“We call it fishing for electrons.” That’s environmental engineer Craig Criddle describing a new way that he and his colleagues have discovered for generating electricity from sewage.

Wait. What?

Brilliant, right? The Stanford team hopes this breakthrough technology will be used to harvest energy in places such as sewage treatment plants, or to break down organic pollutants in the “dead zones” of lakes and coastal waters where fertilizer runoff and other organic waste can deplete oxygen levels and suffocate marine life.

And this new power all starts with wired microbes. The mini power plants produce electricity as they digest plant and animal waste from wastewater. Right now, still in the laboratory phase, their prototype is about the size of a D-cell battery and looks like a chemistry experiment, with two electrodes, one positive, the other negative, plunged into a bottle of wastewater.

Inside that murky vial, attached to the negative electrode like barnacles to a ship’s hull, an unusual type of bacteria feast on particles of organic waste and produce electricity, which is captured by the battery’s positive electrode.

Scientists have long known of the existence of what they call exoelectrogenic microbes—organisms that evolved in airless environments and developed the ability to react with oxide minerals rather than breathe oxygen as we do, to convert organic nutrients into biological fuel.

Over the past dozen years or so, several research groups have tried various ways to use these microbes as bio-generators, but tapping this energy efficiently has proven challenging. Part of that challenge for the Stanford team is the cost of the oxide minerals necessary to make it happen. “We demonstrated the principle using silver oxide, but silver is too expensive for use at large scale,” says team member Yi Cui. “Though the search is underway for a more practical material, finding a substitute will take time.”

The Stanford engineers estimate that the microbial battery can extract about 30 percent of the potential energy locked up in wastewater. That is roughly the same efficiency at which the best commercially available solar cells convert sunlight into electricity.

Their study was published recently in the Proceedings of the National Academy of Sciences.

Image: Xing Xie, Stanford University

Can scientists pull off a real-life version of Jurassic Park?  This intriguing question received a lot of attention earlier this year, when Revive & Restore (a project of the San Francisco-based Long Now Foundation) announced their goal of reviving extinct species using cutting-edge DNA technology. Dinosaurs have been gone too long for DNA to still be intact, but animals that went extinct during human history could potentially make a comeback. One of the first candidates for “de-extinction”—the iconic passenger pigeon (Ectopistes migratorius).

In the early 1800s, the passenger pigeon was the world’s most abundant bird species, even though its range was limited to eastern and central North America. Flocks of passenger pigeons—which sometimes included millions of birds—were so vast, they darkened swaths of sky up to a mile wide. But intensive hunting and habitat destruction by humans drove this species to extinction in a shockingly short span of time. The last passenger pigeon, “Martha,” died in 1914 at the Cincinnati Zoo. Her body remains at the Smithsonian’s National Museum of Natural History.

The Academy’s research collection houses nine specimens and three eggs of this species, dating to the late 1800s. Century-old specimens like these can still provide valuable information for modern-day studies. For example, Academy curator Jack Dumbacher and his colleagues published a paper in 2010 revealing that the closest living relative of the passenger pigeon is not the mourning dove, as many had suspected, but the band-tailed pigeon (Patagioenas fasciata), which is found along the Pacific coast and in the southwestern U.S., and can be seen in oak forests in the Bay Area. DNA sampling from museum specimens provided crucial data for this study. And the study’s conclusion provides critical information about which living relative could serve as a surrogate parent for the passenger pigeon, as scientists move forward with trying to revive this lost species.

Science Today sat down with Jack Dumbacher, who is also a scientific advisor to the Long Now Foundation, for his insights into de-extinction.

Where does the process currently stand?
JD: The Long Now Foundation has assembled a team of scientists to tackle different aspects of this project. Graduate student Ben Novak, working in Beth Shapiro’s lab at UC Santa Cruz, is refining the sequencing of the passenger pigeon genome from museum specimens. The genome of the band-tailed pigeon (the closest living relative) is also being sequenced.

Once the genomes are assembled, what happens next?
JD: You have to compare the genomes to determine which stretches of DNA make a passenger pigeon a passenger pigeon. Then you take the genome of a band-tailed pigeon and convert those important stretches of DNA into passenger pigeon DNA. George Church’s lab at Harvard is working on ways to do this using “CRISPR” technology—using bacterial proteins to genetically engineer specific DNA sequences and direct mutations to occur in a predictable way.

Let’s say scientists successfully get this DNA into an embryo, and the embryo becomes a chick. Is it a true passenger pigeon?
JD: That’s the big challenge. It may still have some band-tailed pigeon DNA. And you have to think about its behavior. How will it learn to be a passenger pigeon, find food, and avoid predators? Teams of researchers are tackling these numerous considerations and challenges.

Some might say that extinct animals went extinct for a reason, and bringing them back is not a good idea. How would you respond
JD: Animals like the passenger pigeon and moa went extinct due to human activity. So going extinct “for a reason” was humans to begin with. Also, developing the technology to successfully de-extinct an animal would itself be an intellectual coup, one that might have unforeseen benefits. The technology could be useful in other aspects of life, like agriculture, animal husbandry, conservation of endangered species, and, potentially, even human health. Think of the Space Race and all the accompanying benefits to society that resulted from that fundamental scientific research and development.

What other ethical concerns have come up?
JD: The ideal goal is to release de-extincted passenger pigeons back into their native habitat. But you have to be careful not to harm any other species whose survival may be on the brink. Their original ecosystem (the forests of the eastern and central U.S.) has changed. You don’t want to upset the balance in a way that threatens additional species. But the idea of restoring a habitat with native species is not a new one. Biologists restore habitats all the time. Had the pigeon survived only in captivity, we would be excited to be able to re-release it. Having survived only in our freezers or museum drawers, is that so different?

How many years away are we from seeing a real, live passenger pigeon?
JD: Optimistically, I would be very excited if this could happen in the next five to ten years. If not, I am confident that some day, we will have the technology to do this. Now is a good time to start thinking critically about what such a technology and ability would mean.

Andrew Ng is Communications Manager at the California Academy of Sciences.

It’s sea otter awareness week, which seems like a great time to reveal something heroic about this charismatic animal. A recent study from UC Santa Cruz concluded that sea otters are helping to save the ocean—with their appetites.

When you think of sea otters, you may think “cute and cuddly,” but these playful marine mammals are top predators, like great white sharks and tigers, and their hunt for food is helping to maintain ecosystem health along portions of California’s coastline.

The sea otter’s role in ecosystem management begins with one of its preferred foods: crabs. Sea otters eat crabs. Crabs in turn eat sea slugs and small crustaceans. The slugs and crustaceans eat algae off sea plants, keeping them green and healthy. It’s a relatively typical food web but now it’s clear: The healthier the crab-eating otter population is, the healthier the plants tend to be.

Sea plants, like eelgrass, along the west coast are important habitat for fish such as Pacific herring, halibut and salmon. They also protect shorelines from storms and waves, and they soak up carbon dioxide from seawater and the atmosphere.  Thus, a healthy coastal ecosystem has the right mix of otters eating crabs and invertebrates eating algae.

Unfortunately, seagrass meadows have been declining worldwide, partly due to excessive nutrients from agricultural and urban runoff entering coastal waters.  When sewage and agricultural waste like fertilizers spill into the sea, ecosystems suffer. Excessive nitrogen and phosphorus in the water spawns excessive algae growth, which can block sunlight and limit plant growth. Coastal areas that would otherwise be swaying in seagrass and kelp turn brown, murky, and barren of important marine species. But, not when sea otters are around.

Brent Hughes from the University of California, Santa Cruz and his colleagues studied 50 years’ worth of data, comparing areas with or without otters. The team discovered that otters trigger the above ecological chain reaction that protects seagrass meadows and can stave off algal blooms.

“The seagrass is really green and thriving where there are lots of sea otters, even compared to seagrass in more pristine systems without excess nutrients,” Hughes says.

Sea otters were hunted to near extinction in the 19^th and 20^th centuries. Populations on the California coast are slowly recovering now, and one of those places otters have called home since the 1980s is Elkhorn Slough, an estuary in Monterey Bay. Hughes and his colleagues determined that the re-colonization of that estuary by sea otters has been an important factor in the seagrass comeback.

In Tomales Bay, a nearby inlet with far lower levels of incoming nutrients, but no otters, the beds don’t look nearly as good. Hughes told Ed Yong of National Geographic:

The seagrass looks relatively unhealthy: it’s brown, covered in algae, and slumped over. The crabs are four times more abundant and 30 percent bigger than they are in Elkhorn Slough.

The findings in Elkhorn Slough suggest that expansion of the sea otter population in California and re-colonization of other estuaries will likely be good for seagrass habitat—and coastal ecosystems—throughout the state.

“This provides us with another example of how the strong interactions exerted by sea otters on their invertebrate prey can have cascading effects, leading to unexpected but profound changes at the base of the food web,” Hughes says. “It’s also a great reminder that the apex predators that have largely disappeared from so many ecosystems may play vitally important functions.”

The study was published last month in the Proceedings of the National Academy of Sciences.

(Sea otters also play a heroic role in the next Academy planetarium show! Currently in production and set for a fall 2014 opening date, the latest production from our visualization studio will highlight complex relationships in ecosystems—and how humans fit into the picture.)

Jami Smith is a science geek-wannabe and volunteers for Science Today.

Image: Robert Scoles/NOAA

Welcome to Sea Otter Awareness Week! Started 11 years ago to increase the public’s awareness about sea otters, the event “is an annual recognition of the vital role that sea otters play in the nearshore ecosystem,” according to seaotterweek.org.

Tomorrow we will explore that vital role a little more; for today’s article, we checked in with Moe Flannery, from the Academy’s Ornithology and Mammalogy department, to better understand the health of local sea otters.

The US Geological Survey’s Western Ecological Research Center conducts annual population surveys of the southern sea otter (Enhydra lutris nereis), a federally listed threatened species found in California. Flannery says the southern sea otter’s range extends from Pigeon Point near Half Moon Bay down to Point Conception in Santa Barbara County.

This year’s USGS survey was released earlier this month and the news is cautiously optimistic: sea otter numbers are up, due largely to an increase in the number of pups.

In its 2013 report, the USGS estimates the population to be 2,941. For southern sea otters to be considered for removal from threatened species listing, the population estimate would have to exceed 3,090 for three consecutive years, according to the threshold established under the Southern Sea Otter Recovery Plan by the US Fish and Wildlife Service. The USGS has been conducting the population surveys since the 1980s.

“Population growth in central California has faltered recently, so the fact that we’re seeing a slightly positive trend is a basis for cautious optimism,” says Tim Tinker, a USGS biologist who supervises the annual survey. “Certainly, sea otters have made an impressive recovery in California since their rediscovery here in the 1930s.”

“We counted a record number of pups this year, which led to the uptick in the 3-year average,” says USGS biologist Brian Hatfield, coordinator of the annual survey. “A high pup count is always encouraging, although the number of adult otters counted along the mainland was almost identical to last year’s count, so we’ll have to wait and see if the positive trend continues.”

USGS scientists also annually update a database of sea otter strandings—the number of dead, sick or injured sea otters recovered along California’s coast each year. Flannery leads the Academy as one of the organizations that responds to these strandings as part of the national Marine Mammal Stranding Network.

This year’s stranding number was 368. Flannery says that a remarkable number of sea otters wash up with shark bites. “The shark populations have been increasing because elephant seal populations are increasing,” she says. “The sharks appear to take a bite of the sea otters, but don’t consume them. As bony, skinny and furry as sea otters are (with up to one million hairs per square inch!), they’re probably less desirable than fat, blubbery elephant seals.”

Sharks aren’t the only threat to sea otters. Mainland diseases, such as toxoplasmosis from cat fecal matter, also plague the animals.

Because of their threatened status, all sea otter necropsies (animal autopsies) are performed by the California Department of Fish and Wildlife. However, many of the specimens end up here, in the Academy’s collections. The result is that we have the largest collection of southern sea otter specimens in the world. The number was up to 1,300 specimens last year, but several hundred have yet to be cataloged and processed, according to Flannery.

Researchers come from all over the world to study the specimens—last year scientists from UC Davis came to study dental pathologies in 1200 sea otter skulls!  They found that 93% of our southern sea otter specimens had problems with their teeth.

Luckily, most of us don’t have to study 1200 sea otter skulls to learn more about these engaging animals. For events around Sea Otter Awareness Week, including this week’s Nightlife at the Academy, click here. Celebrate!

Image: Mike Baird/Wikipedia

Here’s a sampling of a few science headlines from this past week—enjoy!

Grey wolves

When are grey wolves not grey wolves? According to headlines this week in Nature News and New Scientist, the grey wolves are called eastern wolves when the US Fish and Wildlife Service (FWS) wants to de-list the animals from the Endangered Species list.

Citing a publication in FWS’s own North American Fauna journal, the agency claims that the grey wolves were never historically in the regions where the species are being restored. Those were a separate, healthy species, eastern wolves.

But scientists, not to mention genetic testing, describe the eastern wolves as a sub-species of grey wolves. Read more about the science and politics in Nature News.

Crazy, dangerous fungi reproduction

Cryptococcus neoformans is a dangerous fungus that infects individuals with compromised immune systems, such as HIV/AIDS patients. It causes more than 600,000 deaths a year, accounting for a third of all AIDS-related deaths. Some strains can be drug resistant and scientists had a hard time determining why.

Like some other fungi and microorganisms, C. neoformans are both asexual and procreate with exact replicas of themselves, where the expected outcome should simply be more of the same. So how could some individuals develop drug resistance when others do not?

Now researchers, publishing in PLoS Biology, have found the act of sex between such genetically identical organisms can itself be mutagenic, meaning it can create genetic changes and diversity where it did not previously exist. In fact, in the case of the fungus C. neoformans, the process of sexual reproduction can result in extra bundles of genetic material or chromosomes that can be beneficial to the organism’s survival—such as drug resistance.

ScienceNOW has more information.

The chemistry behind whiskey

Thank goodness for Thomas Collins (that’s really his name!) of UC Davis. He’s studying the chemical compounds that make up rye and bourbon whiskeys.

Using chemistry’s latest analytical tools, Collins’s team profiled 60 American whiskeys and found that a single whiskey sample can contain hundreds of nonvolatile compounds, the ones that tend to stay in the liquid rather than evaporate off. Added up across multiple samples, the number of compounds comes to about 4,000 total, a scientific testament to the complex molecular mingling that occurs as a spirit ages, sometimes for decades, in a 53-gallon oak barrel.

Why the in-depth study? “Whiskeys’ chemical profiles could be used for distillers’ quality assurance or process improvement programs,” says Collins, who has conducted similar experiments on wine. “In addition to that, they could be used to help speed up production.”

I’ll drink to that! NPR has more details on the influence of oak barrels on whiskey flavor.

Image (fungus): Joseph Heitman

When are extreme events part of natural climate variability and when are they due to climate change? It’s important to ask—no matter where you stand on the role of humanity’s impact on the environment.

A group of international scientists decided to address this question, focusing on a dozen or so extreme events from 2012. Their results were published last week in the Bulletin of the American Meteorological Society. (The findings are also available in a downloadable report.)

And the results, were, well, variable.

The researchers did not look at Hurricane Sandy, but they did examine the flooding and the inundation it caused. Because of sea-level rise (a direct result of climate change), the researchers determined that the superstorm did far greater damage than it would have with oceans at normal levels.

The team also determined that heavy rains in the United Kingdom, Japan, and China were not due to global warming, and Australia’s above-average rainfall was due to a La Niña event (or short-term climate variability).

However, a deluge in New Zealand was due to climate change. From Wired:

Total moisture available for this extreme event was 1% to 5% higher as a result of anthropogenic greenhouse gas emissions.

And Arctic sea ice melt? The cap of sea ice covering the North Pole shrunk to its smallest extent last summer. The cause? Climate change.

What about last year’s devastating drought in the Midwest? Scientists judged that climate variability was to blame—not global warming.

However, Stanford researchers did find that the extreme heat that came with last summer’s drought could be attributed to climate change. They also found strong evidence that the high levels of greenhouse gases now in the atmosphere have increased the likelihood of severe heat.

In addition, their findings indicate that extreme weather in the north-central and northeastern United States is more than four times as likely to occur than it was in the pre-industrial era.

The Palo Alto scientists hope the results from these studies can help to quantify the true cost of emissions to society, since the cost of the disaster is measurable.

“Knowing how much our emissions have changed the likelihood of this kind of severe heat event can help us to minimize the impacts of the next heat wave, and to determine the value of avoiding further changes in climate,” says lead author Noah Diffenbaugh, a Stanford associate professor of environmental Earth system science.

Image: Theresa L Wysocki/Flickr

When researchers found fire salamanders (Salamandra salamandra) in the Netherlands dying at a rapid rate from a skin fungus, they thought the infection looked familiar.

Globally, amphibian numbers are declining in large part due to a chytrid fungus known as Batrachochytrium dendrobatidis or Bd. Bd attacks the skin of its host causing “the outer layers of the epidermis to thicken,” says the Academy’s amphibian expert, Dave Blackburn. “Bd disrupts the function of amphibian’s skin by interfering with electrolyte transport.”

Bd is quick and deadly: its effects may have wiped out more than 200 species of amphibians worldwide.

Similarly, the fire salamanders are dying at a rapid rate. Since first seeing dead animals in the Netherlands in 2010, scientists have observed that the population has fallen to around 10 individuals, less than four per cent of the original numbers.

But the similarities end there. The infected fire salamanders display skin lesions or ulcers and when the animals were tested, they were negative for Bd.

So what gives? According to a paper published last week in the Proceedings of the National Academy of Sciences, a new chytrid fungus.

Batrachochytrium salamandrivorans or Bs is closely related to Bd, but an entirely new chytrid fungus species.

This study is incredibly important, Blackburn says. “It clearly shows three things: 1) Bs is a new species of chytrid, 2) it presents different pathology than Bd (these lesions), and 3) it may have different host specificity.”

Bs, like Bd, doesn’t kill every amphibian it meets. “Midwife toads, Alytes obstetricans, are among the most susceptible of European frogs to Bd,” Blackburn says. But the study researchers infected the toads with new fungus Bs, and they were not susceptible to that fungus.

But the evidence the study provides only brings more questions for Blackburn. “When we think some amphibians around the world were killed by Bd, could it have been something else? Bs? Yet another species of chytrid?”

He gives an example of the thermal range for Bs and Bd. “People trying to predict how Bd spreads and where it would thrive—the fungus may be absent from that location now, but where it might flourish given the right conditions—by modeling where the disease is now with information on climatic conditions. In the past, have we been looking at the thermal range for Bd only or might we have confused some records of Bd with what we now know as Bs? Each may have different thermal conditions and there could be errors to where we’ve predicted that the disease could thrive.”

Testing for the new chytrid fungus also presents a conundrum. Although tests have been developed to screen for Bd, it is not clear whether these might sometimes be detecting Bs instead. The authors of the new study have developed primers to test for Bs, and Blackburn and his lab will obtain these to test animals here at the Academy.

Blackburn and other scientists came back with live frogs from Cameroon earlier this summer. The team hopes to raise and breed the animals here, displaying them for the public. As we reported in a story a few weeks ago, the frogs are part of a new initiative at the Academy focused on amphibian conservation and biodiversity education.

The Cameroonian frogs were screened and tested positive for Bd. They are being treated with a proven microbial solution, but now Blackburn is worried about Bs. “How widespread is Bs?”

And Blackburn has more and more questions… “Does it only affect salamanders? We’ve seen salamander declines in Central America—it looks like Bd, but could it be Bs? We found skin lesions on amphibians in Cameroon with mortality events, Bd was not present when tested. Could we have found Bs, instead?

“How is it spread, is it totally different from Bd? Why are we seeing these now? How is climate change affecting the emergence, spread, and change of prevalence? How do you stop them?

“Bs really opens the door for further research,” Blackburn says.

Image: Didier Descouens/Wikipedia

The closest I’ve ever come to a whooping crane, perhaps like many folks, is reading Even Cowgirls Get the Blues:

The whooper enters one’s spirit the instant it enters one’s senses. It is perfect radiant sky monster and I cannot describe it.

(Come on, it was written in trippy 1976…)

And it’s likely a good thing that we keep our distance, remarked Greg Smith, of the USGS, on NPR last week:

The more fear they have of humans, the better off we think their survival chances are.

But the potential benefits of staying away from humans makes it difficult to understand the migration patterns of the rebounding bird.

The whooping crane (Grus americana) is North America’s largest bird, standing five feet tall, and survives 30 years or more in the wild. The species neared extinction in the 1940s, as unregulated hunting and habitat loss pushed its population to fewer than 25 individuals. Today there are about 600 whoopers, with more than 150 in captivity.

Humans played and continue to play a huge role in helping the species rebound, despite Smith’s quote above. At captive breeding sites, adult whooping cranes produce chicks which are then hand-raised by biologists using special methods designed to prepare the chicks for life in the wild. Each summer in a Wisconsin marsh, experts train a group of captive-raised chicks to follow an ultralight aircraft, leading them on a 1,300-mile journey to their Florida wintering grounds.

Only this first migration is human-assisted; from then on, the young birds travel on their own, usually in the company of other whooping cranes. Their movements are monitored daily via satellite transmitters, radio telemetry, and on-the-ground observers. All this human activity results in a record of the movements of individual birds over several years, all with known parentage and the same upbringing.

Researchers at the University of Maryland studied these data from whooping crane migrations from 2002 to 2009 to understand whether their migration route is encoded in their genes or is instead a learned behavior.

Publishing their findings in the recent issue of Science, the team determined that the whoopers learn their migration route from older cranes, and get better at it with age.

Whooping crane groups that included a seven-year-old adult deviated 38% less from a migratory straight-line path between their Wisconsin breeding grounds and Florida wintering grounds, the researchers found. One-year-old birds that did not follow older birds veered, on average, 60 miles (97 kilometers) from a straight flight path.

Individual whoopers’ ability to stick to the route increased steadily each year up to about age five, and remained roughly constant from that point on, the researchers found. The scientists hypothesize that older birds are better at recognizing landmarks and coping with bad weather.

“This is a globally unique data set in which we can control for genetics and test for the effect of experience,” says co-author William F. Fagan, of the University of Maryland. “It gives us an indication of just how important this kind of socially learned behavior is.”

So, whatever the role humans play in whoopers’ survival, they clearly need one another to survive and flourish. Here’s to those radiant sky monsters!

Image: US Department of Agriculture