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…]

Neurological conductors that keep the brain in time and tune

Harvard Gazette: Like musical sounds, different states of mind are defined by distinct, characteristic waveforms, recognizable frequencies and rhythms in the brain’s electrical field. When the brain is alert and performing complex computations, the cerebral cortex — the wrinkled outer surface of the brain — thrums with cortical band oscillations in the gamma wavelength. In some neurological disorders like schizophrenia, however, these waves are out of tune and the rhythm is out of sync.

New research led by Harvard Medical School (HMS) scientists at the VA Boston Healthcare System (VABHS) has identified a specific class of neurons — basal forebrain GABA parvalbumin neurons, or PV neurons — that trigger these waves, acting as neurological conductors that trigger the cortex to hum rhythmically and in tune. (GABA is gamma-amniobutyric acid, a major neurotransmitter in the brain.)

The results appear this week in the journal Proceedings of the National Academy of Sciences.

“This is a move toward a unified theory of consciousness control,” said co-senior author Robert McCarley, HMS professor of psychiatry and head of the Department of Psychiatry at VA Boston Healthcare. “We’ve known that the basal forebrain is important in turning consciousness on and off in sleep and wake, but now we’ve found that these specific cells also play a key role in triggering the synchronized rhythms that characterize conscious thought, perception, and problem-solving.” [Continue reading…]

Music: Mike Marshall & Chris Thile — ‘Desvairada’

Music: Mike Marshall & Chris Thile — ‘Sedi Donka’

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…]

Music: Mike Marshall & Chris Thile — ‘Fisher’s Hornpipe’

How to rewild our language of landscape

Robert Macfarlane writes: Eight years ago, in the coastal township of Shawbost on the Outer Hebridean island of Lewis, I was given an extraordinary document. It was entitled “Some Lewis Moorland Terms: A Peat Glossary”, and it listed Gaelic words and phrases for aspects of the tawny moorland that fills Lewis’s interior. Reading the glossary, I was amazed by the compressive elegance of its lexis, and its capacity for fine discrimination: a caochan, for instance, is “a slender moor-stream obscured by vegetation such that it is virtually hidden from sight”, while a feadan is “a small stream running from a moorland loch”, and a fèith is “a fine vein-like watercourse running through peat, often dry in the summer”. Other terms were striking for their visual poetry: rionnach maoim means “the shadows cast on the moorland by clouds moving across the sky on a bright and windy day”; èit refers to “the practice of placing quartz stones in streams so that they sparkle in moonlight and thereby attract salmon to them in the late summer and autumn”, and teine biorach is “the flame or will-o’-the-wisp that runs on top of heather when the moor burns during the summer”.

The “Peat Glossary” set my head a-whirr with wonder-words. It ran to several pages and more than 120 terms – and as that modest “Some” in its title acknowledged, it was incomplete. “There’s so much language to be added to it,” one of its compilers, Anne Campbell, told me. “It represents only three villages’ worth of words. I have a friend from South Uist who said her grandmother would add dozens to it. Every village in the upper islands would have its different phrases to contribute.” I thought of Norman MacCaig’s great Hebridean poem “By the Graveyard, Luskentyre”, where he imagines creating a dictionary out of the language of Donnie, a lobster fisherman from the Isle of Harris. It would be an impossible book, MacCaig concluded:

A volume thick as the height of the Clisham,

A volume big as the whole of Harris,

A volume beyond the wit of scholars.

The same summer I was on Lewis, a new edition of the Oxford Junior Dictionary was published. A sharp-eyed reader noticed that there had been a culling of words concerning nature. Under pressure, Oxford University Press revealed a list of the entries it no longer felt to be relevant to a modern-day childhood. The deletions included acorn, adder, ash, beech, bluebell, buttercup, catkin, conker, cowslip, cygnet, dandelion, fern, hazel, heather, heron, ivy, kingfisher, lark, mistletoe, nectar, newt, otter, pasture and willow. The words taking their places in the new edition included attachment, block-graph, blog, broadband, bullet-point, celebrity, chatroom, committee, cut-and-paste, MP3 player and voice-mail. As I had been entranced by the language preserved in the prose‑poem of the “Peat Glossary”, so I was dismayed by the language that had fallen (been pushed) from the dictionary. For blackberry, read Blackberry.

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I have long been fascinated by the relations of language and landscape – by the power of strong style and single words to shape our senses of place. And it has become a habit, while travelling in Britain and Ireland, to note down place words as I encounter them: terms for particular aspects of terrain, elements, light and creaturely life, or resonant place names. I’ve scribbled these words in the backs of notebooks, or jotted them down on scraps of paper. Usually, I’ve gleaned them singly from conversations, maps or books. Now and then I’ve hit buried treasure in the form of vernacular word-lists or remarkable people – troves that have held gleaming handfuls of coinages, like the Lewisian “Peat Glossary”.

Not long after returning from Lewis, and spurred on by the Oxford deletions, I resolved to put my word-collecting on a more active footing, and to build up my own glossaries of place words. It seemed to me then that although we have fabulous compendia of flora, fauna and insects (Richard Mabey’s Flora Britannica and Mark Cocker’s Birds Britannica chief among them), we lack a Terra Britannica, as it were: a gathering of terms for the land and its weathers – terms used by crofters, fishermen, farmers, sailors, scientists, miners, climbers, soldiers, shepherds, poets, walkers and unrecorded others for whom particularised ways of describing place have been vital to everyday practice and perception. It seemed, too, that it might be worth assembling some of this terrifically fine-grained vocabulary – and releasing it back into imaginative circulation, as a way to rewild our language. I wanted to answer Norman MacCaig’s entreaty in his Luskentyre poem: “Scholars, I plead with you, / Where are your dictionaries of the wind … ?” [Continue reading…]

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…]

Music: Mike Marshall & Chris Thile — ‘Carpathian Mt. Breakdown’

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…]