Eric D. Green, James D. Watson& Francis S. Collins write: Twenty-five years ago, the newly created US National Center for Human Genome Research (now the National Human Genome Research Institute; NHGRI), which the three of us have each directed, joined forces with US and international partners to launch the Human Genome Project (HGP). What happened next represents one of the most historically significant scientific endeavours: a 13-year quest to sequence all three billion base pairs of the human genome.
Even just a few years ago, discussions surrounding the HGP focused mainly on what insights the project had brought or would bring to our understanding of human disease. Only now is it clear that, as well as dramatically accelerating biomedical research, the HGP initiated a new way of doing science.
As biology’s first large-scale project, the HGP paved the way for numerous consortium-based research ventures. The NHGRI alone has been involved in launching more than 25 such projects since 2000. These have presented new challenges to biomedical research — demanding, for instance, that diverse groups from different countries and disciplines come together to share and analyse vast data sets. [Continue reading…]
The Independent reports: The most comprehensive study of the human genome has discovered that a sizeable minority of people are walking around with some of their genes missing without any apparent ill-effects, scientists have found.
A project to sequence and analyse the entire genetic code of more than 2,500 people drawn from 26 different ethnic populations from around the world has revealed that some genes do not seem to be as essential for health and life as previously believed.
The finding is just one to have emerged from the 1,000 Genomes Project set up in 2008 to study the genetic variation in at least this number of people in order to understand the variety of DNA types within the human population, the researchers said. [Continue reading…]
From the earliest of times, philosophers and scientists have tried to understand the relationship between animate and inanimate matter. But the origin of life remains one of the major scientific riddles to be solved.
The building blocks of life as we know it essentially consist of four groups of chemicals: proteins, nucleic acids, lipids (fats) and carbohydrates. There was much excitement about the possibility of finding amino acids (the ingredients for proteins) on comets or distant planets because some scientists believe that life on Earth, or at least its building blocks, may have originally come from outer space and been deposited by meteorites.
But there are now extensive examples of how natural processes on Earth can convert simple molecules into these building blocks. Scientists have demonstrated in the lab how to make amino acids, simple sugars, lipids and even nucleotides – the basic units of DNA – from very simple chemicals, under conditions that could have existed on early earth. What still eludes them is the point in the process when a chemical stew becomes an organism. How did the first lifeforms become alive?
Scientists recently suggested that the Earth’s sixth mass extinction has begun. As terrifying as that sounds, surely humans are too smart and too important to get wiped out? Palaeontologists have long tried to shed light on this question by looking for general rules that might predict the survival of a species.
While this is not exactly a straightforward exercise, research so far indicates that the odds are not in our favour.
Paleogenetics is helping to solve the great mystery of prehistory: How did humans spread out over the earth?
Jacob Mikanowski writes: Most of human history is prehistory. Of the 200,000 or more years that humans have spent on Earth, only a tiny fraction have been recorded in writing. Even in our own little sliver of geologic time, the 12,000 years of the Holocene, whose warm weather and relatively stable climate incubated the birth of agriculture, cities, states, and most of the other hallmarks of civilisation, writing has been more the exception than the rule.
Professional historians can’t help but pity their colleagues on the prehistoric side of the fence. Historians are accustomed to drawing on vast archives, but archaeologists must assemble and interpret stories from scant material remains. In the annals of prehistory, cultures are designated according to modes of burial such as ‘Single Grave’, or after styles of arrowhead, such as ‘Western Stemmed Point’. Whole peoples are reduced to styles of pottery, such as Pitted Ware, Corded Ware or Funnel Beaker, all of them spread across the map in confusing, amoeba-like blobs.
In recent years, archaeologists have become reluctant to infer too much from assemblages of ceramics, weapons and grave goods. For at least a generation, they have been drilled on the mantra that ‘pots are not people’. Material culture is not a proxy for identity. Artefacts recovered from a dig can provide a wealth of information about a people’s mode of subsistence, funeral rites and trade contacts, but they are not a reliable guide to their language or ethnicity – or their patterns of migration.
Before the Second World War, prehistory was seen as a series of invasions, with proto-Celts and Indo-Aryans swooping down on unsuspecting swaths of Europe and Asia like so many Vikings, while megalith builders wandered between continents in indecisive meanders. After the Second World War, this view was replaced by the processual school, which attributed cultural changes to internal adaptations. Ideas and technologies might travel, but people by and large stayed put. Today, however, migration is making a comeback.
Much of this shift has to do with the introduction of powerful new techniques for studying ancient DNA. The past five years have seen a revolution in the availability and scope of genetic testing that can be performed on prehistoric human and animal remains. Ancient DNA is tricky to work with. Usually it’s degraded, chemically altered and cut into millions of short fragments. But recent advances in sequencing technology have made it possible to sequence whole genomes from samples reaching back thousands, and tens of thousands, of years. Whole-genome sequencing yields orders of magnitude more data than organelle-based testing, and allows geneticists to make detailed comparisons between individuals and populations. Those comparisons are now illuminating new branches of the human family tree. [Continue reading…]
As a wildlife veterinarian, I often get asked about bats. I like bats, and I am always eager to talk about how interesting they are. Unfortunately the question is often not about biology but instead “what should I do about the ones in my roof?”.
With some unique talents and remarkable sex lives, bats are actually one of the most interesting, diverse and misunderstood groups of animals. Contrary to popular belief, they are beautiful creatures. Not necessarily in the cuddly, human-like sense – although some fruit bats with doey brown eyes and button noses could be considered so – but they are beautifully designed.
This couldn’t be illustrated better than by the discovery of the oldest known complete bat fossil, more than 53 million-years-old yet with a similar wing design to those flying around today. To put it in perspective, 50m years ago our ancestors were still swinging from the trees and would certainly not be recognised as human. But even then bats already had the combination of thin, long forearms and fingers covered by an extremely thin, strong membrane, which allowed them to master the art of powered, agile flight.
Duncan PJ, CC BY-SA
Soon afterwards, fossils record another game-changing adaptation in the evolution of most bats, and that is the ability to accurately locate prey using sound (what we call echolocation). These two adaptations early in their history gave bats an evolutionary edge compared to some other mammals, and allowed them to diversify into almost all habitats, on every continent except Antarctica.
Carl Zimmer writes: Recently a team of pathologists at Leiden University Medical Center in the Netherlands carried out an experiment that might seem doomed to failure.
They collected tissue from 26 women who had died during or just after pregnancy. All of them had been carrying sons. The pathologists then stained the samples to check for Y chromosomes.
Essentially, the scientists were looking for male cells in female bodies. And their search was stunningly successful.
As reported last month in the journal Molecular Human Reproduction, the researchers found cells with Y-chromosomes in every tissue sample they examined. These male cells were certainly uncommon — at their most abundant, they only made up about 1 in every 1,000 cells. But male cells were present in every organ that the scientists studied: brains, hearts, kidneys and others.
In the 1990s, scientists found the first clues that cells from both sons and daughters can escape from the uterus and spread through a mother’s body. They dubbed the phenomenon fetal microchimerism, after the chimera, a monster from Greek mythology that was part lion, goat and dragon.
But fetal cells don’t just drift passively. Studies of female mice show that fetal cells that end up in their hearts develop into cardiac tissue. “They’re becoming beating heart cells,” said Dr. J. Lee Nelson, an expert on microchimerism at the Fred Hutchinson Cancer Research Center in Seattle.
The new study suggests that women almost always acquire fetal cells each time they get pregnant. They have been detected as early as seven weeks into a pregnancy. In later years, the cells may disappear from their bodies, but sometimes the cells settle in for a lifetime. [Continue reading…]
Roc Morin writes: One of the first words that Koko used to describe herself was Queen. The gorilla was only a few years old when she first made the gesture — sweeping a paw diagonally across her chest as if tracing a royal sash.
“It was a sign we almost never used!” Koko’s head-caretaker Francine Patterson laughed. “Koko understands that she’s special because of all the attention she’s had from professors, and caregivers, and the media.”
The cause of the primate’s celebrity is her extraordinary aptitude for language. Over the past 43 years, since Patterson began teaching Koko at the age of 1, the gorilla has learned more than 1,000 words of modified American Sign Language—a vocabulary comparable to that of a 3-year-old human child. While there have been many attempts to teach human languages to animals, none have been more successful than Patterson’s achievement with Koko.
If Koko is a queen, then her kingdom is a sprawling research facility in the mountains outside Santa Cruz, California. It was there, under a canopy of stately redwoods, that I met research-assistant Lisa Holliday.
“You came on a good day,” Holliday smiled. “Koko’s in a good mood. She was playing the spoon game all morning! That’s when she takes the spoon and runs off with it so you can’t give her another bite. She’s an active girl. She’s always got her dolls, and in the afternoon, her kittens — or as we call them, her kids.”
It was a winding stroll up a sun-spangled trail toward the cabin where Patterson was busy preparing a lunch of diced apples and nuts for Koko. The gorilla’s two kitten playmates romped in a crate by her feet. We would go deliver the meal together shortly, but first I had some questions for the 68-year-old researcher. I wanted to understand more about her famous charge and the rest of our closest living relatives. [Continue reading…]
New Scientist: In an early Star Trek episode, the Enterprise is boarded by human-like aliens, with lives lived so fast that the crew can’t see them. For their part, the aliens see Captain Kirk and his crew as near-static beings whose every action seems to take an age to complete.
Now think about how we view plants. With their slow-lane responsiveness, they could be ticking the boxes for behavioural brightness but they seem too slow, and too different, to register as intelligent.
This is the core of Brilliant Green by Stefano Mancuso and Alessandra Viola and Plant Sensing and Communication by Richard Karban. Plants are smart, they say, but to notice we have to overcome our ingrained cultural biases. As Karban writes: “Ask a child about the differences between plants and animals… They’ll say, ‘Plants can’t move’ or ‘Plants don’t do anything’.”
And, as both books point out, it is but a short intellectual step to allying apparent immobility with a form of mechanistic half-life of simple growth and response – a flatlined existence devoid of subtlety, strategy and learning.
Islam doesn’t consider plants alive at all, Mancuso and Viola remind us. It has a rich tradition of plant and flower illustration, alongside a ban on the physical depiction of living things. And until recently, Western medicine used “vegetative state” to describe people considered to have lost the ability to think or be aware.
Clearly, we will never play chess with a rose, nor ask the orchid on our windowsill for advice. But that is the point: humans are guilty of serious parochialism, of defining intelligence in terms of a nervous system and muscle-based speed that enables things to be done fast, say all three authors.
Plants and animals face similar challenges: to find resources and mates, and avoid predators, pathogens and abiotic stresses. In response, says Karban, “plants communicate, signaling within [themselves], eavesdropping on neighboring individuals, and exchanging information with other organisms”. They have adaptive responses that, if they happened at speeds humans understand, would reveal them to be “brilliant at solving problems related to their existence”. [Continue reading…]
Emily Singer writes: Genes, like people, have families — lineages that stretch back through time, all the way to a founding member. That ancestor multiplied and spread, morphing a bit with each new iteration.
For most of the last 40 years, scientists thought that this was the primary way new genes were born — they simply arose from copies of existing genes. The old version went on doing its job, and the new copy became free to evolve novel functions.
Certain genes, however, seem to defy that origin story. They have no known relatives, and they bear no resemblance to any other gene. They’re the molecular equivalent of a mysterious beast discovered in the depths of a remote rainforest, a biological enigma seemingly unrelated to anything else on earth.
The mystery of where these orphan genes came from has puzzled scientists for decades. But in the past few years, a once-heretical explanation has quickly gained momentum — that many of these orphans arose out of so-called junk DNA, or non-coding DNA, the mysterious stretches of DNA between genes. “Genetic function somehow springs into existence,” said David Begun, a biologist at the University of California, Davis. [Continue reading…]
Nature reports: Researchers want to understand how the cephalopods, a class of free-floating molluscs, produced a creature that is clever enough to navigate highly complex mazes and open jars filled with tasty crabs.
Surprisingly, the octopus genome turned out to be almost as large as a human’s and to contain a greater number of protein-coding genes — some 33,000, compared with fewer than 25,000 in Homo sapiens.
This excess results mostly from the expansion of a few specific gene families, [neurobiologist Clifton] Ragsdale says. One of the most remarkable gene groups is the protocadherins, which regulate the development of neurons and the short-range interactions between them. The octopus has 168 of these genes — more than twice as many as mammals. This resonates with the creature’s unusually large brain and the organ’s even-stranger anatomy. Of the octopus’s half a billion neurons — six times the number in a mouse — two-thirds spill out from its head through its arms, without the involvement of long-range fibres such as those in vertebrate spinal cords. The independent computing power of the arms, which can execute cognitive tasks even when dismembered, have made octopuses an object of study for neurobiologists such as Hochner and for roboticists who are collaborating on the development of soft, flexible robots.
A gene family that is involved in development, the zinc-finger transcription factors, is also highly expanded in octopuses. At around 1,800 genes, it is the second-largest gene family to be discovered in an animal, after the elephant’s 2,000 olfactory-receptor genes. [Continue reading…]
When Morgan Spurlock famously spent a month eating large portions of McDonalds for the purposes of his documentary Supersize Me, he gained weight, damaged his liver and claimed to have suffered addictive withdrawal symptoms. This was popularly attributed to the toxic mix of carbs and fat plus the added chemicals and preservatives in junk foods. But could there be another explanation?
We may have forgotten others who really don’t enjoy fast food. These are the poor creatures that live in the dark in our guts. These are the hundred trillion microbes that outnumber our total human cells ten to one and digest our food, provide many vitamins and nutrients and keep us healthy. Until recently we have viewed them as harmful – but those (like salmonella) are a tiny minority and most are essential for us.
Studies in lab mice have shown that when fed an intensive high fat diet their microbes change dramatically and for the worse. This can be partly prevented by using probiotics; but there are obvious differences between us and lab mice, as well as our natural microbes.
Barbara J. King writes: The idea that our oceans teem with cultural animals — and have for millions of years — is the central conclusion of a new book by two whale scientists. And it’s a convincing one.
Whales and dolphins, as they forage for food and interact with each other in their social units, may learn specific ways of doing things from their mothers or their pod-mates.
Certain killer whales (orcas), for example, learn to hunt communally with such precision that they cause waves to wash seals — of only certain species, because other seals are rejected as prey — off their ice floes and into the sea. And the complex patterned songs of humpback whales evolve so quickly over time and space that only learning can explain it.
“The song being sung at any location can change dramatically into an entirely new form, with new units, new phrases, and new themes within less than a year,” write authors Hal Whitehead and Luke Rendell in their book The Cultural Lives of Whales and Dolphins. “A revolution, rather than an evolution.”
The two scientists, who have been studying sperm whales for a collective half century, offer this working definition of culture: Behavior that is shared by some identifiable group such as a family, community or population, and that is acquired by learning from others.
In order for culture to be ruled in as the primary explanation for some behavior, then, genetics and features of the habitat in which the marine mammals live should be ruled out. [Continue reading…]
Pacific Standard reports: On April 19, 1979, the United States Environmental Protection Agency announced a five-year plan to phase out nearly all uses of polychlorinated biphenyls, or PCBs. The synthetic chemicals had been used in the manufacture of electronic equipment, motor oil, adhesive tapes, paint, and many other products.
“Although PCBs are no longer being produced in this country, we will now bring under control the vast majority of PCBs still in use,” EPA administrator Douglas M. Costle boasted at the time. “This will help prevent further contamination of our air, water, and food supplies from a toxic and very persistent manmade chemical.”
It turns out Costle celebrated too early — way, way too early. More than 36 years after being banned, PCBs continue to pollute ecosystems, according to a study released in the journal PLoS One. They pose a particular challenge to the survival of marine mammals like porpoises, whales, and dolphins. [Continue reading…]
University of Georgia: Unless humans slow the destruction of Earth’s declining supply of plant life, civilization like it is now may become completely unsustainable, according to a paper published recently by University of Georgia researchers in the Proceedings of the National Academy of Sciences.
“You can think of the Earth like a battery that has been charged very slowly over billions of years,” said the study’s lead author, John Schramski, an associate professor in UGA’s College of Engineering. “The sun’s energy is stored in plants and fossil fuels, but humans are draining energy much faster than it can be replenished.”
Earth was once a barren landscape devoid of life, he explained, and it was only after billions of years that simple organisms evolved the ability to transform the sun’s light into energy. This eventually led to an explosion of plant and animal life that bathed the planet with lush forests and extraordinarily diverse ecosystems.
The study’s calculations are grounded in the fundamental principles of thermodynamics, a branch of physics concerned with the relationship between heat and mechanical energy. Chemical energy is stored in plants, or biomass, which is used for food and fuel, but which is also destroyed to make room for agriculture and expanding cities.
Scientists estimate that the Earth contained approximately 1,000 billion tons of carbon in living biomass 2,000 years ago. Since that time, humans have reduced that amount by almost half. It is estimated that just over 10 percent of that biomass was destroyed in just the last century.
“If we don’t reverse this trend, we’ll eventually reach a point where the biomass battery discharges to a level at which Earth can no longer sustain us,” Schramski said.
Working with James H. Brown from the University of New Mexico, Schramski and UGA’s David Gattie, an associate professor in the College of Engineering, show that the vast majority of losses come from deforestation, hastened by the advent of large-scale mechanized farming and the need to feed a rapidly growing population. As more biomass is destroyed, the planet has less stored energy, which it needs to maintain Earth’s complex food webs and biogeochemical balances.
“As the planet becomes less hospitable and more people depend on fewer available energy options, their standard of living and very survival will become increasingly vulnerable to fluctuations, such as droughts, disease epidemics and social unrest,” Schramski said.
If human beings do not go extinct, and biomass drops below sustainable thresholds, the population will decline drastically, and people will be forced to return to life as hunter-gatherers or simple horticulturalists, according to the paper.
“I’m not an ardent environmentalist; my training and my scientific work are rooted in thermodynamics,” Schramski said. “These laws are absolute and incontrovertible; we have a limited amount of biomass energy available on the planet, and once it’s exhausted, there is absolutely nothing to replace it.”
Schramski and his collaborators are hopeful that recognition of the importance of biomass, elimination of its destruction and increased reliance on renewable energy will slow the steady march toward an uncertain future, but the measures required to stop that progression may have to be drastic.
“I call myself a realistic optimist,” Schramski said. “I’ve gone through these numbers countless times looking for some kind of mitigating factor that suggests we’re wrong, but I haven’t found it.”
The study, on “Human Domination of the Biosphere: Rapid Discharge of the Earth-Space Battery Foretells the Future of Humankind,” is available online here.
Mark Spitznagel and Nassim Nicholas Taleb, who both anticipated the failure of the financial system in 2007, see eerie parallels in the reasoning being used by those who believed in stability then and those who insist now that there are no significant risks involved in the promotion of genetically modified organisms (GMOs).
Spitznagel and Taleb write: First, there has been a tendency to label anyone who dislikes G.M.O.s as anti-science — and put them in the anti-antibiotics, antivaccine, even Luddite category. There is, of course, nothing scientific about the comparison. Nor is the scholastic invocation of a “consensus” a valid scientific argument.
Interestingly, there are similarities between arguments that are pro-G.M.O. and snake oil, the latter having relied on a cosmetic definition of science. The charge of “therapeutic nihilism” was leveled at people who contested snake oil medicine at the turn of the 20th century. (At that time, anything with the appearance of sophistication was considered “progress.”)
Second, we are told that a modified tomato is not different from a naturally occurring tomato. That is wrong: The statistical mechanism by which a tomato was built by nature is bottom-up, by tinkering in small steps (as with the restaurant business, distinct from contagion-prone banks). In nature, errors stay confined and, critically, isolated.
Third, the technological salvation argument we faced in finance is also present with G.M.O.s, which are intended to “save children by providing them with vitamin-enriched rice.” The argument’s flaw is obvious: In a complex system, we do not know the causal chain, and it is better to solve a problem by the simplest method, and one that is unlikely to cause a bigger problem.
Fourth, by leading to monoculture — which is the same in finance, where all risks became systemic — G.M.O.s threaten more than they can potentially help. Ireland’s population was decimated by the effect of monoculture during the potato famine. Just consider that the same can happen at a planetary scale.
Fifth, and what is most worrisome, is that the risk of G.M.O.s are more severe than those of finance. They can lead to complex chains of unpredictable changes in the ecosystem, while the methods of risk management with G.M.O.s — unlike finance, where some effort was made — are not even primitive.
The G.M.O. experiment, carried out in real time and with our entire food and ecological system as its laboratory, is perhaps the greatest case of human hubris ever. It creates yet another systemic, “too big too fail” enterprise — but one for which no bailouts will be possible when it fails. [Continue reading…]
Sarah Scoles writes: In the late 1670s, the Dutch scientist Antonie van Leeuwenhoek looked through a microscope at a drop of water and found a whole world. It was tiny; it was squirmy; it was full of weird body types; and it lived, invisibly, all around us. Humans were supposed to be the centre and purpose of the world, and these microscale ‘animalcules’ seemed to have no effect – visible or otherwise – on our existence, so why were they here? Now, we know that those animalcules are microbes and they actually rule our world. They make us sick, keep us healthy, decompose our waste, feed the bottom of our food chain, and make our oxygen. Human ignorance of them had no bearing on their significance, just as gravity was important before an apple dropped on Isaac Newton’s head.
We could be poised on another such philosophical precipice, about to discover a second important world hiding amid our own: alien life on our own planet. Today, scientists seek extraterrestrial microbes in geysers of chilled water shooting from Enceladus and in the ocean sloshing beneath the ice crust of Europa. They search for clues that beings once skittered around the formerly wet rocks of Mars. Telescopes peer into the atmospheres of distant exoplanets, hunting for signs of life. But perhaps these efforts are too far afield. If multiple lines of life bubbled up on Earth and evolved separately from our ancient ancestors, we could discover alien biology without leaving this planet.
The modern-day descendants of these ‘aliens’ might still be here, squirming around with van Leeuwenhoek’s microbes. Scientists call these hypothetical hangers-on the ‘shadow biosphere’. If a shadow biosphere were ever found, it would provide evidence that life isn’t a once-in-a-universe statistical accident. If biology can happen twice on one planet, it must have happened countless times on countless other planets. But most of our scientific methods are ill-equipped to discover a shadow biosphere. And that’s a problem, says Carol Cleland, the originator of the term and its biggest proponent. [Continue reading…]
Tim Flannery writes: In 1609 Galileo Galilei turned his gaze, magnified twentyfold by lenses of Dutch design, toward the heavens, touching off a revolution in human thought. A decade later those same lenses delivered the possibility of a second revolution, when Galileo discovered that by inverting their order he could magnify the very small. For the first time in human history, it lay in our power to see the building blocks of bodies, the causes of diseases, and the mechanism of reproduction. Yet according to Paul Falkowski’s Life’s Engines:
Galileo did not seem to have much interest in what he saw with his inverted telescope. He appears to have made little attempt to understand, let alone interpret, the smallest objects he could observe.
Bewitched by the moons of Saturn and their challenge to the heliocentric model of the universe, Galileo ignored the possibility that the magnified fleas he drew might have anything to do with the plague then ravaging Italy. And so for three centuries more, one of the cruellest of human afflictions would rage on, misunderstood and thus unpreventable, taking the lives of countless millions.
Perhaps it’s fundamentally human both to be awed by the things we look up to and to pass over those we look down on. If so, it’s a tendency that has repeatedly frustrated human progress. Half a century after Galileo looked into his “inverted telescope,” the pioneers of microscopy Antonie van Leeuwenhoek and Robert Hooke revealed that a Lilliputian universe existed all around and even inside us. But neither of them had students, and their researches ended in another false dawn for microscopy. It was not until the middle of the nineteenth century, when German manufacturers began producing superior instruments, that the discovery of the very small began to alter science in fundamental ways.
Today, driven by ongoing technological innovations, the exploration of the “nanoverse,” as the realm of the minuscule is often termed, continues to gather pace. One of the field’s greatest pioneers is Paul Falkowski, a biological oceanographer who has spent much of his scientific career working at the intersection of physics, chemistry, and biology. His book Life’s Engines: How Microbes Made Earth Habitable focuses on one of the most astonishing discoveries of the twentieth century — that our cells are comprised of a series of highly sophisticated “little engines” or nanomachines that carry out life’s vital functions. It is a work full of surprises, arguing for example that all of life’s most important innovations were in existence by around 3.5 billion years ago—less than a billion years after Earth formed, and a period at which our planet was largely hostile to living things. How such mind-bending complexity could have evolved at such an early stage, and in such a hostile environment, has forced a fundamental reconsideration of the origins of life itself. [Continue reading…]