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.  

For 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. 

Unfortunately, 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

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.

The 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?

The 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

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

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!

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

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

Free Stuff!

The enemy of my enemy is my friend

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

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

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!

Wolfram|Alpha is up!

Wolfram|Alpha is an engine that answers computational questions and provides information of all kinds in a clear, concise manner.  It’s a long-term project and so they’re adding new information to it all the time.  

Here is a cool sneak peak of things that you can do with it:

It’s too bad that the camera person spent so much time focused on the bald guy instead of the engine’s output being displayed on the screen, but so it goes.  

Here are some neat things that the engine can do:

1) Calculate nutritional information.  If you give the engine a list of foods (for example, 2 oranges + 1 hot dog), it’ll add up the calories, fats, carbs, cholesterol, etc. and give you a read out with the total amounts of these various measures.

2) Tell you more than you might ever want to know about a particular math formula, including what it looks like when it’s plotted, other ways to write it, its derivative, its series expansion, its maximum and minimum points, etc.

3) Gene information.  It’ll tell you where a particular gene is located in the genome, the length of the sequence, the base pairs in the sequence, etc..  

4) Chemical information.  After being fed information on a chemical compound, it’ll provide you with the compound’s structure, molecular weight, density, melting point, etc. 

The list goes on and on.  If decide to check it out, I suggest starting here.   Pick an area that you’re interested in, test out the examples that they provide and then play around a bit.  It’s a lot of fun!

Unraveling the mystery of the origin of life

For about 40 years now, scientists have been working to recreate the primordial soup.  What I mean by this is we’ve been trying to determine and recreate the original conditions that led to life on this planet.  Powner et al. 2009 have managed to do just that.  

We believe that life originated as RNA, a chain of nucleotides consisting of a nitrogenous base, a ribose sugar and a phosphate.  These nucleotides come in two types, pyrimidines (cytosine and uracil in RNA or thymine in DNA) and purines (adenine and guanine).  Using compounds that were likely present in the early atmosphere and under similar conditions (for example, under high UV radiation), researchers have observed the creation of RNA’s pyrimidines.  This is a major step toward understanding the origin of life on earth. 

 

Pyrimidines

 

 

As an aside, fairly specific conditions that were present millions of years today and are not present today were required for this experiment to work.  For example, the level of UV radiation required to create the pyrimidines is probably much greater than the UV radiation on the planet today, suggesting that we may not be seeing spontaneous new life emerging anytime soon.  A popular creationist argument is that scientists claim life arose spontaneously and therefore we should be seeing spontaneous life emerging all over the place.  The “peanut butter argument” claims that the fact that life doesn’t spontaneously arise in the millions of jar of peanut butter that have been sold throughout the years disproves evolution.

First of all, as I said a moment ago, the conditions necessary for creating life simply aren’t present in a peanut butter jar. Second, we tend to consider the origin of life as a thing somewhat separate from evolution.  As soon as RNA molecules arose, there was certainly evolution occurring as the molecules competed for resources with varying success in the primordial soup. But how these molecules arose in the first place is a matter of chemistry, not evolution.  Anyway, for the sake of a good laugh, here is the argument:

 

Changes in gene expression due to diet!

In an earlier post on epigenetics I mentioned that foods high in methyl groups may be capable of altering epigenetic programming in adults, leading to alterations in stress responsiveness.  

A recent study on cabbage looper caterpillars found here shows that gene expression is indeed responsive to changes in diet.  In this insect, the consumption of plants containing bacteria alters the expression of genes related to immunity AND these changes in gene expression are passed onto their offspring.  Although they haven’t identified the exact epigenetic mechanisms responding to diet in this system, this study provides good evidence that diet is indeed impacting adult epigenomes.    

We now have evidence that the epigenome’s sensitivity to diet can have significant impacts on numerous traits, including behavioral and endocrinological stress responsiveness, immunity and metabolism.  As we learn more and more about these mechanisms I imagine that we’ll use this information to reformulate our thoughts on what makes a healthy diet.  Perhaps we’ll even have epigenetically trained dieticians who will prescribe individual diet plans for people dealing with anxiety issues, metabolic diseases, etc.  Lots of possibilities exist for how this information can be used and epigenetics research seems to be churning out new and exciting findings at an increased pace!

Will mate for water

A recent study published in Behavioral Ecology and Sociobiology by Claudia Ursprung and her colleagues has revealed that thirsty females are more promiscuous.

 

Beetle Lovin'

The literature on sexual selection theory abounds with theories related to why females mate multiply when the sperm from one male is usually sufficient to fertilize all of her eggs.  Not to mention that fact that sex in the animal world is often rough, resulting in costly injuries.  In some systems where males offer large nuptial gifts (often big blobs of nutrients in otherwise nutrient-poor environments), the answer is pretty straightforward.  In these cases, the costs the female incurs while having sex are offset by the resources she gains when she mates with him.  In Callosobruchus maculates, a seed beetle, the benefit that a female gets from mating is surprisingly subtle.

 

Seed beetles spend the first part of their lives living in dried beans before emerging as adults.  Their adult lives last about 8 days which they devote almost entirely to mating and laying eggs.  They often live in dry environments and are able to survive without any food or water for the duration of their adult lives, but will drink and eat if these resources are available.  

A group of researchers studying this system thought to themselves, “Hey, what if parched females are able to absorb water from male ejaculates?  Wouldn’t that be a great way to obtain water in a dry environment?”  If this were indeed the case, then we would expect to see thirsty females mate with lots of males while females who were supplemented with water should be less promiscuous (since sex in this system carries costs to females, including genital tract injury). 

Surprisingly, this is exactly what they found!  Females who were provided with water no longer had to mate to obtain this resource.  These females mated with fewer males, lived longer and were able to produce more eggs than their thirsty, promiscuous counterparts. 

 

"Are you awake up there?"

My favorite part of this article was the description of when they decided the seed beetles were indeed mating.  They described a successful copulation as one in which, “…the male had inserted his aedeagus into the female and was leaning back, motionless.”  Sounds like the seed beetle females are getting a raw deal.

 

I wonder if this information could be used to control pests.  For example, seed beetles often achieve pest status by laying their eggs in legumes.  Could making an extra effort to keep legume storage areas extremely dry control seed beetle populations?  Thirstier females mate with more males, but produce fewer successful eggs.  Perhaps long-term drying could reduce population numbers.  Understanding the subtle mechanisms underlying mating decisions may in some cases provide us with useful information for controlling the population densities. 

In conclusion, it seems as though female seed beetles mate with multiple males in order to obtain “ejaculatory hydration benefits”. Who would have thought?  What other subtle benefits that we have yet to imagine are luring animals into multiple promiscuity?

Reference:

Ursprung, C., den Hollander, M., and Gwynne, D.T. (2009).  Female seed beetles, Callosobruchus maculatus, remate for male-supplied water rather than ejaculate nutrition.  Behavioral Ecology and Sociobiology 63: 781-788.

Grad school admission tips: Picking the right advisor

I’m assuming you’ve done your research and now have a list of professors who study things that interest you.  You now face a massively important decision.  Your choice of an advisor can easily make or break your graduate school experience. A good advisor will challenge you, support you and generally make your life live-able while a bad advisor will make graduate school a truly miserable experience.  The situation is complicated by the fact that the “right” advisor for one person may not be the “right” advisor for someone else.

The most important tip I can give you is to talk to the graduate students already in the lab to which you’re applying. Don’t just chat with them, really grill them for information.  Try to get them to go out to lunch with you or to go out for a drink, just make sure that they’re in an environment where they feel like they can talk about their advisor without him/her overhearing.

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When you have the grad student’s attention, here are some questions that you should ask:

1) How involved does their advisor get in student projects? Some incoming students have never conducted research before and quite honestly require some hand-holding.  Other students are more independent and would prefer to have a professor that lets them do their own thing.  Be honest to yourself about what kind of student you’re likely to be and make sure you match yourself with a professor who can meet your needs.

Some advisors are so busy that they might as well be living on another planet!

2) How often is their advisor around? Some hot shot professors spend a lot of time traveling the globe to give seminars and aren’t around much if at all.  Others are physically on campus, but might as well be on Mars because they have so many things going on they simply aren’t available to you.  Others seem to have so much free time on their hands that they end up micromanaging your project.  Figure out how much time you think you’ll need from an advisor. Do you want an advisor who is always down the hallway with their door open, ready to answer your questions at a moments notice?  Or are you OK with an advisor who you need to schedule an appointment with a few days in advance?

Importantly, find out when potential advisors are planning on taking their next sabbatical.  If you’re looking into a 2-year Master’s program, it’ll be difficult for you to finish on time if your advisor is on another campus for half of your stay in their lab.

3) What is their advisor’s funding situation like? It’s great if you can find an advisor who just received NSF or NIH funding and can afford to fund you on their project.  In general, life is significantly easier when you’re in a lab that has some money floating around.  Especially in programs that don’t guarantee TA positions, being in a funded lab can relieve a lot of stress.   That being said, it would be a bad idea to turn a lab down based solely on a lack of recent funding if the lab has a history of getting funded or if you already have funding yourself.

4) Is their advisor a nice guy/gal? This may sound like a really ridiculous question, but it’s important.  My biggest mistake when applying to graduate schools the first time around was to not grill the graduate students about their advisor’s character.  I ended up changing Master’s programs part-way through because it was clear that I could get a lot more out of my grad school experience elsewhere.  Fortunately, I did things right the next time around and found a pair of professors who made excellent co-advisors.

5) How good is their advisor about getting them connected to the community? Does their advisor go with them to conferences and introduce them to the big names in the field?  Has their advisor helped students in the past get positions after they graduate?  What kind of positions?  Some professors will be better at getting their students government jobs while others will be good at getting their students placed in research labs.  Figure out where you want to end up after you get your degree and find a professor who helps their students reach that goal.

With the right advisor, grad school can be a blast!

6) Does their advisor generally seem to watch out for his/her students? It’s really great to find an advisor who is genuinely invested in their student’s academic lives and research.  Finding a professor who stays on top of your funding situation and helps you find TA positions or fellowships for which you’re eligible is a great catch.  It’s also great to find a professor who helps their students write grant applications, reads their fellowship applications, etc..  There is a lot of variability in how much time and energy a professor will put towards these types of activities, but life runs a lot more smoothly when your advisor wants to help you out.

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If you don’t feel like the graduate students are being honest with you when they’re answering your questions face-to-face, feel free to e-mail them with more questions later on.  This way they can answer at their own leisure and during a time when they’re not worrying about other people overhearing.  I find a good ice breaker is to say something like, “OK, everyone has their weaknesses.  If there were one thing about Dr. X that you would change, what would it be? The guy/gal can’t be perfect!”

I think the most important thing to keep in mind is that you need to be honest with yourself.  If you think you’re going to need a lot of advice and attention from your advisor, then don’t join the lab of an over-extended professor.  Knowing what you want and finding an advisor to match it will make your experience far more pleasant.