Friday, February 27, 2015

The Great Chain of Being is still relevant today and not for the right reasons

The Great Chain of Being, also known as scala naturae, is a concept that was derived from the ideas of Plato and Aristotle. It's the idea that there is an inherent hierarchy of nature with a perfect god at the top, angels right below god, kings below the angels, and animals, birds, worms and then rocks at the very bottom with much in between the kings and the animals. Birds are lower than animals and worms are lower than birds. This method of ranking living and nonliving things classifies them based on perfection with each step down becoming gradually less ideal.

Select portion of Haeckel's Evolution of Man
With a perfect god at the top, this system obviously has religious roots, but it was how naturalists and biologists thought too. The idea has changed over time and eventually living things were grouped based on their anatomy as opposed to this system based on perfection and closeness to a god. It sounds like an archaic way of thinking, yet the idea that some species are higher than others pervades our thinking to this day. Many people believe humans are better or above other animals, that we deserve all of the resources we consume regardless of other species' needs, and even that we deserve these resources because we're more intelligent. We drastically change the landscape and ecology of the planet, building dams, spraying pesticides, logging forests, and so forth, because we believe we're making the world a better place to live in (for humans).

Learning more about wildlife and seeing animals in action, whether it's in a zoo or the wild, is the easiest way I can think of removing these biases. By learning that chimpanzees appear to mourn for their dead, we realize we're not so different. Going on a whale watch and seeing humpback whales with your own eyes is hard to forget and makes these aquatic giants seem more than just another species we need to protect. Learning that the aye-aye's creepy pointed finger has a unique and important function helps us understand that this weird primate is worth saving despite its oddities. Reading about animal intelligence and understanding the tremendous diversity of adaptations animals have to their environments makes it clear that there are multiple ways of measuring importance and worth of a species. One species isn't better than another but each species is different and has its own value. Just because an ant doesn't create art doesn't mean that we should ignore them. Ants wage wars, they are one of the strongest animals in relation to their size, some ants can swim, and some can reproduce asexually. They're more than just an annoyance at a picnic and they're a lot of things we're not. Who are we to judge if they're "better"? Ants aren't humans and humans aren't ants. Different doesn't mean we need to undervalue them.

Monteseny brook newt
Many people also believe that certain animals (usually the photogenic or cute and cuddly ones) are worth protecting over others. This too is similar to the idea that some animals are higher than others. Humans will gladly donate to save the endangered giant panda (Ailuropoda melanoleuca) but saving the critically endangered Montseny brook newt (Calotriton arnoldi) is a lot harder. One species is cute and cuddly and widely recognized and loved whereas the other is unknown to most people. The World Wildlife Foundation uses the giant panda as its symbol or logo. Should the Montseny brook newt remain unknown and ignored because it isn't as cuddly as the panda? Do we really want to base our conservation priorities on which animal takes the best photos and sells the most stuffed animals? Probably not but that's often what happens.

How do we make newts, frogs, insects, snakes, spiders, and other animals more attractive compared to pandas, tigers, orcas, and gorillas? Well, I'm not sure we can. Pandas look good on tee-shirts and there are more tv and movie documentaries on pandas than on newts. Our best bet is likely educating people about how important those less desirable animals are to our world and how interesting they really are. (To learn more about the Montseny brook newt, click here.) This may be one instance where it makes sense to spend more time educating adults than it does children. I'd hope adults are more susceptible to listening to the facts rather than basing their donations and interest solely on the charisma of an animal, but who's to say?

Drumming up support for local species is also a good idea. You're more likely to protect a species that you see in your own neighborhood than one that you'll probably never see because it's on another continent far away. Take for example the California condor (Gymnogyps californianus). This is not a cute species, yet it has rebounded from only a few individuals living in the wild to more than four hundred due to captive breeding programs initiated by the US government. Protecting condors started out as a government initiative, but condors have found their way into our hearts (or at least found their way onto our radar) despite having bald heads and feathers. You can easily donate online to help reintroduction efforts.

The Great Chain of Being should be a concept that pops up only when we're discussing history. Instead, it permeates our ideas about the value of conserving wildlife. This is an outdated idea that doesn't make sense given all we know about the animal kingdom. Gorillas are not higher than rodents and protecting them based on this idea is misguided and outdated. Let's move on from scala naturae and protect species based on other characteristics.

Food for thought: What makes a species worth protecting? How should we judge which species deserve our attention?

Links of interest:
Valuation of species and nature conservation in Asia and Oceania
Science Video: Why do we value some species more than others?
Ethics for Wildlife Conservation: Overcoming the Human-Nature Dualism
TED Talk on bringing the condor back from near extinction

Friday, February 13, 2015

No, humans did not evolve from monkeys

Frequently used image depicting evolution
I often hear, "humans evolved from monkeys" or substitute monkeys for apes or chimps. Unfortunately, this is a common misconception. It's simply inaccurate and a result of poor understanding of how evolution works. Humans did not in any circumstances evolve from monkeys or chimps or lemurs. For the sake of clarity, let me repeat, humans did not evolve from monkeys or chimps or lemurs. I'm not about to go on a creationist rant but I am about to explain hopefully dispel some common misconceptions about evolution. To understand why saying humans evolved from monkeys is so wrong, we first need to take a closer look at how evolution work and we're going to start with phylogenetic trees. A phylogenetic tree is a visual representation of the evolutionary relationships between species. They're often just called trees for short and they're very useful. If we look at the one below, we see multiple species (named "A" and "B" and so forth). The nodes or areas where multiple lines come together represent common ancestors.

For example, if we trace species A back through time we see it eventually connects at a spot I've labeled X. The same is true for species B and C: we can trace their lines back to species X.
Example of a phylogenetic tree

 Species A, B, and C are all descendants of species X, which no longer exists. Species X is the last common ancestor species A, B, and C shared. A common ancestor is simply an ancestor that two or more species have in common, and the last common ancestor is the most recent common ancestor of two or more species. If we keep traveling down the line of A (and back in time), we see that species Z is also a common ancestor of A and B, but the last common ancestor of A and B is species X. There's a slight difference in meaning between common ancestor and last common ancestor. All of the species on this tree originally evolved from species Z, but this was a very long time ago. Usually, trees represent millions of years. Over time, species change. Species Z was one species at the start of this tree, but something happened (either gradually or suddenly) to make this species split into two different species, X and Y. Maybe one population was separated by another due to an earthquake, as time progressed, those two populations became so different from each other, they formed new species (X and Y).  Species X may have been separated from a critical food source, and thus gradually began foraging only at dusk and dawn for insects, whereas the other population started interbreeding with another population made up of only white-colored individuals. Over time, the two become distinct populations and eventually distinct species.

Close-up of some of the phylogenetic tree
Let's take a closer look at another side of the tree and pretend that these alphabetically named species are species of monkeys. D, E, and F separated or diverged from species Y. If I look the tree over from the top to the bottom, I see that species D, E, and F are relatively young (their lines separating them from Y are relatively short), and that species Y spent a great deal of time successfully as species Y before it split into multiple species. Let's say one of the main reasons why species Y split into multiple species was because a new predator was introduced into the habitat. One population of Y changes its behavior and activity patterns to become nocturnal, thus avoiding the diurnal predator entirely. That population becomes E. Enough time passes and E can no longer breed with close relatives, D or F. Another population E finds success in foraging lower in the canopy, thus avoiding the predator, which let's say is some sort of predatory bird. E forages lower in the canopy but has to make behavioral changes to do so, feeding on different items and relying on its tail less to balance on thicker tree branches. Over time, E becomes a distinct species and cannot breed with F or D. It retains some success for a while but eventually it begins to lose numbers due to feeding competition from other animals occupying this part of the canopy, and E goes extinct. This is why species E's line does not extend all the way to the top of the tree, or the present time. It did not survive. The same is true for species D, which managed to adopt certain vigilance behaviors to avoid the predator, but was sadly wiped out from a disease that destroyed the population.

If you follow the lines, you can see that species F eventually splits again into separate species, making species F an ancestral species. It is the last common ancestor to H and I, both of which still survive to this day. Species H is more closely related to species I than it is to species C, which it last shared a common ancestor with a long time ago. That means that H and I will share more characteristics than species I and C.

Tree showing relationship of great apes and humans
Now, all you have to do is apply this to primates. Chimpanzees, lemurs, and so forth are all living species. Replace A with lemurs and I with humans and you can see immediately that we did not evolve from lemurs. A does not come from I. That's obviously wrong. However, A and I do share a common ancestor, Z. Now, these A and I have been evolving, over time, separately for a while. They've taken different paths, but they do share a common ancestor, a common ancestor, Z, which is no longer alive. It may seem like a small difference, but the number of people who actually believe that we did evolve from monkeys is perhaps greater than we'd all like to believe. By saying, we shared a common ancestor with monkeys or we evolved from an ape-like ancestor as did chimpanzees, some of the confusion might be avoided. Or someone may ask you to clarify, and you can explain that humans did not, in fact, evolve from chimpanzees. Looking back to the first image depicting evolution of humans, if you said that first animal was a gorilla, that would be inaccurate. If you said it was an ancestor of both gorillas and humans, you'd be okay.

It's important to remember that while it looks like species H and I separated from each other at a very distinct point according to this tree, that's not always the case. Populations are always evolving, and it may take a few generations or a hundred generations for a species to gradually become a separate one. It is humans who define when exactly a species arises or diverges, but the reality is that it is a process, and the exact time when one species became two is debatable. There usually isn't a right answer. Scientists are forever learning about species, finding new ones, and reassembling these trees using the best information available. The end of the tree, in our case A, B, and so forth, don't need to represent species. You could do a phylogenetic tree and go as far as genera if you'd like or go all the way to subspecies even. It depends on what your purpose is.

True or false: humans are more closely related to orangutans than gorillas.
Answer: false
True or false: humans are more closely related to chimpanzees than bonobos.
Answer: false. If you switch bonobos and chimpanzees in the tree above, you'd be within your right to do so. The same amount of time has passed since we split from the last common ancestor we shared with both species.

Further reading:
Reading trees: a quick review
Chimpanzees and humans may have split much earlier than thought
Phylogenetic tree of primates
Large phylogenetic tree based on genetics

Friday, February 6, 2015

Research experience as an undergraduate student (or earlier)

Courtesy: National Science Foundation
Whether you're an undergraduate biology major or a high-school student figuring out whether or not you want to be a biology major, getting research experience is a wise idea. In fact, it's arguably even essential, depending on what stage of your education/career you're in.

More people are getting their undergraduate degree than ever before. Many students do well in terms of grades and have excellent recommendation letters from their professors. By gaining research experience, you set yourself apart from the majority in a competitive field. You show that you can use all of the knowledge from the books and apply it, and moving beyond the book smarts is important. I think it's in most (if not all) students best interest to gain research experience before graduating.

There are multiple ways to do this: choose coursework that includes independent research as part of the course, do an independent study with a professor in your department or a department you're interested in, do an undergraduate thesis if you're really willing to take on the work load, or gain your research experience over the summer.

Many universities have research experience for undergraduates (REU) programs that take place over the summer. These are programs specifically designed with undergrads in mind. They typically don't require any previous research experience, although some may require certain coursework or that you be in you junior or senior year of your degree. You'll work with a faculty member and you'll be paid to do research. Housing is also usually provided.

Courtesy: National Science Foundation
The experience you have in an REU will depend on the project itself and the faculty member running the project. You may find yourself working under the guidance of a graduate student on a daily basis or you may find that you do your assigned work and check in with the faculty member every few days or so. Most REUs accept only ten or so students and they can be quite competitive. Check out this PDF from the University of Wisconsin-Madison on what an REU is, applying for one, and why you should do one.

If an REU isn't for you, there are still plenty of other options. Doing an independent study for a semester or two allows you to work one-on-one with a professor and assist with his/her research. You can develop a deep understanding of a specific topic, learn about what the research process is like, and earn a grade and credits for your efforts. If you play your cards right and enjoy the experience, that professor you work with can also be a great reference, as he/she will really get to know you over the time.

There are many parts of the research process: the initial design, applying for funding, preliminary data collection, experiment design, redesign, data analysis, and writing up your results. Try and get experience in as many of these areas as possible or talk to your professors or supervisors about their experiences. This is a time in your life when you can gain experience and learn a lot from your supervisors and other project mentors. It may seem a bit intimidating, but everyone knows you're an undergraduate, a newbie. The point is to contribute and learn. 

Whether you choose to do an REU, an independent study, a larger undergraduate thesis, or purposefully enroll in courses with research as a component, there is nothing like gaining hands-on experience. You'll discover whether or not you like working in a lab or want to work in the field. You'll find out if you're great at designing your own projects or if you're better at following directions. A career as a research scientist is not for everyone just as fieldwork is not for everyone or lab work. The only way you will find any of this out is by exploring it yourself. Having these experiences will set you apart and make you more unique as an applicant for jobs or graduate programs. I don't think it's a stretch to say that you need to have some sort of research experience to be a competitive applicant for graduate programs, as more and more people are pursing post-graduate degrees. Potential graduate advisors want to know that you can do the research you're applying to work with them for. They don't want to send you out to the field and find out you can't stand the bugs and want to come home! Regardless of whether you want to apply to grad school, you should gain some research experience because you'll leave university with a better understanding of the work you are best at and the work you enjoy.

This is around the time when some REU applications are due. I've listed some REUs below, some of which are funded through the National Science Foundation (NSF).

NSF-funded project with the Enchinacea Project with opportunities for undergraduates, recent graduates, or even graduate students.
Experience for high-school student, undergraduates, and even teachers with Rocky Mountain Biological Laboratory.
REU with Models in Evolution, Ecology, and Systematics through Kent State.
Aquatic Chemical Ecology REU through Georgia Tech sponsored by NSF.
NSF-sponsored ten week program for undergraduates to do independent and collaborative research in the Chihuahuan Desert

For more REUs, check out the NSF website.