A female coho is examined by a biologist at Sonoma County’s Warm Springs Hatchery. The facility is home to a captive broodstock program that’s trying to both preserve the wild gene pool of Russian River coho and to return the fish to creeks in the river’s watershed.

The National Marine Fisheries Service just unveiled a species recovery plan for Central California's critically endangered coho salmon population. The notes that both recent studies and this winter's generally dismal spawning numbers suggest the region's coho population is collapsing.

How bad is the situation? Charlotte Ambrose, the NMFS biologist who led the team that developed the recovery plan, says that "it's condor time for coho salmon." She's invoking the California condor both as a reminder of the bird's close brush with extinction in the 1980s and also as a spur to the same kind of decisive action and long-term commitment that saved one of the nation’s emblematic species.

The coho plan, which is now open for public comment before final adoption, focuses on 28 watersheds between Mendocino and Santa Cruz counties that still harbor the species. That's about one-third of the coho's historical habitat, but the recovery strategy emphasizes focusing recovery efforts where they have the highest chance of success. Marin County's Lagunitas Creek watershed, the site of concerted local action to save the coho since the late 1990s, is one of the areas targeted for the recovery effort.

And what will the recovery efforts consist of?

The plan lays out a catalog of actions needed to deal with threats posed by water diversions, development, and other activity near salmon streams. Many of these threats are surprisingly mundane. Jon Ambrose, a NMFS biologist in Santa Rosa who has worked on the recovery plan (and spouse of recovery coordinator Charlotte Ambrose), offers "stream simplification" as an example.

"What happens is when you have a lot of people living next to the stream, that there seems to be a tendency for the flood engineer in all of us to come to the forefront, and that worries people," Ambrose says. "Building too close to a stream, putting infrastructure too close to a stream, causes people to want to make sure flooding doesn't happen, so they remove the wood. And removing that wood is removing the habitat necessary for coho, because that large woody debris forms the deep pools that these fish need during the summer, it provides protection against predators, and during big winter flow events it provides protection against being blown out into the ocean."

The recovery plan calls for a sweeping program of habitat restoration to prevent the further decline of coho runs. It would require local governments and agencies to consult NMFS on land-use decisions that might affect the coho. The blueprint also envisions an ongoing cooperative effort involving state and federal wildlife agencies, local government, landowners (including forestry companies along the coast), and local conservation groups such as Marin County's Salmon Protection and Watershed Network (SPAWN).

The recovery strategy also calls for new investment in captive broodstock programs like the one at Warm Spring Hatchery in Sonoma County. That effort, run under the auspices of the Pacific Fishery Management Council, is trying to preserve the genetic diversity of Russian River coho and to restore fish to streams in the river's watershed.

NMFS says if the plan is put into effect, it could take 50 to 100 years for California coho to recover. Citing a 2004 estimate from a state coho recovery plan, the agency puts the cost at $3 billion to $5 billion–maybe more.

Jon Ambrose concedes the project to bring back the coho, a once prolific species that has all but vanished, seems like a daunting one. But he says he's optimistic.

"I gave a presentation on this recovery plan a couple weeks ago, and I was going through the numbers showing the decline, and people got really kind of depressed," he says. "But this is doable. I've worked with a lot of threatened and endangered species throughout my career. Oftentimes people want to throw up their hands and say nothing can be done. And I categorically disagree. This is doable–it's just complex."

The largest land mammal ever to live at 25 feet in length, 17 feet tall and nearly weighing 18 tons.

When I was traveling across the museum floor this morning, I saw four colossal legs splayed out. However many helping hands of the exhibit team were carefully placing those legs all under the canopy of a supporting crane. The area holding the legs was closed off and a sign stanchioned just outside read “I’m pulling myself together: This model of an Indricotherium, the largest land mammal that ever lived on land, is being assembled for our Extreme Mammals exhibit.”

With Extreme Mammals opening in less than a month, new boxes and displays are popping up every day. During NightLife, I got to meet a few members of the exhibit team from the American Museum of Natural History in New York who are overseeing the installment of Extreme Mammals at the Academy. And I was still in the building at 11pm, when a moving truck full of crates for the exhibit pulled into the loading dock.

But the life size replica of the Indricotherium stands taller amongst the rest of specimens – literally. As the largest land mammal ever to live at 25 feet in length, 17 feet tall and nearly weighing 18 tons; this replica dwarfs the T-Rex skeleton that used to take up its footprint but has since moved into the lobby. However, the blue whale still casts a mighty shadow over the Indricotherium. Weighing in at 180 tons, it would take 18 Indricotheriums to match the size of the largest mammal in the oceans today.

The relative today of Indricotheriums are modern day Rhinos and horses. Why are they so tiny in size compared to their prehistoric relative? The Indricotherium lived during the late Oligocene Epoch. During that time the Earth’s topography consisted of dry, seasonal scrublands. The Indricotherium could reach the tops of trees, which was too high for most grazers giving it a food niche that added to its massive size. As well, Indricotherium was well suited to exploit this food source. Its large head was supported by a thick neck, one that was flexible enough to allow the head to point upwards in pursuit of hard to reach vegetation. The Indricotherium had tusk like teeth that could snap off vegetation and molars to then grind it down. Like Rhinos, the Indricotherium also had a prehensile upper lip that allowed it to strip vegetation.

Due to its size, the Indricotherium had very little threat from predators. During the Oligocene, predators were smaller than the Indricotherium. Predators were similar in size to the modern day Rhino so the Indricotherium’s size kept them both in a plentiful food source and free from predation.

Soon, I will be able to walk under the replica of the now extinct Indricotherium to compare my size to the largest living mammal that walked the Earth. I wonder if I will be tall enough to reach his kneecap? And with the blue whale being 18 times bigger, I wonder what my size will feel like in comparison?

23andMe's DNA testing was always fun. Now it is more useful as well.

As anyone who follows this blog knows, I had my DNA tested awhile back by a company called 23andMe.  I wrote about what I learned and didn’t learn from their testing in a bunch of blog entries.

In my mind 23andMe has always been a sort of recreational genetics testing company.  You can find out about your earwax, whether you are likely to have blue eyes or be lactose intolerant and lots of other minor sorts of traits.  This is stuff you probably already know but for geeks it is pretty cool to see them written out in their DNA.

The company always offered some health data too but it wasn’t that strong.  For example, they could tell you if you carried the most common DNA difference that could lead to cystic fibrosis (CF) but not about the less common ones.  In fact, I gave them an incomplete for their carrier testing a few months back.

Since then, the company has gone away from being a place where you get your DNA tested for coolness’ sake to one with a focus on health and/or ancestry.  With this change has come a much-improved product for people interested in what their DNA tells them about their carrier status for a variety of genetic diseases.

Carrier status is important if you are considering having a child.  If you and your partner both carry the broken versions of a gene that could lead to a disease, then your child would be at an increased risk for getting that disease.  For example, if both you and your partner have a nonworking copy of the CFTR gene, then, depending on the exact DNA you each have, your child could have up to a 25% chance of ending up with CF.

This is why the first iteration of 23andMe carrier testing wasn’t as useful as I would have liked.  They tested only one of the 100’s of different DNA variants in the CFTR gene that can lead to CF. Since this DNA variant only accounts for about half the cases of CF, there was a good chance that something would get missed.  This is no longer true.

As part of the refocusing, 23andMe looks for 31 different variants in the CFTR gene that are known to cause CF. Now this isn’t hundreds but is more than the 23 recommended by the American College of Medical Genetics.  And in fact 23andMe includes these 23 in the 31 it tests.

Of course the testing still isn’t perfect but no testing is.  Some of the tests are only useful for certain ethnic groups.  And there is no upfront genetic counseling to help you decide whether or not genetic testing would be useful in your situation anyway.

But the bottom line is that 23andMe’s testing for genetic diseases that you might be carrying is much stronger than it was before.  So much so that it can even give you some piece of mind for many of these diseases.

In some ways I’ll miss the more whimsical look at DNA that 23andMe used to represent.  But this obviously wasn’t a good business model for anyone except those enamored of DNA.  And 23andMe does need to make a profit…

This giant red octopus can be seen at the California Academy of Sciences.

A week ago on Tuesday morning, a co-worker and I were able to go behind the scenes and visit with the Giant Red Octopus and his trainer. To get to his tank, we had to climb a ladder onto a deck surrounding one wall of the tank. There was a detachable wall blocking off the tank from the desk that was covered in astro-turf. Nancy, who works with the octopus, explained that an octopus can’t find suction on astro-turf and therefore cannot get the footing to climb out of the tank. There was also a lip of the tank out of public view. The “octopus garden” was displayed there as dozens of crab shells picked clean.

Nancy was awaiting a crab shipment later that day. She uses live crab as enrichment for the octopus. She also has puzzles made out of PVC piping she hides fish in for the octopus to solve. The octopus gets many visits, much like the one me and my co-worker were on, for enrichment as well.

Nancy took down the detachable wall and we came face to face with the octopus we had only every seen through glass. There were a couple of things I learned that day:

A giant red octopus can drench you in 10 seconds flat if he wants to. The siphon on an octopus is similar to gills on a fish and jettisons water in and out. When he was slightly above the water line, the siphon dumped about two gallons of water over the side and I was directly in the path. It took all day to dry out my jeans.

His skin felt totally different than I expected. I expected something like the scales on a snake. However, his skin was soft, super malleable and slimy. It felt totally weird touching him and my hands were super dry after playing with him for a half hour. I knew that an octopus was boneless before touching him, but it was altogether different to feel him.

Those tentacles have suction power! His trainer showed us how to lay our hands over his suckers and let him grab hold. He had one of his tentacles around my hand and I couldn't get him to let go. His trainer squeezed his tentacle further up and it relieved the suction enough that I could pop his suckers off my hand. They are strong too! At one point, he had suction across my arm and we were playing tug of war.

The giant red octopus knows and is bonded to his trainer. It was amazing watching them interact. I knew the octopus was intelligent before I got a close encounter with him but it was definitely reinforced after I saw how he interacted with us.

Part of why I love working at the Academy is moments like these. It reminds me why I am doing what I am doing for a living and that a special moment with an animal when I was small was what got me where I am today.

Missing two chromosomes but doing fine. A partial karyotype of a man with 44 chromosomes.

A doctor from China contacted me through this blog with some exciting news. He had found a patient with 44 chromosomes instead of the usual 46. And the patient was perfectly normal as far as anyone could tell.

The doctor contacted me because the story of how this patient ended up with 44 chromosomes mirrored my story of how humans may have gone from 48 to 46 chromosomes a million or so years ago. The idea that human chromosome reduction could happen this way was theoretical when I wrote about it. Now we have living proof that it can and does happen.

Sticking Two Chromosomes Together

At first it might seem weird that losing a couple of chromosomes had no real effect on the patient since losing even one is usually fatal. But his case is different because he didn’t really lose two chromosomes (and all of their essential genes). Instead the chromosomes ended up stuck to two other chromosomes. So he has the same genes…they are just packaged differently.

When this happens with a single chromosome, it is called a balanced translocation. These are more common that you might think with about 1 in 1000 people having one.

The way to end up with 44 chromosomes like our patient requires that both parents have the same balanced translocation. The only way this is at all probable is if the parents are closely related. In this case, they are cousins.

I won’t go into the details (click here to learn more) but these parents had a 1 in 36 chance of having a child with a double balanced translocation. And this is our patient.

From 48 to 46 to 44?

As I said before, a big reason why this is all so interesting is because it provides confirmation of one way that humans may have gone from 48 to 46 chromosomes so many years ago. The first step might have been similar to what happened to our patient. Two closely related parents with the same translocation have a child together that has fewer chromosomes.

Back then, chromosomes 12 and 13 fused together to create what we now call human chromosome 2. The fused chromosome then slowly spread through the community. And then, for some reason, the group of humans with 46 chromosomes eventually supplanted the group with 48.

We can’t know for sure, but this may have happened through some random event where the 48 chromosome humans were mostly wiped out and the humans with 46 chromosomes were spared.  Humanity has nearly been wiped our before with the most recent case being a volcanic eruption 75,000 years ago.

If something similar happens in the future, I wonder if people will be questioning our close relationship to chimpanzees. “How could chimpanzees be our closest relatives,” these future folks might ask, “when we have four fewer chromosomes than they do?”  This assumes, of course, that the number of chromosomes has not changed in chimpanzees by then…

Image Credit: Alex Wild.

For those of us fighting losing battles against them in our kitchens, ants are just ants. But the species responsible for the majority of those invasion has a name: the Argentine ant.

Argentine ants have had amazing success as an invasive species in the US. Their West Coast super colony numbers in the billions and spans from Mexico to Oregon. But aside from invading homes, they've had a dramatic effect on native ants and local ecosystems.

While many of us may not think ants are particularly important, ants hold a number of key ecological jobs, as I learned in this week's story. They disperse seeds, aerate soil just like earthworms, and recycle nutrients just like nature's garbage men (well, garbage women. Worker ants are actually female).

Argentine ants are certainly tiny, but thanks to their numbers, they've out-competed native ants for resources and attacked their colonies. So, many of the ecological jobs that native ants do are disappearing. Scientist have also documented the decline of coastal horned lizards, which depend on native ants a food source.

Citizens are helping track Argentine ants and their impact on native ants through a citizen science project, the Bay Area Ant Survey, run by the California Academy of Sciences. You can find more information on how to submit ant specimens of your own here. And for a little more about how they're collected, check out this post by QUEST's Jessica Neely.

In their native range in Argentina, these ants aren't such a nuisance. They don't form the super colonies that we see in North America. It's almost a terrible ecological irony: since the ants in the US descended from a small group introduced by humans, they're genetically similar. So, colonies that would normally fight over resources now see each other as relatives. With no ant wars, they've put that energy into expanding.

So, what can we do when Argentine ants show up in our kitchens? I asked the two scientists I interviewed for this story and their answers were pretty fascinating.

First, Cal Academy's Brian Fisher on the use of chemicals:

Second, UC Berkeley's Neil Tsutsui on what makes our homes look so good to ants:

Listen to the Bay Area Ant Invasion radio report online.

Fisheries technician Wes Hartman (left) and lead biologist Ben White tag a female coho in preparation for spawning at the Warm Springs Hatchery. The tag will help match the female with males that have been selected as mates through genetic screening. Credit: Brandon Beach/U.S. Army Corps of Engineers

A short history of California salmon: Glorious past. Grim present. Dark future. Now, the story I just got done working on for QUEST Radio is about the crisis of coho salmon along our coast. But that short synopsis applies as well to coho in other parts of the state and to their larger and perhaps better-known cousins, the chinook. Wherever you look in California, salmon are in serious trouble if they have not already disappeared. It's evident that their biggest problem is having to live alongside us. Our needs and our ability to exert our will on the world around us–to dam rivers and streams, to clear forests, to replace entire ecosystems with new ones of our own making–has wrought havoc on many species.

The collapse of salmon populations is just one example. Some of the people working to preserve and restore coho along our coasts feel that history–both the natural history of the salmon and their role in human history–can be a powerful teacher and could help save the wild fish from extinction. An egg being squeezed from the vent of a female coho salmon at the Warm Springs Hatchery. Biologists at the facility examine the eggs as part of the process of determining when the females are ready to spawn. Credit: Brandon Beach/U.S. Army Corps of Engineers Biologist Rory Taylor checks on a tray of coho salmon recently hatched at the Warms Springs facility. The coho here are called "alevin"–the salmon's earliest life stage. They'll be reared in the hatchery, then planted in tributaries of the Russian River. Credit: Brandon Beach/U.S. Army Corps of Engineers

Charlotte Ambrose, the National Marine Fisheries Service biologist in charge of coordinating an upcoming recovery plan for coho along our coast, says she has this intertwined history uppermost in her mind. In fact, the draft of the 4-inch-thick recovery plan she's been working on starts with a chapter on the coho's history. Ambrose calls it "a renegade move" to open the document that way, but she says she feels it's crucial to understand the past vitality of coho on the California coast.

She's fond of quoting a 1930s account of a coho run on Northern California's Garcia River: "The water was like glass … the salmon were in rows … they lay there still … every now and then one would wiggle its tail to keep his place in line. They lay there by the thousands as far as my eye could see." That's the glorious past of the coho.

But Ambrose points out that even in that lost age, coho showed a remarkable ability to handle adversity. Drought, flood, or fire might devastate a watershed and wipe out a run. But far from being "hot-house flowers," in Ambrose's phrase, coho are survivors by nature. They're prolific breeders–a single female will lay 2,000 eggs or more in its streambed nest. If they find their natal streams unreachable, they'll wander to new spawning grounds.

Ambrose thinks an understanding of the coho's history–its ever-present drive to perpetuate itself, and its past abundance–are key elements to getting people to act to save the fish. And she says small steps to improve the odds of salmon survival can be as important as sweeping ones. "It’s like a small pebble in a pond. One small action can make a tremendous difference in increasing the probability of survival of the young, of the adults, of the eggs, of the out-migrating smolts." If we want to rewrite the next chapter of the coho's story, she suggests, get to know your watershed, and go out and volunteer to help repair it.

Listen to Saving Salmon radio report online.

One of the most amazing aspects of the cuttlefish is their skin. The skin contains up to 200 pigment cells per square millimeter that enables it to change its camouflage at will.

I have been working for the California Academy of Sciences for five years now this month. I have always held a fondness for the aquarium. On my first day of work, I took a tour with other new hires through the aquarium at Howard Street. We stopped at the giant sea bass’s tank. It was feeding time and we were given sardines to feed him. We were instructed by one of the biologists to hold the fish in two fingers just beneath the surface to let him suck the fish into his mouth. When it was my turn, I dutifully held the fish under the water and watched the huge fish round the tank and head my way. He approached quicker than I had anticipated and I got spooked. So I lifted the fish out of the water. Well he still sucked the fish up; but he also sprayed me with salt water and fish guts. So I started at the office, dripping in salt water and smelling of sardines.

Tonight after work, I descended down into the Steinhart Aquarium. It’s kind of an after-work tradition to tour the aquarium before heading home. I like to stop by and see the same giant sea bass that drenched me and the octopus next door when the lights have been dimmed and the halls are empty. I now often stop at the dwarf cuttlefish tank. Tonight, one of them was swimming around the top of the tank, shimmering in a varied and beautiful color display. The other dwarf cuttlefish was resting at the bottom of the tank, expertly matching the rocks around it.

One of the most amazing aspects of the cuttlefish is their skin. The skin contains up to 200 pigment cells per square millimeter that enables it to change its camouflage at will. It also has muscles in its skin that enable it to change its skin from smooth to rough. Different species of cuttlefish can change the color and texture of their skin to blend in with the environment around them, display spikes and bright colors to ward off predators, or even create a strobe color display to mesmerize prey.

As well, cuttlefish, part of the Cephalopoda family that includes squids and octopi, have one of the largest brain to body ratios of any invertebrate. They can take in input from sight, smell and sound in the form of pressure waves felt through their lateral lines. The reaction of color displays has demonstrated problem solving and biologists study them to learn more about invertebrate and possibly human intelligence.

I now keep a closer watch on this tank, in hope of seeing the new generation of dwarf cuttlefish. The Academy is the first aquarium in the US to have a captive breeding program for dwarf cuttlefish, Sepia bandensis. The program, launched by Academy biologist Richard Ross offers the Steinhart Aquarium and other institutions the chance to feature a species, which is both captivating and less resource-intensive to keep than larger cuttlefish species. Dwarf cuttlefish span only two to four inches in length. “By establishing a stable breeding population,” Ross notes, “our hope is to make it easier for aquariums to showcase cuttlefish and their remarkable characteristics without impacting wild populations.” It’s no wonder that traveling through the Aquarium has become my favorite part of the day. Even after five years of wandering, I still see something amazing with every visit.

For some great footage of cuttlefish in the wild, along with information about research on cuttlefish and an overview of their anatomy – visit this great site provided by NOVA.

Staff at the International Bird Rescue and Research Center caring for oiled birds.

When two gigantic oil tankers collided near Golden Gate Bridge in 1971, more than 900,000 gallons of oil were spilled into the waters of the San Francisco Bay. Thousands of birds and animals were covered in oil and in great danger. Rescue centers to the scale that were needed did not exist. Concerned citizens and professionals snapped to attention and set up emergency centers, one being a facility in Richmond. Alice Berkner was one of those citizens and she was inspired by the efforts of the crew. As a registered nurse, she was also filled with ideas of how to improve on this brand new field. Alice and a group of volunteers were compelled to find the solution that worked best for future injured wildlife and The International Bird Rescue and Research Center (IBRRC) was born.

The center has since been working non-stop to save wildlife that suffers from oil spills and other disasters. In 2001, IBRRC helped to open the state-funded Oiled Wildlife Care and Education Center in Cordelia (Fairfield), California at the northern end of San Francisco Bay, a key facility in California's Oiled Wildlife Care Network. This facility contains IBRRC's new headquarters and the International Training Center for Oiled Wildlife Response. Their work includes training volunteers, consulting with the petrol industry, and managing a professional emergency response team. Their efforts have covered over 200 oil spills in 11 states, including the 1989 Exxon Valdez oil spill in Alaska. A southern rescue center in San Pedro, Los Angeles also contributes to the efforts.

What makes oil spills so toxic for birds?

Birds are made to be buoyant in the water, light in the air and warm and insulated wherever they go. Oil penetrates and opens up the structure of the plumage of birds, reducing its insulating ability, making the birds more vulnerable to temperature fluctuations. It also makes them heavy and less able to float above the water or take off for flight. In this exposed condition, they are unable to escape from predators or find food. As they attempt to preen themselves, they ingest the toxic substances. Unless there is human intervention, most birds affected by an oil spill do not survive.

Fortunate for those birds, and for us humans who are lucky enough to share the planet with them, organizations like the IBRRC exist and are powered by passionate wildlife heroes, like Jay Holcomb.

Jay Holcomb has served as director of the center for the past 24 years and has many amazing stories to tell, from pelicans to penguins.

You can hear these stories at, "Saving Seabirds – Stories from the Frontline" with Jay Holcomb of the International Bird Rescue Research Center. This will be an inspiring benefit presentation by Jay on January 28th at the Oakland Zoo. All proceeds from this event will go support future bird rescue efforts.

Discovered an oiled bird?
In California, call the Oiled Wildlife Care Network at 1-877-823-6926.

Interested in volunteering? Classes are available.

Pepin is famous for going to work after just 9 weeks of training, finding 52 scats in a single day.

This candidate must:

• Follow orders
• Be rough, energetic and adventurous
• Travel around the world
• Find things that are nearly impossible to see
• Be willing to ride in the back of a truck and wear a collar
• Run long distances
• Be a fast learner
• Be obsessed with toys
• Be willing to sniff poop
• Get compensated in rope-tugging with benefits such as scratches and belly rubs
• Come from a background of animal shelter living

Yes, the only qualified species is: Dog.

The Job: Working Dog for Conservation.

I saw these dogs in action at the Wildlife Conservation Network (WCN) Expo in San Francisco in October. The organization, Working Dogs for Conservation and their dog demo with Pepin took center stage during lunch. While Pepin was inside the building schmoozing with the likes of Dr. Jane Goodall, her trainers hid scat in a giant, wide open field area. Once the crowd gathered, Pepin was taken outside, given directions and once released, blasted with determination and blatant glee out into the field. Within 3 minutes she had located the scat and sat proudly next to it, indicating to her trainer that she had done her job; a job that would have taken a human hours.

Being able to find scat helps humans track down various species in the wild and provides needed species conservation information. Deployed conservation dogs have increased scat sample collection rates and have discovered samples that are smaller and more cryptic than people alone are capable of detecting. The working dogs for conservation have found scat of moose, snow leopard, grizzly bear, wolf and cougar, to name a few. The dogs have also been trained to find plants and lost pets and people.

Partnering with dogs is nothing new. Humans have been using the 220 million scent-sensitive cells available for canine olfaction for centuries. These animals are truly man's best friend, but perhaps they are becoming nature's best friend, as well. They certainly deserve to hold this most unusual job.