Saturday, October 27, 2007

From a Few Genes, Life’s Myriad Shapes

Modern Science taking their first feeble steps out of the Dark Ages of Disconnected Specialization?

"......... And what these scientists are finding is that development, a process that has for more than half a century been largely ignored in the study of evolution, appears to have been one of the major forces shaping the history of life on earth. “Do these discoveries blow people’s minds? Yes,” said Dr. Sean B. Carroll, biologist at the Howard Hughes Medical Institute at the University of Wisconsin, Madison. “The first response is ‘Huh?’ and the second response is ‘Far out.’ ” “This is the illumination of the utterly dark,” Dr. Carroll added......."
Explore the Potential of the Possible Human and Michael Murphy's Future of the Body. Understand that to trash and ignore thousands upon thousands of years of mastered wisdom on human nature is dangerous to survival. Highly specialized, yet narrow and shallow vision, breed and fertilize skewed and stale views of our expanding window to reality, which in turn create the trouble with foundational physics, perpetuating stagnant energy evolution, fostering global warming and the coming nuclear resource wars

From a Few Genes, Life’s Myriad Shapes

Since its humble beginnings as a single cell, life has evolved into a spectacular array of shapes and sizes, from tiny fleas to towering Tyrannosaurus rex, from slow-soaring vultures to fast-swimming swordfish, and from modest ferns to alluring orchids. But just how such diversity of form could arise out of evolution’s mess of random genetic mutations — how a functional wing could sprout where none had grown before, or how flowers could blossom in what had been a flowerless world — has remained one of the most fascinating and intractable questions in evolutionary biology.
Now finally, after more than a century of puzzling, scientists are finding answers coming fast and furious and from a surprising quarter, the field known as evo-devo. Just coming into its own as a science, evo-devo is the combined study of evolution and development, the process by which a nubbin of a fertilized egg transforms into a full-fledged adult. And what these scientists are finding is that development, a process that has for more than half a century been largely ignored in the study of evolution, appears to have been one of the major forces shaping the history of life on earth.
For starters, evo-devo researchers are finding that the evolution of complex new forms, rather than requiring many new mutations or many new genes as had long been thought, can instead be accomplished by a much simpler process requiring no more than tweaks to already existing genes and developmental plans. Stranger still, researchers are finding that the genes that can be tweaked to create new shapes and body parts are surprisingly few. The same DNA sequences are turning out to be the spark inciting one evolutionary flowering after another. “Do these discoveries blow people’s minds? Yes,” said Dr. Sean B. Carroll, biologist at the Howard Hughes Medical Institute at the University of Wisconsin, Madison. “The first response is ‘Huh?’ and the second response is ‘Far out.’ ”
“This is the illumination of the utterly dark,” Dr. Carroll added.
The development of an organism — how one end gets designated as the head or the tail, how feet are enticed to grow at the end of a leg rather than at the wrist — is controlled by a hierarchy of genes, with master genes at the top controlling a next tier of genes, controlling a next and so on. But the real interest for evolutionary biologists is that these hierarchies not only favor the evolution of certain forms but also disallow the growth of others, determining what can and cannot arise not only in the course of the growth of an embryo, but also over the history of life itself.
“It’s been said that classical evolutionary theory looks at survival of the fittest,” said Dr. Scott F. Gilbert, a developmental biologist at Swarthmore College. By looking at what sorts of organisms are most likely or impossible to develop, he explained, “evo-devo looks at the arrival of the fittest.”
Charles Darwin saw it first. He pointed out well over a century ago that developing forms of life would be central to the study of evolution. Little came of it initially, for a variety of reasons. Not least of these was the discovery that perturbing the process of development often resulted in a freak show starring horrors like bipedal goats and insects with legs growing out of their mouths, monstrosities that seemed to shed little light on the wonders of evolution.
But the advent of molecular biology reinvigorated the study of development in the 1980s, and evo-devo quickly got scientists’ attention when early breakthroughs revealed that the same master genes were laying out fundamental body plans and parts across the animal kingdom. For example, researchers discovered that genes in the Pax6 family could switch on the development of eyes in animals as different as flies and people. More recent work has begun looking beyond the body’s basic building blocks to reveal how changes in development have resulted in some of the world’s most celebrated of evolutionary events.
In one of the most exciting of the new studies, a team of scientists led by Dr. Cliff Tabin, a developmental biologist at Harvard Medical School, investigated a classic example of evolution by natural selection, the evolution of Darwin’s finches on the Galápagos Islands.
Like the other organisms that made it to the remote archipelago off the coast of Ecuador, Darwin’s finches have flourished in their isolation, evolving into many and varied species. But, while the finches bear his name and while Darwin was indeed inspired to thoughts of evolution by animals on these islands, the finches left him flummoxed. Darwin did not realize for quite some time that these birds were all finches or even that they were related to one another.
He should be forgiven, however. For while the species are descendants of an original pioneering finch, they no longer bear its characteristic short, slender beak, which is excellent for hulling tiny seeds. In fact, the finches no longer look very finchlike at all. Adapting to the strange new foods of the islands, some have evolved taller, broader, more powerful nut-cracking beaks; the most impressive of the big-beaked finches is Geospiza magnirostris. Other finches have evolved longer bills that are ideal for drilling holes into cactus fruits to get at the seeds; Geospiza conirostris is one species with a particularly elongated beak.
But how could such bills evolve from a simple finch beak? Scientists had assumed that the dramatic alterations in beak shape, height, width and strength would require the accumulation of many chance mutations in many different genes. But evo-devo has revealed that getting a fancy new beak can be simpler than anyone had imagined.
Genes are stretches of DNA that can be switched on so that they will produce molecules known as proteins. Proteins can then do a number of jobs in the cell or outside it, working to make parts of organisms, switching other genes on and so on. When genes are switched on to produce proteins, they can do so at a low level in a limited area or they can crank out lots of protein in many cells.
What Dr. Tabin and colleagues found, when looking at the range of beak shapes and sizes across different finch species, was that the thicker and taller and more robust a beak, the more strongly it expressed a gene known as BMP4 early in development. The BMP4 gene (its abbreviation stands for bone morphogenetic protein, No. 4) produces the BMP4 protein, which can signal cells to begin producing bone. But BMP4 is multitalented and can also act to direct early development, laying out a variety of architectural plans including signaling which part of the embryo is to be the backside and which the belly side. To verify that the BMP4 gene itself could indeed trigger the growth of grander, bigger, nut-crushing beaks, researchers artificially cranked up the production of BMP4 in the developing beaks of chicken embryos. The chicks began growing wider, taller, more robust beaks similar to those of a nut-cracking finch.
In the finches with long, probing beaks, researchers found at work a different gene, known as calmodulin. As with BMP4, the more that calmodulin was expressed, the longer the beak became. When scientists artificially increased calmodulin in chicken embryos, the chicks began growing extended beaks, just like a cactus driller.
So, with just these two genes, not tens or hundreds, the scientists found the potential to recreate beaks, massive or stubby or elongated.
“So now one wants to go in a number of directions,” Dr. Tabin said. “What happens in a stork? What happens in a hummingbird? A parrot?” For the evolution of beaks, the main tool with which a bird handles its food and makes its living, is central not only to Darwin’s finches, but to birds as a whole.
BMP4’s reach does not stop at the birds, however.
In lakes in Africa, the fish known as cichlids have evolved so rapidly into such a huge diversity of species that they have become one of the best known evolutionary radiations. The cichlids have evolved in different shapes and sizes, and with a variety of jaw types specialized for eating certain kinds of food. Robust, thick jaws are excellent at crushing snails, while longer jaws work well for sucking up algae. As with the beaks of finches, a range of styles developed.
Now in a new study, Dr. R. Craig Albertson, an evolutionary biologist at Syracuse University, and Dr. Thomas D. Kocher, a geneticist at the University of New Hampshire, have shown that more robust-jawed cichlids express more BMP4 during development than those with more delicate jaws. To test whether BMP4 was indeed responsible for the difference, these scientists artificially increased the expression of BMP4 in the zebrafish, the lab rat of the fish world. And, reprising the beak experiments, researchers found that increased production of BMP4 in the jaws of embryonic zebrafish led to the development of more robust chewing and chomping parts.
And if being a major player in the evolution of African cichlids and Darwin’s finches — two of the most famous evolutionary radiations of species — were not enough for BMP4, Dr. Peter R. Grant, an evolutionary biologist at Princeton University, predicted that the gene would probably be found to play an important role in the evolution of still other animals. He noted that jaw changes were a crucial element in the evolution of lizards, rabbits and mice, among others, making them prime candidates for evolution via BMP4.
“This is just the beginning,” Dr. Grant said. “These are exciting times for us all.”
Used to lay out body plans, build beaks and alter fish jaws, BMP4 illustrates perfectly one of the major recurring themes of evo-devo. New forms can arise via new uses of existing genes, in particular the control genes or what are sometimes called toolkit genes that oversee development. It is a discovery that can explain much that has previously been mysterious, like the observation that without much obvious change to the genome over all, one can get fairly radical changes in form.
“There aren’t new genes arising every time a new species arises,” said Dr. Brian K. Hall, a developmental biologist at Dalhousie University in Nova Scotia. “Basically you take existing genes and processes and modify them, and that’s why humans and chimps can be 99 percent similar at the genome level.”
Evo-devo has also begun to shine a light on a phenomenon with which evolutionary biologists have long been familiar, the way in which different species will come up with sometimes jaw-droppingly similar solutions when confronted with the same challenges.
Among the placental mammals of the Americas and the marsupials of Australia, for example, have evolved the same sorts of animals independently: beasts that burrowed, loping critters that grazed, creatures that had long snouts for eating ants, and versions of wolf.
In the same way, the cichlids have evolved pairs of matching species, arising independently in separate lakes in Africa. In Lake Malawi, for example, there is a long and flat-headed species with a deep underbite that looks remarkably like an unrelated species that lives a similar lifestyle in Lake Tanganyika. There is another cichlid with a bulging brow and frowning lips in Lake Malawi with, again, an unrelated but otherwise extremely similar-looking cichlid in Lake Tanganyika. The same jaws, heads, and ways of living can be seen to evolve again and again.
The findings of evo-devo suggest that such parallels might in fact be expected. For cichlids are hardly coming up with new genetic solutions to eating tough snails as they each crank up the BMP4 or tinker with other toolkit genes. Instead, whether in Lake Malawi or Lake Tanganyika, they may be using the same genes to develop the same forms that provide the same solutions to the same ecological challenges. Why not, when even the beaked birds flying overhead are using the very same genes?
Evo-devo has even begun to give biologists new insight into one of the most beautiful examples of recurring forms: the evolution of mimicry.
It has long been a source of amazement how some species seem so able to evolve near-perfect mimicry of another. Poisonous species often evolve bright warning colors, which have been reproduced by nonpoisonous species or by other, similarly poisonous species, hoping to fend off curious predators.
Now in a new study of Heliconius butterflies, Dr. Mathieu Joron, an evolutionary biologist at the University of Edinburgh, and colleagues, found evidence that the mimics may be using some of the same genes to produce their copycat warning colors and patterns.
The researchers studied several species of tropical Heliconius butterflies, all of which are nasty-tasting to birds and which mimic one another’s color patterns. Dr. Joron and colleagues found that some of the main elements of the patterns — a yellow band in Heliconius melpomene and Heliconius erato and a complex tiger-stripe pattern in Heliconius numata — are controlled by a single region of DNA, a tightly linked set of genes known as a supergene.
Dr. Joron said he and colleagues were still mapping the details of color pattern control within the supergene. But if this turned out to function, as researchers suspected, like a toolkit gene turning the patterns on and off, it could explain both the prevalence of mimicry in Heliconius and the apparent ease with which these species have been shown to repeatedly evolve such superbly matching patterns.
One of evo-devo’s greatest strengths is its cross-disciplinary nature, bridging not only evolutionary and developmental studies but gaps as broad as those between fossil-hunting paleontologists and molecular biologists. One researcher whose approach epitomizes the power of such synthesis is Dr. Neil Shubin, an evolutionary biologist at the University of Chicago and the Field Museum.
Last year, Dr. Shubin and colleagues reported the discovery of a fossil fish on Ellesmere Island in northern Canada. They had found Tiktaalik, as they named the fish, after searching for six years. They persisted for so long because they were certain that they had found the right age and kind of rock where a fossil of a fish trying to make the transition to life on land was likely to be found. And Tiktaalik appeared to be just such a fish, but it also had a few surprises for the researchers.
“Tiktaalik is special,” Dr. Shubin said. “It has a flat head with eyes on top. It has gills and lungs. It’s an animal that’s exploring the interface between water and land.”
But Tiktaalik was a truly stunning discovery because this water-loving fish bore wrists, an attribute thought to have been an innovation confined strictly to animals that had already made the transition to land.
“This was telling us that a piece of the toolkit, to make arms, legs, hand and feet, could very well be present in fish limbs,” Dr. Shubin said. In other words, the genetic tools or toolkit genes for making limbs to walk on land might well have been present long before fish made that critical leap. But as fascinating as Tiktaalik was, it was also rock hard and provided no DNA that might shed light on the presence or absence of any particular gene.
So Dr. Shubin did what more and more evo-devo researchers are learning to do: take off one hat (paleontologist) and don another (molecular biologist). Dr. Shubin oversees one of what he says is a small but growing number of laboratories where old-fashioned rock-pounding takes place alongside high-tech molecular DNA studies.
He and colleagues began a study of the living but ancient fish known as the paddlefish. What they found, reported last month in the journal Nature, was that these thoroughly fishy fish were turning on control genes known as Hox genes, in a manner characteristic of the four-limbed, land-loving beasts known as tetrapods.
Tetrapods include cows, people, birds, rodents and so on. In other words, the potential for making fingers, hands and feet, crucial innovations used in emerging from the water to a life of walking and crawling on land, appears to have been present in fish, long before they began flip-flopping their way out of the muck. “The genetic tools to build fingers and toes were in place for a long time,” Dr. Shubin wrote in an e-mail message. “Lacking were the environmental conditions where these structures would be useful.” He added, “Fingers arose when the right environments arose.”
And here is another of the main themes to emerge from evo-devo. Major events in evolution like the transition from life in the water to life on land are not necessarily set off by the arising of the genetic mutations that will build the required body parts, or even the appearance of the body parts themselves, as had long been assumed. Instead, it is theorized that the right ecological situation, the right habitat in which such bold, new forms will prove to be particularly advantageous, may be what is required to set these major transitions in motion.
So far, most of the evo-devo work has been on animals, but researchers have begun to ask whether the same themes are being played out in plants.
Of particular interest to botanists is what Darwin described as an “abominable mystery”: the origin of flowering plants. A critical event in the evolution of plants, it happened, by paleontological standards, rather suddenly.
So what genes were involved in the origin of flowers? Botanists know that during development, the genes known as MADS box genes lay out the architecture of the blossom. They do so by turning on other genes, thereby determining what will develop where — petals here, reproductive parts there and so on, in much the same manner that Hox genes determine the general layout of parts in animals. Hox genes have had an important role in the evolution of animal form. But have MADS box genes had as central a role in the evolution of plants?
So far, said Dr. Vivian F. Irish, a developmental biologist at Yale University, the answer appears to be yes. There is a variety of circumstantial evidence, the most interesting of which is the fact that the MADS box genes exploded in number right around the time that flowering plants first appeared.
“It’s really analogous to what’s going on in Hox genes,” said Dr. Irish, though she noted that details of the role of the MADS box genes remained to be worked out. “It’s very cool that evolution has used a similar strategy in two very different kingdoms.”
Amid the enthusiast hubbub, cautionary notes have been sounded. Dr. Jerry Coyne, an evolutionary biologist at the University of Chicago, said that as dramatic as the changes in form caused by mutations in toolkit genes can be, it was premature to credit these genes with being the primary drivers of the evolution of novel forms and diversity. He said that too few studies had been done so far to support such broad claims, and that it could turn out that other, more mundane workaday genes, of the sort that were being studied long before evo-devo appeared on the scene, would play equally or even more important roles.
“I urge caution,” Dr. Coyne said. “We just don’t know.”
All of which goes to show that like all emerging fields, evo-devo’s significance and the uniqueness of its contributions will continue to be reassessed. It will remain to be seen just how separate or incorporated into the rest of evolutionary thinking its findings will end up being. Paradoxically, it was during just such a flurry of intellectual synthesis and research activity, the watershed known as the New or Modern Synthesis in which modern evolutionary biology was born in the last century, that developmental thinking was almost entirely ejected from the science of evolution.
But perhaps today synthesizers can do better, broadening their focus without constricting their view of evolution as they try to take in all of the great pageant that is the history of life.
“We’re still a very young field,” Dr. Gilbert said. “But I think this is a new evolutionary synthesis, an emerging evolutionary synthesis. I think we’re seeing it.”

Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift

Modern Science taking their first feeble steps out of the Dark Ages of Disconnected Specialization?

".........Is Darwin due for an upgrade? There are growing calls among some evolutionary biologists for just such a revision. The failure to consider how biodiversity grows reflects an even more troubling flaw in the modern synthesis: it lacks any real sense of history......."
Explore the Potential of the Possible Human and Michael Murphy's Future of the Body. Understand that to trash and ignore thousands upon thousands of years of mastered wisdom on human nature is dangerous to survival. Highly specialized, yet narrow and shallow vision, breed and fertilize skewed and stale views of our expanding window to reality, which in turn create the trouble with foundational physics, perpetuating stagnant energy evolution, fostering global warming and the coming nuclear resource wars

NYT June 26, 2007
Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift
Is Darwin due for an upgrade? There are growing calls among some evolutionary biologists for just such a revision, although they differ about what form this might take. But those calls could also be exaggerated. There is nothing scientists enjoy more than the prospect of a good paradigm shift.
Paradigm shifts are the stuff of scientific revolutions. They change how we view the world, the sorts of questions that scientists consider worth asking, and even how we do science. The discovery of DNA marked one such shift, the theory of plate tectonics another.
Many scientists suffer from a kind of split personality. We believe that this is the most exciting time to be working while yearning for the excitement of a revolution. What ambitious scientist would not want to be part of a paradigm shift? Not surprisingly, this yearning occasionally manifests itself in proclamations that a revolution is at hand.
To understand the current tumult it helps to understand how our evolutionary framework developed. It was constructed from the 1930s to 1950s by early geneticists, paleontologists and others, who disagreed about the efficacy of natural selection in driving evolutionary change (Darwin’s big idea) and about the nature of the underlying genetic variation upon which natural selection could act. What they came to agree on was called the modern synthesis, and it established an intellectual zeitgeist that continues today, and has been continually adapted, in the best evolutionary fashion, to encompass new discoveries.
That synthesis holds that mutations to DNA create new variants of existing genes within a species. Natural selection, driven by competition for resources, allows the best-adapted individuals to produce the most surviving offspring. So adaptive variants of genes become more common. Although selection is often seen, even by biologists who should know better, as primarily negative, removing poorly adapted individuals, Charles Darwin understood that it was a powerful creative tool.
It is the primary agent in shaping new adaptations. Computer simulations have shown how selection can produce a complex eye from a simple eyespot in just a few hundred thousand years.
In the past few years every element of this paradigm has been attacked. Concerns about the sources of evolutionary innovation and discoveries about how DNA evolves have led some to propose that mutations, not selection, drive much of evolution, or at least the main episodes of innovation, like the origin of major animal groups, including vertebrates.
Comparative studies of development have illuminated how genes operate, and evolve, and this places less emphasis on the gradual accumulation of small genetic changes emphasized by the modern synthesis. Work in ecology has emphasized the role organisms play in building their own environments, and studies of the fossil record raise questions about the role of competition. The last major challenge to the modern synthesis came in the 1970s and 1980s as my paleontological colleagues, including the late Stephen Jay Gould, argued for a hierarchical view of evolution, with selection occurring at many levels, including between species.
Transitions between species documented by the fossil record seemed to be abrupt, perhaps too abrupt to be explained by the modern synthesis. If this were generally true, it could render irrelevant much of natural selection occurring within species, because just as mutations are produced randomly with respect to the needs of a species, with selection shaping these into new adaptations, new species might evolve randomly with species selection shaping them into evolutionary trends. This challenge was greeted with less than fulsome praise by evolutionary biologists studying changes within species. The resulting hubbub has yet to fully die down. But the newer work cuts closer to the core of the modern synthesis, and is potentially more revolutionary, because it addresses the fundamental question of how really new things happen in the history of life. What brought about the origin of animals, or the invasion of land?
The Achilles’ heel of the modern synthesis, as noted by the philosopher Ron Amundson, is that it deals primarily with the transmission of genes from one generation to the next, but not how genes produce bodies. The recent discoveries in the new field of evolutionary developmental biology, or evo-devo, that the gene Pax-6 controls the formation of eyes in mice and humans, Nkx2.5 heart formation, and a suite of other genes the formation of the nervous system, has provided a means to investigate the genetic and developmental mechanisms influencing how the form of organisms has evolved, not just their genes. Perhaps the most exciting area in evolution is in exploring how rewiring the circuitry of genes produces different arthropod appendages, or wingspots on butterflies.
Eric H. Davidson, a colleague of mine at CalTech, has dissected the network of interactions between the genes that build the gut of sea urchins and starfish during development. When he compares these gene networks, there is a core of about five genes whose interactions are essential to forming the gut, and which have been preserved for some 500 million years.
One advantage developmental biologists have over paleontologists is that they can experiment on the development of these animals. Most of the genes in this network can be removed, and the developing embryo finds a way to compensate. But these five core genes, which form what Davidson calls a kernel, cannot be modified: change any one of them and no embryo forms at all. There is no reason to think that there was anything unusual about how this kernel first evolved some 500 million years ago (before sea urchins and starfish split into different groups), but once the kernel formed it locked development onto a certain path. These events, small and large, limit the range of possibilities on which natural selection can act. These questions about mechanism were not even being asked under the modern synthesis.
The failure to consider how biodiversity grows reflects an even more troubling flaw in the modern synthesis: it lacks any real sense of history. This may sound odd, as evolution is about history. A geologist would describe evolutionary theory as uniformitarian: “The present is the key to the past.” This is the principle we use that by understanding how processes operate today we can understand past events. Evolutionary theory assumes that the processes we can study among fruit flies disporting themselves in a laboratory capture the broad sweep of evolutionary change.
But just as the erosive power of a river changes the future options for the course of the river, so evolution itself changes future evolutionary possibilities. This can happen in simple ways, as termites construct their own environment by building termite mounds. These mounds may last for dozens or hundreds of years and provide a sort of ecological inheritance for generations of termites.
The first cyanobacteria turned carbon dioxide into oxygen and set off a revolution that completely changed the chemistry of the oceans and atmosphere. Most species modify their environment and this often changes how selection affects them: they construct, at least in part, their own environment. As evolutionary biologists we have little understanding of what these processes mean for evolution.
Does all this add up to a new modern synthesis? There is certainly no consensus among evolutionary biologists, but development, ecology, genetics and paleontology all provide new perspectives on how evolution operates, and how we should study it. None of these concerns provide a scintilla of hope for creationists, as scientific investigations are already providing new insights into these issues. The foundations for a paradigm shift may be in place, but it may be some time before we see whether a truly novel perspective develops or these tensions are accommodated within an expanded modern synthesis.
Douglas H. Erwin is a senior scientist at the National Museum of Natural History at the Smithsonian Institution and a research professor at the Santa Fe Institute.

Humans Have Spread Globally, and Evolved Locally

Modern Science taking their first feeble steps out of the Dark Ages of Disconnected Specialization?

".........Historians often assume that they need pay no attention to human evolution because the process ground to a halt in the distant past. That assumption is looking less and less secure in light of new findings based on decoding human DNA......."
Explore the Potential of the Possible Human and Michael Murphy's Future of the Body. Understand that to trash and ignore thousands upon thousands of years of mastered wisdom on human nature is dangerous to survival. Highly specialized, yet narrow and shallow vision, breed and fertilize skewed and stale views of our expanding window to reality, which in turn create the trouble with foundational physics, perpetuating stagnant energy evolution, fostering global warming and the coming nuclear resource wars

NYT June 26, 2007
Humans Have Spread Globally, and Evolved Locally
Historians often assume that they need pay no attention to human evolution because the process ground to a halt in the distant past. That assumption is looking less and less secure in light of new findings based on decoding human DNA.
People have continued to evolve since leaving the ancestral homeland in northeastern Africa some 50,000 years ago, both through the random process known as genetic drift and through natural selection. The genome bears many fingerprints in places where natural selection has recently remolded the human clay, researchers have found, as people in the various continents adapted to new diseases, climates, diets and, perhaps, behavioral demands.
A striking feature of many of these changes is that they are local. The genes under selective pressure found in one continent-based population or race are mostly different from those that occur in the others. These genes so far make up a small fraction of all human genes.
A notable instance of recent natural selection is the emergence of lactose tolerance — the ability to digest lactose in adulthood — among the cattle-herding people of northern Europe some 5,000 years ago. Lactase, the enzyme that digests the principal sugar of milk, is usually switched off after weaning. But because of the great nutritional benefit for cattle herders of being able to digest lactose in adulthood, a genetic change that keeps the lactase gene switched on spread through the population.
Lactose tolerance is not confined to Europeans. Last year, Sarah Tishkoff of the University of Maryland and colleagues tested 43 ethnic groups in East Africa and found three separate mutations, all different from the European one, that keep the lactase gene switched on in adulthood. One of the mutations, found in peoples of Kenya and Tanzania, may have arisen as recently as 3,000 years ago.
That lactose tolerance has evolved independently four times is an instance of convergent evolution. Natural selection has used the different mutations available in European and East African populations to make each develop lactose tolerance. In Africa, those who carried the mutation were able to leave 10 times more progeny, creating a strong selective advantage.
Researchers studying other single genes have found evidence for recent evolutionary change in the genes that mediate conditions like skin color, resistance to malaria and salt retention.
The most striking instances of recent human evolution have emerged from a new kind of study, one in which the genome is scanned for evidence of selective pressures by looking at a few hundred thousand specific sites where variation is common.
Last year Benjamin Voight, Jonathan Pritchard and colleagues at the University of Chicago searched for genes under natural selection in Africans, Europeans and East Asians. In each race, some 200 genes showed signals of selection, but without much overlap, suggesting that the populations on each continent were adapting to local challenges.
Another study, by Scott Williamson of Cornell University and colleagues, published in PLoS Genetics this month, found 100 genes under selection in Chinese, African-Americans and European-Americans.
In most cases, the source of selective pressure is unknown. But many genes associated with resistance to disease emerge from the scans, confirming that disease is a powerful selective force. Another category of genes under selective pressure covers those involved in metabolism, suggesting that people were responding to changes in diet, perhaps associated with the switch from hunting and gathering to agriculture.
Several genes involved in determining skin color have been under selective pressure in Europeans and East Asians. But Dr. Pritchard’s study detected skin color genes only in Europeans, and Dr. Williamson found mostly genes selected in Chinese.
The reason for the difference is that Dr. Pritchard’s statistical screen detects genetic variants that have become very common in a population but are not yet universal. Dr. Williamson’s picks up variants that have already swept through a population and are possessed by almost everyone.
The findings suggest that Europeans and East Asians acquired their pale skin through different genetic routes and, in the case of Europeans, perhaps as recently as around 7,000 years ago.
Another puzzle is presented by selected genes involved in brain function, which occur in different populations and could presumably be responses to behavioral challenges encountered since people left the ancestral homeland in Africa.
But some genes have more than one role, and some of these brain-related genes could have been selected for other properties.
Two years ago, Bruce Lahn, a geneticist at the University of Chicago, reported finding signatures of selection in two brain-related genes of a type known as microcephalins, because when mutated, people are born with very small brains. Two of the microcephalins had come under selection in Europeans and one in Chinese, Dr. Lahn reported.
He suggested that the selected forms of the gene had helped improved cognitive capacity and that many other genes, yet to be identified, would turn out to have done the same in these and other populations.
Neither microcephalin gene turned up in Dr. Pritchard’s or Dr. Williamson’s list of selected genes, and other researchers have disputed Dr. Lahn’s claims. Dr. Pritchard found that two other microcephalin genes were under selection, one in Africans and the other in Europeans and East Asians.
Even more strikingly, Dr. Williamson’s group reported that a version of a gene called DAB1 had become universal in Chinese but not in other populations. DAB1 is involved in organizing the layers of cells in the cerebral cortex, the site of higher cognitive functions.
Variants of two genes involved in hearing have become universal, one in Chinese, the other in Europeans.
The emerging lists of selected human genes may open new insights into the interactions between history and genetics. “If we ask what are the most important evolutionary events of the last 5,000 years, they are cultural, like the spread of agriculture, or extinctions of populations through war or disease,” said Marcus Feldman, a population geneticist at Stanford. These cultural events are likely to have left deep marks in the human genome.
A genomic survey of world populations by Dr. Feldman, Noah Rosenberg and colleagues in 2002 showed that people clustered genetically on the basis of small differences in DNA into five groups that correspond to the five continent-based populations: Africans, Australian aborigines, East Asians, American Indians and Caucasians, a group that includes Europeans, Middle Easterners and people of the Indian subcontinent. The clusterings reflect “serial founder effects,” Dr. Feldman said, meaning that as people migrated around the world, each new population carried away just part of the genetic variation in the one it was derived from.
The new scans for selection show so far that the populations on each continent have evolved independently in some ways as they responded to local climates, diseases and, perhaps, behavioral situations.
The concept of race as having a biological basis is controversial, and most geneticists are reluctant to describe it that way. But some say the genetic clustering into continent-based groups does correspond roughly to the popular conception of racial groups.
“There are difficulties in where you put boundaries on the globe, but we know now there are enough genetic differences between people from different parts of the world that you can classify people in groups that correspond to popular notions of race,” Dr. Pritchard said.
David Reich, a population geneticist at the Harvard Medical School, said that the term “race” was scientifically inexact and that he preferred “ancestry.” Genetic tests of ancestry are now so precise, he said, that they can identify not just Europeans but can distinguish between northern and southern Europeans. Ancestry tests are used in trying to identify genes for disease risk by comparing patients with healthy people. People of different races are excluded in such studies. Their genetic differences would obscure the genetic difference between patients and unaffected people.
No one yet knows to what extent natural selection for local conditions may have forced the populations on each continent down different evolutionary tracks. But those tracks could turn out to be somewhat parallel. At least some of the evolutionary changes now emerging have clearly been convergent, meaning that natural selection has made use of the different mutations available in each population to accomplish the same adaptation.
This is the case with lactose tolerance in European and African peoples and with pale skin in East Asians and Europeans.

Sunday, October 21, 2007

Scientists Induce Out-of-Body Sensation

Explore the Possibilities of the Possible Human and Michael Murphy's Future of the Body. Understand that to trash and ignore thousands upon thousands of years of mastered wisdom on human nature is dangerous to survival. Highly specialized, yet narrow and shallow vision, breed and fertilize skewed and stale views of our expanding window to reality, which in turn create the trouble with foundational physics, perpetuating stagnant energy evolution, fostering global warming and the coming nuclear resource wars our vaunted scientific institutions spearhead our progress with extremely, very extremely, elementary human nature trivia in the article below

NYT August 23, 2007
Scientists Induce Out-of-Body Sensation
Using virtual reality goggles, a camera and a stick, scientists have induced out-of-body experiences — the sensation of drifting outside of one’s own body — - in healthy people, according to experiments being published in the journal Science.
When people gaze at an illusory image of themselves through the goggles and are prodded in just the right way with the stick, they feel as if they have left their bodies.
The research reveals that “the sense of having a body, of being in a bodily self,” is actually constructed from multiple sensory streams, said Matthew Botvinick, an assistant professor of neuroscience at Princeton University, an expert on body and mind who was not involved in the experiments.
Usually these sensory streams, which include vision, touch, balance and the sense of where one’s body is positioned in space, work together seamlessly, Prof. Botvinick said. But when the information coming from the sensory sources does not match up, when they are thrown out of synchrony, the sense of being embodied as a whole comes apart.
The brain, which abhors ambiguity, then forces a decision that can, as the new experiments show, involve the sense of being in a different body.
The research provides a physical explanation for phenomena usually ascribed to other-worldly influences, said Peter Brugger, a neurologist at University Hospital in Zurich, Switzerland. After severe and sudden injuries, people often report the sensation of floating over their body, looking down, hearing what is said, and then, just as suddenly, find themselves back inside their body. Out-of-body experiences have also been reported to occur during sleep paralysis, the exertion of extreme sports and intense meditation practices.
The new research is a first step in figuring out exactly how the brain creates this sensation, he said.
The out-of-body experiments were conducted by two research groups using slightly different methods intended to expand the so-called rubber hand illusion.
In that illusion, people hide one hand in their lap and look at a rubber hand set on a table in front of them. As a researcher strokes the real hand and the rubber hand simultaneously with a stick, people have the vivid sense that the rubber hand is their own.
When the rubber hand is whacked with a hammer, people wince and sometimes cry out.
The illusion shows that body parts can be separated from the whole body by manipulating a mismatch between touch and vision. That is, when a person’s brain sees the fake hand being stroked and feels the same sensation, the sense of being touched is misattributed to the fake.
The new experiments were designed to create a whole body illusion with similar manipulations.
In Switzerland, Dr. Olaf Blanke, a neuroscientist at the École Polytechnique Fédérale in Lausanne, Switzerland, asked people to don virtual reality goggles while standing in an empty room. A camera projected an image of each person taken from the back and displayed 6 feet away. The subjects thus saw an illusory image of themselves standing in the distance.
Then Dr. Blanke stroked each person’s back for one minute with a stick while simultaneously projecting the image of the stick onto the illusory image of the person’s body.
When the strokes were synchronous, people reported the sensation of being momentarily within the illusory body. When the strokes were not synchronous, the illusion did not occur.
In another variation, Dr. Blanke projected a “rubber body” — a cheap mannequin bought on eBay and dressed in the same clothes as the subject — into the virtual reality goggles. With synchronous strokes of the stick, people’s sense of self drifted into the mannequin.
A separate set of experiments were carried out by Dr. Henrik Ehrsson, an assistant professor of neuroscience at the Karolinska Institute in Helsinki.
Last year, when Dr. Ehrsson was, as he says, “a bored medical student at University College London”, he wondered, he said, “what would happen if you ‘took’ your eyes and moved them to a different part of a room? Would you see yourself where you eyes were placed? Or from where your body was placed?”
To find out, Dr. Ehrsson asked people to sit on a chair and wear goggles connected to two video cameras placed 6 feet behind them. The left camera projected to the left eye. The right camera projected to the right eye. As a result, people saw their own backs from the perspective of a virtual person sitting behind them.
Using two sticks, Dr. Ehrsson stroked each person’s chest for two minutes with one stick while moving a second stick just under the camera lenses — as if it were touching the virtual body.
Again, when the stroking was synchronous people reported the sense of being outside their own bodies — in this case looking at themselves from a distance where their “eyes” were located.
Then Dr. Ehrsson grabbed a hammer. While people were experiencing the illusion, he pretended to smash the virtual body by waving the hammer just below the cameras. Immediately, the subjects registered a threat response as measured by sensors on their skin. They sweated and their pulses raced.
They also reacted emotionally, as if they were watching themselves get hurt, Dr. Ehrsson said.
People who participated in the experiments said that they felt a sense of drifting out of their bodies but not a strong sense of floating or rotating, as is common in full-blown out of body experiences, the researchers said.
The next set of experiments will involve decoupling not just touch and vision but other aspects of sensory embodiment, including the felt sense of the body position in space and balance, they said.

Out-Of-Body Experiences Put To The Test
CBS Aug. 23, 2007
(WebMD) Ever had an out-of-body experience, where you were wide awake and "saw" your body as if you were a bystander? Scientists may have figured out how out-of-body experiences happen. Turns out, it's all about the eyes. Two new studies — both published in tomorrow's edition of the journal Science — put a state-of-the-art spin on out-of-body research. In one experiment, 14 healthy, young adults wore virtual-reality goggles as they stood in the researchers' lab. A few feet behind them, a video camera filmed their backs and projected that image, in real time, into a hologram a few feet in front of the participants. The researchers stroked the participants' real and virtual back at the same time. Afterward, they only stroked the participants' virtual back — but even so, participants said they had the sensation that their real backs were being touched. Participants didn't lose all sense of themselves. They didn't report feeling like they had left their bodies. But they did describe the sensation as weird or strange, according to Olaf Blanke, M.D., Ph.D., and colleagues. Blanke directs the Laboratory of Cognitive Neuroscience at the Ecole Polytechnique Federale de Lausanne in Lausanne, Switzerland. Blanke's team did similar tests on 14 other participants to confirm the findings. The other study also used virtual reality and video cameras to simulate out-of-body experiences. But neuroscientist H. Henrik Ehrsson, M.D., Ph.D., pushed the envelope a little farther. Ehrsson works at University College London and the Karolinksa Institute in Stockholm, Sweden. In a series of experiments, Ehrsson found that participants "felt" touch applied to virtual-reality versions of their bodies. What's more, when Ehrsson pretended to strike participants' virtual bodies — not their true selves — with a hammer, participants were scared for their actual flesh and blood, though they had been promised that they weren't in any danger whatsoever. "This experiment suggests that the first-person visual perspective is critically important for the in-body experience," Ehrsson says in a news release. "In other words, we feel that our self is located where the eyes are."

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I hope more people who have had near death experiences post here. This is a very interesting subject. This study proves nothing...I would like to hear about actual experiences.
Posted by GrammaWhamma at 07:12 PM : Aug 23, 2007+ report abuse
Posted by luvcomments at 06:41 PM : Aug 23, 2007+ report abuse--------------------------------------------------------------------------------****I will not fight science, because I know its futile. However, the experience gave me new energy to go on with life with desire. I cherish every morsel of life. Personally, it did not convert me to a more relgious person (I was catholic turned atheist turned..??) but a more spiritial human being. I know that there is a prupose for everything. I am sorry to be too corney...but I believe in a grand design for each and everyone of us. Most important, now I understand that it is not who you believe but how you lead your life.
Posted by xzavierbrown at 07:05 PM : Aug 23, 2007+ report abuse
xzavierbrownI agree with you. My experience was similar. I experienced total lack of fear, knew I would exist forever (although not as who I was/still am in the flesh, of course), and knew I might or might not get back into my human form I had temporarily left. I saw the doctor, the nurses, everything around me and also in other rooms, as well as saw my own human body. As a result I am not at all afraid of death (maybe afraid of how I die, though). I did see a massive light / energy source and knew even the sun receives its energy from that. They can run all the experiments they want to; I don''t see what difference it makes. The experience left me aware that people are all running around in circles, intent on so many things that really don''t matter one tinker''s cuss in the grand scheme of things.
Posted by luvcomments at 06:41 PM : Aug 23, 2007+ report abuse
does that work for blind people, too?
Posted by luvcomments at 06:31 PM : Aug 23, 2007+ report abuse
"In one experiment, 14 healthy, young adults wore virtual-reality goggles as they stood in the researchers'' lab. A few feet behind them, a video camera filmed their backs and projected that image, in real time, into a hologram a few feet in front of the participants."I dont think anybody would have that as they are dying in an operating table. I had an NDE and what I felt is..*no words can describe it* I am NOT leaning toward a more religious aspect but more or on a spiritual. There is a sense of peace and delight. I did not see jesus nor did I see allah or whatever franchised religion is selling these days, but I sense an entity of power. The most important thing that I learned from it????....LIFE IS TOO PRECIOUS TO WASTE. LIVE IT LIKE YOU ARE GOING TO DIE IN AN HOUR. I can go ahead with this but I am afraid I am going to open myself to the preceeding post to taunts and hollers from both religious and athiest zealots.
Posted by xzavierbrown at 06:30 PM : Aug 23, 2007

Mind Over Matter, With a Machine’s Help

Explore the Possibilities of the Possible Human and Michael Murphy's Future of the Body. Understand that to trash and ignore thousands upon thousands of years of mastered wisdom on human nature is dangerous to survival. Highly specialized, yet narrow and shallow vision, breed and fertilize skewed and stale views of our expanding window to reality, which in turn create the trouble with foundational physics, perpetuating stagnant energy evolution, fostering global warming and the coming nuclear resource wars our vaunted scientific institutions spearhead our progress with extremely, very extremely, elementary human nature trivia in the article below

August 26, 2007
NYT Slipstream
Mind Over Matter, With a Machine’s Help
WOULD that thinking made it so, people sometimes wistfully say. But Christopher deCharms, the chief executive of Omneuron, a start-up in Menlo Park, Calif., believes the adage.
The company he founded has created technologies that teach sufferers to think away their pain, and plans to similarly treat addiction, depression and other intractable neurological and psychological conditions.
Omneuron is one of a number of new companies that are commercializing a brain-scanning technology called real-time functional magnetic resonance imaging, or fMRI. Using large scanners to measure blood flow to different parts of the brain, the technology makes the brain’s activity visible by revealing which of its parts are busiest when we perform different tasks.
While fMRI dates back to the early 1990s, hitherto it has been used mainly by doctors in hospitals to make diagnoses. The commercialization of brain scanning is a recent development, spurred by the refinement of the technology. Omneuron, which Dr. deCharms founded in 2001 and whose research has been funded by the National Institutes of Health, uses fMRI to teach people how to play with their own heads. Other entrepreneurs are working on ways to deploy fMRI as a lie detector, a tool for conducting marketing research or an instrument to make brain surgeries safer and more precise.
Here’s how Omneuron uses fMRI to treat chronic pain: A patient slides into the coffin-like scanner and watches a computer-generated flame projected on the screen of virtual-reality goggles; the flame’s intensity reflects the neural activity of regions of the brain involved in the perception of pain. Using a variety of mental techniques — for instance, imagining that a painful area is being flooded with soothing chemicals — most people can, with a little concentration, make the flame wax or wane. As the flame wanes, the patient feels better. Superficially similar to an older technology, electroencephalogram biofeedback, which measures electrical feedback across multiple areas of the brain, fMRI feedback measures the blood flow in precise areas of the brain.
“We believe that people will use real-time fMRI feedback to hone cognitive strategies that will increase activation of brain regions,” Dr. deCharms said. With practice and repetition, he said, this could lead to “long-term changes in the brain.”
In time, he hopes, a patient could evoke the effect without the machine.
In a 2005 study, Dr. deCharms and Sean Mackey, associate director of the pain management division at Stanford, showed that eight patients with recalcitrant pain felt their discomfort reduced by as much as 64 percent by using Omneuron’s technology.
If fMRI proves effective in treating pain, it could be big business. According to the American Chronic Pain Association, one in three Americans will experience chronic pain at some point in life. At any one time, more than 50 million Americans complain of pain. And Dr. deCharms contends that fully one-third find their pain resistant to traditional treatments like narcotics. Omneuron’s technologies could offer such patients some relief, and without side effects.
The pain-relief industry is huge: the average American spends as much as $900 a year on pain medications, whose effects are generally short-lived.
But Dr. deCharms says that controlling pain is just one of many possible uses for fMRI feedback. Today, Omneuron is also researching treatments for addiction, depression and other psychological illnesses. In addition, he said. the company has contemplated “several dozen applications,” including the treatment of stroke and epilepsy. Brain scanning could even be used to improve athletic performance, he speculated.
Doctors and drug-abuse experts are particularly excited about the idea of treating addiction using fMRI. While scientists have talked about such an application since the technology was invented, Omneuron is the first to work on a real therapy. “We might have a tool to help control the inner sensation of craving,” said Nora D. Volkow, director of the National Institute on Drug Abuse, which helped fund Omneuron’s research into addiction.
A growing number of ventures hope to turn fMRI into a business. The most well-publicized is No Lie MRI, which wants to sell brain scanning to law firms and governmental bodies like police departments or security and intelligence agencies as a replacement for the notoriously unreliable polygraph test. No Lie MRI has already begun selling what it calls its truth verification technology for about $10,000 to individuals keen to prove their innocence.
Joel Huizenga, the chief executive of No Lie MRI, said: “A technology gets known by its first product. For fMRI, that application is going to be truth verification.”
Mr. Huizenga says he would also like to sell fMRI to marketers who wish to determine whether consumers are responding to advertising, a commercial application of an emerging field of research called neuro-economics.
Other brain-scanning ventures include Cephos, another lie-detection company, and Imagilys, which sells fMRI to surgeons who want to map the brains of patients before operations.
For its part, Omneuron would make money not by building fMRI centers — which are expensive and fairly common in larger hospitals — but by selling clinical skills, software and equipment.
“I imagine the business model would be akin to Lasik eye surgery,” Dr. deCharms says. “We’d provide the technology to outpatient treatment centers.”
There are challenges to the commercialization of brain scanning, and the most important may be regulatory. Clinical trials can take many years, and federal approval is famously unpredictable. But until clinical data and federal approval are forthcoming, Dr. deCharms says, Omneuron cannot sell its technology as a clinical treatment.
Ed Boyden, an assistant professor at the Media Lab of the Massachusetts Institute of Technology and a researcher in neuroengineering, distinguishes sharply among different brain-scanning ventures. “If you want to commercialize this technology,” he said, “then the use has to approximate real-world situations.”
In his view, tests of fMRI truth verification don’t meet that criterion. For instance, in studies at the University of Pennsylvania in 2002 and 2005, subjects were told to conceal the identity of a card under questioning. FMRI was able to distinguish falsification 77 percent of the time.
Mr. Huizenga was so inspired by this research that he decided to start his company, confident that fMRI would soon identify lies 90 percent of the time.
But Dr. Boyden says he believes that being asked to tell a falsehood that everyone knows is a falsehood is not the same thing as lying to deceive someone. Thus, whatever brain patterns fMRI detects when a person constructs such a requested fiction may be different from whatever happens when we lie.
By contrast, Dr. Boyden says: “What I like about Omneuron is that it’s working with real-world situations. They gave people visualization strategies which they could monitor — and which produced real, measurable results.”
If Dr. deCharms and Omneuron are successful, and can teach us to train our brains to manage neurological and psychological conditions, they will have given us something that has challenged philosophers, psychologists and yogis alike: gaining some reliable control over our own thoughts.
Jason Pontin is the editor in chief and publisher of Technology Review, a magazine and Web site owned by M.I.T. E