Author Archives: Attention to the Unseen

Introducing ‘dark DNA’ – the phenomenon that could change how we think about evolution

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By Adam Hargreaves, University of Oxford

DNA sequencing technology is helping scientists unravel questions that humans have been asking about animals for centuries. By mapping out animal genomes, we now have a better idea of how the giraffe got its huge neck and why snakes are so long. Genome sequencing allows us to compare and contrast the DNA of different animals and work out how they evolved in their own unique ways.

But in some cases we’re faced with a mystery. Some animal genomes seem to be missing certain genes, ones that appear in other similar species and must be present to keep the animals alive. These apparently missing genes have been dubbed “dark DNA”. And its existence could change the way we think about evolution.

My colleagues and I first encountered this phenomenon when sequencing the genome of the sand rat (Psammomys obesus), a species of gerbil that lives in deserts. In particular we wanted to study the gerbil’s genes related to the production of insulin, to understand why this animal is particularly susceptible to type 2 diabetes.

But when we looked for a gene called Pdx1 that controls the secretion of insulin, we found it was missing, as were 87 other genes surrounding it. Some of these missing genes, including Pdx1, are essential and without them an animal cannot survive. So where are they?

The first clue was that, in several of the sand rat’s body tissues, we found the chemical products that the instructions from the “missing” genes would create. This would only be possible if the genes were present somewhere in the genome, indicating that they weren’t really missing but just hidden.

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Why have we taken so long to catch up with animal consciousness?

Brandon Keim writes: I met my first semipalmated sandpiper in a crook of Jamaica Bay, an overlooked shore strewn with broken bottles and religious offerings at the edge of New York City. I didn’t know what it was called, this small, dun-and-white bird running the flats like a wind-up toy, stopping to peck mud and racing to join another bird like itself, and then more. Soon a flock formed, several hundred fast-trotting feeders that at some secret signal took flight, wheeling with the flashing synchronisation that researchers observing starlings have mathematically likened to avalanche formation and liquids turning to gas.

Entranced, I spent the afternoon watching them. The birds were too wary to approach, but if I stayed in one spot they would eventually come to me. They followed the tideline, retreating when waves arrived, and rushing forward as they receded, a strangely affecting parade. When they came very close, their soft, peeping vocalisations enveloped me. That night I looked at photographs I’d taken, marvelling as the birds’ beauty emerged from stillness and enlargement, each tiny feather on their backs a masterpiece of browns. I looked up their scientific classification, Calidris pusilla, conversationally known as the semipalmated sandpiper — a name derived from a combination of their piping signal calls and the partially webbed feet that keep them from sinking in the tidal sand flats of their habitat, where they eat molluscs, insect larvae and diatom algae growing in shallow, sun-heated seawater.

I learned that semipalmated sandpipers are the most common shorebird in North America, with an estimated population around 1.9 million. My copy of Lives of North American Birds (1996) described them as ‘small and plain in appearance’, which seemed unappreciative, especially in light of their migratory habits. Small enough to fit in my hand, they breed in the Arctic and winter on South America’s northern coasts, flying several thousand miles each spring and fall, stopping just once or twice. The flock I’d watched was a thread in a string of globe-encircling energy and life, fragile yet ancient, linking my afternoon to Suriname and the tundra. At that fact, I felt the sense of wonder and connection that all migratory birds inspire. Yet not once did I wonder what they thought and felt along the way. How did they experience their own lives, not just as members of a species, but as individuals? [Continue reading…]

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Millennia ago, eclipses provided rare opportunities to measure the universe

Tyler Nordgren writes: As a kid visiting the Oregon coast I often wondered, “How wide is the ocean, and what is there beyond the horizon?” As I grew older and turned my sights to the night sky, I wondered something very similar: “How far away are the stars, and are there other planets there?” Even though very few of us have ever circumnavigated the globe, and no human being has ever ventured into space beyond the moon, we do know some of the answers to these questions. Immensity isn’t immeasurable. While these vast numbers may make little sense in our daily lives, we at least know they are known.

Consider what it must have been like to live in a world where this was not true: where the sense of immeasurability, the certainty of the unfathomable, was commonplace, and the thought that the world could be known was a novel idea. The philosopher Anaxagoras was born in about 500 B.C. in the eastern Mediterranean on what is now the coast of Turkey. It was a time when philosophy had only recently turned its attention to the natural world. Less than a hundred years before, Thales of Miletus supposedly predicted the solar eclipse that ended a war, thus implying that our world was predictable and events were not just the random whims of the gods.

In such a world of physical phenomena, Anaxagoras was the first, as far as we know, to understand that eclipses occur when one heavenly body blocks the light from another. This rejection of gods and dragons as the causes of eclipses was a revolutionary thought by itself, but Anaxagoras took it further: If solar eclipses happened only because the Earth had moved into the shadow of the moon, he reasoned, then the size of the shadow must tell us something about the size of the moon. Additionally, since the moon covered the sun, the sun must be farther away. Yet to appear nearly the same size, the sun must be larger than the moon. Herein lies the power of scientific thought: Measure the extent of the shadow sweeping across the Earth, and you know the moon must be at least as big as the shadow, and the sun larger still. Mysticism provided no such opportunity: If eclipses occur when a demon devours the sun, there is no reason to believe that any measurement we make here on Earth should reveal the demon’s size.[Continue reading…]

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Beating the odds for lucky mutations

Jordana Cepelewicz writes: In 1944, a Columbia University doctoral student in genetics named Evelyn Witkin made a fortuitous mistake. During her first experiment in a laboratory at Cold Spring Harbor, in New York, she accidentally irradiated millions of E. coli with a lethal dose of ultraviolet light. When she returned the following day to check on the samples, they were all dead — except for one, in which four bacterial cells had survived and continued to grow. Somehow, those cells were resistant to UV radiation. To Witkin, it seemed like a remarkably lucky coincidence that any cells in the culture had emerged with precisely the mutation they needed to survive — so much so that she questioned whether it was a coincidence at all.

For the next two decades, Witkin sought to understand how and why these mutants had emerged. Her research led her to what is now known as the SOS response, a DNA repair mechanism that bacteria employ when their genomes are damaged, during which dozens of genes become active and the rate of mutation goes up. Those extra mutations are more often detrimental than beneficial, but they enable adaptations, such as the development of resistance to UV or antibiotics.

The question that has tormented some evolutionary biologists ever since is whether nature favored this arrangement. Is the upsurge in mutations merely a secondary consequence of a repair process inherently prone to error? Or, as some researchers claim, is the increase in the mutation rate itself an evolved adaptation, one that helps bacteria evolve advantageous traits more quickly in stressful environments?

The scientific challenge has not just been to demonstrate convincingly that harsh environments cause nonrandom mutations. It has also been to find a plausible mechanism consistent with the rest of molecular biology that could make lucky mutations more likely. Waves of studies in bacteria and more complex organisms have sought those answers for decades. [Continue reading…]

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How color vision came to the animals

Nick Stockton writes: Animals are living color. Wasps buzz with painted warnings. Birds shimmer their iridescent desires. Fish hide from predators with body colors that dapple like light across a rippling pond. And all this color on all these creatures happened because other creatures could see it.

The natural world is so showy, it’s no wonder scientists have been fascinated with animal color for centuries. Even today, the questions how animals see, create, and use color are among the most compelling in biology.

Until the last few years, they were also at least partially unanswerable—because color researchers are only human, which means they can’t see the rich, vivid colors that other animals do. But now new technologies, like portable hyperspectral scanners and cameras small enough to fit on a bird’s head, are helping biologists see the unseen. And as described in a new Science paper, it’s a whole new world. [Continue reading…]

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Moon had a magnetic field for at least a billion years longer than thought

Science News reports: The moon had a magnetic field for at least 2 billion years, or maybe longer.

Analysis of a relatively young rock collected by Apollo astronauts reveals the moon had a weak magnetic field until 1 billion to 2.5 billion years ago, at least a billion years later than previous data showed. Extending this lifetime offers insights into how small bodies generate magnetic fields, researchers report August 9 in Science Advances. The result may also suggest how life could survive on tiny planets or moons.

“A magnetic field protects the atmosphere of a planet or moon, and the atmosphere protects the surface,” says study coauthor Sonia Tikoo, a planetary scientist at Rutgers University in New Brunswick, N.J. Together, the two protect the potential habitability of the planet or moon, possibly those far beyond our solar system.

The moon does not currently have a global magnetic field. Whether one ever existed was a question debated for decades (SN: 12/17/11, p. 17). On Earth, molten rock sloshes around the outer core of the planet over time, causing electrically conductive fluid moving inside to form a magnetic field. This setup is called a dynamo. At 1 percent of Earth’s mass, the moon would have cooled too quickly to generate a long-lived roiling interior.

Magnetized rocks brought back by Apollo astronauts, however, revealed that the moon must have had some magnetizing force. The rocks suggested that the magnetic field was strong at least 4.25 billion years ago, early on in the moon’s history, but then dwindled and maybe even got cut off about 3.1 billion years ago. [Continue reading…]

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Are men seen as ‘more American’ than women?

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Protesters hold signs at the Chicago Women’s March in January 2017.
John W. Iwanski, CC BY-NC

By Laura Van Berkel, University of Cologne; Ludwin Molina, University of Kansas, and Sahana Mukherjee, Gettysburg College

Women make up 50.8 percent of the U.S. population and have equal voting rights, yet are politically underrepresented. The country has never had a female president or vice president. Only 3.5 percent of Supreme Court justices have been women, and women make up only 20 percent of Congress.

Studies have shown that within a country, groups with more power often feel greater ownership over it. Because they control actual resources, like money, and symbolic resources, like writing history, they’re better able to shape the culture in their image. For example, because Christianity is the most prominent religion in the United States, Christmas is a federal holiday.

Because men hold more power than women in the United States, we wanted to explore a simple question: Would people tend to think of men as “more American” than women? And, if so, how does this influence the way American women identify with their country?

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