Fast-Paced Evolution in the Andes
New York Times,
November 7, 2013Link
In 1799 the great naturalist Alexander von Humboldt and his companions set out from Caracas, Venezuela, to climb the Andes. They struggled up a mountainside enveloped in mist so thick they had to clamber over rocks by hand. When the fog cleared, von Humboldt was left astonished by the view. Vast grasslands stretched all around him, home to an astonishing number of different trees, shrubs and flowers.
“Nowhere, perhaps, can be found collected together, in so small a space, productions so beautiful and so remarkable in regard to the geography of plants,” he later wrote.
Von Humboldt had stumbled into a remarkable ecosystem, known as a Páramo. Páramos blanket the Andes in Venezuela, Ecuador and Colombia, growing at altitudes 9,200 to 14,800 feet above sea level.
“They’re like islands in a sea of forest,” said Santiago Madriñán, an expert on Páramos at the University of the Andes in Colombia. All told, Páramos cover about 13,500 square miles — an area the size of Maryland. In that small space, Dr. Madriñán and other researchers have found 3,431 species of vascular plants, most of them found nowhere else on Earth. The Páramos are home to strange variations on familiar forms, such as a daisy known as Espeletia uribei that grows as tall as trees.
Afraid of Snakes? Your Pulvinar May Be to Blame
New York Times,
October 31, 2013Link
Multiple Walter Whites will walk the streets on Thursday in search of candy. But some frights endure the fashion cycle and never go out of style.
This week in Proceedings of the National Academy of Sciences, a team of scientists examines one particularly long-lasting source of fear: snakes. The researchers found that certain neurons in the brain only respond to these legless reptiles. These snake-dedicated neurons, they argue, are a legacy of our distant primate past, when the animals posed one of the greatest threats to our survival.
The new study builds on years of experiments by psychologists. They found that the widespread fear of snakes stems from a perceptual bias: people recognize snakes faster than other objects.
Christening the Earliest Members of Our Genus
New York Times,
October 24, 2013Link
Around 1.8 million years ago, human evolution passed a milestone. Our ancestors before then were little more than bipedal apes. Those so-called hominids had chimpanzee-size bodies and brains, and they still had adaptations in their limbs for climbing trees. But the fossils of hominids from 1.8 to 1.5 million years ago are different. They had bigger brains, flatter faces and upright bodies better suited to walking.
Their geography changed, too. While earlier hominid fossils have only been found in Africa, the newer ones also turn up at sites stretching across Asia, from the Republic of Georgia all the way to Indonesia. These cosmopolitan hominids are so much like modern humans that paleoanthropologists consider them the earliest members of our own genus, Homo.
But they didn’t belong to our species, Homo sapiens. After all, their brains were still no more than two-thirds the size of our own, and they could only make simple hand axes and other crude stone tools. But if not Homo sapiens, then Homo what? What species did these fossils belong to?
That turns out to be a remarkably hard question to answer — in part because it is difficult to settle on what it means to be a species.
Key to Ants’ Evolution May Have Started With a Wasp
New York Times,
October 17, 2013Link
How should we judge the success of an animal? Philip S. Ward, a biologist at the University of California, Davis, offers what could be called the Picnic Test. “Have a picnic anywhere in the world,” he suggests. “Who would pick up the crumbs?”
Unless you happen to lay down your picnic blanket in Greenland, Antarctica, or a few remote islands in the Pacific, the answer will be ants. Ants have spread to just about every corner of earth’s dry land, colonizing virtually every imaginable ecosystem. By one rough estimate, there are 10,000 trillion ants on earth at any moment. In one study in a Brazilian rain forest, scientists discovered that the total mass of the ants that lived there was about four times greater than that of all the mammals, reptiles and amphibians combined.
One factor in the spectacular success of ants is their social life. They live in large colonies in which they divide the labor of finding food, rearing their young and defending their nests. Their societies are so complex that some scientists have studied ants as a way to understand the factors behind our own evolution into a social species.
It’s thus no surprise that many biologists — Dr. Ward among them — have long wondered how ants evolved. In the journal Current Biology, Dr. Ward and colleagues at the University of California, Davis, and the American Museum of Natural History, have now published an evolutionary tree of ants and their closest relatives that may provide the answer.
Elephants Get the Point of Pointing, Study Shows
New York Times,
October 10, 2013Link
We point to things without giving much thought to what a sophisticated act it really is. By simply extending a finger, we can let other people know we want to draw their attention to an object, and indicate which object it is.
As sophisticated as pointing may be, however, babies usually learn to do it by their first birthday. “If you don’t get that they’re drawing your attention to an object, they’ll get cross,” said Richard W. Byrne, a biologist at the University of St Andrews.
When scientists test other species, they find that pointing is a rare gift in the animal kingdom. Even our closest relatives, likes chimpanzees, don’t seem to get the point of pointing.
But Dr. Byrne and his graduate student Anna Smet now say they have discovered wild animals that also appears to understand pointing: elephants. The study, involving just 11 elephants, is hardly the last word on the subject. But it raises a provocative possibility that elephants have a deep social intelligence that rivals humans’ in some ways.
Earth’s Oxygen: A Mystery Easy to Take for Granted
New York Times,
October 3, 2013Link
To Donald E. Canfield, there’s something astonishing in every breath we take. “People take oxygen for granted because it’s just there and we breathe it all the time,” said Dr. Canfield, a geochemist at the University of Southern Denmark. “But we have the only planet we know of anywhere that has oxygen on it.”
What’s even more astonishing is that Earth started out with an oxygen-free atmosphere. It took billions of years before there was enough of the element to keep animals like us alive.
Although scientists have been struggling for decades to reconstruct the rise of oxygen, they’re still making fundamental discoveries. In just the past two weeks, for example, Dr. Canfield and his colleagues have published a pair of studies that provide significant clues about some of the most important chapters in oxygen’s history. They’re finding that our weirdly oxygen-rich atmosphere is the result of a complicated dance of geology and biology.
In Fragmented Forests, Rapid Mammal Extinctions
New York Times,
September 26, 2013Link
In 1987, the government of Thailand launched a huge, unplanned experiment. They built a dam across the Khlong Saeng river, creating a 60-square-mile reservoir. As the Chiew Larn reservoir rose, it drowned the river valley, transforming 150 forested hilltops into islands, each with its own isolated menagerie of wildlife.
Conservation biologists have long known that fragmenting wilderness can put species at risk of extinction. But it’s been hard to gauge how long it takes for those species to disappear. Chiew Larn has given biologists the opportunity to measure the speed of mammal extinctions. “It’s a rare thing to come by in ecological studies,” said Luke Gibson, a biologist at the National University of Singapore.
Over two decades, Dr. Gibson and his colleagues have tracked the diversity of mammals on the islands. In Friday’s issue of the journal Science, they report that the extinctions have turned out to be distressingly fast.
“Our results should be a warning,” said Dr. Gibson. “This is the trend that the world is going in.”
New Approach to Explaining Evolution’s Big Bang
New York Times,
September 19, 2013Link
The name Myllokunmingia may not ring a bell, but it is worth knowing. This 520-million-year-old creature was the size of a guppy, with a tiny swordfish-like fin running high over its back. The fossils it has left behind preserve traces of a skull.
Humans have a skull, too. This and a number of other traits we share with Myllokunmingia reveal it to be one of the oldest, most primitive vertebrates yet found. It is, in other words, a hint of where we came from.
Myllokunmingia emerged during one of the most important phases in the history of life, an evolutionary boom known as the Cambrian explosion (named for the geological period when it took place). Over the course of about 20 million years, the oldest known fossils of most of the major groups of living animals appear, revealing a rapid diversification of life that led directly to humans.
“It’s rapid in geological terms, but it’s probably not rapid to anyone who’s not a geologist,” said Paul Smith, the director of the Oxford Museum of Natural History.
By some estimates, the first animals evolved about 750 million years ago. But it’s not until around 520 million years ago that many major groups of living animals left behind their first fossils. For decades, scientists have searched for the trigger that set in motion this riot of diversity in the animal kingdom.
DNA Double Take
New York Times,
September 16, 2013Link
From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity. Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information — or, as 23andme, a prominent genetic testing company, says on its Web site, “The more you know about your DNA, the more you know about yourself.”
But scientists are discovering that — to a surprising degree — we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people.
“There have been whispers in the matrix about this for years, even decades, but only in a very hypothetical sense,” said Alexander Urban, a geneticist at Stanford University. Even three years ago, suggesting that there was widespread genetic variation in a single body would have been met with skepticism, he said. “You would have just run against the wall.”
But a series of recent papers by Dr. Urban and others has demonstrated that those whispers were not just hypothetical. The variation in the genomes found in a single person is too large to be ignored. “We now know it’s there,” Dr. Urban said. “Now we’re mapping this new continent.”
A Far-Flung Possibility for the Origin of Life
New York Times,
September 13, 2013Link
“We’re All Martians, Scientist Claims,” The Telegraph wrote on Aug. 28. Similar articles showed up in newspapers and on Web sites around the world.
The scientist who inspired all the headlines is a chemist named Steven Benner. Headlines notwithstanding, Dr. Benner is not a wild-eyed U.F.O. advocate claiming to have seen Little Green Men. Instead, he is one of the world’s leading experts on the origin of life.
“Steve is one of the master organic chemists tackling this problem,” said Robert M. Hazen, a mineralogist at the Carnegie Institution and the author of “The Story of Earth.”
The cause for Dr. Benner’s new-found celebrity is a lecture he delivered at a geology conference in Florence on Aug. 29. During his talk, he did not wave satellite pictures of canals on Mars, or of Martian hills that vaguely look like a human face.
Instead, he challenged his fellow scientists to look hard at the evidence we have about how life began.
A Catalog for all the World’s Viruses?
New York Times,
September 5, 2013Link
Viruses have a knack for ambush. Time and again, they have struck our species without warning, producing new diseases. H.I.V. burst on the scene in the early 1980s, and it took years for scientists to figure out that it had evolved from a chimpanzee virus in the early 1900s. In 2003, a previously unknown bat virus in China began to cause SARS in humans. Today we are in the midst of yet another ambush, as a new virus called MERS is infecting people, mostly in in Saudi Arabia. Scientists have yet to definitively pin down its origin, although preliminary evidence points to another species of bat.
We might be able to take away this element of surprise if we had a catalog of all the viruses lurking in mammals. As soon as a mysterious epidemic broke out, scientists could turn to the catalog to figure out where the virus came from, potentially gaining some crucial clues to the virus’s biology. But few scientists have ventured to build such a catalog, perhaps because there seemed to be such a vast number of viruses to contend with.
“No one’s really been addressing this question, even though it seems like such a fundamental one,” said Simon J. Anthony, an associate research scientist at Columbia University and a researcher at EcoHealth Alliance, a New York-based scientific research organization.
Human Microbiome May Be Seeded Before Birth
New York Times,
August 29, 2013Link
We are each home to about 100 trillion bacteria, which we carry with us from birth till death. But when Juliette C. Madan was trained as a neonatologist in the mid-2000s, her teachers told her in no uncertain terms that we only acquire those bacteria after we are born. “It was clear as day, we were told, that fetuses were sterile,” she said.
Dr. Madan is now an assistant professor of pediatrics at the Geisel School of Medicine at Dartmouth, and she’s come to a decidedly different view on the matter. “I think that the tenet that healthy fetuses are sterile is insane,” she said.
Dr. Madan and a number of other researchers are now convinced mothers seed their fetuses with microbes during pregnancy. They argue that this early inoculation may be important to the long-term health of babies. And manipulating these fetal microbes could open up new ways to treat medical conditions ranging from pre-term labor to allergies.
As Humans Change Landscape, Brains of Some Animals Change, Too
New York Times,
August 22, 2013Link
Evolutionary biologists have come to recognize humans as a tremendous evolutionary force. In hospitals, we drive the evolution of resistant bacteria by giving patients antibiotics. In the oceans, we drive the evolution of small-bodied fish by catching the big ones.
In a new study, a University of Minnesota biologist, Emilie C. Snell-Rood, offers evidence suggesting that we may be driving evolution in a more surprising way. As we alter the places where animals live, we may be fueling the evolution of bigger brains.
Dr. Snell-Rood bases her conclusion on a collection of mammal skulls kept at the Bell Museum of Natural History at the University of Minnesota. She picked out 10 species to study, including mice, shrews, bats and gophers. She selected dozens of individual skulls that were collected as far back as a century ago. An undergraduate student, Naomi Wick, measured the dimensions of the skulls, making it possible to estimate the size of their brains.
Two important results emerged from their research. In two species — the white-footed mouse and the meadow vole — the brains of animals from cities or suburbs were about 6 percent bigger than the brains of animals collected from farms or other rural areas. Dr. Snell-Rood concludes that when these species moved to cities and towns, their brains became significantly bigger.
Watching Bacteria Evolve, With Predictable Results
New York Times,
August 15, 2013Link
If we could somehow rewind the history of life to the dawn of the animal kingdom, it would be unlikely that we humans would ever evolve, the evolutionary biologist Stephen Jay Gould argued. The history of life was shaped by too many flukes and contingencies to repeat its course.
Scientists can’t turn back the clock 700 million years, so we can’t know for sure whether Dr. Gould was right on that particular point. But in experiments using bacteria and other fast-breeding organisms, scientists can replay evolution many times over in their labs. And the results of a new experiment published Thursday in the journal Cell Reports demonstrate — with movies — that evolution can be astoundingly predictable.
The experiment was carried out by Joao Xavier of Memorial Sloan-Kettering Cancer Center and his colleagues. They studied a common species of bacteria called Pseudomonas aeruginosa. These microbes live pretty much everywhere — in dirt, in water, on our skin. Under certain conditions, they also invade our bodies and cause dangerous infections. People with cystic fibrosis, for example, can get P. aeruginosa infections in their lungs, which are often impossible to eradicate.
A Family Consents to a Medical Gift, 62 Years Later
New York Times,
August 8, 2013Link
Henrietta Lacks was only 31 when she died of cervical cancer in 1951 in a Baltimore hospital. Not long before her death, doctors removed some of her tumor cells. They later discovered that the cells could thrive in a lab, a feat no human cells had achieved before.
Soon the cells, called HeLa cells, were being shipped from Baltimore around the world. In the 62 years since — twice as long as Ms. Lacks’s own life — her cells have been the subject of more than 74,000 studies, many of which have yielded profound insights into cell biology, vaccines, in vitro fertilization and cancer.
But Henrietta Lacks, who was poor, black and uneducated, never consented to her cells’ being studied. For 62 years, her family has been left out of the decision-making about that research. Now, over the past four months, the National Institutes of Health has come to an agreement with the Lacks family to grant them some control over how Henrietta Lacks’s genome is used.
Monogamy and Human Evolution
New York Times,
August 2, 2013Link
“Monogamy is a problem,” said Dieter Lukas of the University of Cambridge in a telephone news conference last week. As Dr. Lukas explained to reporters, he and other biologists consider monogamy an evolutionary puzzle.
In 9 percent of all mammal species, males and females will share a common territory for more than one breeding season, and in some cases bond for life. This is a problem — a scientific one — because male mammals could theoretically have more offspring by giving up on monogamy and mating with lots of females.
In a new study, Dr. Lukas and his colleague Tim Clutton-Brock suggest that monogamy evolves when females spread out, making it hard for a male to travel around and fend off competing males.
On the same day, Kit Opie of University College London and his colleagues published a similar study on primates, which are especially monogamous — males and females bond in over a quarter of primate species. The London scientists came to a different conclusion: that the threat of infanticide leads males to stick with only one female, protecting her from other males.
Even with the scientific problem far from resolved, research like this inevitably turns us into narcissists. It’s all well and good to understand why the gray-handed night monkey became monogamous. But we want to know: What does this say about men and women?
As with all things concerning the human heart, it’s complicated.
The Fall and Rise of Gene Therapy
Rarely does a whole life’s work crumble in a single week, but james wilson’s did. The first glimmer of impending ruin came on a Tuesday morning—September 14, 1999—as he sat in his office at the University of Pennsylvania. In his role as founder and director of Penn’s Institute for Human Gene Therapy, Wilson was one of the most prominent researchers in the nascent field, which sought to put genes into patients to repair their faulty DNA.
Wilson and his colleagues were adding the final patients to a two-year clinical trial, the ultimate goal of which was to treat a rare but devastating disorder. Called OTCD, or ornithine transcarbamylase deficiency, the genetic disorder renders its victims unable to process nitrogen in their blood. Nitrogen is created when protein is broken down, so the blood of OTCD sufferers becomes poisoned when they eat protein-rich foods: One bite of a hot dog can bring on a coma. As a result, just half of children born with OTCD—estimated at roughly one in 80,000 babies in the US, or 50 per year—live to the age of 5. Wilson and his colleagues hoped to treat this disease by giving sufferers a working copy of the defective gene they carry. To accomplish this, they engineered a virus carrying the functional gene; after successful trials of the virus in mice, they launched a clinical trial to test its safety in humans suffering from OTCD.
The Surprising Origins of Evolutionary Complexity
Quanta Magazine and Scientific American,
Charles Darwin was not yet 30 when he got the basic idea for the theory of evolution. But it wasn't until he turned 50 that he presented his argument to the world. He spent those two decades methodically compiling evidence for his theory and coming up with responses to every skeptical counterargument he could think of. And the counterargument he anticipated most of all was that the gradual evolutionary process he envisioned could not produce certain complex structures.
Consider the human eye. It is made up of many parts—a retina, a lens, muscles, jelly, and so on—all of which must interact for sight to occur. Damage one part—detach the retina, for instance—and blindness can follow. In fact, the eye functions only if the parts are of the right size and shape to work with one another. If Darwin was right, then the complex eye had evolved from simple precursors. In On the Origin of Species, Darwin wrote that this idea “seems, I freely confess, absurd in the highest possible degree.”
But Darwin could nonetheless see a path to the evolution of complexity. In each generation, individuals varied in their traits. Some variations increased their survival and allowed them to have more offspring. Over generations those advantageous variations would become more common—would, in a word, be “selected.” As new variations emerged and spread, they could gradually tinker with anatomy, producing complex structures.
Despite Two New Studies on Motives for Monogamy, the Debate Continues
New York Times,
July 30, 2013Link
The golden lion tamarin, a one-pound primate that lives in Brazil, is a stunningly monogamous creature. A male will typically pair with a female and they will stay close for the rest of their lives, mating only with each other and then working together to care for their young.
To biologists, this deeply monogamous way of life — found in 9 percent of mammal species — is puzzling. A seemingly better evolutionary strategy for male mammals would be to spend their time looking for other females with which to mate.
“Monogamy is a problem,” said Dieter Lukas of the University of Cambridge in a telephone news conference on Monday. “Why should the male keep to one female?”
Looking at Oil Palm’s Genome for Keys to Productivity
New York Times,
July 24, 2013Link
You may have never set eyes on an oil palm tree, but it’s probably an intimate part of your everyday life. Whether you start your day with a shave or an application of lipstick, you are probably putting the oil from the tree’s fruits on your face. You buy a donut on the way to work, and with each bite, you swallow some of the palm oil in which it was cooked. After work, you stop at the supermarket, and about half the products on the shelves contain palm oil. Before bed, you scrub your face with soap and brush your teeth with toothpaste. They’re both palm oil’s way of wishing you good night.
In just the past few decades, the oil palm tree Elaeis guineensis has become a huge global industry. In 1961, the world’s palm oil plantations produced 1.7 million tons of oil; today that figure is up to 64 million tons a year. A single acre of oil palm trees can generate up to $4,500 annually. Those prices will probably stay high in decades to come, as demand for the oil increases. China and India are now shifting to using palm oil for cooking food, for example, and some countries are exploring palm oil as a biofuel.
But the oil palm tree industry is also an environmental disaster, according to many conservation biologists. The tree “grows best in those parts of the world that support tropical rainforests,” said Ben Phalan of the University of Cambridge. “Oil palm expansion in recent decades has been one of the main drivers of deforestation in Southeast Asia.”
Changing View on Viruses: Not So Small After All
New York Times,
July 18, 2013Link
There was a time not that long ago when it was easy to tell the difference between viruses and the rest of life. Most obviously, viruses were tiny and genetically simple. The influenza virus, for example, measures about 100 nanometers across, and has just 13 genes.
Those two standards, it’s now clear, belong in the trash. Over the past decade, scientists have discovered a vast menagerie of viruses that are far bigger, and which carry enormous arsenals of genes. French researchers are now reporting the discovery of the biggest virus yet. The pandoravirus, as they’ve dubbed it, is 1,000 times bigger than the flu virus by volume and has nearly 200 times as many genes — 2,556 all told.
Making the discovery all the more startling is the fact that, of all the genes that pandoraviruses carry, only six percent match any gene known to science.
“We believe we’re opening a Pandora’s box – not so much for humanity but for dogma about viruses,” said Dr. Jean-Michel Claverie of the University of Mediterranée, co-author of the paper that was published online Thursday in the journal Science. “We believe we’re touching an alternative tree of life.”
Looking for Ways to Beat the Weeds
New York Times,
July 16, 2013Link
Depending on your point of view, barnyardgrass is a nightmare or a marvel.
A cotton field was sprayed with residual herbicides before planting to counter glyphosate-resistant weeds.
That’s because it’s a supremely triumphant weed. Barnyardgrass can swoop in to fields and outcompete planted crops. It is particularly devastating on rice farms, where losses sometimes reach 100 percent. It has evolved resistance to a number of herbicides that farmers rely on to control weeds. Even when farmers think they have rid a field of barnyardgrass, they may not have actually won the battle. Each weed can produce up to a million seeds, which nestle into the soil, waiting for a chance to regrow.
Barnyardgrass is but one of many kinds of weeds found around the world. All told, they result in a 10 percent reduction in the productivity of crops. In the United States alone, they cause an estimated $33 billion in losses each year. Herbicides can reduce the toll, but within a few years of the introduction of a new chemical, weeds evolve resistance to it.
Unraveling the Pollinating Secrets of a Bee’s Buzz
New York Times,
July 11, 2013Link
Now is the time of year when bees buzz from flower to flower. And for many plants, the very survival of their species depends on that buzz. The flowers and the insects are joined together in a partnership of sound.
Bumblebees and other insects use buzzing to shake pollen out of flowers for food — and they fertilize flowers along the way. Scientists are exploring this acoustic feat to figure out how it has evolved, and how it helps sustain our own food supply.
Flowering plants typically reproduce by delivering pollen to each other to fertilize seeds. Some flowers, like corn and ragweed, cast their pollen to the wind. Others depend on animals like bees, bats or birds to do the job.
How Simple Can Life Get? It’s Complicated
New York Times,
July 4, 2013Link
In the pageant of life, we are genetically bloated. The human genome contains around 20,000 protein-coding genes. Many other species get by with a lot less. The gut microbe Escherichia coli, for example, has just 4,100 genes.
Scientists have long wondered how much further life can be stripped down and still remain alive. Is there a genetic essence of life? The answer seems to be that the true essence of life is not some handful of genes, but coexistence.
E. coli has fewer genes than we do, in part because it has a lot fewer things to do. It doesn’t have to build a brain or a stomach, for example. But E. coli is a versatile organism in its own right, with genes allowing it to feed on many different kinds of sugar, as well as to withstand stresses like starvation and heat.
In recent years, scientists have systematically shut down each of E. coli’s genes to see which it can live without. Most of its genes turn out to be dispensable. Only 302 have proved to be absolutely essential.
Swan Song for Cicadas, but Many Missed the Show
New York Times,
If you are still waiting for Swarmageddon to break out in your backyard, it is time to stop. The great cicada invasion is winding down for 2013, and it will not be back for another 17 years.
After dwelling in the ground since 1996, the insects began to emerge in May from North Carolina to the Hudson River Valley. In yards, forests and fields up and down the coast, they trilled by the billions, mated, laid their eggs in branches and left exoskeletons on bushes and walkways. Now their song is fading.
But while many people were kept up at night by the roar of this arthropod flash mob, others were left to wonder what all the fuss was about.
“People are disappointed, because the cicadas just aren’t everywhere,” said Chris M. Simon, a biologist at the University of Connecticut.
Studying Tumors Differently, in Hopes of Outsmarting Them
New York Times,
Bert Vogelstein, a cancer geneticist at Johns Hopkins University, says he is haunted by three pictures.
The first shows a man’s upper body studded with large melanomas. The second shows what happened when the man took a drug called vemurafenib. Vemurafenib belongs to a relatively new class of drugs, called targeted cancer therapy. Unlike earlier chemotherapy drugs, they attack specific molecules found only in cancer cells. In response to the vemurafenib, the tumors shrank in a matter of weeks, to the point that the man’s skin looked smooth and healthy.
The third picture is a case of déjà vu. After 16 weeks of treatment, the melanoma returned. “All the lesions reappeared — every single one,” said Dr. Vogelstein. “That struck me as nearly as amazing as the fact that they had disappeared.”
The Man Who Wasn't There (a review of "Permanent Present Tense," by Suzanne Corkin)
The Wall Street Journal,
In 1962, a young graduate student at McGill University named Suzanne Corkin met a 35-year-old man named Henry Molaison. Molaison and his mother had come to Montreal from their home in Connecticut so that Ms. Corkin and her colleagues could run a week-long series of psychological tests on him. Molaison was a sweet, cooperative subject. Ms. Corkin and Molaison talked a lot that week, mostly about Molaison's childhood. Beyond his early years, though, Molaison's recollections faded away.
The reason was both simple and profound. As a child, Molaison had suffered from severe epilepsy. In 1953, a surgeon took the drastic step of removing the part of his brain that was believed to be the cause. While the surgery helped reduce the seizures, it also had a devastating side effect: For the rest of his life, Molaison could hold most new information in his mind for only 30 seconds or so.
After that first meeting in 1962, Ms. Corkin continued to meet with Molaison—first at McGill and then at MIT, where she is a professor—until his death in 2008. In those 46 years, the two of them made scientific history, finding answers to some fundamental questions about how the brain works.
In Glittering Gems, Reading Earth’s Story
New York Times,
A jewelry store is an archive of the Earth. Every gem fixed to every ring or necklace was forged deep inside our planet, according to its own recipe of elements, temperature and pressure.
But it has taken a while for geologists to decode the cookbook for gems. Jade, for example, puzzled geologists for decades. “For a long time people looked at this crazy rock, and it didn’t make any sense,” said George Harlow, a geologist at the American Museum of Natural History. But thanks to the research of Dr. Harlow and other geologists, jade now has a back story: It formed in dying oceans.
The discovery of gems like rubies and jade thus signifies more than just a new supply of bling in jewelry stores. It tells geologists some important things about the planet.
Comfortable in the Cold: Life Below Freezing in an Antarctic Lake
A big part of Ricardo Cavicchioli’s job as a biologist is finding new species. And Cavicchioli, a professor at the University of New South Wales in Australia, has had particular good fortune at a place called Organic Lake, in the Vestfold Hills. “We discovered things we were never even looking for,” Cavicchioli says.
If you actually tagged along with Cavicchioli on one of his trips to Organic Lake, however, you might be deeply skeptical that this was a place where anything could live. The Vestfold Hills are not a rolling tropical landscape. They are located in East Antarctica. Organic Lake gets as cold as -20˚ C. The only reason it doesn’t turn to ice is thanks to its staggering concentration of salt.
Despite these unbearably cold conditions, Organic Lake is home to all manner of microbial life, from fungi to bacteria to viruses. It even has viruses that infect other viruses. Though life in Organic Lake is in many ways the same as elsewhere on Earth, it is also profoundly different in some ways. If Cavicchioli—a warm-blooded mammal—were to fall into the lake, he might die of hypothermia in a matter of minutes. But for the species in Organic Lake, frigid temperatures are comfortable. Warm them up to room temperature, and many would die in the scorching heat.
The Genius of Getting It Wrong (a review of "Brilliant Blunders," by Mario Livio)
New York Times,
In a letter to a fellow physicist in 1915, Albert Einstein described how a scientist gets things wrong:
“1. The devil leads him by the nose with a false hypothesis. (For this he deserves our pity.)
“2. His arguments are erroneous and sloppy. (For this he deserves a beating.)”
According to his own rules, Einstein should have been pitied and beaten alike. “Einstein himself certainly committed errors of both types,” the astrophysicist Mario Livio writes in his enlightening new book, “Brilliant Blunders.”
Apes (a review of "Primates," by Jim Ottaviani)
New York Times,
The stories of scientists create new scientists. Alexander von Humboldt — the most famous naturalist of the early 19th century — chronicled his epic expeditions, between 1799 and 1804, in his “Personal Narrative of a Journey to the Equinoctial Regions of the New Continent.” When a nature-loving student at Cambridge named Charles Darwin read the book, it changed his life. He read passages aloud to his professors and learned Spanish so that he could follow in Humboldt’s footsteps. Humboldt’s “Personal Narrative,” Darwin later wrote, “stirred up in me a burning zeal to add even the most humble contribution to the noble structure of Natural Science.” At age 22, he embarked on his own voyage around the world, out of which he would develop his theory of evolution.
For a long time, such life-changing stories were mostly the stories of men. Biology has changed since the days of Humboldt and Darwin in that respect: today, the majority of Ph.D.’s awarded in biology in the United States go to women. Women regularly head out to sea or into jungles to make new discoveries. They return with their own stories, which can inspire girls and boys alike. And no women have more gripping stories than Dian Fossey, Biruté Galdikas and Jane Goodall, who in their respective ways profoundly changed our understanding of the great apes.
The Sex Life of Birds, and Why It’s Important
New York Times,
For a strange sexual history, it’s hard to beat birds. In some lineages, bird penises have evolved to spectacular lengths. Ducks, for example, have corkscrew-shaped penises that can grow as long as their entire body. They use their baroque genitalia to deliver sperm to female reproductive tracts that are also corkscrew-shaped — but twisted in the opposite direction.
In other lineages of birds, however, the penis simply vanished. Of the 10,000 species of birds on Earth, 97 percent reproduce without using the organ. “That’s shocking, when you think about it,” says Martin Cohn, a biologist at the University of Florida.
Research on the sex life of birds has come under fire from critics who claim that it’s unimportant and a waste of federal money, particularly in times of lean spending. In April the criticism from Fox News and conservative pundits became so intense that Patricia Brennan, an expert on bird genitalia at the University of Massachusetts, wrote an essay for Slate defending the value of her research.
The mystery of the vanishing bird penis is actually an important question — not just for understanding the evolution of our feathered friends, but for clues it may offer to little-understood human genetic disorders.
Growing Left, Growing Right
New York Times,
One day in 1788, students at the Hunterian School of Medicine in London were opening a cadaver when they discovered something startling. The dead man’s anatomy was a mirror image of normal. His liver was on his left side instead of the right. His heart had beaten on his right side, not his left.
Situs inversus, a condition in which the major organs are on the reverse side of what is normal, as seen in an X-ray. Though it is the most dramatic of the left-right disorders, it is not harmful.
The students had never seen anything like it, and they rushed to find their teacher, the Scottish physician Matthew Baillie, who was just as stunned as they were. “It is so extraordinary as scarcely to have been seen by any of the most celebrated anatomists,” he later wrote.
His report was the first detailed description of the condition, which came to be known as situs inversus and is thought to occur in about 1 in 20,000 people. Baillie argued that if doctors could figure out how this strange condition came to be, they might come to understand how our bodies normally tell the right side from the left.
Mountain Populations Offer Clues to Human Evolution
New York Times,
In the hearts of evolutionary biologists, mountains occupy a special place. It’s not just their physical majesty: mountains also have an unmatched power to drive human evolution. Starting tens of thousands of years ago, people moved to high altitudes, and there they experienced natural selection that has reworked their biology.
“This is the most extreme example in humans that you can find,” said Rasmus Nielsen, an evolutionary biologist at the University of California at Berkeley.
Humans have adapted to mountainous environments just as Charles Darwin predicted. To discover how this occurred, scientists are now examining the DNA of people who scaled mountains in different parts of the world.
“There’s this beautiful experiment in natural selection going on,” says Anna Di Rienzo, a professor of human genetics at the University of Chicago. “You can really ask questions central to evolutionary biology.”
Chlorine, Swimming Pool Helper, Has a Checkered Past
New York Times,
With the unofficial start of summer on Monday, many people will get up close and personal with the element that carries 17 protons.
I speak, of course, of chlorine.
Over the next few months, chlorine will ensure that countless swimming pools don’t turn into microbe-choked petri dishes. That’s only one of many uses we’ve found for the element. We sprinkle it on our food as table salt — a k a sodium chloride. We pump water through pipes made of polyvinyl chloride. Perchlorate, a combination of chlorine and oxygen atoms, fuels rockets and ignites fireworks.
But in other incarnations, chlorine is a bane of our existence. In World War I, the German army unleashed clouds of chlorine gas and killed or injured thousands of enemy -soldiers. The Hudson River is burdened with cancer-causing dioxins, chlorine-bearing compounds dumped from factories along its banks.
Still, chlorine’s threats today are nothing compared with its menace on the early Earth.
The Girl Who Turned to Bone
When Jeannie Peeper was born in 1958, there was only one thing amiss: her big toes were short and crooked. Doctors fitted her with toe braces and sent her home. Two months later, a bulbous swelling appeared on the back of Peeper’s head. Her parents didn’t know why: she hadn’t hit her head on the side of her crib; she didn’t have an infected scratch. After a few days, the swelling vanished as quickly as it had arrived.
When Peeper’s mother noticed that the baby couldn’t open her mouth as wide as her sisters and brothers, she took her to the first of various doctors, seeking an explanation for her seemingly random assortment of symptoms. Peeper was 4 when the Mayo Clinic confirmed a diagnosis: she had a disorder known as fibrodysplasia ossificans progressiva (FOP).
The name meant nothing to Peeper’s parents—unsurprising, given that it is one of the rarest diseases in the world. One in 2 million people have it.
Peeper’s diagnosis meant that, over her lifetime, she would essentially develop a second skeleton. Within a few years, she would begin to grow new bones that would stretch across her body, some fusing to her original skeleton. Bone by bone, the disease would lock her into stillness. The Mayo doctors didn’t tell Peeper’s parents that. All they did say was that Peeper would not live long.
“Basically, my parents were told there was nothing that could be done,” Peeper told me in October. “They should just take me home and enjoy their time with me, because I would probably not live to be a teenager.” We were in Oviedo, Florida, in an office with a long, narrow sign that read The International Fibrodysplasia Ossificans Progressiva Association. Peeper founded the association 25 years ago, and remains its president. She was dressed in a narrow-waisted black skirt and a black-and-white striped blouse. A large ring in the shape of a black flower encircled one of her fingers. Her hair was peach-colored.Read the entire article at The Atlantic
From Fearsome Predator to Man’s Best Friend
New York Times,
Imagine a wolf catching a Frisbee a dozen times in a row, or leading police officers to a stash of cocaine, or just sleeping peacefully next to you on your couch. It’s a stretch, to say the least. Dogs may have evolved from wolves, but the minds of the two canines are profoundly different.
Dog brains, as I wrote last month in The New York Times, have become exquisitely tuned to our own. Scientists are now zeroing in on some of the genes that were crucial to the rewiring of dog brains.
Their results are fascinating, and not only because they can help us understand how dogs turned into man’s best friend. They may also teach us something about the evolution of our own brains: Some of the genes that evolved in dogs are the same ones that evolved in us.
To trace the change in dog brains, scientists have first had to work out how dog breeds are related to one another, and how they’re all related to wolves. Ya-Ping Zhang, a geneticist at the Chinese Academy of Sciences, has led an international network of scientists who have compared pieces of DNA from different canines. They’ve come to the conclusion that wolves started their transformation into dogs in East Asia.
17 Years to Hatch an Invasion
New York Times,
From North Carolina to Connecticut, billions of creatures with eyes the color of blood and bodies the color of coal are crawling out of the earth. Periodical cicadas are emerging en masse, clambering into trees and singing a shivering chorus that can be heard for miles.
What makes this emergence truly remarkable, however, is how long it’s been in the making. This month’s army of periodical cicadas was born in 1996. Their mothers laid their eggs in the branches of trees, where they developed for a few weeks before hatching and heading for the ground. “They just jumped out and rained down out of the trees,” said Chris Simon, a cicada biologist at the University of Connecticut.
Those Clinton-era larvae then squirmed into the dirt and spent the next 17 years sucking fluid from tree roots. Now, at last, they are ready to produce the next generation. The adult males are snapping rigid plates on their abdomens to produce their courtship song. The females are clicking their wings to signal approval. They will mate and then die shortly afterward. Their time in the sun is short, but their 17-year life span makes them the longest-lived insects known.
The Rise of the Tick
I’m tailing a Ford pickup truck along the eastern bank of the Connecticut River. When we reach a sign for Lord Creek Farm, the pickup turns off the road and I follow up a dusty driveway. We park in the shadow of an enormous red horse barn, next to paddocks full of jump gates, where riding lessons are under way.
I get out of my car and climb into the passenger side of the pickup. It’s driven by Scott Williams, a wildlife biologist from the Connecticut Agricultural Experiment Station in New Haven. Williams, 38, has the poise and scale of a bear standing upright. He wears a faded peach T-shirt that reads, DO I LOOK LIKE A @@& PEOPLE PERSON? Next to him is Megan Floyd, 24, and riding in the bed in back is Michael Short, 51, both research technicians.
Williams drives us across the farm, past freshly groomed meadows, and into the forest. The morning is magnificent, the sunlight slipping through gaps in the canopy. But we’re not here to admire the scenery. We’re here on a hunt, and our quarry is the black-legged tick. If you want to find black-legged ticks, you could not ask for a more spectacularly infested piece of land than Lord Creek Farm.
“You get absolutely astronomical abundance here—maybe 1,000 ticks an acre,” Williams declares. He sounds both appalled and delighted.
Lord Creek Farm holds another attraction for Williams: it is located in the town of Lyme. As in Lyme disease, caused by bacteria known as Borrelia burgdorferi. As in the town where Lyme disease was first discovered in the late 1970s, before it was recognized across the United States, from New York to California. Today, a quarter of a century after its discovery, Lyme, Connecticut, is still a great place to study Lyme disease. Seventy percent of the ticks on Lord Creek Farm are infected with Borrelia. I’m hoping one of them doesn’t find me today.
Williams, Floyd, and Short climb out of the truck and grab blue plastic crates from the back. I follow Williams into the woods, walking over jewelweed, wine raspberries, and Japanese barberry, which stabs our legs with hypodermic thorns.
A Virtual Pack, to Study Canine Minds
New York Times,
In 1995, Brian Hare began to wonder what his dog Oreo was thinking.
At the time, he was a sophomore at Emory University, where he was studying animal psychology with Michael Tomasello. Dr. Tomasello was comparing the social intelligence of humans and other animals.
Humans, it was known at the time, are exquisitely sensitive to signals from other humans. We use that information to solve problems that we might struggle to figure out on our own.
Bringing Them Back To Life
On July 30, 2003, a team of Spanish and French scientists reversed time. They brought an animal back from extinction, if only to watch it become extinct again. The animal they revived was a kind of wild goat known as a bucardo, or Pyrenean ibex. The bucardo (Capra pyrenaica pyrenaica) was a large, handsome creature, reaching up to 220 pounds and sporting long, gently curved horns. For thousands of years it lived high in the Pyrenees, the mountain range that divides France from Spain, where it clambered along cliffs, nibbling on leaves and stems and enduring harsh winters.
Then came the guns. Hunters drove down the bucardo population over several centuries. In 1989 Spanish scientists did a survey and concluded that there were only a dozen or so individuals left. Ten years later a single bucardo remained: a female nicknamed Celia. A team from the Ordesa and Monte Perdido National Park, led by wildlife veterinarian Alberto Fernández-Arias, caught the animal in a trap, clipped a radio collar around her neck, and released her back into the wild. Nine months later the radio collar let out a long, steady beep: the signal that Celia had died. They found her crushed beneath a fallen tree. With her death, the bucardo became officially extinct.
Interbreeding With Neanderthals
David Reich, a geneticist at the Harvard Medical School, has redrawn our species’ family tree. And today, in his office overlooking Avenue Louis Pasteur in Boston, he picks up a blue marker, walks up to a blank white wall, and shows the result to me. He starts with a pair of lines—one for humans and one for Neanderthals—that split off from a common ancestor no more than 700,000 years ago. The human branch divides into lineages of Africans, Asians, and Europeans, and then into twigs for smaller groups like the people of New Guinea or the residents of the remote Andaman Islands in the Indian Ocean. Reich also creates a branch off the Neanderthal line for the Denisovans, a paleolithic lineage geneticists discovered only a few years ago.
All well and good. This is the sort of picture you’d expect if we and our humanlike relatives diverged neatly through evolution. It looks a lot like the tree of life that Darwin included in The Origin of Species. But then Reich violates his tree.
Can Boosting Immunity Make You Smarter?
After spending a few days in bed with the flu, you may have felt a bit stupid. It is a common sensation, that your sickness is slowing down your brain. At first blush, though, it doesn’t make much sense. For one thing, flu viruses infect the lining of the airways, not the neurons in our brains. For another, the brain is walled off from the rest of the body by a series of microscopic defenses collectively known as the blood-brain barrier. It blocks most viruses and bacteria while allowing essential molecules like glucose to slip through. What ails the body, in other words, shouldn’t interfere with our thinking.
But over the past decade, Jonathan Kipnis, a neuroimmunologist in the University of Virginia School of Medicine’s department of neuroscience, has discovered a possible link, a modern twist on the age-old notion of the body-mind connection. His research suggests that the immune system engages the brain in an intricate dialogue that can influence our thought processes, coaxing our brains to work at their best.
Pigeons Get a New Look
New York Times,
In 1855, Charles Darwin took up a new hobby. He started raising pigeons.
In the garden of his country estate, Darwin built a dovecote. He filled it with birds he bought in London from pigeon breeders. He favored the fanciest breeds — pouters, carriers, barbs, fantails, short-faced tumblers and many more.
“The diversity of the breeds is something astonishing,” he wrote a few years later in “On the Origin of Species” — a work greatly informed by his experiments with the birds.
Raising Devils in Seclusion
New York Times,
In November, a team of biologists journeyed to Maria Island, three miles off the Australian island state of Tasmania, taking with them 15 plastic cylinders. They loaded the cylinders into S.U.V.’s, drove them to an abandoned farm and scattered them in the fields.
Before long 15 Tasmanian devils emerged from the containers, becoming the first ever to inhabit the island.
“All indications are that they’re doing very well,” Phil Wise, a government wildlife biologist who leads the project, said of the devils — fierce-looking, doglike marsupials that have become an endangered species on the much larger island for which they are named.
Black Carbon and Warming: It’s Worse than We Thought
Yale Environment 360,
It rises from the chimneys of mansions and from simple hut stoves. It rises from forest fires and the tail pipes of diesel-fueled trucks rolling down the highway, and from brick kilns and ocean liners and gas flares. Every day, from every occupied continent, a curtain of soot rises into the sky.
What soot does once it reaches the atmosphere has long been a hard question to answer. It’s not that scientists don’t know anything about the physics and chemistry of atmospheric soot. Just the opposite: it does so many things that it’s hard to know what they add up to.
To get a clear sense of soot — which is known to scientists as black carbon — an international team of 31 atmospheric scientists has worked for the past four years to analyze all the data they could. This week, they published a 232-page report in the Journal of Geophysical Research. “It’s an important assessment of where we stand now,” says Veerabhadran Ramanathan of the Scripps Institution for Oceanography, an expert on atmospheric chemistry who was not involved in the study.
February 2013 Link
On September 19, 2011, Evan Snitkin sat staring at a computer monitor, its screen cluttered with Perl script and row after row of 0s sprinkled with the occasional 1. To Snitkin, a bioinformatician at the National Institutes of Health, it read like a medical thriller. In this raw genetic-sequencing data, he could see the hidden history of a deadly outbreak that was raging just a few hundred yards from where he sat.
Snitkin was, in a sense, a medical historian: a genetic epidemiologist who traced the paths of disease outbreaks. But now, for the first time in history, he was trying to use his genetic toolkit to reroute an outbreak while it was in progress—and before it turned disastrous. A few weeks earlier, a handful of patients at the NIH Clinical Center, a 243-bed research hospital on the NIH campus in Bethesda, Maryland, had been hit by a vicious strain of bacteria known as KPC. Shorthand for carbapenem-resistant Klebsiella pneumoniae,
KPC can hitch a ride on healthy people, setting up residence on their skin. From them it can spread to people with weak defenses—like hospital patients—and bloom into an overwhelming infection that spreads via the bloodstream into the whole body, swiftly shutting down one organ after another. In the past decade, KPC has evolved the ability to withstand every known antibiotic. As a result, roughly half of people who develop an active infection of KPC will die.Read the entire article at Wired