Quantum mechanics and Foosball? Credit: RickyDavid.

When I began this story, it seemed pretty simple. I'd heard that scientists at Lawrence Berkeley National Lab were working to mimic photosynthesis and create a man-made version of the process that could supply us with renewable energy.

The premise is to create a "closed-loop" energy system. Artificial leaves would use water, sunlight and carbon dioxide as inputs to create fuels like butane. Those fuels would be used for transportation or fuel cells. And by burning those fuels, we would produce carbon dioxide. The cycle goes on from there.

I never thought that quantum mechanics would enter the picture. That's what I discovered at the UC Berkeley lab of Graham Fleming. He says we have a lot to thank photosynthesis for. It produces the oxygen we breathe and is the basis for the entire food chain on the planet.

Fleming's lab is dedicated to understanding how photosynthesis works so well. And one of the things they've found is that plants are somehow tapping into quantum mechanics to improve their efficiency. It's pretty complicated – but with the help of the folks in Fleming's lab, they helped me understand it through, of all things, Foosball. Here's an audio version of it to help you out.

Listen to the Building an Artificial Leaf radio report online, and listen to our Web Extra: Photosynthesis and Foosball.

David experimenting with EEG

David takes “guinea pig” journalism to super size me heights. He was tested by numerous genetic sequencing companies, had dozens of brain scans, gave gallons of blood for toxicity tests, even had a virtual colonoscopy to understand what “personalized” medicine means for him. His experimentation was divided into 4 categories: genetics, environment, brain, and body.

My favorite experiment was a memory test in which David and I both participated. The study was on how normal aging changes the neural mechanisms of memory and attention; a study run by Dr. Adam Gazzaley of UCSF. His lab uses a combination of techniques including fMRI (functional magnetic resonance imaging -measures blood flow using a big magnet), EEG (electroencephalography – measures electrical signals in the brain), and TMS (transcranial magnetic stimulation – using a magnet to “scramble” regions of the brain).

In this experiment, I was getting an EEG, designed to measure electrical signals of the brain, in this case studying regions controlling memory and attention. I was fitted with a stylish red cap, my head was covered with a conductive gel, and I was seated a few feet from a computer screen. After some careful measurements of my head, I was ready to go.

I was shown either a face or nature scene for a split second, then the screen went blank, then I was shown another face or nature scene. My task was to decide whether the two pictures were the same. Sounds exceedingly simple, but it was far from it. I left absolutely exhausted after just a few hours!

However, my results were excellent. I averaged about 95% correct over 3 hours. According to the researchers, that’s slightly better than the average 18-35 year old. David’s results were about the same, but he is more enthusiastic considering he’s closer to 50. Take a simpler version of a brain age test online.

The Experimental Man with David Ewing Duncan

Where: Atlas Cafe, 3049 20th St @ Alabama St.

When: Monday, October 19th 7-9 PM

Cost: FREE

Details: David Ewing Duncan discusses his new book “The Experimental Man”, his book exploring what cutting-edge technologies in personalized medicine can tell us about individual health and life — past, present and future: genes, environment, brain and body.

David Lindberg, Professor of Integrative Biology at UC Berkeley, and Steve Croft, postdoctoral researcher in the Department of Astronomy at UC Berkeley

How do you connect seemingly separate historical events? Team an astrophysicist and an evolutionary biologist of course. David Lindberg, Professor of Integrative Biology at UC Berkeley, and Steve Croft, postdoctoral researcher in the Department of Astronomy at UC Berkeley will tie these great anniversaries in a unique lecture this weekend.

Starting 14 billion years ago with the Big Bang, Steve will trace the evolution of the universe, from scorching hot gas forming galaxies to the continued birth and death of new stars. David will step in and discuss how the history of our special little planet is inexorably tied to material raining down from space. The water in our oceans, the formation of some organic molecules, and even mass extinctions on this planet have largely been determined by extraterrestrial events. And let's not forget Area 51 (that's a joke!).

Astronomy and Evolution: From the Death of the Dinosaurs to the Stardust in your Bones

When: Saturday, August 15^th 11AM – 12 PM

Where: 100 Genetics & Plant Biology Building, UC Berkeley Campus

Cost: Free

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.

This story marks the first time I've had to use a pseudynm to protect the identity of a horse.

"Disney's" owner's desire for privacy only underscores the stakes here. Performance horses at his level can be worth $60,000 and more. Training, too, is an enormous investment. "Gretchen," as we call her in the piece, has spent years training Disney in English dressage (which, incidentally, makes for some very entertaining YouTube viewing if you have some time to kill). And so when she noticed that her horse's gait had started to suffer, she jumped to find a treatment.

Speed is key here, it was explained to me, because the smaller the injury, the better a horse's chance for recovery. Emphasizing that point is one of the main reasons Gretchen agreed to take part in this program. She says too many owners treat their horses' injuries with ever-greater doses of painkillers, delaying real treatment until it's too late. Gretchen estimated that, including all the preliminary visits and tests, Disney's treatment may reach $7,000.

Davis vets couldn't provide statistics on whether this treatment – injecting a horse's mesenchymal stem cells, drawn from the marrow of the animal's sternum, into the same animal's torn tendon – succeeds in producing new tendon tissue. (Part of the problem is that it's hard to distinguish tendon tissue from scar tissue, seen through an ultrasound.) But if it works, they believe humans may one day have another option for treating our torn ligaments, too.

Listen to the Stem Cells and Horses radio report online, and watch our Web Extra Slideshow.

There is no proven cure for Sudden Oak Death. But that doesn't mean you can't find people selling cures.

In fact, the Internet is full of theories – and their related products – that explain how to treat Sudden Oak Death. The problem with them, says UC Berkeley researcher Matteo Garbelotto, is that they don't work. And in fact, he adds, they could actually harm people's backyard oak trees.

One of the most popular treatments says that part of the problem with oaks is that they're weakened by acidic soils (presumably from acid rain), and the theory is that heavy doses of calcium in the soil could restore natural balance and strengthen trees against the Sudden Oak Death pathogen. In hopes that the theory might bear fruit, the Garbelotto lab recently tested it.

The study found that it did nothing to stop the Sudden Oak Death pathogen. In fact, Garbelotto said, it's like giving a glass of orange juice to someone with a terminal disease. And in some cases, he added, it could have a detrimental effect.

A different Garbelotto study showed that a phosphonate fungicide, brand-named Agri-Fos, can prevent the onset of Sudden Oak Death, for a period of about two years. This is the only product on the market that is effective, he said – not as a cure, but as a two-year preventative.

Some people who love their oak trees decide to try both treatments, Garbelotto said. And since the phosphonate that does work is acidic, and the calcium treatment that doesn't work is basic, then you could end up inhibiting the treatment that actually works. That is, if you use both treatments, he said, the calcium could actually negate the positive effect of the phosphonate.

From 10 a.m. to noon on Sunday, May 16, Garbelotto will lead a "Sudden Oak Death Blitz" at the East Bay Parks Botanic Garden in Berkeley's Tilden Park. The event, sponsored by the California Oak Mortality Task Force, trains participants to spot vegetation infected with P. ramorum and collect samples for testing. The training is useful for homeowners who want to monitor their own trees for Sudden Oak Death.

Listen to the Sudden Oak Death radio report online.

Scientists gather samples on the ocean floor.
Credit: Roger Linington.

What's different about the work being done at the UC Santa Cruz Chemical Screening Center is that it a) looks to a largely unexplored medical resource: the ocean, and b) uses robots, rather than "forlorn-looking grad students" (to quote Center director Scott Lokey) to run the tests.

Here's a video I shot of one of those robots in action, with Lokey narrating.

One thing that didn't make it into the piece is that these researchers — including Lokey and Roger Linington — aren't just studying every disease they can think of. They focus on the diseases that commercial drug companies tend to neglect because there's so little profit in treating them – things like African sleeping sickness and cholera. So far, they're seeing progress on both, as well as breast cancer.

Listen to the Medicine from the Ocean Floor radio report online and check out images from this story in an online slideshow.

Animals generally receive diets that are rich and varied.

Few images will stay as indelibly with me as the sight of a 500 pound grizzly bear devouring a horse bone while standing waist high in water. I should add to that the sight of a geriatric koala slurping his eucalyptus meal. In the aquatic realm, there's something ineffably captivating about watching an anemone's candy-pink arms wrap around its lunch of grain-sized krill.

Witnessing the feeding scenes firsthand, I marveled at the bewilderingly diverse array of mammals, reptiles, amphibians, birds and insects that are fed every day at zoos and aquariums worldwide. Fortunately, to facilitate the feedings and developments of diets, today there are tools like Zootrition, a software program developed by the St. Louis Zoo that allows for the nutritional evaluation and comparison of various diets. Then there's ZuPreem, a manufacturer of ready-made meals for exotic animals. A perusal of their web site reveals such tasty items as "Primate O's" (naturally preserved with vitamins C and E), canned monitor food (boasting nutrient levels comparable to "a mouse in a can"), bags of dry omnivore diet for the hungry bear or boar.

The upshot of this is that animals at facilities accredited by the Association of Zoos and Aquariums generally receive diets that are rich and varied, frequently monitored for the effect they have on the animals to whom they’re served. Not surprisingly, many animals at zoos and aquariums live longer in captivity than they would in the wild, not only because of the high level of care they get in captivity but also because they are safe from predation in the wild.

Jacquelyn Jencek, Chief of Veterinary Services at the San Francisco Zoo, shared with me an amazing story of how they greatly expanded the longevity of koalas with an intervention that has been emulated at other zoos throughout the nation. Most koalas in the wild don’t live past thirteen years of age, when their teeth have been ground down from years of eating coarse eucalyptus leaves and they no longer have enough dental surface to break down the leaves and extract their nutrients. Thus, even if they attempt to eat the leaves, they can still die of malnutrition. So the SF Zoo decided to help the koalas by breaking down dried eucalyptus leaves with a coffee grinder and mixing the powder with water and supplements, turning it into a solution that could be fed by vial to geriatric koalas at the zoo. The zoo first tried administering the eucalyptus solution to Clarry, who lived to be nearly 20 years old, and is now giving it to Clarry's son, Leo, and a few other koalas whose longevity attests to its success. According to Dr. Jencek, "they love the taste of it", and it's clearly good for them.

The story affirms for me the bond of trust that exists between the animals and the zoo and aquarium personnel who take care of them, and how there’s nothing cookie-cutter about feeding the animals and creating their diets.

Watch the Animal Chefs television story online.

Scientists used evolutionary theory to figure out where
to find the bones of this fishibian.

What is so great about this book for a scientist is that it gives the big picture on evolution. This sort of thing can be hard to get sometimes because we scientists are so specialized. As I like to tell people, I worked on a single amino acid of a single human protein for my postdoctoral project. For three years.

Coyne's book synthesizes genetics, anatomy, biogeography, physiology, paleontology, geology, and lots of other "ologies" to show how strong the case is for evolution. This is great for me because, of course, I tend to focus on genetics and molecular biology and spend less time on the other fields. Which means I miss important, subtle nuances to some big findings.

For example, I had heard about the fossil of Tiktaalik roseae that was found in 2004 that linked fish to amphibians. This was a huge deal because the animal that the bones came from had characteristics of both fish and amphibians. And it appeared in the fossil record at the right time to be a transitional animal between the two.

What I hadn't fully appreciated was that the scientists decided to look where they did based on how old they thought the fossil should be. In other words, they were able to use the theory of evolution to predict where to find the fossil they were looking for.

They knew from previous fossil finds that something like Tiktaalik roseae would have appeared between 360 and 390 million years ago. The scientists also knew from previous research that the beast would have been in freshwater. So they got out a geological map and looked for places that met these criteria. They settled on Ellesmere Island in Canada and after five years, they found this marvelous fossil.

This is important for a lot of reasons. One is that it obviously tells us a lot about how vertebrates emerged onto dry land. Another is that it provides further validation of geological dating methods. They had to rely on these methods to know where to look for the fossil and the methods worked.

This find is also important because it is based on a prediction made by evolutionary theory. Around 390 million years ago, the only vertebrates were fish. By 360 million years ago, there were four-footed vertebrates on land. So the scientists looked in a place that was 375 million years old.

Scientists used evolution to make a testable prediction that turned out to be true. And evolution came through with flying colors like any good scientific theory should.

This month marks the 200th birthday of Charles Darwin and the 150th anniversary of On the Origin of Species. If Darwin were alive today, I think he would be very pleased.

He would undoubtedly be very excited about everything we've learned about biology since his time. Like the rest of us, he would be awed by the beauty, grandeur, and complexity of life on Earth.

He would also be pleased that his ideas about natural selection and evolution are to date the only scientific explanation for all of this. His ideas pervade every aspect of modern biology from medicine to genomics to ecology.

His theories dominate because they are supported by mountains of evidence (Read Why Evolution is True to find out more about the data that supports evolution. You can click here for a review of the book.). The evidence in support of evolution is so overwhelming that there is no real debate about it among biologists.

Of course, like any scientific theory, not every "t" is crossed nor every "i" dotted. But that is more of a reflection on how science works rather than the theory itself.

A scientist gathers some data and then proposes a hypothesis to explain that data. Then the scientist does some experiments to test the hypothesis. The new data either supports the hypothesis, requires that the scientist modify the hypothesis to fit the new data, or requires the scientist to come up with a new hypothesis that better explains the data. Then scientists repeat this process over and over again until the hypotheses can be unified into a theory.

This has gone on for 150 years or so for evolution and if anything, evolution is stronger than it was before. Sure, every now and then a hypothesis within the theory needs to be modified but the theory remains as strong as ever.

In fact, no point of contention has yet been raised that is the straw that will break evolution's back. And there is nothing obvious on the horizon that will.

Darwin would also probably not be surprised that his theory remains controversial because it seems to fly in the face of a Creator. Which is of course nonsense. Despite worries about how Earth being the center of the Universe would cast doubts on the Creator, Christianity survived Copernicus and Galileo. And it will survive Darwin as well.

I heard this interesting interview on NPR over the weekend with Richard Dawkins about his book, The God Delusion. In the interview, Dawkins states that it seems unlikely to him that God would create a Universe that could be explained by natural causes. I disagree.

My understanding is that Christianity is based on faith. If a Creator made the Universe in such a way that scientists could show the Earth was 10,000 years old, then of course a Creator exists. That is the only possibility. So where is the faith in that? How would it be different than the Creator greeting each person and welcoming him or her to the Creator's Universe?

To me it makes sense that a Creator would make a world that was or could be formed naturally. In which case it doesn't really matter scientifically whether life arose on Earth through a Creator or by chance. Both ways require evolution. Thank you Charles Darwin for giving us this great framework within which we can understand life here on Earth.