July 25, 2016

Archives for March 2007

Better Know A Scientist – Byron Roberts

Today’s installment of Better Know A Scientist is Byron Roberts. He was kind enough to answer some questions via e-mail recently. Here’s the transcript.

Atoms to Zebras (AZ): Thank you for taking the time to allow us to better know you and your work. Tell us about yourself.
Byron Roberts (BR): I have a somewhat unusual history compared to many graduate students. I grew up in northern California, in Sonoma County, and graduated from high school there in 1991. From high school I went to the local junior college and took courses that pre-med students usually take in their first couple years of college. However, I wasn’t a particularly motivated student at that time, so it took me a few years before I had got enough work done in order to transfer to one of the University of California campuses (UC Riverside). Right about the time that I got accepted for transfer, I decided that I wanted to become a paramedic and work on a 911 ambulance for a couple of years while I finished college. So instead of going to UC, I applied to paramedic school and went through all of that. I had intended to go back to college right after I finished paramedic school, but back when I first got my license, paramedic jobs were hard to come by. My first full-time ambulance job consisted of 24-hour shifts, which made going to school extremely difficult. At any rate, it wasn’t until January 2000 that I was able to switch to 12-hour night shifts and get back to school. However, now I was a much more serious student. I spent another year and a half at the Santa Rosa Junior College and this time got accepted to UC Davis, to which I transferred in 2001, initially as a Cell Biology major. While I was at Davis I participated in undergraduate research, and it was there that I realized that what I really wanted was a career in scientific research and not clinical medicine. However, my research interests are still strongly driven by my past experiences in the clinical world. I graduated from UC Davis in 2003 with a B.S. in Genetics, and took a job there at the Vet School studying the molecular genetics of brain tumors in dogs (pet dogs get brain tumors that are very similar to those seen in humans), as well as developing potential therapies to treat brain tumors. In the summer of 2005 I started graduate school in New York at the Tri-Institutional Program in Computational Biology and Medicine.

AZ: Explain to the readers your general area of research?
BR: In order for our hearts to be effective at doing their job of pumping blood throughout our bodies, they need to function in a certain way. The four chambers of the heart need to work together in a concerted fashion. Also, the heart can’t beat too slowly; otherwise the needs of the various organs and tissues won’t be met. But the heart can’t beat too fast, either, since a heart that is beating too fast won’t have enough time to fill up with blood between beats. The mechanical pumping action of the heart is regulated by an electrical system within the heart. In order for the various parts of the heart to work together, and with the correct timing, electrical impulses must originate in a specific region of the heart and then be conducted throughout the rest of the heart in a specific pattern and in the proper amount of time. Many people aren’t aware, especially on a day-to-day basis, of this electrical activity that’s going on in the background to keep their hearts pumping correctly, but it turns out that this electrical activity is very complex. Even within individual cardiac cells there are a fairly large number of components that must work together to produce the correct electrical series of events. And on top of that, there are billions of cells in a human heart that must work together, adding additional complexity! The people in our lab use computers, in addition to doing wet-lab experiments, to study different aspects of electrical activity in the heart. In particular we are interested in arrhythmias, which are abnormal (and sometimes lethal) electrical conduction patterns in the heart. By learning more about the mechanisms by which arrhythmias arise, better treatments (and prevention) for a wide range of cardiac conditions can hopefully be developed.

AZ: What is your area of focus?
BR: I’m still in a very early phase of my work, but I’ve become extremely interested in what are referred to as reperfusion arrhythmias. When blood flow is cut off to a region of the heart (as during a heart attack, when one or more coronary arteries become blocked) or to the entire heart (as during some surgical procedures which require the heart to be stopped temporarily), changes occur in the tissue that is not being perfused (i.e. tissue is being deprived of blood flow): the cells aren’t getting glucose that is needed to make energy required to carry out work, the inside of the cells become too acidic, etc. When you restore blood flow (the blocked coronary artery is reopened or bypassed, or the heart is restarted at the end of surgery) and the tissue that was previously deprived of a fresh blood supply is reperfused, you might expect everything to return back to normal. However, in some patients, the opposite occurs: the heart actually gets sicker. The affected region of the heart might not be able to pump as strongly anymore, or severe electrical disturbances (arrhythmias) may occur. There has been progress on this problem in the past, and there are certain things that many people agree are happening when these reperfusion arrhythmias occur. But it appears that the causes of the problem have not been completely worked out yet, not to mention that there still appears to be room for improvement in devising therapies. I hope to be able to make some progress in this arena.

AZ: What led you to your current position?
BR: Back when I was working as a paramedic, a lot of what I did revolved around monitoring cardiac electrical activity, as well as treating emergent cardiac problems. I monitored the ECG (an ECG gives a “picture” of the heart’s electrical activity as seen from the surface of the body) in probably the majority of my patients. In addition, some of the most powerful tools at my disposal acted directly on the heart: either drugs or electrical therapy to “reset” the heart in cases of extremely severe cardiac arrhythmias (the familiar paddles that are used to shock patients when they’ve experienced a cardiac arrest). My first exposure to reperfusion arrhythmias came when I was in paramedic school. We had to spend a couple of days doing a rotation in the cardiac cath lab, where images are taken of the coronary arteries, or procedures such as an angioplasty to unblock a coronary artery using a miniature balloon are performed. During one of the angioplasty cases that I was watching, almost immediately after the coronary artery was reopened, all of these extra irregular heart beats (called ectcopy) appeared, and shortly thereafter the patient went into cardiac arrest. The team was able to shock that patient and get the heart restarted, but I remember thinking, “Whoa, what just happened there?” At that time someone explained to me why reperfusion arrhythmias occur, and I came away thinking that the whole mechanism was already worked out. But recently I learned that the whole puzzle is not in fact solved, and now I’m working on this interesting problem that I have seen directly affects real patients.

AZ: What did you want to do when you were growing up?
BR: When I was a kid, I loved to take apart and tinker with all sorts of machines, and later computers. By the time I was in junior high, I had decided that I wanted to work with with computers and/or robots. But later my interests turned more to biology and medicine, so by the time I was half-way through high school I decided that I wanted to become a physician. I guess I’ve landed somewhere in between: using computers to tackle medical problems.

AZ: What do you enjoy most about your work?
BR: I get to continually learn new things about how nature works, and I get to work on a problem that was largely of my own choosing. Being a graduate student means that your time can be relatively free of rigid structure, and it requires a lot of reading, which is something that I love to do.

AZ: What is the most challenging aspect?
BR: Figuring out which questions to ask. There are always lots of questions that can be asked, but I need to formulate my questions in a way that is specific enough to make them scientifically tractable.

AZ: What’s on the horizon in your line of work?
BR: I’m still in the early phase of my program, so my next steps will be to finish courses and take my Advancement to Candidacy Exam.

AZ: Any advice for students interested in your field and science in general?
BR: Communication is an important part of science that I think is too often overlooked. Whether it’s writing or public speaking, try to get feedback from your colleagues after you’ve given a talk or written something. My two pet peeves (actually, I think I have a lot more than just two!) are presentations that have not been targeted to the audience correctly, and presentations that are comprised of disjoint pieces of information that don’t tell a cohesive story. The latter is especially easy in this age of PowerPoint where people tend to put lots of pretty pictures or huge amounts of text onto their slides. My personal feeling is that even if you feel like you’re “dumbing down” your presentation too much, there will probably still be a sufficient number of people in your audience who will appreciate it and actually get more out of your talk or paper than if you had done otherwise.

Many thanks to Byron. For more information on his work check out the website for the Tri-Institutional Program in Computational Biology and Medicine and the Cardiac Electrodynamics Laboratory. Stay tuned to learn more about his and for more chances to Better Know A Scientist (index).

Posted by Tim Roth, author of the political blog Think Anew and Act Anew

The Voyager Message in a Bottle

In a previous article, the topic was the plaques attached to the Pioneer 10 and 11 space probes. This post is about another cosmic message in a bottle, the Voyager Golden Records. As of this writing (March 18, 2007), the probes Voyager 1 and 2 are 101.957 AU and 82.529 AU from Earth. Depending on language use, “AU” or “u.a.” stands for Astronomical Unit, the distance of the semi-major axis (half of the major axis, the longest diameter of an eclipse) of Earth’s elliptical orbit around the Sun. The value of an AU unit is 149,597,870,691 +/- 30 m, about 150 km, or about 93 million miles. This puts Voyager 1 & 2 at about 9.5 billion miles (15.3 billion km) and 7.7 million miles (12.3 billion km) from Earth.

Aboard these two probes is a golden phonograph record that contains sounds and pictures from our planet. Below is a picture of the Voyager craft, at the center of the picture you can see the cover of the 12-inch Golden Record.

NASA illustration of Voyager spacecraft

The cover is a instruction sheet for playing the record that is written in binary code and the spin movements of a hydrogen atom as the timing basis. This far more sophisticated message in a bottle presents has serious limitations as an effective way to communicate with intelligent life. Even if DJ Little Green Man is smart enough to figure out how to scratch out some tracks from this album over the alien airwaves, they may not have the visual or hearing abilities to process the sights and sounds, let alone understand what it’s on it.

Cover of Voyager Golden Record

Here’s here’s larger image of the cover diagram via Wikipedia’s Wikimedia feature.

However, it’s still a romantic idea and as President Jimmy Carter’s printed message on the record said: “We cast this message into the cosmos… Of the 200 billion stars in the Milky Way galaxy, some — perhaps many — may have inhabited planets and space faring civilizations. If one such civilization intercepts Voyager and can understand these recorded contents, here is our message: We are trying to survive our time so we may live into yours. We hope some day, having solved the problems we face, to join a community of Galactic Civilizations. This record represents our hope and our determination and our goodwill in a vast and awesome universe.”

Here’s links to content if you are interested:
Greetings in 55 languages
Sounds of Earth

Posted by Tim Roth, author of the political blog Think Anew and Act Anew

1. Current location data from the probes Pioneer 10, Pioneer 11, Voyager 1, Voyager 2, and last years launch of the New Horizons mission: Spacecraft escaping the Solar System”, Heavens Above website
2. “Astronomical Unit”, Wikipedia entry
3. “Voyager Golden Record”, Wikipedia entry

Better Know A Scientist – Dr. Pete Jordan

Today’s installment of Better Know A Scientist is Dr. Pete Jordan. He was kind enough to answer some questions via e-mail recently. Here’s the transcript.

Atoms to Zebras (AZ): Thank you for taking the time to allow us to better know you and your work. Tell us about yourself.
Dr. Pete Jordan: I’m originally from Australia, where I pursued a degree in mechanical engineering at Queensland University of Technology. After graduating from QUT, I wanted to spend an extended period of time overseas, and fortunately I managed to find sufficient funding to study for a master’s degree in biomedical engineering at the University of British Columbia in Vancouver. However, I left UBC after a year, and started working on a PhD at Cornell University in New York. My PhD research was in the field of cardiac arrhythmias and computational modeling. I successfully defended my doctoral dissertation in December 2006, and am now working as a postdoctoral fellow at the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) at the National Institutes of Health (NIH) in Bethesda, MD.

AZ: Explain to the readers your general area of research?
Dr. Jordan: I am currently working in the area of human metabolism and body composition. We are interested in determining the important factors regulating the long-term composition of the human body, in particular focusing on the sequence of events that lead to obesity. We are looking at these problems using mathematical models of human body composition regulation, as these provide us with insights that cannot easily be obtained experimentally.

AZ: What is your area of focus?
Dr. Jordan: I am currently developing a mathematical model of the way body composition changes during infancy, using data for infants aged 15 days to 2 years to calibrate the model.

AZ: What led you to your current position?
Dr. Jordan: I didn’t ever wake up one morning and think that I was going to be a human body composition researcher. As with so many things in life, it was a lucky confluence of events that lead me to be here. For both professional and personal reasons, coming to the NIDDK made the most sense as the next move in my career – my mentor here at the NIDDK knows my doctoral advisor very well, and thus I know that I am in good hands here; in addition, my fiancee lives here, and we wanted to live in the same city.

AZ: What do you enjoy most about your work?
Dr. Jordan: The eureka moments – those times when you “see” something that you didn’t see before, or when everything that you’ve been working on finally falls into place. The joy of discovery is a great motivator.

AZ: What is the most challenging aspect?
Dr. Jordan: The solitude. Being a researcher can be lonely, and I find that I don’t always have the motivation to keep going. Being part of a team can certainly help offset these concerns – it all depends on the nature of the work that one is doing at any point in time.

AZ: Any advice for students interested in your field and science in general?
Dr. Jordan: No matter what area of science you’re interested in, study as much mathematics as you can. Biology is becoming increasingly quantitative, and having a mathematical structure on which to hang all one’s biological knowledge is extremely helpful for organizing what can appear to be a very disorganized body of knowledge. Similar mathematical “themes” appear in a wide variety of natural phenomena, making mathematical tools a means by which one can study probably a wider array of phenomena than one can study with any other set of scientific tools.

Many thanks go out to Dr. Jordan. Stay tuned to learn more about his work and more chances to Better Know A Scientist (index).

Posted by Tim Roth, author of the political blog Think Anew and Act Anew

Guns, Germs, and Steel Discussion Index

Book Discussion: Guns, Germs, and Steel by Jared Diamond.

1. Introduction: Yali’s Question
2. The Controversy of Yali’s Question

Pioneer Plaques

As you are reading this, the Pioneer 10 and 11 space probes have lost all power and are silently flying in the darkness of space. NASA lost contact with Pioneer 10 in 2003 and Pioneer 11 in 1995. Odds are that they will continue their lonely journey into eternity. However, there is a very slim, but not impossible chance that a intelligent civilization living on a different planet will detect these probes.

If this amazing event were to happen, these beings will find a golden plaque on each probe. On these gold-plated aluminum plaques are a depiction of Earth’s location in the galaxy, a diagram of the hydrogen atom, a map of the Pioneer’s journey through the solar system, and a picture of a man and woman. Pioneer Plaque

Obviously this is a true shot in the dark, but I just love this cosmic “message in a bottle”. One question that comes to mind is: “would an intelligent alien be able to understand the plaque?”

Stay tuned for upcoming articles that take a tour of the plaque. Each element of the plaque is a science lesson in itself. For example, the use of the arrow to describe the gravity slingshot around Jupiter was criticized because an arrow is symbol that stems from the hunter-gather aspects of past (and present in some cases) human civilization. If our intelligent “neighbors” developed their civilization under water, the arrow could be totally meaningless.

Posted by Tim Roth, author of the political blog Think Anew and Act Anew

“Pioneer plaque”, Wikipedia entry

Kelly Egan – Better Know A Scientist

Today’s installment of Better Know A Scientist features Kelly Egan, an undergraduate researcher in Dr. Herb Chen’s lab in the Department of Surgery at the University of Wisconsin Hospital.

Explain to the readers what you do?  
My most recently completed project involved doing a risk-benefit analysis of parathyroidectomy for primary hyperparathyroidism in patients 80 years of age and older. (Parathyroidectomy is removal of parathyroid glands. They glands located behind the thyroid gland in your throat and regulate calcium levels. Hyperparathyroidism is a condition of overactive parathyroid glands that leads to elevated calcium levels). Basically we were trying to prove that surgery (the only cure for primary hyperparathyroidism) is safe and effective in elderly patients.

What led you to your current position?  
I was looking for research experience before I start medical school and a friend of mine had a great experience working for Dr. Chen.

What did you want to do when you were growing up?  
I’ve wanted to be a doctor for as long as I can remember.

What do you enjoy most about your work?  
I like the clinical aspect of research and hearing patient stories on how their quality of life improved after the surgery.  I was also able to scrub in and assist on surgeries this summer, something that is almost unheard of for undergrads.  Every new experience that I have convinces me more that I have chosen the right career path.

What is the most challenging aspect?
My paper that I wrote is going to be published this spring and surgeons all over the world will be reading my research (and critiquing it).  That’s a lot of pressure!  Also, presenting my research at a surgical conference in February was scary, but rewarding.

What’s on the horizon in your line of work?  
I’m starting medical school at the University of Wisconsin in the fall, specialty undecided.

Any advice for students interested in your field and science in general?
Start getting experience while you are young.  I was the only undergraduate at the Academic Surgical Conference, but I didn’t let that stop me from networking and talking to surgeons in many different fields.  Be willing to put in the extra hours and go above and beyond what is required of you.

Kelly Egan is finishing up her senior year at the University of Wisconsin-Madison.  She will be attending the University of Wisconsin School of Medicine and Public Health in the fall of 2007.  Her paper, “A Risk-Benefit Analysis of Primary Hyperparathyroidism in Octogenarians and Nonagenarians” will be published in the Journal of Surgical Research in spring 2007.

Posted by Tim Roth, author of the political blog Think Anew and Act Anew

El Nino winding down and maybe a little La Nina?

Even though predicting weather a mere 24 hours in advance can be very difficult, every month the kind folks at the National Weather Service’s Climate Prediction Center take on the challenge of long term forecasting. While most of us have little practice use for this report, they can be encouraging for those of us still stuck in the dead of winter. I’m definitely getting tired of scraping Wisconsin ice and snow off of my car, so I’m happy to hear that the 3 month outlook forecast calls for warmer temperatures in the western third of country with a pocket of warmer climate that stretches along the northern border states to the Mississippi River Valley. Predictions for the rest of the country are up in the air.

The precipitation forecast calls for below average rainfall in the western and central Gulf Coast Regions along with the Far Southwest. Above average rainfall is predicted for the southern Rocky Mountains and the high plains state. It’s a toss up for the rest of the country.

Can’t forgot about Hawaii – long-term prediction: big surprise….paradise (If you must know, they are predicting average temperature with below average rainfall amounts).

How do they predict the long-term weather?
There are many factors that go into these predictions. An interesting factor is the so-called “memory” effect that ice and snow cover has on climate. For example, if there is a lot of snow on the sun doesn’t heat the ground very well because the energy from the sun is reflected by the snow so the climate “remembers” the recent colder weather. One of the most influential factors is the temperatures of the Atlantic and Pacific Ocean. While El Nino is the most powerful and well-known trend, there are other ocean trends like the Northern Atlantic Oscillation.

Speaking of El Nino, the current El Nino event is winding down and the Pacific Ocean will be ENSO-neutral (El Nino – Southern Oscillation is the full name of the ocean temperature pattern) sometime in the next month or two. In fact, by the summer we may be heading towards La Nina conditions but it’s way too soon to know for sure.

What are El Nino and La Nina?
El Nino and La Nina refers to changes in the average temperatures in the Pacific Ocean that have impacts on weather worldwide. An average increase of 0.5 degrees C in the central topical Pacific is the official definition of El Nino and a decrease of 0.5 degrees C is the definition of La Nina. This doesn’t seem like much, but .5 degrees C of warmer water multiplied by a huge area of ocean is a lot of energy and has a very noticeable effect on global weather.

If you are interested in learning the effects of El Nino on the weather in your location, check out this good website from the National Oceanic and Atomospheric Administartion (NOAA) Here’s a website discussing La Nina effects.

Posted by Tim Roth, author of the political blog Think Anew and Act Anew

1. “Long-Lead Seasonal Outlook – February 15th 2007”, Climate Prediction Center, National Weather Service.

2. “El Nino-Southern Oscillation”, Wikipedia entry

Better Know A Scientist

Short “get to know you” interviews with scientists ranging from professors to the lab technician.

1. Stephen Gaeta – Cardiac Electrodynamics: Alternans

2. Kelly Egan – Risk-Benefit Analysis of Thyroid Surgery

3. Dr. Pete Jordan – Human Metabolism and Body Composition

4. Byron Roberts – Reperfusion Cardiac Arrhythmias

Stephen Gaeta – Better Know A Scientist

Welcome to the first installment of an interview series called Better Know A Scientist (index). Stephen is in the Weill Cornell / Rockefeller / Sloan-Kettering Tri-Institutional MD-PhD program and is a member of David Christini’s Cardiac Electrodynamics Lab.

Explain to the readers what you research?
I’m currently working towards my thesis in David Christini’s Cardiac Electrodynamics laboratory at Weill Cornell Medical College in New York City, where I use a combination of mathematical modeling and more traditional experimental work to research the mechanisms of cardiac arrhythmias.  Specifically, I am currently working to probe the underlying cause of a specific electrical rhythm disturbance, known as “alternans”.  Alternans is a precursor to potentially fatal arrhythmias including ventricular fibrillation, a major cause of death worldwide.  Understanding its genesis and dynamics will allow more insightful research into means of controlling its formation and progression.  Alternans could be controlled through pharmacological means, or through more effective implantable devices.  My research could contribute to advances in either of these approaches.

What led you to your current position?
Starting in this lab was a fairly big departure from my previous work.  As an undergraduate at the University of Wisconsin– Madison, I studied molecular biology and neuroscience, working primarily in a neuroscience laboratory.  The brain has always been my scientific passion, and– for better or worse– until recently i have dedicated most of my work and energies solely into this field.  Following graduation, I began here at the Weill Cornell / Rockefeller / Sloan-Kettering Tri-Institutional MD-PhD program, where I am now nearing the end of my third year.  In the first two years of this program, students complete the first half of medical school, and rotate through multiple labs of their choosing before deciding upon a thesis laboratory.  With the exception of my current lab (which I have declared for my thesis), all of my rotations were in neuroscience labs.  I was drawn to this departure by the power of computational research to answer a different kind of question than is possible in more traditional laboratories, and by the prospect of gaining expertise in computational research, which is becoming an increasingly important and powerful technique in biological research.  Though I retain my passion for the study of the brain, I could not be happier with my decision for this phase of my training.

What did you want to do when you were growing up?
Looking back, I can’t identify a particular job I looked towards, and in a way I find that telling.  I’ve always had diverse interests, and relished learning anything and everything available to me. Deciding to complete a dual degree program has allowed me continue to leave as many doors open as possible for my future, and continue on a path towards an uncertain, but promising future.

What do you enjoy most about your work?
In the right graduate school environment, learning is not only encouraged, but is essential.  My lab is an amazing forum for scientific discussion and education, and I find this both personally satisfying as well as motivational.

What is the most challenging aspect?
As I think any researcher can tell you, science can be a harsh mistress.  Research has been a continuous lesson in perseverance, but fortunately the successes (even the modest ones of my experience) far outweigh the failures.

What’s on the horizon in your line of work?
As I mentioned, computational research is an increasingly powerful and essential tool in research, and I believe as it continues to mature it will become mainstream in more and more fields of research.

Any advice for students interested in your field and science in general?
I have a great deal of advice for students interested in MD-PhD programs, too much to include in a brief interview.  For those interested in science in general, my advice is not to pigeon-hole yourself too early on.  It’s impossible to know if you’re interested in a field until you’ve been properly exposed to it, and I think it’s important to gain a diversity of experience before honing in strongly on one area in particular.  Even if your experience with an area leads you away from it, there are always lessons and skills that you can carry with you from any scientific situation.

Many thanks go out to Stephen. Stay tuned to learn more about his research and for future installments of Better Know A Scientist (index).

Posted by Tim Roth, author of the political blog Think Anew and Act Anew

French paradox

Despite having diets rich in saturated fat, the citizens of France have a remarkably low incidence of coronary heart disease. This is known as the French Paradox.

There are many researchers who believe that the ingredients of wine in regions of France play a role in this paradox. In a recent article, I talked about an ingredient called reservatrol that is found in higher amounts in red wines. Reservatrol is very promising, but this may not explain the French paradox because reservatrol isn’t found in significant amounts in most wine. On the other hand, there is significant amounts of procyanidins in wine. They belong to a class of compounds called polyphenols that are found in plants are believed to protect blood-vessel cells. Interestingly enough, some of most procyanidin-rich wines are found in wine grapes found in South France.

Not surprisingly, it’s not as simple as drinking a few glasses of wine. French diets are rich in folic acid, their portion size are smaller, and the beautiful Mediterranean climate of Southern France leads to more aerobic activities like hiking and bike-riding. However, the moderate consumption of wine definitely helps explain the French paradox.

Stay tuned for more on this subject, especially since I’m now convinced to starting drinking more red wine.

Like every article on the health benefits of alcohol, I must also stress that going beyond low amounts of alcohol on a regular basis is unhealthy for a very long list of reasons.

The consensus opinion for safe, moderate alcohol consumption is currently no more than 2 drinks of day for men and no more than 1 drink a day for women. If you have any health conditions, definitely consult your doctor. While taking nutritional supplements like grape seed extract isn’t nearly as fun as good-tasting wine, drinking wine for health reasons might not be a good idea for you.

Posted by Tim Roth, author of the political blog Think Anew and Act Anew

1. “Alcohol”, Harvard School of Public Health
2. “French paradox”, Wikipedia entry