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.

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

Batrachochytrium dendrobatidis (Bd) is the deadly chytrid fungus killing amphibians worldwide. Researchers have tracked the fungus to African clawed frogs (Xenopus laevis) in South Africa back to 1934, but how did it leave Africa—and those frogs—to cause the recent decline and extinction of 200 frog species worldwide?

Vance Vredenburg of San Francisco State University wants to know. In 2008, he witnessed a population of frogs he studied in Sequoia and Kings Canyon National Park drop 99.9% due to Bd.

Working with a team of researchers at Stanford, Vredenburg began looking at the herpetology collection here at the Academy. Our own Jens Vindum offered the team several specimens of African clawed frogs to swab for DNA samples. The scientists focused on specimens collected from wild populations in California between 2001 and 2010.

African clawed frogs were imported to the US between the 1930s and 1950s for use in pregnancy tests. The frogs ovulate when injected with a pregnant woman’s urine.

“Today, these frog populations are often found in or near urban areas, probably because hospitals released them into the wild when new pregnancy testing methods were invented in the 1960s,” Vredenburg says. Since then, the frogs have established feral populations throughout North America, including Golden Gate Park.

Sure enough, the Academy’s California specimens of African clawed frogs carried Bd. “This is the first evidence of the disease among introduced feral populations in the US, and it suggests these frogs may be responsible for introducing a devastating, non-native disease to amphibians in the United States,” says Vredenburg.

And although the species is a known Bd carrier, these amphibians don’t succumb to the fungus. “It’s amazing that more than half a century after being brought to California, these frogs are still here, and they still carry this highly infectious disease,” remarks Vredenburg. “This implies that there must be a stable relationship between the pathogen and the frogs, whereas there are other frog species, for example in the Sierra Nevada, which have been wiped out by the pathogen.”

The team also tested archived Academy specimens collected in Africa between 1871 and 2010 and found evidence confirming that Bd was present among indigenous populations of this species before they were exported worldwide.

Although no longer used in pregnancy testing, African clawed frogs are still imported to the US for use in biomedical and basic science research. Because of their suspected role as a carrier of the Bd fungus and other potential pathogens, eleven states have already restricted the importation of these frogs, by requiring special permits and not allowing them to be sold as pets.

The study was published last week in PLoS One.

Stay tuned—this summer, Science Today will document Vredenburg’s and Academy researcher Dave Blackburn’s fight against Bd.

Image: Michael Linnenbach/Wikipedia

That’s what a recent paper in PLoS Biology asks—and doesn’t really answer.

Instead, it lays out a great argument, giving the pros and cons of using the controversial technique in addressing conservation issues. It also urges the two parties—synthetic biologists and conservation biologists—to get in the same room and talk about the possibilities and problems with open minds. In fact, the authors of paper organized a meeting this week in the United Kingdom, bringing the two groups of scientists together. (Ed Yong has an article about the meeting at National Geographic.)

The paper describes several examples of how synthetic biology could work to help conservation efforts—restoring habitats, supporting endangered species, and even reviving extinct species. It also lays out several examples of how synthetic biology could wreak havoc on the natural world. (The open-access article is very readable. We encourage you to review it or at least take a look at the examples in Table 1.)

The paper and meeting come on the heels of huge media coverage on de-extinction. National Geographic’s April issue on the topic garnered a lot of press and generated public interest. In some cases, these articles say, de-extinction could be just a few years away, if not closer.

The PLoS paper and de-extinction topic seemed to be a great opportunity to speak to Terry Gosliner, the Academy’s Dean of Science and Research, about the subject.

“Do you really want to encounter a saber-toothed cat in Muir Woods?” Terry joked when we sat down.

He sees huge potential risks in using synthetic biology for conservation, but admits that the meeting and discussion are a great idea. “Open dialogue is the only way to explore the topic, see the potential and understand what the concerns and dangers are,” he says. “Bad things happen when there isn’t discussion. Informed dialogue is the best way to deal with controversial issues.”

Terry believes some aspects of synthetic biology in the natural world could work, with appropriate regulation.

But he also sees that synthetic biology may not be the right approach. When thinking about threatened species, the problem is usually “habitat loss, not necessarily genetic constraints.” He uses the re-emergence of California condors as an example of this.

And in some cases, extinction is a natural process, Terry reminds us. Synthetic biology could just be more of humans interfering with nature, and not in a good way.

The resources going toward de-extinction could be better used to protect life before it goes extinct, Terry thinks. “If we use the same resources to address climate change and how we use energy,” Terry says, “We literally could save hundreds and thousands of species.”

And those energy and climate resources could be from synthetic biology. The PLoS paper cites a 2009 report on synthetic biology: “Many believe that synthetic biology will be one of the transformative technologies necessary to combat climate change, energy shortages, food security issues and water deficits.”

What do you think? Can synthetic biology save wildlife? Where do you stand on the issue?

If geochronology is “the science of determining the ages of earth materials” (according to the center’s website), then Renne must know his gnat’s eyebrow. For those of us lay-folk, it’s about 5,000 years.

Renne and his colleagues have a new paper in Science pinpointing the dates of both the impact and the dinosaur extinction, placing them within the same time of each other—providing evidence, once again, for an asteroid or comet impact being the cause of extinction.

The 110 mile-wide Chicxulub (cheek’-she-loob) crater, off the Yucatan coast of Mexico, is likely the result of a six-mile in diameter asteroid or comet. Using and refining a technique called argon-argon dating, the scientists determined that the impact occurred 66,038,000 years ago, plus or minus 11,000 years.

The same argon-argon dating put the dinosaur extinction at 66,043,000 years ago, with the same margin of error.

The first link between the impact event and dinosaur extinction was published in 1980 by UC Berkeley’s Luis and Walter Alvarez. Since then, many other scientists have supported or refuted the theory, sometimes putting the extinction several hundred thousand years before the impact.

“When I got started in the field, the error bars on these events were plus or minus a million years,” says UC Berkeley paleontologist William Clemens. “It’s an exciting time right now, a lot of which we can attribute to the work that Paul and his colleagues are doing in refining the precision of the time scale with which we work.”

Despite the synchronous impact and extinction, Renne cautions that the impact was not the sole cause of extinction. Dramatic climate variation over the previous million years, including long cold snaps amidst a general Cretaceous hothouse environment, probably brought many creatures to the brink of extinction, and the impact kicked them over the edge.

“These precursory phenomena made the global ecosystem much more sensitive to even relatively small triggers, so that what otherwise might have been a fairly minor effect shifted the ecosystem into a new state,” Renne says. “The impact was the coup de grace.”

The team of researchers, working for the International Union for Conservation of Nature (IUCN), released a report called Priceless or Worthless? In addition to being online and in print, the report was presented at the IUCN World Conservation Congress in South Korea on Tuesday.

The report (a must read!) lays out the statistics of these rapidly declining plants and animals and explains why it’s important to save them, regardless of how much they help the human race.

“The donor community and conservation movement are leaning increasingly towards a ‘what can nature do for us’ approach, where species and wild habitats are valued and prioritized according to the services they provide for people,” says Jonathan Baillie, Director of Conservation at the Zoological Society of London. “This has made it increasingly difficult for conservationists to protect the most threatened species on the planet… While the utilitarian value of nature is important, conservation goes beyond this. Do these species have a right to survive or do we have a right to drive them to extinction?”

As Baillie implies, humans are at the root of most of these threats. The report describes funding, policy, legal and even marketing standpoints of why we need to and how we can save these species.

And while you can see galleries of these threatened species on National Geographic, New Scientist and Wired, really, go read and look at the report online. The images are phenomenal and the urgency of the risks of extinction leap from the page. (Did we mention it’s a must read?)

From plants and fungi to amphibians and mammals, all life is valuable. A quote from Georgina Mace in the report perhaps explains it best:

Every living species represents one unique pathway to success, developed over millions of years. What we lose with each passing species can never be replaced.

Image: Dr. Richard Bartlett/Wikipedia

Until last week, I had no idea what a murmuration was. Did you? Then this amazing video went viral. The science behind starlings flying in unison is stunning and more about physics than biology, says Wired.

Each starling in a flock is connected to every other. When a flock turns in unison, it’s a phase transition.

How does a hummingbird stay dry in the rain? Ask your dog. UC Berkeley researchers, using high-speed video, found that hummingbirds shake off water like dogs do, only in mid-flight, “reaching a G-Force of 34,” according to NPR. Dang!

How can two birds sing a duet so synchronous that it sounds like only one bird singing? Researchers studied Andean wrens’ neurons to understand this phenomenon. They discovered that a pair of male and female wrens memorizes the entire song, coming in when only needed. The female appears to take the lead, so perhaps “the duets are a way for a female to challenge and test a male,” ponders ScienceNOW. You can take a listen here.

Recent studies have shown that many animals are getting smaller as the climate warms. But research conducted by our friends at SF State and PRBO finds the opposite is true with Californian birds. Analyzing data from thousands of local birds caught and released each year over the past 40 years, the scientists discovered that the birds’ wings have grown longer and the birds are increasing in mass.

Extinct birds were the subjects of two separate multimedia articles last week. Cornell University, via the New York Times, has video (the only known video or image) of the imperial woodpecker, extinct since the mid-20^th century. These were beautiful birds, done in by logging in Mexico’s Sierra Madre. Listen to the audio, too. New Scientist has a gallery of “bird ghosts,” that includes drawings by Ralph Steadman and haunting music, too.

Want more? How about rewarding designers and builders for creating bird-friendly buildings? Or robins pleading guilty in spreading the West Nile virus?

Finally, have you read the ongoing “Scientist at Work” blog by the Academy’s own Jack Dumbacher in the New York Times over the past two months? Jack is researching birds in the islands of Papua New Guinea. We’ll feature a video of his work next month, so stay tuned!

Image: User:Mdf/Wikipedia

Well, enough is enough! Over the past two weeks, we have seen some very exciting plant news, including recent funding for new research! From ScienceInsider today:

Long the impoverished Cinderella of the biological research kingdom, plant science has just had a visit from the fairy godmother. Today the Howard Hughes Medical Institute announced it would hire up to 15 plant biologists and spend $75 million over the next 5 years to enable these new HHMI researchers to pursue creative and fundamental research.

This research will also be funded by the local Gordon and Betty Moore Foundation.

Just in time, too. Also in the news today, one-fifth of the world’s plants are at risk of extinction. New Scientist runs the numbers for us:

The Sampled Red List Index for Plants indicates that 22 per cent of all wild plant species face extinction, comparable to the figure for mammals (21 per cent) and higher than that for birds (12 per cent). Of the threatened plant species, 63 per cent are found in tropical rainforest areas which could soon be cleared.

Also in science news recently, daisies. Daisies and their kin (which include sunflowers, dandelions, lettuce, and artichokes) are part of one of the largest plant families in the world. And new research, published last week in Science, confirms that they’re also really, really old. Scientists always thought that the family traced back about 50 million years, and now they have evidence—a fossil found in South America. From Nature News:

Complete with large flower heads, leaf-like structures and slender stems, the remains come from rocks in Patagonia that are 47.5 million years old, dating from the Middle Eocene.

Finally, published last week in the Journal of Ecology, 150 year-old pressed orchids in museum herbaria. That may sound like old news, but these antique flowers provide a new source of data for studying climate change. According to Wired:

Scientists have used the carefully labeled and dated specimens of the early spider orchid, Ophrys sphegodes, to examine the affect of spring temperatures on flowering. The flowers were collected between 1848 and 1958.

The results… found that for a 1.8 degree Fahrenheit increase in the spring temperature, the orchid flowered 6 days earlier.

As The Great Beyond Blog in Nature puts it:

Every year, the media reports that the transition between winter and spring is arriving earlier, and that plants are no longer blooming when they used to. But accurate records of the effects of changing temperatures on plant flowering times are patchy at best… The shortage of available data may not be a problem for much longer.

That’s because in addition to the orchids, there are literally billions more specimens held in natural history collections in museums and herbaria. Some specimens date back to the time of Linnaeus (who devised our system of naming plants and animals) 250 years ago. Climate tracking just got a lot easier, thanks to plants.

So let’s give it up for plants. It’s about time!

Image: Science/AAAS