H5N1

Science march on Washington plagued by organizational turmoil

Via STAT: Science march on Washington plagued by organizational turmoil. Excerpt:

It may be the largest rally in support of science ever. Hundreds of thousands of people have joined the Facebook group for the upcoming March for Science, and tens of thousands have offered to volunteer. Beyond a march in Washington, more than 400 cities worldwide will host simultaneous events on April 22 to repudiate science policies of the new White House and Congress. 

Yet for all the excitement, STAT has found, plans for the march are plagued by infighting among organizers, attacks from outside scientists who don’t feel their interests are fairly represented, and operational disputes. Tensions have become so pronounced that some organizers have quit and many scientists have pledged not to attend. 

What was billed as science advocates speaking with a unified voice, then, has instead surfaced long-lingering tensions within the scientific community.  

Rachel Holloway, a clinical psychologist who chairs the event’s diversity and inclusion committee, conceded that initially the group was overwhelmed by scientists and activists clamoring for a spot at the table. It was “like trying to drink water out of a fire hose,” she said. 

Things have settled down since January, and organizers have begun to address members’ concerns. But many are not satisfied. 

Jacquelyn Gill, a biology and ecology professor at the University of Maine, told STAT that she quit the organizing committee in recent weeks because of leaders’ resistance to aggressively addressing inequalities — including race and gender. 

“We were really in this position where, because the march failed to actively address those structural inequalities within its own organization and then to effectively communicate those values outward, we carried those inequalities forward,” Gill said. “Some of these problems stem from the march leadership failing early on in its messaging.” 

At the heart of the disagreements are conflicting philosophies over the march’s purpose. In one corner are those who assert that the event should solely promote science itself: funding, evidence-based policies, and international partnerships. 

In another are those who argue that the march should also bring attention to broader challenges scientists face, including issues of racial diversity in science, women’s equality, and immigration policy. 

But at the senior levels of march planning, officials say they are concerned about such splintering of the march’s message — even as they combat their own disagreements over what this historic event is meant to accomplish.

Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia

Via Nature, a report on how it is possible to thrive in one place for a very, very long time: Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. The abstract:

Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. 

Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair samples, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49–45 ka. 

After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. 

Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.

You don't do that if you think your environment is something to use and throw away. If you do throw it away, you end up, at best, in the fossil record.

How the fallout from Trump's travel ban is reshaping science

Via Nature News & Comment: How the fallout from Trump's travel ban is reshaping science. Excerpt and then a comment:

Hani Goodarzi is sticking close to home these days. The cancer biologist at the University of California, San Francisco, cancelled a talk at the University of Calgary in late January and has put international travel on hold indefinitely. That’s because Goodarzi, an Iranian citizen who holds a US green card, is afraid that if he leaves the United States he might not be let back in. 

He is not alone. Many foreign-born scientists say they are reconsidering plans to work or study in the United States, even though federal courts have indefinitely blocked US President Donald Trump’s travel ban. The policy, which Trump signed on 27 January, sought to deny entry to citizens of seven Muslim-majority nations for 90 days — including those with valid US visas.  

Some researchers worry that the Trump administration will find a way to reinstate the policy, and perhaps even expand its reach. The government is reportedly preparing a reworked ban that would exclude current visa-holders, and Trump has also made brief mention of instituting a “merit-based” immigration system. The lingering uncertainty over US immigration rules is prompting some scientists to curtail crucial research trips and may dissuade other researchers, students and entrepreneurs from considering the US as a destination. 

“There is this spread of psychology of fear,” says Mustafa al’Absi, a behavioural scientist at the University of Minnesota in Duluth. “This is where the burden is: what’s going on in the air more than the facts.” 

Broken link 

The Trump ban affected citizens of Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen — including those who had already secured permission to visit or live in the United States. In the first days after the policy took effect, numerous reports surfaced of students and faculty from US universities who were trapped overseas or detained in airports. 

Even though the ban has been blocked pending legal challenges, many institutions are still playing it safe. “All foreign nationals should carefully assess whether it is worth the risk to travel outside the country,” the president of Harvard University in Cambridge, Massachusetts, said in a 28 January letter to students and faculty — advice that is still in place for people from the seven countries. Researchers from other universities told Nature that they had received similar guidance.  

Goodarzi says that he won’t leave the country unless it is an emergency, even though the White House moved to exempt green-card holders from the ban before the courts intervened. “I don’t think I can risk it at this time,” he says. That will prevent him from attending international meetings that could help to establish his scientific reputation as he builds a new lab.

After the Soviet suppression of the Hungarian revolt in 1956, Canada accepted something like 30,000 refugees—including an entire college of forestry, which the University of British Columbia happily absorbed as a windfall. No one fretted about secret Red terrorists slipping in among the refugees.

The current political climate in the US promises many more such windfalls for us and other countries. I pointed this out in a Tyee article two days after the election. 

 

When I began my teaching career in 1967, Canada welcomed American draft dodgers and deserters, and prospered. Later it welcomed Ismaili Muslims from Idi Amin's Uganda, Vietnamese boat people, and a host of ex-Yugoslavs. All have enriched Canada. 

 

If Donald Trump wants to scare his base into threatening some of the brightest people in the world, I don't mind...as long as we can go headhunting for people like Dr. Goodarzi, and put them to constructive work here.

A welcome new scientific journal

I am delighted to welcome the journal of alternative facts to Flublogia. We always need another fair and balanced viewpoint on critical issues of public health and science in general. Believe me.

Trump administration imposes freeze on EPA grants and contracts

Via ProPublica: Trump Administration Imposes Freeze On EPA Grants and Contracts. Excerpt:

The Trump administration has imposed a freeze on grants and contracts by the U.S. Environmental Protection Agency, a move that could affect a significant part of the agency’s budget allocations and even threaten to disrupt core operations ranging from toxic cleanups to water quality testing, according to records and interviews. 

In one email exchange obtained by ProPublica on Monday, an EPA contracting officer concluded a note to a storm water management employee this way: 

“Right now we are in a holding pattern. The new EPA administration has asked that all contract and grant awards be temporarily suspended, effective immediately. Until we receive further clarification, this includes task orders and work assignments.” 

Asked about any possible freeze and its implications, EPA officials did not provide an answer. 

One EPA employee aware of the freeze said he had never seen anything like it in nearly a decade with the agency. Hiring freezes happened, he said, but freezes on grants and contracts seemed extraordinary. The employee said the freeze appeared to be nationwide, and as of Monday night it was not clear for how long it would be in place.  

The substance of the email exchange was confirmed by one senior EPA employee with over 20 years at the agency. An EPA lawyer also said that earlier communications had described such a freeze. 

Monday night, Myron Ebell, who ran the EPA transition for the incoming administration, confirmed the basics of the freeze, but said the actions were not unprecedented.  

“They’re trying to freeze things to make sure nothing happens they don’t want to have happen, so any regulations going forward, contracts, grants, hires, they want to make sure to look at them first,” said Ebell, who returned over the weekend to his position directing energy and global warming policy at the Competitive Enterprise Institute, a free-market, industry-aligned group that has long fought the EPA’s growth and influence.  

“This may be a little wider than some previous administrations, but it’s very similar to what others have done,” he said.   

President Trump has nominated Oklahoma Attorney General Scott Pruitt to head the EPA. Pruitt has deep ties to the fossil fuel industry, and formed an alliance between the industry and other attorneys general to fight former President Baracks Obama’s climate proposals. He is seen as a hero among conservatives who believe the EPA oversteps its federal authority.

The hashtag #EPAFreeze is already very busy.

USDA scientists have been put on lockdown under Trump

Via BuzzFeed News: USDA Scientists Have Been Put On Lockdown Under Trump. Excerpt and then a comment:

The US Department of Agriculture has banned scientists and other employees in its main research division from publicly sharing everything from the summaries of scientific papers to USDA-branded tweets as it starts to adjust to life under the Trump administration, BuzzFeed News has learned. 

According to an email sent Monday morning and obtained by BuzzFeed News, the department told staff — including some 2,000 scientists — at the agency’s main in-house research arm, the Agricultural Research Service (ARS), to stop communicating with the public about taxpayer-funded work. 

“Starting immediately and until further notice, ARS will not release any public-facing documents,” Sharon Drumm, chief of staff for ARS, wrote in a department-wide email shared with BuzzFeed News. 

“This includes, but is not limited to, news releases, photos, fact sheets, news feeds, and social media content,” she added. 

Indeed, the last tweet from ARS’s official account was sent the day before Trump’s inauguration on Jan. 20. 

Though the terse internal note did not explicitly mention the new presidential administration, department scientists around the country interpreted it as a message from Trump that changes were coming to the department. 

The memo was also met with some confusion. When asked if the notice constituted a halt on the publication of academic articles, one regional director told scientists that research papers could be published in academic journals and presented at conferences, but that all media interviews must be approved by the office of communications in Washington. 

The Agriculture Department did not reply to a request for comment from BuzzFeed News.

Canadian scientists were muzzled for almost a decade under the Conservative Harper government, so this sounds all too familiar. Scientists should fight this step as if their lives depended on it—because they do.

Dr. Racaniello on why his Zika research proposal was turned down

On his Zika Diaries blog, Dr. Vincent Racaniello has a new post: Zika Critique. He tells us a lot about how science gets done, or doesn't get done. Excerpt:

In the last column I wrote of our first unsuccessful attempt to secure funding for our work on Zika virus. Since then we have received the reviewers' comments and now we can determine what they did not like.  

Applications for research support under the NIH R21 mechanism are reviewed by a study section consisting of ~20 experts in the field. Our application, entitled 'The neurovirulence of Zika virus isolates', was reviewed by three individuals who prepared written critiques. Each reviewer scores (from 1-9 with 1 being the best) the grant application in five different areas: significance, investigator qualifications, innovation, approach, and environment. After the entire panel votes on the scores, the final impact/priority score is calculated by averaging the numbers and multiplying by 10. Currently proposals that are scored over 30 are not funded; ours received an impact score of 41. 

Two of the three individuals assigned scores of between 1 and 3 for each of the five different areas; they were enthusiastic about the proposal and had few criticisms. Unfortunately the third reviewer did not like the proposal and scored it from 2-6 in the five different categories.   

The goal of our proposal was to study the neurovirulence of different Zika virus isolates in brain slice cultures from embryonic mice. We wish to understand how the virus affects brain development, and whether Zika virus isolates differ in their ability to disrupt the brain. 

The main criticism from the negative reviewer was that it is not clear how results obtained in mice would apply to humans. If this criticism were valid, then no virologist would be using animal models to study viruses that cause human disease. They are called 'models' for a reason: the findings might or might not be predictive of what happens in humans. But animal models are invaluable because experimental infections of humans with viruses are not done except with a few viruses that cause little or no disease. Furthermore, experiments in animals can reveal mechanisms of pathogenesis which might be validated by observations of natural infections in humans. 

Dr. Racaniello on the hazards of seeking Zika grants

Dr. Vincent Racaniello, on his blog Zika Diaries, describes the problems involved with obtaining Zika grants. Excerpt and then a comment:

If you have been reading this column from the start, you know that my lab began working on Zika virus early in 2016, switching from poliovirus. Since then we have been generating results with Zika virus and applying for financial support. Unfortunately our first effort to secure funding fell short. 

In August we sent an application to the NIH to support our work on Zika virus. NIH has many different mechanisms to support biomedical research; we chose to apply for an R21. From the NIH website: "The R21 grant mechanism is intended to encourage exploratory/developmental research by providing support for the early and conceptual stages of project development." 

An R21 grant can be for up to two years and $275,000 in direct costs. No preliminary data are required—but in these competitive years, an R21 without some data is not likely to fare well. In our application we included what we think are very interesting findings on the effect of Zika virus infection on the developing brain. We proposed a set of experiments to use our system to answer fundamental questions about how the virus causes brain defects.  

The grant application was reviewed last week, and sadly, the reviewers did not share our enthusiasm for the work: we got a score of 41. An R21 application with a score over 30 will not be funded. We have not yet received the reviewers’ comments, so we don’t know exactly what they didn’t like about the application. When we get the comments we will see if we can revise the application and resubmit it to the NIH.

By coincidence, I'm reading a wonderful book, Lab Girl, by palaeobotanist Hope Jahren, which is both a memoir of her life and career and a brilliant explanation of why plants are so amazing. I don't care what your specialty is—get it and read it. Don't wait for my eventual rave review in The Tyee.

It's also a superb account of how 21st-century science gets done...which involves persuading government bureaucrats to shell out barely enough money to keep you paying your lab assistants. It's almost enough to make you pine for the days when rich hobbyists like Darwin could afford to potter around for decades on whatever interested them.

 

Now, if you can't interest the Bill and Melinda Gates Foundation, you have no patron except the taxpayer—and the effects of Zika virus on developing mouse brains are of little concern to taxpayers in the current US presidential election. God knows if that concern will increase after next Tuesday.

Should we 'gene drive' mosquitoes to extinction?

Via Friends of the Earth, a news release: Genetic "extinction" technology rejected by international group of scientists, conservationists and environmental advocates. Excerpt:

“Gene drives are basically a technology that aims for a targeted species to go extinct,” explains ecologist and entomologist Dr. Angelika Hilbeck, president of the European Network of Scientists for Social and Environmental Responsibility (ENSSER). “While this may appear to some conservationist professionals to be a 'good' thing and a ‘silver bullet’ to handle complicated problems, there are high risks of unintended consequences that could be worse than the problems they are trying to fix.”  

Both the leading developers of the technology and also those concerned about gene drives will be attending this week’s Congress and holding events to raise awareness, hype promises or highlight the potential hazards of gene drives. 

One near-term gene drive proposal, promoted by U.S.-based non-governmental organization Island Conservation, intends to release gene drive mice on islands to eradicate them. Another led by the University of Hawai’i would develop gene drive mosquitoes for use in Hawaii to combat avian malaria which affects honeycreeper birds. 

The debate around gene drives is likely to resurface later this year at the negotiations of the United Nations Biodiversity Convention in Cancun Mexico in December.

“Gene drives, also known as ‘mutagenic chain reactions,’ aim to alter DNA so an organism always passes down a desired trait, hoping to change over time the genetic makeup of an entire species,” explains Dr. Vandana Shiva of Navdanya. “This technology would give biotech developers an unprecedented ability to directly intervene in evolution, to dramatically modify ecosystems, or even crash a targeted species to extinction.”  

“Genetic extinction technologies are a false and dangerous solution to the problem of biodiversity loss,” said Erich Pica, president of Friends of the Earth. “There are real, sustainable, community-based conservation efforts that should be supported. We are concerned that genetic extinction technologies will allow new destructive agricultural practices and even use by the military. Speculative conservation claims are at best an unfounded diversion or smokescreen. We support those in the IUCN who recognize the gravity of irreversible and irresponsible technologies such as gene drives.”

Eurosurveillance: Isolation of H5N6, H7N9, H9N2 from air at live poultry markets in China

Via Eurosurveillance: Isolation of H5N6, H7N9 and H9N2 avian influenza A viruses from air sampled at live poultry markets in China, 2014 and 2015. The abstract:

Zoonotic infections by avian influenza viruses occur at the human–poultry interface, but the modes of transmission have not been fully investigated. 

We assessed the potential for airborne and fomite transmission at live poultry markets in Guangzhou city and in Hong Kong Special Administrative Region (SAR), China, during 2014 and 2015. Viral genome and infectious avian influenza A viruses of H5N6, H7N9, and H9N2 subtypes were detected predominantly from particles larger or equal to 1 μm in diameter in the air sampled with cyclone-based bioaerosol samplers at the live poultry markets in Guangzhou. 

Influenza A(H9N2) viruses were ubiquitously isolated every month during the study period from air and environmental swabs, and different lineages of H9N2 virus were isolated from markets where chickens and minor land-based poultry were sold. 

The use of de-feathering devices increased the quantity of virus-laden airborne particles while market closure reduced the amount of such particles. The results highlight the possibility of airborne transmission of avian influenza viruses among poultry or from poultry to humans within such settings. 

This may explain epidemiological observations in which some patients with H7N9 infection reported being in markets but no direct contact with live poultry or poultry stalls.