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.

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…

So start to things off well, I’ve put up a photo gallery as a penitence for my absence. In March, 2007, I and several others accompanied a friend to Starr County, Texas, where he was conducting research on an endangered cactus, the Star Cactus1 (Astrophytum asterias).

The study involves marking as many cacti as we could find in a quadrat, and then revisiting the areas occasionally to monitor what’s eating the cacti. Other efforts included trapping for small mammals to get a picture of what’s in the area, and using cameras that are triggered by tripping an infrared beam to catch herbivores in the act…

While reaching out to place a flag near a cactus, I noticed an odd rock at arms length. Turns out it was a Common Poorwill sitting on the nest. I had to sprint back to the car to grab my camera, but the shots were pretty amazing.

I’ve put up a handful of pictures of this bird and some other neat highlights from this trip in the photo gallery.

I’ll put up other shots of other trips as time allows.

I want to start using this site again. But instead of providing commentary on the culture wars surrounding evolution, I’m going to simply provide commentary on me. I’m going to use this site as a place to post write-ups and pictures from my various travels.

Hmmm. That sounds familiar.  Perhaps because I wrote almost exactly the same thing on March 29, 2007. I’ll quote myself.

Why did I stop blogging?

The short and sweet answer is that I suddenly got tired of it. It felt more like a chore than it did fun. As the amount of time I poured into school skyrocketed (and so did the amount of writing for school), it was hard to enjoy blogging.

I’m also completely done with these eternal debates about evolution and creationism. At least online anyway. Like the above comments shows, the number of people who froth at the mouth and show up to leave comments far outweighs those interested in learning how science works. We live in the age of Google. In 30 seconds you can get more information about a subject than you can read in 30 days. An understanding of evolution and how it works is not lacking because of a lack of information. Therefore, I’m much more interested in having real conversions with people, face to face, who actually want to learn how things work, not just argue. The time I’ve spent at church talking with people about it on a number of occasions is just so much more fulfilling than blogging about it.

I also face the problem of being a fairly good but extremely slow writer. One story in particular illustrates this better than anything. Not long after we got married, my wife was working on this very lengthy paper for a class. She called me in to ask for help with wording a single sentence. I spent 30 minutes and finally came up with wording that we both liked. So out of 10 pages, I wrote one sentence. When she got the paper back (with a good grade of course), the professor had underline that single sentence and written in the margins, “Nicely worded!” (I’ll smile about that for the rest of my life). But the problem you see is that I can’t spend that long writing a post to Ocellated. There’s not enough hours in the day.

So what’s different this time?

Nothing if I don’t keep posting. But after amassing lots of good pictures, having many excellent adventures, and a likely move within the year to start a doctorate, I really would enjoy a place to share these experiences.

A really cool new way to view pictures

One last word before I put up new pictures. You can now view pictures in the photo gallery using Cooliris. Never heard of it? Follow that link for a flash animation of how it works. It’s a free FireFox plugin (you’re using FireFox, right?) that allows you to view images from the web in a very compelling way. I often use it to search for images with Google and now it works with my own photo gallery.

Once you install Cooliris, visit any of my albums or pictures in the photo gallery and then launch the program. I recommend clicking on the first image to enlarge it, and then using the down arrow to go through the images one by one. This way, you can see the image titles with the images. (You can also view the images full screen or as a slide show, but the title disappear.)

To make the experience even better in Cooliris, I’m going to start uploading larger images in the albums. These larger images will only be visible when in Coolirs, and while you can still view older albums with this tool, the pictures get stretched and may look a little grainy.

Finally, if you’re on a slow connection, you might want to view images just on the website (and not with Cooliris) so they’ll download quickly.

Today I leave for the Davis Mountains to continue my second (and last) field season of thesis research. Last year my adviser was gracious and allowed me the use of his vehicle. This year however, he wasn’t feeling so altruistic. And who can blame him? I had a whole year to arrange for another vehicle.

The problem of course is that I drive a Corolla. She’s light and nimble on her feet and gets a near miraculous amount of miles to the gallon, but she aint exactly renowned for her off road abilities. Her name is Betsy.

I needed more of a bastion of transportation to handle the mountainous terrain. I needed Bertha.

Bertha has a long and storied history. A 1988 GMC suburban that belongs to my parents, she’s like that relative that everyone respects for all they’ve seen and been through, yet no one wants to sit next to at the dinner table because of the smell…

A few years ago in what was expected to be her last hurrah, Bertha embarked with five young gents on a trip deep in the southern bowels of Mexico. She made it all the way to Oaxaca and back. True, she got her gas cap stolen and there were four flat tires in the first six days, but Bertha can hardly be faulted for Mexico’s hooligan youth, shoddy road conditions, and below standard spare tires.

No, Bertha will do quite well for me this summer. She’d better. I just spent $250 to get one of her four windows working (she has no air conditioner) and glue the fabric ceiling back on. She’s just got the right constitution for field work.

I’m really looking forward to these next few weeks. In addition to the research, I’m going to be pulling out the camera in my spare time, catching up on processing all my pictures, and reading lots of books. If my internet connection cooperates, you can expect to see plenty of pictures.

Oh, and by the way, if you’re in the market for a 1988 GMC Suburban with one working window and a glued on ceiling lots of character, I’ll have one for sale in about five weeks.

A new species of hummingbird has just been discovered in the cloud forests of southwestern Colombia. No surprise there. At roughly 1,800 species of birds, Colombia is second to no other country in the total species of birds that it has. Equator + Mountains = ginormous amounts of speciation in lots of different habitat types. With 2,500 species, South America is the bird continent.

Dubbed the Gorgeted Puffleg (Eriocnemis Isabellaea), the bird is quite spectacular.

He’s a puffleg, so he’s got the furry (feathers actually) “disco boots” around his legs. But what struck me the most is that the group of feathers underneath his tail (called the undertail coverts) are iridescent! Lots of hummingbirds have iridescence on their throats, but I can’t recall off the top of my head any that have iridescent undertail coverts. (I’m sure there are plenty in the tropics that I’m just not familar with.)

Despite having so many amazing birds, the article succinctly captures why most birders and even ornithologists don’t usually make it to Colombia.

Investigators caught their first glimpse of the bird while surveying a mountain ridge in the Cauca province in 2005. Braving the zone’s leftist rebels and drug traffickers, they returned to confirm the sighting.

The article also highlights fears that habitat loss from growing drug crops threatens the bird’s existence.

Still, it’s pretty amazing that we’re still discovering new species. There are something like 325 species of hummingbird alone, confined entirely to the new world.

I welcome each and every addition to this group.

I came across a three week old story in the Onion that takes aim at birders, particularly the Sibley Guide. It’s an absolute riot!

Here’s a brief taste, but if you know anything about birding, you’ve got to read the rest of the article.

I don’t understand it. How could it have happened a third time? They’ve had two opportunities to correct it. But there it is, once again. The Sibley Guide To Birds, third printing, page 488: “The dark-eyed junco, a familiar visitor to wintertime bird feeders throughout much of North America, is a species of the junco genus of American finches.”

Mr. Sibley, once again, the dark-eyed junco is not a finch. Its a sparrow. A sparrow.

[...]

Apparently the 42 letters I sent Mr. Sibley, his publisher, and his literary agent either went unread or now line the nests of Carolina wrens. I’m not sure what the mans afraid of, especially since I larded these letters with all kinds of reassurances like “its a common mistake” and “I get all those seed eaters mixed up, too” and other things I didn’t really mean.

And if you’re not laughing, me thinks you need a brief primer on what the Onion is…

Another blogger has used (after getting my permission of course) my recent picture of Burrowing Owls that I put up recently.

Says one of the commenters on the post,

Many thanks for the burrowing-owl photo. It brightened my Monday considerably.

It’s nice to see the shot getting wider exposure.

So I’ve been extremely busy the last few weeks trying to get everything wrapped by the deadlines that always come with the end of the semester. I just completed working on a paper for Molecular Biology about cystic fibrosis. Before I go any further, let me define just a few genetic concepts using the analogy of shoes, so that I don’t have to worry about readers being completely lost. Thirty seconds of biology won’t kill you, I promise.

• allele - alternative version of gene. If shoes are a gene, then cowboy boots, sandals, and tennis shoes would be alleles. For any given gene, you’ve got two alleles - one from mom and one from dad.
• homozygous - you’ve got the same two alleles for a given gene. You’re wearing matching tennis shoes.
  • homozygous dominant - both of your alleles make the same working protein. You’re wearing matching tennis shoes.
  • homozygous recessive - both of your alleles either don’t make a protein or make a protein that doesn’t work. You’re not wearing any shoes and have two bare feet.
• heterozygous - you’ve got different alleles for a given gene. You’re wearing one cowboy boot and one sandal, or one cowboy boot and one bare foot.

Cystic fibrosis is a homozygous recessive trait. You’ve got to get two CF alleles that don’t work right to get the disease.

Enough of the background information. I was focusing on one thing in particular. The allele that causes CF is a lot more common in European populations than one might expect for such a seemingly detrimental allele. In fact in Caucasian populations, the frequency of carriers can reach as high as 1 in 25 people! That’s pretty darn high when you consider that if two copies of those alleles end up in a child, that child’s dead before they’re three years old. How do you explain that? The likely explanation is what’s called heterozygous advantage, where heterozygous are better fit for their environment than homozygotes.

The classic example of this is sickle-cell anemia and malaria. It turns out that heterozygotes are much less likely to get malaria than homozygotes. I was looking on the internet for a reference to the scientific literature that discusses heterozygous advantage with sickle-cell anemia, when I came across this page from the website of a medical doctor at Harvard. (Incidentally, it’s a nice lengthy discussion if you want to learn more about natural selection favoring a detrimental allele through heterozygous advantage.) But it contained one little illustration that immediately caught my eye and made me laugh out loud.

Figure 2. Schematic representation of the effect of the sickle cell hemoglobin gene on survival in endemic malarial areas. People with normal hemoglobin (left of the diagram) are susceptible to death from malaria. People with sickle cell disease (right of the diagram) are susceptible to death from the complications of sickle cell disease. People with sickle cell trait, who have one gene for hemoglobin A and one gene for hemoglobin S, have a greater chance of surviving malaria and do not suffer adverse consequences from the hemoglobin S gene.

Oh, okay. I get it. But still, it’s a rather odd and comical choice for the illustration. It tickled my funny bone so much that I had to share.

So getting back to cystic fibrosis, the main evidence for heterozygous advantage comes from a study1 which showed that the bacteria which cause typhoid fever use the protein that the cystic fibrosis gene creates. Thus, if you’re heterozygous (one good copy, one bad) then you have less of that protein on the surface of your cells lining your digestive tract. Using mice as a model, they showed that typhoid bacteria are 86% less successful at infecting cells of heterozygotes. They also showed that mice containing two bad copies of the CF gene were not infected by any typhoid bacteria. Thus typhoid are using that protein as their entries into the cell.

As typhoid is a disease that has ravaged Europe for many years in premodern time, it now becomes understandable why selection would increase the frequency of the CF allele in European populations.

My wife and ventured to southern Colorado for spring break. I’ve finally gotten around to throwing up the pictures from the trip. They’re heavy on Sandhill Cranes in flight. Why? Because literally tens of thousands of these birds migrate through the San Luis Valley and use it as a staging area on their way back north, and the birds are just about impossible to sneak up on when they’re in the fields feeding. So it’s much easier to take pictures as they fly by.

It was really a magical experience. Most cranes in the world are endangered. These ancient birds haven’t coped well to the changes people have brought. And while it wouldn’t take much too see Sandhill Cranes get in trouble, their populations are currently large and stable. Like all cranes, they’re quite vocal and frequently display towards one another by jumping in the air and flapping their wings. In short, they’re sexy.

Other highlights of the trip included a couple of Burrowing Owls sitting in the rain on the drive up to Colorado, my first Snowshoe Hare (I now understand why they’re in the same genus as our jackrabbits), and an amazing place named the Great Sand Dunes National Park.

I’ll leave you with a selected few pictures. (Click on them to see slightly larger versions in the gallery).

I know many people aren’t into technology, so I’ll make this brief. With overtones of both the mafia and livestock herding, MSNBC has an interesting post up about rival gangs that are fighting to control networks of hijacked computers.

The bot network industry is so profitable, and hijacked computers are so valuable, that rival gangs now fight over them. … Bot herders steal each other’s infected computers, fight off such raids, and often try to knock each other’s computers off-line.

What they’re doing of course is using these computers that they’ve managed to install rogue programs on for the purposes of sending spam and other nefarious activities. What I found so interesting about the article was the level of sophistication these criminals are reaching. They’re not just content to toast your computer through a virus like the good old days of 1999.

The war has escalated to a level where bot herders must jealously guard their hijacked computers. In October, a yet-to-be-named Russian gang released a program called SpamThru that infected machines worldwide and quickly amassed an army of zombies nearly 100,000 strong, capable of sending out 1 billion messages each day.

To protect the investment, the malicious program actually included a stolen copy of the Kaspersky antivirus program, modified to stop all attacks but its own. SpamThru installed the anti-virus program on all infected computers, removing all other viruses. It even sent an infection rate report to the program’s author. The stolen antivirus software continues to defend SpamThru bots from other attacks to this day.

It’s evil. But you’ve gotta admit that’s impressive. Taking a computer that obviously didn’t have anti-virus protection on it in the first place, and then adding anti-virus software to make sure your little parasitic program has a home all to itself.

The article goes on to describe how like any other business, they have to advertise, and that people suspect many attacks seen on the internet may actually be a demonstration to a potential buyer of the strength of a gang’s hijacked computers.

Interesting stuff if you’re even slightly interested in how we use technology and how it affects society and culture.