As part of our grad student concept mapping efforts, I’ve been filming student research to generate video clips to include in our concept maps. Two weeks ago we ventured into the intertidal for some filming in the field. In the coming weeks I’ll be sharing videos highlighting grad student research at NU’s Marine Science Center, but for now, you can watch Val demonstrate intertidal surveys:

And here’s Kate setting up an experimental cage in the field:

This week was packed with Outreach fun. On Wednesday, Thursday and Friday over 100 high school and middle schoolers from far away places like Holliston and Lexington came to take in the beauty of East Point, while also learning about some marine science, history and geology. Mariah (the outreach COOP) and I took them on tours, taught them about the challenges of living in the intertidal zone, and even showed them how to do some real science – in the form of surveys – out on the rocks!

One of my favorite parts of showing the students around is when we see all the animals in our touch tanks. Everyone is always wowed by the rare blue lobster and the giant slimy moon snail. However it is our newest resident a North Atlantic sea cucumber, that has been getting the most wows lately. Even the teacher of the school group today said she had never seen one before. These are pretty neat echinoderms (relatives of seastars and sea urchins). They don’t hav e hard spiny skin like their cousins though, so they have to resort to other strategies to defend themselves. In life or death situations, such as when they are being pursued by a predator, the cucumbers will actually expel their intestines, leaving them behind in hopes that the predator will settle for eating that instead. Obviously this is very tough on the cucumber, and they must invest considerable time and energy to growing back their intestines, so this defense mechanism is likely only used as a last-ditch effort when the only other option is to be eaten. Another neat thing about these animals is that unlike their predatory seastar relatives, sea cucumbers are filter feeders, who catch small particles in the water using a feeding tree which extends from their body, as you can see in the photo below. Sometimes the students are so excited that I am not sure if they digest all this info I tell them, but then I will get an interested question and remember that there is always someone listening.

North Atlantic sea cucumber with feeding tree extended!

My biggest accomplishment of the week was that I managed to make it through all three days of teaching despite the fact that I am losing my voice!

Our department is extremely diverse and the presentations reflected this diversity – biochemistry, microbiology, physiology, developmental biology, bioengineering, ecology, evolution, genetics – pretty much every biological discipline was represented. And this, in my opinion, is the main benefit of the graduate student symposium. With such disparate interests and half of us on main campus and the other half at the Marine Science Center it is almost impossible to interact with everyone on a regular basis and even know who everyone is within the department. The symposium gives us all a chance to interact and present our research in a low key setting with lots of good food!

A very big thanks to those faculty who came out to listen to our talks – especially Drs. Erin Cram and Jon Grabowski who organized the event and secured funding for food and prizes! Dr. Cram personally made over 70 sandwiches to satiate us til BBQ time!

Congrats to those who won best presentation and honorable mentions – chosen by your peers! (A very high honor!)

Picture by Chris Marks (http://www.chrismarksphotography.com/)

Looking forward to next year!

Basically, different groups of people (ie. stakeholders) want to do different things in the ocean. Things like fishing, enjoying nature, transporting goods or acquiring energy. The objective of ocean resource management is to sustainably balance all the stakeholders’ needs.  One way to approach that goal is to only allow certain activities in specified areas in order to reduce the impact on the environment and other stakeholders as much as possible. The process of deciding what to allow where is “marine spatial planning.”

The Sea Education Campus (SEA) in Woods Hole, MA, where the retreat was located. Photo: patricialapadula.com

A lot of the retreat was devoted to the issues surrounding offshore wind farms – which isn’t surprising, considering that Cape Wind is finally supposed to begin construction of a wind farm in Nantucket Sound after spending more than a decade on the approval process. However, the example of marine spatial planning I found the most compelling was a success story involving shipping lanes across Stellwagen Bank, told by David Wiley (the research coordinator for the Stellwagen Bank National Marine Sanctuary).

Stellwagen Bank is a national marine sanctuary located at the mouth of Massachusetts Bay between Cape Cod and Cape Ann. The bank is an underwater plateau, which allows deep nutrient-rich water to upwell to the surface and support a diverse ecosystem, including many species of whales. However, the bank also experiences heavy commercial shipping traffic due to its proximity to Boston. Consequently, increases in the number and speed of ships entering Boston Harbor has caused the number of whales killed by collisions with ships within the sanctuary to also increase.

Scientists from the sanctuary compiled years of data on whale sightings to assess where whales were most likely to be found in Stellwagen Bank. When they plotted the whale data on a map showing shipping traffic, it was revealed that some of the whales’ preferred feeding habitat was directly in the shipping lane!

A map of Stellwagen Bank National Marine Sanctuary. Dots represent right whale sightings, solid lines indicate previous shipping lanes, dotted lines indicate new shipping lanes. stellwagen.noaa.gov

After this discovery, scientists from the sanctuary worked with the shipping companies to reach a solution. Together, they determined that slightly shifting the shipping lane would still allow ships to efficiently reach Boston Harbor while reducing the number of whale strikes by 60%.

The sanctuary also now employs a monitoring system with buoys that detect whales in the shipping lane. Information from the buoys is communicated to ships though the “Whale Alert” iPhone app, which provides detailed information on whale location and makes recommendations for reduced ship speeds. It’s really refreshing to hear about different stakeholders working together and harnessing new technology for a common conservation goal!

Screenshot of the Whale Alert app. Yellow circles indicate that a whale was detected within the past 24 hours. Photo: news.cnet.com

At about the moment this photo was snapped I start to feel a strange tickle in my wetsuit. It’s probably just that my wetsuit got a little bunched up, I tell myself. Snorkeling by myself at night is way more exciting than daytime snorkeling and it can get my senses on edge. As my vision is tunneled to the cone of light thrown out by my torch, I never know what will pop out in front of me. The giant 5 or 6 or 7(!) foot long silvery tarpon fish glide up beside me to share my light in their search for a midnight snack. No matter how many times I’ve seen them before, they always startle me when they appear out of the darkness, sometimes even bumping me with a friendly nudge. Finding the octopus dens I’m tracking at night can be tricky too. We make notes about the precise location of the dens but sometimes it can take some searching to find the landmarks to point you in the right direction. So, long and chilly snorkeling trips can get longer and chillier.

But now I know something is actually moving in my wetsuit. After investigating to find the offending creature, I was relieved to discover this cute baby crab:

To save the crab, I dart back to the beach for its daring return to the ocean:

Swim free baby crab! Now I can sleep well (until my next snorkel, that is).

Bonaire at night

However, if you manage to look beyond the swashbuckling and dragon hatchlings perched atop naked women, you will see that Game of Thrones is chock full of science. And since this blog is an educational and professional forum for academic discussion, I will focus on the scholarly underbelly of GoT rather than the dragons. However, this is in no way a slight to Daenerys Targaryen, whose overall badassery I greatly admire.

So lets get right down to it. I’m going to talk about three fantastical elements from from the show (divided into three scientific fields for your convenience) and discuss their respective merits.

#1: The Ecology of The Wall

One curse of being a grad student is our tendency to be bothered by things that most normal human beings don’t notice. For example, it is often difficult for me to watch sci-fi movies because I’m constantly being bombarded with artistic choices that don’t jive with earth’s natural laws.

This is me every time a movie’s plot revolves around the zombie apocalypse or a viral outbreak.

But I digress. My point is, when I first beheld the Wall, the small part of my brain that wasn’t mooning over Jon Snow became skeptical that such a structure could exist. Turns out I was right. The dimensions of the Wall simply can’t stand up to gravity, leaving the 700 foot high 300 mile long fortification to warp under its own weight. Even though we can safely assume that temperatures are always below freezing at Castle Black, the immense pressure created by the millions of tons of ice would actually melt the lower parts of the Wall. According to glaciologist Bob Hawley of Dartmouth College, the Wall would take on the shape of a glacier flowing downhill, the base pushing outward as the top pushes down. In reality, the biggest problem with the Wall isn’t actually its height or length, but its slope. Martin Truffer, a physicist from the University of Alaska, Fairbanks, estimates that for the Wall to be 700 feet high it must also be 28,000 feet wide. So just take away the 90 degree angle and the Wall goes from fantasy to reality; all that’s missing is a set of gloomy criminals to patrol it. Unfortunately, that slope also makes “climbing” the Wall little more than a chilly jaunt, basically useless against invading wildlings and white walkers.

As a result…

The Wall: MYTH

Which brings us to…

#2: The Biology of Joffrey‘s Parentage

“We’ve had vicious kings, and we’ve had idiot kings… but I don’t know if we’ve ever been cursed with a vicious idiot for a king.” Joffrey Baratheon: taking teenage angst to a whole other level.

Unfortunately for everyone involved, the creator of the series, George R. R. Martin, has a nasty little habit of using incest to drive major plotlines. In fact, it seems that the only thing Martin enjoys more than literal blood is figurative bloodlines. From the Targaryen sibling spouses to Craster and his daughters, each case is more disturbing than the last.

However, today we are concerned with the Lannisters. To give you a brief overview: Cersei Lannister (the deviant lady pictured below) is married to a perfectly unrelated (albeit drunken and irresponsible) king. Despite this arrangement, all three of Cersei’s children (including Joffrey) were fathered by her twin brother (Jaime), who is employed by said king (Robert) due to his uncommon skill with a sword (pun unintended). To make a long story short, Robert dies completely unaware of this horrifying fact and several other folks meet ghastly ends trying to prove it.

Ew. Just… Ew.

But wait a minute, how did anyone figure this out in a world without paternity tests? Turns out that King Robert had some deviant behaviors of his own, namely leaving children in various brothels all over the capitol. Like their father, all of these kids have dark hair. Meanwhile, Cersei, Jamie, and their unnatural brood all sport the trademark Lannister hair color: blonde.

As a human being this whole situation disgusts me. As a geneticist, I see some red flags. Inbreeding is obviously bad for any species but hair color isn’t a great litmus test. Lets look at the facts. First of all, the genetics of human hair color have not been fully established, though many believe it to be under the control of multiple genes. So right off the bat we learn that the heredity of hair color is complex; it is not so black and white – or blonde and brunette – as Martin would have us believe. We do know that hair color comes from two pigments: pheomelanin (blonde and red hair) and eumelanin (black and brown hair). We also know that black/brown hair appears to be dominant over blonde/red hair. Ergo, blonde individuals, like Joffrey, must have inherited only blonde alleles from each of their parents. Cersei obviously passed on her blonde genes to Joffrey, as a blonde herself that is all she can give. She and brother Jamie could certainly have produced the evil blonde sociopath that is Joffrey. However, even though Robert is a brunette, there is no proof that he is homozygous in the eumelanin department! Robert could easily have a blonde allele that is masked by a dominant brunette allele. Indeed, Martin gives no description of his parents. One of them might have been as blonde as a Lannister for all we know! Robert having only dark-haired bastards is simply not enough proof to rule out his role in Joffrey’s conception. After all, we also have no idea what these various mothers look like and they contributed half the genes. So, while Jamie could easily be the father, Robert could be as well.

As a result…

Cersei’s baby daddy: Not enough evidence… MAYBE

Moving on to…

#3: The Chemistry of Wildfire

Ah wildfire. When Martin becomes bored with slashing folks to pieces he simply burns them alive. Wildfire ignites everything it touches, even water, turning your opponent’s fleet into a macabre St. Patrick’s Day barbeque. It’s actually the perfect weapon, if you don’t mind its tendency to explode for no reason.

Silly Stannis, Wildfire is for Targaryens.

But could the Battle of the Blackwater be based on real-life medieval warfare? Did Martin steal this “pyromancer’s piss” from our past? The answer is yes.

Behold, Greek fire, the stuff of nightmares. Just like Wildfire, the recipe for Greek fire was revealed on a need-to-know basis so modern pyros can merely speculate on its biochemical composition. However, most scholars agree that, at its core, Greek fire was based on petroleum and therefore, similar to napalm. This allowed the substance to ignite quickly and spread over large areas as well as burn on water. There was also probably some potassium nitrate and calcium oxide thrown in there for dramatic detonation purposes.

Now all that’s left is the question of the color.

It ain’t easy being green…

Lucky for Tyrion, this is an easy fix. There are plenty of metal compounds that burn green. For instance, trimethyl borate (don’t try this at home) produces a lovely emerald flame. Unfortunately, the liquid itself is colorless. Again, this is not a problem. Copper(II) chloride will greenify the stuff faster than Joffrey can skulk back to the Red Keep during battle.

Team Halfman. This is the last meme, I promise.

As a result…

Wildfire: Totally plausible

So there you have it. Martin’s universe is equal parts fantasy and science because when you play the game of thrones you either create an ad hoc hypothesis or your theory dies.

Here’s a photo of her after her public presentation as she’s preparing to meet with her committee alone for some tough questioning. You can see one of her committee members Skyping in for the event.

Wherever I am, one of the main follow up questions I get is:

why on Earth would someone want to build a robot lobster?

Front view of RoboLobster

Today I’ll tell you why we build biomimetic robots, robots engineered to mimic animals. There are three different but equally important reasons:

1. We can build better robots by learning how animals solve problems.

Animals have evolved for hundreds of millions of years and are very well suited to the environments they inhabit.* If we want to build a robot that can operate in a particular environment, like the ocean floor, why not copy a solution that nature has come up with, like the lobster? We want our robots to be able to overcome any challenges they face, and animals have already figured out how to do that. Rarely do we see animals stuck in the wild. If an animal were to get stuck, it would wiggle and squirm its way to freedom. Traditional autonomous robots can’t really do this as their behaviors have to be programmed ahead of time. In our robot animals we are trying to mimic the way the animal nervous system produces this wiggling and squirming. If our robots can produce new solutions to unforeseen circumstances like animals can, we’ll have some pretty capable robots on our hands.

2. We can learn about the animals by using the robot as a hypothesis-testing platform.

Nervous systems are complicated. The human brain has billions and billions of neurons. Even the relatively simple nervous system of the lobster has over 30,000 neurons. Understanding the connections (synapses) between all these neurons is a tremendous challenge and it still isn’t enough to explain the activity of a nervous system (this leads to a debate about the ongoing efforts to map the human brain which I’ll save for another day).  Substances called neuromodulators can change the activity patterns of neurons and change the synaptic connectivity between neurons. On top of all of that, much of what we know about the nervous system activity in lobsters and other animals has been learned from what are called isolated preparations. This means that neuroscientists remove the nervous system from the animal and then conduct recordings of electrical activity (the language of neurons) in a Petri dish. Networks of neurons often act very differently in a tabletop dish of saline compared to what they do in a freely behaving animal. What I’m trying to tell you is that our understanding of nervous systems, even in supposedly ‘simple’ organisms, is quite limited.

Here’s part of a lobster nervous system pinned out in a Petri dish. [Courtesy: Lin Zhu]

We adopt an approach that uses robots to learn about biology called biorobotics. Based on the biological research evidence available, we come up with a hypothesis for how the nervous system of the lobster controls a particular behavior (e.g. the motor response to visual movement).  The robot lobster gives us a platform to test out this hypothesis. We can run comparative testing between animal and robot in identical situations to see how their behaviors compare. If the response of the robot is different than that of the animal, we know that our hypothesis is deficient and we have an idea of where to focus further biological experiments. We can also validate some of the biological findings through this robot testing.

3. Robot animals are intriguing, charismatic and cute (depending on your tastes) and inspire students and the general public to engage in science.

Robot animals are captivating and quickly garner interest from people of all sorts: from students to neighbors to grandparents. Having such a visually interesting embodiment of my research gets others engaged in the science by asking questions (such as those posed in this post). One major goal of mine is to educate and inspire young scientists and robot animals are a great way to reach a younger audience. Our lab values educational outreach and sharing our work with others whenever possible and I hope that these efforts push more students to pursue careers in science and technology.

I hope this post has given a better understanding of why we build robot lobsters. Now you may be wondering why we chose to mimic lobsters out of all the animals out there. I’ll have to answer that question in my next post.

*Notice I didn’t say that animals are ‘optimized’ or ‘perfectly suited’ to their environments. It’s important to note that animals always continue to evolve over each generation. While natural selection usually pushes evolution towards improving an animal’s characteristics for a given environment, the randomness of the process sometimes leads to unexpected outcomes. Through evolution, animals can change so much that their preferred niche (their location and ecological role) changes. The most prominent evidence for why we can’t use the word ‘optimized’ to explain the result of evolution is that of vestigial organs. Why do ostriches have wings? Or why do we humans have appendixes? These are remnants of previous evolutionary changes that no longer provide much function in the present day and could be described as less than optimal.

I plan on a future career in education/outreach, so this will definitely not be the last time I teach. However, sending in those final grades today still made me realize that the end of grad school brings so many things in my life to a close. Therefore, it’s easy to get sentimental about little things that I never thought I would miss, such as setting up a practical exam, or grading what seem like endless lab reports. Additionally, TAing puts you in a nice spot in terms of your relationship with students, as I think students see TAs as less intimidating than professors, while still respecting us as authority figures.

After teaching this lab for three semesters, I am relatively confident in my ability to convey  the information and run the lab. However I was worried this semester, that I’d be so busy finishing up my research and writing my thesis that I might put less effort into my teaching duties. This fear began to manifest itself at the beginning of the semester when my students seemed disinterested compared to past years students. However as the semester went on I was pleasantly surprised how my students warmed up to the subject matter, and my teaching style, which was reflected by their improving quiz and exam averages.  I even got some positive feedback from students (which is rare to get, in person) several of them telling me how information I presented in the lab really helped them understand key concepts that related to both lab and lecture.

Finally, earlier this week, as I painstakingly graded those last exams and lab reports, I came across several drawings that reminded me why I will probably miss TAing and inspired this blog post. To give these some context, for one of the drawings in this lab report, students were instructed to draw a member of the Class Mammalia. I told them they could draw any mammal they wanted, and cringed as several students said “Sweet! I am just going to draw a stick figure!”, displaying their excitement about the lack of effort required for this drawing. Despite this, I got some very creative,and thoughtful drawings. I have posted my favorite two here.

A terrific drawing of what I assume is my student, me and the fetal pig we dissected in lab.

Even the fetal pig thinks I am a good TA! Thats all the gratification I need….

While these drawing might have simply been unsuccessful attempts to get extra credit, I’d rather think that these students really enjoyed my lab, and that the things I taught them made them appreciate science a bit more. Either way I really appreciate how these students have inspired me to reflect on what a rewarding  experience TAing has been overall.

We (Chris Newton, my fellow TA, and I) were a bit worried about the selection of exhibits that would be available since the NEAq is undergoing some major renovations. But luckily for us many were open – including the rocky intertidal touch area which had just opened that day! Of course as an intertidal ecologist I was drawn to this exhibit. It was there I got to meditate on barnacles feeding – taking advantage of and gaining a bit of energy from some pretty turbulent waters…