Grad School Admission Tips: Picking the right program

Grad school programs can vary quite a bit.  Each program has their own set of course requirements, guidelines for how qualifying exams are run, funding considerations, etc.  Here are some things to think about:

NACA_Physicist_Studying_Alpha_RaysCoursework

There is a lot of variation between programs in how many courses students are required to take and what kinds of courses fulfill these requirements. It may not seem like a big deal to have to sit through a bunch of courses, but significant amounts of coursework can mean that you don’t get to your research project off the ground until your third year of graduate school. That’s a long time to wait if you’re ready to get started when you first arrive. On the other hand, some students benefit greatly from what they learn in class.

If you’re more of a self-learner or feel that you are already sufficiently familiar with the subject material, consider looking for a program with less coursework.

Program Size

Small program:

Pro’s:

1) In a small program you’re far less likely to get lost in the crowd.  It’ll be easier for the program directors to keep track of your progress and funding situation if you’re one of only a handful of students.

2) You get to know the other students in your program really well. Strong bonds formed during graduate school can be important for years to come as the students going through school with you will also be your future colleagues.  These bonds will make graduate school a more pleasant experience and will provide an important support system.

3) You have greater access to professors and their advice by being in a smaller group. If you think you’ll want a lot of input while designing and executing your dissertation project, this may end up being very important to you.

Cons:

1) You get to know other students in your program really well.  If it turns out that you don’t get along well with a handful of people in your program, this could be a big problem.  I’ve heard about cohorts of incoming students containing a few people who bumped heads and this made life pretty miserable for the group as a whole.

2) Small programs often don’t have a lot of money laying around.  This means that they might not be able to help you should you somehow lose your funding and it might mean that they can provide fewer fellowships.

Large program:

Pro’s:

1) Large programs tend to have lots of resources.  They’ll generally have more money for funding students, more money for funding projects, more equipment for running projects and more professors.  The program in which I’m enrolled (the Graduate Group in Ecology at the University of California Davis)  is large enough that we were able to cobble together funds to cover students when the California budget crisis resulted in a loss of funding for several student projects.  I don’t believe that a smaller program would have been able to accomplish this feat.

2) Large programs have lots of people in them. Socially, this means that there is a greater diversity of people with whom you might choose to be friends.  Academically, this means that there are lots of professors and staff available to you.  Having access to a great diversity of professors means it’s more likely that someone will have an answer to whatever question you end up having while working on your project.

Con’s:

1) You can easily get lost in the crowd. You’ll get less attention and because people will be checking in less often, you’ll have to learn how to speak up and be proactive about getting help when you need it.  If you worry about your ability to be pushy to get attention, then maybe you shouldn’t be in a large program.

2) You’ll be competing with all of the other students in the program for time with professors.  Again, you’ll need to be pushy and will need to learn to start asking for help long before a deadline because professors often can’t meet with you right after you contact them.

SalmoQualifying Exams and Exit Exams

Programs can have every different requirements for qualifying and exit examinations, but I personally don’t think that you should pick a program based on these differences.  Unless, of course, a program is particularly well-known for having really unreasonable exams in which most of the students fail even after months of hard studying and preparation.  In general, most programs having fairly reasonable requirements on this front and you’ll just have to jump through the hoops when the time comes.

Other considerations will be important as well, including whether or not you can envision yourself spending 6 years living in whichever city the program is found.

To get information on a particular program, scour the program’s website and then talk to the graduate students in the program about their experience so far.  As I mentioned in the post on picking an advisor, graduate students will be a very important resource and you should pump them for information every chance you get.

Advertisements

Choosy mates

Zach and I have finally completed our move and I will hopefully be able to update at least semi-regularly again. 

Mating_PenguinsI’ve been noticing a lot of articles in the news lately which report on the “surprising” result that human men and women are about equally choosy when picking a mate (in this article, for example).  The articles claim that the result is surprising because of a long-standing belief that women are choosier because they invest more energy into reproduction (larger gametes, gestation, etc.) then men.

Because reproductive investment is low in men, they could potentially produce hundreds of offspring at little cost to themselves. This high potential for reproductive success means that men should mate with lots of females to maximize their fitness. On the other hand, females are only capable of producing a fixed number of offspring during their lifetime and mating is often costly, so females should only mate with a few, carefully choosen males. The main point here is that males have a greater reproductive potential than females. 

DragonfliesThat’s all well and good, but it completely ignores the fact that, in monogamous systems, a male will only end up with as many offsprings as his female partner is capable of producing. Males should therefore be choosy because they want to find a female that will produce as many healthy offspring as possible and females should still be choosy for the same reasons as before.  

Of course, few if any species are completely monogamous.  Genetic studies have revealed that many of the bird species we’ve written songs and poems about because we consider them to be shining examples of monogamy are actually fooling around behind each other’s backs fairly often. So we shouldn’t be surprised when we find that females are willing to sneak around with males of a higher quality than their social partner and males should be willing to sneak around when they get the chance too.  But the point still remains that both sexes in mainly monogamous systems they should be as choosy as possible about the social partner with which they’ll be producing the bulk of their offspring.  

Most human cultures are monogamous (to some degree) and so it doesn’t seem to me that we ought to be too surprised to find that males and females are equally choosy about their partners. The studies examining human mating behavior are certainly interesting, but (despite their claims) they aren’t producing results that are particularly surprising. 

This will certaintly make me unpopular…

One of my biggest pet peeves is when I try to explain something mathematical to a peer and they interupt, explaining that they “don’t understand it because I’m not good at math like you are.”

Good at math? This implies some innate differences in our analytical skills.  If I’m “good” at math it’s only because I’ve spent tons of time hunched over my calculus book struggling to understand the concepts.  

FractalFor a handful of geniuses out there, math comes naturally.  The other 98% of us who are “good at math” are simply patient enough to stare at a problem for hours, hitting it with all of our favorite math tricks until it’s beaten into submission.  Days of hard work and gallons of coffee does a mathematician make.

A false dichotomy has been created between those who are “good at math” and those who aren’t.  People hide behind the excuse that math is hard for them before they’ve even put in the appropriate hours of sweat and toil. Spending an hour looking at a problem without seeing the solution does not mean that you’re bad at math, it only means that the problem is going to require more than an hour of your time. 

EscherUnfortunately, I think the structure of our educational system exacerbates the problem. Plenty of people who are really good at solving math problems need more than a few hours to do it.  Giving people a night or two to solve a homework set or a few hours to complete an exam is a poor way of testing a person’s ability to comprehend complex math concepts and fosters the belief that your’e not good at math unless you can solve math problems quickly.  

Just about anyone can be good at math given enough hours of hard work.  True, some people solve a problem more quickly than others, but it certainly isn’t the case that quick problem solvers are good at math while everyone else is not.  

To anyone who would argue that they’re “not good at math”, I would argue that you haven’t put in enough time. 

“A mathematician is a tool for turning coffee into theorems.” – Alfred Renyi

To kill a killifish

For my dissertation I’m planning on studying California killifish and Euhaplorchis californiensis, my favorite host/parasite system.  The Kuris Lab has done some really excellent work on this system,  providing a great foundation for future studies. 

Euhaplorchis californiensis is a trematode parasite with a complex life cycle.  Its life starts in the digestive tract of waterbirds, where it remains for only a short time before being defecated. Shitty way to start off, huh?   

Cerithidea californica

Cerithidea californica

The horn snails, the parasite’s next host, aren’t especially perceptive and consume E. californiensis while grazing along the bed of the estuary. Once infected, the parasites castrate their snail host and turn the snail into a parasite-making factory.  After a few parasite generations, a significant portion of the snail’s mass will be E. californiensis offspring. When the parasite has completed development, it burrows out of the snail and swims into the water column.

C.californica_parasitizedThe picture on the left is of a deshelled, parasitized horn snail.  If you click on the picture to enlarge it, you’ll notice that much of its back half is white and it almost looks like it’s filled with small grains of white rice.  It’s actually filled with a bunch of trematode parasites (though in this case it isn’t E. californiensis).  

The parasite’s next target is the California killifish (Fundulus parvipinnis).  When a killifish is unfortunate enough to run into the parasite, the parasite will burrow inside and make its way up to the fish’s brain.  Research on closely related species suggests that the parasites find a nerve and follow it up to the brain.  

This is where it gets cool. 

Jenny Shaw and her collaborators looked at how neurotransmitters in killifish brains change as parasites accumulate (the paper can be found here).  They found significant changes in the concentrations of two neurotransmitters, dopamine and serotonin, and found that these changes were more pronounced as parasite density increased.  

One striking finding was that the parasites were suppressing a common stress response.  When vertebrates are stressed, a part of the brain known as the raphe nuclei increases its rate of serotonin metabolism, which essentially means serotonin levels decrease in this part of the brain.  In infected killifish, serotonin levels decreased much less, indicating that the parasites are affecting their host’s responses to stressful situations. As encounters with a predator are clearly stressful, this may be an important mechanism used by the parasites to get the killifish eaten by its next host.  

This poses an interesting possibility – are the parasites altering killifish behavior to make them more likely to be eaten by a particular animal?

Male killifishThe answer is yes, infected killifish do exhibit strange behaviors that make them significantly more likely to be comsumed by waterbirds, the definite host (that is, the host in which the parasite reaches maturity) of E. californiensis.  Lafferty and Morris 1996 observed that infected killifish frequently engaged in behaviors that made them quite conspicuous, including quick trips up to the water surface (which could make the killifish into a quick meal for an awaiting waterbird).  They then set up outdoor enclosures containing killifish that they knew to be infected and those that were uninfected.  Waterbirds were capable of accessing the fish in the enclosure and twenty days after the enclosures were set up the researchers returned to see who was left. 

The results were staggering.  Infected killifish were 30 times more likely to have been consumed by waterbirds than the uninfected fish!  This is immensely strong evidence that the parasites are adaptively manipulating their hosts.  

Much remains to be learned about this system, but parasites like E. californiensis which are capable of behavioral manipulation may tell us important things about how our brain works and perhaps even provide insight into treatments for certain behavioral disorders.  Many behavioral disorders including depression and bipolar disorder are thought to be associated with inappropriate concentrations of neurotransmitters such as dopamine and serotonin in the brain. Understanding how parasites manipulate the concentrations of these chemicals may teach us how we can alter them as well.   

At the moment, we don’t know how parasites are changing neurotransmitter concentrations in the brain.  They could either be secreting the chemicals themselves or they could be manipulating the brain into doing it for them. If they’re manipulating the brain, then the method that they use to do this could provide us with new treatment ideas.

Here comes the fun, wild speculation part. If the technology for nanobots ever gets off the ground then we could use parasites as a model for how to make small-scale changes to neurotransmitters as a way to control behavioral disorders. Alternatively, I wonder if we could create genetically modified parasites capable of altering the concentration of a particular neurotransmitter in specific parts of the brain.  Parasites already know how to get to the brain on their own and we know that controling the number of parasites controls the intensity of the changes in neurotransmitters.  So why not give it a shot (in animal models first, of course)?

California killifish

California killifish

Parasites: a weighty topic

Hey there, blogosphere!  I’m finally back in town and have caught up on the work that I missed while visiting the Kuris Lab at the University of California-Santa Barbara. This group of parasitologists addresses numerous interesting parasite-related questions, including those related to the importance of parasites in food web dynamics and the potential applications of trematodes as bioindicators.  

 

Carpinteria Salt Marsh in Santa Barbara

Carpinteria Salt Marsh in Santa Barbara

Recently, this group intensely studied 3 estuaries and calculated the biomass of the species found at each site.  The prevailing opinion at the time of this study was that parasites are probably not found in high enough abundances to play an important role in ecosystem energetics.  You can imagine how surprised everyone was then when the Kuris Lab showed that parasite biomass was often greater than the biomass of much larger groups of animals.  For example, if you stuck all of the trematode parasites found in an estuary on one scale and all of the estuarine birds on another, you’d find that the parasites weight 3 to 9 times (depending on the estuary) MORE than the birds!  These findings were published in Nature.

 

I think that studies like this are of immense importance because they change the way that we think about parasites.  Parasites capture our imagination by doing things to their hosts that are more gruesome and amazing than just about anything science fictions writers have come up with thus far.  Because of this, I think we tend to think of them as interesting anomalies and forget that parasites make up more than half of the species found on the planet.  Future work will surely continue to enforce that parasites are important in numerous ecological processes and in human culture.  

Next post: The Kuris Lab’s work on brain altering parasites in killifish!

 

Hangin’ with the Reddit guys

My new Reddit bobblehead!

My new Reddit bobblehead!

For a long time now, I’ve been a huge fan of Reddit – the best darned news aggregator out there. My Reddits include cognitive science, science, psyschology, technology, world news, math, and comics.  

Anyway, a while back, Alexis from Reddit contacted my fiance, Zach, to tell him that he enjoys Zach’s comic.  This was super exciting news, and when Zach and the Reddit guys scheduled a lunch date for today, I invited myself along.     

In my mind I had imagined the guys running Reddit to serious, suit-wearing business types. To my surprise, they’re actually laid-back 20-somethings (maybe early 30’s??) who volunteer their spare time to teach the local goldfish how to play soccer.  

For lunch we went to a cute Caribbean restaurant near their office in San Francisco.  The guys were really easy to talk to and even seemed interested in my tales of grad school hardships and rattlesnake-tracking ordeals up in Michigan.    As I love any opportunity to tell a story, and they were kind enough to listen, this immediately put them at the top of my list.  

Back at their office, we learned the following fascinating bits of information about the Reddit guys:

Workin' hard at Reddit.  Notice the penis-arranged desktop icons

Workin' hard at Reddit. Notice the penis-arranged desktop icons

1) They arrange their desktop icons by penis. That’s right, the icons on their desktop form a giant wang.  This is apparently awesome 99.9% of the time, but 0.01% of the time (when 7th graders visit the office to see what running a website is all about) it becomes a bit awkward. 

2) They can feed Mrs. Splashy Pants (their pet goldfish) without being anywhere near his/her tank.  The guys have rigged it up so that remotely opening a CD drive on the computer nearest the fishtank starts up a Rube Goldberg machine, which results in the delivery of fish pellets to the tank. 

3)  They have the power at their fingertips to deliver “Internet Justice.”  They offered to deliver to me the head of my enemy, but I politely declined… for now.  

All in all, it was a great few hours.  Most importantly, they sent us home with free stuff (a graduate student’s favorite thing)!  We received Reddit bobbleheads, t-shirts, and I got a giant squishy sheep.  It was laying around the office and I’m guessing they’ve grown tired of jokes about dirty things to do it, so they were ready to release it to a new home.  I’ll take good care of it guys, I promise.  

The Men of Reddit and Zach Weiner

The Men of Reddit and Zach Weiner

Free Stuff!

Free Stuff!

The enemy of my enemy is my friend

Acanthocephalan

An acanthocephalan parasite

Acanthocephalan parasites are infamous for their ability to dramatically alter the behavior of their hosts.  These parasites often have multi-stage life cycles, meaning that they die unless the host that they’re currently residing in gets eaten by the next host in the cycle. Acanthocephalans are remarkably efficient at manipulating their intermediate hosts into ending up on the dinner plate of the next host in the cycle. 

One well-known example of this manipulation involves the acanthocephalan parasite Polymorphus minutus and its crustacean intermediate host Gammarus roeseli.  The definitive host of P. minutus is a waterbird which scoops G. roeseli out of the water.  The usually defense by G. roeseli to avoid being consumed by the waterbird is to hunker down at the bottom of a streambed and hide in the rubble. The parasite is capable of counteracting this defensive mechanism, presumably by altering the concentration of serotonin in the crustacean’s nervous system. This manipulation causes the the host to swim to the water surface and clamp down on the surrounding vegetation.  In a closely related system (a different species of Gammarus and a different Polymorphus parasite), this behavior has been found to significantly increase consumption of infected gammarids by waterbirds.  In essence, the parasite causes its tiny host to swim up to where the predators are feasting and hang out until it becomes dinner. 

 

Gammarus roeseli

Gammarus roeseli

The interests of G. roeseli and the parasite P. minutus are clearly not aligned when it comes to waterbird predation. There is, however, one thing that they can agree on.  Neither of them want to end up in the stomach of other predators (fishes, crustaceans, etc.). Non-waterbird predators represent a dead end for both members of the party.  The old addage “the enemy of my enemy is my friend” goes a long way here, and recent studies suggest that the parasite enhances the host’s ability to stay out of harm’s way when their interests converge. 

Three-spined sticklebacks
Three-spined sticklebacks

Medoc et al. 2009 have shown that gammarids infected with P. minutus have a leg up on their uninfected counterparts when it comes to avoiding predation by three-spined sticklebacks.   Infected gammarids spent more time hiding in vegetation near the water surface and suffered much lower predation rates.  Additionally, another recent study found that infected gammarids are up to 35% faster when escaping a predatory crustacean.  

This phenomenon has received little attention in the literature.  The few studies that have looked at whether or not parasites “help” their hosts escape from mutually unfavorable predators have reported mixed results.  Some studies have found that infection increased the host’s susceptibility to all predators, whether or not they’re included in the parasite’s life cycle.  

The two studies decribed above showed that the gammarids could escape from predators if escape involved moving fast or hiding near the water surface. But, although the parasites have evolved an excellent host manipulation, it’s probably not perfect.

For example, in the above system where parasites make gammarids cling to water surface vegetation in order to be eaten by birds, it is likely that by doing so the gammarids become vulnerable to other predators. At that water level, there should be a number of other predators that can take advantage of the defenseless gammarids. How fine-tuned the parasite’s control of the gammarid can be is an interesting question deserving future study.

On another note, I’m heading to Santa Barbara tomorrow to meet Armand Kuris and Kevin Lafferty, two immensely awesome parasitologists who I hope to collaborate with for my dissertation work.  When I return on Thursday, I’ll surely have fun stories about the stuff I learned.  Wish me luck!