Posts in Category: School

Playing with DNA

Posted Dec 10th, 2008 at 9:59 am in Research, School, Science | 1 Comment

I had my first really successful day in the molecular lab yesterday.

This is a gel from a PCR reaction of beta fibrinogen intron 7 for eight cockatoo species.

PCR reaction of Beta Fibrinogen intron 7 for eight cockatoo species

While I promise not to show many more of these (it gets boring pretty quick), it’s exciting because everything worked. Lanes 1-8 have a single band, which shows that I successfully amplified the gene I’m interested in. Lane 9 is a negative control. It’s empty as it should be, showing that I didn’t have DNA contamination in the reaction. Lane 10 is a ladder. It has known sizes of DNA so that one can judge what size fragment the PCR reaction returned.

Now I just have to figure out how to sequence DNA…

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I’m Not Dead Yet

Posted Oct 4th, 2006 at 9:17 am in Nature, Photography, School, Science | Comments Off

… as the famous line from Monty Python goes.

I’ve put up some pictures of an outing a couple of weeks ago to a local ranch, where my university’s biology department hosts an annual Bioblitz, identifying every species regardless of taxa they possibly can.

I managed to get one picture in particular that I just really like.

hole in the canopy

Another highlight of the weekend was this Hoary Bat, a species I had previously only seen in pictures. They are arguably the most beautiful of bats found in the U.S.

More from me if I survive today.

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Mentos + Diet Coke = Fun

Posted Sep 19th, 2006 at 9:46 am in Humor, Photography, School | 9 Comments

What do you get when you take The Fresh Maker ® and The Real Thing ® and put them together?

Mentos + Diet Coke = ?

My wife and I heard about this recently on the popular show Myth Busters, and after seeing it, we had to try it out.

Lucky for me, I had a professor that needed a 3 liter bottle. After stopping at four different stores to secure a package of Mentos, the experiment was ready. A biology party was the perfect setting.

So what does it look like?

Diet Coke geyser

Here’s a closeup of that same shot:

Diet Coke geyser closeup

Also, I’ve added a series of photos in the gallery showing the progression as the eruption occurred. The whole thing is extremely fast. It’s over within one to two seconds.

So how does it work?

Upon adding three or four Mentos to the Diet Coke, what happens is that virtually all of the carbon dioxide is released from the Diet Coke in an extremely short amount of time. The resulting pressure forces the liquid out of the bottle with surprising force, resulting in the geyser.

More specifically, the tiny holes on the surface of the Mentos serve as a nucleation site, facilitating the rapid formation and release of tiny bubbles of CO2.

Wikipedia has an article on the subject, with more detailed information on the science behind it.

It’s fun, it’s cheap, you should try it. Just not inside.

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Let Me Share This Funny Story

Posted Jul 25th, 2006 at 3:33 pm in Humor, Life in General, School | 1 Comment

If you’ll indulge me, I have quite a story to share. It’s about life and what we want from life. It’s about what we find important, what we really value, and what we’ll do without in order to get it.

My wife is a waitress this summer. The other day at work, she had a table that was particularly annoying. The moment they walked in, a man in the party did something so bizarre, so shocking, it defies belief. Because it’s the punch line of the story, I’m going to save it till the end. So you’ll have to read the whole post (or just skip to the bottom) to find out what happened…

Now my wife is very slow to get angry. It’s almost annoying how nice, tolerant, and mild mannered she is! But even she has her limits, and they were met and exceeded with this table.

To set the scene, it was a table with an older couple. They quickly became frustrated with the menu. They were trying to order the senior special, but complaining endlessly that the options weren’t comparable to the full menu. Perhaps they had a point. In offering an unequal menu for the seniors, perhaps society was unappreciative of their great contributions. The senior meals come with fries, which separately cost $2.50. Yet they could substitute only one order of vegetables, worth a mere $0.75. “Why the discrepancy?,” the gentlemen wanted to know. Indeed, a great injustice may have been occurring.

But an injustice at my wife’s hands it was not. Seemingly oblivious to the fact that she serves the food rather than makes the menu, they bitterly complained. My poor wife had to finally throw down the gauntlet. “I’m really sorry that your upset, but I don’t make the menu and have no control over these decisions. You can order a regular meal and get what you want, or the senior meal for the reduced price.”

Once the food was out of the way, the real point of contention surfaced. They asked friendly enough personal questions — Where are you from? What are you doing? Oh you’re married? What’s you husband doing? — etc. Friendly enough, that is, until they bluntly decided to share what they thought of our plans…

My wife wants to be an elementary teacher and I a college professor. “Are you independently wealthy?” the women asked with an incredulous scowl upon her face. “How do you expect to pay for any of this?

My wife tried explaining that since you spend most of your adult life at work, we felt it was important to pursue things we were passionate about. That when the day was done and our lives were lived, we would be far happier with a job we cared about than a job we didn’t but which paid us more. This seemed to be lost on them, and they continued insulting her for being so stupid as to help support a husband in grad school. With the excuse of “other customers” my wife walked off, a wee bit ticked off.

So, what’s the surprise waiting for you at the end of the post? The punch line of it all? Well get this. When they walked in, the man had a tape measure. He required at least 14 inches in between the booth and the table to accommodate his stomach. His wife also required the same. And he measured to ensure that he had it.

Yes indeed. When times are tough, and I reflect on the decisions I’ve made in life and the endeavors I’ve decided to pursue, I’ll surely think back to this guy and his wife, squabbling over a few cents on a senior meal, and measuring their booths to make room for their stomachs. And I’ll reflect on the life I never had.

Something tells me I won’t miss it very much.

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On Which My In-laws Undoubtedly Concur

Posted Jul 6th, 2006 at 9:32 am in Humor, School | 1 Comment

Upon my return home from thesis work, my wife had to share a quote she’d gotten a laugh from. It’s from The Simpsons, the modern purveyor of truth that it is.

Bart [after watching a foreign film] : I was so bored I cut the pony tail off the guy in front of us. [holds pony tail to his head] Look at me, I’m a grad student. I’m 30 years old and I made $600 last year.

Marge: Bart, don’t make fun of grad students. They’ve just made a terrible life choice.

What It Is, Exactly, That I’m Doing Out Here

Posted Jun 26th, 2006 at 2:57 pm in Research, School, Traveling About | 2 Comments

Not long after the start of this summer field season, keiths asked if I could explain what I was doing for my thesis in a little more detail. I said I would, I meant to, but somehow I got lazy when it came around to actually doing it. Well, I aim to be a man of my word, and with this summer’s field season coming to a close, I figured I’d better elaborate soon. In terms of humor, interesting writing, and insightful commentary, I promise nothing. This is simply a brief description of what my thesis involves and what my days are like out here in the Davis Mountains. Read the rest of this entry »

Davis Mountains Accomodations

Posted May 21st, 2006 at 9:00 pm in Photography, School, Traveling About | 3 Comments

My I’ve been busy. I finally got around to putting up pictures. They’re not much, but I haven’t been carrying my camera with me yet.

For now, I’m staying in the McIvor Center. It’s a spacious building that’s got nice facilities including a kitchen and an adequate bedroom. It’s also got a wireless internet network via a satellite connection. It’s also a got a nice view. From the center, one can see Mount Livermore in the distance.

And last but not least, I traded cars with my professor to get a vehicle with a little more ground clearance (an absolute necessity on the back roads). The car comes with a colorful bumper sticker.

The thing that’s keeping me so busy is trying to setup my transects. Each point has to be 250 meters apart, and I’m finding that very difficult at times when trying to deal with the terrain. Once those transects are setup, I’ll try to run 20 points each morning in four hours. After that I’m done for the day and will get to enjoy myself a little more. Go birding, take pictures, do all that reading I have planned for this summer, etc. I’m sure blogging will be a little more frequent then too.

A Thesis — Davis Mountains Here I Come

Posted May 15th, 2006 at 11:30 pm in School, Traveling About | 1 Comment

I am excited to announce something I’ve known about for a while but have yet to announce as I worked out the particulars. I’m leaving tomorrow to begin my thesis on avian community ecology in the Davis Mountains. I will spend two field seasons of approximately six to eight weeks focusing on quantitatively describing the bird communities and how they are defined in major habitat types. Also, this type of work has previously been done in many of the other southwest mountain ranges, so I should be able to make comparisons with the Davis Mountains to see if any differences show up.

Most exciting is the place I get to work. I’ll be doing this study on The Nature Conservancy’s Davis Mountains Preserve. This location is an amazing place. It includes Mount Livermore, the fifth highest peak in Texas at 8,378 feet. It also contains habitats (and species associated with them) that are either Rocky Mountain species which barely make it this far south or Mexican species which barely make it this far north. The state’s first record of Buff-breasted Flycatcher was found here, sitting on a nest. The Mexican subspecies of Spotted Owl occurs here. Ten species of hummingbird have been recorded, like Magnificent Hummingbird. It’s also a great place for rare Mexican warblers like Slate-throated Redstart, Red-faced Warbler, and Olive Warbler. It is a place that any biologist would love to work in.

At first, I’ll be extremely busy working on the details of the study and marking my transects. But after things settle down and my surveys begin, I may have time to blog. You can also bet that I’ll be taking pictures, as time allows. We’ll just have to see how things work out. I’m also excited by all the time I’ll have this summer to read. I’m bringing a bunch of books.

One of my biggest goals in my time off however is to make a date with a Flammulated Owl. Of the birds that regularly occur in Texas, I can count the ones I’ve not seen on one hand. Somehow I’ve missed these tiny owls in all my prior birding trips, probably because I’ve not looked for them specifically.

It’s going to be a great summer, but one with its own challenges being away from my wife. I’ve got to give a big shout out for her support and willingness to take care of the homefront while I’m gone.

It’s Finished

Posted May 11th, 2006 at 12:29 am in School | 1 Comment

I can’t begin to tell you how excited I feel right now. I’m done with this semester. Well, the heavy academic part at least. Three finals in the last three days have left me wasted. I studyed my butt off for evolutionary ecology tonight. I don’t even want to hear about an N-dimensional hypervolume for at least a week and anyone leaving comments about them risks my wrath.

But seriously, it’s the best feeling in the world. I’ve finished the semester. I think it’s one of the things I like most about academics. The cycle. The feeling of a new beginning at least twice a year and being completely exhausted and ragged, without a care in the world, when it’s all done in the spring. Oh sure, I’ve got things to do. Lots of things. But for the rest of the week, no more classes and no more tests.

I’ve got a semester of grad school under my belt.

Talk About Inspirational

Posted Apr 10th, 2006 at 9:40 pm in School, Science | 2 Comments

Every year Angelo State has an event called the Moon Lecture where they bring in a top rate scientist to speak on different issues. The night before the lectures, they have an informal BBQ where faculty and certain students can hear the life story of the speaker, meet them, and ask questions. Having just arrived at school, this was my first time to attend.

This year the speaker is Leroy Hood. (And see more on Wikipedia).

He’s a systems biologist who is credited with creating the DNA sequencer, amoung other things. All you lab rats out there who love looking at DNA sequences to study evolution have Dr. Hood to thank. He’s also been involved with the Human Genome Project, various immunology projects, and a host of other biotechnology projects.

He basically spoke of his childhood (grew up in Montana) and how his interest in science was nurtured by parents and childhood teachers. One of those high school teachers convinced him to attend Cal Tech, where he arrived in 1960. He said it was the biggest culture shock of his life. Upon arriving, his roommate asked him if he’d taken some course (cancer research? — I don’t remember). “Not only had I not taken the course, I’d never heard of it.” “You’re in big trouble then, you’re not going to make it,” his roommate responded. Dr. Hood said that his roommate had failed out the first semester from playing 20 hours of bridge a day. Though I’ve never played bridge, I get the idea that it would be an emmensely more enjoyable way to fail out of college than 20 hours of video games a day, as my peers do now.

He spoke of how accessible his professors at Cal Tech were. My jaw dropped when I heard some of his teachers his freshman year. Richard Feynman for physics, Linus Pauling for chemistry, and George Beadle for biology. He had the attention of every single person in the room.

Tomorrow he’ll be giving two lectures which I will attend. As I mentioned, his interest is systems biology. I think it’s essentially the question of how we manage the information we’re getting. When you think about the amount of information contained in the genome and the interactions going on in a biological system, we’ve gotten to the point where we need ways to condense that information and think about it conceptually. Dr. Hood mentioned that medical school was a big disappointment to him because of the rote memorization and the lack of conceptual interest. (Yeah, I personally call it the dark side of biology). I believe his talks will center upon the work being done in these areas.

I’ll take notes and present the highlights. I’m very much looking forward to it.