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.

Can birds read? While a new study provides evidence of avian intelligence, no, our feathered friends aren’t literate (as far as we know).

Canadian researchers, working in France, have found that birds foraging on roads and highways vary the amount of time they take to leave the asphalt when they see a car approaching. And it appears to depend on the posted speed limit.

During Pierre Legagneux’s commute he noticed that birds let him drive closer if he was traveling on a slower road. Using a modern, hi-tech tool—a stopwatch—the scientist monitored the birds’ “flight initiation distances” (FIDs) from the safety of his speeding car.

“FID is basically the distance that the car is from the bird when the bird takes off,” explains Academy bird expert Jack Dumbacher. “When a car is moving slowly, the bird can wait until the car gets pretty close, but when the car is moving fast, it has to begin taking off when the car is still very far away—just to make sure that it can avoid being hit. He was able to measure this pretty easily on his commute by multiplying his speed by the time it took to reach the bird.”

Over a year’s time, Legagneaux measured the FIDs of 134 birds from 21 different species, including many crows (Corvus corone), sparrows (Passer domesticus), blackbirds (Turdus merula) and unidentified songbirds.

And what he found was astonishing! His actual speed had nothing to do with the FID. But the posted speed limit did. The birds’ FID was consistently farther away for faster roads. For roads with a 20 kilometers per hour posted sign, the birds’ FID was 10 meters; 90km/hour signs, 25 meters; and 110km/hour, 75 meters.

“The authors aren’t exactly sure how the birds know, but it appears to have more to do with the AREA than with the oncoming car,” Dumbacher says. “The birds are not assessing the speed of the car, but what speed they THINK the car OUGHT to be going in that area.  And thus, the best predictor in the models was the actual posted speed limit.

“The method is simple and elegant—and something that he was able to do while commuting and paying attention to traffic. (Apparently there aren’t laws against operating a stopwatch while driving in Europe.),” Dumbacher continues.  “All he had to do was jot down 1) his speed, 2) the speed limit, and 3) the time it took to reach the spot where the bird took off.  From his citations, it looks like something like this has been studied before, but this is a cool and interesting article—something that a high school student could do for her science fair project (if she were old enough to drive…).”

The research is published in Biology Letters.

Crow image: Mostly Dans/Flickr

How will climate change affect different species? Will organisms be able to adapt quickly enough to survive in a rapidly changing environment?

Researchers at the University of Oxford are attempting to predict this with small, short-lived birds like the great tit (Parus major). In a study published this week in PLoS Biology, the scientists discovered that great tits living in a forest near Oxford have been able to survive and adapt to a 1°C temperature increase over the past 50 years.

After analyzing those 50-plus years of data collected on the birds in their habitats, the authors studied when the birds lay their eggs relative to spring temperatures, as well as how the birds have tracked the shifts in peak caterpillar numbers caused by the changes in temperature. They found that the birds are now laying their eggs an average of two weeks earlier than they did 50 years ago, primarily as a result of phenotypic plasticity.

Phenotypic plasticity enables organisms to adjust their behavior rapidly in response to short-term changes in the environment. Jack Dumbacher, curator and department chair of Ornithology & Mammalogy here at the Academy, explains, “It’s heritable but it’s not an evolutionary, or genotypic change. There’s no change in the genes.”

The authors’ predictions show that phenotypic plasticity could allow the great tits—and similar birds—to survive warming of 0.5°C per year, easily outpacing the current worst-case scenario of 0.03°C from climate models.

Dumbacher says that while this study is interesting and a good reminder how adaptable one species may be, he emphasizes that temperature increase is just one effect of climate change. Temperature variance and extreme weather are other effects with unknown results to various ecosystems, he says. In addition, Dumbacher reminds us that the great tits and caterpillars play roles in a much larger ecosystem, where the web of relationships is so interdependent that one small change to one small organism in that web could easily affect other species.

One effect of climate change that Dumbacher stresses (and the study does not mention) is invasive species. As temperatures change, habitat ranges change for different species, which can result in one species invading the habitat of another. One example Dumbacher gives is the Northern Spotted Owl (Strix occidentalis caurina). These birds have been able to adapt to a 1°C temperature increase over the past 100 years but are now facing a fierce competitor in the Barred Owl (Strix varia), an eastern species that now finds itself in the same territory as the Northern Spotted Owl.

“Climate change is more than a one degree temperature increase,” Jack says. “And while a species may demonstrate plasticity within different temperature regimes, it’s likely that ecosystems are not as adaptable. This why climatologists have such a difficult time predicting the effect of climate change on organisms.”

Image: Luc Viatour/Wikipedia

Evolution takes time. Or does it?

Evolution can happen rapidly—it all depends upon how strong selection is and how much genetic variation there is in the trait being selected.  We tend to look at fossil bones, for example those along the horse lineage, and it seems like only a few millimeters of length are added per hundreds of thousands of years.  But in fact, these traits can vary quite a bit—even within populations—and if you have lots of individuals and lots of points in time, sometimes you can see really noticeable changes in short times.  The classic examples are Darwin’s Finches, that can significantly evolve larger or smaller bills during times of great stress.

That’s the Academy’s bird expert Jack Dumbacher. I asked him about a paper published this week in Current Biology about birds evolving shorter wings over a time-span of a mere thirty years. The evolutionary advantage? To avoid becoming roadkill.

In the US alone, an estimated 80 million birds are killed each year by cars. But the paper’s two authors, Nebraska researchers Charles and Mary Brown, noticed that fewer of the swallows they’ve studied for the past 30 years were becoming roadkill. This finding was surprising, since there are more cars on the road now than in the 1980s, and more of the swallows make their homes near the highways.

The researchers recently collected hundreds of dead cliff swallows from roadways, railroad tracks and other nesting areas, and noticed that “there were fewer road kills, and the birds found dead along highways had longer wing spans,” Charles Brown says. “I wanted to know if there was selection for particular characteristics in those dead birds.”

So he and his colleagues began a retrospective analysis, measuring the specimens in his 30-year collection. According to ScienceNOW:

The birds that were being killed, further analysis revealed, weren’t representative of the rest of the population. On average, they had longer wings. In 2012, for example, the average cliff swallow in the population had a 106-millimeter wingspan, whereas the average swallow killed on the road had a 112-millimeter wingspan.

The results suggested cliff swallows were undergoing morphological changes through natural selection.

Jack explains this adaptation. “Shorter wings—just like shorter cars – usually means a shorter turning radius. So if the birds need to make a rapid change in course, smaller wings might help facilitate this.”

The cliff swallows aren’t the first bird species to evolve quickly in response to human impacts. “One of my favorite examples is bird song in human habitats,” Jack says. “Our roads and neighborhoods are full of noises—air conditioners, traffic and other machines. Some of these produce noise in certain frequencies that can drown out or obscure bird song.  Researchers here and abroad have shown that many birds have noticeably shifted their song frequencies to avoid our ‘white noise’ and be better heard in human environments.”

Jack appreciates the work of the Browns in determining these shorter wingspans. “We often drive our commute and watch this or that, and sometimes we even ask ourselves whether, ‘Hmm, sure does seem like there are fewer roadkill than last year.’  Even a simple question like this can be incredibly difficult to even verify, but then to do all of the work to find the cause of the change—that can be very difficult to do.  They clearly have that restless scientific mind that doesn’t rest until they find a solid answer…”

I guess it takes one to know one.

Image: Ingrid Taylar/Wikipedia

Scientists who study birds have known this for a while.

The Academy’s Curator and Department Chair of Ornithology & Mammalogy, Jack Dumbacher, explains, “Beaks can tell us many things—often they reveal the foods that birds might eat and how they might forage, but they might also be useful for mating displays, building special nests, or improving the sounds of their vocalizations.”

Does the size of the bill also matter? Russell Greenberg, of the Smithsonian Migratory Bird Center, and his colleagues thought so. They study song sparrows living in the US—near the coast and inland—and noticed something interesting about these familiar feathered friends. For the subspecies closer to the coast, the beak bills were smaller. Those more inland, larger. But why?

“No one could figure out what this is an adaptation for,” Jack says.

Greenberg had a hunch it had to do with heat. See, birds don’t sweat. Or perspire.

“And with a thick downy plumage,” Jack says, “they may have to work to keep cool on a hot summer day.  Birds often pant, ruffle their feathers, and even move air through their feathers to keep cool. They can also radiate heat off their bills.”

Greenberg et al decided to investigate this last point by studying two song sparrow populations on the East Coast and two on the West Coast—inland vs. coastal subspecies.

For the first study, published last week in PLoS ONE, the researchers used thermal imaging to measure body and bill temperature of Eastern song sparrow populations.  The researchers found that the hotter the temperature, the warmer the bill—by about 5-10°C.

The researchers concluded that the birds dissipated heat through their beaks and birds in warmer climates would need larger beaks to do the job. In their studies, the scientists discovered that inland birds with larger bills dissipated over 30% more heat than coastal birds with smaller bills.

For the next study, published in the journal Evolution last week, the researchers took a look California song sparrow specimens housed in various museum collections, including the collection here at the Academy.

Collections like the Academy’s are useful, Jack says, because “each of our specimens has information about when and where they were collected.  Combining this with careful bill measurements allowed the researchers to correlate bill size with locality, and locality with annual temperatures.  It takes thousands of birds to do this kind of comparison, so collections like those of the Academy were critical to the study.”

In fact, the scientists studied almost 1500 specimens from nine different museums.

Not surprisingly, says the article, “song sparrows [specimens] showed increasing body-size-corrected bill surface area from the coast to the interior…” In other words, the hotter the habitat, the larger the beak size for dissipating heat.

“It is exciting to see such compelling explanations for the differences found in the field,” Jack says of his colleagues’ work.  “Interestingly, many of the coastal or sea-side sparrow races also have darker colors—perhaps also better for absorbing the sun’s heat in these cooler environments.”

Image: badjoby/Flickr

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

Despite being in the wrong place, at the wrong time, we were able to catch incredible glimpses of the solar eclipse this week through photos throughout the web.

DNA sequencing started the year off right. Popular Science reported that “For the First Time, DNA Sequencing Technology Saves A Child’s Life.” Doctors, desperate to find the cause of a boy’s severe illness, sequenced his genes, discovered a mutation and were able to prescribe a treatment that appears to be working. A new machine could make this practice more common. An article in the New York Times this week described a more affordable sequencing machine. At $50,000, the Personal Genome Machine is significantly less than standard machines and “could expand the use of DNA sequencing from specialized centers to smaller university and industrial labs, and into hospitals and doctors’ offices.”

What is causing birds to fall out of the sky and fish to die from Arkansas to Maryland and Brazil to Sweden? Cold weather? Hail storms? Fireworks? The end of the world? There’s been much hype and speculation, but scientists don’t appear to be worried. The Academy’s own Jack Dumbacher is getting samples from the southern occurrences—he’s planning on testing the corpses for viruses. You can track these deaths yourself through Google maps or the US Geological Survey.

Finally, after topping the science news headlines last year, oil in the Gulf reappeared this week, at least on news sites. Have bacteria consumed nearly all of the methane from the spill? A study published in Science this week suggests that’s the case. Ed Yong finds a lot of support for the paper in his blog on Discover; Samantha Joye tells Science News, “Just because you can’t find methane in the spot where you lowered your [instruments] doesn’t mean there’s no methane out there somewhere.”

Also, the president’s oil spill commission released the first chapter of its report this week. (The entire report will be available next week.) An excerpt from the chapter in Science Insider reports that the blame for the disaster can be shared among the companies responsible for the well.

Most of the mistakes and oversights at Macondo can be traced back to a single overarching failure—a failure of management.

And sadly, this may not be an unusual event, according to the New York Times:

The commission warned that without major changes, another such accident was likely.

If you want a front seat on a Gulf of Mexico recovery expedition, follow Sylvia Earle and others on National Geographic News Watch this month.

What science news did you dive into this week? Share with us!

Image by Brydzo/Wikimedia