Zoloft is a popular drug used for the treatment of depression symptoms.

Depression is hardly new. The Roman physician Galen, in the second century A.D., expounded on the prevailing medical view that four bodily fluids, or humors, existed within all people but that the unique variation of these humors within people resulted in individual differences among people in their behavior and temperament. An excess of black bile, for example, indicated a melancholic personality.

Fortunately, a lot of scientific progress has been made since then in understanding depression to be an organic, brain-based medical condition that afflicts millions. In fact, an individual has a ten to fifteen percent lifetime risk of developing a major depressive episode. But as Dr. Karl Deisseroth, a Stanford neuroscientist and psychiatrist, told me during our interview for “Illuminating Depression”, “Diagnosis is a big challenge because in psychiatry, we don’t have a lab test. There’s not a blood draw that you can do as you might to check how your liver is doing or how your thyroid function is doing.” So given that the diagnosis of depression is based on clinical observation (most often done by a primary care physician), one can’t help feel that hard, empirical understanding of depression is somewhat lacking, especially when compared to diseases of other organs like the heart and lungs where tests do exist to gauge the presence of pulmonary and cardiovascular diseases.

This was the most interesting observation for me when working on this story. Imagine a medical disease that afflicts eighteen million people in the U.S. (26 million if you include Bipolar Disorder), for which more than 160 million prescriptions were filled in 2008, that is one of the leading causes of disability in the U.S., but a disease for which no definitive medical model of pathology exists. Increasingly, doctors are prescribing antidepressants to treat not just depression but a host of other medical conditions, including chronic pain and insomnia, some of which can co-occur with depression. Sure, we’ve made strides since the time of Galen’s bodily humors and the Freudian view of misplaced hostility and mourning to explain depression, but in some respects, we’re still in the dark about why some people get depression while others don’t, why some people respond to one treatment and not another, or why one person will suffer from a form of depression that is less or more severe than another person. This lack of clear, empirical understanding comes at an awful price to victims of depression, as they encounter remarks from people that tell them to “snap out of it”, implying that they somehow can control the emotional crumbling and dark ideations that accompany the disease.

The consequence of all this is that it’s incredibly tough to create effective, lasting treatments for the disease if we can’t exactly track how the disease affects not only specific regions of the brain but the activity among individual brain cells in regions that may not have even been known to play an integral role in the disease. My layperson’s view is that treating depression currently is a bit like bringing in a car to the mechanic and telling him to fix it but there’s a catch – the mechanic can’t get under the hood to observe directly what’s wrong with the car. We suspect that the problem is with the engine but good luck with opening it up and peering into its pistons. So the mechanic attempts to work on the engine but indirectly, and whatever repairs are attempted may affect the engine but they may also have unwanted effects on the car’s transmission, muffler, timing belt, etc.

Fortunately, advances in imaging techniques like two-photon microscopy and fMRI are elucidating the activity of the depressed brain, allowing the previously impenetrable forest of billions of neurons to be explored, to see their pathways altered, their branches pruned by the disease. And scientists like Philippe Goldin and Kelly Werner are compiling biomarkers like DNA and brain blood flow activity to see if those biomarkers can help predict if people suffering from anxiety and/or depression will respond more favorably to cognitive behavioral therapy than to mindfulness meditation, for example. Dr. Deisseroth is using genetically engineered, photosensitive proteins implanted into rodents’ brains to control brain activity at the level of individual neurons.

Dr. M. Bret Schneider told me during our interview, “A real cure for depression is gonna involve being able to selectively affect those portions of the brain which don’t function properly in depression… But fathoming the huge number of possibilities in each brain with every brain being a little bit different than every other one, is gonna require individualized solutions and will be a scientific feat.” I suppose that with a disease as complex as depression, where one’s individual genetic makeup can influence the kinds of side effects one may experience with an antidepressant, it’s apropos that the future of treating and eventually curing it will entail personalized medicine. Until then, let’s hope that more people bring psychiatry into the research lab to study illnesses like depression, for it’s only through the methodical rigor of science that we have the best hope for curing depression.

Watch the Illuminating Depression television story online.

UCSF biologist Jeff Tabor holds up an ecoli culture designed to display the shape of a squid.

Synthetic biology portends big changes in our lives by ushering in a dizzying array of applications in everything from medicine to biofuels, environmental remediation to agriculture. Though many of these applications haven’t yet come on line, researchers are hard at work to synthesize new drugs and devices made from genetic parts.

For example, there’s an enzyme that exists in plants which makes methyl halides, a molecule which can be catalytically converted into gasoline and other chemicals. Imagine if you could put this enzyme-making gene into yeast, then you could brew the yeast to churn out the methyl halides and after some optimization of the production pathway, you could scale up production to pump out this carbon neutral gasoline precursor for use in today’s automobiles. This is the idea behind an innovative biofuels project that has taken off in the lab of Chris Voigt at UCSF’s School of Pharmacy.

Voigt and his team surveyed the genetic database for the presence of the gene that encodes for the enzyme that makes methyl halides. Lo and behold, the gene exists in plants as diverse as ice plant, which dots the northern California coast, bok choy and pinot noir grapes. After building a library of about 100 enzymes from these diverse plants, the researchers had to determine which of these would function best in the yeast. They zeroed in on an enzyme from ice plant and then used the tool of DNA synthesis to translate the gene for the enzyme that makes methyl halides into something that would work in yeast.

The remarkable thing about this project is that the researchers never actually touched any of the plants. They simply “Googled” a genetic database to find all the genes out there in plants that produce the enzyme that makes methyl halides. As Professor Voigt says, “it’s incredible that synthetic biology is something that could really unlock the potential of using organisms in order to produce fuels.”

Watch the video made by the Voigt Lab demonstrating the combustible property of their synthetically derived methyl halides:

QUEST on KQED Public Media. Video courtesy of
Prof. Chris Voigt, UCSF School of Pharmacy

Watch the Decoding Synthetic Biology television story online.

The Stanford Linear Accelerator. Credit: SLAC.

On the heels of the opening of the Large Hadron Collider last year, I was curious about these particle accelerators: how they work, what research is conducted there, and most importantly why.

Luckily, there is a particle accelerator right here in the Bay Area. Last year, I took an intrepid group down to the Stanford Linear Accelerator (SLAC) to learn more about the these giant expensive research labs.

SLAC maintains an extensive public outreach program. An extensive tour (mine was 2 hours with very in-depth exploration of the facility), public lectures, weekly colloquia, and even science competitions for high schoolers.

I was surprised to find a wealth of research beyond the typical particle colliding at the facility. Many researchers use the state of the art facilities to study basic elements of our life, including water.

On Tuesday, Anders Nilsson is discussing his research on water at SLAC, an in-depth look at some of the stranger properties of water: its high heat capacity, how it is more dense than ice, even insight on using water as a power source (by splitting it into hydrogen and oxygen). Water: The Strangest Liquid, Tuesday February 24th 730-830PM at the Stanford Linear Accelerator.

However, our continued economics woes are threatening physical science research. SLAC is getting the brunt of money cut, missing out on $23 million of requested funding. In response, SLAC laid off 125 of its 1600 employees and shut down its PEP-II collider last year.

SLAC Public Lecture Series
The SLAC Public Lecture Series opens the doors to the inner workings of SLAC for the local nonscientific community. Find out what SLAC is all about: the research, the facilities, and the people that make this a world-class research institute.

SLAC Colloquium
The intellectual watering hole for the entire laboratory, where you can hear talks intended for a general audience on a wide variety of subjects. The colloquium will be returning later this year.

SLAC Science Bowl for High School Students
SLAC hosts an annual Regional Science Bowl for teams of high school students. The Science Bowl is a question-and-answer competition with buzzers, judges, and time keepers for high school teams of 5 students and 1 faculty coach. This year's competition is on February 28th.

SLAC Tour Information
Tours of SLAC will be available again later this year. On the tour, you get an extensive look at the operation of the accelerator, including a peek into the Klystron Gallery.

Is this you in the kitchen?Here in the Bay Area, we're known the world around as foodies, especially given the recent popularity of the Slow Food Festival. As we approach the biggest food holiday of the year, it's a great opportunity to think about the science behind all of these scrumptious meals.

Last year, I stumbled across a new series of lectures on Food Ethics & Environment at Stanford University. Headlining the series was the incomparable Michael Pollan, who led an interactive discussion on the evolution of food culture in the U.S. I was amazed at the level of passion in the audience and moreover the knowledge level of the audience. I left inspired to take my time with food and eat a little healthier (that worked for about a week).

This year, Stanford again delivers a stellar lineup. Over the next few weeks and months– there will be discussions ranging from water, the affect of global warming on our food, fair trade coffee, and even a conversation with a organic farmer (it's Joel Salatin, one of the heroes from the "Omnivore's Dilemma").

So before you give thanks next week, consider a heaping serving of food science.

All events are free. They take place at the Annenberg Auditorium on the Stanford University Campus. The events are usually held on Thursday nights at 7pm. For more info, check out the Stanford Ethics Website.

I was a biologist once, before I got into television, so I find these times particularly trying when I see schoolteachers and otherwise intelligent people calling evolution into question. That's part of the reason that I jumped at the chance to co-produce a story about bio-inspiration (the other reason being that I LOVE geckos…which will make more sense if you watch our QUEST Bio-inspiration segment).

Bio-inspired design borrows its creative inspiration from models and systems in nature, that is, plant and animal parts that have been slowly tweaked for over 3.8 billion years. But that doesn't mean that nature's designs are perfect. In fact, that's what makes the process of engineering things based on natural models so difficult. You have to figure out how to pull the aces from the evolutionary discard pile. As professor Bob Full at U.C. Berkeley explained in our first phone conversation, that's also why scientists now use the term "bio-inspiration" rather than the more commonly known term "biomimicry." Biologists and engineers are not looking to simply mimic nature, because there are all kinds of dead ends and redundancies in natural systems that would be pointless to recreate in an optimized, man-made piece of technology. One of the examples he gave me is a kind of grasshopper that if you were to copy it, you would copy neurons that go to nothing, they don't connect to any muscles, and that's because during evolution the adults lost their ability to fly. The neurons going to the muscles are still there, but the muscles aren't there anymore. No need to copy that, right?

So what a biomimeticist does is look to nature to find plants & animals with remarkable performance abilities, and studies their adaptations for inspiration to design something new. For example, if you want to make a tiny robot that can fly, then look at the best fliers. If you want to design a blade that moves quickly through fluids, or an Olympic swimsuit that minimizes drag, then look to the most efficient swimmers. Now that's what I call "intelligent design!"

Watch the Bio-Inspiration: Nature as Muse television story report online.

The DARPA Grand Challenge is one of the most unusual car races in the world. In this race, the cars drive themselves – no remote controls needed. And the contest is not a game. It could change the way all of us drive. We visited the leading Bay Area team, the Stanford Racing Team, as they geared up for this year’s race.

The race is sponsored by the Department of Defense's research division, known as DARPA. Their goal is to convert one-third of their ground vehicles to unmanned vehicles. That's where the contest comes in– to develop the technology needed for such an application. Early uses could be surveillance on the ground or convoy missions, but they haven't ruled anything out. What are your thoughts on the wartime purpose of this contest?

The Stanford team, like many others, see this technology being used far and wide in the future. The laser sensors that the robots use are much more accurate than human eyes. So, robotic cars could follow each other very closely, which could have major impacts on traffic and the need for new roads. Autonomous vehicles could help elderly and disabled drivers, too. It sounds like science fiction, but scientists are on their way. Would you use a robotic car?

UPDATE: The Stanford Team's car, Junior, took second place in the race this past weekend. I've heard it was a very close race with six team completing the whole course. Check out the full race results or read a San Francisco Chronicle article on the finals.

You may listen to the "Robot Car Race" Radio report online, as well as find more resources. Also, don't miss our behind-the-scenes photos for this story on flickr.com.

Lauren Sommer reports for QUEST and Radio News at KQED-FM.

latitude: 37.4265, longitude: -122.077