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10 Questions for a Signature Scientist: Nathan Baker

June 2, 2011 - 6:28pm

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Nathan Baker  | Photo Courtesy of PNNL

Nathan Baker | Photo Courtesy of PNNL

Meet Pacific Northwest National Laboratory’s Chief Scientist for Signature Science, Nathan Baker. At PNNL, he’s working to advance the innovative application of data analytics and algorithms to real-world challenges, ranging from smart grids and bioforensics to nuclear non-proliferation and medical treatments. Check out our latest 10 Questions below and get the inside scoop on how it’s done.

Question: What sparked your interest in science?

Nathan Baker: It’s hard to point to one thing, but I have been fascinated by computers and programming for a long time; that got me interested in a wider range of science and technology. In addition, I was lucky to have fantastic professors at the University of Iowa. They saved me from the Pre-Medical path and they said ‘Look, there’s so much more to life.’ It was really the chemistry professors there that ultimately set me down the path of research science.

Q: You specialize in computational biophysics, nanotechnology and informatics – what brought you to those fields?

NB: The first thing I was exposed to in depth was chemistry – and chemistry is a great introduction because it overlaps with so many different disciplines: It’s a little bit of physics, a little bit of biology, and embraces computational methods. So, I focused on chemistry for my Bachelor’s degree and continued to pursue chemistry in graduate school at the University of California San Diego. UC San Diego offered me the freedom to pursue a PhD with two fantastic advisors, Andy McCammon in Chemistry and Mike Holst in Mathematics. Andy and Mike provided me numerous scientific opportunities and encouraged me to look at physical chemistry in its broadest definition. Since getting my PhD, my primary interest has been in the very broad area of computational biology/biophysics. However, in order to solve some of those problems I needed more tools from other disciplines, particularly mathematics.

Q: You are the Chief Scientist for Signature Sciences. What does that mean?

NB: A signature is something that pops up in a lot of fields, but very few fields specifically define it in an abstract way. For us, a signature is a set of features or observables that uniquely define a phenomenon of interest. Before moving to PNNL, I worked in computational biology where the idea of signatures is most commonly found in the study of biomarkers. In that case, the signature is the collection of medical observations or biological observables that you can bring together to diagnose a disease or develop a prognosis.

However, the idea of signatures is much more generic. For example, PNNL has a strong history in nuclear signatures for its nonproliferation mission. In the cyber domain, PNNL also has a strong background in thinking about the indicators of different types of cyber activity to answer questions like “Is this a piece of malware or a virus that’s going to take over your computer?” There are several other examples of signature science at PNNL ranging from biomarker signatures for disease and environmental threats to signatures of abnormality in electric power grid infrastructure.

I came to PNNL about eight months ago in response to a search PNNL was carrying out for a new initiative in signature science. When I saw what the Lab had, and how it related to what I’d been doing, it seemed like a great fit – and it still does. As Chief Scientist for the Signature Discovery Initiative, I help lead research activities in signature science which draw on all of these past activities as well as new research projects to build capability in this important area.

Q: Did you have teachers who helped you discover these interests?

NB: Yes, my professors at the University of Iowa. Before interacting with the Chemistry faculty there, I was wandering around the University somewhat bored; Pre Med was not very interesting. It wasn’t until I met Dan Quinn in the Chemistry department that I became excited: research science really opened my eyes to the possibilities of a career in science. Before then I had no clue about research – all my summer jobs had been working on farms, in dish rooms. When I started working in that lab, it was transformative experience. My PhD advisors at UC San Diego also played an essential role in opening my eyes to the broader world of research science and giving me time and space to explore a wide range of research topics. Equally importantly, they both went out of their way to help me and provide outstanding opportunities for my career.

Q: Do you have advice to other wandering young students?

NB: Unlike my high school experience, students don’t have to wait until college to get involved with research. When I went to high school, a summer job was just a summer job. At Washington University, PNNL, and many other research institutions there are many programs to bring students into science before college to give them some exposure. I’ve only been at PNNL for a short time and I’ve already seen some really fantastic interns come into the Lab. It’s a great opportunity, even if you don’t do it for the rest of your life.

Q: You are involved in developing algorithms and software – how are these applied to problem solving?

NB: Signature science and discovery is a great example. As I mentioned earlier, PNNL has a lot of historic investments in signature sciences but they tend to be very domain specific. But the tools used to tackle problems in signatures don’t have to be separate and distinct for each domain. The ideas and methodologies that are used in all of those are actually similar. From my standpoint, algorithms and software development help to pull those pieces together. The wonderful thing about applied mathematics is that it touches on so many different problem areas simultaneously. Often what we’re doing is bringing some of the more abstract aspects of applied mathematics and making them accessible to people who are using them to solve problems.

Q: You also lead a working group for the National Institutes of Health’s Cancer Biomedical Informatics Grid – what is that project advancing?

NB: I lead the NIH NCI caBIG Nanotechnology Working Group. caBIG is an interesting idea that took off five years ago. caBIG is an excellent investment and a great example of team science: the idea of this bigger project is to bring together different types of information from throughout the biomedical research lifecycle – all the way from very basic science research, and up to where it impacts patients, populations and treatments.

Our area of interest in the Working Group is breaking down information barriers in the nanomedicine field which is very diverse. This field involves scientists ranging from synthetic chemists and engineers to clinicians and workplace safety researchers. We want to understand how to get information to flow across this entire spectrum of disciplines. This is especially challenging since many of the different disciplines come with their own language and terminology. However, ultimately, we all want to explain the biological interactions of nanomaterials in a biomedical setting based on their chemical and physical properties. This has a lot of applications ranging from generating new materials for drug delivery, developing better tools for imaging, and understanding the potential threats posed by industrial nanomaterials released into the environment or workplace. In the working group, we’ve been trying to bring these different groups together with their information sets to enable this type of predictive modeling of nanomaterial-biological interactions. caBIG is the perfect home for this activity: its sole purpose is to integrate information across a wide range of sources and disciplines.

Q: It seems like a broad theme across your work is the variety and depth of interactions with other scientists and researchers do you see this playing out?

NB: Absolutely. It was precisely that which got me so excited about joining a National Lab. PNNL has an open campus, an open feel which makes it easy to have those types of collaborations. Every day I get to meet with a wide cross section of people working on everything from basic biology to national security to chemical synthesis.

Q: I imagine keeping up with all of this makes your reading list much longer.

NB: Sure. I use RSS feeds to keep up with all the journals and I think every day I get around 800 journal articles that I need to scan through. And that’s actually fun – if you look at it the right way.

Q: A couple quick last questions, do you have a favorite tool?

NB: It’s got to be my computer. I’m never very far from it.

Q: What do you enjoying in your free time?

NB: Playing with my kids, hiking, reading, and playing video games. I’ve also become very fond of wine since moving to PNNL due to the large number of wineries in the area!

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