QUEST Community Science Blog

I’m the third from left to right.I’m in my late teens in this undated photo. I’m the third from left to right. It’s very likely one of the last times I went camping as a member of the Girl Guide and Boy Scout Association of Costa Rica, which I joined when I was 11. I was very lucky growing up in Costa Rica because the association’s national campground, called Campo Escuela Iztarú, where this photo was taken, was in the hills near my house. From the backyard of my childhood home in Tres Ríos, you can see the national campground. It’s the hill in the background, dotted with a few trees. I thought a lot about this campground while I was working on our QUEST Nature Deficit Disorder TV segment about how kids nowadays in the United States aren’t spending enough time out in nature.

Every year, during the decade or so that I was a Girl Guide in Costa Rica, my fellow guides and I would trek up the steep hill, usually carrying our own sleeping bags and supplies. Once we got to the top, we chopped up wood with machetes and cooked over open fires. We woke up at the crack of dawn and showered in icy-cold water. During the rainy season, we got very wet. During the dry season, we got sunburned.

Camping took precedence over almost everything else. The day I graduated from high school I was in the middle of an international camping trip with girl guides from around the world. My parents drove up the hill, put some ointment on my sunburned ears and whizzed me over to the theater to pick up my diploma. Then they drove me back up the hill to finish the event.

My childhood home in Costa Rica, with the
campground ridge in the backgroundOur trips were always full of that sense of adventure you can only experience as a kid when you’re out in nature and away from your parents. We ran up and down the mountains, crawled in muddy pits, climbed trees and cut ourselves with our machetes. By the end of our trips we were always completely worn out. Once, I sat on my bed and fell asleep with my backpack still on my back.

But all this happiness came to a crashing halt. On Aug. 20, 1988, when I was 16, a young couple my age was murdered in a coffee field on the road to the campground. My sister and I were supposed to go camping a few days later. But my parents wouldn’t hear of it, no matter how much we begged. And who could blame them? The way he had killed his 14 victims was so cruel that it was impossible to incorporate his methods into his moniker, à la The Boston Strangler. So the press simply called him el psicópata, The Psychopath. Fear of el psicópata marked my adolescence and early adult life.

What was near-miraculous was that in time I was allowed to go camping again at Campo Escuela Iztarú. This photo of me is proof, I guess, although it doesn’t make any sense, because my parents were so fearful of everything when it came to their daughters. Perhaps they let me go because they both had good memories of the time they spent outdoors, my mother as a little girl camping all summer long in New England and my father as a teenager pedaling up and down Costa Rica’s mountains to make it to the Pacific coast by sundown. I’m so grateful to them for overcoming their fears (or not - I’m sure they had many sleepless nights). Those fleeting moments of freedom and that sense that anything is possible that I felt when I was camping are so much a part of me that I can’t even really consider them memories. So thank you, Mummy and Daddy, for letting go and letting us go up the mountain.

Watch the “Nature Deficit Disorder” TV Story online, as well as find additional links and resources. Also, please share your own photos of childhood nature experiences in our Flickr Photo Pool.

Gabriela Quirós is a Segment Producer for KQED-TV, and is the producer for this story.

Unless our sewage happens to end up in the Bay and in the headlines, most of us probably never give a second thought to where our wastewater is headed each time we run the tap or flush the toilet.

To learn more about the travels of sewage, I took a tour of the Las Gallinas Valley Sanitary District treatment plant led by Plant Manager Matt Pierce. The plant has been in operation for about 50 years and serves over 30,000 residents in north San Rafael.

After leaving sinks and showers throughout the District, wastewater travels through a network of pipes and pump stations. Once the sewage arrives at Las Gallinas, it passes through an inlet screen and a grit chamber, which together remove much of the dense, inorganic material-”like diamond rings,” Matt jokes.

A lot of what happens at the plant is not that different from what happens in your compost pile: “It’s basically bacteria at work,” Matt points out. (The much bigger challenge for sanitation districts these days are all the unnatural things we’re putting down the drain: household chemicals, personal care products, pharmaceuticals.)

From the grit chamber the sewage heads into a series of clarifiers, where gravity causes the organic solids to settle out. The biosolids pass through a thickener and then an anaerobic digester-the most, ahem, aromatic stop on our tour. After further thickening in storage ponds, the sludge is injected into a disposal field.

Meanwhile, the liquid from the clarifiers travels through two biofilters, where rotating arms spray the water over rock beds. The organic matter in the wastewater is a feast for microbial slime living on the rocks. In the nitrification tower, more microorganisms break down the ammonia in the water. In the final stages of treatment, the wastewater is chlorinated to kill any remaining bacteria, then dechlorinated since the chlorine is toxic to many aquatic species. Finally, the treated water is sprayed onto District fields or discharged into Miller Creek where it flows to San Pablo Bay.

The District has done a lot to minimize the environmental impacts of its operations. The plant is powered by a field of solar panels. The methane released in the sludge treatment process is captured and used to generate power and heat the digester. Some of the treated wastewater supports acres of fresh and saltwater wetlands-in fact the District’s land is a favorite local gem for walkers and birders. And in a partnership with the Marin Municipal Water District, more than a million gallons of treated wastewater are recycled daily for landscape irrigation and other projects.

There are plans to make even fuller use of the reclaimed water. The Bay Institute-in partnership with the Sonoma County Water Agency, Las Gallinas, and three other North Bay sanitation agencies-has developed a plan to use recycled water for wetland and creek restoration and for agricultural irrigation. Legislation sponsored by Congressman Mike Thompson to establish the program passed the House late last year; Senator Dianne Feinstein has introduced similar legislation that we are hopeful will pass this year.

With California’s growing demands for water, such creative means to conserve and recycle are critical to helping prevent this precious resource from just going “down the drain.”


Ann Dickinson is Communications Manager for The Bay Institute (www.bay.org), a nonprofit research, education, and advocacy organization dedicated to protecting and restoring San Francisco Bay and its watershed, “from the Sierra to the sea.”

Is your face giving you away? This week, QUEST met renowned psychologist Paul Ekman, who has spent his life studying how our facial muscles involuntarily reveal emotions like sadness and anger. In 1976, Dr. Ekman and his colleague Dr. Wallace Friesen published the Facial Action Coding System, or FACS, a system that comprehensively inventoried the muscles movements that create smiles, frowns and grimaces.

Each movement is categorized in Action Unit (AUs). When you puff your cheeks, it’s known as AU13. The Frontalis muscle, located on the forehead, is responsible for AU1 or the “Inner Brow Raiser”. Over the course of their extensive research, Ekman and Friesen determined that there are at least 19 different versions of smiles! For more information and additional resources on FACS, visit the Data Face website.

If you live in the Bay Area, you can see a special exhibit at San Francisco’s Exploratorium with more of Dr. Ekman’s photos. It’s open through May 11.

Watch the “Emotions Revealed” TV Story online, as well as find additional links and resources.

Jenny Oh is an Associate Producer for QUEST on KQED Television.

Last week on QUEST, we took a look at the history of the San Francisco Bay’s most dangerous toxin: mercury. This week, now that the mercury is here in the bay, how is it affecting us? The obvious place to go was the Berkeley Marina, one of the bay’s most popular fishing spots. On the day I visited, halibut season had just begun and, even on a Monday morning, the pier was lined with anglers. Halibut contains high levels of mercury, just like other big SF Bay fish but – as you hear in the piece – you wouldn’t know it from talking to the fishermen out that day.

Of course mercury is a problem in many big fish we eat, not just the ones in the San Francisco Bay. Dr. Jane Hightower is one of the leading local doctors diagnosing various levels of mercury poisoning in her patients – many of whom, as she says, do their fishing at places like Whole Foods. We only had time to use a short piece of that interview in the actual story, but anyone who eats fish will want to hear more from Dr. Hightower. A longer version of that interview – including Dr. Hightower’s surprising views on kid staples like canned tuna fish – is right here.

You may listen to the “Mercury in the Bay - Part 2″ Radio report online, as well as find additional links and resources.

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

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In honor of Earth Day, we wanted to take a big look at a chronic environmental issue in the Bay Area, tracing it from its origins to the contemporary strategies to solve it. Mercury was the obvious choice: It’s been flowing into the Bay since before California joined the union, and it continues to trickle in from not just the old culprits, like gold and mercury mines, but a modern crop of industries, like refineries and cement kilns. Even little things – like a broken mercury thermometer dumped into the sink – are part of the problem.

The key fact here is how incredibly potent mercury can be: Just one little globule from an old thermometer can poison all the fish in a 45-acre lake, making them unsafe for humans to eat. Mercury pollution is hardly unique to the Bay Area; what makes us interesting is that local officials are making real strides in trying to clean it up. Over the next 17 years or so, we’ll spend $2.6 billion dollars on the project. Even then, we won’t have a clean bay for 120 years.

For a lot of people, mercury pollution in the Bay is largely theoretical, since few stores sell fish caught in the Bay, and relatively few residents fish for their food. But some still do – including many recent immigrants from fishing-intensive cultures like Laos. We’ll look at how mercury affects the health of local fishermen next week.

This piece marks our first-ever audio slide show, and what a difference it makes! We also hope you’ll check out the mercury map above, where you can see how many pounds of mercury come from each of the Bay Area’s five refineries, plus other mercury sources and the bay’s popular fishing spots.

Watch the audio slide show of “Mercury in the Bay” online, as well as find additional links and resources.

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

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.

By 2050, as our population ages, 15 million Americans will suffer from Alzheimer’s disease – triple today’s number. There is no cure for Alzheimer’s, but several treatments can help alleviate its symptoms, and many research projects aim to understand the disease better and find a way to fight it. In this QUEST story, we visited researchers at San Francisco’s Gladstone Institutes, who are looking for a gene that may hold the key to a cure.

There are many others also working in the field. The Alzheimer’s Association has information about current treatments available. The National Institute on Aging gives a good overview of what avenues of research are being pursued to better diagnose the disease and find a cure. A team of health professionals at the UC Davis Alzheimer’s Disease Center can provide a diagnostic work-up, as well as enroll patients in several ongoing clinical trials.

Watch the “Alzheimer’s: Is the Cure in the Genes?” TV Story online, as well as find additional links and resources.

Gabriela Quirós is a Segment Producer for KQED-TV, and is the producer for this story.

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.

Red hair genes will be diluted but will not go away.I got a call last week from a reporter in Virginia. Someone had come up to her in a bookstore to offer her condolences about her kind dying out. She is a redhead.

The guy from the bookstore must have read one of the stories about the imminent demise of redheads that flashes across the media landscape every few months. People with red hair have to deal with headlines like:

“Redheads Set for Extinction.”
‘Will rare redheads be extinct by 2100?’
“Gingers Extinct in 100 Years.”

The reporter suspected these stories weren’t right and wanted to write a story about it. She called me to get some science to back her up. I was able to reassure her that redheads weren’t going the way of the dodo. They’ll become much less common, but there will probably always be red haired people around.

To understand why redheads will fade but not disappear, we need to dig a bit deeper into how red hair works. Red hair happens when both copies of the MC1R gene do not work properly. (Remember we have two copies of almost all of our genes–one from mom and one from dad.)

So if you’re a redhead, you inherited a nonworking copy of MC1R from both your mom and your dad. If you get a non-working copy from only one of them, then you won’t have red hair. You’ll be a carrier.

Right now redheads are at an artificially high level in the human population because their recessive red hair genes are concentrated in North America, Europe, and Australia. For example, 10% of Ireland and 2-6% of the U.S. has red hair.

These numbers are maintained because carriers and redheads keep making new redheads with each other. But as barriers go down, their red hair genes will flow out of these populations and into the human gene pool.

Red hair genes will become diluted in this pool but they won’t be completely swamped out. Even as redheads decline in numbers, their genes will remain constant. It will just be less likely that two carriers and/or redheads will meet and have babies with red hair.

This is all interesting but it got me to wondering about how many redheads there will be in the distant future when all the mixing is said and done. We can use something called the Hardy Weinberg equation to figure this out.

This equation works great for simple dominant/recessive traits like red hair if we know how many of each gene version there is. To do this, we need to figure out how many redheads and how many carriers there are in the world.

It is easy to figure out how many redheads there are–you can tell who they are just by looking at them. But figuring out carriers is a lot harder. We can make guesses based on the number of redheads (again using Hardy Weinberg) but until we sequence a lot more MC1R genes, they’ll only be guesses.

The numbers I have seen floating around are that around 1% of the world’s population has red hair and that around 4% carry the red hair version of MC1R. This means that there are around 65 million or so redheads in the world and 260 million carriers. (This sounds high to me but these are the numbers out there.)

When we use these numbers and apply the Hardy Weinberg equation, we end up with a final percentage of redheads of 0.1% or 6.5 million. This is quite a fall from current levels but they are hardly wiped out!

There are lots of assumptions* in these calculations that might cause the number of redheads to actually be more or less than 0.1%. But unless there is some red hair specific catastrophe or people start burning them as witches again, redheads are here to stay.

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

*Some assumptions used:

1) There are no barriers to finding partners
2) The 4% carrier number is an accurate one
3) Two non-workingMC1R genes produce red hair in all genetic backgrounds
4) Other assumptions described here