87 posts tagged nature
Researchers analyzing human, fly, and worm genomes have found that these species have a number of key genomic processes in common, reflecting their shared ancestry. The findings, appearing Aug. 28, 2014, in the journal Nature, offer insights into embryonic development, gene regulation and other biological processes vital to understanding human biology and disease. The studies highlight the data generated by the modENCODE Project and the ENCODE Project, both supported by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health. Integrating data from the three species, the model organism ENCyclopedia Of DNA Elements (modENCODE) Consortium studied how gene expression patterns and regulatory proteins that help determine cell fate often share common features. Investigators also detailed the similar ways in which the three species use protein packaging to compact DNA into the cell nucleus and to regulate genome function by controlling access to DNA. Launched in 2007, the goal of modENCODE is to create a comprehensive catalog of functional elements in the fruit fly and roundworm genomes for use by the research community. Such elements include genes that code for proteins, non-protein-coding genes and regulatory elements that control gene expression. The current work builds on initial catalogs published in 2010. The modENCODE projects complement the work being done by the ENCyclopedia Of DNA Elements (ENCODE) Project, which is building a comprehensive catalog of functional elements in the human and mouse genomes. “The modENCODE investigators have provided a valuable resource for researchers worldwide,” said NHGRI Director Eric Green, M.D., Ph.D. “The insights gained about the workings of model organisms’ genomes greatly help to inform our understanding of human biology.”
World next door
Nine theories of the multiverse promise everything and more. But if reality is so vast and varied, where do we fit in?
Our understanding of the fundamental nature of reality is changing faster than ever before. Gigantic observatories such as the Hubble Space Telescope and the Very Large Telescope on the Paranal Mountain in Chile are probing the furthest reaches of the cosmos. Meanwhile, with their feet firmly on the ground, leviathan atom-smashers such as the Large Hadron Collider (LHC) under the Franco-Swiss border are busy untangling the riddles of the tiny quantum world. Myriad discoveries are flowing from these magnificent machines. You may have seen Hubble’s extraordinary pictures. You will probably have heard of the ‘exoplanets’, worlds orbiting alien suns, and you will almost certainly have heard about the Higgs Boson, the particle that imbues all others with mass, which the LHC found this year. But you probably won’t know that (if their findings are taken to their logical conclusion) these machines have also detected hints that Elvis lives, or that out there, among the flaming stars and planets, are unicorns, actual unicorns with horns on their noses. There’s even weirder stuff, too: devils and demons; gods and nymphs; places where Hitler won the Second World War, or where there was no war at all. Places where the most outlandish fantasies come true. A weirdiverse, if you will. Most bizarre of all, scientists are now seriously discussing the possibility that our universe is a fake, a thing of smoke and mirrors. All this, and more, is the stuff of the multiverse, the great roller-coaster rewriting of reality that has overturned conventional cosmology in the last decade or two. The multiverse hypothesis is the idea that what we see in the night sky is just an infinitesimally tiny sliver of a much, much grander reality, hitherto invisible. The idea has become so mainstream that it is now quite hard to find a cosmologist who thinks there’s nothing in it. This isn’t the world of the mystics, the pointy-hat brigade who see the Age of Aquarius in every Hubble image. On the contrary, the multiverse is the creature of Astronomers Royal and tenured professors at Cambridge and Cornell. (via Michael Hanlon – On multiverses)
read of the day: War in the womb
A ferocious biological struggle between mother and baby belies any sentimental ideas we might have about pregnancy
What sight could be more moving than a mother nursing her baby? What better icon could one find for love, intimacy and boundless giving? There’s a reason why the Madonna and Child became one of the world’s great religious symbols. To see this spirit of maternal generosity carried to its logical extreme, consider Diaea ergandros, a species of Australian spider. All summer long, the mother fattens herself on insects so that when winter comes her little ones may suckle the blood from her leg joints. As they drink, she weakens, until the babies swarm over her, inject her with venom and devour her like any other prey. You might suppose such ruthlessness to be unheard-of among mammalian children. You would be wrong. It isn’t that our babies are less ruthless than Diaea ergandros, but that our mothers are less generous. The mammal mother works hard to stop her children from taking more than she is willing to give. The children fight back with manipulation, blackmail and violence. Their ferocity is nowhere more evident than in the womb. This fact sits uncomfortably with some enduring cultural ideas about motherhood. Even today, it is common to hear doctors talking about the uterine lining as the ‘optimal environment’ for nurturing the embryo. But physiology has long cast doubt on this romantic view. The cells of the human endometrium are tightly aligned, creating a fortress-like wall around the inside of the uterus. That barrier is packed with lethal immune cells. As far back as 1903, researchers observed embryos ‘invading’ and ‘digesting’ their way into the uterine lining. In 1914, R W Johnstone described the implantation zone as ‘the ﬁghting line where the conﬂict between the maternal cells and the invading trophoderm takes place’. It was a battlefield ‘strewn with… the dead on both sides’. When scientists tried to gestate mice outside the womb, they expected the embryos to wither, deprived of the surface that had evolved to nurture them. To their shock they found instead that – implanted in the brain, testis or eye of a mouse – the embryo went wild. Placental cells rampaged through surrounding tissues, slaughtering everything in their path as they hunted for arteries to sate their thirst for nutrients. It’s no accident that many of the same genes active in embryonic development have been implicated in cancer. Pregnancy is a lot more like war than we might care to admit.
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(via Pregnancy is a war between mother and child – Suzanne Sadedin – Aeon)
The striking transformation of a caterpillar into a colourful, winged butterfly is one that has captivated scientists for years. The metamorphosis involves the breakdown of most of the caterpillar’s tissues before reassembling to form a butterfly. It therefore seems unlikely that butterflies or moths would remember experiences from their caterpillar days. However, scientists have now established that not only can a moth retain memories formed while it was a caterpillar, but that experiences gained during these early stages can have drastic impacts on adult life.
Memories live long
Moths and butterflies undergo drastic changes throughout their life-cycle, not just in their outward appearance, but also in their diet and overall lifestyle. Metamorphosis occurs within the pupal case. During this period, the larval brain stimulates the release of enzymes which dissolve most of its tissues into their constituent proteins through a process called histolysis. Then a group of specialised cells called histoblasts proceed to reconstruct the broken-down caterpillar body into that of a butterfly or a moth.
A few years ago, Martha Weiss and her group at Georgetown University discovered that aversive memories formed in the tobacco hornworm caterpillar (Manduca sexta) persisted throughout metamorphosis and were retained in adult moths.
Weiss trained caterpillars to avoid the odour of ethyl acetate, a chemical commonly used in nail polish removers. Caterpillars and moths are usually indifferent to the smell of ethyl acetate, but by pairing exposure to the odour with mild electric shocks, the scientists successfully taught these caterpillars to avoid the odour.
When given a choice of air or ethyl acetate, 78% of the caterpillars carefully avoided the odour in favour of air. Then, when adult moths developed from the pupae of trained caterpillars a month later, they continued to show a strong aversion to the smell, with 77% of the moths choosing air over ethyl acetate. Notably, the majority of moths choosing air as adults had also made the same choice as caterpillars, suggesting that individual preferences survived metamorphosis.
Broody octopus keeps record-breaking four-year vigil
For four years and five months, she clung to the rock and guarded her eggs. In a feat that surely made good use of all eight arms, an octopus revealed a new secret of deep sea life when ecologists observed her record-breaking behaviour from a robotic submarine. This doubles the longest brooding time ever seen in the animal kingdom, giving embryos time to develop in the cold. The discovery, published in the journal PLOS One, was made in a canyon 1.4km beneath the Pacific, off California. Dr Bruce Robison led the research at the Monterey Bay Aquarium Research Institute (MBARI). He told BBC News his team had stumbled upon the plucky mother in the days before she settled down and glued her eggs to the rock face. She was heading, slowly, for a known brooding site. By looking at characteristic scars in one of her eight armpits, the team identified the same octopus on the next dive, one month later. (via BBC News - Broody octopus keeps record-breaking four-year vigil)
Odds are, there’s a virus living inside your gut that has gone undetected by scientists for decades. A new study led by researchers at San Diego State University has found that more than half the world’s population is host to a newly described virus, named crAssphage, which infects one of the most common types of gut bacteria, Bacteroidetes. This phylum of bacteria is thought to be connected with obesity, diabetes and other gut-related diseases. The research appears today in Nature Communications. Robert A. Edwards, a bioinformatics professor at SDSU, and his colleagues stumbled upon the discovery quite by accident. Working with visiting researcher and corresponding author on the study Bas E. Dutilh, now at Radboud University Medical Center in The Netherlands, the researchers were using results from previous studies on gut-inhabiting viruses to screen for new viruses. In the DNA fecal samples from 12 different individuals, they noticed a particular cluster of viral DNA, about 97,000 base pairs long, that the samples all had in common. When Edwards and his colleagues checked this discovery against a comprehensive listing of known viruses, they came up empty. The researchers then screened for the virus across the database of the National Institute of Health’s Human Microbiome Project (HMP), and Argonne National Laboratory’s MG-RAST database, and again found it in abundance in samples derived from human feces. To prove that the viral DNA they discovered in their computer data actually exists in nature, fellow SDSU virologist John Mokili used a technique known as DNA amplification to locate the virus in the original samples used to build NIH’s database. “So we have a biological proof that the virus they found with the computer actually exists in the samples,” Mokili said. This was a new virus that about half the sampled people had in their bodies that nobody knew about. “It’s not unusual to go looking for a novel virus and find one,” Edwards said. “But it’s very unusual to find one that so many people have in common. The fact that it’s flown under the radar for so long is very strange.”
Chimpanzee language: Communication gestures translated
Researchers say they have translated the meaning of gestures that wild chimpanzees use to communicate. They say wild chimps communicate 19 specific messages to one another with a “lexicon” of 66 gestures. The scientists discovered this by following and filming communities of chimps in Uganda, and examining more than 5,000 incidents of these meaningful exchanges. The research is published in the journal Current Biology. (via BBC News - Chimpanzee language: Communication gestures translated)
Quantum state may be a real thing
Physicists summon up their courage and go after the nature of reality.
At the very heart of quantum mechanics lies a monster waiting to consume unwary minds. This monster goes by the name The Nature of Reality™. The greatest of physicists have taken one look into its mouth, saw the size of its teeth, and were consumed. Niels Bohr denied the existence of the monster after he nonchalantly (and very quietly) exited the monster’s lair muttering “shut up and calculate.” Einstein caught a glimpse of the teeth and fainted. He was reportedly rescued by Erwin Schrödinger at great personal risk, but neither really recovered from their encounter with the beast. The upshot is that we had a group of physicists and philosophers who didn’t believe that quantum mechanics represents reality but that it was all we could see of some deeper, more fundamental theory. A subclass of these scientists believed that the randomness of quantum mechanics would eventually be explained by some non-random, deterministic property that we simply couldn’t directly observe (otherwise known as a hidden variable). Another group ended up believing that quantum mechanics did represent reality, and that, yes, reality was non-local, and possibly not very real either. To one extent or another, these two groups are still around and still generate a fair amount of heat when they are in proximity to each other. Over the years, you would have to say that the scales have been slowly tipping in favor of the latter group. Experiments and theory have largely eliminated hidden variables. Bohm’s pilot wave, a type of hidden variable, has to be pretty extraordinary to be real.
This has left us with more refined arguments to settle. One of these is about whether the wave function represents reality or just an observer’s view of reality. (via Quantum state may be a real thing | Ars Technica)
Darwin’s Abominable Mystery
Where did flowers come from?
Why flowers, anyhow? Plants began to conquer the land more than 400 million years ago and ruled over it for more than 250 million years without producing a single blossom. Why should they have? Flowers are expensive. Sepals, petals, pigments for color, organic compounds for scent: Creating those fancy clothes and complex perfumes takes a lot of stored energy. Instead of manufacturing flowers, a plant could have used those carbohydrates to make more seeds or grow taller, both proven strategies in the competition for survival. Besides, there seems to be nothing in gymnosperms (nonflowering plants) that corresponds to flowers. Angiosperms (flowering plants) seem to have arisen out of nothing, sui generis. Nonetheless, blossoms—from the oak’s minuscule brown nubs to the green spikelets of rice to the multipetaled splendor of the rose—appear on at least 75 percent of all the world’s plant species. The why and how of angiosperms, Darwin wrote in 1879, are “an abominable mystery.” The mystery still has not been fully solved. Part of the difficulty is that flowers have always been fragile and when they die, they fall apart into easily scattered and perishable pieces. The fossil record of early flowers is therefore exceedingly scant. In recent years, however, evolutionary botanists have come to think the living Amborella trichopoda will help solve the puzzle. (via Why flowers exist: The unlikely genetic mutation of the amborella flower.)
Life Magnified: The Alien Familiarity of the Cellular World
A new collection from the National Institutes of Health offers a zoomed-in perspective of the world.
Our universe is a vast and repeating tapestry of convergences. This how we experience it anyway, and in part because our brains are hardwired to recognize patterns. We can’t help but see the fractal echo of tributaries in a blown-up image of our own capillaries. And it makes sense that a network of Earth’s waterways might resemble a system of human blood vessels; it’s just not the sort of observation that most vantage points allow. Looking at something familiar from an unfamiliar perspective—often from very far away or from very close up—can be revealing this way. Such perspectives abound in science, where microscopes and telescopes allow us to access new worlds over extreme distances and through painstaking repetition. You can catch a glimpse of this world in a new exhibit curated by the National Institutes of Health called Life: Magnified, which includes remarkable scientific images—many come from NIH-backed projects—including a striking forest of gecko toe hair, the sunflower burst of a human liver cell, the fine spiderwebbing that creeps up blood vessel walls, and stunning solar systems of cells. The American Society for Cell Biology’s director calls it a “dazzling trip through the cellular world, which is both foreign and as close as [your] own skin.” (via Life Magnified: The Alien Familiarity of the Cellular World - Adrienne LaFrance - The Atlantic)