These are just some of the beautiful murals adorn the outside of the labs at Schmahl Science headquarters.

Let’s say you’re a student who wants to do a biology experiment for a science fair. Maybe you want to figure out how a certain cancer works or engineer a drought-resistant plant or any other sort of higher level experiment. How in the world do you get started and then do the necessary experiments?

If you know a biologist, then you can get them to help you. Unfortunately most folks don’t know any scientists let alone biologists. What interested people usually have to do is start cold-calling institutions and universities, hoping to find someone willing to help. This is rarely successful.

But if you’re in the South Bay, there is another possibility – Schmahl Science. For around $40/hour, you can do your experiment with the help of a mentor in the lab facilities at Schmahl Science headquarters.

The price is a bargain by science standards but still ain’t cheap. For example, a cancer project can end up costing upwards of $3000! There are scholarships available and there is a sliding scale based on family income, but it will still definitely cost you. However, if you’re interested in doing a top notch science fair project and learning more about science as a career, you can’t beat it.

I recently had the chance to take a tour of the facilities and chat with the executive director, Belinda Schmahl. My first impression of the place was that it was a bit ramshackle. It seemed to have been cobbled together from various spare parts into a Frankenstein sort of creation. This is because it was.

They are able to keep prices so low (and really, they are low) by using other people’s castoffs in a location that is a bit off the beaten track. What it lacks in finish, though, it more than makes up for in personnel.

I was incredibly impressed with the mentors I spoke with. They were knowledgeable and very excited about their students’ projects. And I can see why.

One student I saw there was working on a biochemical experiment to test how well various sunscreens actually protect people from harmful ultraviolet light. One mentor told me about a successful experiment a student had done to generate electricity from bay mudflats. Another mentor told me about a student’s project that was exploring how houseflies were able to fly. Still another told me about a student’s project on the effects of the herbicide RoundUp on certain bacteria rice needs to grow. And so on.

Of the 100 students mentored for the Synopsys science fair last year, 78 received some sort of award. This gives you some idea as to the quality of the work and the guidance each student receives.

These are incredibly interesting and important experiments that the students would not be able to do on their own. What a great service this organization provides for the community. I hope one day it can be cloned over and over again so more students can experience the thrill and excitement of science.

More information on the program

Recent winners of the Synopsys Science Fair. Wow.

Do-it-yourself biology at Biocurious. Photo credit: Maria Chavez.

Let’s say you want to do a little “do-it-yourself” biological tinkering. Maybe you have an idea to make bacteria that can sense or even break down mercury in the environment. Or you want to attract funding for your start up with a few choice experiments. Or you just always wanted to do some biology. Where can you turn?

For people like me, it’s easy. I work for Stanford’s Department of Genetics and so if I were so inclined, I’d have access to the labs there. But this obviously isn’t a typical situation.

For everyone else (at least here in the Bay Area), there is an organization called Biocurious. They are an open lab located in Sunnyvale where you can go and do some biology experiments.

For a monthly fee (currently around $100/month for a year subscription) they provide the equipment, a lab bench and office space. You also get free classes from experts to help you get started.

This lab space is great for folks with some previous lab experience and/or who have an idea of their own they’d like to get started on. The equipment is all there for them to get started and they even get 15% discounts on any reagents they need. Stuff like restriction enzymes, Taq polymerase, nucleotides, etc.

But at least for right now, the space/concept isn’t as useful for the uninitiated. If you just want to come and play, it can be hard to know what to do. Sort of like wanting to design a mobile app but having no experience and having never used one!

One thought I had was maybe membership can come with an optional, relatively simple project that can be done to get the member’s feet wet. Maybe using the mixable and matchable bits of DNA from BioBricks to create a unique, artificial gene. That way the member could create something new but not have it be some cookbook, high school experiment.

This was just one idea off the top of my head. The folks at Biocurious know this is a problem and are brainstorming solutions. Can you think of ways that might help a newbie get started? What would it take to entice you to come join the fun?

Great interview with Eri Gentry, founder of Biocurious

Citizen scientists solved the structure of a viral protein that had been stumping scientists for a decade using the video game Foldit.

Now don’t get me wrong, the system works very well. It isn’t perfect especially as results are based on more complex data but it is self correcting and important discoveries are made all the time. But would it be even better if we opened things up a bit?

A recent story about how gamers solved a scientific riddle that had eluded scientists for ten years suggests that more transparent science might be better science. And this is the goal of the Open Science movement.

I had the opportunity to interview Joseph Jackson about this open science movement and about his upcoming conference, the Open Science Summit. Joseph is a philosopher, entrepreneur, and activist in the Open Science movement. He is the founder of the Open Science Summit, which occurs for the second time on October 22-23, 2011 in Mountain View and co-founder of BioCurious, the Bay Area biology lab for citizen scientists.

Below is an email interview I did with him where I ask about his upcoming summit, what the open science movement hopes to achieve and how someone can get involved if they are interested. Enjoy!

What is the Open Science Summit?

Joseph Jackson at his lab in Menlo Park, CA. May 17, 2011

The Open Science Summit gathers a broad coalition of individuals and organizations striving to transform our science and innovation system to be radically more effective. We examine the biggest opportunities for distributed collaboration and problem solving, while considering the barriers and obstacles standing in the way of the transition to a more fully Open Science paradigm. This year's Summit covers many topics including the future of scientific publishing and peer review (Open Access), data sharing and the future of data driven science, the effects of the patent system on innovation, personal genomics, collaborative (Open Source) models for drug discovery, and new transparent models for clinical trials.

What is the Open Science movement trying to achieve that the current scientific system can't?

By definition, to function, science is supposed to be Open. Indeed, science is arguably humanity's greatest achievement, our most successful, Open Process, for discovering the truths about our universe and then harnessing that knowledge for the benefit of all mankind. In contrast to other human processes (politics, which is an intrinsically contentious undertaking focused on controlling and distributing scarce resources), Science is supposed to be an objective, essentially collaborative endeavor, in which, even when competing, all participants are building on the efforts of one another to improve our collective understanding of reality. In practice, of course science has always been subject to manipulations, government or corporate agendas, distortions, human biases, and other messy realities.

We have the chance to adopt new models and build new institutions better suited to conducting distributed, massively data driven, collaborative science in the 21st century. This means we have to change the incentive structures and reputation systems that govern science; moving away from old metrics like impact factor (which has a near death grip on scientist's career prospects) and toward new ways of measuring reputation that reward participation in other kinds of scientific activity that are new of critical importance (commenting on articles after publication,scientific blogging and communication to the public, data curation, and more).

Do you see Open Science replacing the current system or complementing it?

In the long run, Open Science will transform the way science is done, enhancing the best aspects of science, while helping correct potential abuses and distortions. There are many interrelated components of Open Science, and I don't expect everyone to embrace every part of the vision. Rather, there is a continuum of openness and we're exploring how to improve each dimension of our innovation system by increasing collaboration where and when we can. Quite often, people seize on one aspect or particular argument about Open Science and may have a defensive reaction. They may have a very strongly held or even instinctive position about the role of the patent system or the sanctity of peer review and protest that "X" reform will never work because of "Y and Z" when in fact, all of these components are evolving together: Open Science isn't naively proposing that we abolish a particular institution while holding everything else constant…of course this won't happen overnight.

There is immense inertia surrounding the way science is conducted, measured, and rewarded. Many understand that it is time to embrace change; let's just hope that we don't reprove Max Planck's dictum once again in this context: "Science advances one funeral at a time."

What do you see as the dangers of having people able to do biological experiments in their garage? The benefits?

The idea of garage biology has received tremendous media attention in recent years, as journalists conjure overhyped images both positive and negative ( garage hobbyist as economic savior creating the next billion dollar enterprise or curing cancer vs. the crazed "biohacker" terrorist unleashing a pandemic).

Freedom of scientific inquiry is vital to our society and economy. As terrifying as the thought of garage biology gone wrong is, it is unlikely that regulation is the solution to this concern. Instead, restricting the ability of responsible individuals and groups of independent citizen scientists to conduct research, will not make us safer; though it will make us poorer, both intellectually and materially.

How can your organization help people do science on their own if they are interested?

We're holding a series of classes to introduce the public to the fundamentals of modern biotechnology. Certain activities are best done in a group setting, especially when you are first starting out. We're also able to take care of proper disposal of any waste that may be generated.

Biological experiments are expensive. What resources are available for people who want to do this on the cheap?

Of course, I'll say the best way is for you to come on down to BioCurious in Sunnyvale, where we have everything you need to get started. Additionally, there are a number of great science education companies that sell kits that can help you get started. In San Jose, for example is The Science Shop. Carolina Biology is one of the oldest education companies in the US and more recently, one of our own BioCurious team has launched cofactor bio, a store aimed at the hobbyist biologist.

Stanford researcher Ingmar Riedel-Kruse. Photo by L.A. Cicero

Games are practically omnipresent in our society, filling our social networks, computers and phones. A team led by Stanford researcher Ingmar Riedel-Kruse has taken gaming to an entirely new level, introducing life itself into games.

Riedel-Kruse and his lab have developed the first biotic video games. The player's moves directly influence the behavior of living micro-organisms in real time as the game is being played.

Players are able to influence the basic biological functions of single-celled organisms. The team's goal is for players to learn about biological processes and interact with them without having to go through the rigorous process of formal experimentation.

In total the team has created eight different games that allow players to interact with paramecia (the single-celled organisms used in numerous biology experiments). In one of the games, paramecia move around a small fluid chamber. A camera collects images of the paramecia moving around and sends the images to a video screen that has a game board of a soccer field superimposed on the image. A microprocessor tracks the movements of the paramecia and keeps score as the paramecia "kick" the virtual ball around with their movements in the chamber.

In Biotic Pinball, the player injects a chemical into the fluid at calculated moments, causing the paramecia to swim in one direction or another.

If you're worried about the effects these games may have on single-celled organisms, Riedel-Kruse assures that these organisms have neither a brain nor any ability to feel pain, so they are not causing any harm.

Riedel-Kruse tells the Stanford University News:

"We hope that by playing games involving biology of a scale too small to see with the naked eye, people will realize how amazing these processes are and they'll get curious and want to know more…the applications we can envision so far are on the one hand educational, for people to learn about biology, but we are also thinking perhaps we could have people running real experiments as they play these games."

To learn more about the biotic games being developed, check out this video.

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A tree branch covered in nitrogen-loving lichen. (Credit: Martin Hutton)

Pollution from cars and trucks blows into the Sierra Nevada mountains, where it can have a dramatic impact on the ecosystem. In Yosemite National Park, researchers are trying to gauge that impact by using an unexpected tool: a fungus called lichen.

Yosemite Valley is known for its granite landmarks: Half Dome, El Capitan and the sheer walls that surround the valley. But according to botanist Martin Hutton, the granite isn't really visible.

"Basically what we’re looking at is lichens. We barely even see this rock. It’s all lichens."

Listen to the QUEST radio story Lichen Point to Pollution.

The southern walls of Yosemite Valley are covered in black crust. Last year, Hutton repelled hundreds of feet down the cliffs to survey the species living here. "All sorts of different colors. All sorts of different shapes. They're really special. There are no trees up there. There's no shade." Hutton says there are more than 500 species of lichen in Yosemite and many grow where few other plants can.

Lichens Connected to the Air

Despite looking tough, lichens are some of the most sensitive organisms in the ecosystem. Hutton uses a fallen tree branch to point out the species living there. "I see really deep saturated orange and that is Caloplaca. And there's just this beautiful just deep saturated yellow and that is the yellow of the Candelaira."

The yellow lichen, Candelaira, is warning sign for Hutton. "If you were to go to place with very little air pollution, then you would not be seeing this many of these Candelaria species," said Hutton.

While most plants get nutrients from the ground, lichens get much of what they need from the air. "They are basically directly connected to the atmosphere. They're connected to all of it. They see all of it. It’s one of the reasons they’re so sensitive," said Hutton.

Lichen are sensitive to changes in the air, especially from air pollution. That makes them an indicator of bigger ecosystem changes. Hutton and his team are taking lichen samples at 300 sites around the park and analyzing them to see what story they tell.

Measuring Pollution in the Ecosystem

Further into a nearby pine forest, Hutton and his team have set up funnels that collect air pollution samples. But it's clear something else has gotten there first. Hutton's equipment is strewn across the ground, the victim of a curious black bear.

"Yeah, basically a bear grabbed this funnel and plucked it off the stake. They just want to make sure that there's no food associated with this plastic funnel," said Hutton.

This is one of 12 sites where researchers are measuring a key ingredient of air pollution: nitrogen. Nitrogen oxides are produced by car and truck exhaust. In Yosemite, nitrogen pollution isn’t only from nearby cars. It also arrives from elsewhere in the state.

"We all have experienced the westerly winds that happen that blow stuff essentially from over the ocean, across the Central Valley and up into the mountains," said Lee Tarnay, Air Resource Specialist at Yosemite National Park.

Air pollution from urban areas is blown into the Sierra Nevada mountains by those westerly winds. And the problem is: nitrogen pollution is sticky. "That gas likes to stick to pine needles and just about anything else. And these trees act as a giant collector for the gases that stream through the air," said Tarnay.

When it rains, the nitrogen pollution is washed off the pine needles and deposited on the ground. As any backyard gardener knows: nitrogen is a fertilizer.

"All plants need nitrogen to grow. And some plants need a lot of nitrogen and some need only very little. And so in Yosemite, we already had enough nitrogen to begin with," said Hutton. Sierra Nevada forests are adapted to low levels of nitrogen.

Impact of Nitrogen Pollution in the Ecosystem

"We're worried that additional fertilizer in Yosemite could have effects that we might not anticipate. We think that the Yosemite is system as is it should be now. So we want to make sure that if there's something harming or changing that balance, then we want to know that," said Hutton.

Hutton says that balance is already under threat by invasive plants and many respond to higher nitrogen levels. Nitrogen can also encourage more ground plants to grow, a major concern in fire country. "If you increase the amount of nitrogen, you have plants that basically fill up the space in between these natural patches. And so that means that fires can spread a lot better."

Reducing car traffic in Yosemite could help cut air pollution. It will also depend on regional air districts across California, several of which, like the San Joaquin Valley, exceed federal air pollution limits. Hutton says he's hopeful that research in Yosemite will help them identify pollution hotspots and manage the changes in the field.

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Tamalpais Manzanita, Mount Tamalpais State Park. Photo: randomtruth.

Serpentine, California’s state rock, is feeling some pressure—and not just because it’s a metamorphic rock! The California Legislature is considering a bill that would strip serpentine of its state rock status; geology blogger Brian Romans explained the details in this recent QUEST blog. Basically, proponents of the bill say that because asbestos is made from serpentine rock, and asbestos causes cancer, serpentine should not be the state rock. Never mind that serpentine does not cause cancer. In fact, many organisms thrive on serpentine soils. And that is what today’s post is about—the unique plants and animals that call serpentine soil home.

Serpentine soil is a tough environment: the soil is coarse, so water runs right through it, making it very dry. It is often dark in color, so it heats up in the sun. And its chemical makeup is challenging to plant life, to say the least. The soil has high concentrations of heavy metals, like nickel, iron, and chromium, and low concentrations of nutrients, like nitrogen and phosphorus. It is also really high in magnesium, which makes it hard for plants’ roots to take up those already-scarce nutrients. And it is low in calcium, which causes ion balance problems for plants.

With nutrients scarce, serpentine inhabitants tend to be small in stature—it’s hard to grow big without much food. And, with low water availability, serpentine plants are drought-tolerant. They often have tough little leaves, which don’t lose much water. Some examples are the Tamalpais manzanita (Arctostaphylos montana), and the Leather Oak (Quercus durata).

Plants on serpentine soils also have to deal with those heavy metals, which can interfere with metabolic processes. Some plants, like the Milkwort Jewelflower (Strepthanus polygaloides), have a really high tolerance for heavy metals. Milkwort Jelweflower is a nickel hyperaccumulator—it can take up lots of nickel from the soil, with no ill effects. In fact, some serpentine plants are used in bioremediation; people plant them in contaminated soil, where they pull the heavy metals out of the ground and sequester them in their tissues.

Serpentine soils are home to many endemic species—species that live in a particular habitat type, and nowhere else. Sometimes plants or animals are limited to one habitat because they can’t survive the physical conditions of other habitat types. But in the case of serpentine endemics, many can live in other habitats’ nutrient-rich soils, but are total weaklings when it comes to competition with other plants. They can’t live in other habitats simply because they are out-competed.

Serpentine soils are home to more than just plants—there are butterflies, too, like the beautiful California White (Pontia sisymbrii). Some, like a rare variant of the Edith’s checkerspot butterfly, Euphydryas editha luestherae, are serpentine endemics, because they lay their eggs exclusively on plants living on serpentine soils.

The Geoblogosphere is buzzing with commentary about California’s serpentine bill. If you feel passionate about keeping serpentine as the state rock, by all means write your state representative—but also visit some serpentine habitat! There are lots of places in the Bay Area where you can check out serpentine soils and their inhabitants. There are serpentine outcroppings on Mount Tamalpais, Mount Diablo (be sure to check out QUEST’s Mount Diablo State Park Exploration!), and in the Berkeley and Oakland hills.

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Dowd explores the idea of sin as going backwards on the evolutionary track and that when we are sinning we let the primitive, instinctual, aggressive, fear-driven part of our brain take charge.

Call it the Devil, or evil, or sin, or whatever, something is not quite right in the world. Read a newspaper or turn on the news. Study history. Study your own history. Live life and you’ll find that out. Mystics from all traditions will say that the problem is the way we perceive the world.

Augustine, a Fourth Century Bishop and a Catholic Saint, is credited with conceiving the notion of “original sin”. He found something not quite right in the human mind and human will. But because we have reason, with the help of God, we can chose to do good rather than evil. Julian of Norwich, a Fourteenth Century Christian mystic who lived in Norwich, England, wrote a document describing a series of visions that she had, called Showings or Revelations of Divine Love. Actually, she wrote it about 20 years after she had the visions. She lived in a small room attached to a church. People would come to her to share their problems and pain. She lived through the plague in her town. She would have seen dead bodies in the streets outside her room. But she wrote that sin is “behovely”, or necessary, and that “All shall be well.”

Thomas Merton, a Trappist monk who lived in a Kentucky monastery and died in 1968, thought that life was about recovering our true nature that has been lost. I like this idea of Merton because life, it seems to me, is something like a journey home. As we grow, we can become more comfortable with who we are and less concerned about what others think of us. Paul Tillich, a Protestant theologian and contemporary of Merton thought of sin as separation. We are born separated from our real selves, other people, and God. Modern theologians might add that we also think of ourselves as separated from the Earth and that this sense of separation has led to environmental degradation, species extinction, and perhaps eventually it will lead to our own extinction. Some have called the Devil the Father of Lies. In this case the lie is that we are separated from our best selves, one another, and the Earth.

But what do scientists think about sin? I’ve recently read a book that provided an interesting connection between the biological idea of evolution and sin. The book, by Michael Dowd, an Evangelical Christian, is called Thank God for Evolution. In the book, Dowd explores the idea of sin as going backwards on the evolutionary track and that when we are sinning we let the primitive, instinctual, aggressive, fear-driven part of our brain take charge. We stop thinking and words become weapons; our heart rate goes up and the body releases lots of stress hormones into our bloodstream. Like when we are mad at the person who just cut us off in traffic. We’re not our best selves in these moments, or living as full human beings. And we tend to be selfish and inconsiderate when we’re trying to tailgate the person who cut us off; and we don’t notice the child in the back seat of the other car. Later we might say, “I wasn’t myself”.

(FYI: The Center for Theology and the Natural Sciences at the Graduate Theological Union in Berkeley is sponsoring a two-day event, Exploring the Frontiers of Science and Religion, April 23-24, 2010.)

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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.

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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.

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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

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