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.

Could an odd plant with a terrible name show us that “junk DNA” has value after all?

The carnivorous bladderwort plant, Utricularia gibba, is a lightweight in the genome game. It has about 80 million DNA base pairs. By comparison, its relatives the grape and tomato have about 490 and 780 million base pairs, respectively. (You and I have about 3.2 billion base pairs, but hey, we’re humans.)

Despite its small genome, the carnivorous bladderwort is a complicated plant. Disguised as a lovely flowering beauty, it actually traps organisms such as insects and small fish in a bladder-shaped trap on its water-soaked roots—for nourishment, of course. And while that’s exciting, a new study in Nature has scientists even more excited about the carnivorous plant.

“The big story is that only 3 percent of the bladderwort’s genetic material is so-called ‘junk’ DNA,” says study co-author Victor Albert. The human genome, in contrast, includes about 98% junk DNA. But what kind of “junk” are we talking about?

Junk in the Trunk

“When complete genomes were first being sequenced, it became clear that only a small fraction of the DNA could be assigned a specific function,” explains Brian Simison, curator and director of the Academy’s Center for Comparative Genomics. “The functional regions or genes are primarily those that produce proteins or ribosomes. It has been hypothesized that these vast regions of unknown function were the product of duplications followed by loss of function due to the accumulation of random mutations and/or the accumulation of exogenous DNA from viruses. The term ‘Junk DNA’ emerged from these hypotheses.

“However, research on junk DNA is shedding new insights into these regions,” Simison adds. Last fall, he spoke with Science Today correspondent Barbara Tannenbaum about the ENCODE project. Conducting a huge international effort to look more into the junk part of the human genome, researchers determined that 80% of our genome actually had some function.

Since that time, ENCODE has come under some scrutiny. “I think the ‘controversy’ is overblown,” Simison says. “ENCODE scientists presented a testable hypothesis and it should be pursued as such. My bet is that some junk DNA will, in fact, turn out to be useless baggage from historical genomic events while other bits will prove to be required for normal human functions.”

No Junk in the Trunk

If our junk DNA is worth having around, then why doesn’t a meat-eating plant like the bladderwort need it? “Based on the miniscule number of complete genomes sequenced, it is unusual that the genome of the carnivorous bladderwort is only 3% junk DNA,” Simison says. “It may reveal interesting information about the function and organization of genomes. However, the sample size of complete genomes is so incredibly tiny that junkless genomes may not be that uncommon.”

So what happened to the junk? “That is the big question. Did it get deleted or did the carnivorous bladderwort not have it to begin with?” Simison asks. “To answer this we need to understand more about the evolutionary history of genomes and, in particular, we need to know more about the genomes of this plant’s ancestors.”

The bladderwort’s lack of junk DNA only adds to the mystery. Scientists hope to learn more as additional organisms’ complete genomes are sequenced—and as more research is conducted on the function of junk DNA.

Image: Bruce Salmon/Wikipedia

Not only are they the only mammals that can fly, but bats also show off with their immunity to viruses and other diseases. What gives?

Well, according to a recent study in Science, these two abilities—flight and immunity—might be related in the winged animals.

A group of international researchers sequenced the entire genomes of two species of bats—the fruit bat Pteropus alecto and the insectivore Myotis davidii. These two species are from the two distinct sub-orders of bats—P. alecto is a megabat and M. davidii, a microbat. By comparing and contrasting the two species’ genomes and those of other mammals (human, rhesus macaque, mouse, rat, dog, cat, cow, and horse), the scientists could refine bats’ place in the tree of life as well as determine the evolution of some of their bat-traits.

Study co-author Chris Cowled, of the Australian Animal Health Laboratory, describes how remarkable these traits are. “Bats are a natural reservoir for several lethal viruses, such as Ebola and SARS, but they often don’t succumb to disease from these viruses. They also live a long time compared to animals similar in size.”

It turns out the trick for this trait is flight. Flying is a very energy intensive activity that also produces toxic by-products, and bats have developed some novel genes to deal with the toxins. Some of these genes are implicated in the development of cancer or the detection and repair of damaged DNA.

“What we found intriguing was that some of these genes also have secondary roles in the immune system,” says Cowled. “We’re proposing that the evolution of flight led to a sort of spill over effect, influencing not only the immune system, but also things like aging and cancer.

“A deeper understanding of these evolutionary adaptations in bats may lead to better treatments for human diseases, and may eventually enable us to predict or perhaps even prevent outbreaks of emerging bat viruses,” says Cowled.

Sounds bat-tastic.

Image: James Niland/Wikipedia

An international consortium of researchers recently announced another milestone in the quest to unravel the genetic makeup of the human species. The project—ENCODE, for Encyclopedia of DNA Elements—is a collaborative effort among 440 researchers in 32 global institutions, coordinated by the National Human Genome Research Institute (NHGRI). The results of this international effort will stand alongside such research breakthroughs as Watson and Crick’s 1953 description of DNA’s double helix structure and the Human Genome Project’s 2003 complete sequencing of humanity’s 3.2 billion nucleotides.

ENCODE mapped more than four million non-coding regions of the genome that regulate and interact with protein-producing DNA. The scientific consortium also confirmed that 80 percent of the genome performs specific biological functions. This upends the previous consensus that long stretches of DNA were no more than “junk DNA.”

“This is one of the most important collections of information the world is trying to decode,” explains Brian Simison, head of the Academy’s Center for Comparative Genomics.

Not only does ENCODE solve a bit more of the human genome puzzle, but it offers the potential to accelerate medical research. “We’ve known for a long time that there is a genetic basis to many diseases,” says Simison. “What we didn’t realize is that the source of many diseases would be found in the vast regions of the genome previously known as junk DNA.”

While others describe the project as having found the on/off switches to our genes, Simison prefers the term ‘regulatory function.’

“We are learning that junk DNA has a regulatory role in dosage, duration, timing and other regulatory functions. Understanding these functions will transform Western medicine,” Simison adds. “ENCODE reveals that Western medicine is in its infancy.”

Simison points out that ENCODE is also altering our vision of the genetic composition of life. “Most people think all genetic material is passed down to us by our direct ancestors. Actually,” Simison explains, “the human species is filled with ‘fossil DNA’ transferred to us from viruses.”

As an example, Simison describes a retrovirus that has inserted its DNA into a person’s genome. These endogenous retroviruses (ERVs) are found throughout the genome and it is now believed that some of these have been repurposed.

Finally, Simison explains that it’s not just what ENCODE found but how they found it that is significant.

“The wow factor is enormous,” Simison laughs. As the National Institute of Health reports, hundreds of international researchers performed more than 1,600 sets of experiments on 147 types of tissue with technologies standardized across the consortium.

“Although technology has improved, no single institution could have analyzed the genome data on its own,” Simison remarks. “You need many people sifting through the many layers of data to decode the human genome.”

“I believe it is a positive development that so many nations are sharing this knowledge,” he said, lauding the consortium for its cooperative methods. “These illustrate how the path towards lofty ambitions is often as fruitful as the objectives themselves. Unlike the U.S. space program, the Human Genome Project and ENCODE were international projects where the benefits that emerge are shared with and benefit the world.”

ENCODE’s results were published last month in a wide range of scientific journals and posted online to ensure transparency and public access. To learn more, review the publications here.

Barbara Tannenbaum is a science writer working with the Academy’s Digital Engagement Studio. Her work has appeared in the New York Times, San Francisco Magazine and many other publications.

One way gene expression is altered through epigenetics is called DNA methylation. These are chemical tags that can regulate how genes function. Ed Yong puts it this way in his Discover blog:

These marks, known as methyl groups, are like Post-It notes that dictate how a piece of text should be read, without altering the actual words.

Epigeneticist Andy Feinberg, of John Hopkins, wanted to understand how DNA methylation might be identified in changes in behavior so he teamed up with Gro Amdam, of Arizona State University, a bee behavior expert.

Honeybees make excellent study subjects for this purpose because they are social creatures with very compartmentalized behavior. Female bees are either queens or worker bees, and once the path is chosen, there’s no turning back.

Within the worker bees, however, there are behavior distinctions that are a bit more transient. Workers begin as nurses—tending to the larvae. After two to three weeks, they become foragers, leaving the hive to gather pollen.

The researchers decided to study the chemical tags, DNA methylation, of the two groups—nurses and foragers. “Genes themselves weren’t going to tell us what is responsible for the two types of behavior,” Feinberg says. “But epigenetics—and how it controls genes—could.”

Analyzing the patterns of DNA methylation in the brains of 21 nurses and 21 foragers, the team found 155 regions of DNA that had different tag patterns in the two types of bees. The genes associated with the methylation differences were mostly regulatory genes known to affect the status of other genes.

Then the scientists got tricky. They removed some of the nurses from the hive. When this happens in nature, some of the foragers are able to revert to nursing to fill the gap. Sure enough, the same thing happened in Feinberg’s and Amdam’s experiment—several of the foragers went back to being nurses.

This time, 107 DNA regions showed different tags between the foragers and the reverted nurses, suggesting that the epigenetic marks were not permanent but reversible and connected to the bees’ behavior and the facts of life in the hive.

“It’s like one of those pictures that portray two different images depending on your angle of view,” Amdam says. “The bee genome contains images of both nurses and foragers. The tags on the DNA give the brain its coordinates so that it knows what kind of behavior to project.”

The researchers say they hope their results may begin to shed light on complex behavioral issues in humans, such as learning, memory, stress response and mood disorders, which all involve interactions between genetic and epigenetic components similar to those in the study.

The study is published this week in Nature Neuroscience.

Image: Louise Docker/Wikipedia

Take wild spotted horses depicted by our ancestors as having a white coat with black spots in cave paintings around 25,000 years ago. Scientists had evidence of bay and black horses, including a 2009 published DNA study of ancient horses dating back as far as 12,000 years ago, but no proof of the dappled horses.

A team of international researchers decided to try older samples—31 pre-domestic horses dating back as far as 35,000 years ago from Siberia, Eastern and Western Europe and the Iberian Peninsula, analyzing bones and teeth specimens from 15 locations.

They found that six of the samples shared a genetic variant called LP that is associated with leopard spotting, providing the first evidence that spotted horses existed at this time. In addition, 18 horses had a bay coat color and seven were black, meaning that all color phenotypes distinguishable in cave paintings—bay, black and spotted—existed in pre-domestic horse populations.

The study was published earlier this week in the Proceedings of the National Academy of Sciences.

“Our results suggest that, at least for wild horses, Paleolithic cave paintings, including the remarkable depictions of spotted horses, were closely rooted in the real-life appearance of animals,” says study co-author Michael Hofreiter.

Archeologist Terry O’Connor concurs. “Our research removes the need for any symbolic explanation of the horses. People drew what they saw, and that gives us greater confidence in understanding Paleolithic depictions of other species as naturalistic illustrations.”

Want to learn more? ScienceNOW offers a reason why the LP gene was absent from more recent samples (as studied in the 2009 paper):

As for why the spotted phenotype became more rare after 14,000 years ago, the team points out that some modern horse breeds with two copies of the LP gene suffer from night blindness, which would have made prehistoric horses more vulnerable to predators. The researchers speculate that the gene might have been beneficial during the ice age, when a white spotted coat could serve as camouflage in snowy conditions, but later became rare and disadvantageous until rediscovered by modern horse breeders.

Image: Pruvost et al./PNAS

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

Earth

The Gulf oil spill—the number of gallons spilled and the controversy surrounding the damage seems to top many lists this year. Nature even named Jane Lubchenco, head of NOAA, its newsmaker of the year for how she handled the crisis.

Natural disasters often took the front page in 2010 with the Haitian earthquake and the eruption of Eyjafjallajökull topping many lists. The hard-to-pronounce Icelandic volcano also made many of the best science images of the year lists.

DiscoveryNews ends the year on a positive note with “How Humans Helped the Earth in 2010,” a slide show with text concerning recent strides in alternative energy, species and habitat conservation efforts and individual efforts to go green (electric cars, white roofs and saving energy).

For more environmental news of the year, New Scientist’s Short Sharp Science has a great review and the Nature Conservancy has a best/worst list on its site.

Life

Teeny, modified life stole the spotlight this year—the J. Craig Venter Institute’s so-called “synthetic cell” and GFAJ-1—the bacteria that incorporates arsenic into its DNA—or so NASA scientists claimed.  Science writer Carl Zimmer discredited the arsenic bacteria paper on Slate; NASA author Felisa Wolfe-Simon defended herself in Science. Fun stuff!

The spread of pesky bedbugs was number six in Discover’s “Top 100 Science Stories of 2010.”

Nature’s great article this past summer on eradicating mosquitoes was among its readers’ top choices of the year.

Looking for something a little bigger and less controversial? New Scientist has “The coolest animals of 2010,” which includes a scorpion-eating bat and a fly thought to be extinct for over 160 years!

NPR found it was a very good year for Neanderthals—their genome was sequenced, brain examined and diet expanded.

Remarkably, the Census of Marine Life tops the BP oil spill in the Deep Type Flow blog’s biggest marine science stories of the year for its sheer numbers:

…over 500 research expeditions covering every ocean, over 2,500 scientists and the discovery of over 6,000 species new to science and published in over 2600 peer-reviewed papers.

Space

ScienceNow’s most popular story of all time, not just 2010, was “Does Our Universe Live Inside a Wormhole?” A wonderful theory that we also covered last spring.

Exoplanets, in part thanks to the Kepler mission, were all over the news this year—whether it had to do with size, atmosphere or number within a star system. Discover’s interview with local exoplanet hunter (and California Academy of Sciences Fellow) Geoff Marcy made number 11(!) on their 100 top stories list.

A little closer to home, Jupiter’s missing stripe and Neptune’s tale of cannibalism are included in New Scientist’s most popular space stories of 2010.

Our Moon and Saturn’s moons made news throughout the year and the top lists on Universe Today and Wired this week.

Universe Today also included SDO’s new views of the sun in their top stories list. Stunning!

Hubble celebrated its 20^th year in space this year by taking even more beautiful images. Several are included in Bad Astronomy’s “Top 14 Astronomy Pictures of 2010.”

Technology

Electric cars and NASA’s new foray into commercial spacecraft are included in Scientific American’s top ten stories of the year.

The Large Hadron Collider was very busy this year, and topped many lists. Another machine at CERN made news (and also topped Nature’s readers’ choice list) when it was able to capture antimatter for a sixth of a second!

Graphene not only garnered a Nobel Prize this year, the material (and it’s potential) also made news and top science lists of the year.

DiscoveryNews put plastics on their 2010 list—whether its finding new ways of removing plastic from the oceans or engineering smarter plastics.

What was your favorite science story of the year? Share with us by adding it to the comment section below!

Image by Les Stone, International Bird Rescue Research Center/Wikipedia

When the days grow longer, temperatures begin to rise, and San Francisco Giants’ pitcher Tim Lincecum throws out the first pitch of the season, I know that spring has arrived in San Francisco. As new leaves appear and flowers begin to bloom, we are certain that winter has left us behind. It’s easy for us to know when spring is here, but what about the trees and flowers themselves? How do they know when to drop their leaves, and when to bloom?

Scientists believe they’ve discovered a special molecule in plants that gives them the remarkable ability to “remember” winter and to bloom on schedule in the spring. Their results are reported in the December 2 issue of Science Express.

Sibum Sung, molecular biologist at the University of Texas and one of the paper’s authors, was searching for a mechanism that allows plants to recognize spring and – more importantly – distinguish between spring and a brief warm spell during winter. The key, Sung found, was the plants’ ability to remember that winter had passed.

“Plants can’t literally remember, of course, because they don’t have brains,” says Sung. “But they do have a cellular memory of winter, and our research provides details of how this process works.”

The process Sung referred to is called “vernalization.” It allows a plant to properly come out of hibernation during winter so that it can bloom. But experts have never really understood the genetic basis for how vernalization worked.

Until now. Sung and his co-author Jae Bok Heo dug deep into the DNA of arabidopsis, a small flowering plant related to mustard and cabbage. As they scoured the lines of genetic code, they discovered that arabidopsis’ DNA coded for a molecule they called COLDAIR.

The authors’ experiments revealed that while the plant hunkers down for the winter, COLDAIR is switched off. After 20 days of consistent freezing temperatures, COLDAIR gets switched on. This begins the 10 to 20 day process of preparing the plant for spring. Once complete, the plant is ready for warm temperatures, and other pieces of genetic code help the plant to bloom.

As many of us know, this system isn’t perfect. Sometimes flowers do bloom early, and they pay the price when temperatures quickly return to freezing. But over millions of years of evolution, COLDAIR has helped create a kind of “memory” in generations of plants, telling them when there’s been at least a month of cold and that spring might be just around the corner.

Of course, many questions remain. Sung admits they still don’t have the other pieces of the puzzle, like how does the plant know it’s been at least 20 days of cold temperatures? “That is one of the next questions we have,” he says. “How do plants literally sense the cold?”

The particular mechanisms require further study, but as long as COLDAIR keeps working, flowers will give us one more sign when spring has sprung.

Anne Holden, a docent at the California Academy of Sciences, is a PhD trained genetic anthropologist and science writer living in San Francisco.

Image by Roepers/Wikimedia

Want to get inside a turkey’s head? The Witmer Lab of Ohio University will grant you that access with this video. The technical term for that gray, fuzzy thing?  The snood, of course.

Before you put that bird in the oven check out our San Francisco neighbors the Exploratorium’s Science of Cooking blog. They’ll give you the scoop on (and the science behind) cooking temperatures and times, roasting pans and lids.

Time to set the table. This is a must see! Discover has a super cool Thanksgiving dinner DNA spread. Start off with the turkey genome (recently sequenced in September) and your sides—the corn and potato genomes.  Satisfy your sweet tooth with the apple genome found in your pie and wash everything down with the wine grape genome.  Enjoy some mouth-watering discoveries and images with each course.

The author of the above spread, Emily Anthes, has more to say on her PLoS Blog about the turkey genome. Turns out domestic turkeys are very susceptible to cancer—they could very well be “a great research model for cancer” in the near future.

Pass the mashed potatoes? How are genetically modified foods changing our holiday feast? Popular Science digs deep to discover how biotechnology affects the way we eat.

Stuffed, yet? Scientific American has a 60-Second Science podcast today on eating less. Apparently, simply using a smaller plate or bowl could reduce caloric-intake by 20-50%.

Don’t fight over the wishbone! Our favorite dino-blogger, Brian Switek, has a post today at Smithsonian on something that a turkey and a Tyrannosaurus rex have in common.

Finally, Robert Krulwich, science journalist extraordinaire, has a great blog on NPR today on the first Thanksgiving. More history than science, but still worth the read.

Happy Thanksgiving!