Music: Snarky Puppy — ‘Bent Nails’
Author Archives: Attention to the Unseen
Here’s how genetics helped crack the history of human migration
By George Busby, University of Oxford
Over the past 25 years, scientists have supported the view that modern humans left Africa around 50,000 years ago, spreading to different parts of the world by replacing resident human species like the Neanderthals. However, rapid advances in genetic sequencing have opened up a whole new window into the past, suggesting that human history is much more complicated.
In fact, genetic studies in the last few years have revealed that since our African exodus, humans have moved and mixed a lot more than previously thought – particularly over the last 10,000 years.
The technology
Our ability to sequence DNA has increased dramatically since the human genome was first sequenced 15 years ago. In its most basic form, genetic analysis involves comparing DNA from different sets of people, whether between people with or without a particular type of cancer, or individuals from different regions of the world.
The human genome is 3 billion letters long, but as people differ at just one letter in every thousand, on average, we don’t have to look at them all. Instead, we can compare people where we know there are these differences, known as genetic markers. Millions of these markers have been discovered and, together with a genetic sequencing technology that allows us to cheaply look at these markers in lots of people, there has been an explosion in the data available to geneticists.
Pathogens found in Otzi’s stomach reveal unexpected insights into the coexistence of humans and bacterium
The European Academy of Bozen/Bolzano (EURAC) reports: Scientists are continually unearthing new facts about Homo sapiens from the mummified remains of Ötzi, the Copper Age man, who was discovered in a glacier in 1991. Five years ago, after Ötzi’s genome was completely deciphered, it seemed that the wellspring of spectacular discoveries about the past would soon dry up. An international team of scientists working with paleopathologist Albert Zink and microbiologist Frank Maixner from the European Academy (EURAC) in Bozen/Bolzano have now succeeded in demonstrating the presence of Helicobacter pylori in Ötzi’s stomach contents, a bacterium found in half of all humans today. The theory that humans were already infected with this stomach bacterium at the very beginning of their history could well be true. The scientists succeeded in decoding the complete genome of the bacterium.
When EURAC’s Zink and Maixner first placed samples from the Iceman’s stomach under the microscope in their ancient DNA Lab at EURAC, almost three years ago, they were initially sceptical.
“Evidence for the presence of the bacterium Helicobacter pylori is found in the stomach tissue of patients today, so we thought it was extremely unlikely that we would find anything because Ötzi’s stomach mucosa is no longer there,” explains Zink. Together with colleagues from the Universities of Kiel, Vienna and Venda in South Africa as well as the Max Planck Institute for the Science of Human History in Jena, the scientists tried to find a new way to proceed. “We were able to solve the problem once we hit upon the idea of extracting the entire DNA of the stomach contents,” reports Maixner. “After this was successfully done, we were able to tease out the individual Helicobacter sequences and reconstruct a 5,300 year old Helicobacter pylori genome.” Continue reading
Does our microbiome control us or do we control it?
Dina Fine Maron writes: We may be able to keep our gut in check after all. That’s the tantalizing finding from a new study published today that reveals a way that mice—and potentially humans—can control the makeup and behavior of their gut microbiome. Such a prospect upends the popular notion that the complex ecosystem of germs residing in our guts essentially acts as our puppet master, altering brain biochemistry even as it tends to our immune system, wards off infection and helps us break down our supersized burger and fries.
In a series of elaborate experiments researchers from Harvard Medical School and Brigham and Women’s Hospital discovered that mouse poop is chock full of tiny, noncoding RNAs called microRNAs from their gastrointestinal (GI) tracts and that these biomolecules appear to shape and regulate the microbiome. “We’ve known about how microbes can influence your health for a few years now and in a way we’ve always suspected it’s a two-way process, but never really pinned it down that well,” says Tim Spector, a professor of genetic epidemiology at King’s College London, not involved with the new study. “This [new work] explains quite nicely the two-way interaction between microbes and us, and it shows the relationship going the other way—which is fascinating,” says Spector, author of The Diet Myth: Why the Secret to Health and Weight Loss Is Already in Your Gut. [Continue reading…]
Music: Snarky Puppy feat. Magda Giannikou — ‘Amour T’es Là’
The deep space of digital reading
Paul La Farge writes: In A History of Reading, the Canadian novelist and essayist Alberto Manguel describes a remarkable transformation of human consciousness, which took place around the 10th century A.D.: the advent of silent reading. Human beings have been reading for thousands of years, but in antiquity, the normal thing was to read aloud. When Augustine (the future St. Augustine) went to see his teacher, Ambrose, in Milan, in 384 A.D., he was stunned to see him looking at a book and not saying anything. With the advent of silent reading, Manguel writes,
… the reader was at last able to establish an unrestricted relationship with the book and the words. The words no longer needed to occupy the time required to pronounce them. They could exist in interior space, rushing on or barely begun, fully deciphered or only half-said, while the reader’s thoughts inspected them at leisure, drawing new notions from them, allowing comparisons from memory or from other books left open for simultaneous perusal.
To read silently is to free your mind to reflect, to remember, to question and compare. The cognitive scientist Maryanne Wolf calls this freedom “the secret gift of time to think”: When the reading brain becomes able to process written symbols automatically, the thinking brain, the I, has time to go beyond those symbols, to develop itself and the culture in which it lives.
A thousand years later, critics fear that digital technology has put this gift in peril. The Internet’s flood of information, together with the distractions of social media, threaten to overwhelm the interior space of reading, stranding us in what the journalist Nicholas Carr has called “the shallows,” a frenzied flitting from one fact to the next. In Carr’s view, the “endless, mesmerizing buzz” of the Internet imperils our very being: “One of the greatest dangers we face,” he writes, “as we automate the work of our minds, as we cede control over the flow of our thoughts and memories to a powerful electronic system, is … a slow erosion of our humanness and our humanity.”
There’s no question that digital technology presents challenges to the reading brain, but, seen from a historical perspective, these look like differences of degree, rather than of kind. To the extent that digital reading represents something new, its potential cuts both ways. Done badly (which is to say, done cynically), the Internet reduces us to mindless clickers, racing numbly to the bottom of a bottomless feed; but done well, it has the potential to expand and augment the very contemplative space that we have prized in ourselves ever since we learned to read without moving our lips. [Continue reading…]
The sound of beauty in sadness
Princess Ojiaku writes: Sad music might make people feel vicarious unpleasant emotions, found a study published last year in Frontiers in Psychology. But this experience can ultimately be pleasurable because it allows a negative emotion to exist indirectly, and at a safe distance. Instead of feeling the depths of despair, people can feel nostalgia for a time when they were in a similar emotional state: a non-threatening way to remember a sadness.
People who are very empathetic are more likely to take pleasure in the emotional experience of sad music, according to another study in Frontiers of Psychology. Others enjoy sad songs because they help them return to an emotionally balanced state, according to a review in Frontiers in Human Neuroscience, published in 2015. And those more open to varied experiences might enjoy the songs because the unique emotions that come up when listening to the music fulfill their need for novelty in thoughts and feelings.
In fact, the quest for variety could also explain why some people crave dissonant or experimental music full of uneven, cacophonous or downright disorienting sound. Musical genres such as noise, no wave and experimental rock have a dedicated fan and artist base in thriving underground scenes. Research suggests that people who are more open to novelty are more likely to take pleasure in the uncommon elements found in these non-traditional types of music. A 2012 study in Psychology of Music found a positive correlation between openness to experience and liking jazz, a genre that often defies a traditional pop structure. [Continue reading…]
Arve Henriksen, voice and trumpet, from his album, Chiaroscuro, with an excerpt from the film, Labyrinth of Dreams.
America’s national eating disorder
Julia Belluz spoke to journalist and food advocate Michael Pollan: Julia Belluz: Other countries seem to be doing a much better job of advising people on how to eat, like Brazil. It gives people simple advice — cook at home more often, eat more fruits and vegetables, and eat less meat.
Michael Pollan: That’s an interesting case. The Brazilians have tried to revolutionize the whole concept of dietary guidelines and get away from talking about nutrients completely. They talk not only about foods and science but food culture.
They have recommendations about how you eat, not just what you eat, so for example they encourage Brazilians to eat with other people. What does this have to do with health? It turns out it has everything to do with health. We know that snacking and eating alone are destructive to health.
Julia Belluz: What would it take to see guidelines like Brazil’s in the US?
Michael Pollan: It would take viewing food through a different lens. The mindset that produced those Brazilian guidelines is influenced as much by culture as it is about science — a very foreign idea to us. But food is not just about science. The assumption built into the process here is that it’s strictly a scientific process, a matter of fuel. Eating is essentially a negotiation between the eater and a bunch of chemicals out there. That’s a mistake.
We also have a very powerful food industry that cares deeply about what the government tells the public about food. They don’t want anyone else to be talking to the public about food in a way that might contradict their own messages. So they’re in there lobbying. When the government is deciding about the guidelines for school lunches, industry is in the room, making sure the potato doesn’t get tossed and gets the same respect accorded to vegetables. [Continue reading…]
America is a constipated nation
Ed Wong writes: In the decades after World War II, a one-eyed Irish missionary-surgeon named Denis Burkitt moved to Uganda, where he noted that the villagers there ate far more fiber than Westerners did. This didn’t just bulk up their stools, Burkitt reasoned; it also explained their low rates of heart disease, colon cancer, and other chronic illnesses. “America is a constipated nation,” he once said. “If you pass small stools, you have big hospitals.”
“Burkitt really nailed it,” says Justin Sonnenburg, a microbiologist at Stanford University. Sure, some of the man’s claims were far-fetched, but he was right about the value of fiber and the consequences of avoiding it. And Sonnenburg thinks he knows why: Fiber doesn’t just feed us—it also feeds the trillions of microbes in our guts.
Fiber is a broad term that includes many kinds of plant carbohydrates that we cannot digest. Our microbes can, though, and they break fiber into chemicals that nourish our cells and reduce inflammation. But no single microbe can tackle every kind of fiber. They specialize, just as every antelope in the African savannah munches on its own favored type of grass or shoot. This means that a fiber-rich diet can nourish a wide variety of gut microbes and, conversely, that a low-fiber diet can only sustain a narrower community. [Continue reading…]
Music: Bill Laurance — ‘Gold Coast’
Why we should learn to love all insects – not just the ones that work for us
By Paul Manning, University of Oxford
Insects, which include more than a million described species, represent roughly two-thirds of the biodiversity on Earth. But they have a big PR problem – many think of insects as little more than crop-eating, disease-carrying jumper-munchers. But in reality, species fitting this bill are but a tiny part of an enormous picture.
A dominant narrative has emerged in an effort to clear the good name of our six-legged friends. Insects are the unsung heroes, the little things that run the world. This fact is undeniable. Insects are critical to the existence of the world as we know it, whether through pollinating plants, controlling populations of agricultural pests, or helping with the decomposition of animal waste.
These numerous benefits provided by our environment are known as ecosystem services. A widely cited paper from 2006 estimates that these insect services are worth an annual US$57 billion to the US economy alone. These valuations are an important step in starting conversations about the importance of insect conservation.
However economic arguments can only take us so far.
Music: Bill Laurance — ‘Swag Times’
What is David Bowie’s Blackstar really about?
Spencer Kornhaber wrote last week: The title track of David Bowie’s new album, Blackstar, is about ISIS. Maybe. Bowie reportedly mentioned the Islamic State to the saxophonist and band leader Donny McCaslin when talking about the song, though the drummer Mark Guiliana and the producer Tony Visconti told Rolling Stone they had no idea the haunted and haunting 10-minute opener had anything to do with terrorism. Most anyone who listens to the thing would probably say the same. For starters, its first line mentions the Norse village of Ormen, which is not currently in the caliphate.
But that ISIS comment, relayed second-hand, is about all anyone’s got for now about the intentions and meaning of Blackstar from its author: Bowie doesn’t give interviews anymore. Which you might call frustrating—except for the fact that Blackstar could lose some of its considerable magic were it ever fully explained by its creator. Attempting to interpret its mystery, on your own, is part of the appeal. [Continue reading…]
Music: David Bowie & Pat Metheny Group — ‘This Is Not America’
David Bowie: 1947-2016
An email Brian Eno received from Bowie seven days ago ended: “‘Thank you for our good times, Brian. they will never rot’. And it was signed ‘Dawn’.
“I realise now he was saying goodbye.”
Why life is not a thing but a restless manner of being
Tim Requarth writes: Mike Russell found his moment of inspiration on a warm spring evening in Glasgow in 1983, when his 11-year-old son broke a new toy. The toy in question was a chemical garden, a small plastic tank in which stalactite-like tendrils grew out of seed crystals placed in a mineral solution. Although the tendrils appeared solid from the outside, when shattered they revealed their true nature: each one was actually a network of hollow tubes, like bundles of tiny cocktail straws.
At the time, Russell, a geologist, was struggling to understand an unusual rock he had recently found. It, too, was solid on the outside but inside was full of hollow tubes, their thin walls riddled with microscopic compartments. It dawned on him then that this rock – like the formations in his son’s toy – must have formed in some unusual kind of liquid solution. Russell posited a whole new geological phenomenon to explain it: undersea hydrothermal hotspots where mineral-rich water spewed from Earth’s interior and then precipitated in the cool surrounding water, creating chemical gardens of towering, hollow rocks growing up from the ocean floor.
That was a huge intuitive leap, but it soon led Russell to an even more outlandish thought. ‘I had the epiphany that life emerged from those rocks,’ he said. ‘Many years later, people would tell me the idea was amazing, but it wasn’t to me. I was just thinking in a different realm, in the light of what I knew as a geologist. I didn’t set out to study the origin of life, but it just seemed so obvious.’
What seemed obvious to Russell was that his hypothetical chemical gardens could solve one of the deepest riddles of life’s origin: the energy problem. Then as now, many leading theories of life’s origins had their roots in Charles Darwin’s speculation of a ‘warm little pond’, in which inanimate matter, energised by heat, sunlight or lightning, formed complex molecules that eventually began reproducing themselves. For decades, most origin-of-life research has focused on how such self-replicating chemistry could have arisen. They largely brushed aside the other key question, how the first living things obtained the energy to grow, reproduce and evolve to greater complexity.
But in Russell’s mind, the origin of life and the source of the energy it needed were a single issue, the two parts inextricably intertwined. As a geologist (now working at NASA’s Jet Propulsion Laboratory in California), he came at the problem with a very different perspective from his biology-trained colleagues. Undersea chemical gardens, Russell realised, would have provided an abundant flux of matter and energy in the same place – a setting conducive for self-replicating reactions, and also a free lunch for fledgling creatures. It has long troubled researchers that the emergence of life seems to rely on highly improbable chemical events that lead toward greater complexity. By considering energy first, Russell believed he could address that. In his view, the emergence of biological complexity was not improbable but inevitable. [Continue reading…]
Time’s (almost) reversible arrow
Frank Wilczek writes: Few facts of experience are as obvious and pervasive as the distinction between past and future. We remember one, but anticipate the other. If you run a movie backwards, it doesn’t look realistic. We say there is an arrow of time, which points from past to future.
One might expect that a fact as basic as the existence of time’s arrow would be embedded in the fundamental laws of physics. But the opposite is true. If you could take a movie of subatomic events, you’d find that the backward-in-time version looks perfectly reasonable. Or, put more precisely: The fundamental laws of physics — up to some tiny, esoteric exceptions, as we’ll soon discuss — will look to be obeyed, whether we follow the flow of time forward or backward. In the fundamental laws, time’s arrow is reversible.
Logically speaking, the transformation that reverses the direction of time might have changed the fundamental laws. Common sense would suggest that it should. But it does not. Physicists use convenient shorthand — also called jargon — to describe that fact. They call the transformation that reverses the arrow of time “time reversal,” or simply T. And they refer to the (approximate) fact that T does not change the fundamental laws as “T invariance,” or “T symmetry.” [Continue reading…]
Music: Snarky Puppy — ‘Strawman’
Stories about our deepest values activate brain region once thought to be its autopilot
University of Southern California: Everyone has at least a few non-negotiable values. These are the things that, no matter what the circumstance, you’d never compromise for any reason – such as “I’d never hurt a child,” or “I’m against the death penalty.”
Real-time brain scans show that when people read stories that deal with these core, protected values, the “default mode network” in their brains activates.
This network was once thought of as just the brain’s autopilot, since it has been shown to be active when you’re not engaged by anything in the outside world – but studies like this one suggest that it’s actually working to find meaning in the narratives.
“The brain is devoting a huge amount of energy to whatever that network is doing. We need to understand why,” said Jonas Kaplan of the USC Dornsife Brain and Creativity Institute. Kaplan was the lead author of the study, which was published on Jan. 7 in the journal Cerebral Cortex.
Kaplan thinks that it’s not just that the brain is presented with a moral quandary, but rather that the quandary is presented in a narrative format.
“Stories help us to organize information in a unique way,” he said. Continue reading