Humans have a skull, too. This and a number of other traits we share with Myllokunmingia reveal it to be one of the oldest, most primitive vertebrates yet found. It is, in other words, a hint of where we came from. Myllokunmingia emerged during one of the most important phases in the history of life, an evolutionary boom known as the Cambrian explosion (named for the geological period when it took place). Over the course of about 20 million years, the oldest known fossils of most of the major groups of living animals appear, revealing a rapid diversification of life that led directly to humans. “It’s rapid in geological terms, but it’s probably not rapid to anyone who’s not a geologist,” said Paul Smith, the director of the Oxford Museum of Natural History. By some estimates, the first animals evolved about 750 million years ago. But it’s not until around 520 million years ago that many major groups of living animals left behind their first fossils. For decades, scientists have searched for the trigger that set in motion this riot of diversity in the animal kingdom. Recently, Dr. Smith and his colleague David Harper of the University of Durham took a look at the hypotheses that have been offered about what caused the Cambrian explosion. “It became apparent just how many hypotheses there were out there,” Dr. Harper said. “Thirty-plus over the past 10 years.” The scientists found that many of those explanations had boiled the cause down to just one trigger. Geologists suggested geological causes. Ecologists proposed ecological ones. Many of those ideas have merit, Dr. Smith and Dr. Harper argue in a commentary in this week’s Science, but it’s a mistake to search for a single cause. They propose that a tangled web of factors and feedbacks were responsible for evolution’s big bang. Long before the Cambrian explosion, Dr. Smith and Dr. Harper argue, one lineage of animals had already evolved the genetic capacity for spectacular diversity. Known as the bilaterians, they probably looked at first like little crawling worms. They shared the Precambrian oceans with other animals, like sponges and jellyfish. During the Cambrian explosion, relatively modest changes to their genes gave rise to a spectacular range of bodies. But those genes evolved in bilaterians tens of millions of years before the Cambrian explosion put them to the test, notes Dr. Smith. “They had the capacity,” he said, “but it hadn’t been expressed yet.” It took a global flood to tap that capacity, Dr. Smith and Dr. Harper propose. They base their proposal on a study published last year by Shanan Peters of the University of Wisconsin and Robert Gaines of Pomona College. They offered evidence that the Cambrian Explosion was preceded by a rise in sea level that submerged vast swaths of land, eroding the drowned rocks. “There’s a big kick that correlates with the sea level rise,” Dr. Smith said of the fossil record. He and Dr. Harper propose that this kick happened thanks to the new habitats created by the sea level rise. These shallow coastal habitats were bathed in sunlight and nourished with eroding nutrients like phosphates. Animals colonized these new fertile habitats, Dr. Smith and Dr. Harper argue, and evolved to take up new ecological niches. But these great floods also poisoned the ocean. The erosion of the coastlines released calcium, which can be toxic to cells. In order to survive, animals had to evolve ways to rid themselves of the poison. One solution may have been to pack the calcium into crystals, which eventually evolved into shells, bones, and other hard tissues. Dr. Smith doesn’t think it’s a coincidence that several different lineages of bilaterians evolved hard tissues during the Cambrian explosion, and not sooner. These shells and other hard tissues sped up animal evolution even more. Predators could grow hard claws and jaws for killing prey, and their prey could evolve hard shells and spines to defend themselves. Animals became locked in an evolutionary arms race. This new ecological food web grew even more complex. Bigger predators evolved that could eat smaller predators. Meanwhile, some bilaterians burrowed into the sea floor for the first time, allowing oxygen-rich seawater to flow into the sediment. Those first burrowers profoundly transformed the world’s oceans, creating yet another habitat that other oxygen-breathing animals could also invade. “That drives the diversification onward,” said Dr. Smith. Kevin Peterson, a biologist at Dartmouth, praised Dr. Smith and Dr. Harper for pointing to the right way to study the Cambrian explosion. “We are long past identifying single triggers for the event,” he said. Dr. Peters agreed that taking a holistic view of the Cambrian explosion would lead to a better understanding of it. “It’ll be a fun next decade,” he predicted. But Philip Donoghue of the University of Bristol does not think the links Dr. Smith and Dr. Harper use in their hypothesis are tight enough yet. Questions still remain, for example, about how long vertebrates and other animals groups already existed before they left behind fossils like Myllokunmingia. If animals diversified earlier, then scientists will need to look at earlier causes. “Timing,” said Dr. Donoghue, “is everything.”
Showing posts with label Matter. Show all posts
Showing posts with label Matter. Show all posts
Friday, 20 September 2013
Sunday, 18 August 2013
Matter: Watching Bacteria Evolve, With Predictable Results
Watching Bacteria Evolve, With Predictable Results - NYTimes.com Log In Register Now HelpHome PageToday's PaperVideoMost PopularEdition: U.S. / GlobalSearch All NYTimes.com
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Alice Liang/New York UniversityPseudomonas aeruginosa, a common bacterium, normally has a single tail that it uses to move about. By CARL ZIMMERPublished: August 15, 2013 If we could somehow rewind the history of life to the dawn of the animal kingdom, it would be unlikely that we humans would ever evolve, the evolutionary biologist Stephen Jay Gould argued. The history of life was shaped by too many flukes and contingencies to repeat its course. More 'Matter' ColumnsMatter: Monogamy and Human Evolution(August 6, 2013)Matter: How Simple Can Life Get? It’s Complicated(July 4, 2013)Looking at Oil Palm’s Genome for Keys to Productivity(July 30, 2013)
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Earl Wilson/The New York TimesCarl Zimmer Scientists can’t turn back the clock 700 million years, so we can’t know for sure whether Dr. Gould was right on that particular point. But in experiments using bacteria and other fast-breeding organisms, scientists can replay evolution many times over in their labs. And the results of a new experiment published Thursday in the journal Cell Reports demonstrate — with movies — that evolution can be astoundingly predictable. The experiment was carried out by Joao Xavier of Memorial Sloan-Kettering Cancer Center and his colleagues. They studied a common species of bacteria called Pseudomonas aeruginosa. These microbes live pretty much everywhere — in dirt, in water, on our skin. Under certain conditions, they also invade our bodies and cause dangerous infections. People with cystic fibrosis, for example, can get P. aeruginosa infections in their lungs, which are often impossible to eradicate. To better understand the biology of this pathogen, Dr. Xavier began to study how it searches for food. In a process called swarming, the bacteria spray out gooey molecules that form a slippery carpet; they can then slither over it by whipping their tails, devouring food they encounter along the way. “I just wondered why nobody had filmed them before, because the pattern is so striking,” said Dr. Xavier. He dropped a few hundred microbes in the middle of a petri dish laced with sugar and switched on a camera overhead. By Joao Xavier/Memorial Sloan Kettering Cancer CenterA common species of bacteria called Pseudomonas aeruginosa sprays out gooey molecules that form a slippery carpet that it can slither over. To better understand how the bacteria swarm, Dr. Xavier and his colleagues allowed them to evolve. They seeded petri dishes with a few hundred microbes and gave them a day to swarm and reproduce. The next day, they drew a small sample of the bacteria from the dishes and used them to seed new ones. The scientists reasoned that, with each generation, new mutations would arise from time to time. If a mutation helped bacteria thrive in this new environment, it might become more common because of natural selection. And so it did. Within a few days, the evolution of the bacteria took a dramatic turn. The bacteria became 25 percent faster than their ancestors — Dr. Xavier dubbed them “hyperswarmers.” A movie of hyperswarmers starkly illustrates how different they had become, able to fill up the entire dish. By Joao Xavier/Memorial Sloan Kettering Cancer CenterAfter a few generations, a common species of bacteria called Pseudomonas aeruginosa evolved into a much faster swarmer. “We thought, ‘Something weird has happened,'” said Dr. Xavier. The hyperswarmers emerged in three lines of bacteria overseen by Dr. Xavier’s post-doctoral researcher Dave van Ditmarsch. Dr. Xavier and another lab member, Jen Oyler, each ran the experiment again. “I wanted to make sure this wasn’t just due to Dave’s magic fingers,” said Dr. Xavier. But no matter who applied their fingers to the task, the result was the same. Out of 27 lines of bacteria, 27 evolved into hyperswarmers. When the scientists put the hyperswarmers under a microscope, they could see what had changed. An ordinary P. aeruginosa sports a single tail. The hyperswarmers had evolved so that they had as many as half a dozen tails. Those extra tails gave the bacteria more speed. 
Alice Liang/New York UniversityHyperswarming Pseudomonas aeruginosa bacteria evolved during experiments to have three or more tails. To determine how the bacteria had gained their tails, Dr. Xavier and his colleagues sequenced the DNA of 24 lines of hyperswarmers. In 24 out of 24 cases, they discovered that they have gained a mutation in the same gene, called FleN. FleN encodes a protein that controls other genes involved in building tails. Somehow — Dr. Xavier doesn’t yet know how — the mutations cause FleN to produce a multitude of tails, all of which are fully functional. Using their many tails, the hyperswarmers were able to get out in front of ordinary bacteria and reach fresh food first. They could then reproduce faster, leaving behind more offspring. As a result, each population of the bacteria rapidly turned into pure hyperswarmers. Hyperswarmers evolved so reliably in Dr. Xavier’s experiments that he began to wonder why they had never been seen before. He speculated that, in his lab, the bacteria gained an ability to swim fast at the expense of some other trait that they need in nature. Swarming, after all, is not the only essential task that P. aeruginosa must carry out. When the bacteria find a place that’s good for settling down, they anchor themselves to a surface — on a leaf, for example, or inside a human lung. They form a rubber sheet known as a biofilm. Dr. Xavier and his colleagues found that the hyperswarmers are bad at making biofilms on their own. They then mixed hyperswarmers with normal bacteria and allowed the two types of microbes to make biofilms together. When the biofilm formed, the scientists tallied up how many bacteria in it were ordinary microbes and how many were hyperswarmers. In a video showing the 3-D structure of one of these biofilms, the ordinary bacteria win, and the hyperswarmers have practically gone extinct — confirming that the ability to make microfilms is more important to the bacteria’s survival than being speedier consumers of food. By Joao Xavier/Memorial Sloan Kettering Cancer CenterA 3-D sheet of bacteria called a biofilm, with normal bacteria in red and the few remaining hyperswarmers in green. Dr. Xavier’s discovery could help doctors who are struggling to fight P. aeruginosa. In hospitals around the world, the bacteria are evolving resistance to many antibiotics, and biofilms provide some of their protection by acting like a shield. If scientists could find a way to coax ordinary P. aeruginosa to behave more like hyperswarmers, they might lose their ability to make biofilms. But Dr. Xavier’s research also provides a scientific thrill in itself: the chance to see evolution in action — over and over again. And if there’s one thing Dr. Xavier can now be sure of, it’s that his bacteria will end up as hyperswarmers, thanks to mutations to the same gene. “In this case, it could be that there are only a few solutions in the evolutionary space,” he said. 
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ScienceWorldU.S.N.Y. / RegionBusinessTechnologyScienceEnvironmentSpace & CosmosHealthSportsOpinionArtsStyleTravelJobsReal EstateAutosAdvertise on NYTimes.comMatterWatching Bacteria Evolve, With Predictable Results Alice Liang/New York UniversityPseudomonas aeruginosa, a common bacterium, normally has a single tail that it uses to move about. By CARL ZIMMERPublished: August 15, 2013 If we could somehow rewind the history of life to the dawn of the animal kingdom, it would be unlikely that we humans would ever evolve, the evolutionary biologist Stephen Jay Gould argued. The history of life was shaped by too many flukes and contingencies to repeat its course. More 'Matter' ColumnsMatter: Monogamy and Human Evolution(August 6, 2013)Matter: How Simple Can Life Get? It’s Complicated(July 4, 2013)Looking at Oil Palm’s Genome for Keys to Productivity(July 30, 2013) Connect With Us on Social Media @nytimesscience on Twitter. Science Reporters and Editors on Twitter Like the science desk on Facebook. Enlarge This ImageEarl Wilson/The New York TimesCarl Zimmer Scientists can’t turn back the clock 700 million years, so we can’t know for sure whether Dr. Gould was right on that particular point. But in experiments using bacteria and other fast-breeding organisms, scientists can replay evolution many times over in their labs. And the results of a new experiment published Thursday in the journal Cell Reports demonstrate — with movies — that evolution can be astoundingly predictable. The experiment was carried out by Joao Xavier of Memorial Sloan-Kettering Cancer Center and his colleagues. They studied a common species of bacteria called Pseudomonas aeruginosa. These microbes live pretty much everywhere — in dirt, in water, on our skin. Under certain conditions, they also invade our bodies and cause dangerous infections. People with cystic fibrosis, for example, can get P. aeruginosa infections in their lungs, which are often impossible to eradicate. To better understand the biology of this pathogen, Dr. Xavier began to study how it searches for food. In a process called swarming, the bacteria spray out gooey molecules that form a slippery carpet; they can then slither over it by whipping their tails, devouring food they encounter along the way. “I just wondered why nobody had filmed them before, because the pattern is so striking,” said Dr. Xavier. He dropped a few hundred microbes in the middle of a petri dish laced with sugar and switched on a camera overhead. By Joao Xavier/Memorial Sloan Kettering Cancer CenterA common species of bacteria called Pseudomonas aeruginosa sprays out gooey molecules that form a slippery carpet that it can slither over. To better understand how the bacteria swarm, Dr. Xavier and his colleagues allowed them to evolve. They seeded petri dishes with a few hundred microbes and gave them a day to swarm and reproduce. The next day, they drew a small sample of the bacteria from the dishes and used them to seed new ones. The scientists reasoned that, with each generation, new mutations would arise from time to time. If a mutation helped bacteria thrive in this new environment, it might become more common because of natural selection. And so it did. Within a few days, the evolution of the bacteria took a dramatic turn. The bacteria became 25 percent faster than their ancestors — Dr. Xavier dubbed them “hyperswarmers.” A movie of hyperswarmers starkly illustrates how different they had become, able to fill up the entire dish. By Joao Xavier/Memorial Sloan Kettering Cancer CenterAfter a few generations, a common species of bacteria called Pseudomonas aeruginosa evolved into a much faster swarmer. “We thought, ‘Something weird has happened,'” said Dr. Xavier. The hyperswarmers emerged in three lines of bacteria overseen by Dr. Xavier’s post-doctoral researcher Dave van Ditmarsch. Dr. Xavier and another lab member, Jen Oyler, each ran the experiment again. “I wanted to make sure this wasn’t just due to Dave’s magic fingers,” said Dr. Xavier. But no matter who applied their fingers to the task, the result was the same. Out of 27 lines of bacteria, 27 evolved into hyperswarmers. When the scientists put the hyperswarmers under a microscope, they could see what had changed. An ordinary P. aeruginosa sports a single tail. The hyperswarmers had evolved so that they had as many as half a dozen tails. Those extra tails gave the bacteria more speed. Alice Liang/New York UniversityHyperswarming Pseudomonas aeruginosa bacteria evolved during experiments to have three or more tails. To determine how the bacteria had gained their tails, Dr. Xavier and his colleagues sequenced the DNA of 24 lines of hyperswarmers. In 24 out of 24 cases, they discovered that they have gained a mutation in the same gene, called FleN. FleN encodes a protein that controls other genes involved in building tails. Somehow — Dr. Xavier doesn’t yet know how — the mutations cause FleN to produce a multitude of tails, all of which are fully functional. Using their many tails, the hyperswarmers were able to get out in front of ordinary bacteria and reach fresh food first. They could then reproduce faster, leaving behind more offspring. As a result, each population of the bacteria rapidly turned into pure hyperswarmers. Hyperswarmers evolved so reliably in Dr. Xavier’s experiments that he began to wonder why they had never been seen before. He speculated that, in his lab, the bacteria gained an ability to swim fast at the expense of some other trait that they need in nature. Swarming, after all, is not the only essential task that P. aeruginosa must carry out. When the bacteria find a place that’s good for settling down, they anchor themselves to a surface — on a leaf, for example, or inside a human lung. They form a rubber sheet known as a biofilm. Dr. Xavier and his colleagues found that the hyperswarmers are bad at making biofilms on their own. They then mixed hyperswarmers with normal bacteria and allowed the two types of microbes to make biofilms together. When the biofilm formed, the scientists tallied up how many bacteria in it were ordinary microbes and how many were hyperswarmers. In a video showing the 3-D structure of one of these biofilms, the ordinary bacteria win, and the hyperswarmers have practically gone extinct — confirming that the ability to make microfilms is more important to the bacteria’s survival than being speedier consumers of food. By Joao Xavier/Memorial Sloan Kettering Cancer CenterA 3-D sheet of bacteria called a biofilm, with normal bacteria in red and the few remaining hyperswarmers in green. Dr. Xavier’s discovery could help doctors who are struggling to fight P. aeruginosa. In hospitals around the world, the bacteria are evolving resistance to many antibiotics, and biofilms provide some of their protection by acting like a shield. If scientists could find a way to coax ordinary P. aeruginosa to behave more like hyperswarmers, they might lose their ability to make biofilms. But Dr. Xavier’s research also provides a scientific thrill in itself: the chance to see evolution in action — over and over again. And if there’s one thing Dr. Xavier can now be sure of, it’s that his bacteria will end up as hyperswarmers, thanks to mutations to the same gene. “In this case, it could be that there are only a few solutions in the evolutionary space,” he said. This article has been revised to reflect the following correction:
Correction: August 15, 2013
An earlier version of this article misstated the name of a scientific journal. It is Cell Reports, not Cell Communications.
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