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

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

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

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

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

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

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

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

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

Areas where the oil spread after the spill. See this map and others.

And November's the month last year when the Cosco Busan crashed, leaking 53,000 gallons of black goo into San Francisco Bay.

So biologists will be particularly attentive this November, one year after the oil spill, to see if there's a noticeable dip in the numbers of herring in the Bay, or the number of migratory birds that alight here.

The number of birds harmed by the oil spill is not really known. More than 2,000 birds were killed – but those are simply the birds that were identified, not the total number. Since many dead birds in remote areas were never found, and since predators took away many of the hurt birds, the estimate for the total number of birds harmed by the spill is many times higher than that. So researchers are conducting experiments to determine a provable, scientific estimate of the number of birds killed or harmed by the oil spill.

According to California Fish and Game scientist Julie Yamomoto, it only takes a spot of oil the size of a nickel to harm a bird. It's not just uncomfortable, she says, it's actually lethal – because the oil is like a hole in a wetsuit, and birds that have been oiled become hypothermic. And they also lose buoyancy, so birds can actually sink and drown in the ocean.

All the experiments and data on habitats, fish, birds and other wildlife will be compiled into something called the Natural Resource Damage Assessment.

It's nicknamed NRDA (pronounced "nerd-a") and that's pretty apt. It's a little wonky, to say the least. The data is supposed to be completed by the end of next year, and then the NRDA report is expected to be compiled and submitted sometime in 2010.

Listen to the Oil Spill Anniversary radio report online.

Having extra copies of certain genes helps fish live in Antarctica

What I like is learning how these beasts have adapted to their incredibly harsh environment. More specifically, what changes have happened in their DNA that allow them to live where no other animal could.

In this blog I'll focus on those poor fish living in the waters off Antarctica. These waters are icy cold and the fish aren't warm blooded. Which means their body temperature is the same as the water around them.

Most biological processes do terribly under these conditions. Proteins don't fold right, enzymes work incredibly slowly, fats glob up. It is astonishing that these fish survive at all.

Scientists figured out back in the 70's that these fish evolved a special antifreeze protein to keep their blood from freezing. Since then they've done other experiments that show other adaptations to the cold too.

In a new study, scientists from the University of Illinois and the Chinese Academy of Sciences decided to take a look at as many genes and as much of the DNA of these fish as they could. What they found was that lots of genes are turned up in these fish compared to relatives that live in warmer waters. And that many of these genes are turned on higher because the Antarctic fish have extra copies of them.

The genes they found that were different made sense. For example, there are a bunch of genes that make proteins called chaperones. Chaperones help other proteins fold up right. In this cold, proteins need all the help they can get!

Also they found that there were more of the proteins that scavenge reactive oxygen species (ROS) in these fish. This makes sense because colder water has more oxygen.

O2 is a pretty nasty molecule that tends to create even nastier chemicals (ROS) that beat up on DNA and proteins. We all have proteins whose job it is to defuse these chemicals. These fish make more of these proteins.

A few years ago it would have been surprising to find that the way these genes made more proteins was by duplicating themselves. Not anymore.

As we look closely at the DNA of various creatures, we are finding that gene duplications (and deletions) happen a lot. Even in people.

For example, people from cultures that eat a lot of starch have extra amylase genes. (This gene makes amylase, a protein that helps breakdown starch.) Some people are resistant to HIV (the virus that causes AIDS) because they have extra copies of the CCL3L1 gene. And so on.

Our DNA is much less stable than we thought. Which is one way we can better adapt to our surroundings. I can't wait to see what they learn about those tubeworms!

This sushi is good enough to eat.
Photo credit: Andrea Kissack.

There is a new trend in town. Sustainable sushi. The Monterey Bay Aquarium, and two other ocean conservation groups (Blue Ocean Institute and Environmental Defense Fund), have come out with new advice for making better sushi choices. Modeled after the Monterey Bay Aquarium’s popular Seafood Watch Pocket Guide, the new sustainable sushi guide helps consumers make informed choices by categorizing seafood into three areas: Green (or best choice), Yellow (or good alternative) and Red (what to avoid). Just what kind of sushi you should avoid may surprise you. Until now, Unagi (bbq eel with avocado), seemed pretty harmless and a good choice for reluctant sushi eaters. Well, Unagi is farmed, freshwater juvenile eel so that definitely gets a red light from the Seafood Watch folks. You can try a sustainable alternative to Unagi at Tataki Sushi Bar in San Francisco. It may be the only restaurant of it’s kind in the country. The owners of the all sustainable sushi restaurant say they don’t want to become a niche as much as they want to influence the rest of the industry to change its’ practices. And with sushi a growing multibillion dollar industry, consumer preferences can have a big impact.

So how do you green your sushi? Try Pacific Halibut, farmed scallop or North American Albacore. Monterey Bay Aquarium biologists consider these among the “best” seafood because they come from abundant, well-managed fisheries or are raised using sustainable aquaculture methods.

But even though it's in our own backyard, this place remains mostly unknown… probably due to its chilly temperatures. Let's face it, most of us are not donning our masks and snorkels and swimming in the hypothermic Pacific Ocean off our coast.

Lucky for us, some intrepid scientists and students are diving into this amazing place. Their job is to monitor how the ecosystems are responding to the new restrictions and protections taking place in the Marine Protected Areas. They gave us an amazing opportunity to see the natural world beneath the surface. And the world they shared with QUEST is truly inspiring. Playful harbor seals tease the divers while they weave through the gently swaying kelp forests. Fish dart through the rays of sunshine that cascades down to where starfish slowly go about their day. Through the eyes of these scientists, we witness the undersea life in bloom. They clearly have one of the best offices to go to work to each day.

Watch the Underwater Wilderness: Creating Marine Protected Areas television story report online.

Mary Collins School teacher Blythe Shelley touching
a leopard shark at the Aquarium of the Bay

So, how do the Bay's leopard sharks, soupfin sharks, sevengill sharks, spiny dogfish, and other shark species differ from "non-shark" fishes? Here are a few key distinctions:

#1. You could say that sharks don't have a bad bone in their bodies. In fact, sharks don't have any bones in their bodies. Sharks-along with their relatives skates, rays, and ratfish-belong to a diverse class of fish that have cartilaginous skeletons, unlike the bony skeletons of other fish.

#2. Body shape. If you look at most fish head on, they have a generally oval shape. Sharks, in contrast, tend to be more triangular with a wide, flat under-surface. Their broad pectoral fins give them lift as they move through the water, not unlike the wings of an airplane. This hydrodynamic shape is key to keeping sharks afloat (you'll see why as we move on to difference #3).

#3. Besides bones, sharks lack the air-filled swim bladders that most fish use for buoyancy (If sharks are airplanes, does that mean bony fish are hot air balloons?) Instead, sharks keep afloat with the help of a large, low-density liver, their unique body designs, and the physics of forward motion. If a shark stops swimming it won't necessarily drown-only some sharks need to swim to breath-but it will sink!

#4. While most fish have gills tucked behind a bony flap called an operculum, sharks exhale water through gill slits located behind their head. Five gill slits are typical, but some sharks -like the sevengill shark found in the Bay-have more. Most sharks use ram ventilation to breath, swimming constantly with their mouths open to keep water flowing over their gills. Bottom dwelling sharks, whose mouths may be buried in the sand, inhale water through an opening on the top of their head called a spiracle and pump water past their gills.

#5. A shark's skin is covered with tiny dermal denticles that differ from scales on most fish. As their name indicates, they bear a physiological similarity to teeth. Their unique structure helps reduce drag as the shark moves through the water-in fact, sharkskin helped inspire the high-tech swimsuits we saw at the Summer Olympics.

#6. Most fish spawn by releasing large numbers of unfertilized eggs and sperm into the water. Sharks, in contrast, reproduce via internal fertilization. Depending on the species, they then lay a much smaller number of fertilized eggs, or carry the eggs inside until they hatch, giving birth to live pups.

Old Adobe Elementary teacher Juliet James examining shark teethSadly, these unique creatures are declining all over the world due to overfishing, pollution, loss of habitat from coastal development, and climate change. And that's bad news not just for sharks but also for their ecosystems. Like lions and wolves, most sharks sit atop the food chain as apex predators; thus their disappearance can trigger a cascade of disruption up and down the chain.

All the more reason for us to study up.

On July 16th, my Mom and I left San Francisco by boat to tour the Southeast coastal islands of Alaska. I have been hearing stories about the untamed Alaska since I was a small child. My mom lived in Kodiak as a girl. Her father and my grandfather had his last tour of Naval duty on Kodiak. His assignment was to survey the numbers of Kodiak bears for the sake of conservation. So I was more than eager to see the wildness and wildlife of Alaska.

While at sea, I've seen common Alaskan wildlife. Humpbacks have spouted and breached, raven and eagles have dived at the water for a dinner of spawning salmon. But I keep looking at the water, hoping to glimpse Orcas. The next opportunity to do so will be tomorrow coming out of the port of Victoria, British Columbia. Orcas, or killer whales as they are commonly known, are not whales at all. They are the largest species of the dolphin family and they are prominent along the Southeast islands of Alaska. They have captured the spirit of natives in these lands. They are alive in their legends and are carved into totem poles that are being preserved in the towns and museums along the coast. Both the native people here and Orcas form matriarchal societies and many native people believe that members of their tribe are reincarnated as killer whales.

Resident Orcas are just one type of Killer Whale. Three groups of Orcas have been found to be genetically separate on the nuclear and mitochondrial DNA level here. Resident Orcas stay close to the shore of the Alaskan islands in herds of up to 200. They have strongly bonded familial ties and are the fisherman of the Orcas, as their diet consists only of fish. Transient Orcas, on the other hand, live also in groups of up to 200 but will split off for the sake of the hunt. They hunt small marine mammals and migrate a great deal more, going where they can find food. While residents have a small and predictable migration route, transients are harder to research because of an unpredictable migration route. Researchers in Alaska have been able to collect more data on resident pods because of their predictability. They identify each individual by their Saddle-patch, or the white markings adjacent to the dorsal fin. It is like a fingerprint, identifying individual Orcas. The third group of Orcas is even more elusive than the transient pods. They are known as the Offshore Orcas. They are known as the rogue of the species and have been very difficult to research because of their unpredictability and often solo migration.

I am most interested in Orcas because of the question of Orca culture. They are seen as very intelligent animals by Native tribes as well as researchers. There is a controversy in the scientific field if Orcas have culture. Traits of fishing or hunting seem to be passed down to offspring denoting learning and hence culture. However, the science community is still split on learning behavior. One story I heard while here paints them as creatures of learning and remorse. One sick Orca was found in a pod. Fisherman noticed the other pod-mates line up and the sick Orca went through the line giving attention to each pod member and then left the pod after what looked like "saying his goodbyes". Was this a goodbye ritual for sending off a dying pod-mate? Whether is was or not, such unusual behavior is well worth more research. Hopefully, I will be able to see some of their behavior myself before returning to San Francisco.

Every year, millions of fish make a strange and harrowing detour through the Skinner Fish Facility, part of the State Water Project's facilities in the Delta.

In my last post, I wrote about my visit to the Banks Pumping Plant, whose giant pumps slurp water from the Delta to help quench California's thirst. As the volumes of water are sucked up, both resident and migrating fish come along for the ride. The Skinner Facility, in operation since 1968, was built to protect fish from being killed at the pumps–an effort that sadly is not as successful as one would hope (more on that below).

I was amazed to learn there is a whole art and science to fish screens, which range from physical barriers–called positive barriers–like perforated plates or wire mesh, to behavioral barriers like sound, light, or other stimuli aimed at keeping fish away. Well-designed screens minimize both entrainment (fish being pulled into the pump or diversion) and impingement (fish being trapped or injured against the screen itself due to water velocity).

Both physical and behavioral barriers are used at the Skinner Facility. Fish being pulled toward the pumps first encounter a trash rack that diverts many bigger fish, along with floating debris. Next, fish encounter a large, v-shaped array of metal louvers. The louvers create turbulence that functions as a behavioral signal, encouraging the fish to swim away into bypass pipes that function, as our tour guide put it, like "a big vacuum system."

From the bypass pipes fish travel to another set of louvers and pipes, concentrating them into a smaller volume of water, and then into holding tanks in a nearby warehouse. Giant, suspended cone-shaped buckets are used to periodically sample the fish, which are identified, counted, and measured. Some 90 species turn up in the facility, including Chinook salmon, steelhead, white sturgeon, and delta smelt. (I asked our guide if delta smelt really do smell like cucumbers. He confirmed it. In fact, when a school of smelt comes through–an event that has become rare–the warehouse smells "like a salad.") When enough fish have been collected, they are loaded into trucks and driven back to the Delta.

Here's the rub. Many fish caught in the pull of the pumps are lost to predation before even reaching the screening facility. Then, the facility does not effectively screen fish smaller than about 1.5 inches, meaning that littler, less powerful species and juveniles are still vulnerable to the pumps. For the fish that make it to the holding tanks, the process is such a trauma–with big and little fish squashed together in the tanks, buckets, and trucks–it's no surprise there are casualties; in fact, the delicate delta smelt often do not survive. And even for fish that make it through the entire process and out the other end, there's a final, fatal hurdle: the trunks routinely dump salvaged fish at the same locations, where more predators have learned to cluster for a free lunch.

Scientists agree that the loss of fish at the huge state pumps–and other pumps and intake pipes throughout the Delta–is a major contributor to plummeting populations. How much water we use makes a difference: The higher the export rates, the more fish are entrained. There also is broad consensus that more state-of-the-art fish screening facilities are needed. That could come with a hefty price tag. But with our fish disappearing, can we afford not to invest in their survival?

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.

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.