31 January 2007

what are these bacteria telling us?

Inteterdepence and cooperation, not isolation and selfishness, are the key to survival, to the degree that we may need to discard the notion of separate species, report two theoretical biologists, N. Goldenfeld and C. Woese. ScienceWeek observes that their Nature article concludes:
…the convergence of fresh theoretical ideas in evolution and thecoming avalanche of genomic data will profoundly alter our understanding of the biosphere -- and is likely to lead to revision of concepts such as species, organism and evolution.The place to start is horizontal gene transfer (HGT), the non-genealogical transfer of genetic material from one organism to another -- such as from one bacterium to another or from viruses to bacteria. Among microbes, HGT is pervasive and powerful -- for example, in accelerating the spread of antibiotic resistance. Owing to HGT, it is not a good approximation to regard microbes as organisms dominated by individual characteristics. In fact, their communications by genetic or quorum-sensing channels indicate that microbial behaviour must be understood as predominantly cooperative….In the wild, microbes form communities, invade biochemical niches and partake in biogeochemical cycles. The available studies strongly indicate that microbes absorb and discard genes as needed, in response to their environment. Rather than discrete genomes, we see a continuum of genomic possibilities, which casts doubt on the validity of the concept of a "species" when extended into the microbial realm.… Recent work suggests that viruses are an important repository and memory of a community's genetic information, contributing to the system's evolutionary dynamics and stability. [...]

30 January 2007

nonhumancommunications Photo of the Day

"She says she's willing to wash the windshield for spare change."

surprise! animals suffer PTSD, too

…from Science Week:

The following points are made by G. A. Bradshaw et al (Nature 2005 433:807):

1) Psychobiological trauma in humans is increasingly encountered as a legacy of war and socio-ecological disruptions. Trauma affects society directly through an individual's experience, and indirectly through social transmission and the collapse of traditional social structures. Long-term studies show that although many individuals survive, they may face a lifelong struggle with depression, suicide, or behavioral dysfunctions. In addition, their children and families can exhibit similar symptoms, including domestic violence. Trauma can define a culture.

2) How posttraumatic stress disorder (PTSD) manifests has long been a puzzle, but researchers today have a better idea as to why the effects of violence persist so long after the event. Studies on animals and human genocide survivors indicate that trauma early in life has lasting psychophysiological effects on brain and behavior. Under normal conditions, early mother-infant interactions facilitate the development of self-regulatory structures located in the corticolimbic region of the brain's right hemisphere. But with trauma, an enduring right-brain dysfunction can develop, creating a vulnerability to PTSD and a predisposition to violence in adulthood. Profound disruptions to the attachment bonding process, such as maternal separation, deprivation, or trauma, can upset psychobiological and neurochemical regulation in the developing brain, leading to abnormal neurogenesis, synaptogenesis, and neurochemical differentiation. The absence of compensatory social structures, such as older generations, can also impede recovery.

3) Elephant society in Africa has been decimated by mass deaths and social breakdown from poaching, culls, and habitat loss. From an estimated ten million elephants in the early 1900s, there are only half a million left today. Wild elephants are displaying symptoms associated with human PTSD: abnormal startle response, depression, unpredictable asocial behavior and hyperaggression. Elephants are renowned for their close relationships. Young elephants are reared in a matriarchal society, embedded in complex layers of extended family. Culls and illegal poaching have fragmented these patterns of social attachment by eliminating the supportive stratum of the matriarch and older female caretakers (allomothers).

4) Calves witnessing culls and those raised by young, inexperienced mothers are high-risk candidates for later disorders, including an inability to regulate stress-reactive aggressive states. Even the fetuses of young pregnant females can be affected by pre-natal stress during culls. The rhinoceros-killing males may have been particularly vulnerable to the effects of pre- and postnatal stress for two reasons. Studies on a variety of species indicate that male mammalian brains develop at a slower rate relative to females, but also that elephant males require a second distinct phase of socialization. As with females, male socialization begins during infancy with the mother and a tight constellation of allomothers. But in adolescence, males leave the natal family to participate in older all-male groups, a period coincident with a second major stage of brain reorganization identified in humans.[1-3]


1. Clubb, R. & Mason, G. A Review of the Welfare of Elephants in European Zoos (RSPCA, Horsham, 2002)

2. Schore, A. N. Affect Dysregulation and Disorders of the Self (W. W. Norton, New York, 2003)

3. Slotow, R. et al. Nature 408, 425-426 (2000)

Nature http://www.nature.com/nature

ScienceWeek http://scienceweek.com

"I used to be really hard. But they taught me how to be soft"

….Sometimes, when Deborah Cooper looks a troubled horse in the eye, she knows exactly how it feels. She knows what it's like to be expected to do something that goes against your nature, to be considered something of a rebel. Which may be why some believe her to be one of the top horse trainers in the county, a real-life horse whisperer whose livelihood depends on her talent for turning a bucking, bolting, biting animal into something that's close to a friend.…What she does, she says, is finds out what an animal's talents are, listens to what it is saying by how it behaves, and then sets out to get it to trust a human, so its owners can trust it again. "It's: How can we create the ambiance where a horse wants to play with me or ride with me," Cooper says as she heads into the ranch's cool, dark tack room, her spurs leaving small punctuation marks in the dust.…She's got 70 horses — 15 of them, her own — and people bring their animals from all over California so she can "fix" them.

A horse isn't exactly glad to see a human, she says as she heads into the bright winter sun where her stallion waits in a round corral. "A horse is a prey animal, and we're predators. Our eyes are in front to focus on our prey. A horse's are on the side of their heads to see what's going on." Which, she says, makes them frightened of people, movement and changes in things around them — one example, she says, of how a horse views the world differently than a human and why they act in ways that a rider might not appreciate.

The trick, she says, is to figure out what an animal is experiencing or trying to say, and then learning ways to communicate with them. It's not making a horse more like us, she says, but making us more like a horse.

These are the things she learned when she studied with Pat Parelli, one of the masters of what has become known as Natural Horsemanship — popularized in the 1995 novel by Nicholas Evans, "The Horse Whisperer"

The idea behind his, and other "whisperers' " training, is to understand and use a horse's natural instincts and communication, in order to teach it.

"They've taught me to be soft," she says. They've taught her to observe and listen and to be courageous. Some of them come in so fried and so scared," she says, her voice breaking. I used to be really hard," she says. "But they taught me how to be soft"…

Deborah Cooper may just be a horse's best friend
By PEGGY TOWNSEND, 28 January 2007, Santa Cruz Sentinel

29 January 2007

"a metaphysical difference between humans and nonhuman animals"

….For researchers, however, “there’s nothing sacramental about the boundaries between the species,” and interbreeding, therefore, “is just moving around cellular or genetic materials in the world,” says Arizona State University bioethicist Jason Robert. Esmail Zanjani, an animal biotechnologist at the University of Nevada School of Medicine, has grown sheep with human livers; Irving Weissman, director of the Institute for Stem Cell Biology and Regenerative Medicine at Stanford University, has created mice with human brain cells; and many researchers are taking the first steps toward stem cell therapy by injecting human cells into mice, monkeys, and other animals. Evan Snyder of the Burnham Institute in La Jolla, California, argues that these sorts of experiments allow scientists to work out the kinks in such therapies on a monkey or rat rather than “your child or grandmother.”

Like Snyder, most biologists working to combine species aim to help humans or to advance scientific knowledge, not to selfishly cook up a Frankensteinian manimal. Zanjani, for instance, hopes human organs grown in animals could help shorten transplant waiting lists. Still, the intermingling makes many uneasy. Robert and other bioethicists have identified some potential underlying reasons for these fears: In essence, man-animal chimeras and hybrids could lead to a type of moral confusion, leaving us unsure of how we are supposed to treat the resulting creatures and whether we should be performing medical research on them at all. Regardless of their religious beliefs or lack thereof, most people do find something “special” about the human species, Robert says. “For people of faith, it’s going to be a metaphysical difference between humans and nonhuman animals. For others, it’s going to be something else, such as culture or self-consciousness, that explains the differences between human and nonhuman animals.”

This sense of specialness also underlies many of the negative responses the researchers at the Broad Institute received. “The reason there is all this discussion is because a lot of people still today simply can’t wrap their minds around the idea that we’re animals,” says Pigliucci, who has a particular interest in the way we think about evolutionary theory. “We may be special animals, we may be particular animals with very special characteristics, but we’re animals nonetheless; we have cousins and relatives all over the animal world, and, therefore, by implication of course, we were not created from nothing by an intelligent designer. That really hurts a lot of people.”

Sara Via, an evolutionary biologist at the University of Maryland, echoed this sentiment in a recent AAAS talk on speciation: “Many people don’t want to accept that humans aren’t on the top of the heap evolutionarily and certainly not that humans may have evolved from something that resembles a lowly monkey.”

Scientists are not immune to illusions of distinct separation, says Pigliucci. “I am certainly not going to claim that at a subconscious level, there’s been no bias amongst scientists themselves in terms of human biology,” he says. “I’m sure that it is difficult to look not only at humans, but at our closest relatives, in a completely detached way. I know several primatologists, and I don’t know any of them who doesn’t feel more than just a scientific curiosity toward their subject of investigation. They clearly understand and they feel that they’re dealing with very special animals because they’re so closely related to us.” But new information, such as the complete sequence of human and some animal genomes, is allowing scientists to factually confirm, again and again, our similarities to other species. We share with chimpanzees more DNA than previously thought; other primates, known as bonobos, have constructed societies in which they display moral rules; and elephants and other long-living species are now believed to suffer from psychiatric conditions like post-traumatic stress disorder. The ability to uncover these commonalities—and to be surprised by them—highlights the true benefit of the scientific worldview, Pigliucci says: its flexibility.

“Your regular person on the street thinks of a scientist as someone who’s certain. Scientists know facts. They’re objective. But that’s not science at all,” says Via. “Science is a view of life in which new information is admitted, not denied, and we use that information to always make that view better.” ….


Of Manimals and Humanzees
The idea that humans and chimps interbred causes discomfort in some circles, even as science explores the potential benefits of hybrids and the blurring of what was once a bright line between species.

by Cindy Kuzma

nonhumancommunications Headline of the Day

Mysterious source jams satellite communications

...in New Scientist.

bad idea: "companion animals function as a blank slate" for human projection

There seems to be an inverse relationship between the amount of emotion people associate with their dog and the amount of concrete knowledge they have about his physical and behavioral needs," says veterinarian Myrna Milani, who has written extensively on the human-animal bond. "Dogs, cats and other companion animals function as a blank slate on to which people can project what emotions they want - including the belief that sharing food with their pet is a form of communion."

Fat-pet pill? Try common sense
by Denise Flaim, Newsday.com, January 29, 2007

a reasonable approach: "try to communicate with them on their level"

What exactly constitutes "dog psychology?"

It's more of a direct communication with your dog instead of training them through human psychology, like "sit" and "stay." You're actually acting like the "alpha" member of the pack, talking to them the way that they understand. Most of the behavioral problems that are dogs have are created by (humans), by mixed messages. Our policy is to respect the dog and try to communicate with them on their level.

-Didi Tremblay
Manager of Dogma Grooming and Pet Needs
Richmond, VA

communications between Kenyans, elephants reach a low point

"Elephant handlers at the Daphne Sheldrick Elephant Orphanage walk animals to their bath." [Photo by Nick Wadhams, special to the Chronicle]

In Kenya, elephants are hated
As people move closer to wildlife, clashes increase

by Nicholas Wadhams, San Francisco Chronicle Foreign Service
Sunday, January 28, 2007

(01-28) 04:00 PST Narok, Kenya -- Mary Sinigi hates elephants.

In December, an elephant terrorized her village, chased her husband down a dirt path and ripped the roof off her home while she and her five children cowered inside.

"Because of elephants, we never rest," Sinigi said, recalling the predawn invasion. "When the kids leave in the morning to go out to school, we are not certain they will come back until we see them again."

Most Kenyans do not share the common Western belief that the elephant is a lovable beast in desperate need of protection and worth the several thousand dollars' cost of a safari vacation. To them, the elephant is a 6-ton garden pest, a wrecking ball that kills, tramples and terrifies.

That anger reflects what conservationists say is a worrisome trend: Conflict between humans and wildlife -- and particularly elephants -- is on the rise, sparking a backlash among Kenyans against the very animals that are considered treasured assets.

[...] "The problem is, of course, expanding human population that's taking up a lot of the space that elephants traditionally use on their migratory travels," said Daphne Sheldrick, a conservationist who runs an elephant sanctuary outside Nairobi. "Where elephants come into conflict with humans, those elephants will have to disappear or be moved."

Newspapers across East and southern Africa are filled with stories about elephants destroying crops, killing farmers, wandering into slums where they've never appeared before. In 2005, an elephant trampled an old man and then crashed his funeral -- spurring irate mourners to block a road and pelt passing cars with rocks in frustration.

Anecdotal evidence points to a rise in the illegal trade of bush meat, and poaching continues to be a problem in many parks. Statistics show that some 90 percent of Kenyans value wildlife in the abstract -- but only 5 percent value wildlife on their own land.

Current laws have stripped people of the right to kill problem animals themselves, and punishment for doing so can include prison time. Yet if an elephant, a lion or a buffalo kills a person, the victim's relatives receive just 30,000 Kenyan shillings -- about $400 -- if they get anything at all. There is no compensation for destruction of livestock or crops.

"If I'm not getting benefit, I would rather kill the animal than have my brother or sister killed," said Yusuf Ole Petenya, a Maasai who works with the African Conservation Centre, a Nairobi-based research group. "Of course, we have an interest in wildlife, but I'm also interested in seeing my brother or my sister alive. How can I have happiness if I wake up in the morning and my brother is dead because he's been mauled by a lion next door?"

The resentment toward the rules on wild animals was evident at a mid-December meeting to discuss the national review in Narok, a town outside the renowned Masai Mara game reserve. This is a place where everyone knows someone who has been killed by a charging buffalo. A nearby orphanage is populated by children who lost their parents to two main killers: HIV/AIDS and animals.

The new elephant problem is gripping much of Africa, not just Kenya. In Botswana, Namibia, South Africa and Tanzania, elephant populations stabilized at about 600,000 -- down from 1.5 million in the 1970s -- and are beginning to rise.

Capable of consuming several hundred pounds of food and at least 30 gallons of water a day, elephants have the capacity to turn heavily vegetated ecosystems into near desert. They also kill other species that crowd them.

Villagers say any policy change will have to address not only the changes in Kenya, but also the changes in the wildlife that surrounds them.

In the Rift Valley south of Nairobi, a flash point in the conflict between humans and elephants, the once-skittish beasts seem to have figured out that the laws are working in their favor.

"The elephants are very polite," said Steven Nteetu, a cattle owner and farmer near the village of Olkirimatian. "Even if they come here to the farms, you can shout and shout, but they can look at you and continue with eating. What we have seen now is that the animals are not wild. They are coming nearby. They are not afraid of the human being."

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URL: http://sfgate.com/cgi-bin/article.cgi?file=/c/a/2007/01/28/MNG7SNQDHR1.DTL

27 January 2007

the beetles are coming!

Some 8,000 species of beetles in California alone, and humans can't communicate worth a darn with any of them.

That's one conclusion to draw from a new book from Cal State Northridge biologist James N. Hogue, Field Guide to Beetles of California, which looks like the guide to California beetles.

shine your love light, baby!

Spiders do it, too:
Ultraviolet light found to promote romance among jumping spiders

The dpa German Press Agency article says the study reveals "the first connection between light and sex in the animal kingdom."

No word, however, from these National University of Singapore researchers as to whether the eight-legged romantics have begun decorating their student dorm room walls with Day-Glo posters and burning incense, to help a date get in the mood.

[Cosmophasis umbratica, pix from msnbc.com]

animal behavior sound & video

…from Cornell Lab or Ornithology's library of animal behavior recordings:

Recordings from the archive play a role in “The Birds That Roar,” reports the Ithaca Journal. According to the newspaper, a performance tomorrow in Ithaca, New York:

begins with fascinating bird and animal sounds from the archive, presented by Cornell Professor Ron Hoy, an animal communication expert, and Cornell physicist John Greenly. They will show how these sounds have inspired composers and musician-scientist John Greenly will provide musical examples with his quartet and solo on his clarinet.

The second part of the finale will be presented by Oscar-winning sound designer and director Gary Rydstrom of Pixar. He'll discuss his work on the Jurassic Park movies and how he used bird sounds from the Cornell Lab of Ornithology's Macaulay Library to give computer-generated dinosaurs a voice.

The archive of animal sounds (and a growing collection of behavioral video) at the Lab's Macaulay Library is the largest in the world. Sounds from the collection have been used in everything from research to museum exhibits, toys, games and, of course, movies. Anyone wishing to explore animal sounds can listen to the collection online by visiting www.animalbehaviorarchive.org.

"we must do all we can to open lines of communication between man and, uh, Dumbo"

A letter to the editor in today's San Francisco Chronicle:

Robber pachyderms

The world has seen enough and it is time to take action.

Your Jan. 20 Earthweek article involving the "brazen hijacking" in Thailand of as many as 10 trucks loaded with sugar cane and tapioca by a herd of elephants raises the specter of a potential conspiracy by 20 pachyderms. I ask: How did we miss signs of this felonious act, and will they do it again?

According to the chief of the Khao Ang Rue Nai Wildlife Sanctuary, this was the "first highway robbery by elephants we recorded." Maybe so, but what's to say this wasn't a serial crime spree in the making? Wildlife science says elephants don't easily forget. One can only imagine their next larceny might include a weapon.

As we recover from this deplorable event, we should investigate what could have allowed these large friends to meander down this path of crime. Has society completely neglected the criminal behavior of these four-legged vandals with trunks?

These elephants may have been "encouraged to hijack the tasty cargo by the many passers-by," but now we must do all we can to open lines of communication between man and, uh, Dumbo. In so doing, we can work to prevent future "white-collar" crimes of the pachyderm.

Mill Valley

Say what?

26 January 2007

who needs to wake up?

…picked this up on Boing Boing some time ago:

I think that the lower animals, with all their reactions and adjustments made and established are in a somnambulic state, like the Chinese. But the Chinese are waking up! Do you think that anything could wake up the ants and start them plotting against human civilization?
–Charles Fort, 1925 letter

next they'll try talking to potatoes

Next month, the College of Southern Idaho will offer an "Introduction to Animal Communication" that will employ a hands-on approach to help students "fine tune their feelings and realize that communication with animals is real and possible," says course developer, Cindy Lee Simeon, according to the Idaho Mountain Express. The class promises to "not only teach students how to communicate with pets and other animals, but will "help add another dimension to the relationship between the two." Simeon said.


Warnings for humans, but none for the mountain lions, since we don't know how to communicate directly with them (pix opportunistically grabbed from a Google search):

…from Lisa Leff of the Associated Press:

Wildlife officials on Thursday credited a woman with saving her husband's life by clubbing a mountain lion that attacked him while the couple were hiking in a California state park. Jim and Nell Hamm, who will celebrate their 50th wedding anniversary next month, were hiking in Prairie Creek Redwoods State Park when the lion pounced.

"He didn't scream. It was a different, horrible plea for help, and I turned around, and by then the cat had wrestled Jim to the ground," Nell Hamm said in an interview from the hospital where her husband was recovering from a torn scalp, puncture wounds and other injuries.

After the attack, game wardens closed the park about 320 miles north of San Francisco and released hounds to track the lion. They later shot and killed a pair of lions found near the trail where the attack happened. The carcasses were flown to a state forensics lab to determine if either animal mauled the man.

Although the Hamms are experienced hikers, neither had seen a mountain lion before Jim Hamm was mauled, his wife said.

Nell Hamm said she grabbed a four-inch-wide log and beat the animal with it, but it would not release its hold on her husband's head.

"Jim was talking to me all through this, and he said, 'I've got a pen in my pocket and get the pen and jab him in the eye,'" she said. "So I got the pen and tried to put it in his eye, but it didn't want to go in as easy as I thought it would." When the pen bent and became useless, Nell Hamm went back to using the log.

The lion eventually let go and, with blood on its snout, stood staring at the woman. She screamed and waved the log until the animal walked away.

"She saved his life, there is no doubt about it," said Steve Martarano, a spokesman for the Department of Fish and Game.

Nell Hamm, 65, said she was scared to leave her dazed, bleeding husband alone, so the couple walked a quarter-mile to a trail head, where she gathered branches to protect them if more lions came around. They waited until a ranger came by and summoned help.

"My concern was to get Jim out of there," she said. "I told him, 'Get up, get up, walk,' and he did.
Jim Hamm, 70, was in fair condition Thursday. He had to have his lips stitched back together and underwent surgery for lacerations on his head and body. He told his wife he still wants to make the trip to New Zealand they planned for their anniversary, she said. Nell Hamm warned people never to hike in the backcountry alone.

Park rangers told the couple if Jim Hamm had been alone, he probably would not have survived.
"We fought harder than we ever have to save his life, and we fought together," she said.

…from an earlier AP report of the same incident:
Based on their weight of between 70 and 100 pounds, officials think the lions were relatively young. The incident about 320 miles north of San Francisco was the 16th mountain lion attack reported to the state since 1890. It was the first attack since three people were injured, one of them fatally, in separate incidents in Orange and Tulare counties in 2004, Martarano said.
Since 1990, the 4,000 to 6,000 mountain lions estimated to be in California have been protected from hunting, although residents can get special permits to shoot a lion if it is perceived as a danger to people, pets or livestock.

Sightings of the animals have increased in the past decade as housing has spread into their habitat, but attacks are relatively rare since mountain lions tend to be wary of people, said Karen Kovacs, a senior wildlife biologist with the Department of Fish and Game.

"For the most part, their natural inclination is to go the other way when humans are around," Kovacs said. "This was atypical because this person was with somebody. Usually they attack someone who is alone."

The park was reopened to the public Thursday after the second lion was killed, Banko said.

25 January 2007

stacking the totem pole

Watching a fight and knowing who wins or loses lets some fish figure out the local hierarchy, reports National Geographic, pre-empting the journal, Nature. The African cichlids that were the object of this research, Astatotilapia burtoni, sound like some people I know. Nothing here about onlookers turning into brown-nosers, after the fight.

20 January 2007


Time running out for NY dolphins

Rescuers in a boat near the trapped dolphins

A last-ditch attempt to rescue a pod of common dolphins trapped in a shallow cove off Long Island near New York appears to be failing.

About 20 dolphins were stranded in the shallow waters north of East Hampton over a week ago, after swimming through a gap in the sandbanks at high tide.

Although eight or nine were coaxed back into open waters, most of the others have now died - leaving three dolphins.

But forecast gales and low temperatures make their chances of survival slim.

The BBC's Jeremy Cooke in New York says these are increasingly frustrating times for the 80 or so volunteers who have spent much of the last week braving high winds and freezing temperatures to rescue the dolphins.

"Rescuers are standing by to pick up any of the living dolphins that may wash up on shore and take them for treatment.Time is not on our side. We're looking at a gale wind tomorrow and Sunday doesn't look good, which makes boat operations almost impossible," said Charles Hamilton, regional emergency response co-ordinator for the Department of Environmental Conservation.

There was some early success when eight or nine of the dolphins were herded through a tiny gap in the sandbanks and into the safety of the open waters.

Since then, all of the efforts which have included using several boats emitting high frequency sound pulses to corral the rest of the dolphins to safety, have failed.

Three days ago the remaining dolphins began to die. Marine biologists blamed stress and hunger. Gales and low temperatures predicted over the next few days make the chances of survival for the remaining dolphins extremely slim. Common, or white-sided, dolphins normally stay 30-80 miles (50-130km) offshore.