Each of us is, genetically, more microbial than human

The New York Times reports: Since 2007, when scientists announced plans for a Human Microbiome Project to catalog the micro-organisms living in our body, the profound appreciation for the influence of such organisms has grown rapidly with each passing year. Bacteria in the gut produce vitamins and break down our food; their presence or absence has been linked to obesity, inflammatory bowel disease and the toxic side effects of prescription drugs. Biologists now believe that much of what makes us human depends on microbial activity. The two million unique bacterial genes found in each human microbiome can make the 23,000 genes in our cells seem paltry, almost negligible, by comparison. “It has enormous implications for the sense of self,” Tom Insel, the director of the National Institute of Mental Health, told me. “We are, at least from the standpoint of DNA, more microbial than human. That’s a phenomenal insight and one that we have to take seriously when we think about human development.”

Given the extent to which bacteria are now understood to influence human physiology, it is hardly surprising that scientists have turned their attention to how bacteria might affect the brain. Micro-organisms in our gut secrete a profound number of chemicals, and researchers like [Mark] Lyte have found that among those chemicals are the same substances used by our neurons to communicate and regulate mood, like dopamine, serotonin and gamma-aminobutyric acid (GABA). [Continue reading…]

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The Earth stands on the brink of its sixth mass extinction and the fault is ours

Jan Zalasiewizc writes: Life on Earth is in trouble. That much we know. But how bad have things become – and how fast are events moving? How soon, indeed, before the Earth’s biological treasures are trashed, in what will be the sixth great mass extinction event? This is what Gerardo Caballos of the National Autonomous University of Mexico and his colleagues have assessed, in a paper that came out on Friday.

These are extraordinarily difficult questions. There are many millions of species, many elusive and rare, and inhabiting remote and dangerous places. There are too few skilled biologists in the field to keep track of them all. Demonstrating beyond reasonable doubt that any single species is extinct is arduous and painstaking (think how long it took to show – to most people, at least – that Loch Ness probably does not harbour a large monster).

And it’s not just a case of making a head-count of modern extinctions. This needs to be compared with a long-term “baseline” rate of extinctions in our planet’s long geological history. This can only be extracted via the equally painstaking and difficult work of excavating and identifying millions of fossils from the almost endless rock strata. Not surprisingly, different studies made so far on different fossils have yielded different baseline rates.

Caballos and colleagues have thought through these difficulties, and come up with probably the most robust estimate yet of how severe the modern crisis is.

They have been deliberately conservative – they’re well aware of the dangers of crying wolf on a topic of such importance, and where passions run so high. For a start, they limit themselves to the best-studied group of organisms, the vertebrates. Then, they take a high estimate of background extinctions to compare with, to make the modern figures as undramatic as possible. And then, they either consider only those animals known to be extinct (the “highly conservative” scenario), or they add in those extinctions in the wild that are likely to have happened, but are not yet verified.

Even with this caution, the figures are still shocking. [Continue reading…]

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Everything we thought we knew about the genome is turning out to be wrong

Claire Ainsworth writes: Ask me what a genome is, and I, like many science writers, might mutter about it being the genetic blueprint of a living creature. But then I’ll confess that “blueprint” is a lousy metaphor since it implies that the genome is two-dimensional, prescriptive and unresponsive.

Now two new books about the genome show the limitation of that metaphor for something so intricate, complex, multilayered and dynamic. Both underscore the risks of taking metaphors too literally, not just in undermining popular understanding of science, but also in trammelling scientific enquiry. They are for anyone interested in how new discoveries and controversies will transform our understanding of biology and of ourselves.

John Parrington is an associate professor in molecular and cellular pharmacology at the University of Oxford. In The Deeper Genome, he provides an elegant, accessible account of the profound and unexpected complexities of the human genome, and shows how many ideas developed in the 20th century are being overturned.

Take DNA. It’s no simple linear code, but an intricately wound, 3D structure that coils and uncoils as its genes are read and spliced in myriad ways. Forget genes as discrete, protein-coding “beads on a string”: only a tiny fraction of the genome codes for proteins, and anyway, no one knows exactly what a gene is any more.[Continue reading…]

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DNA deciphers roots of modern Europeans

Carl Zimmer writes: For centuries, archaeologists have reconstructed the early history of Europe by digging up ancient settlements and examining the items that their inhabitants left behind. More recently, researchers have been scrutinizing something even more revealing than pots, chariots and swords: DNA.

On Wednesday in the journal Nature, two teams of scientists — one based at the University of Copenhagen and one based at Harvard University — presented the largest studies to date of ancient European DNA, extracted from 170 skeletons found in countries from Spain to Russia. Both studies indicate that today’s Europeans descend from three groups who moved into Europe at different stages of history.

The first were hunter-gatherers who arrived some 45,000 years ago in Europe. Then came farmers who arrived from the Near East about 8,000 years ago.

Finally, a group of nomadic sheepherders from western Russia called the Yamnaya arrived about 4,500 years ago. The authors of the new studies also suggest that the Yamnaya language may have given rise to many of the languages spoken in Europe today. [Continue reading…]

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Direct connection discovered between the brain and the immune system

Science Daily reports: In a stunning discovery that overturns decades of textbook teaching, researchers at the University of Virginia School of Medicine have determined that the brain is directly connected to the immune system by vessels previously thought not to exist. That such vessels could have escaped detection when the lymphatic system has been so thoroughly mapped throughout the body is surprising on its own, but the true significance of the discovery lies in the effects it could have on the study and treatment of neurological diseases ranging from autism to Alzheimer’s disease to multiple sclerosis.

“Instead of asking, ‘How do we study the immune response of the brain?’ ‘Why do multiple sclerosis patients have the immune attacks?’ now we can approach this mechanistically. Because the brain is like every other tissue connected to the peripheral immune system through meningeal lymphatic vessels,” said Jonathan Kipnis, PhD, professor in the UVA Department of Neuroscience and director of UVA’s Center for Brain Immunology and Glia (BIG). “It changes entirely the way we perceive the neuro-immune interaction. We always perceived it before as something esoteric that can’t be studied. But now we can ask mechanistic questions.”

“We believe that for every neurological disease that has an immune component to it, these vessels may play a major role,” Kipnis said. “Hard to imagine that these vessels would not be involved in a [neurological] disease with an immune component.”

Kevin Lee, PhD, chairman of the UVA Department of Neuroscience, described his reaction to the discovery by Kipnis’ lab: “The first time these guys showed me the basic result, I just said one sentence: ‘They’ll have to change the textbooks.’ There has never been a lymphatic system for the central nervous system, and it was very clear from that first singular observation — and they’ve done many studies since then to bolster the finding — that it will fundamentally change the way people look at the central nervous system’s relationship with the immune system.” [Continue reading…]

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Warming waters may lead to unprecedented biodiversity shifts across world’s oceans

Climate Central reports: The world’s oceans could face a massive reshuffling by the end of the century – the likes of which hasn’t been seen in as many as 3 million years – due to warming waters.

Changes are already afoot in the oceans. Roughly 93 percent of the heat trapped by human greenhouse gas emissions is ending up in the world’s seas and already contributing to changes from slowing plankton growth to recent incursions of tuna near Alaska, thousands of miles from their normal range.

If greenhouse gas emissions continue to build, that heat could create wholesale changes for the vast majority of the world’s oceans (which, of course, make up the vast majority of the world).

The findings come from a new study published in Nature Climate Change, which looks at future climate projections and the distant past when 60-foot sharks prowled the oceans, sea levels were 100 feet higher and the globe was about 11°F hotter. Oh, and humans weren’t around, either. [Continue reading…]

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From chimps to bees and bacteria, how animals hold elections

By Robert John Young, University of Salford

Lots of people find elections dull, but there’s nothing boring about the political manoeuvres that take place in the animal kingdom. In the natural world, jockeying for advantage, whether this is conscious or merely mechanical, can be a matter of life or death.

Chimpanzees, our closest relatives, are highly political. They’re smart enough to realise that in the natural world brute strength will only get you so far – getting to the top of a social group and remaining there requires political guile.

It’s all about making friends and influencing others. Chimps make friends by grooming each other and forming alliances; this behaviour is especially prominent in males wishing to be group leader. In times of dispute they call upon their friends for assistance or when they sense a coup may be successful. And the ruling group either reaffirms its position or a new group grabs control – but having the weight of numbers is normally critical to success.

You’ve got my vote.
IFAW, CC BY-NC

Back in the 1980s, the leading Dutch primatologist Frans de Waal spent six years researching the world’s largest captive colony for his classic book Chimpanzee Politics. He soon realised that, in addition to forming cliques, chimp politics still involves some degree of aggression.

Humans in modern societies have largely replaced antagonistic takeovers with voting. Chimps do not, however, live in a democratic society. For them, the social structure of the ruling party is usually one based on male hierarchy, where dominant individuals have best access to the resources available – usually food and females.

[Read more…]

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Resurrecting ancient proteins to illuminate the origins of life

Emily Singer writes: About 4 billion years ago, molecules began to make copies of themselves, an event that marked the beginning of life on Earth. A few hundred million years later, primitive organisms began to split into the different branches that make up the tree of life. In between those two seminal events, some of the greatest innovations in existence emerged: the cell, the genetic code and an energy system to fuel it all. All three of these are essential to life as we know it, yet scientists know disappointingly little about how any of these remarkable biological innovations came about.

“It’s very hard to infer even the relative ordering of evolutionary events before the last common ancestor,” said Greg Fournier, a geobiologist at the Massachusetts Institute of Technology. Cells may have appeared before energy metabolism, or perhaps it was the other way around. Without fossils or DNA preserved from organisms living during this period, scientists have had little data to work from.

Fournier is leading an attempt to reconstruct the history of life in those evolutionary dark ages — the hundreds of millions of years between the time when life first emerged and when it split into what would become the endless tangle of existence.

He is using genomic data from living organisms to infer the DNA sequence of ancient genes as part of a growing field known as paleogenomics. In research published online in March in the Journal of Molecular Evolution, Fournier showed that the last chemical letter added to the code was a molecule called tryptophan — an amino acid most famous for its presence in turkey dinners. The work supports the idea that the genetic code evolved gradually. [Continue reading…]

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The man who drank cholera and launched the yogurt craze

Lina Zeldovich writes: What do Jamie Lee Curtis, gut bacteria, and a long forgotten Russian scientist have in common? Why, yogurt, of course. But wait, the answer is not that easy. Behind it stretches a tale that shows you can never predict cultural influence. It wends its way through the Pasteur Institute, the Nobel Prize, one of the hottest fields of scientific research today, the microbiome, and one of the trendiest avenues in nutrition, probiotics. It all began in the 19th century with a hyperactive kid in Russia who had a preternatural ability to connect dots where nobody saw dots at all.

When Ilya Metchnikoff was 8 and running around on his parents’ Panassovka estate in Little Russia, now Ukraine, he was making notes on the local flora like a junior botanist. He gave science lectures to his older brothers and local kids whose attendance he assured by paying them from his pocket money. Metchnikoff earned the nickname “Quicksilver” because he was in constant motion, always wanting to see, taste, and try everything, from studying how his father played card games to learning to sew and embroider with the maids. His wife later wrote in The Life of Ellie Metchnikoff that Metchnikoff asked the “queerest” questions, often exasperating his caretakers. “He could only be kept quiet when his curiosity was awakened by observation of some natural objects such as an insect or a butterfly.”

At 16, Metchnikoff borrowed a microscope from a university professor to study the lower organisms. Darwin’s On the Origin of Species shaped his comparative approach to science during his university years — he viewed all organisms, and physiological processes that took place in them, as interconnected and related.

That ability led him to the discovery of a particular cell and enabled him to link digestive processes in primitive creatures to the human body’s immune defenses. In lower organisms, which lack the abdominal cavity and intestines, digestion is accomplished by a particular type of cells — mobile mesodermal cells — that move around engulfing and dissolving food particles. While staring at mesodermal cells inside transparent starfish larvae, Metchnikoff, 37 at the time, had a thought. “It struck me that similar cells might serve in the defense of the organisms against intruders,” he wrote. He fetched a few rose thorns from the garden and stuck them into the larvae. If his hypothesis was correct, the larva’s body would recognize thorns as intruders and mesodermal cells would aggregate around the thorns in an attempt to gobble them up. As Metchnikoff expected, the mesodermal cells surrounded the thorns, proving his theory. He named his cells phagocytes, which in Greek means “devouring cells,” and likened them to an “army hurling itself upon the enemy.” [Continue reading…]

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How artificial sweeteners could lead to obesity

Scientific American reports: Many of us, particularly those who prefer to eat our cake and look like we have not done so, have a love-hate relationship with artificial sweeteners. These seemingly magical molecules deliver a dulcet taste without its customary caloric punch. We guzzle enormous quantities of these chemicals, mostly in the form of aspartame, sucralose and saccharin, which are used to enliven the flavor of everything from Diet Coke to toothpaste. Yet there are worries. Many suspect that all this sweetness comes at some hidden cost to our health, although science has only pointed at vague links to problems.

Last year, though, a team of Israeli scientists put together a stronger case. The researchers concluded from studies of mice that ingesting artificial sweeteners might lead to—of all things—obesity and related ailments such as diabetes. This study was not the first to note this link in animals, but it was the first to find evidence of a plausible cause: the sweeteners appear to change the population of intestinal bacteria that direct metabolism, the conversion of food to energy or stored fuel. And this result suggests the connection might also exist in humans.

In humans, as well as mice, the ability to digest and extract energy from our food is determined not only by our genes but also by the activity of the trillions of microbes that dwell within our digestive tract; collectively, these bacteria are known as the gut microbiome. The Israeli study suggests that artificial sweeteners enhance the populations of gut bacteria that are more efficient at pulling energy from our food and turning that energy into fat. In other words, artificial sweeteners may favor the growth of bacteria that make more calories available to us, calories that can then find their way to our hips, thighs and midriffs, says Peter Turnbaugh of the University of California, San Francisco, an expert on the interplay of bacteria and metabolism. [Continue reading…]

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Stardust

Ray Jayawardhana writes: Joni Mitchell beat Carl Sagan to the punch. She sang “we are stardust, billion-year-old carbon” in her 1970 song “Woodstock.” That was three years before Mr. Sagan wrote about humans’ being made of “star-stuff” in his book “The Cosmic Connection” — a point he would later convey to a far larger audience in his 1980 television series, “Cosmos.”

By now, “stardust” and “star-stuff” have nearly turned cliché. But that does not make the reality behind those words any less profound or magical: The iron in our blood, the calcium in our bones and the oxygen we breathe are the physical remains — ashes, if you will — of stars that lived and died long ago.

That discovery is relatively recent. Four astrophysicists developed the idea in a landmark paper published in 1957. They argued that almost all the elements in the periodic table were cooked up over time through nuclear reactions inside stars — rather than in the first instants of the Big Bang, as previously thought. The stuff of life, in other words, arose in places and times somewhat more accessible to our telescopic investigations.

Since most of us spend our lives confined to a narrow strip near Earth’s surface, we tend to think of the cosmos as a lofty, empyrean realm far beyond our reach and relevance. We forget that only a thin sliver of atmosphere separates us from the rest of the universe. [Continue reading…]

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How useful is the idea of the Anthropocene?

Jedediah Purdy writes: As much as a scientific concept, the Anthropocene is a political and ethical gambit. Saying that we live in the Anthropocene is a way of saying that we cannot avoid responsibility for the world we are making. So far so good. The trouble starts when this charismatic, all-encompassing idea of the Anthropocene becomes an all-purpose projection screen and amplifier for one’s preferred version of ‘taking responsibility for the planet’.

Peter Kareiva, the controversial chief scientist of the Nature Conservancy, uses the theme ‘Conservation in the Anthropocene’ to trash environmentalism as philosophically naïve and politically backward. Kareiva urges conservationists to give up on wilderness and embrace what the writer Emma Marris calls the ‘rambunctious garden’. Specifically, Kareiva wants to rank ecosystems by the quality of ‘ecosystem services’ they provide for human beings instead of ‘pursuing the protection of biodiversity for biodiversity’s sake’. He wants a pro‑development stance that assumes that ‘nature is resilient rather than fragile’. He insists that: ‘Instead of scolding capitalism, conservationists should partner with corporations in a science-based effort to integrate the value of nature’s benefits into their operations and cultures.’ In other words, the end of nature is the signal to carry on with green-branded business as usual, and the business of business is business, as the Nature Conservancy’s partnerships with Dow, Monsanto, Coca-Cola, Pepsi, J P Morgan, Goldman Sachs and the mining giant Rio Tinto remind us.

Kareiva is a favourite of Andrew Revkin, the roving environmental maven of The New York Times Magazine, who touts him as a paragon of responsibility-taking, a leader among ‘scholars and doers who see that new models for thinking and acting are required in this time of the Anthropocene’. This pair and their friends at the Breakthrough Institute in California can be read as making a persistent effort to ‘rebrand’ environmentalism as humanitarian and development-friendly (and capture speaking and consultancy fees, which often seem to be the major ecosystem services of the Anthropocene). This is itself a branding strategy, an opportunity to slosh around old plonk in an ostentatiously shiny bottle. [Continue reading…]

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Inside the new social science of genetics

David Dobbs writes: A few years ago, Gene Robinson, of Urbana, Illinois, asked some associates in southern Mexico to help him kidnap some 1,000 newborns. For their victims they chose bees. Half were European honeybees, Apis mellifera ligustica, the sweet-tempered kind most beekeepers raise. The other half were ligustica’s genetically close cousins, Apis mellifera scutellata, the African strain better known as killer bees. Though the two subspecies are nearly indistinguishable, the latter defend territory far more aggressively. Kick a European honeybee hive and perhaps a hundred bees will attack you. Kick a killer bee hive and you may suffer a thousand stings or more. Two thousand will kill you.

Working carefully, Robinson’s conspirators — researchers at Mexico’s National Center for Research in Animal Physiology, in the high resort town of Ixtapan de la Sal — jiggled loose the lids from two African hives and two European hives, pulled free a few honeycomb racks, plucked off about 250 of the youngest bees from each hive, and painted marks on the bees’ tiny backs. Then they switched each set of newborns into the hive of the other subspecies.

Robinson, back in his office at the University of Illinois at Urbana-Champaign’s Department of Entomology, did not fret about the bees’ safety. He knew that if you move bees to a new colony in their first day, the colony accepts them as its own. Nevertheless, Robinson did expect the bees would be changed by their adoptive homes: He expected the killer bees to take on the European bees’ moderate ways and the European bees to assume the killer bees’ more violent temperament. Robinson had discovered this in prior experiments. But he hadn’t yet figured out how it happened.

He suspected the answer lay in the bees’ genes. He didn’t expect the bees’ actual DNA to change: Random mutations aside, genes generally don’t change during an organism’s lifetime. Rather, he suspected the bees’ genes would behave differently in their new homes — wildly differently.

This notion was both reasonable and radical. Scientists have known for decades that genes can vary their level of activity, as if controlled by dimmer switches. Most cells in your body contain every one of your 22,000 or so genes. But in any given cell at any given time, only a tiny percentage of those genes is active, sending out chemical messages that affect the activity of the cell. This variable gene activity, called gene expression, is how your body does most of its work. [Continue reading…]

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Your gut tells your mind, more than you may imagine

Charles Schmidt writes: The notion that the state of our gut governs our state of mind dates back more than 100 years. Many 19th- and early 20th-century scientists believed that accumulating wastes in the colon triggered a state of “auto-intoxication,” whereby poisons emanating from the gut produced infections that were in turn linked with depression, anxiety and psychosis. Patients were treated with colonic purges and even bowel surgeries until these practices were dismissed as quackery.

The ongoing exploration of the human microbiome promises to bring the link between the gut and the brain into clearer focus. Scientists are increasingly convinced that the vast assemblage of microfauna in our intestines may have a major impact on our state of mind. The gut-brain axis seems to be bidirectional — the brain acts on gastrointestinal and immune functions that help to shape the gut’s microbial makeup, and gut microbes make neuroactive compounds, including neurotransmitters and metabolites that also act on the brain. These interactions could occur in various ways: microbial compounds communicate via the vagus nerve, which connects the brain and the digestive tract, and microbially derived metabolites interact with the immune system, which maintains its own communication with the brain. Sven Pettersson, a microbiologist at the Karolinska Institute in Stockholm, has recently shown that gut microbes help to control leakage through both the intestinal lining and the blood-brain barrier, which ordinarily protects the brain from potentially harmful agents.

Microbes may have their own evolutionary reasons for communicating with the brain. They need us to be social, says John Cryan, a neuroscientist at University College Cork in Ireland, so that they can spread through the human population. Cryan’s research shows that when bred in sterile conditions, germ-free mice lacking in intestinal microbes also lack an ability to recognize other mice with whom they interact. In other studies, disruptions of the microbiome induced mice behavior that mimics human anxiety, depression and even autism. In some cases, scientists restored more normal behavior by treating their test subjects with certain strains of benign bacteria. Nearly all the data so far are limited to mice, but Cryan believes the findings provide fertile ground for developing analogous compounds, which he calls psychobiotics, for humans. “That dietary treatments could be used as either adjunct or sole therapy for mood disorders is not beyond the realm of possibility,” he says. [Continue reading…]

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The genetic code is less like a blueprint than a first draft

Nessa Carey writes: When President Obama delivered a speech at MIT in 2009, he used a common science metaphor: “We have always been about innovation,” he said. “We have always been about discovery. That’s in our DNA.” Deoxyribonucleic acid, the chemical into which our genes are encoded, has become the metaphor of choice for a whole constellation of ideas about essence and identity. A certain mystique surrounds it. As Evelyn Fox Keller argues in her book The Century of the Gene, the genome is, in the popular imagination at least, the secret of life, the holy grail. It is a master builder, the ultimate computer program, and a modern-day echo of the soul, all wrapped up in one. This fantasy does not sit easily, however, with geneticists who have grown more aware over the last several decades that the relationship between genes and biological traits is much less than certain.

The popular understanding of DNA as a blueprint for organisms, with a one-to-one correspondence between genes and traits (called phenotypes), is the legacy of the early history of genetics. The term “gene” was coined in 1909 to refer to abstract units of inheritance, predating the discovery of DNA by forty years. Biologists came to think of genes like beads on a string that lined up neatly into chromosomes, with each gene determining a single phenotype. But, while some genes do correspond to traits in a straightforward way, as in eye color or blood group, most phenotypes are far more complex, set in motion by many different genes as well as by the environment in which the organism lives.

It turns out that the genetic code is less like a blueprint and more like a movie script, subject to revision and reinterpretation by a director. This process is called epigenetic modification (“epi” meaning “above” or “in addition to”). Just as a script can be altered with crossed-out words, sentences or scenes, epigenetic editing allows entire sections of DNA to be activated or de-activated. Genes can be as finely tuned as actors responding to stage directions to shout, whisper, or cackle. [Continue reading…]

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Darwin learned more about evolution from plants than Galapagos Finches

Henry Nicholls writes: When the HMS Beagle dropped anchor on San Cristobal, the easternmost island in the Galapagos archipelago, in September 1835, the ship’s naturalist Charles Darwin eagerly went ashore to gather samples of the insects, birds, reptiles, and plants living there. At first, he didn’t think much of the arid landscape, which appeared to be “covered by stunted, sun-burnt brushwood…as leafless as our trees during winter” But this did not put him off. By the time the Beagle left these islands some five weeks later, he had amassed a spectacular collection of Galapagos plants.

It is fortunate that he took such trouble. Most popular narratives of Darwin and the Galapagos concentrate on the far more celebrated finches or the giant tortoises. Yet when he finally published On the Origin of Species almost 25 years later, Darwin made no mention of these creatures. In his discussion of the Galapagos, he dwelt almost exclusively on the islands’ plants.

By the early 19th century, there was increasing interest in what we now refer to as biogeography, the study of the distribution of species around the globe. Many people still imagined that God had been involved in the creation of species, putting fully formed versions down on Earth that continued to reproduce themselves, dispersing from a divine “center of creation” to occupy their current habitats. To explain how the plants and animals reached far-flung places such as the isolated Galapagos, several naturalists imagined that there had to have been land bridges, long-since subsided, that had once connected them to a continent. But in the wake of the Beagle voyage, the collection of Galapagos plants suggested an alternate scenario.

Even if there had once been a land bridge to the islands, it could not account for the fact that half of the plant species Darwin collected were unique to the Galapagos, and that most of them were particular to just one island. “I never dreamed that islands, about fifty or sixty miles apart, and most of them in sight of each other, formed of precisely the same rocks, placed under a quite similar climate, rising to a nearly equal height, would have been differently tenanted,” wrote Darwin in his Journal of Researches. His observations could be best explained if species were not fixed in nature but somehow changed as the seeds traveled to different locations. [Continue reading…]

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DNA contains no information

Regan Penaluna writes: When we talk about genes, we often use expressions inherited from a few influential geneticists and evolutionary biologists, including Francis Crick, James Watson, and Richard Dawkins. These expressions depict DNA as a kind of code telling bodies how to form. We speak about genes similarly to how we speak about language, as symbolic and imbued with meaning. There is “gene-editing,” and there are “translation tables” for decoding sequences of nucleic acid. When DNA replicates, it is said to “transcribe” itself. We speak about a message — such as, build a tiger! or construct a female! — being communicated between microscopic materials. But this view of DNA has come with a price, argue some thinkers. It is philosophically misguided, they say, and has even led to scientific blunders. Scratch the surface of this idea, and below you’ll find a key contradiction.

Since the earliest days of molecular biology, scientists describe genetic material to be unlike all other biological material, because it supposedly carries something that more workaday molecules don’t: information. In a 1958 paper, Crick presented his ideas on the importance of proteins for inheritance, and said that they were composed of energy, matter, and information. Watson called DNA the “repository” of information.

Less than a decade later, George Williams, an influential evolutionary biologist, elaborated on this idea. He described genes to have a special status distinct from DNA, and to be the message that the DNA delivers. In a later work, he likened genes to ideas contained in books. A book can be destroyed, but the story inside is not identical to the physical book. “The same information can be recorded by a variety of patterns in many different kinds of material. A message is always coded in some medium, but the medium is really not the message.” In his book The Blind Watchmaker, Dawkins gives perhaps the most forthright description of this view: “airborne willow seeds… are, literally, spreading instructions for making themselves… It is raining instructions out there; it’s raining programs; it’s raining tree-growing, fluff-spreading, algorithms. That is not a metaphor, it is the plain truth. It couldn’t be any plainer if it were raining floppy discs.”

But do genes truly contain information in the same sense as words, books, or floppy discs? It depends on what we mean by information. If it’s the meaning represented by the words, books, or floppy disks, then no. Many philosophers agree that this kind of semantic information requires communication: an agent to create the message and another to interpret it. “Genes don’t carry semantic information, though. They weren’t made as part of an act of communication. So genes don’t literally represent anything, as people sometimes say,” explains Peter Godfrey-Smith, a professor of philosophy at CUNY. [Continue reading…]

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Crows understand analogies

crow

Scientific American reports: People are fascinated by the intelligence of animals. In fact, cave paintings dating back some 40,000 years suggest that we have long harbored keen interest in animal behavior and cognition. Part of that interest may have been practical: animals can be dangerous, they can be sources of food and clothing, and they can serve as sentries or mousers.

But, another part of that fascination is purely theoretical. Because animals resemble us in form, perhaps they also resemble us in thought. For many philosophers — including René Descartes and John Locke — granting intelligence to animals was a bridge too far. They especially deemed abstract reasoning to be uniquely human and to perfectly distinguish people from “brutes.” Why? Because animals do not speak, they must have no thoughts.

Nevertheless, undeterred by such pessimistic pronouncements, informed by Darwin’s theory of evolution, and guided by the maxim that “actions speak more loudly than words,” researchers today are fashioning powerful behavioral tests that provide nonverbal ways for animals to disclose their intelligence to us. Although animals may not use words, their behavior may serve as a suitable substitute; its study may allow us to jettison the stale convention that thought without language is impossible. [Continue reading…]

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