QUEST Community Science Blog

The day was hot, the owl was angry… we shot this really fast. It’s not Olivia the owl’s fault, it was just one of those days. As we all know, owls are nocturnal creatures, and we happened to be filming Olivia during the hottest, brightest part of the day. If your eyes were that big and we made you perform for us on camera at high noon, you’d be squinting and hissing at us too!

But the greatest disappointment, in the end, was that I did not have enough time in this segment to tell our audience about all of the amazing adaptations that this creature has. Their claws are enormous and powerful, they have excellent hearing, and fantastic vision in low light. But perhaps one of the coolest things about the Great Horned Owl is that they can fly almost silently due to “fringes” on their feathers that help to break up the sound of air passing over their wings.

The other thing people might not know is that the famous “hoo-hoo-hoo” sound that we make when we are imitating owls comes from the Great Horned Owl. People tend to think all owls sound like this because the male GH owl’s call is often used in Hollywood movies, no matter what kind of owl is being depicted on screen.

Olivia and her ilk are well adapted, formidable hunters, and truly gorgeous to look at… go and see for yourself at the Oakland Zoo.

Watch theCool Critters: Owls story online, as well as find additional links and resources.

Joan Johnson is an Associate Producer for QUEST on KQED Television.

Human and chimpanzee chromosomes are very similar.
Note that human chromosome 2 is very similar to a
fusion of two chimpanzee chromosomes.

For the last few weeks I have been corresponding with someone about intelligent design (ID). More specifically, we have been chatting about why humans have 46 chromosomes and most of the great apes have 48.

To me, this is great evidence for evolution. Why? Because if you look at the chromosomes closely, you can see that human chromosome 2 is really just a fusion of two great ape chromosomes.

The idea is that a few million years ago, a common human-chimpanzee ancestor of ours had two of his or her chromosomes fused together. This sort of thing happens all the time even today. Around 1 in 1000 live births has one of these kinds of fusions.

Then, probably through chance,this ancestor with the fused chromosomes went on to found the human race. Now people have 46 chromosomes and chimpanzees have 48.

An alternative explanation is that the designers fused the two chromosomes together when they created humans. The idea would be that the designer wouldn’t create every plant, animal, bacteria, and virus from scratch–why reinvent the wheel every time? Instead the designers would mix and match parts that worked.

So as part of the process of designing a human, the designer fused two ape chromosomes together. This would presumably be simpler than creating a human chromosome 2 the way the other chromosomes were made.

The difficulty with this idea is that there is no obvious advantage to having 46 chromosomes instead of 48. What matters is our DNA, not how it happens to be packaged.

It is possible that there was some advantage to fusing the chromosomes together. For example, maybe a new gene was created at the fusion point. Or maybe genes that were shut off before were now turned on in the new fused chromosomes.

There isn’t any evidence of these kinds of things. And even if there were, a designer who can easily put in the 60 million or so differences between humans and chimpanzees should be able to accomplish whatever results a chromosome fusion gives more elegantly than sticking two ape chromosomes together.

Also, when you look at the fusion point, you can see that the DNA isn’t exactly what you would expect if a fusion happened in the last 10,000 or even 100,000 years. The results look more like an event that happened millions of years ago.

The ends of a chromosome have a defined sequence of DNA repeats called a telomere. The DNA at the fusion point looks very similar to a string of telomeres (as we would expect from a fusion) but it isn’t perfect. This is just what you would expect if the fusion happened millions of years ago. Because our DNA gets changed a little all of the time.

The environment or even our own cells can cause the wrong letter to end up in our DNA. Our cells are pretty good at fixing these mistakes but they don’t catch them all. What this means is that our DNA builds up mutations over time.

When an unfixed change happens in a sperm or egg, then it is passed down to the next generation. If the changes that aren’t fixed happen somewhere important, then they are selected for or against. But if they’re neutral, then they just build up over time. Scientists can even use these sorts of errors to predict how long ago something happened. Or to trace human migration patterns.

These DNA changes at the fusion point do not fit with ID if they don’t serve a purpose. Otherwise, why put them there? It will be interesting to see the results of experiments that might show if these sequences matter or not.

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

Why do Moon Bears need you to knit?

Once upon a time in the far away land of Hong Kong, a woman named Jill Robinson discovered that beautiful moon bears where being held captive in tiny cages in China and farmed (through their bellies) as a living source for bear bile, which is used in traditional medicines. She decided to do something heroic about the issue and founded the Animals Asia Foundation. Animals Asia became a thriving organization, dedicated to ending cruelty and restoring respect for all animals in Asia.

For many moon bears, their stories have a happy ending. Jill and the AAF crew have rescued 500 bears, releasing them into their idyllic sanctuary in Chengdu China. Newly rescued moon bears tentatively step on fresh grass, slowly learn to climb, socialize, scamper through bamboo, wrestle and eat honey, finally becoming a real bear.

Of course, the bears can’t go from cages to sanctuary directly; they must endure urgent veterinary care and often surgery to remove the bile equipment from their bodies. Bears must be anaesthetized to receive this care and it is important that they stay warm and comfortable during the process. Just as with humans, the bears’ extremities are the first things to get cold and that is where knitters on the West Coast of the United States, worlds away, come in. They must knit giant bear mittens!

The Oakland Zoo is hoping to have some mittens knitted in order to hand them directly to Jill Robinson on May 21, when she speaks at the Oakland Zoo. We will have a knitting party at the zoo on Friday, May 9, from 1pm-3pm. However, mittens can be turned in to the Oakland Zoo at anytime and mailed to China in the hopes that the thousands of moon bears still in captivity will need them soon.

The mitten pattern allows for several weights of yarn and includes instructions for knitting in the round with one circular, two circulars, double-pointed needles, or knitting flat. Finished mittens are about 7″ wide (14″ circumference) with a 12″ foot and 6″ cuff. The pattern is intended to be beginner level, but if you have any questions about the techniques mentioned, you might find the website knittinghelp.com helpful.

Click here for the pattern and try it yourself:

bearbooties.pdf

The Oakland Zoo will be working with Article Pract in Oakland on more mittens for bears.

Find out more about Moon Bears and their plight, and meet Jill Robinson on Wednesday, May 21 at 6:30 for the lecture entitle, “From Prison to Paradise: Rescuing the Endangered Asian Moon Bear. Bring the family to Bear Day at the Oakland Zoo on Saturday, May 17.

Some of this information is thanks to Twisted, the Knit Shop in Oregon who is helping the Oregon zoo knit mittens.


Amy Gotliffe is Conservation Manager at The Oakland Zoo.

A Pacific Chorus FrogWhen I was growing up in the Bay Area the chirping croaks of native tree frogs often serenaded us to sleep. The sound of those little Pacific Chorus frogs calling to each other was always familiar background music to long summer nights. Those were days of catching pollywogs down at the creek and finding Western Toads in our backyard garden. My brother and I knew exactly where the toads liked to sit during the hot summer afternoons. And like most young boys it was nearly impossible to resist picking them up and interrupting the poor animals’ siestas. Of course the toads always expressed their irritation in the same way, leading us to immediately put them back down in gleeful disgust. This was a wonderful part of each summer’s routine.

I’m sad to say my daughter probably won’t share those same experiences I had. I could say it’s because we live in San Francisco and cities aren’t as amphibian-friendly as the suburbs. But my parents still live in the same house where I grew up. Unfortunately, it has been years since we’ve seen toads in the garden there. And the quiet singing of the tree frogs seems much lonelier today.

Amphibian decline is happening all over the world. And as depressing as it is not to have those fun childhood experiences of catching, playing with and hearing frogs in the garden, there is a much more serious problem going on. This can have some serious consequences to local food webs. It is also an alarming sign that there is something really unusual happening with the world’s environment.

There are many reasons for the decline in the world’s amphibian populations. And it seems that each region of the globe, and maybe even each species, may have its own ticking time bomb. Some places may be experiencing rapid habitat decline. There is pollution in the rainwater and chemical run-off in lakes and streams. Some places are seeing a sharp increase in parasites and diseases. Scientists are even looking at increased UV radiation. Or maybe it’s a combination of multiple factors. The result is part of what some scientists are now calling the “sixth wave of extinction.”

That’s a lot of doom and gloom. Luckily, scientists are racing to understand this decline and hopefully may come up with a means of curbing it before it is too late. We were fortunate to meet some of the best. We joined herpetologists Karen Swaim and Vance Vredenburg out into the field to learn more about what is happening to our local California red-legged frogs. We also visited the laboratory of Professor Tyrone Hayes at UC Berkeley to learn what his team is discovering about the connection between agricultural pesticides and frog decline. (See our additional web-only interview with Professor Hayes) You can test your amphibian knowledge by taking our QUEST quiz. Do you know why my brother and I always put down those toads?

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

Chris Bauer is a Segment Producer for television on QUEST.

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.”

Nobody likes moving. The packing, taping, lifting, shipping… it can be major hassle. But nobody’s experience compares to what’s going on at the California Academy of Sciences. They’re moving to their new 400,000 square-foot building in Golden Gate Park after three years in downtown San Francisco. But they’ve got a lot more to move than most people. Try 38,000 live animals and 20 million scientific specimens.

From fossils and gemstones to bird eggs and a stuffed Kodiak bear, it takes a lot of creativity to pack their collection. Everything seems to have special requirements. Their fish collection is made up of 200,000 jars - all filled with alcohol. And since it’s a flammable liquid, they’ll need a licensed hazmat driver to take it across town.

The live animals take extra care, of course. In this story, we followed the move of three black tip reef sharks. They hadn’t been fed in a few days (so they wouldn’t make any, um, deposits in their holding tank) and they weren’t easy for the staff to catch, but they made it safely to their new exhibit. Even the largest of the three, F3 as she’s known, made it ok, despite being a little groggy at first from too much oxygen.

As curator Bart Shepherd put it, their new Philippine Coral Reef Exhibit is a giant science experiment. The water for the 200,000 gallon tank comes straight from the Pacific Ocean through a four mile pipe. But most impressively, the Academy has been growing coral just for the exhibit. Just managing the water chemistry alone has been a major project, but now several dozen colonies of coral are happily planted in their new home.

Make sure to check out the audio slide show for this story to see how the new building is shaping up. And check out a few of the posts from QUEST science blogger Cat Aboudara, who is an Academy staff member, for more details on what it takes (here, here and here).

Watch the “Moving Day” audio slide show online, as well as find additional links and resources.

Lauren Sommer is an Associate Media Producer for QUEST.

A “penguin suit” doesn’t just refer to a tuxedo anymore.

Why does Pierre, the Academy’s 25-year-old penguin
need a wetsuit?Thanks to an innovative treatment at the California Academy of Sciences. Pierre, the Academy’s 25-year-old penguin was recently fitted with a wetsuit! Pierre’s feathers were thinning and not growing back. Because penguins rely on their feathers for warmth, Pierre was often shivering and uncomfortable without the protection of his feathers. When medical tests concluded there was no medical reason for the feather loss and more conventional treatments proved unsuccessful, senior aquatic biologist & penguin handler, Pam Schaller came up with a more creative approach to keep Pierre warm.

Pam was very familiar with the warmth of wetsuits. She then mused why couldn’t a wetsuit be designed for a penguin? She approached Academy veterinarian, Freeland Dunker with her left field idea. At first, he was dubious but after talking with Pam, he agreed it was worth a try as long as the wetsuit was fitted to insure it did more good than harm. In other words, as long as the wetsuit was fitted not to impede movement or cause rashes, it was worth a shot. Pam knew the best person to design a custom wetsuit would be Celeste Argel, the Early Childhood Specialist at the Academy, who is an excellent and creative seamstress. Celeste was asked to collaborate with Pam to develop and fit a wetsuit just Pierre’s size.

But how do you go about designing a penguin wetsuit? The answer seems to be trial and error. Celeste sat down with me and went over the details about the unusual experience. The process from idea to creation required a great deal of patience and re-fitting.

Celeste, Pam and Pierre met several times in order to customize dimensions. The first fitting consisted of Pam restraining Pierre in order for Celeste to take measurements. From the start, Celeste marveled at the strength of Pierre. “From far away,” she commented, “penguins just look so cute and cuddly but being up close gave me an appreciation for just how strong penguins really are.” With measurements in hand, Celeste drafted up a pattern for the wetsuit and created the first prototype from white cotton bed linens.

On the second fitting, Celeste was faced with a new challenge - getting Pierre’s flippers through the armhole. Pam wanted to keep the armholes as small as possible to maximize warmth. In doing so, Pierre’s flippers had to be bent at the joint and folded in upon themselves in order to thread them though the armholes. While Pam again restrained Pierre, Celeste applied pressure at the joint to fold his wings. “It was amazing and scary to fold up Pierre’s flipper. I wanted to make sure I wasn’t hurting him but to fold his flipper required a bit of pressure at the joint,” Celeste related. With the prototype on, Celeste was able to use a marker and note where the suit had to be taken in or taken out to make Pierre more comfortable. And then again, it was back to the drawing board.

A few more fittings took place to streamline the suit and to ensure that Pierre’s flippers had full mobility. Then Velcro was added to the back of the suit. Pierre was let loose in the penguin enclosure to see how he moved. Both Celeste and Pam sat down to watch his movements and observed where the fabric was bunching. Pierre seemed to be adjusting to his suit quite well but the other penguins, new to a mostly white Pierre, started poking and prodding to investigate the newly adorned bird. Because of the interest from the other birds, the session in the suit only lasted a few minutes. Celeste changed the color of the prototype to a dark brown to see if the other penguins would respond differently and they did. They accepted Pierre with a dark physique. More sessions in the new prototype followed and when Pierre jumped into the water and swam around with the suit on, Celeste and Pam knew it was time for the neoprene fitting.

Celeste conducted research to see how neoprene would act differently than cotton. From her research, she concluded that the whole suit would have to be taken in at least an inch because of the give of the material. However, Celeste didn’t have a machine to sew neoprene effectively so Pam asked Oceanic Worldwide, who supplied wetsuits to the human staff at the Academy, to manufacture a neoprene suit. Pam delivered the working prototype and the patterns to Oceanic who agreed to donate their time and materials. “We were really excited to do it,” said Teo Tertel, company marketing specialist. “We heard most of these penguins only live to 20, and our little buddy there was already 25. Anything we could do to help them, we were all for it.”

When the suit from Worldwide was delivered, it still wasn’t quite ready. The neoprene suit fit differently than expected and had to be re-fitted all over again. However neoprene can be glued instead of sewn so it was a matter of trying the suit on Pierre, marking where it didn’t fit snugly and adjusting. “I would walk behind him and look at where there were any gaps, and cut and refit and cut and refit until it looked like it was extremely streamlined,” Pam remarked on the final alterations. There were hiccups with a penguin being in a wetsuit for the first time and being curious about the Velcro and tabs. So nothing was left unaltered for Pierre’s comfort and mobility.

With all the alterations finally done, a final set of patterns was delivered to Oceanic Worldwide and they again donated their time to manufacture the final wetsuit for Pierre. All the hard work paid off for all involved when Pierre became warm again. It was a huge bonus when he also started to gain weight and his feathers began to grow back. The goal of designing the wetsuit for Pierre was to keep him comfortable and warm and the custom suit worked much better than expected. Having Pierre happy and healthy without the further need of the wetsuit was a perfect outcome for a very unusual treatment.

Cat Aboudara is the Special Projects Manager at California Academy of Sciences and works in the public programs division. The Academy is a wonderful fit for her because of her curiosity about the natural world and her experience in working with native California wildlife.

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.

These fish can tell us a lot about ourselves.

Species often end up a different color when their environment changes. And humans are no exception.

When people moved out of Africa tens of thousands of years ago, they were dark-skinned. Now when we look around Northern Europe or parts of Asia, we see much lighter people. What happened?

A common explanation has to do with sunlight and vitamin D. When people moved north, they got less sun. Less sun means less vitamin D and awful diseases like rickets.

Anyone who moved north and had lighter skin ended up getting more vitamin D and did better than their darker neighbors. After awhile, most of the population had light skin.

This is all well and good, but what happened at the gene level to cause this transformation? One way scientists are learning about how humans ended up with lighter skin is by studying fish. For example, the zebrafish has taught us a lot about why Europeans are often so pale.

The zebrafish is an important model system that scientists use to study vertebrate development, human disease, and lots of other things. A common mutant fish that scientists use in these studies is called “golden.” These fish have lighter, yellowish stripes instead of black ones.

Scientists discovered that these mutant fish had yellow stripes because of a single DNA difference (or SNP*) in their SLC24A5 gene. When fish have this DNA difference, they have yellow stripes.

These scientists next looked for this gene in people. What they found was that most of the people they looked at had two copies of the “black stripe” version of the gene. Except for Europeans. They tended to share a common SNP in their SLC24A5 gene that the scientists went on to show is a big part of why many Europeans have lighter skin.

Another group of researchers decided to dig a bit deeper and find out when this transformation happened. By looking at the DNA around SLC24A5, they found that lighter skin came to dominate Europe around 6,000-12,000 years ago. At first this result is a bit confusing because humans moved into Europe around 40,000 years ago. Why did it take so long for lighter skin to become the norm?

Scientists can’t know for sure but one idea is diet. Around this time, Europeans started to grow their own food. And a farmer’s diet has less vitamin D than does a hunter-gatherer’s diet. Maybe the lack of sun only started to affect Europeans after they started growing their own food. Then, after a relatively brief time, most Europeans ended up fair-skinned to get enough vitamin D.

This gene doesn’t explain all of skin color. For example, it doesn’t explain the difference in color between Northern and Southern Europeans. Or why some Asians have fair skin. But it does explain a good deal of European coloration. Thanks, zebrafish!

*SNP=single nucleotide polymorphism

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

And live in an aquarium in my living room?

A fish tank calms my nerves. A fish tank connects me to the sea. A fish tank brings peacefulness into my hectic world. These are the words of marine aquarium owners. The lure of a tropical fish tank is clear: they are mesmerizing and colorful, they are relaxing to gaze at and they bring real sea creatures right into one’s home. In fact, between 1.5 and 2 million people worldwide feel this way, and keep marine aquariums, including 800,000 households in the United States alone.1,471 species of fish are traded worldwide, with global trade ranging between 20 and 24 million individual fish annually.

Unfortunately, not enough aficionados of tropical fish know how these beautiful beings got to their local tropical fish store. Fewer than 10% of the fish are captive-bred, meaning most are collected from their coral reef habitats off of places such as Indonesia.

Most collectors are men from small villages, who make mere pennies on their catches. Though they sometimes use nets and their own hands, often they employ squirt bottles full of cyanide. As a result of cyanide use, mortality rates of captured fish are between 5% and 75% within hours of collection, with 20% to 50% of survivors dying soon thereafter. Of those that survive the collection process, another 30% on average die prior to export. Collection using cyanide results in an overall survival rate of less than 1 in 10 fish, at best, and often produces 100% mortality.

For those that make it out of their country of origin and onto a plane, eight out of ten will die en route from lack of oxygen, stale water and trauma. For U.S. export, most of these bagged fish are sent to “fish row” in Los Angeles where they are distributed to fish supply stores all over the country.

The good news is that once tropical fish collectors know more, they tend to act. More and more collectors are asking suppliers about their collection techniques and making informed decisions. Reef Project International is a project of Earth Island Institute (and the supplier of most of this information). They have created a Reef Fish Guide for the aquamarine hobbyist that lets them know if a particular fish falls under “Take it Home” or “Keep it Wild”. The guide is available at (www.reefprotect.org). The hope is that when consumers demand sustainable and humane tropical fish, suppliers will respond, and fish and their habitats will benefit.

By the way, Clownfish, like Nemo, are one of the few species that can be captive-bred.

Amy Gotliffe is Conservation Manager at The Oakland Zoo.