Instituto de Biología, UNAM, Mexico City

Posting has been slow because I recently went back to Mexico City for a visit. Most of my time was spent researching (i.e., drinking) the ancient and unsettling alcoholic beverage called pulque for an upcoming article, but I started off my trip with a visit to a few labs at the Biology Institute at the UNAM, the public university of 250,000 students where I spent the last two years studying comparative literature.

Biology is perhaps the science I am least familiar with; years spent running around physics labs can sadly sort of make you forget about the life sciences. High energy physics, particularly, operates simultaneously at two scales that seem pretty removed from life on Earth: the very small (quarks, neutrinos) and the very large (black holes, the origins of the universe). I was delighted and a bit surprised to see a similar conflation of disparate scales in the Biology Institute labs I visited. By studying the genetics of specific animal populations, my tour guides Noemi Matías Ferrer, a graduate student in biological sciences working on her Ph.D., and Patricia Rosas Escobar, a staff biologist originally from Baja California, are able to learn about entire ecosystems, humans’ effect on the environment, and life on our planet more generally.

Some of the chemical buffers Paty and Noemi use to extract DNA from their samples. Paty is in the background.

Paty is studying the genetics of guacamaya roja (otherwise know as the scarlet macaw) populations as part of a project to reintroduce the bird to protected areas of the Yucatán. Illegal trade of these dramatically plumed parrots has dramatically reduced their populations, and all surviving guacamayas now live in some form of captivity. Paty studies the DNA of guacamayas to ensure that only birds from populations that originated in Mexico are being reintroduced to the peninsula. This type of environmental intervention, in which intense human management is required to merely get an ecosystem back to “normal,” flies in the face of the assumption that the best thing we can do for the environment is to just leave it alone. (I saw something similar at work at Fermilab’s prairie preserve back in 2005.)

The group in charge of the guacamaya reintroduction effort in the Yucatán sends Paty these blood samples from the birds, from which she extracts their DNA. The paper is specially designed to preserve the genetic information in the blood without refrigeration, making it an ideal tool for rural fieldwork. In this (slightly blurry; sorry!) picture, you can see the small holes where Paty has removed part of the sample on the right in order to analyze it.

Noemi, on the other hand, studies two species of tree frog in southern Veracruz. Unlike Paty, who analyzes samples that are sent to her, Noemi spends a lot of time in the field collecting specimens and observing the frogs’ behavior. When she first went to Veracruz to do fieldwork in 2009, there was a drought and the frogs were extremely hard to find—a worrying discovery. But thanks to increased rain in 2010 and 2011 (she usually goes during September and October, the height of the rainy season), the populations seemed to bounce back.

But that doesn’t mean that the frogs Noemi studies are out of the woods (so to speak). One of the reason that Noemi is interested in studying tree frogs is because, as she said in Spanish, “amphibians reflect [environmental changes] in a more immediate manner than mammals do” and are, therefore, considered bioindicators. Noemi’s frogs have lost much of their habitat over the years, and she is studying their genetics and morphology to determine how that stress is affecting them. Studying their DNA reveals which individuals in a population are reproducing, while weighing and measuring the frogs helps Noemi pick out physical changes and asymmetries that can be responses to environmental stress.

Noemi studies the physical traits of these tree frogs under a microscope. Afterward, she removes their hearts and livers for further study. If you look closely at the frogs lying on their backs, you can see the incisions she makes on their abdomens.

All of Noemi’s specimens are males, partly because her research does require killing the frogs she studies and she prefers to leave the egg-laying females alone to minimize her effect on their populations. But the male tree frogs are also much easier to find, as they spend their nights singing to attract mates. In addition to the challenge of finding the frogs, Noemi is increasingly confronting issues related to declining security in Veracruz. Her fieldwork often involves wandering around private property at night, which is the first thing you learn NOT to do if you visit rural Mexico.

The heart (below) and liver of a tree frog. Noemi leaves their other organs intact so that other scientists can use them for future studies.

Back at the lab, Noemi will often spend seven or eight hours measuring and dissecting frogs under a microscope, but she says that after about four hours she starts to burn out. The fine motor skills and intense concentration required for her hands-on work reminded me of the arts and crafts sensibility of Steph’s chemistry lab.

Perhaps the most time consuming part of both Noemi and Paty’s research is extracting DNA from their samples and preparing it for analysis.

Noemi and Paty use these micropipettes to measure out extremely small quantities of the buffers in the first picture as part of the process of DNA extraction.

Once the sample has been treated with the buffers, it goes into this centrifuge to separate out the DNA and force it to clump together.

Tubes containing extracted frog DNA.

Once they have extracted the DNA, Noemi and Paty must isolate the fragments of genetic information they are most interested in. To make those fragments easier to study, they amplify them using what they charmingly referred to as “a copy machine.”

The "copy machine" that Noemi and Paty use to amplify the fragments of DNA they want to study.

When the extraction and amplification is complete—which can take hours—Paty and Noemi look at the DNA under UV light to make sure they actually have the sample they need. This is the moment of truth, since if nothing shows up they have to repeat the tedious and time consuming process until they get it right.

By looking into the eye piece on the top of this box, Paty and Noemi can view the DNA they have extracted and amplified under UV light.

The result of a successful DNA extraction and amplification as seen under UV light. This picture is of a fragment of pine tree DNA.

All this work is just a prelude to the analysis that Noemi and Paty will ultimately produce.

A page from Noemi's lab book.

Mexico is often described as one of the most beautiful countries in the world, and it certainly contains an impressive variety of ecosystems (my favorite is the huatesca, a truly bizarre combination of desert and rain forest). I asked Noemi and Paty what they thought about the recent push to increase ecotourism in Mexico in hopes of protecting some of these areas, and their answers were some of the most thoughtful I’ve ever heard on the subject. Paty pointed out that ecotourism often favors certain species over others; she recalled seeing whale watchers in Baja California trample plants and litter during their excursion. Noemi, for her part, wondered if ecotourism can be sustainable without economically benefiting the local populations of humans, who are often more generously rewarded for exploiting the environment around them than for protecting it—think of how lucrative selling a captured guacamaya on the black market could be, especially for a person without many other options.

In her work with amphibians, Noemi also runs up against the issue of how to convince people to protect an animal that isn’t, to be blunt, cuddly or conventionally beautiful. A lot of people think frogs are pretty gross and don’t want to go out of their way to help them out. (For more on this issue, check out Robert Krulwich’s story about efforts to reintroduce the world’s largest stick insect to its natural habitat.) What’s more, the habitat her tree frogs need to reproduce—deep pools of standing water surrounded by vegetation—is also conducive to dengue-carrying mosquitos, making it a target for well-meaning and necessary public health efforts as well as simple deforestation.

Our relationship to the environment is never a simple issue, and the first step toward improving it is figuring out just what is going on out there anyway. A big thank you Noemi and Paty for taking time away from their work to show me what they do.

¡Gracias, Noemi!

And of course a big thank you to aluminum foil, without which no science would ever be done.

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