Chimp ‘culture’ paper retracted after authors spot errors, now has home at another journal

thanks to Geraldine F for the link!
from retraction watch

The authors of a 2011 paper claiming that chimp “culture” has more to do with local habitats than with where the chimps live have retracted it after finding mistakes in their work.

Here’s the notice for the paper, “Variation in chimpanzee ‘culture’ is predicted by local ecology, not geography:”

Shortly after our above paper was published in Biology Letters, we discovered several coding errors in the dataset we analysed. After re-analysing a corrected dataset, we did not find the same results as in our publication. In contrast, we found that no ecological variable was a statistically significant predictor of behavioural variation. Consequently, we do not feel that the main result of our publication is valid and have requested retraction of this manuscript.

So how did the errors come to light? Corresponding author Jason Kamilar, formerly of Yale and now at Midwestern University in Glendale, Arizona, tells Retraction Watch:

A colleague contacted me about a week after the paper appeared on Biology Letters’ Early View to request the dataset. We originally used a couple of different methods to code the data and we conducted the analyses about 2 years ago. After looking at the datasets in more detail I noticed several errors that likely was likely due to coding the data from a separately coded dataset instead of the original dataset. I confirmed the problem by re-analyzing the correct dataset and I obtained different results. I contacted the editors of Biology Letters and we agreed that retracting the paper was the best course of action.

We wanted to know whether the retraction would have a significant effect on the field.

I think the impact will be quite minor. The retraction occurred less than 2 months after the paper appeared online, and it was never actually published in an issue. In addition, I submitted a new version of the manuscript that contained the correct dataset and analysis, which is now in press in Journal of Human Evolution.

Not surprisingly, the new paper found the opposite of the original results:

…geography, and longitude in particular, was the best predictor of behavioral variation.

The authors were also transparent in the new paper, which includes a line noting the retraction:

Our paper also serves as correction to our recently retracted study (Kamilar and Marshack, 2011), which contained several coding errors in the dataset.

Kamilar, we should note, is as critical of others’ work as he is of his own. Late last year, he was a co-author of a Comment in Science alleging flaws in a May 2011 report on whether dinosaurs were nocturnal. Its abstract:

Schmitz and Motani (Reports, 6 May 2011, p. 705) claimed to definitively reconstruct activity patterns of Mesozoic archosaurs using the anatomy of the orbit and scleral ring. However, we find serious flaws in the data, methods, and interpretations of this study. Accordingly, it is not yet possible to reconstruct the activity patterns of most fossil archosaurs with a high degree of confidence.

The response from the original paper’s authors wasn’t anything like a retraction; it was more like doubling down:

Hall et al. claim that it is not yet possible to infer the diel activity patterns of fossil archosaurs with high confidence. We demonstrate here that this assertion is founded on unscreened data, untenable assumptions, and inappropriate methods. Our approach follows ecomorphological and phylogenetic principles in a probabilistic framework, resulting in statistically well-supported reconstructions of diel activity patterns in Mesozoic archosaurs.

See no evil, hear no evil?

Extinct Giant Tortoise May Still Be Alive in Galapagos

A hybrid C. becki tortoise. Photo: Claudio Ciofi

From Wired.com
by Brandon Keim

Genetic traces of a supposedly extinct giant tortoise species have been found in living hybrids on the Galapagos island of Isabela.

A few pure Chelonoidis elephantopus almost certainly still exist, hidden in the island’s volcanic redoubts. The hybrids have so much C. elephantopus DNA that scientists say careful breeding could resurrect the tragically vanished behemoths.

“To our knowledge, this is the first rediscovery of a species by way of tracking the genetic footprints left in the genomes of its hybrid offspring,” wrote researchers led by Yale University biologists Ryan Garrick and Edgar Benavides in a Jan. 9 Current Biology paper.

At the beginning of the 16th century, before humans arrived, an estimated 250,000 giant tortoises representing 15 different species lived in the Galapagos. Once fully grown, the tortoises had no natural predators — except people.

For whalers and pirates, the slow-moving animals were like walking grocery stores. They weighed up to 900 pounds; their flesh was tasty and rich in oil. They could survive for months, even years, without eating or drinking, and sailors stored tortoises alive in the hulls of their ships for future consumption.

By the time a young Charles Darwin surveyed the tortoises, they were being indiscriminately slaughtered. (“The inhabitants believe that these animals are absolutely deaf; certainly they do not overhear a person walking close behind them,” he wrote.) Five species, including C. elephantopus, would eventually go extinct. But the tortoises’ long-term storage convenience had one unexpected benefit.

“If a ship was under siege, sailors would unload it by throwing things overboard,” said Garrick. “The first thing to go was stuff stored in the hull. Tortoises don’t swim, but they float like wine corks, and it so happens that the prevailing current runs northeast through the islands. The last place a tortoise might catch land before being swept into the ocean was the northern part of Isabela island. This is where they would have washed up.”

Three years ago, Garrick and Colleagues sequenced the genomes of museum specimens of C. elephantopus and Chelonoidis becki, a closely related tortoise found on the northern part of Isabela island. They found C. elephantopus genes in a few C. becki, suggesting that some castaway tortoises historically made landfall and mated with the locals.

For the new study, the researchers traveled to Isabela island. On the island’s northern tip, on the slopes of Volcano Wolf, they took genetic samples from 1,600 C. becki individuals. Of these, 84 contained so much C. elephantopus DNA that at least one recent ancestor must have been a purebred C. elephantopus.

None of the purebreds was spotted, but because of the genetic signals’ strength and the hybrids’ youth — many were juveniles — the researchers estimate that about 40 purebreds still survive. Given that individual tortoises from other giant Galapagos species have lived for 170 years in captivity, some of the survivors could conceivably have been thrown from ships themselves.

Later this year the researchers will return to Isabela, where they hope to establish a captive breeding program using hybrids and, if they can find them, a few true C. elephantopus. The tortoises could roam again, their slaughter an evolutionary chapter rather than an end.

“The way they were moved around creates a rare opportunity to resuscitate a species that we thought we’d lost,” said Garrick.

Citation: “Genetic rediscovery of an ‘extinct’ Galápagos giant tortoise species.” By Ryan C. Garrick, Edgar Benavides, Michael A. Russello, James P. Gibbs, Nikos Poulakakis, Kirstin B. Dion, Chaz Hyseni, Brittney Kajdacsi, Lady Márquez, Sarah Bahan, Claudio Ciofi, Washington Tapia, and Adalgisa Caccone. Current Biology, January 9, 2012.

The Photographic Fascination With Twins

the spring board is a national geographic article on epigenetics but the photos are captivating as well -MA

from NPR
by Claire O'Neill

One of the photos that made photographer Diane Arbus famous was Identical Twins, Roselle, New Jersey, 1967; it reverberated in The Shining and probably influenced Mary Ellen Mark's twin photos.

It goes without saying that twins long have fascinated photographers — as well as scientists. How is it that identical twins with virtually identical DNA can be so different? Conversely, how is it that identical twins separated at birth can still have so much in common? An article in National Geographic's January issue explores the focus of recent research: How a third factor, beyond nature and nurture, might have a vital role in making us who we are. The term is epigenetics and the article explains it best.

Photographer Martin Schoeller must have jumped at the chance to shoot the portraits for this story. Once you know his style, you'll start to recognize his photos on the covers of major magazines — or in museums. I saw his enormous portraits for the first time at the National Portrait Gallery a while back. He uses a huge camera with a depth of field so famously narrow that the eyes are in focus and the nose is not.

In Schoeller's portraits, eyes are like an open book. His portraits are studies of the face's physical topography, but also of our irrepressible emotions — how they translate to the twinkle of an eye or the wrinkle on a forehead.

It's fascinating to see his style in this context. How identical are identical twins? What do you think?

--
gallery here: http://ngm.nationalgeographic.com/2012/01/twins/schoeller-photography and more here: http://ngm.nationalgeographic.com/2012/01/twins/miller-text

Identical twin boys with different gender identifications

From Boston.com
by BELLA ENGLISH
Led by the child who simply knew
The twin boys were identical in every way but onehttp://www.blogger.com/img/blank.gif. Wyatt was a girl to the core, and now lives as one, with the help of a brave, loving family and a path-breaking doctor’s care.

Jonas was all boy. He loved Spiderman, action figures, pirates, and swords.

Wyatt favored pink tutus and beads. At 4, he insisted on a Barbie birthday cake and had a thing for mermaids. On Halloween, Jonas was Buzz Lightyear. Wyatt wanted to be a princess; his mother compromised on a prince costume.

Once, when Wyatt appeared in a sequin shirt and his mother’s heels, his father said: “You don’t want to wear that.’’

“Yes, I do,’’ Wyatt replied.

“Dad, you might as well face it,’’ Wayne recalls Jonas saying. “You have a son and a daughter.’’

That early declaration marked, as much as any one moment could, the beginning of a journey that few have taken, one the Maineses themselves couldn’t have imagined until it was theirs. The process of remaking a family of identical twin boys into a family with one boy and one girl has been heartbreaking and harrowing and, in the end, inspiring - a lesson in the courage of a child, a child who led them, and in the transformational power of love.

Wayne and Kelly Maines have struggled to know whether they are doing the right things for their children, especially for Wyatt, who now goes by the name Nicole. Was he merely expressing a softer side of his personality, or was he really what he kept saying: a girl in a boy’s body? Was he exhibiting early signs that he might be gay?Was it even possible, at such a young age, to determine what exactly was going on?

Until recently, there was little help for children in such situations.But now a groundbreaking clinic at Children’s Hospital in Boston - one of the few of its kind in the world - helps families deal with the issues, both emotional and medical, that arise from having a transgender child - one who doesn’t identify with the gender he or she was born into.

The Children’s Hospital Gender Management Services Clinic can, using hormone therapies, halt puberty in transgender children, blocking the development of secondary sexual characteristics - a beard, say, or breasts - that can make the eventual transition to the other gender more difficult, painful, and costly.

Founded in 2007 by endocrinologist Norman Spack and urologist David Diamond, the clinic - known as GeMS and modeled on a Dutch program - is the first pediatric academic program in the Western Hemisphere that evaluates and treats pubescent transgenders. A handful of other pediatric centers in the United States are developing similar programs, some started by former staffers at GeMS.

It was in that clinic, under Spack’s care, that Nicole and her family finally began to have hope for her future.

The Maineses decided to tell their story, they say, in order to help fight the deep stigma against transgender youth, and to ease the path for other such children who, without help, often suffer from depression, anxiety, and isolation.

“We told our kids you can’t create change if you don’t get involved,’’ says Wayne, 53, sitting in the living room of their comfortable home in a southern Maine community they do not want identified.

They have good reason for caution. Their journey has included a lawsuit to protect their daughter’s rights, and a battle against bullying and insensitivity that led them to move to a new place and new schools.

It has been a hard road, but nothing that compares with the physical transformation of Wyatt into Nicole.

“I have always known I was a girl,’’ says Nicole, now 14. “I think what I’m aiming for is to undergo surgery to get a physical female body that matches up to my image of myself.’’

Early confusion

When Wyatt and Jonas were born, their father was thrilled. Wayne looked forward to the day when he could hunt deer with his boys in the Maine woods. The family lived in Orono, near the University of Maine campus, where Wayne is the director of safety and environmental management.

They had no preparation for what would come next.

When Wyatt was 4, he asked his mother: “When do I get to be a girl?’’ He told his father that he hated his penis and asked when he could be rid of it. Both father and son cried. When first grade started, Wyatt carried a pink backpack and a Kim Possible lunchbox.

His parents had no idea what was going on. They had barely heard the term “transgender.’’ Baffled, they tried to deflect Wyatt’s girlish impulses by buying him action figures like his brother’s and steering him toward Cub Scouts, soccer, and baseball.

When the boys were 5, Kelly and Wayne threw a “get-to-know-me’’ party for classmates and parents. Wyatt appeared beaming at the top of the stairs in a princess gown, a gift from his grandmother.

Kelly whisked him off and made him put on pants. Though she and Wayne were accustomed to his girly antics, they were afraid of what others might think.

To this day, she feels guilty about it. “I know she was totally confused and felt like she had done something wrong,’’ says Kelly, 50, who works in law enforcement.

“Even when we did all the boy events to see if she would ‘conform,’ she would just put her shirt on her head as hair, strap on some heels and join in,’’ Kelly says. “It wasn’t really a matter of encouraging her to be a boy or a girl. That came about naturally.’’

Kelly and Wayne didn’t look at it as a choice their child was making.

“She really is a girl,’’ Kelly says, “a girl born with a birth defect. That’s how she looks at it.’’

Fear of the unknown

After Wyatt began to openly object to being a boy, his mother started doing research on transgender children. There was little out there; it seemed they would have to find their way largely on their own.

During those early years, while Kelly was doing her research, Wayne was hoping that this was no big deal, that this was a stage Wyatt just had to go through.

“I felt it had nothing to do with how they would grow up,’’ he says.

But as they grew older, his concern grew. “I feared the unknown,’’ he says.

Even the family Christmas card became a challenge. They would write about Jonas’s affinity for sports and Wyatt’s “flair for the dramatic.’’

Their elderly pediatrician, nearing retirement, did not want to discuss the matter with them. Finally, Kelly picked another pediatrician out of the phone book. “I told her how it was, and it turned out that she understood and was very supportive.’’

When the twins were in the first grade, their parents found a therapist for Wyatt, who was starting to act out. In the third grade, before the GeMS Clinic was even open, Kelly heard about Dr. Spack and made an appointment with him.

“He told us everything,’’ Wayne says, recalling that first meeting. “I didn’t understand it all, but I saw the weight lift off Kelly’s shoulders and a smile in Nicole’s eyes. That was it for me. There were tons of challenges for us after that, but I knew my daughter was going to be OK, medically.’’

Elementary school changes

In elementary school, Wyatt told classmates that he was a “girl-boy.’’ In the fourth grade, he grew his hair longer and started talking about a name change. That same year, he drew a self-portrait as a girl, and in a class essay, wrote: “Wyatt needs hair accessories, clothes, shoes . . . likes to wear bikinis, high heels, mini-skirts.’’

Emma Peterson of Orono, a close friend from the elementary years at the Asa Adams School, recalls playing dolls with Nicole’s giant dollhouse, and the two of them putting on makeup. “Before Nikki started growing her hair out, she looked exactly like Jonas,’’ Emma says.

In fourth grade, Wyatt started using “Nicole’’ as a name, and many classmates were calling him “Nikki.’’ The next year, the family went to court and had the name legally changed to Nicole.

To Kelly, it seemed the next logical step. Family discussions merely centered around what the name would be. In the end, Nicole chose it. “I believed in Nicole,’’ her mother says. “She always knew who she was.’’

Wayne was nervous. Could he call his son Nicole? As usual, he relied on his wife’s instincts. “I have to tell you, Kelly’s the leader in our family,’’ he says. “Both she and Nicole are extremely strong-willed, and I went with the flow.’’

At first, though, he couldn’t bring himself to use the new name. An Air Force veteran and former Republican, he realizes now he was grieving the loss of a son. “But once you get past that, I realize I never had a son,’’ he says.

Legal battles

When fifth grade started, Wyatt was gone. Nicole showed up for school, sometimes wearing a dress and sporting shoulder-length hair. She began using the girls’ bathroom. Nikki’s friends didn’t have a problem with the transformation; there were playdates and sleepovers.

“They said, ‘It was about time!’ ’’ Nicole says. She was elected vice president of her class and excelled academically.

But one day a boy called her a “faggot,’’ objected to her using the girls’ bathroom, and reported the matter to his grandfather, who is his legal guardian. The grandfather complained to the Orono School Committee, with the Christian Civic League of Maine backing him. The superintendent of schools then decided Nicole should use a staff bathroom.

“It was like a switch had been turned on, saying it is now OK to question Nicole’s choice to be transgender and it was OK to pursue behavior that was not OK before,’’ Wayne says. “Every day she was reminded that she was different, and the other kids picked up on it.’’

According to a 2009 study by the Gay, Lesbian and Straight Education Network, 90 percent of transgender youth report being verbally harassed and more than half physically harassed. Two-thirds of them said they felt unsafe in school.

To protect her from bullying at school, Nicole was assigned an adult to watch her at all times between classes, following her to the cafeteria, to the bathroom. She found it intrusive and stressful. It made her feel like even more of an outsider.

“Separate but equal does not work,’’ she says.

It was a burden that Jonas shouldered as well. The same boy who in fifth grade objected to her using the girls bathroom made the mistake of saying to Jonas in sixth grade that “freaking gay people’’ shouldn’t be allowed in the school. Jonas jumped on him and a scuffle ensued.

“He’s taken on a lot,’’ Wayne says. “Middle school boys and sexuality, you know . . . boys can get picked on.’’

Nicole and her parents filed a complaint with the Maine Humans Right Commission over her right to use the girls bathroom. The commission found that she had been discriminated against and, along with the Maines family, filed a lawsuit against the Orono School District. The suit is pending in Penobscot County Superior Court, and the Maines family is represented by lawyers from the Gay & Lesbian Advocates & Defenders (GLAD) in Boston and by Jodi Nofsinger, who serves on the Maine ACLU board.

“What Nicole and Jonas both went through in school was unconscionable,’’ says Jennifer Levi, one of the GLAD lawyers on the case. “Their one huge stroke of luck was having Kelly and Wayne as parents.’’

A huge relief

Since that first visit to Spack when Nicole was 9, her parents discussed putting her into the GeMS Clinic when the right time came. They were glad there was time to adjust to the idea. “Baby steps,’’ Kelly calls their path toward treatment.

“I wasn’t always on board,’’ Wayne says. “Kelly and I were not on the same page. My question was, what is this doctor doing? It scared me. I was grieving. I was losing my son.’’

But the more he watched his child struggle, the better he felt about going to Spack. And once he got there, he says, it was a huge relief. “Not only does he know what he’s doing, he’s extremely comforting. He’s got to deal with a ton of dads who are just freaking out, and he made me feel good.’’

Spack’s experience runs deep; before the clinic was established, he had long worked with transgender youth, as well as with adults. “The most striking thing about these kids was the fact that they were just normal young people who had this incredibly unusual and problematic situation,’’ says Spack, 68.

He believes it is crucial to intervene with such children before adolescent changes begin in earnest.

“Most of us look pretty similar until we hit puberty,’’ he says. “I bet I could go to any fourth or fifth-grade class, cut the hair of the boys, put earrings on various kids, change their clothing, and we could send all those kids off to the opposite-gender bathrooms and nobody would say boo.’’

He adds: “We can do wonders if we can get them early.’’

Second-guessing

Not everyone agrees that they should, of course, and Spack has heard the arguments: Man should not interfere with what God has wrought. Early adolescents are too young for such huge decisions, much less life-altering treatment.

Though GeMS treatment is now considered the standard of care by mainstream medical groups, some have their doubts. Dr. Kenneth Zucker, a psychologist and head of the gender-identity service at the Center for Addiction and Mental Health in Toronto, says he worries about putting youngsters on puberty blockers, drugs that suppress the release of testosterone in boys and estrogen in girls.

“One controversy is, how low does one go in starting blockers?’’ Zucker says. “Should you start at 11? At 10? What if someone starts their period at 9?’’ Nicole started on the blockers at age 11.

He also questions the role the parents have played; have they simply followed the child’s lead? “Say a 5-year-old says repeatedly that he wants to be a girl,’’ Zucker says. “The parents deduce this must mean the child is transgender, so they socially transition him to living in the other gender.’’

Spack and others, however, say the issue is a medical one and that early intervention makes sense. “We’re talking about a population that has the highest rate of suicide attempts in the world, and it’s strongly linked to nontreatment, especially if they are rejected within their family for being who they think they are,’’ says Spack, who adds that nearly a quarter of his patients admitted to “serious self-harm’’ before coming to him.

As for the criticisms about “playing God,’’ Spack quotes from the Old Testament: “Leviticus says, ‘If thy neighbor is bleeding by the side of the road, you shall not stand idly by the blood of thy neighbor.’ It’s a mandate. I think these kids have been bleeding.’’

The next step

The clinic, which includes geneticists, social workers, psychiatrists, psychologists, and nurses, has so far treated 95 patients for disorders that range from babies born with ambiguous genitalia to cases where normal sexual development does not occur.

About a third of the patients have undergone puberty suppression.

Each patient must have been in therapy with someone familiar with transgender issues and who writes a letter recommending the treatment. The child’s family also must undergo extensive psychological testing before and during treatment. And the patient must be in the early stage of puberty, before bodily changes are noticeable.

Nicole and Jonas are the first set of identical twins the program has seen, and they have provided critical comparative data, Spack says.

The effects of the blockers - an injection given monthly to prevent the gonads from releasing the unwanted hormones - are reversible; patients can stop taking them and go through puberty as their biological sex. This is critical, Spack says, because a “very significant number of children who exhibit cross-gender behavior’’ before puberty “do not end up being transgender.’’

Since the 1970s, the blockers have been used for the rare condition of precocious puberty, when children as young as 3 can hit puberty. They are kept on the blockers until they are of appropriate age. “The drugs have a great track record; we already know that these kids do fine,’’ says Spack. “There are no ill consequences.’’

It is the next big step - taking sex hormones of the opposite gender - that creates permanent changes, such as breasts and broadened hips, that cannot be hormonally reversed.

“In puberty,’’’ Spack says, “when your body starts making a statement, you either have to accept it or reject it.’’

There is no definitive answer to the question of what causes gender identity disorder, though studies suggest a genetic contribution. “It’s still a very open question,’’ Zucker says. And how could it affect just one of two identical twins? “There can be genetic changes during fetal development that maybe hit one twin but not the other.’’

Changed atmosphere

After the family’s lawsuit against the Orono schools was publicized, the atmosphere in town changed. When they went to the movies, people pointed and whispered. There were fewer party invitations, fewer sleepovers.

In the sixth grade, the twins joined the school’s Outing Club. All year they attended meetings to prepare for the crowning event: a whitewater rafting trip. Wayne went to several meetings, too, so he could serve as a chaperone.

Wayne thought he had a good relationship with the club leader. But then the man informed him that Nicole would not be allowed to sleep in the tent with the girls - the same girls who had slept over her house several times. She and her father could have a separate tent.

A difficult family conversation followed. Jonas and Wayne went on the trip. Nicole stayed home.

After that episode, Kelly and Wayne decided a new start would be good for the family. The summer after the sixth grade, they moved to a larger, more diverse community in southern Maine, and the twins enrolled in public school. Wayne still works at UMaine and stays in Orono during the week, spending weekends with his family.

For two years, in seventh and eighth grade, Nicole went “stealth,’’ as she calls it: passing as a girl. She did not tell anyone that she was biologically male. Though she made friends at school, she never brought them to the house. After that hard last year in Orono, the family was afraid to come out.

This fall the twins entered high school, transferring to a smaller, private school known for open-mindedness. Before they arrived, the school changed its bathrooms to unisex. And before classes started, the family met with members of the school’s Gay Straight Alliance - “so she’d have older kids watching her back,’’ says Wayne. After the meeting, the group changed its name to include transgender; it is now the Gay Straight Transgender Alliance.

“It made me a lot more comfortable,’’ Nicole says. “I thought, this is OK. I can do this.’’

She recently started telling some of her new friends her story. One girl replied: “Does this mean you’re going to start wearing boys’ clothes to school?’’

“No,’’ replied Nicole. “I’m male to female.’’

The girl’s reaction? “She was like, ‘Ohhhhhhhhhhhhhhh.’ ’’

Concerns about safety

The male hormone suppressors have done their job, and the next step is to add female hormones so that Nicole will undergo puberty as a girl and develop as a woman, with breasts and curvy hips. She is due to see Spack in January, and a date may then be set for adding estrogen, which she will take every day for the rest of her life. Though she will have a higher risk of breast cancer than if she were a male, she will have a lower risk of prostate cancer, Spack says. The treatment will leave her infertile.

But before the estrogen is administered, the GeMS clinic will reevaluate Nicole to make sure that she still identifies as a female and wants to continue.

“In my experience, the patients just blossom physically and mentally when they get the hormones of the gender they affirm,’’ Spack says. “It’s quite amazing. I feel good about Nicole and who she is and where she’s going.’’

An endocrinologist in Maine now administers the blockers Nicole needs, but Spack still sees her in Boston every four to six months. The Maines family has grown close to him and others in the clinic. “I love going to see him,’’ says Wayne, who has thanked Spack for “saving my daughter’s life.’’ The Maines family declined to talk about the cost of the treatment but said insurance has covered much of it.

But as well as things are going, the Maines family still worries about Nicole’s safety. Last year Wayne and Nicole attended Transgender Day of Remembrance in Maine, which honors those who have been killed in hate crimes.

Wayne spoke to the crowd, telling them that as much as Nicole is loved at home, her family cannot always protect her.

“I remind her that she needs to always be aware of her surroundings, to stay close to friends and her brother if she feels uncomfortable, and to call me anytime she feels threatened,’’ he said.

Lobbying the Legislature

Last winter, Maine state representative Kenneth Fredette, a Republican from Penobscot County, sponsored a bill that would have repealed protections for transgender people in public restrooms, instead allowing schools and businesses to adopt their own policies. The bill was a response to the Maines’ 2009 lawsuit against the Orono School District.

Last spring Wayne and Nicole roamed the halls of the State House, button-holing legislators and testifying against the bill. “I’d be in more danger if I went into the boys bathroom,’’ Nicole told the lawmakers, who ultimately rejected the bill.

“She knows how to work a room,’’ her father says proudly. “She even convinced a cosponsor to vote the other way.’’

In October, the family was honored for its activism in helping defeat the transgender bathroom bill. The Maineses received the Roger Baldwin Award, named for a founder of the American Civil Liberties Union, from the Maine chapter of the ACLU.

Surrounded by Kelly and the kids, Wayne told the audience that he and his wife have had top-notch guides as they confronted the unknown.

“As a conventional dad, hunter, and former Republican, it took me longer to understand that I never had two sons,’’ he told them. “My children taught me who Nicole is and who she needed to be.’’

Typical teens

In some respects, Jonas has had as tough a time as Nicole. For one thing, there’s the personality difference: Nicole is the dominant twin, talkative and tough, while Jonas is cautious and reserved.

“If this had been Jonas, I would have had to home school him,’’ his mother says.

The twins have always been close. During an interview, Nicole sits next to her brother on the couch and occasionally lays her head on his shoulder. At one point, when Jonas goes silent as the twins talk of their lives, she whispers words of encouragement into his ear.

But the next minute, like typical teenage siblings, they’re teasing and tussling. Jonas displays a faint scar on his arm where Nicole jabbed him with a pencil. Both have black belts in tae kwon do, which they started at age 5.

They often hang out in Jonas’s spacious basement room, where they watch TV and play video games.

“I love having a sister,’’ says Jonas, who acknowledges being protective of her. “We have a very strong relationship.’’

Nicole calls Jonas her closest friend.

“I would say my brother got lucky with me. Because we grew up with only boy neighbors, I developed a liking to shoot-’em-up and military video games,’’ she says. “I could have come out a lot girlier.’’

At 14, Jonas is handsome, Nicole pretty. Jonas is midway through puberty. His shoulders have broadened, his voice has deepened, and there’s a shadow on his upper lip. He’s 5 feet 6 and weighs 115 pounds, with a size 11 shoe.

Nicole is petite: 5 feet 1, 100 pounds. She’s got long, dark hair and she wears girls’ size 14-16. Her closet contains nice shirts and jeans, party dresses, glittery shoes, and a pair of footy pajamas.

“The thought of being a boy makes me cringe,’’ she says. “I just couldn’t do it.’’

Excited, worried about surgery

Nicole’s final step on her journey to womanhood would be gender reassignment surgery. Doctors generally won’t perform it until the age of consent, which is 18. No hospitals in New England perform such surgery, says Spack. The nearest that do are in Montreal and Philadelphia.

Nicole says she’s excited about the idea of surgery, though a bit worried about the results - “and maybe the pain, too.’’

While she’s interested in boys, she has expressed fear that “nobody is ever going to love me.’’

She has gone on weekend retreats sponsored by the Trans Youth Equality Foundation and to summer camp for transgender children, where she developed her first crush on a boy.

Over the years, the family has become close to several adult transsexuals, and Nicole has seen that some have found happy marriages. “She says she does feel better about it,’’ Kelly says, “but still wonders if she ever met a boy who falls for her, and then found out that she was trans, if he would still like her, or say awful things as he skedaddled out the door.’’

Nicole knows there is a long road ahead, but she feels she’s on the right path.

“Obviously my life is not going to be as easy as being gender-conforming, but there are perks like being able to get out there and do things that will benefit the [transgender] community,’’ she says. “I think everything’s going to turn out pretty well for me.’’

For now, at least, life feels more normal to the Maines family.

Wayne recently spoke at GLAD’s Spirit of Justice dinner in Boston and was introduced by Nicole. She kept her composure in her brief remarks and thanked GLAD for giving them a rare chance to “safely speak out.’’

Wayne choked up when thanking the group for its support. He recounted young Wyatt asking him, sadly, “Daddy, why can’t boys wear dresses?’’ Wayne hated to tell his son that society wouldn’t accept that.

But today, when Nicole asks her father what he thinks of a certain dress she’s wearing, his typical response, he told the audience, is: “That dress is too short. Go change your clothes.’’

In conversation later, Wayne tells another story of how things have changed, for good and forever. He and the twins were getting out of the car recently, and he grabbed their hands to walk with them.

Jonas, being a teenage boy, shook his father off, while Nicole was happy to walk hand-in-hand, swinging arms.

“She’ll do that the rest of her life,’’ Wayne says with a wide grin. “It was an epiphany for me.’’

Jonas and Wyatt Maines were born identical twins, but from the start each had a distinct personality.

Molecular Anthropology Group - University of Oregon

My friend and Colleague Nelson Ting's Molecular Anthro page is now up and running - "like" it on facebook to stay up to date on his group's research and job opportunities!

Scientists a step closer to cloning mammoth

from Japantimes

The thighbone of a mammoth found in August in Siberia contains well-preserved marrow, increasing the chances of cloning one of the extinct beasts, Japanese and Russian scientists confirmed recently.

The teams from the Sakha Republic's mammoth museum in eastern Russia and Kinki University's graduate school in biology-oriented science and technology will launch full-fledged joint research next year to clone the giant mammal, which is believed to have become extinct about 10,000 years ago, they said.

By transplanting nuclei taken from the marrow cells into elephant egg cells whose nuclei have been removed through a cloning technique, embryos with a mammoth gene could be produced and planted into elephant wombs, as the two species are close relatives, they said.

Securing nuclei with an undamaged gene is essential for the nucleus transplantation technique, but doing so from mammoths is extremely difficult and scientists have been trying to reproduce a mammoth since the late 1990s, they said.

In the Sakha Republic, global warming has thawed its almost permanently frozen ground, leading to numerous discoveries of frozen mammoths. But cell nuclei are usually damaged or have not been kept in a frozen state even when they have been found in a good overall condition, a Russian museum official said.

This time, however, there is a high likelihood that biologically active nuclei can be extracted as the frozen marrow found when museum scientists cut open the thighbone Nov. 13 was fresh and in excellent condition, according to the official. The bone was found near Batagay in northern Sakha.

The technique for extracting nuclei, meanwhile, has improved dramatically in the past few years and some undamaged nuclei have been successfully taken from badly preserved mammoth tissue fragments, albeit at low rates, said the Kinki University team based in Osaka Prefecture.

The museum, located in the republic's capital, Yakutsk, soon notified the Japanese side, with which it has had close ties through joint research since 1997, including professor Akira Iritani and associate professor Hiromi Kato.

Iritani confirmed that the outstanding condition of the marrow has increased the chances of cloning a mammoth, and said the Japanese team will try to obtain elephant eggs for the research project, although he added this would not be easy.

NewYorker article on Neanderthals (and Svante Pääbo)

New Yorker article on Neanderthals

Dolphins team up to get the girl

by ABBIE THOMAS
from abc.net

An alliance of four male dolphins, dubbed The Beatles have shown that when blokes co-operate, they have more sexual success.

The research by a team at Macquarie University is published in the Journal of Animal Ecology.

The study found that male dolphins who form an alliance fathered far more babies than those who worked in smaller groups or alone.

The researchers studied a population of 70 male and 64 female Indo-Pacific bottlenose dolphins living in Port Stephens, New South Wales. They collected skin samples from males and calves and looked for genetic markers which would reveal the paternity of the calves.

They found that 14 different males had sired 32 calves. However, nearly half of the calves - 13 individuals - were sired by a single alliance of four dolphins known as The Beatles.

Three calves were sired by a three-male alliance and five calves were sired by another three-male alliance.

The remaining 11 calves sired by pairs or lone males.
Teaming up works

Males are known to form alliances in a number of species, including lions, chimpanzees, horses and, some would argue, humans.

"But there has not been any evidence to show why an alliance might be preferable," says co-author Dr Jo Wiszniewski.

"This research shows that male dolphins need to cooperate with each other to maximise their reproductive success."

Up to 80 per cent of males form alliances to seek out and reproduce with females during the spring/summer breeding season, says Wiszniewski.

"Males in alliances have better control of the females - we often see the males swimming around the females one on each side, sometimes one at the back. The female can't get away from them," she says.

"They basically herd the female - they try to keep her away from other males. They would swim by her and when she was feeding, they would feed too."

"These kind of herding events can last just from a few hours up to a few weeks at a time," says Wiszniewski.
Pressure to form alliances

Female dolphins only have a calf every two to five years, so in any particular year there are very few females available and ready to mate with.

"That's why there's so much pressure for males to form alliances, to become more competitive," she says.

Previous research from Western Australia also found that male dolphins who form alliances breed more successfully. But in this case, forming cooperative alliances was less surprising, Wiszniewski says, because those dolphins were related.

"If one of those males helps another reproduce, he still gets benefits because his genes still get passed on," she says.

But in Port Stephens, the cooperating dolphins weren't related.

"That's what's so fascinating. By helping another male, they are actually risking the chance that they won't reproduce with a female. So they really need a high level of cooperation and trust so then the male knows that by helping another male, he's also going to get helped."

Wiszniewski points out that one of The Beatles - John - doesn't seem to have fathered any calves.

"We have a feeling he was not a full part of the alliance. He was what we call the odd male out - he wasn't really 'in' with the group."

Orangutan Culture Develops Like Human Culture

Thanks to Geraldine F and Zoran A for the link
from WIRED.com
By Olivia Solon

A team of anthropologists have shown that orangutans may have the ability to learn socially and pass these lessons down through generations — evidence that culture in humans and great apes has the same evolutionary roots.

In humans, certain behavioral innovations tend to be passed down from generation to generation through social learning. Many consider the existence of culture in humans to be one of the key factors that differentiates us from other animals.
Around a decade ago, biologists observing great apes noticed geographical variations in behavior that suggested that they were passing certain innovations down through generations, just as humans do. To this day, there is much debate about whether geographical variations in behavior is driven culturally or through genetic and environmental factors.

Researchers from the University of Zurich have now studied whether the geographic variation of behavioral patterns in nine orangutan populations in Sumatra and Borneo can be explained by cultural transmission. They have concluded that it can.

The team analyzed more than 100,000 hours of behavioral data and created genetic profiles of more than 150 wild orangutans. They measured the ecological differences between the habitats of the different populations using satellite imagery and remote sensing techniques.

Co-author of the study, published in Current Biology, Carel van Schaik said: “The novelty of our study is that, thanks to the unprecedented size of our dataset, we were the first to gauge the influence genetics and environmental factors have on the different behavioral patterns among the orangutan populations.”

Environmental influences and, to a lesser degree, genetic factors did play an important role in defining differences in social structure and behavioral ecology between the populations. However, these factors did not explain the behavioral patterns.

Michael Krützen, the first author of the study, said: “The cultural interpretation of the behavioral diversity also holds for orangutans — and in exactly the same way as we would expect for human culture. It looks as if the ability to act culturally is dictated by the long life expectancy of apes and the necessity to be able to adapt to changing environmental conditions.”

How Do Giant Pandas Survive on Bamboo?

Panda poop held clues to how bears break down plant fibers, study says.
From National Geographic
by RACHEL KAUFMAN

A new analysis of panda poop has finally answered an age-old question: How do giant pandas survive on a diet that's 99 percent bamboo when they have the guts of carnivores?

Plant-eating animals tend to have longer intestines to aid in digesting fibrous material, a trait the black-and-white bears lack.

What's more, when the giant panda's genome was sequenced in 2009, scientists found that the creature lacks the genes for any known enzymes that would help break down cellulose, the plant fibers found in bamboo and other grasses.

This led researchers to speculate that panda intestines must have cellulose-munching bacteria that play a role in digestion. But previous attempts to find such bacteria in panda guts had failed.

The new study looked at gene sequences in the droppings from seven wild and eight captive giant pandas—a much bigger sample than what was used in previous panda-poop studies, said study leader Fuwen Wei, of the Chinese Academy of Science's Institute of Zoology in Beijing.

Wei and colleagues found that pandas' digestive tracts do in fact contain bacteria similar to those in the intestines of herbivores.

Thirteen of the bacteria species that the team identified are from a family known to break down cellulose, but seven of those species are unique to pandas.

"We think this may be caused by different diet, the unique inner habitat of the gut, or the unique phylogenetic position of their host," since pandas are on a different branch of the tree of life than most herbivores, Wei said.

Humans Drove Pandas to Bamboo?
Even with help from gut bugs, pandas don't derive much nutrition from bamboo—a panda digests just 17 percent of the 20 to 30 pounds (9 to 14 kilograms) of dry food it eats each day. This explains why pandas also evolved a sluggish, energy-conserving lifestyle.

So how and why did pandas became plant-eaters in the first place?

Some scientists theorize that, as the ancient human population increased, pandas were pushed into higher altitudes. The animals then adopted a bamboo diet so they wouldn't compete for prey with other meat-eaters, such as Asiatic black bears, in their new homes, said Nicole MacCorkle, a panda keeper at the Smithsonian's National Zoo in Washington, D.C.

Pandas will eat meat if it's offered to them, MacCorkle added, but they won't actively hunt for it.

Stephen Fry's Planet Word (featuring a lot of the MPI-EVA)

Thanks to Richard M for the link!

Computer gamers solve problem in AIDS research that puzzled scientists for years

FROM DISCOVER MAGAZINE

When scientists struggle with a problem for over a decade, few of them think, “I know! I’ll ask computer gamers to help.” That, however, is exactly what Firas Khatib from the University of Washington did. The result: he and his legion of gaming co-authors have cracked a longstanding problem in AIDS research that scientists have puzzled over for years. It took them three weeks.
Khatib’s recruits played Foldit, a programme that reframes fiendish scientific challenges as a competitive multiplayer computer game. It taps into the collective problem-solving skills of tens of thousands of people, most of whom have little or no background in science.

Here’s what I wrote about Foldit last year:

The goal of the game is to work out the three-dimensional structures of different proteins. Proteins are feats of biological origami; they consist of long chains of amino acids that fold into very specific and complicated shapes. These shapes can reveal how proteins work, but solving them is fiendishly challenging. To do it, scientists typically need to grow crystals of purified protein before bouncing X-rays off them.
Foldit takes a different approach, using the collective efforts of causal gamers to do the hard work. And its best players can outperform software designed to do the same job. Best of all, you don’t need a PhD to play Foldit. Barely an eighth of the players work in science, and two-thirds of the top scorers have no biochemistry experience beyond high school. The controls are intuitive; tutorial levels introduce the game’s mechanics; colourful visuals provide hints; and the interface is explained in simple language. While protein scientists concern themselves with “rotating alpha-helices” and “fixing degrees of freedom”, Foldit players simply ‘tweak’, ‘freeze’, ‘wiggle’ and ‘shake’ their on-screen shapes.

Foldit’s success relies on the fact that it doesn’t shallowly flirt with interactivity – it’s a true game. Its creator Seth Cooper designed it to “attract the widest possible audience… and encourage prolonged engagement”. It’s competitive: players are scored based on the stability of the structures they end up with and a leader board shows how they rank against other gamers. There’s also a social side: gamers can chat on online forums, work in groups to solve puzzles and share solutions on a wiki. And just like real game development, everything was tuned according to feedback from the players. Tools were added and refined, the difficulty of the tutorials was tweaked to stop frustrated beginners from leaving, and puzzles were matched to the skills of the players.

There’s the thrill of contributing to genuine scientific research, but that motivates less than half of the community. The rest do it for the achievement, the social aspects and largely, because the game was fun and immersive.

Foldit’s origins lie within Rosetta, a piece of software designed to solve protein structures by simulating and testing thousands of different folds. Rosetta is an example of ‘ distributed computing’, where volunteers run the program on their home computers when they don’t need it. They effectively donate their computing power to speed up the laborious task of solving protein structures. But the volunteers wanted to use their biological computers – their brains – as well as their man-made ones. They suggested an interactive version of the programme and in May 2008, they got their wish with Foldit.

Last year, Cooper showed that Foldit’s gamers were better than the Rosetta programme at solving many protein structures. They used a wide range of strategies, they could pick the best places to begin, and they were better at long-term planning. Human intuition trumped mechanical number-crunching.

This year, Khatib wanted to see if the Foldit community could solve fresh problems. He entered the players into a twice-yearly contest called CASP (Critical Assessment of Techniques for Protein Structure Prediction), where structural biologists from all over the world compete to predict the structures of proteins that have almost been solved. They get the best predictions from Rosetta to begin with. Then, they’re on their own.

Khatib’s gamers, bearing names such as Foldit Contenders Group and Foldit Void Crushers Group, had varying degrees of success in the contest. In many of the categories, they did reasonably well but they couldn’t match the best groups. They weren’t as good at using the structures of similar proteins to tweak the ones they were working on. They could also head down dead ends if they started at the wrong place. In one case, their strategy of refining their starting structures to the best possible degree led to one of the “most spectacular successes” in the contest. But mostly, they focused too heavily on tweaking already imperfect solutions that other teams achieved better results by making large-scale changes.

Learning from that lesson, Khatib stepped in himself. He agitated the initial protein structures in many random ways, to create a wide variety of terrible answers that the gamers could then refine. In their attempts, they came up with the best-ranked answer to the most difficult challenge in the competition.

It was a success, and more would follow. After the competition, the players solved an even more important problem. They discovered the structure of a protein belonging to the Mason-Pfizer monkey virus (M-PMV), a close relative of HIV that causes AIDS in monkeys.
These viruses create many of their proteins in one big block. They need to be cut apart, and the viruses use a scissor enzyme –a protease – to do that. Many scientists are trying to find drugs that disable the proteases. If they don’t work, the virus is hobbled – it’s like a mechanic that cannot remove any of her tools from their box.

To disable M-PMV’s protease, we need to know exactly what it looks like. Like real scissors, the proteases come in two halves that need to lock together in order to work. If we knew where the halves joined together, we could create drugs that prevent them from uniting. But until now, scientists have only been able to discern the structure of the two halves together. They have spent more than ten years trying to solve structure of a single isolated half, without any success.
The Foldit players had no such problems. They came up with several answers, one of which was almost close to perfect. In a few days, Khatib had refined their solution to deduce the protein’s final structure, and he has already spotted features that could make attractive targets for new drugs.

“This is the first instance that we are aware of in which online gamers solved a longstanding scientific problem,” writes Khatib. “These results indi­cate the potential for integrating video games into the real-world scientific process: the ingenuity of game players is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems.”

Update: Stephen Curry, who works on protein structures, had this to say about the paper: “Credit where it’s due: this is certainly an innovative approach to the problem of determining crystal structures of proteins. And I do like the idea of ‘citizen science’. Although it’s probably questionable how much science the gamers are understanding, the involvement in this sort of research, even if it is just at the level of playing a game, is undoubtedly a good thing.”
Curry also points out that a structure for this protein was published in 2003 using a different method called nuclear magnetic resonance. Khatib says that this is “quite inaccurate” and that people have struggled to use it to progress any further, but Curry says that they don’t say much about the differences between the old and new structures.

Likewise, Khatib doesn’t mention how closely related the M-PMV protease and the HIV ones are. “This information is crucial for deciding whether a structure of M-PMV protease is going to be any use as a template for the design of novel classes of drug targeted to HIV protease. If I had reviewed this paper, I would have asked for that information to be included because it is needed to make sense of observed differences in structure,” he says.

Reference: Khatib, DiMaio, Foldit Contenders Group, Foldit Void Crushers Group, Cooper, Kazmierczyk, Gilski, Krzywda, Zabranska, Pichova, Thompson, Popović, Jaskolski & Baker. 2011. Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural and Molecular Biology http://dx.doi.org/10.1038/nsmb.2119

More on Foldit: Foldit – tapping the wisdom of computer gamers to solve tough scientific

How "Zombie" Virus Liquifies Caterpillar Hosts

Single gene allows virus to brainwash caterpillars, turn them to goo, study says.

by Brian Handwerk

From National Geographic

Scientists have identified a single gene that allows a caterpillar-brainwashing virus to do its dirty work, a new study says.

The virus forces the "zombie" caterpillars to climb trees, where the invader eventually liquifies its hosts' bodies into a dripping goo.

"When gypsy moth caterpillars are healthy and happy, they go up into the trees at night to feed on leaves, and then climb back down in the morning to hide [in bark crevices or soil] from predators during the day," said study co-author Kelli Hoover, an entomologist at Penn State University.

But caterpillars infected with a baculovirus—a type of virus that infects invertebrates—are driven to the treetops and reprogrammed to stay there until they meet a doom worthy of a horror film.

"When they are infected, as they get sicker they stay up in the trees and die up there," Hoover explained.

The virus "ends up using just about all of the caterpillar to make more virus, and there are other genes in the virus that then make the caterpillar melt. So it becomes a pool of millions of virus particles that end up dropping onto the foliage below where it can infect other moths that eat those leaves."


Viruses Are Master Manipulators
Though such zombie-making viruses were previously known, their genetics have been a mystery.

So Hoover and colleagues infected gypsy moth caterpillars with half a dozen different types of baculovirus and placed the bugs in tall bottles with food on the bottom. Viruses that the scientists had determined carried a specific gene, called egt, drove caterpillars to climb to the top of the container and stay there to die.

Researchers then removed egt from some viruses, reinfected the caterpillars, and found that the zombie behavior stopped. When the team inserted the gene into a virus that previously lacked it, the zombie behavior returned.

"Somehow or other, using this gene, the virus is able to manipulate the behavior of the caterpillar to go to the right location in the tree to enhance transmission to new hosts. It's really amazing," Hoover said.

The gene may work by deactivating its hosts' molting hormone, according to the study, published tomorrow in the journal Science.

"That would be an advantage to the virus because it keeps the insect in a feeding state, so that they get bigger and bigger and make more and more virus."

Viruses and Moths-Natural Enemies
There are many different types of baculovirus, Hoover said, and almost all caterpillar species are infected by one or more of them.

But the virus, which is naturally occurring, doesn't greatly impact gypsy moths as a species, Hoover said. Gypsy moth populations are prone to cycles of boom and bust, so when caterpillar numbers are in check, the virus remains so as well.

When gypsy moth invasions grow, the virus may go into outbreak mode-serving as a natural control mechanism for caterpillar infestations.

"This virus probably came to North America when the caterpillars did," Hooever explained. "It's just a natural enemy of the gypsy moth."

--

if you liked this you might also like: http://dnapes.blogspot.com/2010/09/zombie-fying-parasites.html

In the lab at night...

Thanks to Mark W for the link (original here: http://i.imgur.com/lEZEV.jpg)

PAN African chimpanzee census, counting chimps and mapping culture

Apes in Africa: The cultured chimpanzees
by Gayathri Vaidyanathan
From NATURE NEWS

pdf can be downloaded here

Do chimpanzees have traditions? As wild populations dwindle, researchers are racing to find out.

Thump! Thump! Thump! As the hollow sound echoes through the Liberian rainforest, Vera Leinert and her fellow researchers freeze. Silently, Leinert directs the guide to investigate. Jefferson 'Bola' Skinnah, a ranger with the Liberian Forestry Development Authority, stalks ahead, using the thumping to mask the sound of his movement.

In a sunlit opening in the forest, Skinnah spots a large adult chimpanzee hammering something with a big stone. The chimpanzee puts a broken nut into its mouth then continues pounding. When Skinnah tries to move closer, the chimp disappears into the trees. By the time Leinert and her crew get to the clearing, the animal is long gone.

For the past year, Leinert has been trekking through Sapo National Park, Liberia's first and only protected reserve, to study its chimpanzee population. A student volunteer at the Max Planck Institute for Evolutionary Anthropology (EVA) in Leipzig, Germany, Leinert has never seen her elusive subjects in the flesh but she knows some of them well. There's an energetic young male with a big belly who hammers nuts so vigorously he has to grab a sapling for support. There are the stronger adults who can split a nut with three blows. And there are the mothers who parade through the site with their babies. They've all been caught by video cameras placed strategically throughout Sapo.

Chimpanzees in the wild are notoriously difficult to study because they flee from humans — with good reason. Bushmeat hunting and human respiratory diseases have decimated chimpanzee populations1, while logging and mining have wiped out their habitat. Population numbers have plunged — although no one knows by exactly how much because in most countries with great apes, the animals have never been properly surveyed.

The Pan Africa Great Ape Program, the first Africa-wide great-ape census to be mounted, could change that. In addition to surveying chimpanzee numbers (see 'How many chimpanzees are left?'), project scientists plan to set up automated video and audio recording devices at 40 research sites in 15 countries with chimp populations. Led by Christophe Boesch, director of the primatology department at the EVA, and Hjalmar Kühl, also at the EVA, the programme aims to get a picture of how chimpanzee behaviour — from nut cracking to vocal calls — varies across Africa. Ultimately, the hope is to learn about the origins and extent of what, in humans, would be called culture.

Until recently, scientists regarded culture — defined as socially transmitted behaviours — as exclusive to humans, but there is growing recognition that many animals exhibit some sort of culture. Chimpanzees, which share 98% of their genes with humans, have the most varied set of behaviours documented in the animal world. The difference between humans and animals is growing less distinct, say some researchers. "It is not black and white," says Kühl, who is Leinert's supervisor at the EVA.

In the old scenario, "only humans have culture", says Jason Kamilar, a biogeographer in the department of anthropology at Yale University in New Haven, Connecticut. "Then, culture would be the defining feature of humanity, which evolved some time after the split between the human and chimp lineages," he says. But "if chimps have culture, then presumably the last common ancestor of chimps and humans had culture".

Mapping Behaviour
Some chimps dance slowly at the beginning of rain showers, others don't; some use long sticks to dig up army ants; others use short sticks. In West Africa, some chimp groups hammer nuts with a stone or a piece of wood to open them. But east of the river Nzo-Sassandra, which cuts across Côte d'Ivoire, only one group has been seen cracking nuts.

So far, researchers have observed these variations over years spent studying groups of chimpanzee that have been carefully habituated to the presence of humans. There are just 12 such colonies in Africa (see 'Chimpanzee census'), the most famous of which is in Gombe Stream National Park in Tanzania, where primatologist Jane Goodall worked.

In 1999, evolutionary psychologist Andrew Whiten of the University of St Andrews, UK, and his colleagues compiled a list of behaviours seen in seven of those groups and showed that chimpanzees have unique traditions depending on where they live2. They identified at least 39 behaviours from a list of 65 that varied between groups for no obvious reason.

In humans, culture is passed on from one person to another, and in laboratory studies chimpanzees have shown the capacity to pass on learned customs. In one experiment, Whiten and his colleagues taught two chimps a complex series of steps for getting food from a box. Soon after the chimps were reunited with their groups, all the animals were using this method to get their food3. But whether such social learning happens in the wild is less clear. Gorillas and bonobos can also learn to use tools in the lab, but rarely use them in their natural habitat4.

Deciphering culture in the wild is difficult because researchers must ensure that behavioural differences between groups do not have other causes, such as variation in genetics or environmental conditions. "Why is it all chimps don't do everything? One solution is that there are hidden ecological differences between populations," says primatologist Richard Wrangham at Harvard University in Cambridge, Massachusetts. A behaviour could be linked to any number of variables such as amount of rainfall, the types of tree available, or the kinds of predator in the area, he says.

These influences can be subtle, as researchers found while studying how chimps use sticks to harvest army ants. Chimpanzees in Guinea sometimes use short sticks and sometimes use sticks up to twice as long. No reason for this was obvious until Tatyana Humle, an anthropologist at the University of Kent, UK, found that some ants are more aggressive, with longer legs and larger mandibles; they run up sticks quicker and bite harder5. This might explain why chimps elsewhere in Africa also choose tools of varying lengths to get at ants.

But researchers have not been able to find obvious explanations for other variations related to ant harvesting. Chimpanzees in Cote d'Ivoire sweep the ants off their sticks and into their palms before eating; in Guinea, only about 320 kilometres away, the animals stick the ant-laden sticks directly into their mouths. The same type of ant is present in both places.

Ruling out genetic influences is equally complicated. This year, molecular ecologist Kevin Langergraber at the EVA and his colleagues compared genetic and behavioural data for nine groups of chimpanzee. They found that communities with greater overlap in their mitochondrial DNA showed more similarities in their behaviour6. "What we are saying is, you haven't really ruled out the genetic explanation," says Langergraber.

There may be a few hundred thousand chimpanzees in Africa, but researchers have studied just 700–1,000 chimpanzees at the dozen sites with well habituated colonies, says Whiten. The available information from those groups is too little to determine how genes and the environment influence behavioural variations. Kühl compares the situation to using a handful of villages scattered around the world to draw basic conclusions about all the rituals that define human culture.

Whiten and his colleagues are now carrying out more detailed comparisons of the behaviour and ecology of chimps at all the habituated sites. But it has taken 50 years to capture the data they are using, most of which were recorded by painstaking observational studies.

The way forward may be the use of cameras hidden in strategic sites, like those Leinert and her team are setting up in Liberia. Such techniques have already proved their worth. Two years ago in Gabon, Boesch and his team were puzzled by random pits they observed in the ground. They set up camera traps and obtained video recordings of chimps digging to extract honey from underground bees' nests — something that had never been seen before7. "Camera traps are proving to be an exciting way to reveal new and often complex behavioural techniques in wild chimpanzee communities," says Whiten.
Caught in the act

At the site in Sapo, Leinert pulls on gloves to measure the rock used by the chimp to crack open nuts of the Guinea plum, Parinari excelsa. The rock is sizeable, weighing in at 880 grams. She collects nuts for later analysis, as well as hair and dung samples for genetic studies.

Leinert may later put up a video camera at the location to collect more data on the nut-cracking behaviour. The cameras are mounted in boxes on tree trunks at the height of a chimp's shoulder, and powered by rechargeable batteries. An infrared motion detector activates the camera for one minute when anything moves in its range.

Near the nut-cracking site, a solar-powered audio device is already continuously recording the forest sounds. Chimpanzees emit a range of calls, including short, high-pitched 'pant hoots' that are unique to each individual, and researchers can use them to identify individuals and to tally the size of a community. These calls may be a form of vocal culture, somewhat like human dialects8.

Over the next five years, the Pan Africa Great Ape Program will establish similar recording stations at locations across Africa. "So potentially we might have, in a few years, behavioural differences from 40 different populations, which is, as you know, four times more than what we have now," says Boesch.

Kühl proposes that these data could help in designing computer models to test how genes, ecology and social transmission influence the distribution and spread of behaviours such as nut cracking. One idea is that when female chimpanzees reach sexual maturity and move to new communities, they pass along their learned behaviours. Another possibility is that each group invents its own behaviours, some of which catch on and become a culture. Individual practices can die out in particular groups but thrive in others. Or, it might be that some chimp groups refuse to take up new ways of doing things from incoming individuals. This could explain why some populations show similar behaviours and others do not.

Before Kühl and his colleagues can conduct the modelling work, they need to devise a faster way to go through the recordings made by the camera and audio traps, which are accumulating at a rate of hundreds of hours each month. Students are currently carrying out the analysis but it can take 10 hours to go through an hour of video, according to Kühl. So engineers at the Fraunhofer Institute for Digital Media Technology, based in Ilmenau, Germany, have developed a computer algorithm to recognize individual chimpanzees from their facial patterns and distinctive features, such as the wrinkles under their eyes. In tests of zoo animals, the software can correctly identify individual chimpanzees 83% of the time, and it processes recordings ten times faster than a person can.

Nevertheless, the cameras cannot reveal how an adult chimp patrols its range, or other actions that play out over a wide area. The full portfolio of traditions in the community will remain a mystery. And automated recordings will never capture the subtle ecological information — such as the mandible size and leg length of army ants — that may eventually explain particular behaviours. These require boots on the ground, and long-term behavioural studies are needed to see how chimpanzees pass traditions on to each other as a driver of culture.

But already, the 30 cameras that Leinert has set up in Sapo Park have delivered some tantalizing clues. She is most interested in the lively young male she calls 'Janosch', whom she likes for "his big belly and the way he strikes out to crack the nuts". Besides being entertaining, he sometimes carries his pounding rock away with him, something Leinert hasn't seen with most other chimpanzees in Sapo. The practice may yet catch on with others there. If so, Leinert could be seeing the beginnings of a cultural variation, captured by the cameras she set up in the forest.

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Box: How many chimpanzees are left?

Jacob the chimp, now two years old, spends most of his day in a wooden box not much bigger than himself. Born in Sapo National Park in Liberia, he was rescued by a forest ranger, who found Jacob and his dead mother in the arms of a poacher.

Such tales are common in Africa. Bushmeat is a vital source of protein and a dead chimpanzee can fetch US$200 in Nigeria. No one knows exactly how many chimps there are in the wild: in 2003, the International Union for Conservation of Nature made a very rough estimate of 172,700–299,700. But the population is declining rapidly, and many communities are likely to disappear in the next few decades. A study in 2008 found that the population in Côte d'Ivoire had decreased by 90% in 17 years.

In 2010, the dearth of data prompted the Max Planck Institute for Evolutionary Anthropology (EVA) in Leipzig, Germany, to team up with the Wild Chimpanzee Foundation, headquartered at the EVA, and Conservation International, based in Arlington, Virginia, to launch the Pan Africa Great Ape Program. They aim to conduct nationwide surveys in 15 countries to estimate how many chimps are left in Africa. The scientists involved would not disclose the project's budget, but acknowledged that the surveys will be expensive and that they do not yet have all the necessary funding.

As part of the survey, graduate student Jessica Junker of the EVA and her Liberian team of graduate students and rangers from the Forest Development Authority are walking some 400 kilometres to survey 68 squares laid out on a grid across the country. They trek through uncut bush and overgrown farms, across rivers, and into deep muddy valleys to look for chimpanzee nests. Each chimp usually builds a new nest every day, and the researchers can estimate the age of a nest from its state of decomposition. They can then extrapolate to get an idea of the number of animals in an area. Their findings so far suggest that Liberia holds at least 3,300 chimpanzees.

Using similar methods in Sierra Leone, the 2008–10 Tacugama National Chimpanzee Census estimated that more than 5,500 chimpanzees live in that country. This is much higher than a 1981 estimate of 2,500, probably because the earlier survey used less systematic survey methods.

Christophe Boesch of the EVA, who co-heads the Pan Africa Great Ape Program, says that it will guide conservation efforts to where they can do the most good. But getting precise numbers on the great apes in each country is expensive because of the labour involved, and some conservationists would rather see the money spent on enforcing laws against poaching.

“We don't need a nationwide survey to tell us we are losing the battle,” says David Greer, who coordinates the African Great Apes Program for the conservation group WWF. “We need to be more assertive, more aggressive with intervention measures, trying to stop the decline.”

In celebration of Mendel's birthday Google has a great doodle :)

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Mystery of mole's second thumb solved

By Jennifer Carpenter
The extra digit plays a crucial role in mole digging proficiency

Scientists have discovered how one of the world's best diggers got its "extra thumb".

Comparing the mole's digits with those of its close relative, the researchers looked for molecular clues to the anatomical oddity.

The results show that the mole's second thumb is not a real digit but starts out as a wrist bone, the scientists report in Biology Letters.

The extra appendage helps propel the mole through its subterranean world.

The very early four-legged land vertebrates, such as Acanthostega and Ichthyostega, that dragged themselves from the muddy waters on to land had five, six, seven, even eight fingers. But evolution seems to have favoured the five-fingered.

And so today, whether they have paws, claws or hands, most vertebrates have five digits. The exceptions, such as hoofed animals and birds have all descended from five-fingered ancestors.

In today's world, the giant panda and the mole are anomalies among vertebrates: both have a second thumb, giving them a total of 12 digits.

A fake
Their extra thumbs are considered adaptations to their modes of life.

The panda uses its thumbs to better grip its favourite bamboo food, while the mole's shovel-like claws are probably an adaptation to its dirt-filled tunnels.

Now new research suggests that the mole's second thumb, just like the Giant panda's, is a fake.

Developmental biologist Christian Mitgutsch, and his colleagues, from the University of Zurich, Switzerland, looked at the hands of eight mole species, and compared them with those of their close relative, the shrew.
Skeletal image of hand (Credit: C.Mitgutsch/Zurich)

By looking at the developing paws of the mole, Dr Mitgutsch was able to see that genes that usually turned on at the beginning of digit development did not show up when the mole's thumb started to form.

What is more, these cells did not start to extend into a finger-like protrusion until after the five other digits were well on their way to being fully formed.

Them wrist bones
However, what clinched it for Dr Mitgutsch was when he and his team showed that the second thumb seems to grow from tissue that usually develops into wrist bone, and not finger bone.

All of the eight mole species had some form of extra thumb, Dr Mitgutsch explained, but some did not develop past a small milimetre-long bone at the bottom of their paws, while others, like the Iberian mole, Talpa occidentalis, had a second thumb that matched the length of its five other fingers.

The researchers suspect that the mole's hormones are responsible for the six-finger quirkiness.

Female moles possess both ovararian and testicular tissue, and therefore have high levels of testosterone compared to species where individuals are either one sex or the other.

Exposure to high levels of testosterone - a known bone builder - in the uterus has been linked to polydactylism, a condition where people are born with extra fingers and toes.

However, there is more work to do before researchers can point the finger at testosterone when it comes to the mole's extra digits.

Reference
Mitgutsch C, Richardson MK, Jiménez R, Martin JE, Kondrashov P, de Bakker MAG, Sánchez-Villagra1 MP, Sánchez-Villagra1 MR (2011) Circumventing the polydactyly ‘constraint’: the mole's ‘thumb’. Biology Letters doi: 10.1098/rsbl.2011.0494

Abstract
Talpid moles across all northern continents exhibit a remarkably large, sickle-like radial sesamoid bone anterior to their five digits, always coupled with a smaller tibial sesamoid bone. A possible developmental mechanism behind this phenomenon was revealed using molecular markers during limb development in the Iberian mole (Talpa occidentalis) and a shrew (Cryptotis parva), as shrews represent the closest relatives of moles but do not show these conspicuous elements. The mole's radial sesamoid develops later than true digits, as shown by Sox9, and extends into the digit area, developing in relation to an Msx2-domain at the anterior border of the digital plate. Fgf8 expression, marking the apical ectodermal ridge, is comparable in both species. Developmental peculiarities facilitated the inclusion of the mole's radial sesamoid into the digit series; talpid moles circumvent the almost universal pentadactyly constraint by recruiting wrist sesamoids into their digital region using a novel developmental pathway and timing.

Missing Gene Helps Mice Run for Hours

by Sarah C.P. Williams
from Sciencemag

Lab mice usually take only an occasional jaunt on their exercise wheels. But mice missing a gene called IL-15Rα run for hours each night, a new study reveals. And the gene doesn't just make a difference to mice—it might also be linked to the ability of long-distance athletes to outperform the rest of us.

Previous studies had suggested that IL-15Rα is important for muscle strength. In experiments on cells grown in a Petri dish, the gene seemed to control the accumulation of proteins necessary for muscle contraction. But IL-15Rα had never been studied in a living animal.

In the new research, physiologist Tejvir Khurana of the University of Pennsylvania and his colleagues genetically engineered mice to lack the IL-15Rα gene. The changes were dramatic. Each night, according to sensors on the wheels in the mice's cages, the modified mice ran six times farther than normal mice.

But these behavioral quirks weren't quite enough to convince Khurana of the effect on muscles. Lack of the IL-15Rα gene could just be making the mice jittery or giving them extra energy. So the researchers dissected muscles from the longer-running mice. The muscles sported increased numbers of energy-generating mitochondria and more muscle fibers, indicating that they tired less easily. And when the researchers stimulated them with electricity, the muscles continued to contract for longer than normal, taking longer to use up their energy stores, the team reports today in The Journal of Clinical Investigation.

Mice, like humans, have two types of muscles. Fast-twitch muscles, such as the muscles in our fingers, allow more precise movements but tire faster, whereas slow-twitch muscles, like those in our back, are more resistant to fatigue but don't allow such precise movements. Removing the IL-15Rα gene, Khurana says, coaxed the mice's fast-twitch leg muscles to turn into slow-twitch muscles.

To study whether IL-15Rα might also affect human endurance, Khurana collaborated with a group of researchers in Australia who keep a library of genetic samples from Olympic and world-class athletes. They found that certain variants of the IL-15Rα gene were more common in endurance athletes like long-distance cyclists and rowers than they were in sprinters. More than three-quarters of long-distance triathletes had one type of variant, for example. Although researchers don't know yet what functional differences the gene variants might have, the finding suggests that the most successful endurance athletes might have a variant that gives their muscles extra endurance.

Biologist Ronald Evans of the Salk Institute for Biological Studies in San Diego, California, says the new study adds to the picture of how endurance is controlled at a molecular level. Evans has characterized the effects of a separate protein called PPARδ, which gives mice extra running endurance as well as enhanced fat-burning abilities. Mice lacking IL-15Rα showed an increase in PPARδ activity, though it's not clear whether the genes directly interact and work through the same mechanisms.

Psychological factors could also be at play. "In a case like this, it's hard to know how to connect the hyperactivity component to the endurance component," Evans says. Even if the mice's muscles have extra endurance, he says, why do they voluntarily run so much more than normal mice?

Still, Khurana says the work raises the possibility that drugs blocking IL-15Rα could one day enhance endurance. Of course, researchers don't know whether such a drug would have other side effects, because the IL-15Rα gene is expressed in many tissues in the body, not just muscles. So for now, if you want to become a better athlete, it's probably best to just lace up your sneakers and get some old-fashioned exercise.

Reference
Pistilli1 EE, Bogdanovich S, Garton F, Yang N, Gulbin JP, Conner JD, Anderson BG,Quinn LS, North K, Ahima RS, Khurana1 TS (2011) Loss of IL-15 receptor α alters the endurance, fatigability, and metabolic characteristics of mouse fast skeletal muscles J Clin Invest. doi:10.1172/JCI44945.

Abstract
IL-15 receptor α (IL-15Rα) is a component of the heterotrimeric plasma membrane receptor for the pleiotropic cytokine IL-15. However, IL-15Rα is not merely an IL-15 receptor subunit, as mice lacking either IL-15 or IL-15Rα have unique phenotypes. IL-15 and IL-15Rα have been implicated in muscle phenotypes, but a role in muscle physiology has not been defined. Here, we have shown that loss of IL-15Rα induces a functional oxidative shift in fast muscles, substantially increasing fatigue resistance and exercise capacity. IL-15Rα–knockout (IL-15Rα–KO) mice ran greater distances and had greater ambulatory activity than controls. Fast muscles displayed fatigue resistance and a slower contractile phenotype. The molecular signature of these muscles included altered markers of mitochondrial biogenesis and calcium homeostasis. Morphologically, fast muscles had a greater number of muscle fibers, smaller fiber areas, and a greater ratio of nuclei to fiber area. The alterations of physiological properties and increased resistance to fatigue in fast muscles are consistent with a shift toward a slower, more oxidative phenotype. Consistent with a conserved functional role in humans, a genetic association was found between a SNP in the IL15RA gene and endurance in athletes stratified by sport. Therefore, we propose that IL-15Rα has a role in defining the phenotype of fast skeletal muscles in vivo.