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Scientists have discovered water that was sealed in Canadian bedrock for nearly half of Earth's history. It may contain the descendants of ancient microbes. The discovery could give scientists new insights into early life on Earth and inform the search for life on other planets.

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Social media shows hundreds gathering in southern city of Kunming as officials deny refinery will produce carcinogen PX

Thousands of protesters have gathered in the southern Chinese city of Kunming for the second time this month to voice concerns over the environmental impact of a planned chemical plant, according to uncorroborated posts on Twitter and Chinese social networking sites.

The protesters gathered in front of the provincial government headquarters at the intersection of Zhengyi Road and Renmin Road at about 10am, according to the posts. The demonstration has drawn a large police presence and began with one arrest, but has remained largely peaceful.

Kunming's first environmental protest this month was held, without arrests, on 4 May after China National Petroleum Corporation announced plans to build the chemical plant in Anning, 17 miles (28km) south-west of the city centre.

Every year the refinery would produce 500,000 tons of paraxylene (PX), a carcinogenic chemical used in production of polyester, according to the state-run China Daily newspaper.

Thursday's demonstrators donned face masks displaying anti-PX messages, shouted "roll out, protest!" and sang the national anthem in unison, according to Twitter reports.

Photos posted online show a thick line of police pressed tightly against rows of protesters, many of them documenting the standoff with smartphones and digital cameras.

"Protest activities only happen on the precondition that the government doesn't offer opportunities for information transparency, dialogue and negotiation," said an influential Kunming-based blogger who uses the name Bianmin, or "frontier person", in an email interview before Thursday's protest.

"If the government clings to its position, the public's resistance will only increase."

According to pictures posted on the popular Chinese microblogging website Sina Weibo, protesters held banners reading: "Save Kunming! Help us! We love Kunming, oppose pollution" and in English, "Save the water for the life!" The pictures have since been deleted, and searches for Kunming PX have been blocked.

Many university students in Kunming have been blocked from leaving their campuses, according to reports online. On Saturday the municipal government sent text messages to Kunming residents claiming that the project "will not produce PX".

Many Kunming residents appear unconvinced. "If the refinery is [as] clean and safe they claim it to be, why does the government not dare to publish the environmental review report," a demonstrator told the South China Morning Post.

A similar protest earlier this month in Chengdu, the capital of adjacent Sichuan province, was suppressed by police.

Environmental protests have become more common in recent years, as many Chinese people become increasingly exasperated by the government's growth-first development strategy and lack of transparency.

A Shanghai battery manufacturer announced on Wednesday that it would cancel plans for a new plant after hundreds of people staged three protests to voice concerns about its possible environmental impact.

In August 2011 a protest in the north-eastern city Dalian led local authorities to announce that they were would relocate a polluting PX plant. The following summer, the coastal city Qidong scrapped a pipeline plan after about a thousand protesters stormed government offices and overturned cars.

• China
• Asia Pacific
• Pollution
• Oil and gas companies
• Energy industry

Jonathan Kaiman
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Climate-induced forced migration requires a governance framework that can respond faster and more dynamically

It is now two decades since the community of Newtok, a village of around 350 people on the west coast of Alaska, first documented the need to relocate. But despite the concerted efforts of at least 25 tribal, governmental and non-governmental organisations, including the herculean efforts of the Newtok Traditional Council, progress has been painfully slow.

Significant statutory limitations prevent the government from responding effectively and dynamically to the climate-induced environmental changes that are forcing communities like Newtok to relocate in Alaska. In the United States, the Federal Emergency Management Agency (Fema), whose activities are defined by the 1988 Stafford Disaster Relief and Emergency Assistance Act, is the federal agency responsible for hazard mitigation and disaster relief in the US.

The act requires a presidential disaster declaration to access federal funding for post-disaster recovery as well as most hazard-mitigation activities. Under the Stafford Act, the president is authorised to declare a disaster for natural catastrophes such as hurricanes and tornados. Drought is the only gradual environmental process listed in the statute as a potential catalyst for a presidential disaster declaration.

Erosion, the principal reason Newtok must relocate, is not included in the list of major disasters in the Stafford Act. As a consequence, the Newtok Traditional Council is not now eligible for disaster relief funding despite the fact that erosion is causing an ongoing disaster and a humanitarian crisis in the community.

This post-disaster recovery and hazard mitigation statutory framework encourages rigid responses to specifically defined random extreme weather events and is primarily aimed at rebuilding and repairing infrastructure in place and protecting them from future hazards through erosion and flood protection. However, the standard, defensive adaptation strategies to protect coastal communities, such as rock walls and sandbags, have been largely unsuccessful in Alaska despite government spending millions of dollars.

This fact is best illustrated by the experience of Kivalina, an Inupiat Eskimo community located north of Newtok and the Arctic circle. In September 2006, after finalising the construction of a multimillion dollar seawall, federal government leaders arrived to celebrate its completion. But before the celebrations could begin, a storm damaged the seawall and caused the officials to cancel the celebration. One year later, in September 2007, a storm, with a forecasted 12 to 14-foot surge for the 10-foot elevation village, threatened the community. Residents feared that the seawall would not protect them, and 250 Kivalina residents evacuated their community in search of safety. The inability of technology to protect people who reside in vulnerable risk-prone coastal and riverine communities is an issue that could affect millions of people all over the world.

Disaster-relief and hazard-mitigation measures are important when protection in place is possible. However, this approach may be futile when climate-induced environmental changes repeatedly alter ecosystems, damage or destroy public infrastructure, and endanger human lives, in which case community relocation involving permanent population displacement may be the only viable adaptation.

The need to relocate entire communities as a result of climate-induced environmental change is an extreme form of adaptation. If climate-induced environmental change renders entire communities uninhabitable, it is critical to understand the governance tools and human rights protections that can foster community resilience. Newtok's relocation provides an example of a model governance structure where the Newtok Traditional Council is leading the community's relocation effort and federal, state and tribal governmental and non-governmental organisations are providing the community with the technical assistance needed to build the infrastructure at the relocation site. However, despite this model working group, the institutional barriers to the relocation process have been enormous.

For these reasons, climate-induced forced migration requires a governance framework that is based in human rights doctrine and that can respond quickly to communities at risk. Adaptive governance, in this context, means that institutions need a range of options, including post-disaster recovery, protection in place (seawall/shoreline protection), hazard mitigation, and relocation, to respond to the humanitarian needs of communities. Human rights protections must be embedded in this governance framework because the failure to fully consider the welfare of the population and empower people of a community to make decisions about issues such as site selection and community lay-out, are the principal reasons that relocations have been unsuccessful.

Amendment of US federal policies such as the Stafford Act to include gradual and recurring climate-induced environmental processes and creation of a relocation institutional framework are critical first steps to facilitating the relocation of communities threatened by climate-induced environmental change and unable to be protected in place. The creation of this institutional framework in the US could be a model for other countries needing to design and implement a response for climate-induced relocations.

• Climate change
• Sea ice
• Sea level
• Polar regions
• Arctic
• Alaska
• United States

Robin Bronen
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Overwhelming majority of peer-reviewed papers taking a position on global warming say humans are causing it

Our team of citizen science volunteers at Skeptical Science has published a new survey in the journal Environmental Research Letters of over 12,000 peer-reviewed climate science papers, as the Guardian reports today. This is the most comprehensive survey of its kind, and the inspiration of this blog's name: Climate Consensus – the 97%.

The survey

In 2004, Naomi Oreskes performed a survey of 928 peer-reviewed climate papers published between 1993 and 2003, finding none that rejected the human cause of global warming. We decided that it was time to expand upon Oreskes' work by performing a keyword search of peer-reviewed scientific journal publications for the terms 'global warming' and 'global climate change' between the years 1991 and 2011.

Our team agreed upon definitions of categories to put the papers in: explicit or implicit endorsement of human-caused global warming, no opinion, and implicit or explicit rejection or minimization of the human influence, and began the long process of rating over 12,000 abstracts.

We decided from the start to take a conservative approach in our ratings. For example, a study which takes it for granted that global warming will continue for the foreseeable future could easily be put into the implicit endorsement category; there is no reason to expect global warming to continue indefinitely unless humans are causing it. However, unless an abstract included language about the cause of the warming, we categorized it as 'no opinion'.

Each paper was rated by at least two people, and a dozen volunteers completed most of the 24,000 ratings. The volunteers were a very internationally diverse group. Team members' home countries included Australia, USA, Canada, UK, New Zealand, Germany, Finland, and Italy.

We also decided that asking the scientists to rate their own papers would be the ideal way to check our results. Who knows what the papers say better than the authors who wrote them? We received responses from 1,200 scientists who rated a total of over 2,100 papers. Unlike our team's ratings that only considered the summary of each paper presented in the abstract, the scientists considered the entire paper in the self-ratings.

The results

Based on our abstract ratings, we found that just over 4,000 papers took a position on the cause of global warming, 97.1% of which endorsed human-caused global warming. In the scientist self-ratings, nearly 1,400 papers were rated as taking a position, 97.2% of which endorsed human-caused global warming. Many papers captured in our literature search simply investigated an issue related to climate change without taking a position on its cause.

Our survey found that the consensus has grown slowly over time, and reached about 98% as of 2011. Our results are also consistent with several previous surveys finding a 97% consensus amongst climate experts on the human cause of global warming.

Why is this important?

Several studies have shown that people who are aware of scientific consensus on human-caused global warming are more likely to support government action to curb greenhouse gas emissions. This was most recently shown by a paper just published in the journal Climatic Change. People will generally defer to the judgment of experts, and they trust climate scientists on the subject of global warming.

However, vested interests have long realized this and engaged in a campaign to misinform the public about the scientific consensus. For example, a memo from communications strategist Frank Luntz leaked in 2002 advised Republicans,

"Should the public come to believe that the scientific issues are settled, their views about global warming will change accordingly. Therefore, you need to continue to make the lack of scientific certainty a primary issue in the debate"

This campaign has been successful. A 2012 poll from US Pew Research Center found less than half of Americans thought scientists agreed humans were causing global warming. The media has assisted in this public misconception, with most climate stories "balanced" with a "skeptic" perspective. However, this results in making the 2–3% seem like 50%. In trying to achieve "balance", the media has actually created a very unbalanced perception of reality. As a result, people believe scientists are still split about what's causing global warming, and therefore there is not nearly enough public support or motivation to solve the problem.

Check our results for yourself

We chose to submit our paper to Environmental Research Letters because it is a well-respected, high-impact journal, but also because it offers the option of making a paper open access, free for anyone to download.

We have also set up a public ratings system at Skeptical Science where anybody can duplicate our survey. Read and rate as many abstracts as you like, and see what level of consensus you find. You can compare your results to our abstract ratings, and to the author self-ratings.

Human-caused global warming

We fully anticipate that climate contrarians will respond by saying "we don't dispute that humans cause some global warming." First, there are a lot of people who do dispute that humans cause any global warming. Our paper shows that their position is not supported in the scientific literature.

Most papers don't quantify the human contribution to global warming, because it doesn't take tens of thousands of papers to establish that reality. However, as noted above, if a paper minimized the human contribution, we classified that as a 'rejection'. For example, if a paper were to say "the sun caused most of the global warming over the past century," that would be included in the less than 3% of papers rejecting or minimizing human-caused global warming.

Many studies simply defer to the expert summary of climate science research put together by the Intergovernmental Panel on Climate Change (IPCC), which says that most of the global warming since the mid-20th century has been caused by humans. And according to recent research, that statement is actually too conservative. Of the papers which specifically examine the contributors to global warming, they virtually all conclude that humans are the dominant cause over the past 50 to 100 years.

Most studies simply accept this fact and go on to examine the consequences of this human-caused global warming and associated climate change.

Another important point is that once you accept that humans are causing global warming, you must also accept that global warming is still happening. We cause global warming by increasing the greenhouse effect, and our greenhouse gas emissions just keep accelerating. This ties in to the fact that as recent research has showed, global warming is accelerating. If you accept that humans are causing global warming, as over 97% of peer-reviewed scientific papers do, then this conclusion should not be at all controversial. Global warming cannot have suddenly stopped.

Spread the word

Given the importance of the scientific consensus on human-caused global warming in peoples' decisions whether to support action to reduce greenhouse gas emissions, and the public lack of awareness of the consensus, we need to make people aware of these results. To that end, design and advertising firm SJI Associates generously created a website pro-bono, centered around the results of our survey. The website can be viewed at TheConsensusProject.com, and it includes a page where consensus graphics can be shared via social media or email. Skeptical Science also has a new page of consensus graphics.

Quite possibly the most important thing to communicate about climate change is that there is a 97% consensus amongst the scientific experts and scientific research that humans are causing global warming. Let's spread the word and close the consensus gap.

• Climate change
• Climate change

Dana Nuccitelli
guardian.co.uk © 2013 Guardian News and Media Limited or its affiliated companies. All rights reserved. | Use of this content is subject to our Terms & Conditions | More Feeds

Ben just got a new tip to tip measurement this afternoon... 24.5",  He is only getting more lovable as he grows - which is good because he is big enough to kill me now.  Hardly horns me anymore...just wants to be scratched.  Bud has come along quite well.  He hand feeds from strangers now and reluctantly loves getting scratched and brushed...but not into the tape measure yet.  They were romping around like crazy last night after the cool temps and rain we got.  

Looks like summer is finally getting here.  87,97,55,0,B,.32

Of more than 4,000 academic papers published over 20 years, 97.1% agreed that climate change is anthropogenic

• Dana Nuccitelli: how we reached the findings

A survey of thousands of peer-reviewed papers in scientific journals has found 97.1% agreed that climate change is caused by human activity.

Authors of the survey, published on Thursday in the journal Environmental Research Letters, said the finding of near unanimity provided a powerful rebuttal to climate contrarians who insist the science of climate change remains unsettled.

The survey considered the work of some 29,000 scientists published in 11,994 academic papers. Of the 4,000-plus papers that took a position on the causes of climate change only 0.7% or 83 of those thousands of academic articles, disputed the scientific consensus that climate change is the result of human activity, with the view of the remaining 2.2% unclear.

The study described the dissent as a "vanishingly small proportion" of published research.

"Our findings prove that there is a strong scientific agreement about the cause of climate change, despite public perceptions to the contrary," said John Cook of the University of Queensland, who led the survey.

Public opinion continues to lag behind the science. Though a majority of Americans accept the climate is changing, just 42% believed human activity was the main driver, in a poll conducted by the Pew Research Centre last October.

"There is a gaping chasm between the actual consensus and the public perception," Cook said in a statement.

The study blamed strenuous lobbying efforts by industry to undermine the science behind climate change for the gap in perception. The resulting confusion has blocked efforts to act on climate change.

The survey was the most ambitious effort to date to demonstrate the broad agreement on the causes of climate change, covering 20 years of academic publications from 1991-2011.

In 2004, Naomi Oreskes, an historian at the University of California, San Diego,surveyed published literature, releasing her results in the journal Science. She too came up with a similar finding that 97% of climate scientists agreed on the causes of climate change.

She wrote of the new survey in an email: "It is a nice, independent confirmation, using a somewhat different methodology than I used, that comes to the same result. It also refutes the claim, sometimes made by contrarians, that the consensus has broken down, much less 'shattered'."

The Cook survey was broader in its scope, deploying volunteers from the SkepticalScience.com website to review scientific abstracts. The volunteers also asked authors to rate their own views on the causes of climate change, in another departure from Oreskes's methods.

The authors said the findings could help close the gap between scientific opinion and the public on the causes of climate change, or anthropogenic global warming, and so create favourable conditions for political action on climate.

"The public perception of a scientific consensus on AGW [anthropogenic, ie man-made, global warming] is a necessary element in public support for climate policy," the study said.

However, Prof Robert Brulle, a sociologist at Drexel University who studies the forces underlying attitudes towards climate change, disputed the idea that educating the public about the broad scientific agreement on the causes of climate change would have an effect on public opinion - or on the political conditions for climate action.

He said he was doubtful that convincing the public of a scientific consensus on climate change would help advance the prospects for political action. Having elite leaders call for climate action would be far more powerful, he said.

"I don't think people really want to come around to grips with the fact that climate change is a highly ideological issue and it is not amenable to the information deficit model," he said.

"The information deficit model, this idea that if you just pile on more information people will get convinced, is just completely inadequate, he said. "It strengthens the people who actually read and pay attention but it is certainly not going to change or shift the opinions of others."

Jon Krosnick, professor in humanities and social sciences at Stanford university and an expert on public opinion on climate change, said: "I assume that sceptics would say that there is bias in the editorial process so that the papers ultimately published are not an accurate reflection of the opinions of scientists."

• Climate change
• Climate change scepticism
• Climate change
• Peer review and scientific publishing
• United States

Suzanne Goldenberg
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Your article (European energy chief puts forward case for funding coal, 12 May) says the European Bank for Reconstruction and Development has "hinted it may expand funding of high-carbon coal projects despite mounting pressure from climate change campaigners to rule out such investments". This suggestion is wrong. The EBRD is not considering an expansion of its funding of coal projects. The EBRD has been pioneering in its development of a sustainable energy initiative which is actively promoting energy efficiency and the use of renewable energy sources across the regions where it invests. The EBRD may, on a selective basis and taking into account the lack of availability of alternative sources of energy, consider financing coal-fired projects that would replace highly polluting existing plants with new state of the art ones, thus improving energy efficiency and lowering emissions. But there is no consideration of a policy of expanding its funding for coal projects.
Anthony Williams
European Bank for Reconstruction and Development 

• It is disappointing that the transport select committee (Report, 10 May) calls for the expansion of Heathrow, given that millions of Londoners already suffer from the excessive noise and air pollution of an airport that was built in the wrong place. However, in recognising that Britain needs a competitive hub airport and that Heathrow would need a fourth runway, the committee has accidentally made clear why the Davies commission must reject Heathrow expansion and recommend a new airport to the east of London.
Richard Tracey
Transport spokesman, GLA Conservatives

• Coal
• Energy
• Fossil fuels
• Heathrow third runway
• Airline industry
• London
• Air transport

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Canvey Wick, Essex: Sitting on our egg boxes are about 20 moths from nine species, including the reed dagger and sloe carpet

Evening falls on this wildlife jewel of a brownfield site. The hazy southern horizon is crenelated with giant fuel storage tanks and chimneys, and dotted with sodium yellow lights. Metallic clanks and distant radio music drift over from an industrial estate. Close by a cuckoo calls enthusiastically from the birch scrub. Our little two-stroke generator is obstinate – coughing, spluttering, smoking and stalling. Eventually it comes to life and we plug in the moth trap; the big mercury vapour bulb flickers on and its glow builds from pink to brilliant white.

Despite the clear sky the air is still and reasonably balmy. We set off on a torch-lit bug hunt, stalking through soggy low-lying areas, striding over the broad asphalt discs where fuel tanks briefly stood in the 1970s, and sweeping nets through herbs growing in sandy areas. Where the vegetation is sparse and sand exposed we find marble-sized, white puffballs on short stems, winter stalkballs (Tulostoma brumale), more usually encountered on sand dunes. We find weevils, shiny round beetles, a variety of spiders, ladybirds, leafhoppers, picture-wing flies and a wealth of other animals – everything is less than 6mm long. Then we spot a bigger beetle climbing nonchalantly on the trunk of a small sallow tree: the blue darkling beetle (Helops caeruleus), a chunky, black, deadwood-feeder with a glorious sheen of metallic blue.

There has been a reasonable catch at the moth trap. The much-delayed spring has been disappointing for moth recorders with low catches widely reported. Sitting safely on our egg boxes are about 20 moths from nine species. Concerns about low numbers are mitigated by the quality of the species. Two are nationally scarce: the reed dagger, a khaki moth with two diffuse black streaks on each forewing, is a wetland-living reed feeder; and the sloe carpet is a delicate grey-brown moth with arched wings and a penchant for blackthorn scrub in Essex and Suffolk. Satisfied by our nocturnal hunt on this enigmatic and wonderful habitat we pack up to the sound of motorbikes speeding up and down the adjacent dual carriageway.

• Rural affairs
• Insects

Matt Shardlow
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New life is coming to Washington State's Olympic Peninsula. Two dams along the Elwha River are being removed, bringing a rush of sediment downstream and exposing hundreds of acres of once-submerged land. The dams were built in the early 1900s to power nearby timber mills. But they blocked salmon migration and their power is no longer needed, so they're coming out. This story originated as part of the public media collaboration, EarthFix.

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Fish are moving away from the equator and toward the poles to maintain their preferred water temperature. That means, for example, that fishermen are seeing swordfish normally found in the Mediterranean swimming near Denmark. But in the tropics, there are no fish to replace the ones that are leaving.

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Leaked papers show UK rejects proposal to classify oil from tar sands as highly polluting, a label that would deter EU countries from importing it

Britain has given its clearest signal yet that it wants to allow European countries to import carbon-intensive tar sands oil from Canada.

Leaked papers seen by the Guardian show that in EU negotiations on laws intended to encourage the use of low-carbon transport fuels, the UK has rejected language that would class tar sands oil as more polluting than conventional crude or other fuels.

The European commission has proposed labelling the oil as "highly polluting" under its fuel quality directive, a move that would deter countries importing it. Studies suggest that oil from tar sands produces more than one-fifth more greenhouse gas emissions than conventional crude.

But of six options put to EU countries in April on how to implement the proposal, the UK chose the two that would make no differentiation between the carbon content of fuels.

"Based on the findings so far, it seems clear that [these two] seem to meet the policy aims of the directive with the least risks of unexpected consequences," the UK said in the documents. It firmly rejected others that allowed a difference.

Previously the UK left open the possibility that it would abstain.

The papers were released by Greenpeace as Norman Baker, a minister at the Department for Transport, prepared to meet former Nasa climate scientist Jim Hansen in London. Hansen has been an outspoken critic of tar sands, saying last year "it will be game over for the climate if development of the oil sands isn't stopped".

Charlie Kronick, senior climate campaigner at Greenpeace, said: "Labelling oil from tar sands as highly polluting would strongly discourage tar sands imports into the Europe and possibly other markets. It could also discourage planned tar sands extraction projects in other parts of the world, such as Madagascar.

"If you're not serious about keeping tar sands oil out of Europe, then you're not serious about climate change. This could be the biggest decision Norman Baker will make in his entire career, and right now he's on the wrong side of the science and the wrong side of history."

But Baker said: "Our position has not changed, nor have we chosen any options – Greenpeace is simply wrong. We are committed to reducing greenhouse gas emissions and want the fuel quality directive to be a key tool in achieving this aim. We take the treatment of high-emitting oil sands seriously but we want an effective solution to address the carbon emissions from all highly polluting crudes, not simply those from oil sands.

"We continue to encourage the commission to consider and assess options which account for the carbon intensity of all crude oils, including Canadian oil sands. I take this issue seriously and that is why I have arranged to meet Jim Hansen this week to discuss the matter."

• Oil sands
• Energy
• Fossil fuels
• Oil
• Oil
• Canada
• Americas
• European Union
• Europe
• Energy industry

John Vidal
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The newly-sequenced scarlet macaw genome will provide many important insights into avian and human biology, behaviours and genetics and will contribute to parrot conservation

After many years of research into the behaviours, diseases, genetics and life history of scarlet macaws, a team of scientists have taken their studies to the next level. Christopher Seabury, an Assistant Professor of Genetics at Texas A&M University's college of Veterinary Medicine and Biomedical Sciences, and Ian Tizard, Director of the Schubot Exotic Bird Health Center and a Professor of Microbiology & Immunology at Texas A&M University's college of Veterinary Medicine and Biomedical Sciences, spearheaded an international collaboration of scientists that sequenced the genome of the scarlet macaw, Ara macao. This work significantly expands the range and depth of research opportunities involving scarlet macaws and other parrots. In addition to important conservation applications, this research may provide insights into the genetics that contribute to key traits of parrots, such as cognitive and speech abilities as well as longevity.

Scarlet macaws are large and showy parrots with brilliant red, yellow and blue plumage and long pointed tails. Endemic to Central and South America, this impressive neotropical parrot occupies a large range from southeastern Mexico throughout the Amazon basin region of Peru, Bolivia and Brazil. Easily trained to do complex tasks and to mimic human speech, wild scarlet macaws have been persecuted by the caged bird trade. Additionally, their preferred habitat of lowland evergreen rainforests makes them vulnerable to deforestation and habitat destruction.

To do this work, Drs Seabury and Tizard and their team obtained a blood sample from an adult female scarlet macaw known as "Neblina" who resides at the Blank Park Zoo in Iowa. A wild-caught parrot from Brazil, Neblina had been seized in 1995 by the US Fish and Wildlife Service after she illegally entered the United States.

Unlike mammals, avian red blood cells are nucleated, so a small sample of whole blood from a bird is an excellent source of DNA for molecular, chromosomal and cytological studies. Some cells were grown in cultures so the intact chromosomes could be harvested and examined whilst DNA was extracted from other cells for sequencing. These gene sequences were then assembled into the complete scarlet macaw genome by Seabury and his team.

Similar to almost all vertebrates, scarlet macaws are diploid; having two copies of each chromosome type, one contributed by each parent. Like all birds except birds of prey (Falconiformes), parrot genomes contain macrochromosomes and a larger number of microchromosomes.

Macrochromosomes are what most people think of when they hear the word "chromosome" and they are the type of chromosomes that are typically found in mammals. Macrochromosomes, which include autosomes and sex chromosomes, are large -- generally more than 40 megabases (Mb) in size (1 megabase is 1,000,000 nucleotide basepairs in length).

Microchromosomes, on the other hand, are very small -- usually less than 20 Mb in size. Due to their small size, microchromosomes are often impossible to distinguish when creating a traditional karyotype, as you see in Figure 1 (larger view):

Scarlet macaws have somewhere between 62 and 64 chromosomes; including 22 macrochromosomes (10 pairs of autosomomes and two sex chromosomes) and between 40 and 42 microchromosomes.

To identify similar regions between scarlet macaw and chicken macrochromosomes, the team used chromosome painting. This method uses fluorescently labeled chromosome-specific DNA probes that hybridise to complementary DNA regions, thereby identifying macaw chromosome regions that are similar to chicken chromosomes (Figure 2; larger view):

As expected, the final completed scarlet macaw genome shows similarities to that of the domestic chicken. However, there are a number of important differences, which are to be expected since parrots and chickens (taxonomic order: Galliformes) diverged approximately 122–125 million years ago. For example, several macaw macrochromosomes (1, 6 & 7) show significant rearrangements. The sex chromosome W shows no similarities at all between chicken and macaw, indicating that this chromosome is changing rapidly and thus, has not been conserved across such a large evolutionary distance.

As typical for other avian genomes studied so far, scarlet macaw genomes are smaller than mammalian genomes.

"The final analysis showed that there are about one billion DNA bases in the genome, which is about one-third of that found in mammals," Dr Tizard explained in a written press release.

"Birds have much less DNA than mammals primarily because they do not possess nearly as much repetitive DNA."

Repetitive DNA has no currently known function. The amount of repetitive DNA varies greatly between taxa: for example, more than 50 percent of the human genome is repetitive DNA [doi:10.1038/nrg3117].

According to Dr Seabury, comparing the scarlet macaw genome to other avian genomes will provide scientists with a better understanding of avian biology.

"The Scarlet Macaw Genome Project opens a variety of doors ranging from modern forensics to determining how the macaws utilize their natural habitat and landscape, as inferred from variable genetic markers," said Dr Seabury in a written press release.

In addition to research into evolution and population genetics, and conservation biology applications, what can we learn from the scarlet macaw's genome? First, even though birds have higher metabolisms than mammals, they enjoy much longer life spans than do mammals with the same body mass. In the case of scarlet macaws, adults weigh somewhere between 1000 and 1200 grams (roughly 2.2 pounds), and they reach sexual maturity at 5 years of age, yet their life span rivals that of humans. By comparing avian genomes to those obtained from other animals, it may be possible to identify which genes contribute to birds' remarkable longevity.

Other genes of interest are those involved in heart and cardiovascular fitness, and those that contribute to the risk for diabetes. But perhaps most interesting are those genes involved with cognition and brain size.

"A preliminary analysis of their genome suggests that [macaws] have a lot of genes involved in brain development", said Dr Tizard in a video press release. "Which fits, knowing how smart they are."

Despite differences from humans in brain development and structure, macaws are much like humans: they are very intelligent and live in highly complex social groups. Additionally, when corrected for differences in body size, macaws' brains are twenty-one percent larger than those of zebra finches, Taeniopygia guttata, which are the model system for vertebrate learning and memory. Thus, comparing the scarlet macaw, zebra finch and human genomes could provide greater insight and understanding into important genetic differences in brain development, structure and volume.

Sources:

Seabury C.M., Dowd S.E., Seabury P.M., Raudsepp T., Brightsmith D.J., Liboriussen P., Halley Y., Fisher C.A., Owens E. & Viswanathan G. & Tizard, I.R. (2013). A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao), PLoS ONE, 8 (5) e62415. doi:10.1371/journal.pone.0062415.s019

TAMU written and video press releases.

Also cited:

Treangen T.J. & Salzberg S.L. (2012). Repetitive DNA and next-generation sequencing: computational challenges and solutions, Nature Reviews Genetics 13: 36-46. doi:10.1038/nrg3117

Ried T., Schröck E., Ning Y. & Wienberg J. (1998). Chromosome painting: a useful art, Human Molecular Genetics, 7 (10) 1619-1626. doi:10.1093/hmg/7.10.1619 [OA PDF]

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GrrlScientist is an evolutionary biologist, ornithologist and freelance science writer who writes about the interface between evolution, ethology and ecology, especially in birds. You can follow Grrlscientist's work on her other blog, Maniraptora, and on facebook, Google +, LinkedIn, Pinterest and of course, on twitter: @GrrlScientist

• Genetics
• Birds
• Zoology
• Biology

GrrlScientist
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Comedian opposes Tattingstone solar farm but it's not clear how he'd keep the lights on and tackle climate change

In opposing a solar farm near his home in Suffolk, Griff Rhys-Jones makes the point that the government is struggling with its energy policy, and has made a "willy nilly" decision to allow such developments. I feel like saying to Griff, look we need lots of solar, and it's got to be near someone.

The government is indeed struggling with its energy policy. So are most if not all other governments. Many countries live with the threat of their lights going out. All countries live with the threat of unchecked climate change. For we are en route both to recurrent energy crisis and to six degrees of global warming, unless we accelerate the deployment of low carbon technologies like solar.

One of the reasons governments are struggling so badly is that there are no free lunches with energy. All forms of energy have downsides, somewhere. All of them have their opponents, as well as their supporters.

We know that the lights will start going out in Britain in 2016, unless new electricity generation comes onstream. It can't be coal. That much most of us agree on, if not because of the emissions, then because the EU has already made the decision, in its Large Combustion Plants Directive and other climate commitments.

Could it be gas? In principle yes. But increasingly we'd have to rely on overseas favour, because anyone outside the Treasury who knows what happens in a Texan shale-gas fracking operation knows in their hearts that – whatever we might feel about the desirability of gas – there would be civil war in rural England if there are attempts to produce it on land at any scale here.

So maybe nuclear. But even if you could tolerate a nuclear power plant or two in Suffolk, just check the builders' track record in recent years, and how much taxpayers' money would be needed to underwrite their ten-year – if they are lucky – build cycle.

That leaves renewable energy. Wind has largely been driven offshore in the UK, unlike Germany. A marked minority in the population is succeeding, in that regard, in imposing their preferences on a consistent majority, so polls on the issue tell us.

So what are we left with? Solar. That's it. Biomass and marine renewables are in their infancy in the UK still, long held back by the conventional-energy incumbency. Hydro power has limited additional potential.

I have said that all forms of energy have their downsides. Solar's are that it doesn't work at night, and yes, can be a bit on eyesore if you don't like blue or black marble. But solar sits low to the ground, can be surrounded by hedges and screened from view, can be mixed-use land with sheep grazing, plants growing, biodiversity thriving between the rows of panels.

Most forms of energy also have upsides, and in the case of solar, these greatly outweigh the downsides. They start with the fact that solar is set on becoming the cheapest option, within a few years. Many analysts forecast that solar electricity will cost less than any other form in multiple countries by 2015, or not long thereafter. It works really well when mixed in strategic harness with otherforms of renewable energy, as experience in Germany is showing.

And it offers hope, amid all the gloom about the future.

Griff should visit one of the hundreds of solar schools around the country, and talk to the kids about it. He should check out what solar can do for developing countries, where it is way cheaper than extending the grids, and as such is often the only option.

The more solar we do in cloudy Britain, the easier it becomes for developing countries – often sunny places – to believe it can work for them, and not replicate the same mistakes we have made with conventional energy.

• Solar power
• Energy
• Renewable energy
• Rhys Jones

Jeremy Leggett
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Waste and recycling handlers in Portland, Ore., say they're seeing an unfortunate side effect of the city's reduction in garbage pickups: 120 pounds of dirty diapers a day, tucked into recycling bins.

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How big would Noah's ark need to have been? Wouldn't it be possible to get two of every species on a ship such as MS Oasis of the Seas?

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• The Bible
• Cruises
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Warmer temperatures, heavy rain, flooding, sea-level rise and retreating sea ice are stealing the ground from beneath Alaskans' feet

Guardian US interactive teamGreg ChenGabriel DanceFeilding CageSuzanne Goldenberg

Tensions are running high in an Alaskan village immediately threatened by climate change

Guardian US interactive teamGabriel DanceFeilding CageRichard SprengerSuzanne Goldenberg

A debate over food standards with the largest US trading partner could affect what Americans are eating for dinner

As President Obama and Prime Minister David Cameron stood smiling for the cameras at a press conference on free trade this week, a secret lurked behind them: the average American couldn't care less about whether the US has a good trade deal with Europe, or whether Europeans buy our products or we buy theirs. With over 12 million unemployed people at home, no one's worried about whether we have enough ripe cheese from France or beer from Germany.

Yet a confluence of events over the past week shows that Cameron's visit is important to Americans. One of the things he and other leaders will be negotiating are what kinds of American food they want brought into their countries cheaply.

Here's why what Europe wants matters: the EU, which loathes American food safety practices, could, by exerting pressure on the negotiations, actually end up improving the quality or variety of food available to Americans.

Right now, the American food supply is an issue of perpetual controversy. Hormones in meat and milk have many families – at least those who can afford organic options – rushing to pay more for a sense of safety.

The US food supply lacks variety: only a few crops dominate and major companies determine the extent and quality of the food supply – and they often prefer genetically modified seeds, bred to withstand herbicides but not fully tested in their long-term effect on human health. As the Guardian reported: "three big companies now control more than half of the global seed market.. … the average cost of planting an acre of soybeans had risen 325% between 1995 and 2011."

Not surprisingly, this corporate pressure has induced American agriculture to favor the kind of crops that corporations can best control: genetically modified crops. About 93% of the soybean seeds in the United States are genetically modified, along with 88% of corn, 94% of cotton and 90% of sugarbeets, which provide about 54% of the sugar sold in America, as the HuffPo's blog has pointed out. McDonald's, one of the biggest buyers of potatoes, has an outsize influence on the shape of the US potato supply. This week, one of its major potato processors, JR Simplot, raised the possibility of growing genetically modified potatoes again.

A lot is at stake: the EU is a powerful economic force and the US's most important trading partner, and this potential trade deal is an important one. It is worth at least $97bn to the United States and as much as $132bn to the rest of the world.

The sheer dollar value of a trade agreement – think of all those lovely dollars that we could use to boost our anemic GDP – means that the EU has financial clout in the US.

In fact, the EU has enough clout to finally convince the US government to clean up America's food supply, long given over to factory farming and the economic demands of agribusiness. If America wants to export more beef, chicken and crops to the European Union, it will have to make better products. The EU won't stand for the ones we're peddling now.

The EU looks down on American food safety and production practices, and with good reason. American meat production is heavily reliant on chemicals, from hormones to chlorine-bleach baths, and European officials and consumers largely reject these treatments and standards.

American farmers and food industry officials find this European exactitude on food practices bewildering, as captured in the comment of Ron Frye, the marketing manager for a Montana ranch, when talking with the Financial Times: "If it's good enough for us it ought to be good enough for them."

The US government is friendly to agribusiness interests; from the supreme court to the State Department, it's hard to find a government department hostile to corporate interests like those of, say, Monsanto. Yesterday, Monsanto won a supreme court case that allowed it to claim a patent on its genetically modified seeds no matter how farmers came by them. The justices ruled that whether farmers come across Monsanto seeds in grain silos, as useless among feed, or from third parties, the company must be paid for its patented seeds.

Monsanto also spurred a legislative provision preventing the government from taking action to stop genetically modified seeds, even if they were found to be harmful to the health of consumers. The GM giant's influence also seems to reach into the State Department, where officials travel the world singing the praises of genetically modified crops.

As Wenonah Hauter, the head of Food and Water Watch, wrote for the Guardian this week:

"We have spent months looking at the extent to which the US State Department is working on behalf of the GM seed industry to make sure that biotech crops are served up abroad whether the world wants them or not."

Her organization, scanning 900 diplomatic cables, found the State Department encouraging US embassies across the world to "pursue an active biotech agenda" and "encourage the use of agricultural biotechnology."

With the support of the government, Monsanto is a key force in American agriculture. Its sells a popular and powerful herbicide, Roundup, alongside the only seeds that are really resistant to it: soybeans named Roundup Ready, for which it charges twice the price of normal seeds. Strong herbicide has led, predictably, to stronger superweeds; now Monsanto is creating seeds that are resistant to even more powerful weedkillers.

The US Department of Agriculture dealt Monsanto a rare blow merely by insisting that its new seeds – the ones resistant to powerful herbicides – require at least another year of examination for safety. The delay was met with surprise.

In the US, Big Agriculture calls the shots; the European Union argues that it shouldn't. A trade deal would be the testing ground for a battle over food standards to play out.

The EU has little love for Monsanto or other chemical companies with a stake in agribusiness, like Germany's BASF. The EU has approved only two genetically modified crops – corn from Monsanto and potatoes from BASF. Even those modest approvals have met cultural roadblocks. Around eight EU, including France, Italy and Poland, have taken steps to ban Monsanto's GM corn. BASF, after seeking approvals for three of its potato varieties in Europe, gave up trying after a regulatory quest that took nearly four years.

All of which tells us that if the US wants to export more agricultural products through its trade agreement with the EU, things are probably going to have to change here, as well.

• GM
• United States
• Farming
• European Union
• US politics
• US supreme court
• Agriculture
• Food & drink industry

Heidi Moore
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Green campaigners disappointed as ministers agree on phased in 5% discard rate from 2015, with exemptions on some species

Fisheries ministers from across Europe came to an agreement on a sweeping reform of fisheries policies early on Wednesday morning, but fell short of the most ambitious changes that green campaigners had demanded.

They agreed to ban the wasteful practice of discarding healthy fish at sea, but most of the ban will be phased in from 2015 instead of this year as had been proposed, and there are significant caveats for some species. Fish quotas will be based on scientific advice on what is the "maximum sustainable yield" for each stock, but there is no date on when stock levels must be restored, to the deep disappointment of greens for whom this was a central issue. Key aspects of the management of stocks will be devolved to member states instead of decided centrally in Brussels.

But details of the deal were still sketchy on Wednesday morning as the full results of the negotiations had not yet been officially released. The ministers' meeting is also not the final stage of the process – their document will be discussed by the European parliament and commission before the end deal is reached, which could take months.

Maria Damanaki, the EU fisheries commissioner, said: "[This is] a good step forward. We need a fast deal and this can give the opportunity to the commission to focus on issues relating to the implementation. We need to solve the practicalities and at the same time we need to help our fishermen to adjust to the new situation, because this is a radical change for the way we fish. We have to give all possible support to our fisheries sector and our administrations. We have positive news this morning and I hope that in the coming weeks we can work we can work together with the parliament and the council to facilitate the procedure to come to a deal."

Fleets would still be able to discard 5% of their catch under the council of ministers' plans, because ministers argued that some inadvertent catch was unavoidable, and there are exemptions covering some species, such as sea bass, and mixed fisheries, where several species inhabit the same area. The 5% level was regarded by many as the best that could be done – some member states wanted a discard rate of 10%, which greens rejected as too high. Sweden was unhappy about the compromise, however, having pushed for a zero limit.

However, the compromise means that those member states which were trying to scupper the ban altogether have effectively been thwarted.

The parliament and commission will now use the draft document from the council of ministers to come up with a further compromise position which will be thrashed out in the coming months.

"We are hoping to see something stronger than what was produced last night. We welcome it but it has not gone far enough. We think there can still be more ambition – that is possible in the next round of negotiations and a proper compromise can be achieved," said Ian Campbell, senior associate of the Pew Trusts Environment Programme.

Under the text agreed, if it is passed by the parliament, a ban on discards of pelagic fish such as mackerel and herring would come into force in 2015, and for other fisheries from 2016. Some had been hoping that a ban on mackerel and herring discards could be brought in at the end of this year.

There was also disappointment at the lack of a firm date for moving to a scientifically set maximum sustainable yield for fish quotas, which would be based on the need to restore stocks. A date of 2020 for a legally binding requirement to this effect had been proposed.

Richard Benyon, UK fisheries minister, said: "This package of reforms fulfils our promise to make discards a thing of the past and ensure sustainable fishing for future generations. The next step is for the European parliament to agree these reforms which are set to bring about real benefits for our fishermen and the marine environment for years to come. We have worked hard on these negotiations, and I hope that parliament supports our agreement and brings negotiations to a swift conclusion. The wait is nearly over."

Saskia Richartz, fisheries policy adviser at Greenpeace, said that with a 5% discard rate allowed and with exemptions in some cases the restrictions on discards could not be regarded as an outright ban. "This has pushed the door open enough to a better agreement – it is not a failure, but it depends on finding common ground on the detail, and that remains a challenge for the coming weeks," she said. "This is ultimately a decision for the parliament, to see how far they compromise or stick to their position."

She said EU citizens should write to their MEPs as soon as possible on the issue to urge them to go for a strong deal to protect Europe's dwindling fish stocks, emphasising a deadline for stock recovery. "The message of reform must be sent to the parliament. We are now in the end game and the next few weeks will be critical," she said.

Hugh Fearnley-Whittingstall, the chef who has spearheaded a campaign to ban discards, told the Guardian: "It's been a long grind to get to this point, but the news this morning is broadly good. There will be a discards ban – and that is a vindication of the huge public support for our Fish Fight campaign to end this disgraceful waste of good fish. It's a credit to our fisheries minister Richard Benyon that he and his allies managed to largely restrict attempts by the French and Spanish to water down the ban and create easy loopholes for their fishermen. There's still scope to improve on the details of the ban in the final negotiations with MEPs, who are rightly pushing for even tougher measures against discards. We'd really like to see that happen. It's also great news that the revised CFP will commit to ending overfishing and restoring fish stocks – but we still need to see hard dates to make that sticks, and that it applies across all fisheries. If we get that in the next few weeks then we should see the signing of a new CFP that can finally put European fishing on a sustainable track."

The exhaustive process of fisheries reform – the biggest shake-up of fishing in the EU for four decades – has taken more than two years of close negotiations.

• Fishing
• Food
• Wildlife
• Conservation
• Animals
• Marine life
• Fish
• Food & drink
• Seafood
• European commission
• European Union
• Europe

Fiona Harvey
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Spraying of west Berkshire woodland to kill oak processionary moth could affect local allotments and other species

A helicopter will spray insecticide on woodland in west Berkshire on Wednesday in a bid to destroy an infestation of pest caterpillars, despite complaints that not enough has been done to consult local residents.

After 1pm, if the weather is suitable, a Forestry Commission team will spend 10-15 minutes using aerial spraying to eradicate the caterpillars of the oak processionary moth (Thaumetopoea processionea), which defoliates oaks and whose thousands of hairs cause itchy rashes upon contact with people. The insecticide is a widely used toxin produced by a bacteria that occurs naturally in soil called Bacillus thuringiensis (Bt), which could kill other species of butterflies and moths known to inhabit the site.

Officials have previously reassured residents that Bt poses no risk to human or animal health. But a spokesman said they would not spray between 3 and 4.30pm because school-run traffic could be on the road through the 25-hectare woodlands, Herridge's Copse and Broom Copse, which are south-east of Pangbourne.

If delayed by bad weather, another attempt will be made on Thursday, with a second bout of spraying later this month under the terms of the licence issued by the regulator, Natural England. The site is the only location outside of London where the moth has taken hold, and tree experts are determined to stop the species from spreading throughout the UK. An extra £1.5m of government funding was announced last week to step up spraying to eradicate the moth.

But local residents and environmentalists have raised concerns over the impact of the aerial spraying, on both local allotments and other butterfly and moth species in the woods.

Green party member Jenny Hicks, who lives in Reading, said the "major concern is whether this spraying will affect allotments". Antoinette Earl, who lives nearby, said she is "very concerned" at the impact on her allotment 500 yards from site, which is designated as a site of special scientific interest. "I am aware of the toxic nature of the caterpillars, but also aware that previous control methods have reduced the number of caterpillar nests from several dozen in 2011 to only three last year. The aerial spraying approach feels like using a sledgehammer to crack a nut," said Earl.

Other species of butterflies and moths at the site include the silver-washed fritillary (Argynnis paphia), white admiral (Limenitis camilla), and the scarlet tiger moth (Callimorpha dominula).

Labour's parliamentary candidate for Reading West, Victoria Groulef, said the commission had not done enough to communicate with residents.

"Residents say that a short article in the local newsletter and a few scattered posters have said that spraying will take place, but have not indicated when it will happen, what the impact will be, or who to contact if you have concerns. Despite leaving messages on the Forestry Commission's own help line, nobody has called residents back. This is totally unacceptable.

"Residents are being very reasonable. They understand that the oak processionary moth caterpillars, a native of southern and central Europe can cause health problems. But likewise they want reassurances that the spraying will not have an impact on human health or on the local environment," she said.

• Insects
• Wildlife
• Animals
• Invasive species
• Conservation
• Trees and forests

Adam Vaughan
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