Saturday, March 06, 2010

Methane on the Move?

Arctic Methane on the Move?

Methane is like the radical wing of the carbon cycle, in today’s atmosphere a stronger greenhouse gas per molecule than CO2, and an atmospheric concentration that can change more quickly than CO2 can. There has been a lot of press coverage of a new paper in Science this week called “Extensive methane venting to the atmosphere from sediments of the East Siberian Arctic Shelf”, which comes on the heels of a handful of interrelated methane papers in the last year or so. Is now the time to get frightened?

No. CO2 is plenty to be frightened of, while methane is frosting on the cake. Imagine you are in a Toyota on the highway at 60 miles per hour approaching stopped traffic, and you find that the brake pedal is broken. This is CO2. Then you figure out that the accelerator has also jammed, so that by the time you hit the truck in front of you, you will be going 90 miles per hour instead of 60. This is methane. Is now the time to get worried? No, you should already have been worried by the broken brake pedal. Methane sells newspapers, but it’s not the big story, nor does it look to be a game changer to the big story, which is CO2.

[Note: Edited Toyota velocities to reflect relative radiative forcings of anthropogenic CO2 and methane. David]

For some background on methane hydrates we can refer you here. This weeks’ Science paper is by Shakhova et al, a follow on to a 2005 GRL paper. The observation in 2005 was elevated concentrations of methane in ocean waters on the Siberian shelf, presumably driven by outgassing from the sediments and driving excess methane to the atmosphere. The new paper adds observations of methane spikes in the air over the water, confirming the methane’s escape from the water column, instead of it being oxidized to CO2 in the water, for example. The new data enable the methane flux from this region to the atmosphere to be quantified, and they find that this region rivals the methane flux from the whole rest of the ocean.

What’s missing from these studies themselves is evidence that the Siberian shelf degassing is new, a climate feedback, rather than simply nature-as-usual, driven by the retreat of submerged permafrost left over from the last ice age. However, other recent papers speak to this question.

Westbrook et al 2009, published stunning sonar images of bubble plumes rising from sediments off Spitzbergen, Norway. The bubbles are rising from a line on the sea floor that corresponds to the boundary of methane hydrate stability, a boundary that would retreat in a warming water column. A modeling study by Reagan and Moridis 2009 supports the idea that the observed bubbles could be in response to observed warming of the water column driven by anthropogenic warming.

Another recent paper, from Dlugokencky et al. 2009, describes an uptick in the methane concentration in the air in 2007, and tries to figure out where it’s coming from. The atmospheric methane concentration rose from the preanthropogenic until about the year 1993, at which point it rather abruptly plateaued. Methane is a transient gas in the atmosphere, so it ought to plateau if the emission flux is steady, but the shape of the concentration curve suggested some sudden decrease in the emission rate, stemming from the collapse of economic activity in the former Soviet bloc, or by drying of wetlands, or any of several other proposed and unresolved explanations. (Maybe the legislature in South Dakota should pass a law that methane is driven by astrology!) A previous uptick in the methane concentration in 1998 could be explained in terms of the effect of el Nino on wetlands, but the uptick in 2007 is not so simple to explain. The concentration held steady in 2008, meaning at least that interannual variability is important in the methane cycle, and making it hard to say if the long-term average emission rate is rising in a way that would be consistent with a new carbon feedback.

Anyway, so far it is at most a very small feedback. The Siberian Margin might rival the whole rest of the world ocean as a methane source, but the ocean source overall is much smaller than the land source. Most of the methane in the atmosphere comes from wetlands, natural and artificial associated with rice agriculture. The ocean is small potatoes, and there is enough uncertainty in the methane budget to accommodate adjustments in the sources without too much overturning of apple carts.

Could this be the first modest sprout of what will grow into a huge carbon feedback in the future? It is possible, but two things should be kept in mind. One is that there’s no reason to fixate on methane in particular. Methane is a transient gas in the atmosphere, while CO2 essentially accumulates in the atmosphere / ocean carbon cycle, so in the end the climate forcing from the accumulating CO2 that methane oxidizes into may be as important as the transient concentration of methane itself. The other thing to remember is that there’s no reason to fixate on methane hydrates in particular, as opposed to the carbon stored in peats in Arctic permafrosts for example. Peats take time to degrade but hydrate also takes time to melt, limited by heat transport. They don’t generally explode instantaneously.

For methane to be a game-changer in the future of Earth’s climate, it would have to degas to the atmosphere catastrophically, on a time scale that is faster than the decadal lifetime of methane in the air. So far no one has seen or proposed a mechanism to make that happen.


Dlugokencky et al., Observational constraints on recent increases in the atmospheric CH4 burden. GEOPHYSICAL RESEARCH LETTERS, VOL. 36, L18803, doi:10.1029/2009GL039780, 2009

Reagan, M. and G. Moridis, Large-scale simulation of methane hydrate dissociation along the West Spitsbergen Margin, GEOPHYSICAL RESEARCH LETTERS, VOL. 36, L23612, doi:10.1029/2009GL041332, 2009

Shakhova et al., Extensive Methane Venting to the Atmosphere from Sediments of the East Siberian Arctic Shelf, Science 237: 1246-1250, 2010

Shakhova et al., The distribution of methane on the Siberian Arctic shelves: Implications for the marine methane cycle, GEOPHYSICAL RESEARCH LETTERS, VOL. 32, L09601, doi:10.1029/2005GL022751, 2005

Westbrook, G., et al, Escape of methane gas from the seabed along the West Spitsbergen continental margin, GEOPHYSICAL RESEARCH LETTERS, VOL. 36, L15608, doi:10.1029/2009GL039191, 2009

Friday, March 05, 2010

Welcome Our Microbial Overlords

The New Carnival of Evolution Is Up
Synthetic Biology: Ten Years Old, Ten Years On »
I For One Welcome Our Microbial Overlords


Can the bacteria in our bodies control our behavior in the same way a puppetmaster pulls the strings of a marionette? I tremble to report that this wonderfully creepy possibility may be true.

The human body is, to some extent, just a luxury cruise liner for microbes. They board the SS Homo sapiens when we’re born and settle into their assigned quarters–the skin, the tongue, the nostrils, the throat, the stomach, the genitals, the gut–and then we carry them wherever we go. Some of microbes deboard when we shed our skin or use the restroom; others board at new ports when we shake someone’s hand or down a spoonful of yogurt. Just as on a luxury cruise liner, our passengers eat well. They feed on the food we eat, or on the compounds we produce. While the biggest luxury lines may be able to carry a few thousand people, we can handle many more passengers. Although the total mass of our microbes is just a few pounds, the tiny size of their cells means that we each carry about 100 trillion microbes–outnumbering our own cells by more than ten to one.

It’s important to bear in mind that you can carry this galaxy of microbes around and enjoy perfect health. These microbes, for reasons that are not entirely clear, behave like well-mannered passengers. They do not barge into the kitchen, take a cleaver to the cooks, and then eat all the food. Aboard the SS Homo sapiens, the crew includes a huge staff of security guards armed with lethal chemical sprays and other deadly weapons, ready to kill any dangerous stowaway (also known as the immune system). For some reason, the immune system does not unleash its deadly fury on the microbes–even when the microbes are fairly close relatives to truly dangerous pathogens.

In fact, our microbial passengers may actually help out the cruise liner’s crew. They can close up the ecological space in our bodies, so that invading pathogens can’t get a solid foothold. Some species in our guts can break down our food in ways that we can’t, and synthesize certain vitamins and other compounds beyond our biochemistry. The genes that the microbes carry–millions of them–expand our biochemical powers enormously.

To understand the human microbiome better, scientists have been cataloging the microbes in and on people’s bodies, and they’ve been sequencing their DNA. (Listen to my recent podcast with biologist Rob Knight for more.) Yesterday, Nature published a head-spinningly huge study on the microbiome from a team of European and Chinese researchers. Lurking in the stool of 124 volunteers, the scientists found, were 3.3 million microbial genes. The scientists identified a core of bacteria species carried in most people’s guts, as well as other species that varied from person to person.

As Ed Yong rightly points out, this study is most impressive as a titanic database. It is not the Theory of Everything for the human microbiome. That will take a lot longer to build, because the microbial ecosystem inside of us is so complex. Individual species don’t just sit in isolation, surviving in their own special way. Microbes cooperate with one another to get the food they need and produce the conditions in which they can thrive. In Microcosm, for example, I write about research suggesting that E. coli–a minor member of the gut ecosystem–may keep oxygen levels low enough for other species to invade and dominate. And it’s not as if there is some Platonic ideal of a microbiome that we all carry around with us from birth to death. The diversity of microbes I carry is different from the one you carry, and they both change over our lifetimes. Every time we take a dose of antibiotics, for example, the balance can change dramatically. And as the diversity of microbes changes, so do its ecological functions.

Which brings me, at last, to the possibility that the human microbiome can become our puppetmaster.

First some background. A lot of parasites have evolved the ability to manipulate their hosts for their own benefit. (I get into more detail about this in my book Parasite Rex and in this segment of the show Radio Lab.)

Very often, the parasites cause hosts to do things that help the parasites, instead of themselves. For example, a protozoan called Toxoplasma needs to get from rats to cats, and to help the process along, it makes rats lose their fear of cats. Parasites can also change the diet of their host as well as the way in which their hosts digest their food. Parasitic wasps living inside caterpillars, for example, cause catepillars to convert the plants they eat into compounds that supply quick energy (good for wasp larvae growing quickly) instead of storing them as fat for their own metamorphosis.

I was reminded of this sinister manipulation by a paper that was published in Science today by Rob Knight and his colleagues. They built on previous research that revealed that mice genetically engineered to be obese have different kinds of microbial diversity in their guts than normal mice. Scientists have found that if they transfer microbes from an obese mouse to a regular mouse that has had all its own germs stripped out, the recipient mouse will develop extra fat. In the case of these obese mice, it appears that the microbes become less efficient at helping the animals digest food, triggering a series of changes that leads the mice to be fat.

Knight and his colleagues discovered a different–and more disturbing–way that microbes can make mice fat. They started out by engineering mice so that they didn’t produce a protein normally found on the surface of gut cells, called TLR5. TLR5 can recognize bacteria, and some studies suggest that the cells can then pass along signals to the immune system, possibly sending a stand-down command so that the immune system doesn’t start trying to kill the microbes (and end up killing gut cells too).

Born without TLR5, mice got 20% fatter than normal. Not only that, but the mice had lots of other familiar symptoms that go along with being overweight, such as high levels of triglyceride, cholesterol, and blood pressure. Without TLR5 exerting its soothing influence, the mice suffered from chronic inflammation, probably thanks to the low-level war they were waging on their microbes. And things got worse for the mutant mice when they had to eat a high-fat diet. They gained more weight on a high-fat diet than regular mice, suffered even more inflammation, and even ended up diabetic.

The obesity of these TLR5-deficient mice was not the result of inefficiency, as in previous studies. Instead, the mice wanted to eat more–about 10 percent more than regular mice. Knight and his colleagues restricted the diet of the mutant to what the regular mice ate. A lot of their symptoms went away. So the change in their behavior was critical to their weight change.

The scientists also discovered that the make-up of the microbial diversity changed significantly in the mutant mice. Were the microbes giving the mice their symptoms? To find out, Knight and his colleagues knocked out the microbes with antibiotics. The mice ate less, put on less fat, and showed less diabetes-like symptoms.

To isolate the effects of the microbes even more, the scientists transferred them from mutant mice into the bodies of ordinary mice that had first had all their own germs stripped out. Remember–these mice have a normal set of TLR5 receptors. The scientists found that the microbes made the recipient mice hungry–and also made them obese, insulin resistant, and so on.

So here we are. Mice with a genetic make-up that alters the diversity of their gut microbes get hungry, and that hunger makes them eat more. They get obese and suffer lots of other symptoms. Get rid of that particular set of microbes, and the mice lose their hunger and start to recover. And that distinctive diversity of microbes can, on its own, make genetically normal mice hungry–and thus obese, diabetic, and so on.

When I first learned of this work, I asked Knight–with a mix of dread and delight–whether the microbes were manipulating their hosts, driving them to change their diet for the benefit of the microbes. He said he thinks the answer is yes.

This discovery doesn’t just have the potential to change the way we think about why we eat what we eat. (Am I really hungry? Or are my microbes making me hungry?) It also provides a new target in the fight against obesity, diabetes, and related disorders. What may be called for is some ecological engineering.

Thursday, March 04, 2010

Fallujah's Genetic Legacy

Disturbing story of Fallujah's birth defects

By John Simpson
BBC News, Fallujah
Many parents blame the American attacks

Six years after the intense fighting began in the Iraqi town of Fallujah between US forces and Sunni insurgents, there is a disturbingly large number of cases of birth defects in the town.

Fallujah is less than 40 miles (65km) from Baghdad, but it can still be dangerous to get to.

As a result, there has been no authoritative medical investigation, certainly by any Western team, into the allegations that the weapons used by the Americans are still causing serious problems.

The Iraqi government line is that there are only one or two extra cases of birth defects per year in Fallujah, compared with the national average.

'Daily cases'

But in the impressive new Fallujah General Hospital, built with American aid, we found a paediatric specialist, Dr Samira al-Ani, who told us that she saw two or three new cases every day.

Most of them, she said, exhibited cardiac problems.

I have nothing documented. But I can tell you that year by year the number [is] increasing
Dr Samira al-Ani
Fallujah General Hospital

When asked what the cause was, she said: "I am a doctor. I have to be scientific in my talk. I have nothing documented. But I can tell you that year by year, the number [is] increasing."

The specialist, like other medical staff at the hospital, seemed nervous about talking too openly about the problem.

They were well aware that what they said went against the government version, and we were told privately that the Iraqi authorities are anxious not to embarrass the Americans over the issue.

There are no official figures for the incidence of birth defects in Fallujah.

The US military authorities are absolutely correct when they say they are not aware of any official reports indicating an increase in birth defects in Fallujah - no official reports exist.

Mothers warned

But it is impossible, as a visitor, not to be struck by the terrible number of cases of birth defects there.

We heard many times that officials in Fallujah had warned women that they should not have children.

We went to a clinic for the disabled, and were given details of dozens upon dozens of cases of children with serious birth defects.
Baby girl with birth defect
Dozens of children were being treated at a clinic for the disabled

One photograph I saw showed a newborn baby with three heads.

While we were at the clinic, people kept arriving with children who were suffering major problems - a little girl with only one arm, several children who were paralysed, and another girl with a spinal condition so bad I asked my cameraman not to film her.

At the clinic we were told that the worst problems were to be found in the neighbourhood of al-Julan, near the river.

This was the heart of the resistance to the Americans during the two major offensives of April and September 2004, and was hit constantly by bombs and shells.

River water

We went to a house where three children, all under six, were suffering from birth defects.

Two boys were partially paralysed, and their sister clearly had serious brain damage.

Like all the other parents we spoke to, their mother had no doubt that the American attacks were responsible.

Outside, a man who had heard we were there had brought his four-year-old daughter to show us. She had six fingers on each hand, and six toes on each foot.

She was also suffering from a number of other serious health problems. The father told us that the house where they still lived had been hit by an American shell during the fighting in 2004.

There may well be a link with drinking-water, especially in al-Julan.

After the fighting was over, the rubble from the town was bulldozed into the river bank, and most people in this area get their water from the river.

The true causes of the problem, and the question of the effects of the weapons the Americans used, can be resolved only by a proper independent inquiry by medical experts.

And until the security situation in and around Fallujah improves, it will be difficult to carry that out.

Sunday, February 28, 2010

No Alternatives for Harper Israel Policy

Canadian aid groups told to keep quiet on policy issues
Earthquake survivors in Port-au-Prince wait in line to collect water this week. Aid groups in Canada say they've been warned by the Conservatives not to weigh in on policy.

Non-governmental organizations say they're receiving veiled warnings about positions that clash with Ottawa's

See also:

* Tories' hard line on criticism of Israel could spark backlash, MP says
* Harper must make abortion part of health pledge, Ignatieff says
* Gerald Caplan: If the PM is serious about the plight of mothers...

Campbell Clark

Ottawa — From Friday's Globe and Mail Published on Thursday, Feb. 11, 2010 9:30PM EST Last updated on Tuesday, Feb. 16, 2010 4:14PM EST

Aid groups say the federal government is casting a chill over advocacy work that takes positions on policy or political issues – and one claims a senior Conservative aide warned them against such activities.

An official with a mainstream non-governmental aid group said that Keith Fountain, policy director for International Co-operation Minister Bev Oda, gave a verbal warning that the organization's policy positions were under scrutiny: “Be careful about your advocacy.”

The official did not want to be identified out of concern that it might jeopardize funding for the group's aid projects from the Canadian International Development Agency, or CIDA.

That's a concern voiced by some other NGO leaders, who said they have received hints the government dislikes their policy advocacy or criticisms of the government policies, but did not want to be identified.

Most aid organizations, from church-based organizations such as Anglican and Mennonite aid agencies to big agencies such as World Vision, Oxfam and CARE, take public positions on some policy issues, and some organize letter-writing campaigns or publish pamphlets.

The aid groups use CIDA money to finance 75 per cent of specific programs, but don't use it for advocacy.

Some have had veiled warnings about positions that clash with Ottawa's on issues such as climate change, free trade with Colombia, or the Middle East, said Gerry Barr, president of the Canadian Council for International Co-operation, an umbrella group.

“NGOs are being positively invited to remain silent on key questions of public policy,” he said.

Cheryl Curtis, executive director of the Anglican Church's Primate's World Relief and Development Fund, said government officials have never warned her organization about public-policy positions, but other aid organizations have reported such messages.

“We've certainly heard that amongst colleagues,” she said, adding: “There clearly is a conversation that's brewing at the government level.”

But the government insists that is not so.

A spokesman for Ms. Oda, Jean-Luc Benoit, did not specifically respond to a question about whether Mr. Fountain had warned an aid agency about its advocacy work. But he said an NGO's funding is evaluated on effectiveness in delivering aid and matching CIDA's aid priorities.

“This is about best use of taxpayers' dollars to help the poor, not about what these organizations do with their own money,” Mr. Benoit said in an e-mail.

The fears among the NGOs have been amplified by the government's move to reject a $7-million funding request from Kairos, an aid organization backed by a coalition of churches.

Immigration Minister Jason Kenney said publicly that Kairos was de-funded because it supported a boycott campaign against Israel. (Kairos insists it doesn't support a boycott.)

The government later backtracked and said the agency's funding was turned down because it did not meet CIDA's new areas of focus. But Ms. Curtis, who is also chair of Kairos's board of directors, said the feeling that the agency lost funding for political reasons has not gone away.

“Each and every one of us who are members of Kairos feel that keenly,” she said.

Another aid NGO, the left-leaning Montreal-based Alternatives, can't get CIDA to return its calls since the National Post – citing unnamed government sources – reported that the organization's long-standing $2.1-million funding proposal would be rejected because of its political advocacy. Its most recent aid funding ran out last March.

Alternatives produces a newspaper that has published left-wing commentators and, for example, a piece that made a controversial argument for a “united Israel” and against Israel's status as a Jewish state – rather than the internationally endorsed “two-state solution” of Israel existing beside a separate Palestinian state.

“Everything we hear is that Alternatives' advocacy work is the main reason we'll eventually be cut,” said the organization's executive director, Michel Lambert.