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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Humans and animals — the power and limitations of language

Stassa Edwards writes: In his Apology for Raymond Sebond (1576), Michel de Montaigne ascribed animals’ silence to man’s own wilful arrogance. The French essayist argued that animals could speak, that they were in possession of rich consciousness, but that man wouldn’t condescend to listen. ‘It is through the vanity of the same imagination that [man] equates himself with God,’ Montaigne wrote, ‘that he attributes divine attributes for himself, picks himself out and separates himself from the crowd of other creatures.’ Montaigne asked: ‘When I play with my cat, who knows if she is making more of a pastime of me than I of her?’

Montaigne’s question is as playful as his cat. Apology is not meant to answer the age-old question, but rather to provoke; to tap into an unending inquiry about the reasoning of animals. Perhaps, Montaigne implies, we simply misunderstand the foreign language of animals, and the ignorance is not theirs, but ours.

Montaigne’s position was a radical one – the idea the animals could actually speak to humans was decidedly anti-anthropocentric – and when he looked around for like-minded thinkers, he found himself one solitary essayist. But if Montaigne was a 16th century loner, then he could appeal to the Classics. Apology is littered with references to Pliny and a particular appeal to Plato’s account of the Golden Age under Saturn. But even there, Montaigne had little to work with. Aristotle had argued that animals lacked logos (meaning, literally, ‘word’ but also ‘reason’) and, therefore, had no sense of the philosophical world inhabited and animated by humans. And a few decades after Montaigne, the French philosopher René Descartes delivered the final blow, arguing that the uniqueness of man stems from his ownership of reason, which animals are incapable of possessing, and which grants him dominion over them.

Everyone know what it’s like to forget someone’s name. It could be the name of a celebrity and the need to remember might be non-existent, and yet, as though finding this name might be an antidote to looming senility, it’s hard to let go of such a compulsion until it is satisfied.

From infancy we are taught that success in life requires an unceasing commitment to colonize the world with language. To be lost for words, is to be left out.

Without the ability to speak or understand, we would lose our most vital connection with the rest of humanity.

Montaigne understood that it was a human conceit to imagine that among all creatures, we were the only ones endowed with the capacity to communicate:

Can there be a more formall and better ordained policie, divided into so severall charges and offices, more constantly entertained, and better maintained, than that of Bees? Shall we imagine their so orderly disposing of their actions, and managing of their vocations, have so proportioned and formall a conduct without discourse, reason, and forecast?

What Montaigne logically inferred in the 1500s, science would confirm centuries later.

While Stassa Edwards enumerates the many expressions of a human desire for animals to speak, my sense is that behind this desire there is an intuition about the limitations of language: that our mute companions often see more because they can say less.

We view language as a prism that allows us perceive order in the world and yet this facility in representation is so successful and elegantly structured that most of the time we see the representations much more clearly than we see the world.

Our ability to describe and analyze the world has never been more advanced than it is today and yet for millennia, humans have observed that animals seem to be able to do something that we cannot: anticipate earthquakes.

Perhaps our word-constructed world only holds together on condition that our senses remain dull.

The world we imagine we can describe, quantify, and control, is in truth a world we barely understand.

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Birds can hear sounds hundreds of miles away

The Atlantic: In April, a massive thunderstorm unleashed a series of tornadoes that tore through the central and southern United States. The 84 twisters decimated homes and buildings, causing more than $1 billion in damage across 17 states. In the wake of the natural disaster, 35 people lost their lives.

Now, scientists say a peculiar event took place just two days before the storm: Flocks of songbirds fled the area en masse. Many golden-winged warblers had just finished a 1,500-mile migration to Tennessee when they suddenly flew south on a 900-mile exodus to Florida and Cuba. At that time, the storm was somewhere between 250 and 560 miles away. The researchers said that the birds somehow knew about the impending storm.

“At the same time that meteorologists on The Weather Channel were telling us this storm was headed in our direction, the birds were apparently already packing their bags and evacuating the area,” Henry Streby, a population ecologist from the University of California, Berkeley, said in a statement. He and his research team had been examining the birds’ migratory patterns when they made their discovery.

Initially, the team was studying if warblers, which weigh the same as four dimes, could carry half-gram geo-locators over long distances. After retrieving data from five of the 20 tagged birds, the team noticed the birds were nowhere near the path they’d expected. Why, the researchers wondered, would these tiny birds travel so far from their already-grueling migratory route? Upon further inspection, the scientists found that the dates the birds broke with the pattern coincided with the beginnings of the storm. In a paper reported today in the journal Current Biology, the team suggests that the birds made their “evacuation migration” because their keen sense of hearing alerted them to the incoming natural disaster. [Continue reading…]

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What is it like to be a bee?

honey-bee

In the minds of many humans, empathy is the signature of humanity and yet if this empathy extends further and includes non-humans we may be suspected of indulging in anthropomorphism — a sentimental projection of our own feelings into places where similar feelings supposedly cannot exist.

But the concept of anthropomorphism is itself a strange idea since it seems to invalidate what should be one of the most basic assumptions we can reasonably make about living creatures: that without the capacity to suffer, nothing would survive.

Just as the deadening of sensation makes people more susceptible to injury, an inability to feel pain would impede any creature’s need to avoid harm.

The seemingly suicidal draw of the moth to a flame is the exception rather than the rule. Moreover the insect is driven by a mistake, not a death wish. It is drawn towards the light, not the heat, oblivious that the two are one.

If humans indulge in projections about the feelings of others — human and non-human — perhaps we more commonly engage in negative projections: choosing to assume that feelings are absent where it would cause us discomfort to be attuned to their presence.

Our inclination is to avoid feeling too much and thus we construct neat enclosures for our concerns.

These enclosures shut out the feelings of strangers and then by extension seal away boundless life from which we have become even more estranged.

Heather Swan writes: It was a warm day in early spring when I had my first long conversation with the entomologist and science studies scholar Sainath Suryanarayanan. We met over a couple of hives I had recently inherited. One was thriving. Piles of dead bees filled the other. Parts of the comb were covered with mould and oozing something that looked like molasses.

Having recently attended a class for hobby beekeepers with Marla Spivak, an entomologist at the University of Minnesota, I was aware of the many different diseases to which bees are susceptible. American foulbrood, which was a mean one, concerned me most. Beekeepers recommended burning all of your equipment if you discovered it in your hives. Some of these bees were alive, but obviously in low spirits, and I didn’t want to destroy them unnecessarily. I called Sainath because I thought he could help me with the diagnosis.

Beekeeping, these days, is riddled with risks. New viruses, habitat loss, pesticides and mites all contribute to creating a deadly labyrinth through which nearly every bee must travel. Additionally, in 2004, mysterious bee disappearances began to plague thousands of beekeepers. Seemingly healthy bees started abandoning their homes. This strange disappearing act became known as colony collapse disorder (CCD).

Since then, the world has seen the decline of many other pollinating species, too. Because honeybees and other pollinators are responsible for pollinating at least one-third of all the food we eat, this is a serious problem globally. Diagnosing bee problems is not simple, but some answers are emerging. A ubiquitous class of pesticides called neonicotinoids have been implicated in pollinator decline, which has fuelled conversations among beekeepers, scientists, policy-makers and growers. A beekeeper facing a failing hive now has to consider not only the health of the hive itself, but also the health of the landscape around the hive. Dead bees lead beekeepers down a path of many questions. And some beekeepers have lost so many hives, they feel like giving up.

When we met at my troubled hives, Sainath brought his own hive tool and veil. He had already been down a path of many questions about bee deaths, one that started in his youth with a fascination for observing insects. When he was 14, he began his ‘Amateur Entomologist’s Record’, where he kept taxonomic notes on such things as wing textures, body shapes, colour patterns and behaviours. But the young scientist’s approach occasionally slipped to include his exuberance, describing one moment as ‘a stupefying experience!’ All this led him to study biology and chemistry in college, then to work on the behavioural ecology of paper wasps during his doctoral studies, and eventually to Minnesota to help Spivak investigate the role of pesticides in CCD.

Sainath had spent several years doing lab and field experiments with wasps and bees, but ultimately wanted to shift from traditional practices in entomology to research that included human/insect relationships. It was Sainath who made me wonder about the role of emotion in science – both in the scientists themselves and in the subjects of their experiments. I had always thought of emotion as something excised from science, but this was impossible for some scientists. What was the role of empathy in experimentation? How do we, with our human limitations, understand something as radically different from us as the honeybee? Did bees have feelings, too? If so, what did that mean for the scientist? For the science? [Continue reading…]

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How broken sleep can unleash creativity

Karen Emslie writes: It is 4.18am. In the fireplace, where logs burned, there are now orange lumps that will soon be ash. Orion the Hunter is above the hill. Taurus, a sparkling V, is directly overhead, pointing to the Seven Sisters. Sirius, one of Orion’s heel dogs, is pumping red-blue-violet, like a galactic disco ball. As the night moves on, the old dog will set into the hill.

It is 4.18am and I am awake. Such early waking is often viewed as a disorder, a glitch in the body’s natural rhythm – a sign of depression or anxiety. It is true that when I wake at 4am I have a whirring mind. And, even though I am a happy person, if I lie in the dark my thoughts veer towards worry. I have found it better to get up than to lie in bed teetering on the edge of nocturnal lunacy.

If I write in these small hours, black thoughts become clear and colourful. They form themselves into words and sentences, hook one to the next – like elephants walking trunk to tail. My brain works differently at this time of night; I can only write, I cannot edit. I can only add, I cannot take away. I need my day-brain for finesse. I will work for several hours and then go back to bed.

All humans, animals, insects and birds have clocks inside, biological devices controlled by genes, proteins and molecular cascades. These inner clocks are connected to the ceaseless yet varying cycle of light and dark caused by the rotation and tilt of our planet. They drive primal physiological, neural and behavioural systems according to a roughly 24-hour cycle, otherwise known as our circadian rhythm, affecting our moods, desires, appetites, sleep patterns, and sense of the passage of time.

The Romans, Greeks and Incas woke up without iPhone alarms or digital radio clocks. Nature was their timekeeper: the rise of the sun, the dawn chorus, the needs of the field or livestock. Sundials and hourglasses recorded the passage of time until the 14th century when the first mechanical clocks were erected on churches and monasteries. By the 1800s, mechanical timepieces were widely worn on neck chains, wrists or lapels; appointments could be made and meal- or bed-times set.

Societies built around industrialisation and clock-time brought with them urgency and the concept of being ‘on time’ or having ‘wasted time’. Clock-time became increasingly out of synch with natural time, yet light and dark still dictated our working day and social structures.

Then, in the late 19th century, everything changed. [Continue reading…]

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The life cycles of flowers and bees are getting thrown out of balance by climate change

bee-pollination

The Guardian reports: Sexual deceit, pressed flowers and Victorian bee collectors are combined in new scientific research which demonstrates for the first time that climate change threatens flower pollination, which underpins much of the world’s food production.

The work used museum records stretching back to 1848 to show that the early spider orchid and the miner bee on which it depends for reproduction have become increasingly out of sync as spring temperatures rise due to global warming.

The orchid resembles a female miner bee and exudes the same sex pheromone to seduce the male bee into “pseudocopulation” with the flower, an act which also achieves pollination. The orchids have evolved to flower at the same time as the bee emerges.

But while rising temperatures cause both the orchid and the bee to flower or fly earlier in the spring, the bees are affected much more, which leads to a mismatch.

“We have shown that plants and their pollinators show different responses to climate change and that warming will widen the timeline between bees and flowers emerging,” said Dr Karen Robbirt, at the Royal Botanic Gardens, Kew and the University of East Anglia (UEA). “If replicated in less specific systems, this could have severe implications for crop productivity.”

She said the research, published in Current Biology on Thursday, is “the first clear example, supported by long-term data, of the potential for climate change to disrupt critical [pollination] relationships between species.” [Continue reading…]

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The complex, varied, ever changing and context-dependent microbiome

Ed Yong writes: In the late 17th century, the Dutch naturalist Anton van Leeuwenhoek looked at his own dental plaque through a microscope and saw a world of tiny cells “very prettily a-moving.” He could not have predicted that a few centuries later, the trillions of microbes that share our lives — collectively known as the microbiome — would rank among the hottest areas of biology.

These microscopic partners help us by digesting our food, training our immune systems and crowding out other harmful microbes that could cause disease. In return, everything from the food we eat to the medicines we take can shape our microbial communities — with important implications for our health. Studies have found that changes in our microbiome accompany medical problems from obesity to diabetes to colon cancer.

As these correlations have unfurled, so has the hope that we might fix these ailments by shunting our bugs toward healthier states. The gigantic probiotics industry certainly wants you to think that, although there is little evidence that swallowing a few billion yogurt-borne bacteria has more than a small impact on the trillions in our guts. The booming genre of microbiome diet books — self-help manuals for the bacterial self — peddles a similar line, even though our knowledge of microbe-manipulating menus is still in its infancy.

This quest for a healthy microbiome has led some people to take measures that are far more extreme than simply spooning up yogurt. [Continue reading…]

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The biology of deceit

Daniel N Jones writes: It’s the friend who betrays you, the lover living a secret life, the job applicant with the fabricated résumé, or the sham sales pitch too good to resist. From the time humans learnt to co‑operate, we also learnt to deceive each other. For deception to be effective, individuals must hide their true intentions. But deception is hardly limited to humans. There is a never-ending arms race between the deceiver and the deceived among most living things. By studying different patterns of deception across the species, we can learn to better defend ourselves from dishonesty in the human world.

My early grasp of human deception came from the work of my adviser, the psychologist Delroy Paulhus at the University of British Columbia in Canada, who studied what he called the dark triad of personality: psychopathy, recognised by callous affect and reckless deceit; narcissism, a sense of grandiose entitlement and self-centered overconfidence; and Machiavellianism, the cynical and strategic manipulation of others.

If you look at the animal world, it’s clear that dark traits run through species from high to low. Some predators are fast, mobile and wide-ranging, executing their deceptions on as many others as they can; they resemble human psychopaths. Others are slow, stalking their prey in a specific, strategic (almost Machiavellian) way. Given the parallels between humans and other animals, I began to conceive my Mimicry Deception Theory, which argues that long- and short-term deceptive strategies cut across species, often by mimicking other lifestyles or forms.

Much of the foundational work for this idea comes from the evolutionary biologist Robert Trivers, who noted that many organisms gain an evolutionary advantage through deception. [Continue reading…]

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The healing power of silence

Daniel A. Gross writes: One icy night in March 2010, 100 marketing experts piled into the Sea Horse Restaurant in Helsinki, with the modest goal of making a remote and medium-sized country a world-famous tourist destination. The problem was that Finland was known as a rather quiet country, and since 2008, the Country Brand Delegation had been looking for a national brand that would make some noise.

Over drinks at the Sea Horse, the experts puzzled over the various strengths of their nation. Here was a country with exceptional teachers, an abundance of wild berries and mushrooms, and a vibrant cultural capital the size of Nashville, Tennessee. These things fell a bit short of a compelling national identity. Someone jokingly suggested that nudity could be named a national theme — it would emphasize the honesty of Finns. Someone else, less jokingly, proposed that perhaps quiet wasn’t such a bad thing. That got them thinking.

A few months later, the delegation issued a slick “Country Brand Report.” It highlighted a host of marketable themes, including Finland’s renowned educational system and school of functional design. One key theme was brand new: silence. As the report explained, modern society often seems intolerably loud and busy. “Silence is a resource,” it said. It could be marketed just like clean water or wild mushrooms. “In the future, people will be prepared to pay for the experience of silence.”

People already do. In a loud world, silence sells. Noise-canceling headphones retail for hundreds of dollars; the cost of some weeklong silent meditation courses can run into the thousands. Finland saw that it was possible to quite literally make something out of nothing.

In 2011, the Finnish Tourist Board released a series of photographs of lone figures in the wilderness, with the caption “Silence, Please.” An international “country branding” consultant, Simon Anholt, proposed the playful tagline “No talking, but action.” And a Finnish watch company, Rönkkö, launched its own new slogan: “Handmade in Finnish silence.”

“We decided, instead of saying that it’s really empty and really quiet and nobody is talking about anything here, let’s embrace it and make it a good thing,” explains Eva Kiviranta, who manages social media for VisitFinland.com.

Silence is a peculiar starting point for a marketing campaign. After all, you can’t weigh, record, or export it. You can’t eat it, collect it, or give it away. The Finland campaign raises the question of just what the tangible effects of silence really are. Science has begun to pipe up on the subject. In recent years researchers have highlighted the peculiar power of silence to calm our bodies, turn up the volume on our inner thoughts, and attune our connection to the world. Their findings begin where we might expect: with noise.

The word “noise” comes from a Latin root meaning either queasiness or pain. According to the historian Hillel Schwartz, there’s even a Mesopotamian legend in which the gods grow so angry at the clamor of earthly humans that they go on a killing spree. (City-dwellers with loud neighbors may empathize, though hopefully not too closely.)

Dislike of noise has produced some of history’s most eager advocates of silence, as Schwartz explains in his book Making Noise: From Babel to the Big Bang and Beyond. In 1859, the British nurse and social reformer Florence Nightingale wrote, “Unnecessary noise is the most cruel absence of care that can be inflicted on sick or well.” Every careless clatter or banal bit of banter, Nightingale argued, can be a source of alarm, distress, and loss of sleep for recovering patients. She even quoted a lecture that identified “sudden noises” as a cause of death among sick children. [Continue reading…]

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Why the symbol of life is a loop not a helix

Jamie Davies writes: Here is a remarkable fact about identical twins: they have the same DNA, and therefore the same ‘genetic fingerprint’, yet their actual fingerprints (such as they might leave behind on a murder weapon) are different, and can be told apart in standard police observations. Fingerprints are, of course, produced by the pattern of tiny ridges in skin. So, it would appear that certain fine-scale details of our anatomy cannot be determined by a precise ‘genetic blueprint’.

It isn’t only fine details that seem open to negotiation in this way: anyone who has seen Bonsai cultivation knows how the very genes that would normally build a large tree can instead build a miniature-scale model, given a suitable environment. Bonsai trees aren’t completely scaled down, of course: their cells are normal-sized – it’s just that each component is made with fewer of them.

In the 1950 and ’60s, many children were affected by their mothers taking the drug thalidomide while pregnant, when the drug blocked growth of the internal parts of their limbs. Even though growth of the skin is not directly affected by thalidomide, the very short limbs of affected children were covered by an appropriate amount of skin, not the much larger amount that would be needed to cover a normal limb. The growth of the skin cannot, therefore, just be in response to the command of a hard-wired internal blueprint: something much more adaptive must be going on.

Such observations are not troubling for biological science as such. But they are troubling for a certain picture of how biology works. The symbol for this worldview might be the DNA double helix, its complementary twisting strands evoking other interdependent pairs in life: male and female, form and function, living and non-living. DNA on its own is just a chemical polymer, after all, essential for life but not itself alive. Yet it holds out the promise that we can explain living processes purely in terms of the interactions between simple molecules. [Continue reading…]

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Ants are cool but teach us nothing

E.O. Wilson writes: For nearly seven decades, starting in boyhood, I’ve studied hundreds of kinds of ants around the world, and this qualifies me, I believe, to offer some advice on ways their lives can be applied to ours. I’ll start with the question I’m most often asked: “What can I do about the ants in my kitchen?” My response comes from the heart: Watch your step, be careful of little lives. Ants especially like honey, tuna and cookie crumbs. So put down bits of those on the floor, and watch as the first scout finds the bait and reports back to her colony by laying an odor trail. Then, as a little column follows her out to the food, you will see social behavior so strange it might be on another planet. Think of kitchen ants not as pests or bugs, but as your personal guest superorganism.

Another question I hear a lot is, “What can we learn of moral value from the ants?” Here again I will answer definitively: nothing. Nothing at all can be learned from ants that our species should even consider imitating. For one thing, all working ants are female. Males are bred and appear in the nest only once a year, and then only briefly. They are pitiful creatures with wings, huge eyes, small brains and genitalia that make up a large portion of their rear body segment. They have only one function in life: to inseminate the virgin queens during the nuptial season. They are built to be robot flying sexual missiles. Upon mating or doing their best to mate, they are programmed to die within hours, usually as victims of predators.

Many kinds of ants eat their dead — and their injured, too. You may have seen ant workers retrieve nestmates that you have mangled or killed underfoot (accidentally, I hope), thinking it battlefield heroism. The purpose, alas, is more sinister. [Continue reading…]

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Evolution’s random paths lead to one place

Quanta Magazine: In his fourth-floor lab at Harvard University, Michael Desai has created hundreds of identical worlds in order to watch evolution at work. Each of his meticulously controlled environments is home to a separate strain of baker’s yeast. Every 12 hours, Desai’s robot assistants pluck out the fastest-growing yeast in each world — selecting the fittest to live on — and discard the rest. Desai then monitors the strains as they evolve over the course of 500 generations. His experiment, which other scientists say is unprecedented in scale, seeks to gain insight into a question that has long bedeviled biologists: If we could start the world over again, would life evolve the same way?

Many biologists argue that it would not, that chance mutations early in the evolutionary journey of a species will profoundly influence its fate. “If you replay the tape of life, you might have one initial mutation that takes you in a totally different direction,” Desai said, paraphrasing an idea first put forth by the biologist Stephen Jay Gould in the 1980s.

Desai’s yeast cells call this belief into question. According to results published in Science in June, all of Desai’s yeast varieties arrived at roughly the same evolutionary endpoint (as measured by their ability to grow under specific lab conditions) regardless of which precise genetic path each strain took. It’s as if 100 New York City taxis agreed to take separate highways in a race to the Pacific Ocean, and 50 hours later they all converged at the Santa Monica pier.

The findings also suggest a disconnect between evolution at the genetic level and at the level of the whole organism. [Continue reading…]

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The thermodynamic theory of ecology

Quanta Magazine: The Western Ghats in India rise like a wall between the Arabian Sea and the heart of the subcontinent to the east. The 1,000-mile-long chain of coastal mountains is dense with lush rainforest and grasslands, and each year, clouds bearing monsoon rains blow in from the southwest and break against the mountains’ flanks, unloading water that helps make them hospitable to numerous spectacular and endangered species. The Western Ghats are one of the most biodiverse places on the planet. They were also the first testing ground of an unusual new theory in ecology that applies insights from physics to the study of the environment.

John Harte, a professor of ecology at the University of California, Berkeley, has a wry, wizened face and green eyes that light up when he describes his latest work. He has developed what he calls the maximum entropy (MaxEnt) theory of ecology, which may offer a solution to a long-standing problem in ecology: how to calculate the total number of species in an ecosystem, as well as other important numbers, based on extremely limited information — which is all that ecologists, no matter how many years they spend in the field, ever have. Five years ago, the Ghats convinced him that what he thought was possible from back-of-the-envelope calculations could work in the real world. He and his colleagues will soon publish the results of a study that estimates the number of insect and tree species living in a tropical forest in Panama. The paper will also suggest how MaxEnt could give species estimates in the Amazon, a swath of more than 2 million square miles of land that is notoriously difficult to survey.
John Harte thinks it is possible to predict the behavior of ecosystems using just a few key attributes. His method ignores nature’s small-grained complexities, which makes many ecologists skeptical of the project.

If the MaxEnt theory of ecology can give good estimates in a wide variety of scenarios, it could help answer the many questions that revolve around how species are spread across the landscape, such as how many would be lost if a forest were cleared, how to design wildlife preserves that keep species intact, or how many rarely seen species might be hiding in a given area. Perhaps more importantly, the theory hints at a unified way of thinking about ecology — as a system that can be described with just a few variables, with all the complexity of life built on top. [Continue reading…]

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True Darwinism is all about chance

Noah Berlatsky writes: Chance is an uncomfortable thing. So Curtis Johnson argues in Darwin’s Dice: The Idea of Chance in the Thought of Charles Darwin, and he makes a compelling case. The central controversy, and the central innovation, in Darwin’s work is not the theory of natural selection itself, according to Johnson, but Darwin’s more basic, and more innovative, turn to randomness as a way to explain natural phenomena. This application of randomness was so controversial, Johnson argues, that Darwin tried to cover it up, replacing words like “accident” and “chance” with terms like “spontaneous variation” in later editions of his work. Nonetheless, the terminological shift was cosmetic: Randomness remained, and still remains, the disturbing center of Darwin’s theories.

Johnson, a political theorist at Lewis & Clark College, explains that there are two basic kinds of chance in Darwin’s thought. The first—most familiar and least disconcerting—is chance as probability. According to the theory of natural selection, individuals with advantageous adaptations are most likely to survive. A giraffe with a longer neck has a better shot of reaching those lofty leaves and living to munch another day; a polar bear blessed with a warmer coat has a higher probability of surviving a frigid winter than one with less hair. The long-necked giraffe may not always win—it may, for example, be pulverized by a meteor before it can pass on its long-necked genes. But over time, the odds will go its way. There is randomness here, but it is controlled and predictable: It works in accordance with a rule. Natural selection makes sense.

The second kind of chance in Darwin’s work, though, is more mysterious. For natural selection to work, you need to have a range of traits to select among. That range is provided by individual variation, the fact that two different animals (whether giraffe or bear) are different from each other. Some giraffes have longer necks than others. Some bears have thicker fur than others. Why should this be? Darwin’s answer was chance. [Continue reading…]

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How to save Earth from a cataclysmic extinction event

Tony Hiss talks to E.O. Wilson, the great evolutionary biologist, about how to save life on Earth: Throughout the 544 million or so years since hard-shelled animals first appeared, there has been a slow increase in the number of plants and animals on the planet, despite five mass extinction events. The high point of biodiversity likely coincided with the moment modern humans left Africa and spread out across the globe 60,000 years ago. As people arrived, other species faltered and vanished, slowly at first and now with such acceleration that Wilson talks of a coming “biological holocaust,” the sixth mass extinction event, the only one caused not by some cataclysm but by a single species—us.

Wilson recently calculated that the only way humanity could stave off a mass extinction crisis, as devastating as the one that killed the dinosaurs 65 million years ago, would be to set aside half the planet as permanently protected areas for the ten million other species. “Half Earth,” in other words, as I began calling it—half for us, half for them. A version of this idea has been in circulation among conservationists for some time.

“It’s been in my mind for years,” Wilson told me, “that people haven’t been thinking big enough—even conservationists. Half Earth is the goal, but it’s how we get there, and whether we can come up with a system of wild landscapes we can hang onto. I see a chain of uninterrupted corridors forming, with twists and turns, some of them opening up to become wide enough to accommodate national biodiversity parks, a new kind of park that won’t let species vanish.”

I had also begun to think about such wildland chains as “Long Landscapes,” and Wilson said he liked the idea that they could meet climate change head on: Those that run north-south, like the initiative in the West known as Yellowstone-to-Yukon, can let life move north as things warm up, and those that run east-west may have the benefit of letting life move east, away from the west, which in the future may not see as much rain. “Why, when this thing gets really going,” Wilson said, “you’ll be so surrounded, so enveloped by connected corridors that you’ll almost never not be in a national park, or at any rate in a landscape that leads to a national park.”

Is this Half Earth vision even possible, I wondered, and what might it look like? [Continue reading…]

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