A Conversation with George Locke

We all know how beneficial it can be to hear about the journey famous scientists have traveled. Seeing the more human (and less glamorous) side reminds us of how much dedication and diligence comes into success. But hearing from folks just starting out can also be extremely helpful.

Here, Visionlearning sits down for a conversation with George Locke, a PhD candidate in Biological Physics at Rutgers University, for a brief chat about his experiences, and the advice he would offer young folks interested in the sciences. Locke’s current research is on the DNA sequence-specificity of nucleosome formation and transcription factor binding. His first publication is currently under review with Proceedings of the National Academy of Sciences (PNAS).

Visionlearning: George, could you tell us a little about yourself?

Locke: Sure. I was born in Medford, Massachusetts in June of 1982 to two loving parents.  Both had PhDs in Ethnomusicology from Wesleyan, but my mother chose to work in insurance to support the family while my father pursued an academic career.  I benefited from a private school education in middle school and high school and went on to college at Tufts where my father is a professor.  I took piano lessons from a young age and began to write music on the computer in junior high.  I maintain a passion for making music, and I also continue the visual arts I picked up in high school.  I have always been good at math and science and had a knack for abstract reasoning, so I naturally gravitated toward physics, with the help of a gifted teacher in high school.  I continued in all these pursuits in college, focusing on physics.  I spent the two years in between my undergraduate and graduate education working for my senior thesis advisors in a supporting role in a neutrino physics experiment.  In this time, I came to feel that physics would provide an exciting and rewarding career, and now I am studying for my PhD.  I married my longtime girlfriend 15 months ago.  I love her more every day. 

VL: How long have you been studying and working in your physics?

Locke: If you start with my first research project, that was in 2004.  My first course in basic physics was as a junior in high school, 1998–89, and I have been working in and studying physics since then.

VL: You’ve described your current research to be about DNA sequence-specificity of nucleosome formation and transcription factor binding. Can you translate that into layman’s terms?

Locke: Sure. If you were to take all of the DNA in one of your cells and lay it out in a straight line, it would be more than six feet long.  However, the cell nucleus where all of that DNA lives has a diameter one millionth of that length.  In order to put so much DNA in such a small space, eukaryotic organisms (everything but bacteria) do a great deal of work to compact the size of their genomes.  The collection of DNA and the architectural elements that pack it so tightly is called chromatin.  The structure of chromatin has implications for how the cell operates, since the more tightly a particular gene is packed, the harder it is to use (transcribe).  My work is a study of the fundamental unit of chromatin: the nucleosome.  Nucleosomes are tiny bundles of DNA wrapped around a core of stiff proteins called histones.  Nucleosomes cover about 80% of the genome in every living animal, plant, and fungus, and they form the basis of larger chromatin structures.  I and my collaborators seek to predict what DNA sequences are more or less likely to form nucleosomes, using statistical physics to analyze experimental data.  (Statistical physics is the branch of physics which describes the aggregate behavior of systems with many particles, e.g. molecules in a gas.) We are currently extending our methods to study the general case of protein-DNA binding.

VL: Was studying physics something you always knew you wanted to do, or did you start out on a different path?

Locke: In college, I considered a music major but found that writing about music was impossible for me, at least the sort of analysis my teachers expected.  Prior to college I considered pursuing a BFA in visual art after my BA, but by the time I finished my Bachelor’s that seemed like an unrealistic career path.

VL: What is it about physics that you find exciting and/or inspiring?

Locke: Science as a project is something I find very exciting in general.  I want to know about the world, and I like the idea that I can contribute to the body of human understanding, producing knowledge that will be valuable after I am dead and gone.  Physics in particular is a way of looking at the world.  Physicists like to see the world in the simplest terms possible, reducing a physical system to its essence.  Sometimes this means ignoring fine points, but the goal is to arrive at fundamental parameters controlling large-scale behavior.  Explaining the collective in terms of the participant is fun, elegant, beautiful, and exciting. 

Biological physics involves the application of ideas in physics to biological problems.  It is fun to see how theories designed to explain the behavior of gases and particles can describe the behavior of living things.  This historical moment seems to be the perfect time to enter the broader field of quantitative biology, now that we understand enough of the basic physical mechanisms and we have the computing power to apply this understanding.  In particular, the idea that biological physics can contribute to medical applications down the line is exciting, and the idea of improving quality of life through basic research is very attractive.  

The whole business seems like it’s worth doing in terms of ethics – science is a valuable contribution to culture and the technology deriving from it can solve human problems (it can create them too, but on balance it’s a win).  I’m happiest when I exercise my faculties in the service of a goal that I find worthwhile.  Summing up: I value the product, and the process is rewarding in itself.

VL: When you first started out, what did you find was the most surprising about conducting research? Did you have any misconceptions going into it?

Locke: I can’t think of any big surprises.  One thing that I guess surprised me is how much factors besides science influenced my choice of field.  Factors such as duration of experiment/project (in high energy physics one begins planning an experiment 10 years in advance of getting data), size of research group, the kinds of analysis one does (using pre-made computational tools vs. making your own, data analysis versus simulation, etc).  Each sub-field has its own culture.

VL: How does creativity come into play with your work? How would you describe your process of discovery?

To be honest, I am having a lot of trouble finding my own creativity in my work.  At least in the large scale of choosing projects and choosing analytical tools, I feel more like I’m picking through a tool-box rather than creating anything new.  This isn’t so bad, it just doesn’t feel very creative.  I find myself dissatisfied with my creative output vis a vis my research, but I’m still relatively early in my career so I’m not too exasperated just yet.  It’s not unlikely that I’m just being too hard on myself and fail to see my own strengths.

VL: How did you end up studying and working at Rutgers?

Locke: Well, I wanted to move away from Boston, where I had spent my whole life, and learn what it was like to make my own space.  I chose Rutgers for several reasons: it was well located, highly regarded, had an excellent student-faculty ratio (about 1.5:1 !), and the department was large, which was important to me since I wasn’t sure what sub-field I was going into as an entering student.  Plus, I knew a member of the department who could support me, which was nice since it allowed me to avoid being a Teacher’s Assistant during the first year of classes, which is very demanding.

VL: Do your hobbies and interests outside of work influence your research?

Locke: It’s hard to say.  I have diverse interests (drawing and painting, experimental music, cooking, philosophy).  I think my interest in philosophy is helpful in making and analyzing scientific arguments.  Whatever influence there is, and there must be significant influence, is more or less out of my awareness.  To a certain extent, my interest in matters outside of physics distracts me from my research – many academic researchers seem to be single-minded in their devotion to their work, and that is not for me.

VL: What do you think is the most exciting recent development or discovery in science?

Locke: Oh, gee…maybe mapping the human genome?  I see a lot of developments in biology that show great potential for medicine but the applications are still a ways out of reach.  Our dramatically increasing understanding of genetic networks may create a paradigm shift in terms of drug design: if we know which genetic pathways are messed up in a certain disease then we should, in principle, be able to set them right. 

I also see huge potential for nanomaterials.  There was a recent publication of a way to extend the life of a battery 10-fold or something by putting carbon nanotubes inside the battery.

VL: In the last decade, we’ve seen a lot of advancements in science and technology. With this in mind, what do you think the future is for physics? Is technology changing the way you think about and conduct research?

Locke: 100%.  Computational power opens up so many doors in research, at least the sort of research I do – bigger simulations, more data, etc.  Astrophysics benefits a lot from computational power – the first simulations of galaxy mergers involved ~30 particles per galaxy and more recently this explodes into the hundreds of thousands, with more and more complex physics included.  Same for particle and solid state physics, or any other sub-field you care to mention.  Experimental particle physics may be hitting a barrier in terms of the size of their accelerators.

VL: We really appreciate your taking the time to chat with us, George. My last question is this: What advice would you give to students or young people thinking about a career in the sciences?

Locke: If you know you want to go into science and you’re considering what specific area you want to go into, consider what kinds of activities someone in that field engages in on a day-to-day level.  You have to be passionate about the science, but you also have to enjoy the practicum.  Pick a school that fits your personality.  Your relationship with your grad advisor is of prime importance.  If you’re in undergrad, don’t forget to have fun!!  If you’re in high-school, try your best to find good teachers, as basically every scientist I know decided what area of science to pursue based on their high school experiences.

Use the EPA in Classroom Reseach Projects

It's no secret that finding quality information on the Internet can be hit or miss. As educators working with a large body of students, helping students conduct online research can leave you needing a time out in the teacher's lounge! And yet, data collection and analysis is such an important part of learning about science that it can't be skipped. Fortunately, many government bodies and environmental organizations are working to make quality, reliable information easier to come by. Today, we're highlighting the wonderful resource that the Environmental Protection Agency has put together.

First off, the EPA home page gives easy links to current news events. Today's page highlights the latest information on the EPA's response to the oil spill in the Gulf of Mexico, comments from Administrator Lisa P Jackson (yes, she tweets), and a list of the most popular topics people are concerned about.

The Learn the Issues page lets visitors gather comprehensive, detailed information on water and water pollution, climate, green living, ecosystems and other areas of concern. This is a particularly good starting place for students who are in their general information gathering phase. The page also lists a series of popular questions posed to the EPA, with complete answers.

The Science and Technology page provides information on research that the EPA is currently conducting. Today's articles include a discussion on the use of nanotechnology for breaking down pollutants, and tracking air pollution.

But, probably the most useful tool for your classroom is the EPA's featured item: MyEnvironment. For such a great feature, it can be a little difficult to find. On the home page, down near the bottom (in the middle), is the small green 'MyEnvironment' text with an empty box for inserting a zip code or town name. Type in the information for a specific US location, et voila! What you get is a page filled with information on everything from pollutant risks for the area, to air quality, to the locations that report data to the EPA. There are lists (by street) of businesses that use hazardous materials in their work, statistics on ozone and radon concentrations, even a list of what EPA cleanups are taking place in the community. For example, the image above shows the cancer risks for midtown Manhattan in 2002 (the latest statistics).

This compendium of information is easily accessible and may just be the key to helping your students on their next data collection project. If you want to direct them in their environmental research and fact-gathering, but don't have the time for weeding through reliable resources, make this your first classroom stop.

Have other sites you think are worth mentioning? Share them here, or on our Facebook page.

Vote for Your Favorite Microbe

Joseph Heintz, University of Wisconsin, Madison

Wisconsin legislators voted this month to pay tribute to Lactococcus lactis by making it the official Wisconsin State Microbe. Why Lactococcus and not, say, Bacillus or Saccharomyces? Because good old L. lactis is the microbe responsible for turning the curdled rennet, milk, and salt mixture into what we've come to know and love as Cheddar cheese. (It is also used in the making of Colby and Monterey Jack.) The honor makes sense, after all, as Wisconsin is the country's number one cheese producing state.

In light of this, the question begs to be asked: What about the other microbes that are just as hard working? Take our poll on the left to decide which microbe you think deserves such an honor. The winner will be featured in our blog on May 7th. The nominees are:

• Saccharomyces cerevisiae -- otherwise known as baker's yeast, for making leavened bread products.
• Pseudomonas putida -- cleans wastes from sewage water at water treatment plants.
• Escherichia coli -- lives in the human digestive system and allows us to digest the food we eat. 
• Streptomyces -- a soil bacteria that is used to treat infections. 

When the Valve Doesn't Work and the Boom's Not Enough

"Oil spill" -- it's a dirty noun, and with good reason. For many of us who have been around for more than a few decades, it even triggers some residual trauma. Who can forget the images of dying fish and seabirds washing up on the shores of Prince William Sound, Alaska, courtesy of the Exxon Valdez? Or the ban on fishing that lasted for over 5 months in the fertile Narraganset Bay off of Rhode Island because of a tanker-tug boat collision? Yes, there are many serious consequences to oil contamination in our oceans, and this latest event in the Gulf of Mexico is going to be no exception.

Though the International Tanker Operators Pollution Federation Limited proudly explains how the incidences of oil spills -- regardless of their source -- has significantly declined in the last thirty years (see the graph at right), it doesn't negate the fact that when they do happen, the results aren't pretty. Efforts to stop the leak in the Gulf through the use of robot submarines (closing the well's valve manually) have been unsuccessful, and in the three days since they started trying, the oil slick has moved more than ten miles closer to the shore, threatening wetlands, beaches, and wildlife from Louisiana to Florida. As of Wednesday morning, the slick is 40 miles wide, 80 miles long, and growing by the hour.

The viscosity and density of oil is different than water, and so tends to float on top of it. That is why the early deployment of booms is an important first step in containing spills. Unfortunately, wave action churns crude oil under, creating what looks like "chocolate mousse", and then that oil sinks -- contaminating the delicate ecosystem.

Responses to such spills can take many forms. Boats crews with booms and skimmers can try to contain and mop up the oil before it spreads too far. Planes and helicopters can dump dispersant chemicals into the slick to help the oil break down faster and be less harmful to the ecosystem (think: dropping some Dawn into a sink full of greasy dishes). Pollution containment devices can be constructed at the source, such as a leaking well, to capture the oil. And the oil can be lit on fire, about 95 percent of which is released as carbon dioxide and water into the atmosphere.

While the efforts of the Coast Guard and BP are noble and appreciated -- they are trying a blend of all these techniques -- it appears that they are still weeks away from full containment, and a good three months away from stopping the leak permanently. In the meantime, the oil is expected to reach the Gulf shores as early as this weekend.

Are you using this important news event in your classroom and teaching? We would love to hear how. Share with us and other educators here, or on our Facebook page, how you are talking with students or colleagues about oil spills and cleanups. we would also love to hear about preventative measures folks along the Gulf can take now to protect their shoreline.

Using Skype in the Classroom

One of the benefits of incorporating new technology into the classroom is that it allows the teacher and students access to things they otherwise wouldn't have access to. In today's post, we'd like to highlight the benefits and uses of Skype -- the free software that allows for video conferencing.

What you need:
Skype is installed onto a computer (PC or Mac), so it goes without saying that your classroom will need a computer with internet access. Because it is a video conferencing tool, you will also require a camera and microphone. These last two do not need to be particularly hi-tech. In fact, combination units can easily be picked up at many stores for around $10. If your computer system happens to accommodate an overhead projector, that will be of use as well because it will allow all the students in the class to see the person/people they are speaking with.

How you can use Skype:
In the 'old days' -- meaning, pre-1990s -- it was quite common to be set up with a pen pal through school. Writing to a pal on the other side of the country or ocean helped young people practice their penmanship, learn about other cultures, and build communication skills. In today's day and age, pen pal programs are less common. However, new technology (like Skype) can be used to interact with folks outside of the classroom in other ways. For example, you can use video conferencing to:

• talk with students in classrooms in other states or countries.
• have discussions with scientists working in different fields (it's far easier than trying to bring that scientist into your classroom proper).
• create research projects with students or classes in another place.
• have specialists provide tours of places students would never have access to.
• provide students access to lectures or presentations they can't physically travel to (with permission).

The initial set-up of the computer takes a matter of minutes, and making the connections for such video conferences can be built into classroom activities. Make students responsible to contacting potential scientists or specialists for conferences (with instructor direction). Ensure that students do their research prior to any conference so that they have thoughtful questions to pose. With a little bit of planning and preparation, you can have your students building important connections in no time at all!

Do you use multimedia or new technology in your classroom? We'd love to hear how you incorporate them. How does it affect your teaching and students' learning?

E. O. Wilson Takes to Writing Fiction

E. O. Wilson, renowned biologist and one of (if not THE) foremost experts on ant biology and ecology has put pen to paper once again. Only this time, it's to appeal to fiction readers who might not have the time or interest to pick up his more comprehensive nonfiction works.

The novel takes place by the side of a lake in rural southern Alabama. While the story focuses on a young boy who grows up to be a lawyer, the majority of characters, which probably comes as no surprise, are ants. In this undertaking, Wilson says he "had in mind a message, although I hope it doesn't intrude too badly, persuading Americans, and especially Southerners, of the critical importance of land and our vanishing natural environment and wildlife." Read more of his interview with Steve Ross of the Huffington Post here.

It's a unique and interesting undertaking, to say the least. Here, Nature is not just present to provide atmosphere to the story -- it's a main character. Wilson is giving voice to an 'entity' that we typically don't hear from (at least not in the conventional sense). Interestingly, the writer's voice has remained intact during this jump from nonfiction to fiction. The phrasing and terminology used is not unlike that of Wilson's very readable nonfiction books. While it isn't always the most conversational of tones, it is nevertheless quite engaging and gets across a sense of character that many writers of fiction would envy.

What intrigues us more, though, is Wilson's intent before writing -- to create a work of fiction that not only is entertaining, but puts across a sociological message: human beings are a biological species, acting in a biological environment and everything we do impacts all that is around us.

What do you think? Could the new wave of eco-activism be subterfuge? Will making us empathetic to creatures through fiction help a conservation movement that has taken quite a few hits in the last year?

Listen to the NPR podcast on this remarkable new story by clicking here.
Or read a book review by Barbara Kingsolver in the New York Times here.

40 Years On -- How Proud Would Rachel Carson Be?

Forty years ago today, Senator Gaylord Nelson held the first environmental teach-in we know as Earth Day. Partly in response to the growing eco-activism of the 1950s and '60s, and the overwhelming evidence presented to the public through works like Rachel Carson's Silent Spring, Nelson organized this national event in the hopes that a "grassroots outcry about environmental issues" might motivate the folks in Washington to do something to stop environmental damage. A New York Times article highlighting Nelson's efforts commented: "Rising concern about the 'environmental crisis' is sweeping the nation's campuses with an intensity that may be on its way to eclipsing student discontent over the war in Vietnam."*

Forty years on, with controversy about another war on the lips of most Americans, the question begs to be asked: "Have we come far enough in our thinking?" There is no doubt that there is much to celebrate: the Clean Water Act, the Endangered Species Act, mandatory recycling in many communities throughout the nation. The activism work of the 1950s, '60s, and '70s also did much to raise the awareness of science as a discipline. But as we pat ourselves on the back for our earth-consciousness today, we might also take some time to think about the environmental issues we're now presented with and ways they might be addressed. Has the battle become weary, or are we starting to rally again?

With that in mind, we'd like to hear from you about what environmental concerns are at the top of your list. What should we as a larger community, and the government in Washington, be paying attention to most? We would also love to hear how teachers are choosing to honor this occasion in the classrooms around the country. Share your thoughts with us here, or on our Facebook page!


*"Environmental Crisis' May Eclipse Vietnam as College Issue," New York Times, 11/30/1969