QUEST Community Science Blog

Image Source: luxomediaSan Francisco’s got lofty plans to improve safety and convenience for cyclists. And with gas prices rising, parking a headache, and a desire to reduce their carbon footprint, more and more San Franciscans are cycling in the city to work and to do errands. Cycling rose 15% between 2006 and 2007, and injuries from bicycle collisions are down over a 10-year period, according to municipal studies. But the city’s been spinning its wheels to increase bike lanes because a 2006 injunction has barred their installation. And it’s still an uphill climb, even here where environmental consciousness is high, to convince people to cut their car use.

Quest follows a recent convert as they negotiate the treacherous streets of S.F., guided by a member of the city’s bicycle coalition. We add up the gas and carbon emissions they are saving and find out what has prevented would-be riders from commuting on bike. lastly, we talk with city traffic managers and find out what the most bike-friendly cities are doing. Marjorie Sun reports.

You may listen to the “Bike to Work” Radio report online, as well as find additional links and resources. And please share your San Francisco Bike Commute photos with us in our Bike to Work Day Flickr Pool.

Andrea Kissack is Senior Editor for QUEST at KQED Public Radio.

What does our use of bottled water say about us? View our 2-minute TV short “Future History: Plastic Water Bottles” to take a look from the perspective of an anthropologist from the distant future, and the take our poll below:

Josh Rosen is Series Producer for QUEST on KQED Television.

Making Every Photon Count

Last week I went to a talk given by the leader of the Supernova Factory collaboration at LBNL. What is SN factory? This is an ambitious project to study supernovae like never before. I mentioned this project briefly in a previous post , now that they are so close to releasing their results I want to discuss it a bit more.

The main idea of this project is to study several hundred nearby supernovae using an instrument known as the Supernova Integral Field Spectrograph, or SNIFS. This type of instrument is essentially a blend between a traditional imaging camera and a spectrograph.

The resolution in an integral field spectrograph is defined in spaxels instead of the pixels that have become all too familiar with the advent of digital cameras. A spaxel is quite similar to a pixel, there aren’t nearly as many and each one carries at least a 1000 times as much information.

In your digital camera, the light passes through the lens and directly onto the CCD. Each pixel on the CCD counts the number of photons in the red, the blue, and the green. Typically, there are millions of pixels, each counting photons from a slightly different region of the subject of your photograph.

Now imagine that instead of just counting red, green, and blue, that each pixel counts the entire rainbow of light from your subject. Now you have a spaxel. In an intregral field unit, the light passes through an array of microlenses and prisms before landing on the detector. We would call each set of microlenses and prisms a spaxel. The resulting image carries information about every wavelength of light from every region of your target.

Spectrum of the first SN observed with SNIFSThe advantage to an integral field spectrograph like SNIFS is that you gain a lot more information than either an imager or spectrograph alone. With an integral field spectrograph you can basically identify and organize every photon that reaches the telescope.

Specifically designed to observe supernovae, SNIFS is being operated at the 88-inch telescope on Mauna Kea. Spaxels are quite expensive - this particular instrument has only 225. However, this is more than enough to observe the entirety of a galaxy, a supernova, and the background.

The members of the SN Factory have now observed over 100 SNe using this new camera. Last Thursday, I saw the data from the first 25 well-calibrated supernovae and was very impressed. The data showed the evolution of each supernova and the properties of the host galaxy in great detail. I’m sure the supernova community will be equally impressed when they first see these new results.

Kyle S. Dawson is engaged in post-doctorate studies of distant supernovae and development of a proposed space-based telescope at Lawrence Berkeley National Laboratory.

DNA magnified 850,000 times through a scanning electron
microscope
DNA day is coming up on Friday April 25th. This annual celebration of genetics and genomics was set up in 2003 to commemorate the sequencing of the human genome and the 50th anniversary of the solving of the structure of DNA.DNA day was thought of as an opportunity for teachers, students, and the general public to learn about DNA. And to have fun with it.

This should be a chance to pull DNA out of beef, strawberries, kumquats or even yourself and learn that you have around 100 billion miles* of DNA inside of you. In case you’re interested, that’ll reach from the Earth to Pluto and back when Pluto is farthest from Earth. And that is one person’s DNA.

Add up everyone’s DNA in the world and you get 125 million light years of DNA. (At least I think you do… these numbers are getting ridiculous!) That’ll get us to the galaxy Andromeda and back 25 times. Add up all the DNA on Earth and… OK, that’s probably enough of that.

There isn’t just a lot of the stuff but it is amazing to me how similar all human DNA is. The latest estimates are that people are around 99.5% the same at the DNA level. That means that all those light years of DNA are mostly the same old thing just copied over and over.

Notice the mostly. With 6 billion letters of code in every person, a 0.5% difference means 30 million differences between you and me. It is these differences that make me look different than you. And to a varying degree, make me act differently than you.

This code doesn’t work in a vacuum either. The environment can change how it works which is a big reason identical twins aren’t really identical. And one of the reasons why it is so hard to figure out the genetics of complicated diseases like diabetes or heart disease.

Our DNA also changes with time. Things in the environment might damage it. Or our own cells can make mistakes when they make copies of themselves. What this means is that today’s light years of human DNA will be different than the same stretched out DNA in 100 years.

This also means that you have some cells in your body have different DNA than the rest of your cells. And if a DNA change happens in sperm or egg cells, then they are passed on to the next generation. Which is where all the wonderful diversity around us originally came from.

As you can see, there is a lot about DNA to celebrate. It is huge and mysterious and we’re just starting to get a good grasp on what it is all about.

I plan to spend the morning of DNA day at The Tech Museum in San Jose exciting kids (and hopefully some adults) about DNA by running five different hands on genetics programs all at once. It’ll be a blast!

I have searched high and low for a list of DNA day activities here in the bay area but I haven’t come across any. Does anyone know about other DNA day celebrations here in the bay area?

* Each cell has 6 feet of DNA and we are made up of around 50-100 trillion cells.

Dr. Barry Starr is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA.

There is a lot we don’t know about our DNA and how it works. While there seems to be news every week about genetics, scientists are still in the early stages of finding out what effect our genes have on us (check out this post from another QUEST blogger, Dr. Barry Starr). That’s what the researchers at the Canine Behavioral Genetics Project are doing. But in this case, they’re looking at dog DNA.

It turns out that human intervention in the form of hundreds of years of dog breeding has created a unique genetic experiment. Because purebred dogs are in essence closed gene pools, it’s much easier for scientists to compare of DNA of dogs within a breed. The Canine Behavioral Genetics Project is doing this to find the genes that are associated with behavioral disorders, like anxiety and fear. They also hope to use that information to find the genes in humans that are associated with similar disorders.

Millions of problematic dogs are given up each year in the U.S. And while the UCSF team definitely believes that training is a huge part of dealing with dog behavioral disorders, they’re also hoping to understand the genetic influences. Many owners are starting to use medications to help treat these problems, like doggie Prozac. But Melanie Chang, a member of the UCSF team, made a good point to me. Owners tend to think their dog’s problems are the owner’s fault. Sometimes there are other forces at work.

Listen to “Doggie DNA: Human Genetics through Dogs” online, as well as find additional links and resources. Also, check out the photo set with behind-the-scenes photos.

Lauren Sommer is an Associate Media Producer for QUEST.

Raise your hand if you live in a watershed! Are all of your hands up? We all live in a watershed, an area of land that all water (from rain, snow and springs) flows across, under and through on its way into a common body of water, such as a creek, river, bay or ocean. The water may travel through city streets and into storm drains, over the surface of the ground and across farm fields, or suburban lawns, or it may seep into the soil and travel as groundwater. Along the way, water picks up and carries materials.

Everything we do impacts our watershed. Use of land and water from any part of the watershed, such as polluted run-off from farms, forests, ranches, and cities, eventually affects the health of the whole watershed – as well as the plants, animals and people within it.

A healthy watershed is important to everyone! Animals find food, water and shelter near creeks and waterways. Humans enjoy clean water and places to relax, swim and appreciate nature. One of the best ways to help your local watershed is to connect with it.

So, may I suggest a visit to that creek in your neighborhood for an old-fashioned, low-tech exploration? Bring binoculars, a nature journal, a creek creature identification sheet, and empty baby food jars. Bring some kids and all your senses.

At the creek, sit quietly and listen for the sound that is the nearest or the sound that is farthest away. Can you hear the creek running or the birds calling?

Notice the variety of habitats in the creek. Look for a place in the creek where there is a riffle: a shallow area where water breaks over rocks, promoting high oxygen levels. Invertebrates and the small fish that feed on them live here, in a pool: a deeper area with slower moving water. Pools provide a spawning, feeding and resting site for fish, or a run: a straight, fast moving, section of a creek between riffles that has a diverse mixture of aquatic life. Look for tracks and scat along the creek banks. Use the baby food jars to carefully capture aquatic life. Observe, sketch and release.

Smell the variety of plants and flowers now blooming in the riparian zone. Notice that the bushes, trees and roots are all home to various wildlife. Draw a guide to the plants and trees in one small area of the creek.

Blindfold a friend or sibling and carefully lead them to a tree near the creek. Allow them to touch it, then give them a spin and lead them away. Remove the blindfold and challenge them to find their tree using their eyes.

Find edibles along the creek, like wild onion, miner’s lettuce or blackberry and taste wild food right off the vine.

Once connected, it is easy to care, and help keep our watersheds clean, in simple ways such as monitoring what you allow down the storm drains, refraining from flushing cat feces, or participating in a creek clean up. Please add your own ideas!

The Oakland Zoo has restored a section of the Arroyo Viejo Creek on the zoo grounds with support from City of Oakland, the California Coastal Conservancy, the California Department of Parks and Recreation, Alameda County Flood Control and Water Conservation District, and the City of Oakland Measure DD Bond. With six outdoor classrooms featuring educational signage and seating on logs, the creek will offer an exploration experience for all. Help us celebrate with a ribbon cutting ceremony at noon on Saturday, April 12, as part of the Oakland Zoo’s Earth Day celebration.

See you down at the creek!

Amy Gotliffe is Conservation Manager at The Oakland Zoo.

Last night we completed our observations for the Supernova Legacy Survey. This was a five year program to study supernovae using a 4-meter telescope in Hawaii in combination with several of the largest optical telescopes in the world.

The project was headed by a group at a university in Toronto and a group at a university in Paris. Canada and France sponsor the 4-meter telescope that is used to discover and observe the supernovae from the point of explosion to the final days when the supernova fades from view. We call this the imaging part of the program. This data constrains the apparent brightness and life cycle of the supernova, and eventually the absolute distance to the supernova.

Our contribution to the project was primarily through our affiliation with Keck Observatory. We were typically awarded four nights a year to observe recently discovered supernovae spectroscopically. The data is used to determine the redshift and the kind of supernova explosion.

The supernovae are used to study the rate of expansion of the universe. It was this type of experiment that was first used to discover that the universe is actually dominated by dark energy.

No one really suspected the presence of dark energy for almost the entirety of the 20^th century. Now, we not only know it exists but are actually trying to understand it in the same way we understand gravity, protons, and electrons. That is where projects like the Supernova Legacy Survey come in. With projects like this, we work to collect enormous samples of well-studied supernovae that can improve our understanding of dark energy.

We use a certain type of supernova as yardsticks to measure distances in the universe. We then model the affects of dark energy on the expansion history of the universe by comparing distances and rates of expansion. This comparison is typically represented in a Hubble Diagram.

The Supernova Legacy Survey has been very successful in its attempts thus far. On the right, I show the Hubble Diagram from the first year of data. This is less than 20% of the full sample. The dotted line outlines the expectations of the 1990’s cosmology crowd. The solid line shows the prediction from the more sophisticated cosmologists of the 21^st century. As you can see, the original expectations were pretty far off the mark - the supernovae just don’t lie on top of the dotted line.

Now that this program is finishing up, we should be seeing similar figures that are teeming with supernovae. Future programs should do an even better job of making these measurements. Someday we may actually understand this dark energy thing, it may turn out to be something else completely new and unexpected!

Kyle S. Dawson is engaged in post-doctorate studies of distant supernovae and development of a proposed space-based telescope at Lawrence Berkeley National Laboratory.

A sample of switchgrass at Sandia National
LaboratoriesIt doesn’t need to be said that there’s a heated debate about how to mitigate greenhouse gas emissions with actions that lessen our society’s carbon footprint. Biofuels like ethanol or biodiesel are one option. They’re touted as being carbon neutral because the CO2 they emit comes from crops which had previously sequestered them in the atmosphere. In contrast, petroleum produces CO2 emissions that had previously been buried deep in the earth’s crust, adding to the other green house gases in the environment. For example, the U.S. Department of Energy - citing research by the Argonne National Laboratory – states that ethanol derived from corn emits 25% less greenhouse gas emissions than petroleum and that the savings with cellulosic ethanol, made from a feedstock like switchgrass, are much higher, in effect producing no additional greenhouse gases.

So when QUEST decided to move forward on producing a story about biofuels, I welcomed the opportunity to assist Series Producer Josh Rosen in its crafting. Being QUEST, we weren’t content to merely renumerate the different kinds of biofuels and how cellulosic ethanol is more efficient than corn-based ethanol. Instead, our story focuses on the pioneering work being done by researchers affiliated with the Joint BioEnergy Initiative (JBEI), a multi-billion dollar research initiative based in Emeryville, as they look beyond ethanol to the next generation of biofuels. So not only is JBEI looking at various feedstocks like switchgrass, rice, poplar and innovative ways to “deconstruct” the cellulosic material, it also attempts to synthesize fuels that work more efficiently in America’s automotive fleet, still overwhelmingly reliant on gasoline.

But even top researchers at JBEI like Jay Keasling and Blake Simmons caution that this next generation of biofuels won’t be coming online for years. Moreover, new research suggests that the net production cycle of biofuels, from the clear-cutting of trees to grow the crops to their transport to markets far away, may yield as many or more emissions as the use of petroleum-based fuel. A recent Op-Ed piece in the San Francisco Chronicle by UC Berkeley Alex Farrell cites the reason for this as primarily one of production– the way we clear land for growing biofuels, as well as our emphasis on the use of food-based crops like corn and soybean, which aren’t terribly efficient sources of ethanol to begin with.

Tad Patzek, also at UC Berkeley, has been an ardent critic of the carbon-neutral reputation of biofuels, garnering controversy for conducting studies that some other researchers have criticized for their calculations of emissions arising from biofuel production. (See Patzek’s co-authored article on page 19 of the March 2007 edition of Energy Tribune). Earlier this year, a study by researchers at the Smithsonian Tropical Research Institute suggests that biofuels are not created equal, as those made from U.S. corn, Malaysian palm oil and Brazilian soy yield more emissions than their petroleum-based counterparts, given the environmental damage they reap when grown for fuel. The study cites recycled cooking oil and biofuel made from grassy and woody cellulosic material as being more intelligent choices for cutting down on emissions.

And so the debate continues, struggling to keep pace with the technological progress made by scientists toiling away in their quest to find the holy grail of an efficient, cheap and environmentally-friendly biofuel.

Watch the “Biofuels: Beyond Ethanol” TV Story online, as well as find additional links and resources.

Sheraz Sadiq is an Associate Producer for QUEST on KQED Television.

First things first: If you swim in the bay, no need to worry about sharks. None of the experts we spoke to could remember a single instance of someone getting bitten. And you can rest easy about Great Whites too; they don’t seem to have a taste for Bay waters. For more on this, see the Aquarium’s Chris Spaulding’s blog post.

The San Francisco Bay is much more of a mystery to scientists than I, at least, had realized. Why? It’s simply too hard to peer into. There’s no point in scuba diving. The bay is thick with sediment, much of it a legacy of gold mining explosions in the Delta. So if you want to know what’s swimming around in those murky waters, you have to go fishing.

At first glance, this struck me as both laborious and tough on the animals – catch and release may spare lives, but not without putting a lot of stress on whatever’s on the other end of the line. But when you think about how heavily we humans use the bay – sewage leaks, oil spills, urban runoff, coastal development — it becomes clear we have to take a closer look at how its inhabitants are faring. Sharks are at the top of the food chain, which means they’re a great indicator of how everything underneath them is doing.

Of course, tagging is only worth the effort if you catch enough animals to have meaningful data – which means this project requires tenacity on the part of Aquarium researchers. For updates (as well as info on what to do if you catch a tagged shark) check out the Aquarium’s website. Also, here’s the radio piece we did on the same project.

Watch the “Cool Critters: Sharks of the Bay” TV Story online, as well as find additional links and resources. Also don’t miss our behind-the-scenes photos for this story.

Amy Standen is a Reporter for QUEST and Radio News at KQED-FM.

Thought California has consigned coal-burning to the scrap bin? Think again! California has 11 coal-fired power plants, all used to heat limestone into cement — making us one of the biggest cement-producing states in the country. In addition to cement, these kilns produce 95% of the state’s airborne mercury pollution and 2% of its greenhouse gas emissions. Mostly, they’ve slipped under the radar of regulators, but that is changing fast.

You may listen to the “Cement - A Dirty Business” Radio report online, as well as find additional links and resources. Also don’t miss our behind-the-scenes photos for this story.

Amy Standen is a Reporter for QUEST and Radio News at KQED-FM.