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May 31, 2004

journey to Luckenbach

Per Marcella's helpful guidance, Tim and I took a drive today through the Hill Country. Our destination: Luckenbach, Texas, the city "Where Everybody is Somebody", made famous by the song of its name by Willie Nelson and Waylon Jennings in 1978. Today Luckenbach considers itself a "social center" for music, beer, and bikers.

We took the long route to our destination, up through Johnson City and west along FM 1323. FM 1323 was lined with beautiful "wild" flowers and offered plenty of nice views. The best part though was the biker bar called Harry's in Willow City. We each had a beer and a rest and even got to chat with Harry for a while. Not bad for noon on Sunday.

We sped through Fredericksburg because that town isn't much fun for anyone under 60 years old. We made it to Luckenbach in one piece. Sure enough, this teeny town was crawling with people (apparently this was a big weekend: it marks the town's 150th anniversary). We chilled, had a beer. Tim had a pork loin sandwich 'cos Marcella said so. There was some kind of Corvette convention in town, as well, which was kind of neat. Overall, it's a cute little venue. The whole thing made me wish I bought that motorcycle.

If you care, here's a link to a short history of Luckenbach.

Link to Photos.

Other trips I'd like to take (or re-take) in the near future, while the H is O:

Willow City Loop / Enchanted Rock
Real Ale Brewing Company in Blanco, TX!!! (on the map above)
Mount Bonnell at Sunset

Any hidden gems I'm missing?

May 30, 2004

HHGTTG official weblog

In case you haven't noticed, the upcoming Hitchhikers Guide To The Galaxy movie has an official weblog. I'm not looking forward to this movie coming out so much because I'm a big geek, but also because it's starring my man Martin Freeman as Arthur Dent. He's got movie updates on his site, as well.

No wonder I can't sleep...

Scary:
Crash Test comparison of the Mini Cooper vs. the Ford F-150

"Are the best performers the biggest and heaviest vehicles on the road? Not at all. Among the safest cars are the midsize imports, like the Toyota Camry and the Honda Accord. Or consider the extraordinary performance of some subcompacts, like the Volkswagen Jetta. Drivers of the tiny Jetta die at a rate of just forty-seven per million, which is in the same range as drivers of the five-thousand-pound Chevrolet Suburban and almost half that of popular S.U.V. models like the Ford Explorer or the GMC Jimmy. In a head-on crash, an Explorer or a Suburban would crush a Jetta or a Camry. But, clearly, the drivers of Camrys and Jettas are finding a way to avoid head-on crashes with Explorers and Suburbans. The benefits of being nimble--of being in an automobile that's capable of staying out of trouble--are in many cases greater than the benefits of being big." (From the New Yorker according to the above article.)

Scarier?
The Way We Eat Now by Craig Lambert of Harvard Magazine

GREAT Article... sums up the current state of us fat Americans: corn syrup guzzling, hydrogenated oil drinking, restaurant frequenting, bloated, clogged gluttons. The trouble is, if we can eat a greasy, high-energy meal, we will eat a greasy, high-energy meal. In America, calories are everywhere and in abundance. They're in our faces - how many gigantic glowing fast food signs do you drive by everyday? This article talks about a lot of good stuff: the fast food culture, childhood obesity, the television effect, evolution... I was really really happy to see them busting the US government on the USDA "food pyramid":

Ironically, U.S. government agencies' attempts to deal with obesity during the last three decades—encouraging people to eat less fat and more carbohydrates, for example—actually may have exacerbated the problem. Take the Department of Agriculture's (USDA) Food Guide Pyramid, first promulgated in 1992. The pyramid's diagram of dietary recommendations is a familiar sight on cereal boxes—hardly a coincidence, since the guidelines suggest six to 11 servings daily from the "bread, cereal, rice, and pasta" group. The USDA recommends eating more of these starches than any other category of food. Unfortunately, such starches are nearly all high-glycemic carbohydrates, which drive obesity, hyperinsulinemia, and Type II diabetes. "At best, the USDA pyramid offers wishy-washy, scientifically unfounded advice on an absolutely vital topic—what to eat," writes Willett in Eat, Drink, and Be Healthy. "At worst, the misinformation contributes to overweight, poor health, and unnecessary early deaths."

Note that the pyramid comes from the Department of Agriculture, not from an agency charged with promoting health, like the National Institutes of Health or the Department of Health and Human Services (DHHS). The USDA essentially promotes and regulates commerce, and its pyramid (currently under revision; expect a new version in 2005) was the focus of intensive lobbying and political struggle by agribusinesses in the meat, sugar, dairy, and cereal industries, among others.

It also mentioned that obesity is inversely proportional to education level. While this article is awesome and everyone should read it, somehow I don't think that most of the nation subscribes to Havard Magazine. So for now, the billboards and flashy commercials and curly fries win. Diet in America is so messed up at the moment, I wouldn't even know where to begin changing it. I wonder how much this bad press is helping? Are articles like this and movies like Supersize Me getting in the faces of its target audience? Or is diet just like any philosophy: beautiful in the hands of its believers. We can publish as many papers as we like, but is it actually changing how overweight people think about food? I'm skeptical. Health, like philosophy, is a personal choice. Also like philosophy, old habits are hard to break. I'm always amazed that to some people, McDonalds tastes good. Is it a matter of upbringing? Can people raised on tv, video games, Cocoa Pebbles, and McDonalds Happy Meals ever turn around?

Right, I'm going to stop thinking about this for the time being and worry about myself. I get really sad by the the number of people I see every day who don't take care of their bodies. Where's the respect?

Who needs sleep?

There's so much joy in life, so many pleasures all around But the pleasure of insomnia is one I've never found With all life has to offer, There's so much to be enjoyed But the pleasures of insomnia are ones I can't avoid

Lids down, I count sheep
I count heartbeats
The only thing that counts is
that I won't sleep
I countdown, I look around

Hala Hala Hala...

*sigh*

Food Heads and Isuzu Poopers

It's 12:38am here in Austin. Just an hour ago, Tim and I went out for a walk, and within a couple of minutes I was sweating bullets. A Walk-By-Moore ended up at the Crown, where my grease face enjoyed an Amstel Light. The beer must have raised my body temperature, because the walk home had me dripping with sweat. GROSS. What is UP with this Austin heat? I'm averaging 3 showers a day here. It's making my skin dry. And it sucks that if I want to be responsible and walk to a bar, by the time I get there I'm Nasty-Master General. And I won't even get into the bug factor...

But speaking of swatting away bugs, Tim and I discovered a great two-years-new sandwich shop today called Food Heads in a cute old house on 616 W 34th St. You can order a customized sandwich or one of their specialties. I had their special: grilled eggplant sandwich with blue cheese, spinach, tomato, and balsamic on sourdough. It was really tasty and the atmosphere was pleasant. They had tables inside and out. I'd say it compares to the sandwiches at Avenue B Grocery (4403 Ave B), which I must go back to soon. Sadly, I always seem to be in the mood for their avocado sandwich on Sundays, when they are closed.

This Isuzu Pooper cracks me up:

May 28, 2004

Up way too late...

... late enough to catch the CD comp advertisements. But Red Hot looks really REALLY good! Alias, More than words can say I need you now.... this CD was made for me. Check out this track list:

Disc 1:
1. Something So Strong - Crowded House
2. Obsession - Animotion
3. Something About You - Level 42
4. Is This Love - Whitesnake
5. Every Rose Has Its Thorn - Poison
6. All I Need - Jack Wagner
7. More Than Words Can Say - Alias
8. Some Like It Hot - The Power Station
9. Touch Me (I want Your Body) - Samantha Fox
10. Never Gonna Give You Up - Rick Astley
11. Touch Me - Cathy Dennis
12. Need You Tonight - INXS
13. The Flame - Cheap Trick
14. Black Velvet - Allanah Myles
15. Save Your Love - Great White
16. When I'm With You - Sheriff
17. Can't Stop - After 7
18. Addicted To Love - Robert Palmer

Disc 2:
1. Feel Like Makin' Love - Bad Company
2. I Want To Know What Love Is - Foreigner
3. Suddenly Last Summer - The Motels
4. Too Shy - Kajagoogoo
5. Shattered Dreams - Johnny Hates Jazz
6. We Belong - Pat Benatar
7. Caribbean Queen - Billy Ocean
8. I Get Weak - Belinda Carlisle
9. Take Me Home Tonight/Be My Baby - Eddie Money with Ronnie Spector
10. Hold On To The Nights - Richard Marx
11. Listen To Your Heart - Roxette
12. Missing You - John Waite
13. I Touch Myself - Divinyls
14. Simply Irresistible - Robert Palmer
15. Sugar Walls - Sheena Easton
16. I Can Dream About You - Dan Hartman
17. Freeway Of Love - Aretha Franklin

May 27, 2004

Sweet love showin' us a heavenly light...

I discovered a great new song tonight. I'm not usually a fan of Sheryl Crow, but "If You Ever Did Believe", performed with Stevie Nicks, made me hurt in the way that sad songs do. But I can't seem to turn it off. In fact, I am so pleased this discovery, that I'm posting a link to it (that will only remain active for 24 hours): enjoy.

Since we're on the topic of bittersweet songs and Sheryl Crow duets, check out her duet with Kid Rock.

If You Ever Did Believe Lyrics

You've left me now
And it's seasoned my soul
And with every step you take,
I watch another part of you go

I continue to build a wall
You were so strong,
I fell to my knees
And I don't think I can handle this at all

Well one more night
I'd like to lie and hold you
Yes and feel
To make you smile,
I'd like to be there for you--
Have you forgotten me?

And the days go by
Doing nothing about them
How much time
Will I have to spend?

My mind won't rest
And I don't sleep
Not even in my dreams

If you ever did believe
For my sake
If you ever did believe

And the days go by
Doing nothing about them
How much time
Will I have to spend?

And the days go by
Doing nothing about them
How much time
Will I have to spend?

Well one more night
I'd like to lie and hold you
Yes and feel
To make you smile,
I'd like to be there for you--
Have you forgotten me?

ooo....ooo.....ooo...
Ooo baby don't leave me
ooo..ooo...ooo...ooo
I'm down on my knees...
ooo..ooo...ooo...ooo
Begging you please...
ooo...ooo...ooo...ooo
Baby don't leave me....
Did you ever believe?

May 26, 2004

Happy Birthday Stevie

Stevie Nicks turns 56 today. She rocks so hard, that I'm only listening to Stevie (and Fleetwood Mac) today. My playlist includes:

Whenever I Call You Friend (with Kenny Loggins) Leather and Lace Stand Back (with Don Henley) Stop Draggin' My Heart Around (with Tom Petty) Free Fallin' (Tom Petty Cover) Landslide Dreams Silver Spring
My favorites at the moment are Stop Draggin' My Heart Around and Whenever I Call You Friend.

May 25, 2004

soft fruit

I bought some wonderful strawberries today at Central Market. They were incredibly sweet and delicious! They reminded me of the poem, "This is Just to Say", by William Carlos Williams:

I have eaten the plums that were in the icebox

and which
you were probably
saving
for breakfast

Forgive me
they were delicious
so sweet
and so cold


Speaking of fruit, if you're a fan of Australians and naughty words, might I recommend the film, Soft Fruit? It is rated R for sexuality/nudity, language and drug content and also features the algorithmic Russell Dykstra as "Bo".

If you're in the D.C. area, might I also recommend you invite my friend James along? He's such a fan of this film, and it might distract him from the Honey Bunches of Oats for a while.

Tim's House

Lia's boy, Rob, is in town. Tim and I joined them this evening at the Clay Pit to enjoy some delicious food and get to know Rob a little bit better. It was a really nice time. The Clay Pit's vindaloo is DELICIOUS. But tonight I controlled myself and ordered the tandoori vegetables instead. They really know how to cook their veggies - crisp, flavorful, tasty.

Snapped some photos at Tim's place this afternoon. That was fun.

May 24, 2004

austin scraps

happiness is

happiness is being drunk enough to feel warm and fuzzy inside without needing to barf.

sadness is realizing you're sober enough to know you're going to feel hungover tomorrow. =(

May 23, 2004

one week closer to englightenment

a beloved friend of mine once told me "It's all about the zen...'when the student is ready, the master will appear.'  i would tell you what it meant, but that would mean that i was trying to understand what it meant, and that is not the way to enlightenment.  by trying to understand, one makes understanding impossible.  that or i just don't know."

i don't know either, but i wish i had listened more closely... because i'm only barely starting to get what he was talking about in that i feel completely and utterly not in tune with this so-called zen. in this very simplistic case, i feel like i haven't been feeling the writing zen as of late. but it's not just writing, as that's just my confused manifestation of electrons. no, this weekend i can't quite get into the zone with anything, be it food or play or exercise. i have an anxiety in the pit of my stomach that permeates up through my throat, causing me to choke on my words and my St. Pauli Girl. and when it happens, i am immediately reminded of my friend's words and think "i gotta get me some zen." it's getting me down. you know how it is: sometimes i want so hard for something to happen. and i believe it's right in the very depth of my soul. when it doesn't work out, i'm confused and sad. and then i get angry with myself for believing in faith when i don't really believe in god.

i get entirely too introspective when i don't have a regular job or something definitely good on the horizon.

so i'm trying to find my zen, or at least become ready for it to appear. will the master be in the form of a hairy scary boosh? or the evil dirty laundry monster? (if you haven't heard, the "dirty laundry monster" is my latest idea for a halloween costume ... think about it, everyone gets scared in the face of dirty gym socks and used underwear ... fuck elvira and princess leia and catholic school girls, halloween is about FEAR.)

what was i saying? right, zen. in light of recent stress, in about one hour i will celebrate 1 week without cigarettes. i've come close to failing, but stayed strong, which is more than i can say for past quitting attempts. how will i celebrate? well, i'll probably just go to sleep. i should be punished for ever starting to smoke, rather than lauded for having quit.

right, my weekend in a nutshell: for all my whining about zen or lack thereof, it's been a very full weekend. friday i tooled around with ginger for a bit before heading home to watch Sports Night and get an early sleep. i woke up at 7am on saturday to go garage sale shopping with one of the math flunkies. it was extremely fun. getting up early is soooo good during austin summers. it's cool outside until about 10am. and it was really fun driving around austin, hanging out outside, looking at people's junk, talking about people's junk, and meeting the interesting people who were selling the junk. the math flunkie also purchased a 7up for us to share, which came in a glass bottle imported from Mexico, made with sugar instead of corn syrup. it was the best pop i've ever had. i was raised on Diet Rite, so never really had a taste for full-syrupped soda. but this 7up was something special.

a funny thing happened: driving around we spotted a yard sale sign and i recognized the address. the address was next door to the one i used to live at on Harris Park. immediately i realized it was tracey's as she was also shipping off and out from UT, so i stopped by to say hello before moving on. when flunkie and i were done, tim and i went back to tracey's to visit with her and jesse and enjoy a few last moments with our old neighbors. tracey is moving back to New Orleans. this is exciting because NOLA is one of my favorite places and now i have an excuse to visit before i ship off. i also scored some eats from her fridge and a pair of Solomon shoes.

another point of note: cowboy hats make summer life in austin infinitely more tolerable. although i never considered such a hat to be my style, after a particularly hot weekend while my mom was in town, i decided to defy my own personal laws of fashion and go for comfort instead. it's taking a while, but by the end of the summer i think the cowboy hat will be fully integrated into my personal repertoire. i am more comfortable, cooler, and generally happier. and i think the Brits will love it. (hah)

after hanging with tracey for a long time, i headed to Opal Divines. they have the best fries in austin, by the way. later i rode my bike to the gym. the bike ride to and from the gym was nice, but the workout at the gym was sub-par. saturday was graduation day, and seeing all the professors in their robes got me a little hot and bothered. i couldn't really focus at the gym. no one was there, which sounds nice, but really i felt too exposed. i left after about 35 minutes, biked home, and lifted weights while i watched Jurassic Park on network TV. I don't care what you say, Jurassic Park is a great action flick, and its soundtrack moves me to tears!

Sunday, fairly uninspiring but positive in terms of planning. Woke up, enjoyed some 100% whole wheat toast courtesy of the bread machine. Kinda sorta watched some political round tables on pbs. Cleaned out my office at ACES. Was touched by office-mate Paul's farewell; he's a really good guy. Had a conversation. Figure out some zen. Had some pizza at the Parlor. Drank some beer. Came home. Drank some more beer. And did not smoke! And only missed smoking about once! I felt so good and relaxed that I'm having a St. Pauli Girl as I type. So forgive me if I'm not entirely sensical. I'm a little tipsy!!!

As for zen, well, I'm a little behind but slowly catching up to my friend. Damn those people who get it right before I do. Tomorrow I'll wake up and eat breakfast and look for jobs and ride my bike and feel a tiny bit enlightened. But I'll try not to think about it too much. I should just enjoy the ride, 'cos if there's anything deeper there, my feeble mind will never understand it. Just like the way my feeble mind has poorly articulated the correlation between the zen speak and my weekend. Aargh, I think too much!

May 21, 2004

Dog Phylogeny in the news

I smiled yesterday afternoon when I heard some talk on All Things Considered about DNA studies to determine the evolution of man's best friend.

Today, I found this article on CNN about the study. Many breeds turned out to be relatively "new" on an evolutionary scale, including the Pharaoh Hound and the Ibizan Hound, once thought to be 5,000 years old. The recent spur of diversity in dogs is due to, you guessed it, human breeding. According to the article

a surprising 30 percent of genetic differences among dogs can be accounted for by a few hundred years of intense inbreeding -- far more than the so-called racial differences between humans.

Genetic profiling may be taboo among humans, but I wonder if it will ever become a part of "Best in Show" type competitions. Or indirectly, could studies like this cause dogs like the Pharoah Hound to go out of style because they are not as ancient as once believed?

But more to the point... would it be at all possible to genetically isolate the "yappy" dog gene in order to weed out that irritating trait in smaller dogs? Please?

May 20, 2004

Andy Kaufman back from the dead?

And with a blog to boot?

So is it true? Kaufman himself said that were he to fake his death, he would return 20 years later, on May 16, 2004. I'd imagine there are plenty of fake Kaufmans out there, excited that the time has finally arrived for their own ultimate hoax. Even Yahoo news states, "[This particular Andy Kaufman] has subjected himself to medical examination and submitted DNA, hair, blood and fingerprint samples to the auditors. Ernst & Young and the Kaufman family report that with a 99% probability, this is indeed the real Andy Kaufman."

But according to snopes.com, it's all bologna. All technical evidence aside, snopes makes the best point here:

If the real Andy Kaufman were back, his story would be picked up by every major news service in the U.S. and a good many abroad, not merely a single "anybody can submit a story" free publicity service. And if the real Andy Kaufman genuinely wanted to demonstrate he was still alive, just one public appearance would serve that purpose far more convincingly than an unverifiable DNA test. Most important, if the Andy Kaufman I remember — the brilliant, unpredictable, erratic, and unique comic genius — had finally emerged from hiding twenty years after faking his own death, I have no doubts that he'd find a much more imaginative way of revealing his return than a free press release and a rather ordinary blog.

GMail buzz

Most of you may have heard that Google is starting up its own webmail service called GMail, and the buzz is quite astounding. I forget that the majority of the world's people aren't academics or techsters privy to ad-free POP e-mail accounts with heaps of storage space. Knowing now that my university e-mail address will soon be expired, I can better relate to the hoi polloi.

Contrary to the rumor, GMail does not offer a terrabyte of storage space. What it does offer is a clean, easy interface, free of banner adds, and a spam blocker PLUS 1 gig of storage space.

The trouble is, at the moment, you can't get a GMail account unless you've been invited by Google or a GMail member (Google is still "smoothing out the kinks"). Although most people aren't in a huge hurry to get an account, people are worried about ending up with a crap e-mail address. I'd definitely be bummed if I got stuck with monica_l_sha_1979@gmail.com rather than monica@gmail.com. In fact, so many people are worried about this, that there's now a website called GMail Swap specifically designed for anxious future GMailers to swap personal items for a desired (but already taken by a "nefarious hooligan") GMail user name. It's amazing what people will do for an e-mail account...

Yum! Fresh baked goodies!
Fresh baked cookies or rice crispy treats (the marshmellowie cereal delight)*. Next day aired to the location of your choice. Cooked with love by a professionally trained chef (gradute of the peter kumps cooking school).

Pics of my ex-girlfriend
She cheated on me about 2 months ago, and I have a folder filled with her pics as well as having in them in a yahoo profile - if you want them, plus some that aren't on the profile, give me the invite. She's 5'10", blonde, thin, 36c breasts, bi, great in bed... and you'll see her in action (I've edited myself out of the pics)

Lessons from World's Fastest Bagger !!
Everyone hates going to the grocery store and waiting while some incompetent high school kid smashes your bread and crushes your eggs...As a former World's Fastest Grocery Bagger, as seen on David Letterman, I can teach you the skills necessary to bag your groceries fast and get out of that crowded supermarket !!...You get all this for only a measely little Gmail account !! What a deal !!

turning things around

quit smoking
spastic anxious edgy
focussed? not so much.
and yet feeling super great (on a scale from 1 to awesome)
and mega productive

energies redirected to:

cooking
training (or at least rambling about it)
burninating the cocoa
cleaning

no booooze. no superman. but i wake up in the morning and ride my bike to rec sports where it is almost empty. a crevice-shaped mp3 player nestled in my sports bra, tucked between my bosoms. cold water.

no homework. just grillin' and chillin'.

summer's here.

May 19, 2004

Cocoa Java Grande Latte

Check out my new blog:

Cocoa Java Grande Latte

This is where I post my progress as I learn how to program in Cocoa using Java!!

I started this task just a few weeks ago, and quickly discovered that there are very little resources or tutorials for Java-based Cocoa apps. This site is intended to keep track of what I learn. I plan to post Java versions of some the Objective-C examples in O'Reilly's Learning Cocoa as well as samples of my own personal projects.

May 17, 2004

i am a nonsmoker...

... and i have a very nice reward in store for me in one month's time if i keep it up. motivation!

school's out and i'm broke. when money's tight, i always manage to find more things to sell on amazon. i am featuring a wide collection of books -- science, math, fiction -- and even a few DVDs!

it is very strange not having any classes to think about. even on previous summer vacations, i always knew that the summer would end and i'd have to go back to a classroom desk that wasn't made for a left-handed person.

i'm not quite sure what to do with myself but stay in bed and hide! this isn't true. i'm glad i'm the sort of person who knows what to do with her free time -- clean, haxx0r, haxx0r some more, blogg0rbate, work out, have a nooner. still, i'm a little concerned that it's 11:21am and i'm still in bed. so i'll allow myself this morning of lethargy because i happened to quit smoking today. tomorrow it's back to discipline. cos' really, it sucks losing the morning, and i try never to do it. so many things are good in the morning, like eggs and tea and the news and walks and sunglasses.

so a couple points of note:

the texas brewers festival kind of sucked. it was held in a parking lot on a very hot afternoon. i felt inundated by asphalt and bbq fumes. the only place with shade and seating was under a tent that also happened to house the band which was entirely too loud. full pints of beer were not available. furthermore, all of the beer stands were located all in a row in the same place, creating a funnel of confusing lines and lecherous crowds. drinking beer is about chillin' out with friends and the beer festival provided no opportunity for such leisure. fortunately, the fest was located down the street from opal divines.

been watching Sports Night on DVD... great show, often cheesy but very funny. the laugh track is a little strange, but i got over it fairly quickly.

cutting my own hair is not terribly difficult and takes less time and far less money than going to a "salon". whether or not i cut my own hair well is, i suppose, a matter of opinion.

tonight i am going to attempt cooking pizza on the grill. i'm not sure if i'm going to utilize the pizza stone (dough cooked right on the grill might be really tasty!). i found a couple fairly comprehensive websites on grilled pizza, i'll let you know how mine turns out:

Grilled Pizza on pizzatherapy.com

grilled pizza @ epicurious

May 15, 2004

haxx0rbating the peasants

Now that school's out I have time to pursue my Mac OS X training software. I just finished the first installment, MetCalc: a metabolic calculator. If you know anything about these calculators, their estimates are very rough. But without any expensive machinery, it's the best I can do. Well, second best thing -- I want to write a metabolic calculator that computes an hour-by-hour estimate of calories burned (that is, take into account sleep, exercise, waking activity, household chores, etc.). But first I'm going to dive headfirst into a calorie log.

If anyone is interested in trying out MetCalc.app, you can d/l the tar file.

MetCalc.tar (192kb)

The illustrious screen shot:

May 14, 2004

o sweet bliss

i had a prototypical bio-disaster nightmare last night. i can't explain the entire plot, as i was a player. only there was a women, and a virus, and open sores. a brief scuffle by the car. i touched her hand. i was infected. there was a vaccine. i had to get to the hospital. searching for help. i hijacked a horse and buggy. but at the hospital, everyone was already dead. then there were zombies. and i woke up , because i was scared, and i couldn't go back to sleep for a little while.

I can't draw any parallel between my dream and my sudden liberation from university. cuz that feels pretty good.

and yet somehow anticlimactic.

anyway, i celebrated by going to a uShip happy hour where i met the rest of the founders and the other potential interns. the guys who run it are pretty cool. they are excited about their product and really like beer; what more could you want from a boss? oh right, a paycheck. hopefully things will look up for my finances next week.

there was also a parlor outing. it was fun, same ol' same ol'. plus pool. i don't know why, but i feel like playing pool lately.

marc, a guy i know from way back when, is currently working in Japan and has posted some cool pictures of monkeys on his blog. (Links are in the right column to his albums.)

May 13, 2004

hybrids... a little late

Yet another installment of dry biology ...

Hybridization occurs when a species introduces its alleles to another species. Many hybrids are sterile and do not survive to form their own species. This can be overcome by polyploidy, the doubling of chromosomes in alleles. Polyploids are interfertile among themselves, but not with the parent species. Hence, a new species is born!

Selection for hybrids is typically not in their favor. Often they are unable to overcome ecological competition or find a mate (two species with the same ecological need cannot coexist!).


Areas in which hybridization is common is called a "hybrid zone". These are examples of "stepped clines". A cline is a geographic gradient in the frequency of genes; in a stepped cline, the gradient is more dramatic.

In a primary hybrid zone, two populations that have been kept apart come back together. Either reproductive isolation is complete or incomplete. If it is complete, then the two populations cannot mate and speciation has occurred. If it is incomplete, the two populations can mate and produce hybrids. If these hybrids are unfavorable, the two populations will continue to separate and form new species by parapatric or sympatric speciation.

In a secondary hybrid zone, two previously separate populations which speciated allopatrically come in contact and cross-fertilize. Isolation is increased if the hybrids are unfavorable.

A graduate slide back into the same species is possible by gene flow.

An area in which hybridization with selection against hybrids is called a "tension zone."

In practice it is difficult to distinguish between secondary and primary hybrid zones. Secondary hybrid zones are believed to be more common. Certain landscapes are more apt to have hybrid zones than others.

In nature, certain hybrid zones demonstrate the existence of "novel alleles", alleles that were not present in the parents. It is probably that natural selection favors these alleles.

But when do we define a new species?

Some examples of hybrid animals:

Mule - female horse / male donky
Hinny - female donkey / male horse
Wolfdog - domestic dog / wolf
Beefalo - American bison / domestic cow
Liger (or Tigon) - Tiger / Lion
Cama - camel / llama
Wolphin - false killer whale / bottlenose dolphin

May 12, 2004

biogeography: the plot thickens

This is it... my last night of biology ... and only biology. I'm dying of boredom. Don't get me wrong, I think evolution is cool as hell, and I've been occasionally awed but some of the stuff I've learned. But at the moment, preparing for this test somewhat dull, and I'm only brushing the service of all the topics I'm studying. I'm the kind of person who likes to know the details. In fact, I need to know the details, otherwise I feel like I don't truly understand what I'm reading. Maybe that's why I studied math.

So on with it. Tonight's motivation... get through biogeography and hybrids, and I will reward myself with a beer. This I must do before midnight, as that is when the store closes!

Let's start with a definition:

Biogeography is the study of the spacial patterns of biodiversity. In other words, it is the study of the distribution of past and present organisms, and the patterns of variation in which they live and evolve.

There are three fundamental processes in biodiversity:

1. Lineage splitting (evolution)
2. Lineage extinction
3. Lineage movement (dispersal)

Co-evolution exists at three levels: the gene and species trees, areas and biotas, and hosts and parasites.

As their names suggest, gene trees describe the lineage of the genes (alleles), while species trees describe the lineage of the species themselves (domestic cat, african wild cat, etc.). These trees don't always agree due to a little process we call stochastic lineage sorting.

Consider two daughter species A or B. In the presence of stochastic lineage sorting, their gene tree will reflect different relationships over time. At an earlier time, the gene tree will appear polyphyletic; some lineages of A will be closer to B and vice versa. Later, due to stochastic extinction, B's lineages will "die out" and only A's lineage will seem closer to B (paraphyly). At a later time, both of A's and B's lineages dye out, resulting in a monophyletic relationship between A and B.

In the case of 3 species, A, B, and C, their species tree may suggest that B is closer to C than A is. However, the gene tree may reflect differently if the divergence of alleles predates species divergence.

(This is better illustrated with a picture that I may add later.)

Ecological biogeography deals with processes on a small spacial and temporal scale, while historical biogeography is more concerned with the big picture.

Two functions dominate historical distributions: dispersal and vicariance.

Dispersal occurs when an organism is able to cross a barrier, or a barrier disappears.

Vicariance occurs when a barrier is introduced, causing the separation of species and potential divergence.

We typically describe distributions in terms of vicariance rather than dispersal because dispersal could potentially describe any form of speciation while vicariance is more discriminating.

Several methods exist to study these patterns.

Center of Origins

The Garden of Eden! Species originate at a "center of origin". New species appear which displace the older species. The result is: new species at the center, older species around the edges.

Phylogenetic biogeography

Closely related species tend to replace each other in space, that is, species are either allopatric or parapatric. If two species share a similar biogeographic pattern, then they probably share the same history. Two rules are associated with patterns:

The deviation rule states that of two daughter species, one is more apomorphic than the other.

The progression rule states that primitive species occupy the center of origin while apomorphic groups exist progressively away from the center; allopatric speciation by peripheral isolation allows the dispersal of the clade.

Panbiogeography rejects the idea of dispersal and center of origins. This theory speculates that the earth and its biota evolved as one and should be treated as such. "In the beginning", all organisms were closely related and evolved apart as the earth did. Panbiogeography uses the concept of tracks to study patterns. A track is the circumspection of the entire range of a clade or species. A generalized track describes congruous patterns in two otherwise unrelated clades. Think of a track as a minimum spanning phylogeny that represents the phylogenetic estimate of the group.

Vicariance biogegraphy seems to be most important/useful.

This method attempts to describe distributions among unrelated clades without no prior assumptions about dispersals. The method has bears a flavor of Panbiogeography.

We take a bunch of groups and, for each group, define an area cladogram. This is simply a species cladogram with taxa name replaced by area names. From these cladograms, we combine them into one. This gives us a generalized area cladogram which we can compare to a geographical cladogram. If the two are similar, then we might have a pattern!

Synthesizing the generalized cladogram is a bit complicated because typically there is not a one to one correspondence between area and taxa. Sometimes a taxon appears in more than one area (widespread taxa), or sometimes one area has more than one taxon (redundant distribution), or sometimes an area is not present in all cladograms (missing areas). A resolved area cladogram is constructed, taking into account some assumptions: widespread taxa may be paraphyletic and may be located anywhere in the tree.

A reconciled tree approaches the problem differently: we determine under what conditions all trees are true. This is typically done when we have two trees and uses an optimality criterion to find the best generalized tree. Hopefully the tree will maximize shared history and minimize extinctions.

molecular clocks

Here's a good question:

AIDS was first detected in 1981, and soon thereafter was HIV. So when did the HIV virus originate in humans?

We don't have a time machine, but since the HIV virus erupted relatively recently, we do have molecular data.

Is it possible to extrapolate an HIV "timeline" from current molecular data?

(Scroll to the section "The HIV Question" for the answer if you don't want to read about the fascinating theory of molecular clocks.)

The question has to do with molecular clocks. The molecular clock idea stipulates that genes evolve at a rate that is constant enough to be used to predict times of divergence. A couple of dudes, Zukerkandl and Pauling, determined that this rate is close to a Poisson distribution. The Poisson distribution exhibits very wide confidence intervals over time. This makes sense for our case... as molecules evolve, our ability to predict their structure over time diminishes.

As you might suspect, this theory is highly debated. Many genes exhibit variable substitution rates across genes and lineages. It is natural to wonder if this clock is close enough to the truth to be used.

"You can't handle the truth!"

Formally, the molecular clock theory makes 6 assumptions. How accurate are they?

❶ Molecular change is a linear function of time; these changes follow a poisson distribution.

Empirical data show that the rates fit the clock decently but have broader 95% confidence limits.

❷ Rate of change is equal across all sites and lineages.

This assumption is often violated for both sites and lineages. Recent molecular clock studies attempt to account for rate heterogeneity at the sites. The constant rate along lineages is still a problem.

❸ The phylogenetic tree can be reconstructed with out error and each branch can be analyzed independently.

There is error here, but pairwise distances can mask them. Studies have shown that the confidence limits are more narrow than the desired Poisson limits.

❹ The number of substitutions across lineages can be reconstructed without error.

Unsure about this, but my guess is that this assumption is usually violated.

❺ Calibration dates are known without error.

Easy opportunities for error here. Suppose you have a tree depicting the evolution of some species of frog. You calibrate a node at 90mil yrs ago, and infer that its offspring diverged 40mil yrs ago. However, you know for a fact that the offspring diverged due to allopatric speciation by continental drift, and geography studies have show the drift to occur 80mil yrs ago. Hmm. Are these frogs distance swimmers? Or did we make a mistake?.

❻ A regression of time of molecular divergence can be conducted without error.

The 95% confidence intervals for the regression slope can lead to very wide and unuseful 95% confidence intervals on the new time predictions -- yikes!

So how do we test if the molecular clock is accurate when our physical evidence of the fossil record is so minimal and the rates of evolution are so temperamental?

"The HIV Question"

Since we have HIV samples from the past several decades, why not test our molecular clock on this sample?

The earliest HIV cases were found in blood samples from the 1950s obtained in Africa. One theory asserts that HIV originated as a result of oral polio vaccinations that were cultured in the kidneys of chimpanzees and given to a large number of people in the Congo between 1957 and 1960.

The theory is not conclusive, however, so we turn to our trusty phylogenetic methods.

Korbet et al. did this and the results were published in Science (unfortunately you need a subscription to read the article online).

Assuming a constant rate of evolution, the study estimated that HIV arose in humans in 1931 with a confidence interval of 1915-1941. Furthermore, the phylogenetic tree predicted correct origination times for certain known cases of HIV. In this case, the molecular clock was very accurage!

Bayesian studies incorporating rate heterogeneity achieved similar results.

Here's a link to a paper that discusses the Science paper.

Although the molecular clock was a good model for HIV, it is not always as pretty for predicting molecular changes over millions of years. There are many inconsistencies between the fossil records and the molecular clock predictions. It has been shown that an exponential distribution shows a tighter fit.... where do we go from here?

Only time will tell!

(hahahah)

Size matters

I know I said I wasn't going to post this because it's so damn boring, but I'm going to anyway so I can read it from other computers in case I don't have my ibook with me.

In today's exciting segment on systematics, we delve into the perplexing topic of size and shape measurement of species. I'm sorry if you were looking forward to reading about hybrids, but I'm a little bored with speciation at the moment so I thought I'd move on to something that's, oh maybe not less boring, just different.

For us women, if someone asks us what "size" we are, we usually refer to the arbitrary scale of pant sizes. I think of "8" as being fairly average and healthy. Then again, I'm a size "8", but I'm also 5 feet tall and have a tummy ridden with beer plague. I don't think pant size should define my "size".

So biologists have a problem. Frogs come in different lengths and girths, so how do you tell which one is the biggest?

First of all, we can measure size as a linear function of certain factors and weights.

size = w1 * x1 + w2*x2 + ....

For instance, the size of people might be better described by body fat percentage instead of pant size or weight. With the use of calipers, we can measure the fat in various places on our body, and use a linear equation to approximate percentage body fat. This data, which combines several variables, would be more accurate for comparison than single variable size measurements.

In this respect, it is often better to compare individual species in terms of "shape" rather than "size". How do we do this?

One might consider using a ratio, but this causes problems if the species grows or shrinks symmetrically across all axes: the ratio may not reflect dramatic growth.

It may be helpful to treat a ratio as a linear combination by using logs since

z = x / y <==> log z = log x - log y

It may be useful to add weights. We consider

log z = w1*log x - w2*log y

We can improve the usefulness of this equations by setting the weights to reflect maximal differences among groups, adding new variables, and deciding whether the log or the ratio or some other combination best illustrate correlations in the data.

Math at last...but not really

Do you know how difficult it is to talk about mathematical concepts without being very specific? If were ahead of the game, I'd talk about it anyway, but there isn't time and the specifics aren't important to biologists.

Principal Component Analysis (PCA) is one method to determine variable correlations in a data set. It changes the coordinate system of the data to a system that displays the most variance. This is useful if we have measured a large amount of variables in a group; we can take this data and transform it into a 2-variable system.

The math of it all involves eigenvectors and covariance matrices and other "complicated" mathematical concepts. Let's just say that the data gets projected onto a plane, and we find the axis through the data that exhibits the most variation of the data on that axis (this is the "PC I" axis). "PC II" does the same thing in the other direction, and is orthogonal to "PC I". PC I is typically considered the size axis, while PC II reflects shape.

Suppose we already know a priori that the groups we are comparing are different. Then "discriminant function" analysis is appropriate for reduction.

A discriminant function is a linear function that maximally separates two groups. These functions can be used in canonical variance analysis (CVA) and multivariate analysis of variance (MANOVA).

CVA is a method that is similar to PCA but operates on the centroids of the group data.

Suppose we have 7 groups whose data form elliptical clusters when plotted. Each cluster has a centroid. PCA is performed on the centroids and the ellipses are scaled to be circles. CVA attempts to maximize variance between groups relative to the variance within groups.

MANOVA tests the null hypothesis that all of the centroids are the same. If the null is rejected, a posterior analysis must be done to determine which centroids are different. The difference between the centroids tells us how different the groups are.

AWESOME.

good things

the interview went pretty well. the job looks interesting and the people seem very warmhearted. they are selecting 2 from the 10 applicants they chose to interview. i hope i get it; that would take a great deal of stress off my mind.

still, with finances tight, my jeans feel even tighter. and since i'm going to quit smoking (again) this monday, i decided a gym membership for the summer would be worth my $78 and a better way to spend my money than on cigarettes. (the nice thing about quitting smoking all the time are the multiple excuses to reward myself.) i considered doing without the gym this summer and get my exercise by running, cycling, using my freeweights in my apartment, walking, et cetera. but then i thought about how much i really like going to the gym and how much i miss it when i don't go.

i also thought about how much i hate austin's oppressive summer heat.

the texas craft brewers festival is this saturday. they claim it is the largest beer tasting in texas! they're doing a cool session on food and beer pairing. apparently Calloway's Vanilla Porter at the Draught House goes beautifully with Apple & Raisin Bread Pudding. On Fireman's #4:

This light bodied blonde ale is perfectly balanced with a touch of Crystal hops for bittering and aromatics. Fireman's #4 is a great choice on any hot Texas summer day or pair it with spicy foods to help you put out the fire.

see you there!

May 11, 2004

no science today

i wrote some stuff about hybrids and how to measure species, but it was really boring and i was too embarrassed to put it up.

instead i'm going to talk about my legs.

i've been feeling a little inadequate lately in the calve department. i feel like i rarely do anything with them these days, and sometimes when i look in the mirror, i feel like my calves are not what they once were.

tomorrow morning i have a job interview, so i decided to put on my heel-shoes to make sure i can still walk in them. i'm wearing shorts at the moment, so when i had a look in the mirror i could see how funny my legs look in heels. i no longer have any doubt about my calves. i see other women in heels, and the effect is usually that of a long streamlined calve. mine, however, due to the inherent pointy-toe effect of high-heeled shoes, look like calve with a big plateau-esque chunk jutting out of the top half.

this made me happy to know that i still have super-calves, but a little sad to know that i have cross-dresser man legs.

tomorrow i shall be wearing pants.

since i'm on the subject, an update on the job front:

i have one internship secured with an internet start-up company, uShip.com. i think it will be very fun and educational. it will not, however, make me rich. so i continue my search for a part-time job. it's nerve-wrecking, but i feel lucky to have found something interesting and resume-worthy to do this summer.

I will not abide another toe.

The Big Lebowski Random Quote Generator

May 10, 2004

What is a Species?

The question seems simple enough. But how would you describe a "species"? How would you describe the difference beween human beings and cats, for instance?

Are species defined as organisms with distinctive characteristics that distinguish them from other species? (morphological)

Are species groups of organisms that reproduce with one another? (biological)

Are species defined by their ancestors? (Darwinian)

Are species determined by the organisms that individual members would choose as mates? (mate-recognition)

Given our prior discussion on taxonomy, you can see how the ambiguity in definitions can cause some problems. Biologists have long debated which species concept accurately describes the notion of a species. Clearly the biological and mate-recognition approaches seem wrong because they exclude organisms that produce asexually. But this still doesn't leave us with a clear definition of species.

The problem seems to be that different people want to answer different questions.

What are species?

How do we identify species?

Why are there species?

What factors are important in speciation, the creation of new species?

Certain species concepts seem inappropriate for discussion of some of these issues. Disagreement on the answers to these questions make the issue that much more problematic.

What are species?

Many biologists in the phylogenetics realm (that's me for the purpose of this discussion) currently adhere to the Darwinian (or evolutionary) species concept: species are lineages of ancestor-dependent populations. Relationships between species form a network of "reticulations". A species starts when an organism diverges from its lineage, and ends at extinction or the creation of new daughter lineages.

We've seen trees in the taxonomy article. Imagine the "Tree of Life", the tree that describes the relationship between all species. The tree is a hierarchy of historical lineages and current species.

Construction of the Tree of Life is a fascinating and enormous task. There are people who devote a great deal of time to building this tree. The Tree of Life Project website is a great resource if you're curious about how far along we are in understanding the evolutionary history of all organisms. The site includes an impressive guide to the tree, along with pretty pictures and extensive discussions.

How do we identify species?

Clearly we want to identify species by their character evidence. In terms of phylogeny, we identify character traits unique to lineages. It's a fuzzy description: how do we determine the cut-off? Often times we define "clusters" of characteristics as species descriptors.

Why are there species?

This is like asking "why do we evolve"? Natural selection and adaptation would be my answer. It turns out there are a few theories, some completely bonko:

Typological species: species are creations rather than evolved entities. (Move aside, god-people, that's just rediculous!)

Biological species: species are maintained by reproductive boundaries; a new species is created when the boundary is crossed (e.g. a horse mates with a donkey).

Ecological species: species are groups of organisms that occupy specific ecological niches. (this doesn't seem to tell the whole picture to me)

Cohesion species: emphasizes cohesion mechanisms that hold species together like reproduction and demographics.

Some hippies argue that species don't really exist except for in the minds of the biologists. Please. Because there is language, there is an inherent necessity to define and categorize everything. So in that case, nothing exists except for in our own minds. Like, dude, like, maybe we don't really exist except for in the minds of some bigger super-dude.

Are you a living computer simulation?

A philosopher's playground

You may have noticed that organism distinction is as much a philosophical issue as it is a biological issue. If you're at all like me, you tend to veer from the latter topic, as it can be most excruciating and (this is coming from someone who doesn't like philosophy) usually a waste of time. Still, even for me, the topic is interesting in its inherent social dilemma. Do categories really exist in nature? If you're at all interested in this, here's an article on the philosophy of species concepts with some references.

What mechanisms are important in speciation?

According to different species concepts, different mechanisms are more important than others: mates, physical characteristics, evolutionary history, ecological demographic. Are these characteristics at all compatible so we can at least define the concept of a speciation event?

The evolutionary definition is defined by the evolution of characters. Often new lineages arise as a result of ecological or reproductive change. So perhaps we can bring it all together at the speciation level. Let's consider what has to happen in order for speciation to occur.

Why can't we have sex?

Let's think about the reproductive aspect. We have some vague idea that many new species come about as a result of reproduction. So what keeps this from happening?

Prezygotic Isolating Mechanisms:

-Incompatible or absent mating calls.
-Different sub-habitats of the same habitat.
-Incompatible sex organs.
-Different breeding times.
-The gametes don't combine.

Postzygotic:

The species might reproduce, but the resulting organism has a low chance of survival. (We'll talk about hybrids soon, I promise!)

Horse + Donkey = sterile donkey = bad news for the ladies

So how does speciation occur in light of these isolating barriers?

Basically, a lineage splits when the two or more resulting species can no longer reproduce due to isolation barriers. This can occur in several ways.

Allopatric model: The formation of two of more species due to geographic separation (e.g. continental drift, a river, etc.).

Peripatric model: A small popluation of an existing population becomes isolated at the "edge".

Parapatric model: The two species exist in the same geographical area in groups that abut one another but never overlap. For instance, the dividing line may be the edge of a forest or a crossable river.

Sympatric model: Two or more dependent species evolve from the same ancestral species in the same geographic location. (Many biologists don't think this exists, as the conditions for such speciation are rare.)

Next time: Hybridization

Cute site: Evolution 101

haaaaaawwwwt

i'm sorry about that last post. it made me sound really pathetic.

i'll attempt to make up for it by turning you on with hugh's beautiful package of pecs and strategically placed body hair.

for the boys and vegelesbians: check out portfolio 1.

there is some regret...

This morning I had a look on my CS test and although my grade wasn't as good as I had hoped, I was pleased to find that my mistakes weren't horrible indications that I did not know material, but rather further evidence that I don't know how to read.

Still, I got my credit for the course, so I am happy.

Walking out from his office towards the bio lab, I started to feel a bit sad. He had asked me if I "planned to go into CS" and I said, "well, no, 'cos I'm already a grad student in TICAM". He seemed surprised that I hadn't made it aware to him previously that I was a grad student, "too". Once again, another chance for comraderie thwarted by my own social anxiety. The brief chat made me realize how painfully shy I am in so many social situations, especially classes. It made me wish I had been more outspoken and assertive, because the thing is, I thought my TA was pretty cool, as were a couple students in my class, as were a bunch of people I've met in grad school, only to let pass me by because I'm too embarassed to make my presence known.

So I'm filled with an overwhelming amount of regret at the moment. I'm sad that I never really found my social niche. I'm regretful because it's my own fault.

Fortunately there isn't any time for any serious moping... I have much work to do before Thursday.

Kings Play Chess On Funny Green Squares

The last exam of my life (potentially) is this Thursday in Systematics. Thus far, I've performed vaguely crappy on all of our exams. It's a biology course, and I'm so paranoid about not knowing the facts that I over-focus on memorizing details instead of getting the big picture. So this time around I've decided to take a different approach to exam preparation. I've decided to write a series of essays on what I've learned. Hopefully this will help me connect the lecture dots. My first discussion concerns the interesting, yet tedious, subject of taxonomy, the study of the hierarchical classification of things.

Since the 18th century, zoologists and botanists have adopted the scientific classification system of Linnaeus. Most of us became familiar with his binomial nomenclature system in high school biology. The groupings (taxa) of taxonomy are classified according to observed trait similarities. From general to most specific, the groupings of taxa are


Kingdom
Phylum
Class
Order
Family
Genus
Species

You can use the mnemonic in the subject of this post to remember the order. In binomial nomenclature, the "scientific name" of an organism consists of two words (often of Latin origin): the first half is the genus and is capitolized, and the second half is the species epithet. For example, Homo sapiens, Escherechia Coli, etc.

Classification rules are in place to maintain universality, uniqueness, and stability of names. When scientists discover a new species, they give it a name and publish it in a prestigious academic journal. A name is considered "scientifically complete" if the author and publication details are printed after the name. Exciting.

But there is a problem: synonyms and homonyms threaten the stability of binomial nomenclature. As the names imply, synonyms are two different names for the same species, while a homonym is the same name given to two different species. These kinds of discrepancies pop up when, for example, two independent scientists discover the same species and publish two different names, or when two previously named taxa are discovered to be from the same species.

When two synonymous taxa are discovered, priority is given to the name with the older publication date.

In order to keep up with the changes, biologists keep a "type specimen" described by its "type description". The single specimen designated as the type for a species is called a "holotype", and its description is the official description of the new species. The holotype is stored and maintained in a collection so that the description can be modified if it becomes necessary as new research and new questions arise. The type specimen is an objective point of reference for determining which organisms go with which species name.

A Quick Run-Through of Cladistics

Cladistics (phylogenetic systematics) is a branch of biology that studies the evolutionary relationships among organisms based on derived similarity. These relationships are plotted on trees intended to illustrate these relationships (see images above and below). Monophyletic taxa evolve from a single ancestor, pharaphyletic taxon include an ancestor and organisms which descended form it, and polyphyletic taxon include unrelated organisms that evolved from more than one common ancestor. Check out Steven Carr's website for a good pictorial example.

The trouble with the Linnean system is that grouped taxa can by monophyletic, polyphyletic, or paraphyletic. Most biologists today consider monophyly (also called a clade) to be a requirement for taxon grouping. "Grade taxa" (polyphyletic or paraphyletic taxa) lead to inappropriate comparisons such as reptiles to mammals.

The Linnean system breaks down with ongoing progress in phylogenetics.

Requiring each species to belong to each category (kingdom, phylum, etc.) is redundant. That is, distantly related species and their respective monophylies will have a similar order producing names that are redundant.

The convention often results in non-monophyletic taxa, especially when relationships among certain species are not always well-understood.

The use of exhaustive categories means then if a species is assigned a subgenus, then all other similar species must include that subgenus, even if that species displays no evidence for that subgenera. In order to avoid this, an overabundance of subcategories must be invented: Subphylum, Superphylum, Infraclass, etc.

Even worse, aside from species, these categories are completely arbitrary; there is no biological basis to the ranking system.

A Phylogenetic Solution

The Linnean system must be abandoned or de-emphasized in favor of a new naming standard that uses the principal of common descent as the basis for taxonomy, and evolutionary relationships to organize groupings. A code of phylogenetic nomenclature, called PhyloCode, is currently underway. The new system means that binomial names are no longer necessary. Names will reflect evolutionary relationships rather than characteristics. There are a number of ways in which this can work. A taxa can be associated with its ancestor and all its descendants (node-based names). Stem-based names associate a taxa with a clade of all organisms sharing a more recent common ancestor. Another system bases name on apomorphies, or derived characteristics. Apomorphy-based names base a taxa on the clade stemming from the ancestor from which a certain apomorphy evolved.

The PhyloCode system means that taxon names are only synonyms if they belong to the same clade. Priority is date-based by clade rather than category. Redundancy is less of an issue.

It has been suggested that names be standardized according to a "crown clade", the smallest clade that contains the last common ancestor of a living group and all of its descendants. This would discourage unfounded generalization based on extrapolation of extinct organisms.

My thoughts on the matter:

After studying taxonomy, I realize it's not as boring a field as I thought. But it's still pretty damn dull. I would have to eat my own face if I were on the PhyloCode committee.

References:

-Stephen Carr's Concepts of monophyly, polyphyly, & paraphyly

-Wikipedia: Cladistics, Scientific Classification

-My Bio384K notes - not in the public domain

Dinosaurs are cool.

May 09, 2004

Happy Mother's Day

♥ Happy Mother's Day to my wonderful mother, Dorothy, who has always encouraged me to follow my dreams. Thank you, mom, for your support and love. Without you, I would not be the independent, creative, and passionate person I am today. ♥