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Note: My

Note: My Anthropic Trilogy web-book, evolving since 1997, is a chronicle of my passing all considered opinion
through the lens of my Nirvikalpa Samadhi with both an open-mind and healthy skepticism.

Examining the Continuum of Evolution of Animals, Plants and Humans
NY Times Special March 14, 2011

From Single Cells, a Vast Kingdom Arose by Carl Zimmer - NY Times: March 14, 2011

Lurking in the blood of tropical snails is a single-celled creature called Capsaspora owczarzaki. This tentacled, amoebalike species is so obscure that no one even noticed it until 2002. And yet, in just a few years it has moved from anonymity to the scientific spotlight. It turns out to be one of the closest relatives to animals. As improbable as it might seem, our ancestors a billion years ago probably were a lot like Capsaspora.

The origin of animals was one of the most astonishing and important transformations in the history of life. From single-celled ancestors, they evolved into a riot of complexity and diversity. An estimated seven million species of animals live on earth today, ranging from tubeworms at the bottom of the ocean to elephants lumbering across the African savanna. Their bodies can total trillions of cells, which can develop into muscles, bones and hundreds of other kinds of tissues and cell types.

The dawn of the animal kingdom about 800 million years ago was also an ecological revolution.

Animals devoured the microbial mats that had dominated the oceans for more than two billion years and created their own habitats, like coral reefs.

The origin of animals is also one of the more mysterious episodes in the history of life. Changing from a single-celled organism to a trillion-cell collective demands a huge genetic overhaul. The intermediate species that might show how that transition took place have become extinct.

“We’re just missing the intervening steps,” said Nicole King, an evolutionary biologist at the University of California, Berkeley.

To understand how animals took on this peculiar way of life, scientists are gathering many lines of evidence. Some use rock hammers to push back the fossil record of animals by tens of millions of years. Others are finding chemical signatures of animals in ancient rocks. Still others are peering into the genomes of animals and their relatives like Capsaspora, to reconstruct the evolutionary tree of animals and their closest relatives. Surprisingly, they’ve found that a lot of the genetic equipment for building an animal was in place long before the animal kingdom even existed.

It was only in the past few years that scientists got a firm notion of what the closest relatives to animals actually are. In 2007, the National Human Genome Research Institute started an international project to compare DNA from different species and draw a family tree. The cousins of animals turn out to be a motley crew. Along with the snail-dwelling Capsaspora, our close relatives include choanoflagellates, amoebalike creatures that dwell in fresh water, where they hunt for bacteria.

Now scientists are trying to figure out how a single-celled organism like Capsaspora or choanoflagellates became a multicellular animal. Fortunately, they can get some hints from other cases in which microbes made the same transition. Plants and fungi evolved from single-celled ancestors, as well as dozens of other less familiar lineages, from brown algae seaweed to slime molds.

Primitive multicellularity may have been fairly easy to evolve. “All that has to happen is that the products of cell division stick together,” said Richard E. Michod of the University of Arizona. Once single-celled organisms shifted permanently to colonies, they could start specializing on different tasks. This division of labor made the colonies more efficient. They could grow faster than less specialized colonies.

Eventually, this division of labor could have led many cells in proto-animals to give up their ability to reproduce. Only a small group of cells still made the proteins required to produce offspring. The cells in the rest of the body could then focus on tasks like gathering food and fighting off disease.

“It’s not a hurdle,” said Bernd Schierwater of the University of Veterinary Medicine in Hanover, Germany. “It’s a very good way to be very efficient.”

Yet multicellularity also threw some new challenges at the ancestors of animals.

“When cells die in a group, they can poison each other,” said Dr. Michod. In animals, cells die in an orderly fashion, so that they release relatively few poisons. Instead, the dying cells can be recycled by their living brethren.

Another danger posed by multicellularity is the ability for a single cell to grow at the expense of others. Today that danger still looms large: cancer is the result of some cells refusing to play by the same rules as the other cells in our body.

Even simple multicellular organisms have evolved defenses to these cheaters. A group of green algae called volvox have evolved a limit to the number of times any cell can divide. “That helps reduce the potential for cells to become renegades,” said Dr. Michod.

To figure out the solutions that animals evolved, researchers are now sequencing the genomes of their single-celled relatives. They’re discovering a wealth of genes that were once thought to exist only in animals. Iñaki Ruiz-Trillo of the University of Barcelona and his colleagues searched Capsaspora’s genome for an important group of genes that encode proteins called transcription factors. Transcription factors switch other genes on and off, and some of them are vital for turning a fertilized egg into a complex animal body.

In the current issue of Molecular Biology and Evolution, Dr. Ruiz-Trillo and his colleagues report that Capsaspora shares a number of transcription factors that were once thought to be unique to animals. For example, they found a gene in Capsaspora that’s nearly identical to the animal gene brachyury. In humans and many other animal species, brachyury is essential for embryos to develop, marking a layer of cells that will become the skeleton and muscles.

Dr. Ruiz-Trillo and his colleagues have no idea what Capsaspora is doing with a brachyury gene. They’re now doing experiments to find out; in the meantime, Dr. Ruiz-Trillo speculates that single-celled relatives of animals use the brachyury gene, along with other transcription factors, to switch genes on for other tasks.

“They have to check out their environment,” said Dr. Ruiz-Trillo. “They have to mate with other organisms. They have to eat prey.”

Studies by other scientists point to the same conclusion: a lot of the genes once thought to be unique to the animal kingdom were present in the single-celled ancestors of animals. “The origin of animals depended on genes that were already in place,” Dr. King said.

In the transition to full-blown animals, Dr. King argues, these genes were co-opted for controlling a multicellular body. Old genes began to take on new functions, like producing the glue for sticking cells together and guarding against runaway cells that could become tumors.

Paleontologists have searched for decades for the fossils that chronicle this transition to the earliest animals.

Last year, Adam Maloof of Princeton and his colleagues published details of what they suggest are the oldest animal fossils yet found. The remains, found in Australia, date back 650 million years. They contain networks of pores inside of them, similar to the channels inside living sponges.

Sponges may have also left behind other ancient traces. Gordon Love of the University of California, Riverside, and his colleagues have drilled down into deposits of oil in Australia dating back at least 635 million years. In the stew of hydrocarbons they’ve brought up, they have found cholesterol-like molecules that are produced today only by one group of sponges.

The fact that sponges show up so early in the fossil record is probably no coincidence. Recent studies on animal genomes indicate that sponges are among the oldest lineages of living animals — if not the oldest. Sponges are also relatively simple compared with most other animals. They have no brains, stomachs or blood vessels.

Despite their seeming simplicity, sponges are card-carrying members of the animal kingdom. Like other animals, sponges can produce eggs and sperm, which can then produce embryos. Sponge larvae swim through the water to find their way to a good spot where they can settle down for a sedentary life and grow into adults. Their development is an exquisitely sophisticated process, with stem cells giving rise to several different cell types.

The first sponge genome was only published in August. It offered scientists an opportunity to compare the DNA of sponges to that of other animals as well as to Capsaspora and other single-celled relatives. The researchers looked at each gene in the sponge genome and tried to match it to related groups of genes in other species, known as gene families. All told, they were able to find 1,268 gene families shared by all animals — including sponges — but not by other species.

Those genes were presumably passed down to living animals from a common ancestor that lived 800 million years ago. And by surveying this catalog, scientists can infer some things about what that ancestor was like.

“It wasn’t just an amorphous blob of cells,” said Bernard M. Degnan of the University of Queensland. Instead, it was already setting aside eggs and sperm. It could produce embryos, and it could lay down complicated patterns in its body.

Animals didn’t just evolve multicellular bodies, however. They also appear to have evolved new ways of generating different kinds of bodies. Animals are more prone to mutations that shuffle sections of their proteins into new arrangements, a process called domain shuffling. “Domain shuffling seems to be a critical thing,” Dr. Degnan said.

Dr. Degnan and his colleagues have found another source of innovation in animals in a molecule called microRNA. When cells produce proteins from genes, they first make a copy of the gene in a molecule called RNA. But animal cells also make microRNAs that can attack RNA molecules and destroy them before they have a chance to make proteins. Thus they can act as another kind of switch to control gene activity.

MicroRNAs don’t seem to exist in single-celled relatives of animals. Sponges have eight microRNAs. Animals with more cell types that evolved later also evolved more microRNAs. Humans have 677, for example.

MicroRNAs and domain shuffling gave animals a powerful new source of versatility. They had the means to evolve new ways of reshaping their embryos to produce a wide range of forms — from big predators to burrowing mud-feeders.

That versatility may have allowed early animals to take advantage of changes that were unfolding all around them. About 700 million years ago, Earth emerged from the grips of a worldwide ice age. Noah Planavsky of the University of California, Riverside, and his colleagues have found evidence in rocks of that age for a sudden influx of phosphorus into the oceans at the same time. They speculate that as glaciers melted, phosphorus was washed from the exposed land into the sea.

The phosphorus may have acted as a pulse of fertilizer, stimulating algae growth. That may have been responsible for the rapid rise of oxygen in the ocean at the same time. Animals may have been prepared to use the extra oxygen to fuel large bodies and to use those bodies to devour other species.

“It was a niche to be occupied,” said Dr. Ruiz-Trillo, “and it was occupied as soon as the molecular machinery was in place.”

The Creature Connection by Natalie Angier NY Times, March 14, 2011

“She draws the whole family together,” said Pamela Fields, 52, a government specialist in United States-Japan relations. “Even when we hate each other, we all agree that we love the dog.” Her husband, Michael Richards, also 52 and a media lawyer, explained that the name Bashert comes from the Yiddish word for soul mate or destiny. “We didn’t choose her,” he said. “She chose us.” Their 12-year-old daughter, Alana, said, “When I go to camp, I miss the dog a lot more than I miss my parents,” and their 14-year-old son, Aaron, said, “Life was so boring before we got Bashert.”

Yet Bashert wasn’t always adored. The Washington Animal Rescue League had retrieved her from a notoriously abusive puppy mill — the pet industry’s equivalent of a factory farm — where she had spent years encaged as a breeder, a nonstop poodle-making machine. By the time of her adoption, the dog was weak, malnourished, diseased, and caninically illiterate. “She didn’t know how to be a dog,” said Ms. Fields. “We had to teach her how to run, to play, even to bark.”

Stories like Bashert’s encapsulate the complexity and capriciousness of our longstanding love affair with animals, now our best friends and soul mates, now our laboratory Play-Doh and featured on our dinner plates. We love animals, yet we euthanize five million abandoned cats and dogs each year. We lavish some $48 billion annually on our pets and another $2 billion on animal protection and conservation causes; but that index of affection pales like so much well-cooked pork against the $300 billion we spend on meat and hunting, and the tens of billions devoted to removing or eradicating animals we consider pests.

“We’re very particular about which animals we love, and even those we dote on are at our disposal and subject to all sorts of cruelty,” said Alexandra Horowitz, an assistant professor of psychology at Barnard College. “I’m not sure this is a love to brag about.”

Dr. Horowitz, the author of a best-selling book about dog cognition, “Inside of a Dog,” belongs to a community of researchers paying ever closer attention to the nature of the human-animal bond in all its fetching dissonance, a pursuit recently accorded the chimeric title of anthrozoology. Scientists see in our love for other animals, and our unslakable curiosity about animal lives, sensations, feelings and drives, keys to the most essential aspects of our humanity. They also view animal love as a textbook case of biology and culture operating in helical collusion. Animals abound in our earliest art, suggesting that a basic fascination with the bestial community may well be innate; the cave paintings at Lascaux, for example, are an ochred zooanalia of horses, stags, bison, felines, a woolly rhinoceros, a bird, a leaping cow — and only one puny man.

Yet how our animal urges express themselves is a strongly cultural and contingent affair. Many human groups have incorporated animals into their religious ceremonies, through practices like animal sacrifice or the donning of animal masks. Others have made extensive folkloric and metaphoric use of animals, with the cast of characters tuned to suit local reality and pedagogical need.

David Aftandilian, an anthropologist at Texas Christian University, writes in “What Are the Animals to Us?” that the bear is a fixture in the stories of circumpolar cultures “because it walks on two legs and eats many of the same foods that people do,” and through hibernation and re-emergence appears to die and be reborn. “Animals with transformative life cycles,” Dr. Aftandilian writes, “often earn starring roles in the human imagination.” So, too, do crossover creatures like bats — the furred in flight — and cats, animals that are largely nocturnal yet still a part of our daylight lives, and that are marathon sleepers able to keep at least one ear ever vigilantly cocked. Page 2: Before long, humans were committing wholesale acts of anthropomorphism, attributing human characteristics and motives to anything with a face, a voice, a trajectory — bears, bats, thunderstorms, the moon.

James Serpell, president of the International Society for Anthrozoology, has proposed that the willingness to anthropomorphize was critical to the domestication of wild animals and forming bonds with them. We were particularly drawn to those species that seemed responsive to our Dr. Dolittle overtures.

Whereas wild animals like wolves will avert their eyes when spotted, dogs and cats readily return our gaze, and with an apparent emotiveness that stimulates the wistful narrative in our head. Dogs add to their soulful stare a distinctive mobility of facial musculature. “Their facial features are flexible, and they can raise their lips into a smile,” Dr. Horowitz said. “The animals we seem to love the most are the ones that make expressions at us.”

Dogs were among the first animals to be domesticated, roughly 10,000 years ago, in part for their remarkable responsiveness to such human cues as a pointed finger or a spoken command, and also for their willingness to work like dogs. They proved especially useful as hunting companions and were often buried along with their masters, right next to the spear set.

Yet the road to certification as man’s BFF has been long and pitted. Monotheism’s major religious texts have few kind words for dogs, and dogs have often been a menu item. The Aztecs bred a hairless dog just for eating, and according to Anthony L. Podberscek, an anthrozoologist at Cambridge University, street markets in South Korea sell dogs meant for meat right next to dogs meant as pets, with the latter distinguished by the cheery pink color of their cages.

As a rule, however, the elevation of an animal to pet status removes it entirely from the human food chain. Other telltale signs of petdom include bestowing a name on the animal and allowing it into the house. Pet ownership patterns have varied tremendously over time and across cultures and can resemble fads or infectious social memes.

Harold Herzog, a professor of psychology at Western Carolina University, describes in his book “Some We Love, Some We Hate, Some We Eat” how the rapid growth of the middle class in 19th-century France gave rise to the cartoonishly pampered Fifi. “By 1890, luxury and pet ownership went hand in hand,” he writes, and the wardrobe of a fashionable Parisian dog might include “boots, a dressing gown, a bathing suit, underwear and a raincoat.”

In this country, pet keeping didn’t get serious until after World War II. “People were moving to the suburbs, ‘Lassie’ was on television, and the common wisdom was pets were good for raising kids,” said Dr. Herzog in an interview. “If you wanted a normal childhood, you had to have a pet.”

Pet ownership has climbed steadily ever since, and today about two-thirds of American households include at least one pet.

People are passionate about their companion animals: 70 percent of pet owners say they sometimes sleep with their pets; 65 percent buy Christmas gifts for their pets; 23 percent cook special meals for their pets; and 40 percent of married women with pets say they get more emotional support from their pets than from their husbands. People may even be willing to die for their pets. “In studies done on why people refused to evacuate New Orleans during Katrina,” said Dr. Herzog, “a surprising number said they could not leave their pets behind.”

Pets are reliable from one year to the next, and they’re not embarrassed or offended by you no matter what you say or how much weight you gain. You can’t talk to your teenage daughter the way you did when she was 3, but your cat will always take your squeal. And should you overinterpret the meaning of your pet’s tail flick or unflinching gaze, well, who’s going to call you on it?

“Animals can’t object if we mischaracterize them in our minds,” said Lori Gruen, an associate professor of philosophy at Wesleyan University. “There’s something very comforting about that.” http://www.nytimes.com/2011/03/15/science/15food.html?src=un&feedurl=http%3A%2F%2Fjson8.nytimes.com%2Fpages%2Fscience%2Findex.jsonp No Face, but Plants Like Life Too By CAROL KAESUK YOON Published: March 14, 2011 Several years ago, after having to drive for too long behind a truck full of stinking, squealing pigs being delivered for slaughter, I gave up eating meat. I’d been harboring a growing distaste for the ugliness that can be industrial agriculture, but the real issue was a long-suppressed sympathy for its — or really, my — victims. Even screaming, reeking pigs, or maybe especially screaming, reeking pigs, can evoke stark pity as they tumble along in a truck to their deaths.

If you think about it, and it’s much simpler not to, it can be hard to justify other beings suffering pain, fear and death so that we can enjoy their flesh. In particular, given our many connections to animals, not least of all the fact that we are ourselves animals, it can give a person pause to realize that our most frequent contact with these kin might just be the devouring of them.

My entry into what seemed the moral high ground, though, was surprisingly unpleasant. I felt embattled not only by a bizarrely intense lust for chicken but nightmares in which I would be eating a gorgeous, rare steak — I could distinctly taste the savory drippings — from which I awoke in a panic, until I realized that I had been carnivorous only in my imagination.

Temptations and trials were everywhere. The most surprising turned out to be the realization that I couldn’t actually explain to myself or anyone else why killing an animal was any worse than killing the many plants I was now eating.

Surely, I’d thought, science can defend the obvious, that slaughterhouse carnage is wrong in a way that harvesting a field of lettuces or, say, mowing the lawn is not. But instead, it began to seem that formulating a truly rational rationale for not eating animals, at least while consuming all sorts of other organisms, was difficult, maybe even impossible.

Before you hit “send” on your hate mail, let me say this. Different people have different reasons for the choices they make about what to kill or have killed for them to eat. Perhaps there isn’t any choice more personal or less subject to rationality or the judgment of others. It’s just that as far as I was concerned, if eating a tofu dog was as much a crime against life as eating bratwurst, then pass the bratwurst, please.

So what really are the differences between animals and plants? There are plenty. The cells of plants, and not animals, for example, harbor chloroplasts, tiny green organelles that can turn the energy of light into sugar. Almost none of these differences, however, seem to matter to any of us trying to figure out what to eat.

The differences that do seem to matter are things like the fact that plants don’t have nerves or brains. They cannot, we therefore conclude, feel pain. In other words, the differences that matter are those that prove that plants do not suffer as we do. Here the lack of a face on plants becomes important, too, faces being requisite to humans as proof not only that one is dealing with an actual individual being, but that it is an individual capable of suffering.

Animals, on the other hand — and not just close evolutionary relations like chimps and gorillas, but species further afield, mammals like cows and pigs — can experience what pretty much anyone would agree is pain and suffering. If attacked, these animals will look agonized, scream, struggle and run as fast as they can. Obviously, if we don’t kill any of these animals to eat them, all that suffering is avoided.

Meanwhile, whether you pluck a leaf or slice a trunk, a plant neither grimaces nor cries out. Plants don’t seem to mind being killed, at least as far as we can see. But that may be exactly the difficulty.

Unlike a lowing, running cow, a plant’s reactions to attack are much harder for us to detect. But just like a chicken running around without its head, the body of a corn plant torn from the soil or sliced into pieces struggles to save itself, just as vigorously and just as uselessly, if much less obviously to the human ear and eye. Page2: When a plant is wounded, its body immediately kicks into protection mode. It releases a bouquet of volatile chemicals, which in some cases have been shown to induce neighboring plants to pre-emptively step up their own chemical defenses and in other cases to lure in predators of the beasts that may be causing the damage to the plants. Inside the plant, repair systems are engaged and defenses are mounted, the molecular details of which scientists are still working out, but which involve signaling molecules coursing through the body to rally the cellular troops, even the enlisting of the genome itself, which begins churning out defense-related proteins.

Plants don’t just react to attacks, though. They stand forever at the ready. Witness the endless thorns, stinging hairs and deadly poisons with which they are armed. If all this effort doesn’t look like an organism trying to survive, then I’m not sure what would. Plants are not the inert pantries of sustenance we might wish them to be.

If a plant’s myriad efforts to keep from being eaten aren’t enough to stop you from heedlessly laying into that quinoa salad, then maybe knowing that plants can do any number of things that we typically think of as animal-like would. They move, for one thing, carrying out activities that could only be called behaving, if at a pace visible only via time-lapse photography. Not too long ago, scientists even reported evidence that plants could detect and grow differently depending on whether they were in the presence of close relatives, a level of behavioral sophistication most animals have not yet been found to show.

To make matters more confusing, animals are not always the deep wells of sensitivity that we might imagine. Sponges are animals, but like plants they lack nerves or a brain. Jellyfish, meanwhile, which can be really tasty when cut into julienne and pickled, have no brains, only a simple net of nerves, arguably a less sophisticated setup than the signaling systems coordinating the lives of many plants. How do we decide how much sensitivity and what sort matters?

For those hoping to escape these quandaries with an all-mushroom diet, forget it. In nearly every way that you might choose to compare, fungi are likely to be more similar to us than are plants, as fungi are our closer evolutionary relations.

If you think about it, though, why would we expect any organism to lie down and die for our dinner? Organisms have evolved to do everything in their power to avoid being extinguished. How long would any lineage be likely to last if its members effectively didn’t care if you killed them?

Maybe the real problem with the argument that it’s O.K. to kill plants because they don’t feel exactly as we do, though, is that it’s the same argument used to justify what we now view as unforgivable wrongs.

Slavery and genocide have been justified by the assertion that some kinds of people do not feel pain, do not feel love — are not truly human — in the same way as others. The same thinking has led to other practices less drastic but still appalling. For example, physicians once withheld anesthetics from infants during surgery because it was believed that these not-quite-yet-humans did not feel pain (smiles were gas, remember).

Yet even as we shake our heads over the past, we continue to fight about where to draw the line around our tribe of those deemed truly human. We argue over whether those who love others of the same gender deserve full human rights. We ask the same about fetal humans.

The dinner menu pushes us further still. Do other species of animal deserve our consideration? Do plants? Fungi? Microbes?

Maybe this seems all nonsense to you. Perhaps you’re having trouble equating a radish to a lamb to a person whose politics you hate to your beloved firstborn. It’s not surprising. It is reliably difficult for us to accept new members into our tribe, the more so the less like us they seem. It can be infinitely inconvenient to take the part of every individual we come across, to share with it that most precious of commodities: compassion.

What should we have for dinner tonight? Who knows?

Human beings survive by eating other living things. I really want not only to eat, but to survive. Yet a nakedly logical way to judge the value of one kind of organism over another — the rightness of a plant’s death versus an animal’s — seems, to me, out of reach.

My efforts to forgo meat didn’t last more than a couple of years. Still, I wonder what our great-grandchildren will think of us. Will we have trouble explaining to them why we killed animals or perhaps even plants for food? And if so, what on Earth will we be eating?

Supremacy of a Social Network by Nicholas Wade - NY Times: March 14, 2011

Every time some human attribute is said to be unique, whether tool-making or language or warfare, biologists soon find some plausible precursor in animals that makes the ability less distinctive.

Still, humans are vastly different from other animals, however hard the difference may be to define. A cascade of events, some the work of natural selection, some just plain accidents, propelled the human lineage far from the destiny of being just another ape, down an unexpected evolutionary path to become perhaps the strangest blossom on the ample tree of life.

And what was the prime mover, the dislodged stone that set this eventful cascade in motion? It was, perhaps, the invention of weapons — an event that let human ancestors escape the brutal tyranny of the alpha male that dominated ape societies.

Biologists have little hesitation in linking humans’ success to their sociality. The ability to cooperate, to make individuals subordinate their strong sense of self-interest to the needs of the group, lies at the root of human achievement.

“Humans are not special because of their big brains,” says Kim Hill, a social anthropologist at Arizona State University. “That’s not the reason we can build rocket ships — no individual can. We have rockets because 10,000 individuals cooperate in producing the information.”

The two principal traits that underlie the human evolutionary success, in Dr. Hill’s view, are the unusual ability of nonrelatives to cooperate — in almost all other species, only closely related individuals will help each other — and social learning, the ability to copy and learn from what others are doing. A large social network can generate knowledge and adopt innovations far more easily than a cluster of small, hostile groups constantly at war with each other, the default state of chimpanzee society.

If a shift in social behavior was the critical development in human evolution, then the answer to how humans became unique lies in exploring how human societies first split away from those of apes.

Paleoanthropologists often assume that chimp societies are a reasonably good stand-in for the ancestral ape society that gave rise to the chimp and human lineages. Living hunter-gatherers may reflect those of long ago, since humans always lived this way until the first settled societies of 15,000 years ago.

The two species’ social structure could scarcely be more different. Chimp society consists of a male hierarchy, dominated by the alpha male and his allies, and a female hierarchy beneath it. The alpha male scores most of the paternities, cutting his allies in on others. The females try to mate with every male around, so each may think he’s the father and spare her child. How did a chimplike society ever give rise to the egalitarian, largely monogamous structure of hunter-gatherer groups?

A new and comprehensive answer to this question has been developed by Bernard Chapais of the University of Montreal. Dr. Chapais is a primatologist who has spent 25 years studying monkey and ape societies. Recently he devoted four years to reading the literature of social anthropology with the goal of defining the transition between nonprimate and human societies. His book, “Primeval Kinship,” was published in 2008.

Dr. Chapais sees the transition as a series of accidents, each of which let natural selection exploit new opportunities. Early humans began to walk on two legs because it was a more efficient way of getting around than knuckle-walking, the chimps’ method. But that happened to leave the hands free. Now they could gesture, or make tools.

It was a tool, in the form of a weapon, that made human society possible, in Dr. Chapais’s view. Among chimps, alpha males are physically dominant and can overpower any rival. But weapons are great equalizers. As soon as all males were armed, the cost of monopolizing a large number of females became a lot higher. In the incipient hominid society, females became allocated to males more equally. General polygyny became the rule, then general monogamy.

This trend led to the emergence of a critical change in sexual behavior: the replacement of the apes’ orgiastic promiscuity with the pair bond between male and female. With only one mate, for the most part, a male had an incentive to guard her from other males to protect his paternity. Page 2: The pair bond was the pivotal event that opened the way to hominid evolution, in Dr. Chapais’s view. On the physiological level, having two parents around allowed the infants to be dependent for longer, a requirement for continued brain growth after birth. Through this archway, natural selection was able to drive up the volume of the human brain until it eventually reached three times that of a chimpanzee.

On the social level, the presence of both parents revealed the genealogical structure of the family, which is at least half hidden in chimp societies. A chimp knows who its mother and siblings are, because it grows up with them, but not its father or father’s relatives. So the neighboring bands to which female chimps disperse at puberty, avoiding incest, are perceived as full of strange males and treated with unremitting hostility.

In the incipient hominid line, males could recognize their sisters and daughters in neighboring bands. They could also figure out that the daughter’s or sister’s mate shared a common genetic interest in the welfare of the woman’s children. The neighboring males were no longer foes to be killed in sight — they were the in-laws.

The presence of female relatives in neighboring bands became for the first time a bridge between them. It also created a new and more complex social structure. The bands who exchanged women with each other learned to cooperate, forming a group or tribe that would protect its territory from other tribes. Though cooperation became the norm within a tribe, tribes would wage warfare just as relentlessly as chimpanzee bands.

“There is no single pressure that made us human,” Dr. Chapais said in an interview. He sees human evolution as having progressed through a series of accidents. “The fact that you can recognize patrilineal kin was not selected for, but as soon as you had that you could move forward and establish peaceful relations with other groups,” he said.

The new social structure would have induced the development of different social behaviors. “I personally am hung up on cooperation as being what really differentiates humans from nonhuman apes,” said Michael Tomasello, a developmental psychologist at the Max Planck Institute for Evolutionary Anthropology in Germany. A system of cooperative bands “provides the kind of social infrastructure that can really get things going,” he said.

In a series of experiments comparing human and chimpanzee infants, Dr. Tomasello has shown that very young children have an urge to help others. One of these skills is what he calls shared intentionality, the ability to form a plan with others for accomplishing a joint endeavor. Children, but not chimps, will point at things to convey information, they will intuit others’ intentions from the direction of their gaze, and they will help others achieve a goal.

Early humans venturing out into the savannah from the apes’ ancestral forest refuge would have been surrounded by predators and in fierce competition for food. Cooperation may have been forced on them as a condition of existence. “Humans were put under some kind of collective pressure to collaborate in their gathering of food — they became obligate collaborators — in a way that their closest primate relatives were not,” Dr. Tomasello writes in a recent book, “Why We Cooperate.”

Humans wear the mark of their shared intentionality, he notes, in a small but significant feature — the whites of their eyes, which are three times larger than those of any other primate, presumably to help others follow the direction of gaze. Indeed, chimps infer the direction of gaze by looking at another’s head, but infants do so by watching the eyes.

So if ever a visiting Martian biologist should ask you what made your species the master of its planet, point first to your mother and all her relatives, then to the whites of your eyes, and only lastly to your prominent forehead.

Emotional Power Broker of the Modern Family by Benedict Carey - NY times, March 14, 2011

First, he tore up his dog toys. Then shredded the furniture, clothes, schoolbooks — and, finally, any semblance of family unity. James, a chocolate-brown pointer mix, turned from adorable pet to problem child in a matter of weeks.

“The big bone of contention was that my mom and my sister thought that he was too smart to be treated like a dog; they thought he was a person and should be treated as such — well, spoiled,” said Danielle, a Florida woman who asked that her last name not be published to avoid more family pet strife. “The dog remains to this day, 10 years later, a source of contention and anger.”

Psychologists long ago confirmed what most pet owners feel in their bones: that for some people bonds with animals are every bit as strong as those with other humans. And less complicated, for sure; a dog’s devotion is without detectable irony, a lap cat’s purring without artifice (if not disapproval).

Yet the nature of individual human-pet relationships varies widely, and only now are scientists beginning to characterize those differences, and their impact on the family. Pets alter not only a family’s routines, after all, but also its hierarchy, its social rhythm, its web of relationships. Several new lines of research help explain why this overall effect can be so comforting in some families, and a source of tension in others. The answers have very little to do with the pet.

“The word ‘pet’ does not really capture what these animals mean in a family, first of all,” said Froma Walsh, a psychologist at the University of Chicago and co-director of the Chicago Center for Family Health. The prevalent term among researchers is now “companion animal,” she said, which is closer to the childlike role they so often play.

“And in the way that children get caught up in the family system as peacekeepers, as go-betweens, as sources of disagreement, the same happens with pets.”

People cast these roles in part based on the sensations and memories associated with their first Princess or Scooter, psychologists say — echoing Freud’s idea of transference, in which early relationships provide a template for later ones. In many families, this means that Scruffy is the universal peacemaker, the fulcrum of shared affection.

In a family interview reviewed by Dr. Walsh in a recent paper, one mother said that the best way to end an argument between siblings was to bark, “Stop fighting, you’re upsetting Barkley!” “This is always more effective than saying, ‘Stop hitting your brother,’ ” the mother said. (Barkley made no comment.)

Animals often sense these expectations and act on them. In a video recording of another family discussed in the paper, the cat jumps on a woman’s lap when it senses an impending argument with her husband. “And it works,” Dr. Walsh said. “It reduces tension in both; you can see it happening.”

“She’s my first child,” said Adrienne Woods, a cellist in Los Angeles, of Bella, the Husky puppy that she and her fiancé just got. “The biggest upside is this sense of inner peace. I feel like a grandma, like I have a companion I’ve been wanting for 30 years.”

Yet pets can also raise tension, as millions of couples learn the hard way. The Animal Planet show “It’s Me or the Dog” is built on such cases. And Cesar Millan, a dog behavior specialist, has become a celebrity by helping people gain control over unruly hounds, bringing order into households with uncertain lines of authority.

Perhaps more often, pets become a psychological wedge not from lack of boundaries but because family members have diverging views of what a pet should be. And those views are shaped by cultural inheritance, more so than people may realize.

In a study of dog ownership, Elizabeth Terrien, a sociologist at the University of Chicago, conducted 90 in-depth interviews with families in Los Angeles, including Ms. Woods. One clear trend that has emerged is that people from rural backgrounds tend to see their dogs as guardians to be kept outside, whereas middle-class couples typically treat their hounds as children, often having them sleep in the master bedroom, or a special bed.

When asked to describe their pets without using the word “dog,” people in more affluent neighborhoods “came up with things like child, companion, little friend, teenage son, brother, or partner in crime,” Dr. Terrien said. In neighborhoods with a larger Latino immigrant population, owners were more likely to say “protector,” or even “toy for the children,” she found. “In those neighborhoods you’ll sometimes see kids yanking around a dog on the leash, pushing and playing, the sort of behavior that some middle-class owners would think of as abuse,” she said. Page 2: And there are countless single people out there all but married to some hairy Frida or Diego — banishing any potential partner who doesn’t fall quickly, and equally, in love.

The reason these feelings run so deep is that they are ideologies, as well as cultural and psychological dispositions. In the summer of 2007, David Blouin, a sociologist at Indiana University, South Bend, conducted extensive interviews with 35 dog owners around the state, chosen to represent a diverse mix of city, country and suburban dwellers.

He found that, as a rule, people fall into one of three broad categories of beliefs concerning pets. Members of one group, which he labels “dominionists,” see pets as an appendage to the family, a useful helper ranking below humans that is beloved but, ultimately, replaceable. Many people from rural areas — like the immigrants Dr. Terrien interviewed — qualified.

Another group of owners, labeled by Dr. Blouin as “humanists,” are the type who cherish their dog as a favored child or primary companion, to be pampered, allowed into bed, and mourned like a dying child at the end. These include the people who cook special meals for a pet, take it to exercise classes, to therapy — or leave it stock options in their will.

The third, called “protectionists,” strive to be the animal’s advocate. These owners have strong views about animal welfare, but their views on how a pet should be treated — whether it sleeps inside or outside, when it should be put down — vary depending on what they think is “best” for the animal. Its members include people who will “save” a dog tied to tree outside a store, usually delivering it home with a lecture about how to care for an animal.

“These are ideologies, and so protectionists are very critical of humanists, who are very critical of dominionists, and so on,” Dr. Blouin said. “You can see where this can create problems if people in a family have different orientations. Every little decision about the pet is loaded.”

Up until, and including, the end: Couples may not only disagree over when to put an animal down but also have vastly different emotional reactions to the loss. “For someone who’s been treating the pet like a child, it can feel like the loss of a child — and of course children are not supposed to die before their parents,” Dr. Terrien said. It’s an end-of-life crisis, which often begins a lengthy period of grieving. Whereas for the partner who sees the pet differently, the death may bring relief.

None of which is to say that a resourceful pet — using the combined power of cuteness, doleful stares and episodes of getting stuck in boxes or eating crayons — cannot bridge such opposing religions. But family therapists say that, usually, four-legged diplomats need some help from the two-legged kind to succeed.

“Families either figure it out and manage these differences,” Dr. Terrien said, “or they give up the pet — which happens far more often than people think.”

Why Dogs Bark by Raymond Coppinger and Mark Feinstein (Excerpts: Smithsonian Magazine, January, 1991)

A dog's barking actually may have no primary function at all, not one. Instead, it may be just an artifact of prehistoric domestication, a result of Darwinian evolution that created a tame, but yapping, juvenile dog. That means when natureís forces built the domestic dog, barking just happened to get left in the genetic mix. It is repetitious, meaningless and functionless.

That notion may be hard to believe for any dog owner who they believe their pet has chased off a burglar, saved a child from a burning building or just woofed in happy greeting. But six years of research convinced Coppinger and Feinstein that barking is merely a byproduct.

Before we could answer why dogs barked, we looked at what might motivate dogs to bark. The answer was nothing and everything. They bark at everything and nothing, any time of the night or day. We watched dogs bark at the wind and at leaves, at the ground and the night sky, at people coming and people going, at people they knew and people they didnít. Sometimes a dog will bark so hard and long it will inflame its vocal cords until it no longer can make a sound. Still, it will try to bark. We observed a livestock-guarding dog on a cold winter night, no predators around, just out there, nothing around. The dog barked for seven hours straight. Dogs sometimes bark at each other, or join a chorus of barking, but these dogs often are not directing their barks at each other. They are just barking randomly with no apparent point. Barking does not look like a very efficient communications system and often goes out without any response.

When domestic dogs are compared to coyotes and wolves, the dogís closest cousins that might offer hints to its prehistoric behavior - again, we found differences. Wild animals in general are very quiet. In wolves, barking accounts for about 2.5 percent of their vocalizations; in dogs, it makes up about 95 percent. Then we looked at environment. When domestic dogs are released in the wild, they bark, but how about wolves and coyotes? Would they bark if kept in a domesticated setting? Our finding: Dogs bark. Coyotes donít. When you put coyotes in a kennel when dogs are barking incessantly, they just sit there not interested.

Finally we noticed something in wolves that formed the basis of oyur theory. While adult wolves donít bark, young wolves do. They bark in their dens. They begin to bark at about the same point dog pups do. At six to seven weeks after birth, however, when dog pups still are barking continuously, wolf pups stop. Dog pups will continue barking even after the noise fails to elicit any kind of nurturing response from their mothers.

But for dog lovers who insist that dogs communicate, take heart. Feinstein and Coppinger donít completely disagree. Just because barking is a genetic holdover with no primary function, they donít mean it is completely meaningless.

For Whom the Cell Mutates: The Origins of Genetic Quirks by Sean B. Carroll NY Times: March 14, 2011

There was very little that was safe or conventional in Ernest Hemingway’s life. The great writer hurled himself into danger in three wars, managed to survive two plane crashes on the same big-game safari in remote Africa, and precipitated many domestic dramas with a variety of love affairs in the course of his four marriages. “Moderation” appears to have been one word lacking from his otherwise superb vocabulary, even when it came to cats.

The image of the macho big-game hunter and marlin fisherman is hard to reconcile with that of a pet-hoarder, but Hemingway surrounded himself with felines. The author loved the animals and took in so many strays that at one point his house in Cuba, Finca Vigia (Lookout Farm), had 57 cats. Every animal had a name, including such unmasculine monikers as Princessa, Furhouse, and Littless Kitty. Hemingway loved their company when writing, especially when he was alone for lengths of time on the island. He incorporated many favorite pets into his short stories and novels. His loyal, longtime companion Boise merited 35 pages in “Islands in the Stream,” including this autobiographical passage:

“That night, when he had sat in the big chair reading with Boise at his side in the chair, he had thought that he did not know what he would do if Boise should be killed. He thought, from his actions and desperation, that the cat felt the same way about the man.”

But of all the cats in Hemingway’s life, the most famous are those that have taken up residence at his former home in Key West, Fla. In late 1931, Hemingway and his second wife, Pauline, moved into a two-story house on Whitfield Street. It was in Key West that Hemingway established a routine of writing in the morning, and then spending the hot afternoons fishing from the bridges, docks or a boat, or relaxing with friends.

It was an extremely productive lifestyle. Over a 12-year span in Key West, he worked on or completed “A Farewell to Arms,” “Green Hills of Africa,” “Death in the Afternoon,” “For Whom the Bell Tolls,” “To Have or Have Not,” and the short stories “The Snows of Kilimanjaro” and “The Short Happy Life of Francis Macomber.”

The house in Key West, which the author owned until his death 50 years ago this summer, is now a museum and a permanent home to about 50 cats. But of course, such an extraordinary man would not be associated with just ordinary cats; about half of the animals bear extra toes, typically on their forepaws. Most cats are, like humans, pentadactyls. That is, they have five digits on their forepaws. The so-called Hemingway cats have six digits, with the extra digit the homolog of the human thumb, which gives the paw a mittenlike appearance. When found in felines, the condition, formally known as preaxial polydactyly, is now commonly referred to as a “Hemingway cat.”

The origins of the cats on the Hemingway grounds are shrouded in legend, and it remains difficult to sort out facts from tall tales in many matters concerning the famous writer. One version of the cat story offered today is that Hemingway was given a six-toed tomcat, Snowball, by a ship’s captain in the mid-1930s, and that all of the six-toed residents are descended from this founding father.

Another account is that Hemingway had no housepets at the time and that the six-toed cats are descended from strays that came onto the property from time to time and took up residence after the writer was gone. Cats have long been present in Key West for controlling the rodent populations, and six-toed cats were popular with ship captains and sailors for the same purpose, as well as being considered good luck on voyages.

While the origins of the Hemingway House cats remains murky, the cause of their polydactyly is no longer a mystery. Researchers have recently pinpointed the precise mutation in the cats’ DNA responsible for the formation of the extra digit. The story of the origin of Hemingway’s cats is one of finding deep genetic connections among very different animals — from fruit flies to chickens, mice, cats, and yes, even humans.

In the late 1970s, one of the most challenging puzzles in all of biology was that of embryonic development — how a complex creature formed from a single fertilized egg cell. Two researchers, Christiane Nüsslein-Volhard and Eric Wieschaus, led a bold undertaking to identify all of the genes that were responsible for the process in fruit flies, then and now one of the main workhorses of basic genetic research. They identified scores of genes that played roles in building the fruit fly body and its body parts, work that led to their sharing of the 1995 Nobel Prize in Physiology or Medicine with the late Edward B. Lewis, another pioneer fruit fly geneticist. Page 2:

One of the reasons for that honor was the discovery that, contrary to all biologists’ expectations, similar sets of genes to those involved in building fruit flies were also involved in building the bodies of such different animals as mice, frogs and other vertebrates, including humans. Indeed, by the 1990s, one common strategy for discovering genes involved in building vertebrate bodies, organs or body parts was to look for the counterparts of fruit fly genes in those vertebrates.

That was the approach taken by one team led by Prof. Cliff Tabin at Harvard Medical School that was eager to find the genes responsible for the formation and patterning of vertebrate limbs. Decades of research on the chicken wing had shown that the formation of the pattern of digits across the entire structure depended on some signal produced by cells in the most posterior part of the developing embryo’s wing bud. Professor Tabin’s team sought to identify that signal by isolating the chicken’s counterparts of certain fruit fly genes.

They isolated a chicken homolog of a fruit fly gene called “hedgehog.” The name had been given by Dr. Nüsslein-Volhard and Dr. Wieschaus because mutations in the fly gene caused the fruit fly larva to be covered with fine hairs, like a hedgehog.

Professor Tabin’s team was stunned and delighted to find that the chicken gene, dubbed “Sonic hedgehog” after the video game character, was turned on in the posterior of the limb bud, right where the digit-patterning activity was also located. They then found that the Sonic hedgehog protein was indeed the long-sought digit-patterning signal. For instance, they demonstrated that turning Sonic hedgehog on in the anterior part of the limb bud had the same effect as transplanting posterior tissue to the anterior part of the limb — it caused the formation of extra digits.

The induction of polydactyly by Sonic hedgehog in laboratory experiments raised the possibility that inherited cases of polydactyly might be caused by mutations in the Sonic hedgehog gene. Polydactyly is well known in mice and in humans, as well as cats, and sure enough, cats, mice and humans all have Sonic hedgehog genes. But inspection of the Sonic hedgehog genes of polydactyl individuals did not reveal any mutations that would cause the Sonic hedgehog signal to be defective.

So what role, then, does Sonic hedgehog play in the syndrome? It turns out that polydactyly is not due to disruptions of Sonic hedgehog function, but of its regulation. In order to make the proper five-digit, pinky-to-thumb pattern, the production of the Sonic hedgehog protein must be restricted to posterior cells. The pattern of the digits depends upon the relative concentration of Sonic hedgehog, which is greatest in the posterior (where the pinky will form) and lowest in the anterior where the thumb will form. Mutations that disrupt Sonic hedgehog regulation such that some protein is made in the anterior of the limb bud cause the formation of an extra thumb.

These mutations were difficult to find in DNA at first because they were not located in the part of the gene that encodes the protein. Rather, they occurred far away in a stretch of DNA sequence that acts like a switch to turn Sonic hedgehog on in the posterior part of the limb bud and to keep the gene off in cells in the anterior part of the limb bud.

A team led by Robert Hill of the Medical Research Council Human Genetics Unit in Edinburgh showed that the Sonic hedgehog switch that controls gene activity in the limb is located about one million base pairs from the part of the gene encoding the Sonic hedgehog signal. On the scale of DNA, finding the mutations so far away from the gene was much like looking for one’s car in a parking lot, and eventually finding it in a vacant field in another town.

Mutations that scramble the switch are responsible for polydactyly in mice and humans. But further work has shown that even slight mutations substituting just a single letter of the DNA sequence can also cause the syndrome, not only in mice and humans, but in Hemingway’s cats.

Mr. Hill’s team analyzed one line of affected Key West cats and found a perfect association between polydactyly and a substitution at one position in the cat Sonic hedgehog gene switch. They also examined other unrelated polydactylous North American cats and found the same substitution, which indicates that all North American polydactylous cats may be descended from one polydactylous ancestor. If that is indeed the case, that ancestor may date back as early as pre-Revolutionary times in New England, and its descendants probably reached Key West by ship long before Hemingway did.

Like Hemingway’s cats and the writer himself, we all have our quirks, some more visible than others. Genetics has made huge strides in understanding the basis of many physical characteristics, like extra toes and fingers. In time, we can look forward to learning more about the genetics of deeper mysteries, like the cause of the profound depression that overtook Hemingway and many of his close relatives or, on the brighter side, perhaps some insights into the source of his great talent.

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