl wasn’t bad enough, Kelly decided to follow up by inflicting the worst piece of music in American history upon the public consciousness. Kelly claims he is a genius for squeezing out what are so far 12 installments of his “hip hopera,” “Trapped in the Closet” like so many virtually identical turds, with no variation in musical content and a story line so patently terrible that it soon became the subject of a parody-frenzy involving Saturday Night Live, South Park, Mad TV, Jimmy Kimmel, and the Upright Citizens brigade, among many others. Even his good songs all seem to be about fucking underage girls.

Exhibit A: Seriously—pissing on an underage girl.

Sentence: Trapped in a closet. Eventually dies of thirst.

There are also some good "bend over and fuck me" Democrats, like Hillary Clinton and Joe Loserman, and your usual stable of Republican colostomy bags. Don't miss the surprise at #4.

(via Pale Blue Dot)

Does Being a Horse Count as an Ethnicity

A high school teacher who happens to be a Pittsburgh Steelers fan (or is he a Steelers fan who happens to be a teacher?) made one of his students take a midterm exam on the floor last Friday because that student was wearing a Denver Broncos John Elway jersey. The kid didn't get the memo: if you're gonna wear a John Elway jersey, go with the Orange Crush look, not the ugly ass angry horsey jersey.

Kid wearing new Broncos jersey (left) and John Elway wearing orange crush jersey (right).

Sunday, January 22, 2006

Is Everyone On Earth Named Steve Smith?

In honor of our favorite punt returner who's quarterback can't get him the ball, here is list of all of the Steve Smith's I know of. Feel free to add more in the comments.

Here's the Carolina Panthers wide receiver (the guy who's quarterback can't get him the ball) and Chad Johnson's junior college teammate that inspired this list. This dude's got a pretty bad-ass tattoo on his upper arm; that distinguishes from the other Steve Smiths. He's the only Steve Smith playing in the NFL (for now), but not the only football playing Steve Smith.

Steve Smith is also the #2 receiver on the USC Trojans. This Steve Smith will be playing in the NFL in two years, only adding to the confusion of players playing the same position with the same name (see here for another example). It doesn't help that USC's Steve Smith is an undersized receiver, meaning not only do Steve Smith and Steve Smith play the same position, they play the same position in the same way.

At least this Steve Smith plays a different sport than the previous two Steve Smiths. Well, technically he no longer plays his sport professionally. Looking at him in the USA Basketball uniform reminds me of how Steve Smith never quite lived up to expectations. This is the opposite of Steve Smith the Panther, who was never supposed to amount to anything, but ended up a pro-bowl quality receiver.

This Steve Smith (actually, Stephen A. Smith) used to be a respectable sports writer. Now he's become a sports talking head and D-list celebrity. Oh, and he writes his columns on a Blackberry. And he's really annoying when he opens his mouth and tries to talk -- not a good quality for a TV personality (but, surprisingly, one that a lot of TV personalities share).

Ok, so Steve Smith is not a real person, but what is "real" anyway? He's a character on American Dad . . . you know, that show that comes on after Family Guy. Never mind.

Weekly Random Ten (22 January 2006)

New Rules Edition

Alright, we're gonna try something new with the evolgen Weekly Random Ten. Here's the new rule: I get 10 songs worth of time to write an entry. I've used this as a rough guideline for the random ten in the past, but I never put it in writing. Once the last note in the last song is played, I must stop writing -- even if it's in mid sentence.

So, I'm sitting in front of the TV in between playoff games. I blew my pick in the first game. Looks like I went with the wrong road underdog to win. I still think the Panthers can win, but it will be quite a feat if both road dogs win in the conference championship. At least neither Delhomme nor Hasselbeck have a goofy beard -- of course, Hasselbeck's got that bald thing going against him.

I'm gonna do that stupid sports commentator thing and stand by my pick in the second game despite how things have changed. Does that piss anyone else off? An expert analyst will pick a team to win the Super Bowl at the beginning of the season. Then, halfway through the season, the team falls to 4-4, and they're still saying, "I picked them at the start of the season and I'm standing by my pick." That just shows you're too stupid to realize you were wrong and don't know how to reevaluate your position with further evidence. It's bullheaded; it's stupid. At least they're only talking heads (talking about sports, even), and not politicians responsible for making important decisions about the country. It would really suck if politicians were so stubborn and refused to change their stance on an important issue like war in light of new information . . . oh, wait, nevermind. Asshats.

Ok, I've got a couple more songs to kill. How about the size of the American flag that they busted out for the national anthem at the start of the Seahawks game. They love America a lot more than I do. Shit. All that's missing is an F-14 flyover and a huge fireworks display. That would really show those terrorist bastards. Why does the beginning of a sporting event turn into a caricature of patriotism, or even a celebration of a military state. By the way, the Seahawks have the fugliest uniforms ever.

That's enough from me for now. Here are the ten songs I listened to while writing this crappy entry:
  1. Sublime - Get Out!
  2. Gorillaz - Feel Good Inc.
  3. Living End - So What
  4. 311 - Light Years
  5. Tilt - Bad Seed
  6. The Hives - A.K.A. I-D-I-O-T
  7. NOFX - Eat the Meek
  8. Jurassic 5 - React
  9. The Ataris - Neilhouse
  10. Pete Townshend - Let My Love Open the Door

Last Second Picks

It's a few hours before the games begin and here are my picks (see the last edition for how it works):

Pittsburgh Steelers at Denver Broncos
Who I want to win: I'm a Raiders fan, so I hate the Broncos. There is no way I can pull for them. That means that I'm rooting for the Steelers by default. Plus, how can you not be for Troy Polamalu and his hair. And I live in Steelers country, so it's hard to not get sucked into the black and gold fever.

Who I think will win: On a neutral field, the Steelers would win. Too bad this game is being played at Mile High Invesco Field. Broncos will win . . . as long as Plummer doesn't blow it.

Carolina Panthers at Seattle Seahawks
Who I want to win: Ever wonder what a seahawk is? Of course, the Panther is one of the archetypes of conservation genetics. I would be happy to see either of these teams go to the Superbowl. I'm kinda sick of Sean Alexander, though. If Alexander plays well, I wanna see the Panthers win. If Alexander sucks it up big time, go Seahawks.

Who I think will win: The Panthers have won their last five road games (including two playoff road wins). There is no way they can win another road game. There is no way they make it to the Super Bowl. There is no way I'm not picking the Panthers. Yes, the Panthers will win. Plus, when I see someone as tall as I am excelling at receiver in the NFL, I can't help but pull for him.

Enjoy the games.

Sports Reporters

What the hell was going on with the Sports Reporters this morning? It was like the editor was playing a practical joke on all of us.

Thursday, January 19, 2006

Prove It!

The Quote of the Day goes to Brent Rasmussen of Unscrewing the Inscrutable:
"Proof" is a word that only applies to mathematics and liquor.
I now return you to your regularly scheduled podcast . . .

Monday, January 16, 2006

Haven't You Seen My Movies?

Something Awful is missing the caption to this image:

There's a motherfucking snake on the motherfucking plane . . . motherfuckers!


If you don't get it, you need to get it.

Sunday, January 15, 2006

One Bourbon, One Scotch, and One Double Black Diamond

America's favorite drunk-ass skier, Bode Miller (who looks a lot like Edward Burns), has come under fire for boozing while slaloming. Turns out Bode's a drinker with a skiing problem. Slate offers a nice editorial clarifying the whole thing:
Miller tried to clarify his statements, explaining that he didn't actually drink on race mornings, but that, on occasion, he'd arrived at the start with a hangover from the night before.
So, Bode goes out and wins the downhill on Saturday, gets hammered that night, then shows up for the Slalom with some knockin' in his noggin. Sounds ok to me. Rage on Bode, rage on.

More Sunday Afternoon NFL Blogging

Is this confusing for anyone else?

Adrian Peterson the Chicago Bear (left) and Adrian Peterson the Oklahoma Sooner (right).

One thing that comes with having a good season is increased TV coverage. I've seen a lot more of the Chicago Bears this year (and now in the playoffs), and I've become familiar with some of their players. When I heard that Adrian Peterson was their running back, I thought, "Wow, he wasn't at Oklahoma very long." It turns out there are two Adrian Petersons. In a couple of years, Adrian Peterson, the younger, will be starring in the NFL, only adding to the confusion.

At least the Jason/Jayson Williams had the decency to stand out by playing different positions. Additionally, only Jayson Williams was charged with manslaughter, only one of the Jason Williams has the motorcycle riding skills of Kellen Winslow Jr., and only one of the Jason Williams tokes with Randy Moss.

Why The Patriots Lost

They didn't give the ball to the Diet Pepsi Machine. Tom Brady threw 36 passes, none of them to the Machine, despite the fact that machine has good hands (what hands?). Let's just hope Pepsi stops running those stupid commercials. Pepsi should take a lesson from Burger King if they wanna incorporate NFL footage into their adds. The latest one with the King as Steve Young is absolute magic (I can't find a link to the ad).

Toni Tony Tone & A Tribute to Troy

We're all gonna rag on Peyton Manning for losing the game (or Mike Vanderjagt if you hate idiot kickers) -- Manning has never been able to win in college or the pros, providing solid evidence for the Ewing theory when Tee Martin won a national championship at Tennessee after Peyton graduated.

But I'm gonna be a total asshole and claim Tony Dungy should shoulder a lot of the blame. Sure, his son just died. And, yeah, the dude's a man of faith (whatever the hell that's worth). But Dungy's got a bit of Ewing theory going for him, seeing as how the Tampa Bay Buccaneers won a Super Bowl the year after firing Dungy. Dungy deserves some props for turning the Bucs into winners and leading them to the playoffs, but he's gonna be remember as a guy who couldn't win it all.

The Dungy-Manning pairing may make it impossible for the Colts to ever make it to the Super Bowl. The Patriots seemed to be Manning's NFL version of the Florida Gators, but this year (following one of the best starts to season in NFL history) the Colts couldn't even win a single playoff game. It's another year and another flop in the playoffs for Dungy and Manning. I wonder if Dungy never bothered to come back to Indianapolis after his son died or if Peyton got injured while his offensive line could not protect him, would the Colts have fared better in the Playoffs?

So, let's stop treating Dungy like a sacred cow -- the dude's got more choke in him than Michelle Kwan. Yeah, I went there. Whatcha gonna do about it?

Oh, and my boy Troy was all over the place today. Even if he can't catch, the man can defend the pass better than any other safety out there. Don't let anyone cut those Samson locks; his hair is the secret to his power.

Saturday, January 14, 2006

Detecting Natural Selection (update)

I previously remarked that I would be posting my series "Detecting Natural Selection" at Clash, Culture and Science. Well, I changed my mind. The newest installment of "Detecting Natural Selection" has been posted at ScienceBlogs.

Friday, January 13, 2006

Happy Friday the 13th

It's Friday, January Thirteenth. Don't walk under no ladders. Don't let no black cats walk in your path. And don't shake hands with no lepers.

Ok, I made that last one up.

Thursday, January 12, 2006

Fuck You, Rate My Professor

To anyone who has ever received a poor review on, you can now stake your revenge at Rate Your Students.

The Best Things Ever Since Anything Ever

A few things on the internets made me laugh out loud recently. Here they are:
Maybe the last one isn't that funny, but I wanted to post a link to the first two, and "a few things" sounds better than "two things", and everyone knows you need at least three things to make it a few . . . exemplary run-on, don't you think?

This Is What Happens When You're Culturally Illiterate

You misread obituaries. Crooked Timber, far more cultured than I, reports that Birgit Nilsson has passed away. Being uncultured, I read it as saying that Brigitte Nielson had died. This would be a very different story. Nilsson was a top soprano in her day (no, not a Soprano, but a singer) hailing from Sweden -- I only learned that from reading her Wikipedia entry.

Birgit Nilsson on the left, and Brigitte Nielson on the right. Notice the differences (ie, Birgit seems to live in some sort of gray-scale world).

Brigitte Nielson, on the other hand, earned fame in the 1980s for her appearance in Beverly Hills Cop II, her marriage to Sylvester Stallone, and her fling with Mark Gastineau. She disappeared (as much as a 6 foot 1 inch, platinum blonde, Dane can disappear) from the limelight until she co-starred in the television opiate, VH1's The Surreal Life. It was during her time on that show that she "fell in love" with Public Enemy's Favor Flave. They then starred in a spinoff show devoted to their disturbing relationship. Apparently, they're splitsville, and Brigitte is planning to marry some guy half her age even though she still hasn't completed the divorce with her previous husband.

Birgit and Brigitte have something in common: both had careers as singers . . . Birgit far more successful and talented.

Wednesday, January 11, 2006

NFL Playoff Picks

I promised you more diversity, and now I'm gonna deliver. Today, I give you my way of picking the winners of sporting events. The premise is, a sports fan has the team he thinks is going to win a game and the team he wants to win. Sometimes they are the same team, sometimes they are not (this leads to hedging your bets by laying down money on a team you don't want to win). I got this idea a couple of weeks ago, and I wish I had done it for the wild-card weekend, but I did not. So, here is the first "who I want to win, and who I think will win". Most of the time it comes down to which team I hate the least.

Washington Redskins at Seattle Seahawks
Who I want to win: That's easy: the Redskins. If you paid attention, you'd know that I'm pulling for the racist epithets to go all the way just so I can watch Clinton Portis play dress up. That, and I have a hard time pulling for a bald quarterback.

Who I think will win: The Seahawks will probably win seeing how they have the best running back in the NFL (yes, better than Southeast Jerome), and the 'Skins set the record for fewest yards in a playoff win.

New England Patriots at Denver Broncos
Who I want to win: Neither team. I'm hoping an avalanche buries the city of Denver this weekend, and the game gets cancelled, so the winner of the other AFC divisional game gets an automatic trip to the Super Bowl. I'm sick of the Patriots -- they beat my beloved Raiders in the tuck game. I hate the Broncos (and the Chiefs) because I'm a Raiders fan.

Who I think will win: The fucking Patriots. They always win these games. Even though Denver beat them earlier in the season. Even though Denver had a better regular season. Even though New England has a bunch of injured players. New England will still win.

Pittsburgh Steelers at Indianapolis Colts
Who I want to win: Colts, I guess. The Steelers busted up Carson Palmer's knee. They also knocked off the Bengals, which means no more Chad Johnson touchdown celebrations.

Who I think will win: The Colts have a better defense, a better offense, and home field advantage. They also have a Manning at quarterback, which means look out for the choke. That said, I still think the Colts will win.

Carolina Panthers at Chicago Bears
Who I want to win: I'm apathetic about this one. When in doubt, pull for the underdog. So , let's go Panthers. Besides, if the Bears win, the final score will be 5-3. At least if the Panthers win there's a chance that some points will be scored.

Who I think will win: The Bears are favored, but I think the Panthers will pull it out. The Bears have a great defense and no offense. The Panthers have a solid defense and an ok offense. Unless the Bears D puts up two scores, they ain't gonna win.

There they are, my picks. Let's see how I do.

Evolgen Jumps the Shark

In a classic episode of Happy Days the Fonz goes water skiing and (in a moment of pure special effects glory) jumps over a shark. It is said that the show was never the same again. Hence, the term “Jumping the Shark” was born to describe the moment when a TV show (or any other pop-culture item) tries some gimmicky trick to lure in viewers because they have run out of good ideas -- see, also, it’s all downhill from here.

In announcing its move to the new Seed Media Group blog consortium, Science Blogs, Dispatches from the Culture Wars proclaimed that Ed is Selling Out, conjuring up images of Pete Townshend and Roger Daltrey hawking deodorant and baked beans on an album cover. I too am moving over to Science Blogs, but while Ed may be doing it for the money, evolgen’s move over to Seed is motivated by sheer masochism. You see, I’m jumping the shark, shooting myself in the foot so to speak.

Don’t expect evolgen to ever be the same again. This humble little blog is movin’ on up to the east side (to a deluxe website in the sky) to live with George and Weezie. You can say that we finally got a piece of the pi (bad, nay, horrible science joke).

Most of the science content of evolgen will be posted at my new Science Blogs url ( Bookmark that link, write it down, tattoo it on your ass, or do whatever you need to do to remember my new internet location. But don’t lose this url. My current plan is to continue posting non-science related stuff here at Blogger (and we will maintain this site as an archive of previous evolgen posts) such as the apathetically enjoyed Weekly Random Ten and some stuff on sports and pop culture. While most of the science content will be posted over at Science Blogs, I will keep posting my Detecting Natural Selection series at Blogger.

Given the shift in focus of this blog, and the fact that the Science Blogs site will contain the bulk of the evolution and genetics that make up evolgen, I will be moving the description “AT THE CONVERGENCE OF EVOLUTION AND GENTICS” over to the Science Blogs version of evolgen. The Blogger version of evolgen will now be known as:

Clash, Culture and Science

The name comes from the title of a Rancid song (Cash, Culture and Violence), with some slight modifications. “Clash” refers to the only band that matters, but also the general idea of confrontation, disagreement, and antagonism. You will be seeing more posts on things that piss me off (ala another mad biologist you may be familiar with), and these will not be limited to intelligent design creationism. As you may have noticed, I am a pop-culture whore. You can expect a lot of posts on this guilty pleasure (along with some posts on sports) in the “Culture” section of Clash, Culture and Science. Finally, I would be remiss to leave out any “Science” writing. While the new Science Blogs version of evolgen will have the bulk of the science content, Clash, Culture and Science will also have a science angle.

I’m not the only one to jump the shark (or sell out, whatever the case may be). Here are some friends of evolgen that will be joining me over at Science Blogs:

Dispatches from the Culture Wars
Stranger Fruit
The Intersection
Gene Expression
Living the Scientific Life

Give the British Some Spare Time . . .

. . . and they'll give you a neat little web-ap. The author a popular molecular evolution text has heeded the call of E.O. Wilson and created a webpage for every species known to man. He actually didn't make a separate page for each species, but rather created a website that searches three databases for information on a query species: it looks up the taxonomic name for the species on NCBI, searches the web (using Yahoo) to find up to five images of the query organism, and searches Google Scholar for articles related to that species.

The application (known as iSpecies, which I don't think has anything to do with iMac, iBook, iPod, or I, Robot) is available here.

(via Rod Page's blog)

Are Deletions Deleterious? Part 2

In a previous post I mentioned three recent papers from Nature Genetics that deal with detecting and describing polymorphic deletions using SNPs. I only described the content of one of the papers, as I spent about half of the post trying to give readers some background as to why this is an interesting issue (ie, the idea that deletions are deleterious). In this post I will describe one of the other two papers and, hopefully, formulate some sort of unified idea of why we (by we I mean humans, but these findings should be expected in all other eukaryotes) harbor deletion polymorphisms. I will then add a third (and, probably, final) post on linkage disequilibrium and SNPs.

The approach I previously described uses allele and genotype frequencies to identify clusters of SNPs that are not in Hardy-Weinberg equilibrium. This involves analyzing all of the SNPs in the entire population simultaneously. Another approach, described in the paper from Jonathan Pritchard’s group, uses known relationships of family members (so called “parent-offspring trios”) to identify SNPs that are transmitted from parents to offspring in a non-Mendelian fashion. They start with the observation that individuals carrying a deletion at a SNP locus will appear to be homozygous when genotyped at that SNP (this same assumption was made by Altshuler). They then examined the progeny from the parent-offspring trios for individuals that are homozygous for a particular SNP (note: there will be a lot of homozygous SNPs in any one individual) and see if they could have inherited the same allele from each of their parents. For example, if the parents are genotyped as “AA” and “TT” at a particular SNP, and their child is genotyped as “AA”, either there was a mutation in the germline of the TT parent (changing one of the T alleles to A), or the TT parent is actually “T-“ (where the “-“ means that parent is missing a second copy of the SNP). If one of the parents is T- then the child’s genotype is actually “A-“, and that child inherited the deletion from the parent with the genotype T-.

Figure 1. Examples of four of the seven types of trio genotype configurations used in this analysis.
The true genetic state of each individual is depicted within his or her pedigree symbol. The called genotype, when it differs from the true genotype, is shown outside the pedigree symbol. The three upper configurations (A and C) all result in mendelian incompatibilities. We define 'Type I mendelian incompatibilities' as those that are compatible with a deletion transmitted from parent to child and 'Type II mendelian incompatibilities' as those that are incompatible with the deletion model. Key to figure: A: mendelian incompatibility, genotypes compatible with a deletion transmitted from the mother; C: mendelian incompatibility, genotypes incompatible with a transmitted deletion; E: no mendelian incompatibility, genotypes compatible with a deletion transmitted from the mother (but not the father); G: no mendelian incompatibility, genotypes incompatible with a transmitted deletion. Candidate deletion regions are runs of consecutive SNPs with at least two Type I mendelian incompatibilities and other SNPs that are compatible with a deletion; all the SNPs must suggest transmission from the same parent. See further details in Methods.

Any run of at least two Mendelian inconsistencies was labeled as a deletion. They examined parent-offspring trios from two populations: a European derived population (CEU) harbored 345 deletions and one from Nigeria (YRI) harbored 590. Just like the other paper I described, they validated some of the deletions using quantitative PCR and confirmed that the PCR products from all 12 candidates were in fact valid. They also using an oligonucleotide microarray to test for false positives in 9 of the offspring at 93 deletions and confirmed all but 13 of the deletions (14% false positives). I won’t get into the details of it, but they assessed their power to detect deletions given the amount of polymorphism in the SNP data set, the spacing of SNPs, and the size of the deletions they were identifying.

The median deletion size was 10.6 kb and 8.5 kb in the CEU and YRI samples, respectively, and the size distribution is L-shaped (many small deletions, and a tail containing the large deletions). Most of the deletions were segregating at low frequencies, and 39% were identified in only one trio. Interestingly, some of the deletions at the same locus appear to have different breakpoints, and some deletions sit on multiple haplotype backgrounds, suggesting that certain loci have been deleted independently in multiple lineages. This is nothing new, as many factors (such as repeat sequences flanking a region) can make a particular locus more prone to deletion and duplication (more on this later).

Finally, they took a closer look at deletions that contained genes (exons and introns) and found 267 genes within their entire sample of deleted regions (201 of which were deletions of coding sequence, and 92 were completely deleted genes). There was a deficiency of SNPs in genic regions within deletions compared to genic regions with no association to a deletion, suggesting that purifying selection against haplotypes carrying deletions of genes decreases the variation at these loci. They assigned each gene to a functional class and found an overrepresentation of genes involved in immunity, sensory perception, cell adhesion and signal transduction in their set of 267 deleted genes. These functional classes are similar to those identified in screens for segmental duplications, genes with signatures of positive selection, and lineage specific gene family expansions.

I think the two most interesting finds are the reuse of deletion breakpoint regions (independent origins of the same deletion) and the analysis of functional classes. Many human diseases are the result of the deletion, duplication, or relocation of a particular genomic region. These chromosomal aberrations often occur in somatic cell lines (ie, they are not inherited per se, but the mutation happens some time during the individual’s life history). There is some aspect of heritability when it comes to these types of mutations, as you can inherit a predisposition to a certain genetic disease if you get a defective allele from one parent or you inherit a locus that is predisposed to a deleterious mutation. How can you be predisposed to get a particular mutation? Well, if you have some sort of repetitive sequence (transposable element, segmental duplication, etc) flanking a “disease gene”, that repeat can induce a genomic rearrangement that leads to some deleterious change in that disease gene. The same idea is behind the independent origins of similar deletions that Pritchard’s group proposes.

It appears that certain functional classes of proteins are more prone to rapid evolution, duplication, and deletion. One explanation for the differences in “evolvability” between classes of proteins lies in the differences in purifying selection on different genes. Let’s assume that genes that carry out a more important function than other genes are less robust to mutation (both in amino acid sequence and expression), so that changes to the copy number of particular genes will have deleterious effects. Not only will natural selection remove haplotypes that carry a deletion or duplication of that gene, it will also select against repetitive sequences flanking that gene that would allow for the duplication and deletion events to occur. We see this type of pattern when we look at the location of transposable elements (TEs) in a genome -- they are clustered in intergenic regions, although this may also be due to the effects of TEs on the expression of nearby genes. If only certain genes can withstand having rearrangement inducing repeats in their vicinity, then certain functional classes will be overly duplicated and deleted. Furthermore, some genes (such as large gene families like the odorant receptors) appear to be overly duplicated, suggesting natural selection may favor repetitive sequence near these genes (in fact, duplicated genes alone can spur on more duplication because they are repetitive sequences themselves).

If we imagine that certain classes of genes are under more purifying selection than other classes, then we can expect to see the same types of genes in the rapidly evolving class regardless of how we measure the rate of evolution (nucleotide sequence, segmental duplication, deletion, flanked by repeats, or any other technique). I hope to finish my discussion of SNPs and deletions with my next post in which I will attempt to write about linkage disequilibrium (a subject that gives me trouble).

Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. 2006. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 38:75-81

Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA. 2006. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet. 38:82-85

McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB Lee C, Daly MJ, Altshuler DM, & The International HapMap Consortium. 2006. Common deletion polyrmorphisms in the human genome. Nat Genet. 38: 86-92.

Tuesday, January 10, 2006

Creationist Genome Rearrangements

Following in the footsteps of John Davison, Disco fan and (bad) IDEA club head honcho Casey Luskin has delved into the genome rearrangements discussion. The premise of his argument (from what I can gather seeing as this guy ain't no Dobzhansky) is that humans and other apes do not share a common ancestor because they differ in chromosome number, and that karyotypic change would have been selectively deleterious. There goes the research plan for my postdoc! Anyway, PZ Myers frisks him pretty good, and I added a comment to Myers's post:
Even an argument about duplication would be bogus because of the amount of substantial duplications segregating in populations as Mendelian variants (aka, not mutations in the germline of the previous generation). Luskin doesn't understand how to distill information - yes, there are deleterious rearrangements, but there are also a whole bunch of (nearly) neutral ones. It's just that there has been an ascertainment bias in discovering fussion/fissions, deletions/duplications, and inversion associated with disease. That bias is now fading with population genomic studies of human variation -- there are a lot of structural differences between two "normal" humans.
For an example of the amount of structural variation in the genome, see here. I've also dealt with this when I wrote about a human inversion under selection. And, don't forget that the Robertsonian fusion is probably not responsible for the incompatibility between chimps and humans. Hell, you can take a chunk out of our genome and it still works ok.

Monday, January 09, 2006

Weekly Random Ten (9 January 2006)

"Where the Hell am I?" Edition

Football (or "American Football" to my international readers) is a dangerous sport full of high impact collisions and body contortions. The power at which the hits occur is made worse by the impression of invincibility the athletes receive from their heavy padding. The average football player wears a helmet with face mask, shoulder pads, hip pads, thigh pads, knee pads, and a tail bone pad. Additionally, many players choose to wear add ons to their shoulder pads (lower back padding, pads that go around the entire lower torso, pads that extend to the biceps, neck rolls), elbow pads, lower arm padding, and a mouthpiece is required in youth leagues, high school, and college (but not in the professional leagues) to reduce the risk of concussions. All of this equipment makes a player (one who's in good shape) look like the caricature of masculinity -- large head and shoulders, narrow waist, and spandex pants that accentuate the shape of the legs.

As I mentioned, it has been argued that the pads make the players feel invincible, so they hit harder than if they were not wearing any protection (the type of tackling in football differs from that in rugby where the padding is minimal). And, as someone who has worn a football helmet, I can say that they are not very comfortable and actually make minimal collisions feel a lot worse. Additionally, they press up against your forehead in an uncomfortable manner that takes getting used to. The helmets (along with mouth pieces), however, do reduce the chance of a concussion, and the facemask protects your pretty face from getting all mashed up.

Two helmets with the classic design (left two), and one with the new Revolution design (right). Notice the additional area to the right of the earhole in the Revolution.

The modern football helmet is a combination of a plastic outer shell with soft padding (often times air cushioned) inside, and it is held on by a chin strap. The facemask is made up of metal bars coated in rubber (much like a hockey goalie's or baseball catcher's facemask). The design used by most players has been around for decades, but was not constructed to any definitive specifications to reduce the impact of a collision. That has changed with Riddell's Revolution helmet, which was designed to reduce the impact of a collision to the side of the head (the area shown to be mostly responsible for concussions). A medical study has confirmed that the new design reduces the chance of a concussion among high school football players:
"Across the three years of this initial study, the annual concussion rate was 5.4 percent in athletes wearing the Revolution helmet, compared to a 7.6 annual percent rate in athletes wearing standard helmets, representing a 2.3 percent decreased absolute risk of concussion for high school football players. In terms of relative risk, Revolution wearers were 31 percent less likely to sustain a concussion compared to athletes who wore standard football helmets."
With a more intelligent design (sorry, couldn't resist) and evidence to support its efficacy, you'd think that all players would jump at the opportunity to wear this safer helmet. In doing so you'd be forgetting about the machismo and image that go into a football player's wardrobe. Defensive backs and wide receivers (players who do a lot of running) have been known to favor playing without knee, hip, thigh, and tailbone pads because they impede movement. Many professional players don't wear mouthpieces (the single best protection against a concussion), especially quarterbacks who must bark out audibles at the line of scrimmage. It's not uncommon to see a player with his chin strap not fully buckled -- something I can only attribute to style over substance (or safety). That said, it suprises me to watch football games (collegiate and professional) and see so many players still wearing the old design when a superior (or, at least, potentially safer although definitely not more dangerous) helmet is available.

Before I start sounding too much like your mom, let me remind you to wear your mittens because it's cold outside. Now that you know more that you would ever want to know about football padding, here is this week's evolgen Random Ten:
  1. Antiflag - She's My Little Go Go Dancer
  2. The Ataris - 1-2-3-4
  3. Ol' Dirty Bastard - Shimmy Shimmy Ya
  4. Guns N' Roses - Oh My God
  5. Catch 22 - Learning the Truth
  6. No Use For a Name - Best Regards
  7. Less Than Jake - Out of the Crowd
  8. Sonic Youth - Tunic (Song for Karen)
  9. Garbage - Push It
  10. Steppenwolf - Magic Carpet Ride

Sunday, January 08, 2006

Separated at Birth?

That's Chris Mooney (one of the few decent science journalists) and Seth MacFarlane (creator of one of the greatest TV shows of all time). Is it just me, or does Chris (on the left) look an awful lot like Seth (on the right)?

Semester Plans

A new semester begins tomorrow, and this provides some structure to an academic’s life even if he does not take classes. As an aside, I often have difficulty communicating to those ignorant what exactly a graduate student does if he does not take classes. They ask me if I’m working on my thesis, and I say, sort of. I try to explain to them what “research” means, and how I’m trying to build a collection of findings that will eventually make up my thesis. Anyway, there still is structure to be derived from an academic calendar for those of us who must also teach (or, as I prefer to view it, baby sit the lazy).

Considering the new semester begins tomorrow, now seems as good a time as any to lay out some plans for the upcoming semester. Here are the ten things I need to do before the end of May:

  1. Do some wet lab work (I’ve become quite computational).
  2. Push some flies (see #1).
  3. Write at least one good science blog post a day to make me think about the literature I’m reading (unless there aren’t enough articles published worthy of writing about, a decision that will be determined based on whether I feel like writing a blog post).
  4. Read every article that I’ve downloaded to my hard drive (and put into a folder called “To Read”).
  5. Master Perl, R, and MySQL (just because I’m computational, doesn’t mean I know what I’m doing).
  6. Publish three papers in Nature, one in science, and a couple each in Genetics, MBE, and Evolution (because my CV looks more barren than Gilda Radner . . . too soon?).
  7. Sequence five eukaryotic genomes in my spare time.
  8. Get a stalker.
  9. Derive the grand unifying theory of everything.
  10. Figure out a tenth goal for the upcoming semester.

Too much? Maybe it’s a bit ambitious. The way I see it, at least if I shoot for the moon and miss, I’ll end up in the stars . . . or some bullshit like that.

Find Religion

The Carnival of the Godless is up. I don't usually advertise this carnival, but I have submitted an entry so I figured I'd reciprocate some of the traffic it's sending over here.

As you may have noticed, there have been a few of non evolution/genetics posts recently (ie, my post on the Rose Bowl and religion featured by the COTG). Does this hint that there is a change on the way? Wait and see. I promise you'll always be able to get your evolutionary genetics from evolgen.

Saturday, January 07, 2006

Are Deletions Deleterious? Part 1

Large scale deletions have been used by geneticists for a long time. A Drosophila geneticist can order a line (a small population of nearly identical flies characterized by some genetic similarity) carrying a deletion for practically any segment on any chromosome (this is only true for D. melanogaster). These so called “deficiency” stocks are useful as they can be used to expose recessive mutations for a particular region of the chromosome (creating hemizygous individuals). They are also used to map the genomic location of recessive mutations, in a process known as deficiency mapping. Overlapping deletions either expose the mutant phenotype or do not, allowing the geneticist to determine the section of the chromosome containing the mutated gene.

Large scale deletions in Drosophila are assumed to be deleterious because they eliminate multiple genes within the deleted region; flies homozygous for these deficiencies probably do not survive to adulthood, and if they do, they most likely suffer major fitness costs. What about smaller deletions? We can assume that the deletion of a coding region (either partial or complete) is probably not appreciated by the organism if the deleted sequence encodes some important protein. Also, if the deletion leads to a frameshift, the encoded protein will be dramatically changed. Many non-coding sequences contain important regulatory elements, the deletion of which is probably ill advised if they control the expression of a vital gene. But many eukaryotic genomes (including all of the mammalian genomes studied) have huge chunks of non-coding DNA, much of it probably not involved in the regulating gene expression.

If we examine a genome, we can identify deletions and determine whether they are more common in coding or non-coding regions. With the influx of whole genome sequences, much has been made about copy number variation in humans. Variation in copy number can be due to a duplication in one genome or a deletion in the other genome. If, however, one genome has a single copy of a sequence and the other genome has no copies, deletion in one genome seems like a very likely scenario. Three papers published in Nature Genetics report the identification of polymorphic deletions in human populations and some analysis of their distribution (for a review of these articles, go here).

David Altshuler’s group (along with the HapMap Consortium) present a single nucleotide polymorphism (SNP) based approach for identifying deletions. Their design is quite elegant and is based on the expected relationship of allele and genotype frequencies at neutral loci. The observed genotype frequencies of a particular SNP in a population can be used to determine the allele frequencies. We can then use the allele frequencies to calculate the expected genotype frequencies under Hardy-Weinberg equilibrium. If the observed genotype frequencies deviate from the expected frequencies, we have too few individuals with a particular genotype and too many with some other genotype. In the case of polymorphic deletions, an individual that is hemizygous (has only one copy of a locus) will appear to be homozygous when a SNP within that deletion is genotyped. If there are an excess of apparent homozygotes (based on the SNP data) clustered in a particular region, we have reason to suspect that there is a deletion of that region segregating in the population.

They identified 541 deletions (507 of which had not been identified previously) ranging in size from one to 745 kilobases long (with an average of 7.0 kb). They confirmed five of the larger deletions using in situ hybridization to chromosomes, and they tested 60 using PCR (51/60 were confirmed). In total, the deletions contained 266 genes that were either partially or entirely located within deleted regions. They used the expression of these genes to determine whether an individual was homozygous for both copies (wild type, normal level of expression), homozygous for the deletion (no expression), heterozygous/hemizygous (half the expected level of expression), and they found that the deletions were inherited according to Mendelian expectations.

Many deletions are associated with diseases and cancers, but others are probably not very deleterious as they are at appreciable frequencies in human populations. While we can expect that deletions that fail to remove coding sequences may be common, it seems surprising to find that some gene deletions are also found in many individuals (additionally, they appear quite old as they are found in different populations). This begs the question, are all of our genes necessary? Do we have certain expendable coding sequences that we can live without? Maybe they were of important at some time in our evolutionary history, but they are no longer needed. Whatever the case may be, there is no single human genome in terms of sequence or structure, only a rough sketch that we all follow, with our own little quirks and idiosyncrasies (this is true for all other species as well). This, of course, leads us to question how much of our phenotypic uniqueness is due to genetic differences, something I am neither qualified nor prepared to discuss.

In a subsequent post I will describe the other two papers.

Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. 2006. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 38:75-81

Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA. 2006. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet. 38:82-85

McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB Lee C, Daly MJ, Altshuler DM, & The International HapMap Consortium. 2006. Common deletion polyrmorphisms in the human genome. Nat Genet. 38: 86-92.

Thursday, January 05, 2006

Does God Give A Shit?

Before we can ask whether God cares about you, me, or anyone else, we should probably determine whether God exists or not. Well, due to limitations in religion (or, Judeo-Christian religion) we can do no such thing as God's existence must be taken on faith. I'm using the European paradigm of religions because 1) that's what I'm most familiar with and 2) most of the crap I hear about God doing something for people comes from the fundy Christian sects. So, let's assume that God exists (whatever God may be). Does he intervene in our daily lives?

This is question is inspired by Mike the Mad Biologist's problem with athletes thanking God (which came while he was praising PZ Myers for his take on God and the West Virginia miner story):

"I realize that many religious people think God directly intervenes in daily events, but I think that's just silly religion (an aside: on a less serious note, I've wondered the same thing about athletes. If you lost, does that mean Jesus wanted you to miss that tackle?)."

If you were under the impression that I was going to philosophize as to whether God gives a shit about you and me, I apologize for misleading you. I just wanted to pose the question and use the words "God" and "shit" in the same sentence. The same thing could have been accomplished by asking whether God takes a shit. You see, I don't even think God exists, so I feel foolish working under the assumption that he does in order to ask whether he cares. Or she cares. Or it cares. Whatever.

Anyway, the real motivation was to point out the foolishness of thinking you won the big game because God was pulling for your team (if you can imagine the classic image of God sitting on his couch with a beer in one hand, a remote control in the other, and a bowl of popcorn in front of him yelling at Mrs. God to shut the hell up, there's less than two minutes left, and the Packers are driving down the field).

As I was walking out of the Rose Bowl last night (yes, I was at the game, and I don't feel like talking about it . . . yet, but there may be a more detailed post in a couple of days after I have had a chance to mull everything over in my head), I happened to be next to a couple of really tall dudes. One of them looked remarkably like former NBA player Sean Rooks. Given that there aren't that many 6'10" guys in the world, I am fairly comfortable assuming that it was, in fact, Mr. Rooks. There were two other tall guys with Rooks, neither of which I recognized.

One of the other tall guys said something along the lines of, "Both USC and Texas were praying hard for a win, I guess the people in Texas just prayed harder." Some girl who was near us, less than half of the size of Rooks and his tall friends, turned around to agree with the tall dude. I shuttered. Anyone who has ever been to the Rose Bowl knows that the stadium is surrounded by Christians hawking their “God loves you, and if you don’t love him back he’s going to make you suffer forever” message along with the largest density of Jews for Jesus on Earth. The giant Christian signage already had me bitching about proselytizers, and then this comment sent me over the edge.

Apparently, the outcome of the game had nothing to do with the fact that Vince Young has super human strength and speed, the mental discipline to avoid mistakes, and has worked his ass off (along with the rest of his teammates) to earn a National Championship. Nope. Maybe Reggie Bush’s ill advised lateral was an act of God -- something beyond Bush’s control. Or Vince Young’s knee touched the ground on Texas’ first touchdown, but the TV in the replay booth suddenly stopped working because God’s got a few C-notes running on the game. All of this happened because the people in the lone star state convinced God to wear a burnt orange #10 jersey. What a douche bag (the tall dude, not Vince Young or God). If I put a shit load of effort into something, I want to be getting the credit for it, not my imaginary super friend.

High School Biology

PZ Myers (and others) had a different experience in high school biology than I did. When I first arrived in high school I had aspirations of becoming a screen writer (growing up in Los Angeles does that to you). I took biology in 9th grade (freshman year of high school) and found the class easy, but boring; most science and math classes came easy to me growing up because I realized that if I paid attention in class and did the homework, I was guaranteed a good grade (this actually works all the way through college, but in college the "homework" often consists of reading 100 pages from a textbook every couple of days in each of your courses).

But that was biology in my freshman year of high school. I happened to attend a school that offered a ton of Advance Placement (AP) courses (it was a public school as well, which is a rarity). AP courses, for those of you aren't hip with the lingo, are high school courses designed to be taught at an introductory college level (usually taken in 11th or 12th grade). The premise is that these courses will prepare you for college by allowing you to either test out of an introductory level course in college (by scoring well on the AP exam at the end of the year) or make those introductory courses less challenging by exposing you to more of the material before you arrive at college. I also happened to have very competitive friends in high school, and we considered it a challenge to see who could take the most AP courses and score the best on the exam at the end of the year.

That brings me to the second biology course I took in high school -- the one that got me interested in genetics. I had a great AP biology teacher who had an excellent grasp of the material and could present it very clearly. He was well prepared, and often finished his teaching well within the allotted time allowing us to ask questions and begin on our homework assignments. Prior to taking the class, I viewed science as a stagnant collection of facts (of which, there was not much left to learn), but throughout that year I decided that I wanted to be a scientist. It was during the unit on genetics (there was something about transcription and translation that piqued my interest) that I decided I wanted to pursue a PhD in genetics. I even included this fact in my essays for college applications. A lot of kids apply to college planning on becoming a doctor or a lawyer, but how many enter college with the intent of getting a PhD and know in which field that want to pursue it?

I took AP biology my junior year of high school (11th grade), but I wanted to learn more about biology with one year of high school remaining. Luckily, my AP biology teacher also offered a course in marine biology. He had a close relationship with a marine biology lab at UCLA (he had a masters degree, but I’m not sure if it was in education or biology), which meant we not only had access to specimens for observation and dissection, but we also got to do experiments. I guess this requires another bit of clarification. You see, not only was my high school a public school with good academic facilities, it was also located about five blocks from the Pacific Ocean. That meant we could take monthly field trips to the nearby pier to collect samples, take depth and temperature readings, and study the waves and tidal patterns. We would later analyze our data and observe the specimens we collected in our nets (usually planktonic larvae and crustaceans). We also took a special field trip to tidal pools to observe some of the species we had learned about in class.

I am glad I took AP biology in high school because it meant I did not have to take introductory biology in college. Nowadays, introductory courses are affectionately referred to as “weed out” courses for their notorious ability to eliminate a substantial fraction of freshman students from a particular major. After having been a teaching assistant in introductory biology course as a graduate student, I can confidently say that I’m glad I never had to take such a course as an undergrad. I’m not sure if it’s the impersonal feel of one instructor and hundreds of students, or the absolute rush to cover so many aspects of biology in one semester. Whatever it is, it definitely does not stack up to my AP biology course.

Wednesday, January 04, 2006

Tangled Bank #44

The Tangled Bank

Tangled Bank #44 has been posted by Afarensis. Lots of good science to read, so get started.

Tuesday, January 03, 2006

Red State, Blue State, Rose Bowl

At first glance, the Rose Bowl (College Football's National Championship game this season) appears to be a clash between the prototypical Red State and the ultra-liberal Blue State. The University of Southern California is located in one of the few liberal strongholds remaining in America, despite its Republican governor (who is actually liberal on social issues despite his blind allegiance to the Republican party). The University of Texas, on the other hand, is located in the home state of his holiness, the unquestionable leader of this nation, Commander Cuckoo Bananas.

Upon further inspection, one quickly finds that the red state school is not so red and the blue state school is the prototype of George W's base. I have never been to Austin, Texas, but from how I have heard it described it sounds like an island of reason in a sea of faith. It's supposed to be eco-friendly, tolerant toward alternative lifestyles, and having a large academic institution to flood the city with ivory tower types couldn't hurt either.

I am quite familiar with the USC crowd, however, growing up with a diehard Trojan fan as a parent. The University of California, Berkeley (long known as a liberal center) contrasts nicely with the private school in southern California -- take this jacket designed by a USC fan for the annual game against Cal as an example. While using stereotypes are not a good way to develop an argument, USC is known for attracting very affluent students (although it's hard to imagine they are any more well off than students at other private universities) and looking down on its cross town neighbor, UCLA, for their middle class lifestyle. Hell, even the gay alumns are log cabin republicans -- ok, a sample size of one hardly makes a case.

But wealth is by no means a perfect indicator of political position, and it appears that USC may be becoming more liberal. I'm having a hard time putting my finger on it, but hanging around USC alumni I have definitely noticed a conservative (read, Republican) slant to their politics. California's affluent communities are known for their strong support of the Republican party and probably wield more strength within the GOP than most any red state. It's these people that probably contribute to the conservative image at USC.

Anyway, if you find yourself thinking red state versus blue state while watching The President (Reggie Bush, not George W Bush) try to outrun the Longhorns' speedy defenders, take a second to reconsider which school is red and which is blue . . . ok, one of them is Cardinal and Gold and the other is Burnt Orange, but you know what I mean.

Detecting Natural Selection (Part 6)

Calculating Nucleotide Sequence Polymorphism

This is the seventh of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). The first post contained a brief introduction and can be found here. The second post described the organization of the genome, and the third described the organization of genes. The fourth post described codon based models for detecting selection, and the fifth detailed how relative rates can be used to detect changes in selective pressure. The sixth post dealt with classical population methods for detecting selection using allele and genotype frequencies.

Much of the popular press surrounding recent publications that proclaim to detect natural selection does not adequately detail whether the researchers have identified purifying selection (selective constraint) or positive (aka Darwinian) selection. See here for a particularly poor article that confused the heck out of me (and I claim to understand genome analysis). Recall from our discussion of codon based models for detecting selection that we can distinguish between these two selection regimes, although the codon based models are not very powerful. We can also use relative rates to identify differences in selective constraint between lineages, but it is difficult to differentiate relaxed constraint from positive selection using these analyses. Furthermore, there are a lot of computational biologists interested in identifying highly conserved regions between genomes under the assumption that these sequences are probably under strong purifying selection.

But what if we’re interested in finding signatures of positive selection? In my opinion, the best data for this type of analysis is DNA sequence polymorphism. This post will detail some of the core concepts in calculating polymorphism from DNA sequences. Subsequent posts will detail the statistical analyses that can be performed on this data.

Signatures of selection can be detected using either protein coding or non-coding DNA; the statistical techniques differ for analyzing these two types of sequences, but the initial steps are very similar. We will refer to region of the genome we are sequencing as a locus. The length of this region can range anywhere from about 500 nucleotides to thousands of nucleotides (the longer the region, the more work the grad student or undergrad doing the lab work must put in). Once a researcher has chosen a particular locus (either because they know sequencing it will be feasible or because it is a near a gene of particular interest), she will sequence it in approximately 20-30 individuals from some population (although it is common to sequence in as few as 10 or as many as hundreds of individuals). Choosing which individuals to sample (and which populations to sample from) is beyond the scope of this entry and often depends greatly on the natural history of the species in question.

DNA alignment. Click on the image for a larger version.

Once all of the “wet-lab” work is completed (which can take weeks if you are lucky or years if you chose a poorly studied taxon and tricky locus), the sequences must be aligned (see above). To read the alignment above, you need a quick primer on the nomenclature. The column on the left contains the identifiers (or names) of the sequences. The first set of sequences is the alignment of the first 50 nucleotides from the locus, followed by numbers that indicate the position of each nucleotide. Below that, we have positions 51-100, then 101-150, etc. Ideally, we would have all the positions aligned in a single block, but the limitations of printed paper prevent such a representation. The color coding is just there to make distinguishing the nucleotides from each other.

I will assume we have a good alignment, although the alignment process can be quite tricky. Each homologous nucleotide can be compared between all of the sequences in an alignment. Sites at which all sequences have the same nucleotide (position 1 above, where all sequences have a G) are monomorphic. If there are different nucleotides at a site (position 6, where some sequences have a C and the others have a T), that site is said to be polymorphic. We can count the number of sites that are monomorphic and the amount that are polymorphic.

We will discuss two types of polymorphism. The first, the number of segregating sites (Sn), is just the amount of polymorphic nucleotide sites in the data set. As the number of sequences in the data set increases, so too do the number of segregating sites. If this is not obvious to you, imagine we have sampled five sequences from a population (if you need a picture, imagine it’s the first five sequences listed above: D_yakuba, RPU74073, RPU74053, PSU74068, TJU74075). We can calculate the number of segregating sites using these five sequences, and this number will usually be less (and never be more) than if we added five more sequences to our sample. Each time we add a sequence, we identify more segregating sites, although there are diminishing returns as more sequences get added -- eventually (ok, after a really long time) you identify all of the segregating sites in a population, and adding more sequences will only result in adding the same polymorphic sites that you have already identified.

The number of segregating sites depends on the number of sequences in your data set, and we will need to apply a simple correction to take this into account (I will address this in a later post). The second type of polymorphism, the average pairwise differences (p), does not suffer from this problem. To calculate p we must first compare all pairwise combinations of sequences in the data set (compare the first sequence to the second, the first to the third, the first to the forth, all the way to the second to the last and the last). In each pairwise comparison we calculate the number of nucleotide sites that differ between those two sequences. Once we have calculated the number of differences between each pair, we divide by the number of comparisons made to get the average pairwise differences. Because we are taking an average, this estimate of polymorphism does not depend on the number of sequences in the sample.

In future posts we will discuss the theoretical framework behind detecting selection using nucleotide polymorphism and how our two estimates of polymorphism can be used to detect natural selection.