Wednesday, August 28, 2013

Some City Birds Are Changing Their Tune

European starlings are one of the many bird species changing their songs
 in urban environments. Image by 4028mdk09 at Wikimedia Commons.
The human world population has climbed to over 7.1 billion people and for the first time ever, more than half of us live in an urban area. Urban areas are spreading and more animals are either getting pushed out or are becoming urbanized in the process. Birds are among the many species we are used to seeing and hearing in our cities, but how exactly are they and their songs being affected by urban spread?

This week at Accumulating Glitches I tell the story of how urbanization is changing our avian soundscape. Check it out here.

And to learn more, check this out:

Slabbekoorn, H. (2013). Songs of the city: noise-dependent spectral plasticity in the acoustic phenotype of urban birds Animal Behaviour (85), 1089-1099 DOI: 10.1016/j.anbehav.2013.01.021

Wednesday, August 21, 2013

How To Get Into An Animal Behavior Graduate Program: Getting Good Grades

There's a strategy to doing well
in college courses. Image by
I showed up to my first year of college wide-eyed and ready to take life by the horns. It was the first time I had lived away from my parents’ rules and I was surrounded by an exciting new world of dorms, Outdoor Clubs, new friends and parties… Oh, the parties. Needless to say, I was distracted. And by the end of my freshman year, my grades showed it. If I was going to get into a graduate program after I graduated (which was already my goal), I was going to have to turn things around.

Getting good grades in a rigorous college course requires more finely-tuned study skills than getting good grades in a high school class. Simply showing up to classes and skimming through your notes the night before the exam may have gotten an “A” in high school, but it’s barely enough for a “C” in college. Unfortunately, many of us get into college (and sometimes a few years in) without having learned these critically important study skills that in the end will make you less stressed, more prepared, and more impressive. Here is some advice on how you can get the most out of your college classes and get good grades while doing it (That is, after all, why you’re paying all that college tuition, right?).

There are two essentials to getting good grades in college courses, and no, being a talented genius is not one of them. They are simply to be organized and put in the time.

If you haven’t gotten one yet, go and get yourself an academic planner (at any bookstore or office supply store). There are many different types, but my preference is for a monthly/weekly planner, which has monthly calendars followed by sections for daily notes. Once you get your planner, fill each week out with your scheduled obligations: class times, work schedule, club meetings, etc. Don’t forget to include workouts, meals and sleep (which can be as important to your grades as studying).

An organized planner is your secret weapon to achieving your goals.
Photo by electrictuesday at flickr.
Once your “fixed” schedule is written in the planner, you should be able to see blocks of time that are still available (if you don’t, you should consider cutting back on work hours, cutting back on the number of clubs you’re participating in, or dropping a class). These are the blocks of time where the real course work happens. For each course, calculate roughly how much weekly study time you should be putting in. Each college and course is a little different, but a general rule is that you should expect to put in 3 hours of time per week for each college credit. That means that for a 4 credit class, you should put in 12 hours per week. It may seem like a lot, but full-time students generally take 12-14 credits in a semester, which would translate to 36-42 hours per week, which is roughly equivalent to a full-time work week for any job. Subtract the time you spend in classes and labs (yes, that counts) from the total time you should spend on a class per week to get the amount of time you should schedule to study for that class. Now, find blocks of time to schedule your studying time for each course. You can make those blocks as long or short as you like, depending on your studying stamina. Just make sure that the total for each course adds up and doesn’t include time spent on Facebook or watching ridiculous YouTube videos.

Now the question is, what should you do with your studying time? Most professors give required or recommended readings to accompany their lectures. It is a good idea to read these before the lecture they are paired with. This will allow your brain to process the topic and the concepts and will often generate questions. Don’t expect to memorize or even understand every word, but do jot down the parts that you find confusing or have questions about.

In class, take notes. Even if the professor gives you handouts or printouts of slides, it is important for you to write down terms, diagrams and concepts. This is because the physical act of writing these down will help you remember them (Remember in elementary school when the teacher would make you write down vocabulary words over and over?) Also, now is the time to ask about the parts that you found confusing in the reading.

After you have been exposed to the material is when the learning really takes place. This is the integration phase. Using your notes from class, your readings and any materials your professor may have given you, reorganize and rewrite your notes in a format that makes sense to you. You may want to do this as an outline, a set of flash cards, or in diagrams. The most important thing is that it makes sense to you and includes everything the professor says you need to know. As you run into concepts you discover you don’t fully understand, look them up in your assigned readings, in other books or on the internet (But go to credible sites only – There’s a lot of misinformation on the internet). If you still need clarification, ask your professor.

A good way to test your understanding is with a study group. Going through the concepts with friends can help you find out if there are still details you don’t understand. And if there are details a friend doesn’t understand, nothing will help you understand the material better than teaching it to someone else.

By the time the exam comes around, you will have read the material, been lectured to about the material, studied the material and taught the material. You should know it pretty well. Now you just need to look over your notes one last time and maybe test yourself on some memorization or practice questions, but you don’t need to have a major pre-exam cramming session. Just eat well, work out and get 8 hours of sleep.

If this is all new to you and you have some semesters of grades you are not so proud of behind you, don’t think the graduate school doors have closed on you. There are two stages in the application process when grades are important. Your application is first examined to see if you meet the program’s basic requirements. At this point, you must have met their minimum GPA (and perhaps minimum GPA for science and math classes by themselves). If your current GPA does not meet this minimum (which is generally announced on their web page) you need to take more courses to get that GPA up before it will even be worth your time and money to apply.

If your application passes the first round of cuts, it will typically be given to the professors/researchers you would like to work with. They will usually assess what courses you have taken and how well you did in them. They are often looking either for consistently high grades or a strong pattern of improvement. This means that if you have some less-than-desirable grades in your past, they could be tolerated if your grades dramatically improve and remain high. If you apply these study skills to your courses from here on out, you could make yourself a major contender for one of those prized slots for incoming graduate students. Whether you’ve been distracted by the social aspects of college like I was or you’ve just realized that you want to pursue a graduate degree in a subject that has caught your imagination, these study tips will help you get there.

Good luck!

Did I miss your favorite study tip? Write it in the comment section below! And for more advice on applying to graduate programs, go here.

Wednesday, August 14, 2013

Epigenetics: The Fusion of Nature and Nurture (A Guest Post)

By Tricia Horvath

For decades scientists have been debating what makes a person who they are. Is someone’s personality, appearance, and medical history determined by their nature (their hardwired genes with the environment playing no role) or nurturing (how they were raised, and what they encountered in their environment growing up)? Many scientists were convinced that only one of these things, nature or nurture, could be responsible for determining a person’s fate. For instance, those who believed in nurture as the prevailing force thought that a person’s specific genes had nothing to do with how they behaved. Although ample evidence has been built up on both sides, scientists now know that the answer is actually both!

If you need convincing, just think about identical twins. Identical twins are genetic clones (all of their genes are exactly the same). These twins are very similar to each other in many ways such as physical appearance and personalities, even if they are separated at birth and raised apart from one another. However, anyone who has spent significant time with identical twins knows that each twin is their own person, and as they get older and spend less time together the personalities of the twins will continue to diverge. If nature (just genes) was in charge, identical twins would be the same in every respect. If nurture (just environment) was in charge, identical twins would be no more similar than any pair of siblings.

Genes are like pages in an
instruction manual for ourselves.
If genes are the pages in our
instruction manual, then DNA
is the actual book. Image by
tungphoto at
So how is any of this possible? The answer lies in a field called epigenetics. Epigenetics studies how the environment interacts with genes to change their expression. Genes are like pages in an instruction manual for ourselves. In order for certain traits to be expressed, these genes/pages need to be read. If a gene cannot be read, then the trait it represents will not be expressed.

The environment plays a large role in determining which genes can be read, and therefore what traits are expressed. However, if a person does not have the genes for a specific trait (their book does not have those pages) that trait could never be expressed. For example, no matter how much time you spend in the water growing up, you will never grow a mermaid tail because you don’t have the genes for a mermaid tail. In this example, spending a lot of time in the water growing up would be part of your nurturing, and the lack of genes for a mermaid tail would be part of your nature. Even though having a mermaid tail would be beneficial in the water, the environment cannot interact with your genes to give you a mermaid tail because you simply don’t have the genes. Therefore epigenetics only works if you have the right genes.

How does epigenetics work?

DNA is the long strings of genetic material that are found in every cell (and every cell has exactly the same DNA). Genes are strung together on the DNA strings: If genes are the pages in our instruction manual, then DNA is the actual book. Each gene has a section with “read” or “don’t read” signs. The gene will be read, or not read depending on which of these signs is showing. The environment can determine which genes are read (and therefore which traits are expressed) by covering up these signs.
You’re less likely to stop if you don’t see the sign.
Photo by Nicholas A. Tonelli at Flickr.

The first player in covering up one of these signs is a methyl mark. Methyl marks are little chemical tags that get attached to certain parts of DNA. Methyl marks have two jobs. First, they partially cover up one of the signs (“read” or “don’t read”). Second, they help attract proteins that can help completely cover up the sign.

Before we talk about these other factors, it is important to understand a few structural aspects of DNA. DNA exists in cells loosely wrapped around proteins called histones. This looks like beads (histones) on a string (DNA). DNA wraps around histones easily because DNA is negatively charged and histones are positively charged, and oppositely charged things attract one another. (Think about magnets that stick together when the opposite poles are facing each other, but repel each other when the same poles are facing each other.) In order to keep the DNA from wrapping too tightly around the histones, acetyl groups are added to the histones. Acetyl groups cover up the positive charges on the histones. This makes the histones less positively charged so they don’t attract the DNA as strongly. (This would be like making one of the magnets less strong. It is easier to pull apart two magnets that aren’t strongly attracted to each other.)

This diagram of epigenetic mechanisms is by NIH at Wikimedia Commons.

When methyl marks are present on DNA they attract proteins that remove the acetyl groups. This causes the DNA to wrap around the now more positively-charged histones very tightly. (The magnet is stronger now). When a whole section of a gene becomes wound up this tightly it leads to a complete covering up of the “read” or “don’t read” sign. Sometimes this can also happen on part of the gene that would normally be read (the actual page of the instruction manual). If enough of the gene is covered up by the DNA wrapping too tightly around the histones, then the gene cannot be read (imagine if there was a large object covering the page you wanted to read in the instruction manual).

Once a “read” or “don’t read” sign is covered up, it is not necessarily covered up for the rest of your life. Instead, the environment can remove methyl marks from DNA and add acetyl groups back onto the histones (covering up the positive charge on the histones, making them attract the DNA less strongly). This would uncover the sign and allow it to be read once more.

All of this means that traits (including behavior) may be influenced by both genes and the environment. Although the genes we are born with only make it possible for us to express certain traits, our environment helps determine which of those traits are actually expressed. If our environment changes, the traits we express can change! Because we can change our environments, we have the power to change ourselves!

Wednesday, August 7, 2013

What Comes First: The Signal or the Response?

Jewel wasps show us how new communication systems may have come to be.
Photo by M.E. Clark at Wikimedia Commons.
Finding and attracting a mate is tricky business for most species. It can be quite helpful then to have a species-specific signal that is sent and received by members of your own species, but not perceived as well by predators. Chemical signals (those we perceive through smell and taste) are among the most diverse and specific signals produced in the animal kingdom, so they make good candidates for these species-specific mating signals. Sex pheromones are chemical compounds released by an animal that attract animals of the same species but opposite sex. They are often so specific that other species can’t smell them at all, which makes them useful as a secret communication line for just that species. But this specificity raises an intriguing question: What develops first: the ability to make the pheromone or the ability to perceive it?

This week I tell the story of how jewel wasps shed light on this chicken-or-the-egg problem at Accumulating Glitches. Check it out here.

And to learn more, check these out:

1. Lassance, J., & Löfstedt, C. (2013). Chemical communication: A jewel sheds light on signal evolution Current Biology, 29 (3) DOI: 10.1016/j.cub.2013.03.055

2. Niehuis, O., Buellesbach, J., Gibson, J.D., Pothmann, D., Hanner, C., Mutti, N.S., Judson, A.K., Gadau, J., Ruther, J., & Schmitt, T. (2013). Behavioural and genetic analyses of Nasonia shed light on the evolution of sex pheromones Nature, 494, 345-348 DOI: 10.1038/nature11838