Study Guide

Taxonomy In the Real World

  • Health

    Pathology

    The TV show House has popularized medical mysteries, like the following story that relies on taxonomy for the proper treatment of patients.

    A pathologist is a doctor who specializes in figuring out what is making someone sick. This might entail looking at biopsies to determine if a tumor is benign or malignant, or testing blood and tissue samples for the presence of genes that would identify which viruses, bacteria, protozoa, or fungi are infecting a patient.

    A new patient comes in who is suffering from damage to his lungs from some sort of invader (or a pathogen). A tissue sample is taken and sent to the pathology lab to start unfolding the mystery.

    A quick look under the microscope shows a filamentous fungus. That's already bad because, since fungi's cells are more similar to our cells than bacterial cells. It's harder to kill them without also killing the human cells that they are invading. The pathologist's first thought is that it is Paecilomyces variotii. Then she remembers reading a paper published in 2011 that reported that P. variotii can easily be mistaken for Geosmithia argillacea. She decides to use genetic sequencing to identify the fungus, knowing that correct treatment relies on correct identification.

    The sequence data comes back showing that the fungus in the patient's lungs is definitely G. argillacea. That means that it is an aggressive infection that may be able to cross into other tissues. It will probably be resistant to most oral antifungal medicines and surgery might be the patient's best option. Unfortunately, a really effective drug isn't known. As more patients are correctly diagnosed with G. argillacea, instead of P. variotii, a clearer picture will develop. In the meantime, at least patients won't be given false hope.

    See P. variotii here.

  • Policy

    Biodiversity is just what it sounds like: diversity of living organisms. In general, we tend to think that diversity is a good thing. The variation among living organisms is breathtaking. It makes sense that we would try to preserve it. Imagine a world in which all the trees were the same kind, all the dogs were the same kind, all the flowers were just one single kind. BO-RING.

    Besides being awesome to observe and study, biodiversity also helps species by giving them many different types of other organisms to interact with, thus honing their fitness. Think of a runner training for the Olympics 200 m dash. If she only practiced by running 200 m on a track over and over, she would have little chance of winning because her muscles would only be given one type of challenge. Instead, she will do all sorts of exercises and training regimens to strengthen her heart, lungs, and all of the muscles in her legs. When species interact with each other, they compete for resources and put pressure on each other to survive.

    Cheetahs are only the fastest animals in the world because, gradually over time, the slower cheetahs died off, probably because they couldn't run fast enough to kill enough food to survive and reproduce well; they couldn't hack it with the big boys. Biodiversity is like Olympic training for the evolution of species.

    For most of the history of the Earth, biodiversity just followed its own course. Species interacted and competed with each other and the environment. Some became extinct, others went on to thrive, and still others came into being. For most of the history of human beings on Earth, biodiversity continued to follow its own course. But we're a powerful species. We can alter the land and oceans, and mess up other species' habitats, very rapidly and quite drastically. Habitat destruction, overhunting, and overfishing have caused many species to go extinct.

    On the up side, we know how to use our technology to track species and study them and their habitats in ways that were never before possible. We are also learning ways to use the resources of the Earth (through mining, agriculture, etc.) in ways that do as little damage as possible. Whether or not we use this knowledge is another question.

    In 1973, Congress passed the Endangered Species Act (ESA) in order to protect species from going extinct and "encourage" businesses to choose environmentally friendly options. The US Fish and Wildlife Service (FWS) maintains the official list of endangered species. The law has several consequences. Probably the most infamous one is that businesses must apply for permits from the Environmental Protection Agency before they build anything. They must check the land and verify that their building will not harm any endangered species. This is where science meets policy.

    An endangered species is one that "is in danger of extinction through all or a significant portion of its range." (A species' range is all of the territory where it lives.) It's a tricky thing to determine that a species is endangered. 5,000 water buffalo is a very different number from 5,000 mosquitoes. That brings up another point. The FWS doesn't give priority to higher forms of life. You might think it would be just fine if mosquitoes went extinct but the FWS will protect them just the same.

    What are most commonly reported in the news are stories about a human endeavor harming the habitat of an endangered species. For example, in Pacifica, CA, there is a golf course that the Wild Equity Institute is suing to shut down because they claim that the lawn watering and mowing are harming the San Francisco garter snake and the California red-legged frog, both of which are endangered species. Snakes and frogs can't vote no matter how much you might like them. Would you like to be the politician that works to take away your constituents golf course?

    Ironically, the ESA can even pit one species against another. That's what's happening in litigation over species that inhabit the Bonneville Dam, which is on the Columbia River located along the border between Oregon and Washington. There are two endangered species of fish (salmon and rainbow trout) that travel along the river each year to reach the Pacific Ocean after spawning inland in freshwater. A population of California sea lions (not an endangered species) preys on the fish as they work their way through the Bonneville Dam system. In order to help the endangered fish, the National Marine Fisheries Service has been authorized to remove (and kill) 92 sea lions each year through 2016. The Humane Society challenged this and a judge has reduced the number from 92 to 30. The policy question that this raises, of course, is what efforts are legitimate in helping endangered species to survive? Where do we find the balance between helping one species and hurting another? Do we know enough to be able to decide how many predators are sufficient to keep a species "on its toes" evolutionarily but not sufficient to drive it to extinction?

    Finally, our desire to protect habitats for endangered species can also conflict with our desire to find more environmentally friendly ways of obtaining energy. Solar energy is an up-and-coming renewable source of energy. Obviously deserts are a great place to put solar panels because of the intense sunlight that they receive. Plus, there aren't many people living in the desert to complain about the unsightly panels blocking their views of nature. But what if the panels will interrupt the habitat of an endangered species? That is what's at issue in lawsuits that seek to require the inclusion of a desert tortoise on the endangered species list- so that further interruption of their habitat would be forbidden. The litigation has already limited solar development in the Mojave Desert in California and seeks to do the same in the Sonoran Desert in Arizona.

    Stories like these show us that science cannot direct policy decisions on its own. Science can help us to determine what species need in order to thrive. Then we must make value judgments and do the best we can after weighing the importance of many different issues. How would you rank the following good things? Would your rankings depend on specific scenarios?

    a) Biodiversity, b) Environmental protection, c) Increasing your country's energy production, d) Increasing renewable energy production, e) Increasing jobs and helping the economy.

  • History

    Paleontology

    In 2007, two University of Florida graduate students made an HUGE discovery (literally). Their lab had been exploring a coal mine (Cerrejón) in Colombia for several years, looking for fossils in the exposed rocks. These fossils dated back about 60 million years. After each trip, they brought their loot back to the lab in Florida to study and preserve the specimens.

    One night, after most of the lab had already gone home, Alex Hastings had a hunch that the huge vertebral bone he was holding was not from a crocodile, as it had been labeled. His labmate Jason Bourque was a specialist in reptiles, among other things, so Hastings checked with him. Without skipping a beat, he identified it as coming from a snake. Suddenly, Hastings knew that he was holding a bone from the largest snake ever discovered. It was at least ten times bigger than the vertebrae of anacondas, the largest extant (living) snakes on Earth (see picture). So they dubbed their snake Titanoboa cerrejonensis, after the coalmine where it was found it.

    After looking through their bone collection again, they went to Colombia to dig some more. Everything they found confirmed their guess that the bone came from a huge snake. In total, they found 100 fossilized vertebrae from 28 different snakes of the same kind, plus there was a preserved skull, which is really rare for snakes since their skull bones are so delicate. Comparing their sizes and shapes and the number of vertebrae in the longest intact fossils, the experts deduced an approximate size for the snake: about 43 feet long, 3 feet in diameter and weighing in at one ton.

    After estimating the snake's size, the team could even estimate what the temperatures must have been in that region of the world at that time. Snakes are ectothermic (cold-blooded), which means that their bodies cannot warm themselves. They derive all of their warmth from the environment. The smaller the snake, the less heat it takes to get warm. The bigger the snake, the more heat it needs.

    Indeed, we see this trend throughout the world. The biggest snakes live closest to the equator. The trend is so consistent that we can predict the climate of a snake based on its size. And that is what scientists have done for Titanoboa, concluding that average temperatures were warmer than they thought, hovering between 86 ºF and 93 ºF. Because Earth is cooler now than it was then, we no longer have such huge snakes, or other enormous reptiles, for that matter—something to be grateful for.

    Now for its taxonomic classification and name. As a snake, the scientists already knew its taxonomy to a certain extent. It belongs to Domain Eukarya, Kingdom Animalia, Phylum Chordata, Subphylum Vertebrata, Class Reptilia, Order Squamata, and Suborder Serpentes. What was unclear at that point was whether it should be classified in the Family Boidae (as a boa) or Phythonidae (as a python). Carefully comparing the bones of boas, phythons, and their huge mystery snake, the experts decided that it's more similar to a boa than a phython, so it was classified in the Family Boidae and the Subfamily Boinae. Now the question is whether it is part of the Genus Boa, or the Genus Eunectes (the anacondas), or whether it needs its own genus. It is more similar to a boa than an anaconda except that it has more teeth than boas normally do (nowadays). That fact, plus its enormous size, led the team to classify it as a new genus, Titanoboa, think Titanic. The species gets the full name Titanoboa cerrejonensis, named for the coal mine where it was found. And there you have it: a modern day taxonomy story of gigantic proportions.

    The story about how the fossils were found can be found here.

    Learn about how a life-size model was made here.

    Videos can be found here.