MIT's ocean model precisely mimics microbes' life cycles

MIT's ocean model precisely mimics microbes' life cycles

Scientists at MIT have created an ocean model so realistic that the virtual forests of diverse microscopic plants they "sowed" have grown in population patterns that precisely mimic their real-world counterparts.

This model of the ocean is the first to reflect the vast diversity of the invisible forests living in our oceans-tiny, single-celled green plants that dominate the ocean and produce half the oxygen we breathe on Earth. And it does so in a way that is consistent with the way real-world ecosystems evolve according to the principles of natural selection.

Scientists use models such as this one to better understand the oceans' biological and chemical cycles and their role in regulating atmospheric carbon dioxide, an important greenhouse gas.

The output of the new model, the brainchild of oceanographer Mick Follows, has been tested against real-world patterns of a particular species of phytoplankton, called prochlorococcus, which dominates the plant life of some ocean regions.

Follows and co-authors report this work, part of the MIT Earth System Initiative's new Darwin Project, in the March 30 issue of Science. The Darwin Project is a new cross-disciplinary research project at MIT connecting systems biology, microbial ecology, global biogeochemical cycles and climate.

"The guiding principle of our model is that its ecosystems are allowed to self-organize as in the natural world," said Follows, a principal research scientist in MIT's Department of Earth, Atmospheric and Planetary Sciences (EAPS), lead author on the paper and creator of the model. "The fact that the phytoplankton that emerge in our model are analogous to the real phytoplankton gives us confidence in the value of our approach."

One of Follows' collaborators, Penny Chisholm, the Lee and Geraldine Martin Professor of Civil and Environmental Engineering and Biology and director of the Earth Systems Initiative, has made prochlorococcus her focus of study for 20 years. Stephanie Dutkiewicz, a research scientist in EAPS, and Scott Grant, a graduate student at the University of Hawaii, who was an MIT physics undergraduate during this project, collaborated with Chisholm and Follows on the new model.

Chisholm believes that because previous ocean models did not convey the diversity of phytoplankton, they did not well represent the systems they modeled. The new model remedies that.

"Now we are finally modeling the ocean systems in a way that is consistent with how biologists think of them-water filled with millions of diverse microbes that wax and wane in relative abundance through interactions with each other, and the environment, as dictated by natural selection," said Chisholm.

Indeed the guiding principle of the new model is natural selection. It simulates the physical and chemical characteristics of the oceans, but adds to the virtual soup about 100 random types of phytoplankton. The model randomly generates the single-celled plants, which differ primarily in their size, and in their sensitivity to light, temperature and nutrient availability, then allows the ocean to self-select those most fit for survival in any particular area.

What emerged after the model completed its 10-year virtual evolution -which took four to five days on a cluster of parallel computers-is a phytoplankton community with members that are characteristic of observed phytoplankton communities, including plants similar to prochlorococcus that are extremely abundant in the warm mid-latitude Atlantic and Pacific oceans.

Chisholm said this is the first major change in the way scientists approach ocean models in many years. She believes it will serve to break down disciplinary barriers between the physical and biological ocean sciences.

Follows attributes this new approach to three factors: the emergence of new information about the genetic diversity of marine microbes, recent advances in computational capability and a simple recognition of his own bias.

"Physicists, like myself, have a bit of a reductionist view. We often shy away from the complexity of the real world in our models and prefer to reduce things to the simplest case with fewest factors," said Follows, who went through a sort of conceptual evolution after collaborating with Chisholm for several years. "I finally said, 'Yes, real world ecosystems are messy and complex. But let's embrace it.'"

The Paradigm Consortium of the National Ocean Partnership Program, the National Science Foundation, the Department of Energy, the Gordon and Betty Moore Foundation, and the MIT Global Habitat Longevity Award provided funding for the research.

Chisholm, Follows and Dutkiewicz plan to use this new type of model to look in more detail at what shapes the habitats of the phytoplankton and to link this to other, larger scientific issues about oceans, the plants and creatures living in them and global climate.

"This is just the beginning," said Chisholm. "Now we can begin to ask the model questions and test hypotheses about the role of oceanic microbes in global processes. This will help guide decisions about responsible use of the oceans in this era of global change."

Green Counsel: San Francisco Bans Plastic Bags

Green Counsel: San Francisco Bans Plastic Bags

San Francisco just passed a law -- the first in the United States -- that bans petroleum-based plastic bags by large grocery and drug chains. According to the city, plastic bags litter the streets and are responsible for choking marine life. As an alternative, stores may offer paper bags or compostable plastic.

According to Craig Noble, a San Francisco-based spokesperson for NRDC, "America consumes 30 billion plastic bags and 10 billion papers ones each year," he says, which use up 14 million trees and 12 million barrels of oil. The biodegradable bags, he says, "give consumers a way out of making this false 'paper or plastic' choice."

The California Grocers Association opposed the ban, partly because of cost, and supported recycling. They argued that plastic bags cost pennies, while paper bags cost 4 to 5 cents, and compostable plastic bags run from 6 to 10 cents; and these costs will have to be passed on to consumers.

Shark disappearance threatens sea life: Report

TheStar.com - News - Shark disappearance threatens sea life: Report

HALIFAX – The near extinction of several species of sharks is causing a dangerous ripple effect through the marine food chain, according to a new study that links their virtual disappearance to depletions of other sea life.

The report by a team of researchers at Dalhousie University in Halifax has found that species that were once the primary food source for certain types of large sharks are undergoing a population boom because there aren't as many sharks to prey on them.

The scientists contend that the explosive increase in about a dozen types of smaller sharks, rays and skates has caused a cascading effect throughout the ecosystem as they begin to deplete limited nutrient sources and alter nature's complex food web.

"It's incredibly serious," said Julia Baum, who co-wrote the report to be released Friday in the journal Science. "Everyone knows that the oceans are being overfished and it's the top predators that are being disproportionately hit by overfishing.

"Because they structure everything underneath them in the food web, we may be drastically changing and restructuring how the oceanic food web functions and operates."

The report states that shark populations off the eastern United States are in an even steeper decline that originally thought. Using data from fisheries logs and research surveys from 1970 to 2005, the team discovered that the abundance of several types of so-called great sharks has dropped by more than 99 per cent.

The bull and dusty sharks are verging on extinction, while hammerheads and great white sharks are in dangerously low numbers, Baum said, due largely to overfishing.

The controversial practice of finning – slicing the shark's fin off and then tossing the carcass overboard – has led to precipitous drops in most strains of the large predators globally, the report said.

"What we're seeing is a higher risk of extinction of these species in these areas, and the term we use as ecologists is functional elimination," Baum said, adding that finning kills as many as 73 million sharks a year worldwide for an industry that supplies fins for soups and other uses.

"It means that these great predators can no longer play their roles in the ecosystem as top predators. So they're no longer controlling the species in the food web below them."

The researchers, including the late Ransom Myers who passed away Tuesday, cited a specific example of how the removal of sharks is affecting other species.

Baum, a marine biologist, said they have for the first time linked the decimation of bay scallops in waters off North Carolina to an increase in cownose rays, which eat the delicacy. Sharks feed on the rays, but because there are now so few sharks, the ray population has been allowed to grow to more than 10 times what it was a decade ago.

Cownose rays have wiped out scallop beds to the point that the fishery has been closed every year off North Carolina since 2004.

"This ecological event is having a large impact on local communities that depend so much on healthy fisheries," said Charles Peterson, a professor of marine sciences and biology at the University of North Carolina and co-author of the report.

Baum said it's not clear what the increase in the other species will mean for the food chain and the wider ecosystem, but it's likely skates, rays and smaller sharks are disrupting the wider natural order in oceans around the world.

The loss of the bay scallop has already caused disruptions to seagrass, an important habitat for other marine life, because rays plow through the growth in search of scallops. Rays may also be inhibiting the recovery of oysters, hard clams and soft-shell clams.

Ken Frank, a fisheries scientist with the federal Fisheries Department, said the findings add to what he had discovered in an earlier research paper that looked at how the disappearance of cod affected the food chain.

Frank, whose study was published in Science in 2005, found that the collapse of cod and other large species led to a cascade effect. As the number of large predators declined dramatically, the fish they preyed on – herring, capelin, shrimp and snow crab – experienced a population explosion.

"There are interdependencies among the species, and when you cause these imbalances, you're going to get some effect elsewhere," he said from his office in Halifax.

"For many decades, it was thought this type of cascade effect was possible only in simplified systems like ponds, so seeing this occur in the marine system is alarming. It means we're modifying the way energy is flowing through these systems."

This latest scientific paper follows groundbreaking research Myers and Baum did in 2003 that found shark populations in the Atlantic had plunged dramatically since the mid-1980s.

"We know better now why sharks matter," Baum said. "Keeping top predators is critical for sustaining the health of the ocean."

Arctic sea ice decline may trigger climate change cascade

Arctic sea ice decline may trigger climate change cascade
 

Arctic sea ice that has been dwindling for several decades may have reached a tipping point that could trigger a cascade of climate change reaching into Earth's temperate regions, says a new University of Colorado at Boulder study.

Mark Serreze, a senior research scientist at CU-Boulder's National Snow and Ice Data Center who led the study synthesizing results from recent research, said the Arctic sea-ice extent trend has been negative in every month since 1979, when concerted satellite record keeping efforts began. The team attributed the loss of ice, about 38,000 square miles annually as measured each September, to rising concentrations of greenhouse gases and strong natural variability in Arctic sea ice.

"When the ice thins to a vulnerable state, the bottom will drop out and we may quickly move into a new, seasonally ice-free state of the Arctic," Serreze said. "I think there is some evidence that we may have reached that tipping point, and the impacts will not be confined to the Arctic region."

A review paper by Serreze and Julienne Stroeve of CU-Boulder's NSIDC and Marika Holland of the National Center for Atmospheric Research titled "Perspectives on the Arctic's Shrinking Sea Ice Cover" appears in the March 16 issue of Science.

The loss of Arctic sea ice is most often tied to negative effects on wildlife like polar bears and increasing erosion of coastlines in Alaska and Siberia, he said. But other studies have linked Arctic sea ice loss to changes in atmospheric patterns that cause reduced rainfall in the American West or increased precipitation over western and southern Europe, he said.

The decline in Arctic sea ice could impact western states like Colorado, for example, by reducing the severity of Arctic cold fronts dropping into the West and reducing snowfall, impacting the ski industry and agriculture, he said. "Just how things will pan out is unclear, but the bottom line is that Arctic sea ice matters globally," Serreze said.

Because temperatures across the Arctic have risen from 2 degrees to 7 degrees F. in recent decades due to a build-up of atmospheric greenhouse gases, there is no end in sight to the decline in Arctic sea ice extent, said Serreze of CU-Boulder's Cooperative Institute for Research in Environmental Sciences. Arctic sea ice extent is defined as the total area of all regions where ice covers at least 15 percent of the ocean surface.

"While the Arctic is losing a great deal of ice in the summer months, it now seems that it also is regenerating less ice in the winter," said Serreze. "With this increasing vulnerability, a kick to the system just from natural climate fluctuations could send it into a tailspin."

In the late 1980s and early 1990s, shifting wind patterns from the North Atlantic Oscillation flushed much of the thick sea ice out of the Arctic Ocean and into the North Atlantic where it drifted south and eventually melted, he said. The thinner layer of "young" ice that formed it its place melts out more readily in the succeeding summers, leading to more open water and more solar radiation being absorbed by the open ocean and fostering a cycle of higher temperatures and earlier ice melt, he said.

"This ice-flushing event could be a small-scale analog of the sort of kick that could invoke rapid collapse, or it could have been the kick itself," he said. "At this point, I don't think we really know."

Researchers also have seen pulses of warmer water from the North Atlantic entering the Arctic Ocean beginning in the mid-1990s, which promote ice melt and discourage ice growth along the Atlantic ice margin, he said. "This is another one of those potential kicks to the system that could evoke rapid ice decline and send the Arctic into a new state."

The potential for such rapid ice loss was highlighted in a December 2006 study by Holland and her colleagues published in Geophysical Research Letters. In one of their climate model simulations, the Arctic Ocean in September became nearly ice-free between 2040 and 2050.

"Given the growing agreement between models and observations, a transition to a seasonally ice-free Arctic Ocean as the system warms seems increasingly certain," the researchers wrote in Science. "The unresolved questions regard when this new Arctic state will be realized, how rapid the transition will be, and what will be the impacts of this new state on the Arctic and the rest of the globe."

Global warming is very real and very serious

http://www.da.wvu.edu/XMLParser/printstory.phtml?id=27022

Global warming is very real and very serious

By Travis Doyle
Columnist

It has recently been brought to my attention that global warming is a very serious problem and that we, as human beings, must treat it with all the seriousity that we can muster. First and foremost, we must destroy all volcanoes. After that, we have to consider the facts.
The biggest fact is that carbon dioxide, or CO2, causes global warming. We all have seen this on television, we all have heard the disaster reports, and it really doesn't matter that at times in Earth's history there have been three to 10 times as much CO2 in the atmosphere without the world coming to an end, because now it will cause the world to end. There are no hidden agendas, there is no propaganda in regards to this subject, there are just people dying from global warming. And those people could be you.
Another big fact that people should know is that Al Gore supports efforts to reduce global warming, and he was almost president. Why would anyone who isn't president lie to us? Why would his ice core samples show a correlation between CO2 in the atmosphere and warming temperatures, yet fail to comment on the fact that the correlation is skewed in the opposite direction? Just because CO2 levels in his core samples rise 800 years later than global temperatures themselves have raised doesn't mean we shouldn't believe him. After all, he was almost president.
Furthermore, just because in the post-war economic boom between 1940 and 1970, when our nation was increasing its CO2 emissions by the greatest leaps and bounds in history, and global temperatures were lowering, doesn't mean that global warming isn't happening now. Even though the same types of environmental scientists who are propagating global warming now are the ones that were predicting global cooling in the '70s, they have it right this time, and we need to listen to them or die.
Look, I know what a lot of you are thinking: ''But I went on Google Video and watched the UK documentary called, 'The Great Global Warming Swindle,' which clearly points out, with the aid of scientists from around the world, that global warming really isn't feasible.''
Well, there are a lot of scientists supporting global warming as well, and they're getting a lot of grant money for doing it. Who are you going to trust: scientists ��?or scientists? I am going to put my life in the hands of scientists. Do whatever you want with yours.
And I'm sure that there are some people out there are going to say, ''But I read the article in The New York Times by Frederick Seitz, the former president of the National Academy of Sciences, and he said that there were a great deal of omissions in the global warming report shown to the UN, and that scientists who dropped out of the project still had their names added to it, despite the fact that they didn't support the text within.'' Do I really have to ask if you're going to put stock in what the former president of the National Academy of Sciences says about anything scientific? Just because he has all the credibility a man could ever need on the subject doesn't mean that he is right. And he is not right, and if you believe him, you will die.
But the real issue that I'm going to encourage people to take up, in writing this column, is to destroy volcanoes. Volcanoes produce more CO2 than any man, machine or industry on the planet combined. Volcanoes are going to kill us if we don't kill them first. Everyone needs to look around, grab something pointy and start stabbing at the nearest volcano.
Remember, folks, if you don't agree with me, then you don't believe in global warming.
And if you don't believe in global warming, then nobody is going to die because of it, and the world will probably be a better place without all that grant money being wasted and all that media airtime being spent on the same footage of a glacier cracking.

Bioenergy pact between Europe and Africa

Bioenergy pact between Europe and Africa

According to a new study by researchers at the Carnegie Institution and Lawrence Livermore National Laboratory, warming global temperatures have already caused annual losses of roughly US$5 billion for major food crops over the past two decades.

From 1981-2002, warming reduced the combined production of wheat, corn, and barley—cereal grains that form the foundation of much of the world's diet—by 40 million metric tons per year. The diagram with scatter plots ( click to enlarge ) shows first-differences of yield (kg ha–1) and first-differences of average monthly minimum and maximum temperatures (°C) and precipitation (mm) during the growing season, along with best-fit trend lines (in grey). Each decade is shown with a different colour, indicating that the relationships do not appear to change through time.

The study, titled "Global scale climate–crop yield relationships and the impacts of recent warming" [*abstract], is published in the current online edition of the journal Environmental Research Letters, and demonstrates that this decline is due to human-caused increases in global temperatures. The article is freely accessible [ *.html version / *.pdf version]. Do check it out, as the evidence is represented in a very straightforward way, and it offers a - scaringly clear - signal of the potential disaster climate change has in store for global agriculture.

"Most people tend to think of climate change as something that will impact the future," says Christopher Field, co-author on the study and director of Carnegie's Department of Global Ecology in Stanford, Calif. "But this study shows that warming over the past two decades has already had real effects on global food supply."

The study is the first to estimate how much global food production has already been affected by climate change. Field and David Lobell, lead author of the study and a researcher at Lawrence Livermore National Laboratory, compared yield figures from the Food and Agriculture Organization with average temperatures and precipitation in the major growing regions.

They found that, on average, global yields for several of the crops responded negatively to warmer temperatures, with yields dropping by about 3-5 percent for every 1 degree F increase. Average global temperatures increased by about 0.7 degrees F during the study period, with even larger changes in several regions:
  "Though the impacts are relatively small compared to the technological yield gains over the same period, the results demonstrate that negative impacts are already occurring," said Lobell.

The researchers focused on the six most widely grown crops in the world: wheat, rice, maize (corn), soybeans, barley and sorghum—a genus of about 30 species of grass raised for grain. These crops occupy more than 40 percent of the world's cropland, and account for at least 55 percent of non-meat calories consumed by humans. They also contribute more than 70 percent of the world's animal feed.

The main value of this study, the authors said, was that it demonstrates a clear and simple correlation between temperature increases and crop yields at the global scale. However, Field and Lobell also used this information to further investigate the relationship between observed warming trends and agriculture.

"We assumed that farmers have not yet adapted to climate change—for example, by selecting new crop varieties to deal with climate change. If they have been adapting—something that is very difficult to measure—then the effects of warming may have been lower," explained Lobell.

Most experts believe that adaptation would lag several years behind climate trends, because it can be difficult to distinguish climate trends from natural variability. "A key moving forward is how well cropping systems can adapt to a warmer world. Investments in this area could potentially save billions of dollars and millions of lives," Lobell added.