Monthly Archives: December 2018

Amazon Turtles are Back! Thanks to Local Vigilantes

The historically over-exploited Giant South American Turtle is making a significant comeback on river beaches in the Brazilian Amazon thanks to local protection efforts, say researchers at the University of East Anglia.  Their results, published in Nature Sustainability, show that Giant Turtle populations are well on their way to full recovery on beaches guarded by local vigilantes. There are now over nine times more turtles hatching on these beaches than there were in 1977, equivalent to an annual increase of over 70,000 hatchlings.  The beach survey showed that, of over 2000 turtle nests monitored on protected beaches, only two per cent were attacked by poachers. In contrast, on unprotected beaches, poachers had harvested eggs from 99 per cent of the 202 nests surveyed.The beach protection programme along the Juruá river is part of the largest community-based conservation programme in the Brazilian Amazon. Beaches are guarded on a shoestring budget by local communities carrying out round-the-clock beach surveillance throughout the five-month turtle breeding season.

Prof Carlos Peres, from UEA’s School of Environmental Sciences and a senior author on the study, said: “This study clearly demonstrates the effectiveness of empowering local management action by stakeholders who have the largest stake and a 24/7 presence at key conservation sites. The beaches protected by local communities represent noisy islands of high biodiversity, surrounded by lifeless unprotected beaches, which are invariably empty and silent.”

Excerpts from Amazon turtle populations recovering well thanks to local action, Nov. 3, 2018

Devil’s Idea for Tokyo’s End: Fukushima

By late March 2011… after tsunami struck the Fukushima Daiichi plant—it was far from obvious that the accident was under control and the worst was over. Chief Cabinet Secretary Yukio Edano feared that radioactive material releases from the Fukushima Daiichi plant and its sister plant (Fukushima Daini) located some 12 km south could threaten the entire population of eastern Japan: “That was the devil’s scenario that was on my mind. Common sense dictated that, if that came to pass, then it was the end of Tokyo.”

Prime Minister Naoto Kan asked Dr. Shunsuke Kondo, then-chairman of the Japanese Atomic Energy Commission, to prepare a report on worst-case scenarios from the accidenta .  Dr. Kondo led a 3-day study involving other Japanese experts and submitted his report (Kondo, 2011) to the prime minister on March 25, 2011. The existence of the report was initially kept secret because of the frightening nature of the scenarios it described. An article in the Japan Times quoted a senior government official as saying, “The content [of the report] was so shocking that we decided to treat it as if it didn’t exist.” …

One of the scenarios involved a self-sustaining zirconium cladding fire in the Unit 4 spent fuel pool. Radioactive material releases from the fire were estimated to cause extensive contamination of a 50- to 70-km region around the Fukushima Daiichi plant with hotspots significant enough to require evacuations up to 110 km from the plant. Voluntary evacuations were envisioned out to 200 km because of elevated dose levels. If release from other spent fuel pools occurred, then contamination could extend as far as Tokyo,…There was particular concern that the zirconium cladding fire could produce enough heat to melt the stored fuel, allowing it to flow to the bottom of the pool, melt through the pool liner and concrete bottom, and flow into the reactor building.

Lessons Learned from the Fukushima Daiichi Accident for Spent Fuel Storage: The U.S. nuclear industry and its regulator should give additional attention to improving the ability of plant operators to measure real-time conditions in spent fuel pools and maintain adequate cooling of stored spent fuel during severe accidents and terrorist attacks. These improvements should include hardened and redundant physical surveillance systems (e.g., cameras), radiation monitors, pool temperature monitors, pool water-level monitors, and means to deliver pool makeup water or sprays even when physical access to the pools is limited by facility damage or high radiation levels….

[At nuclear power plants there must be…adequate separation of plant safety and  security systems so that security systems can continue to function independently if safety systems are damaged. In particular, security systems need to have independent, redundant, and protected power sources…]

Excerpts from Lessons Learned from the Fukushima Accident for Improving
Safety and Security of U.S. Nuclear Plants: Phase 2, US National Academies, 2016

Sequencing All Species: the Earth BioGenome Project

In the first attempt of its kind, researchers plan to sequence all known species of eukaryotic life—66,000 species of animals, plants, fungi, and protozoa—in a single country, the United Kingdom. The announcement was made here today at the official launch of an even grander $4.7 billion global effort, called the Earth BioGenome Project (EBP), to sequence the genomes of all of Earth’s known 1.5 million species of eukaryotes within a decade.

In terms of genomes sequenced, the eukaryotes—the branch of complex life consisting of organisms with cells that have a nucleus inside a membrane—lag far behind the bacteria and archaea. Researchers have sequenced just about 3500 eukaryotic genomes, and only 100 at high quality.

The U.K. sequencing effort—dubbed The Darwin Tree of Life project—will now become part of the EBP mix…Also announced today was a memorandum of understanding for participating in EBP. It has been signed by 19 institutions, including BGI Shenzhen, China; the Royal Botanic Gardens, Kew; and Sanger. 

Excerpts from Erik Stokstad, Researchers launch plan to sequence 66,000 species in the United Kingdom. But that’s just a start, Science, Nov. 1, 2018

Eradicate Mosquitoes Forever: Gene Drives

The mosquitoes are being fitted with a piece of dna called a gene drive. Unlike the genes introduced into run-of-the-mill genetically modified organisms, gene drives do not just sit still once inserted into a chromosome. They actively spread themselves, thereby reaching more and more of the population with each generation. If their effect is damaging, they could in principle wipe out whole species.. If gene drives were to condemn to a similar fate the mosquitoes that spread malaria, a second of humankind’s great scourges might be consigned to history.

Gene drives can in principle be used against any creatures which reproduce sexually with short generations and aren’t too rooted to a single spot. The insects that spread leishmaniasis, Chagas disease, dengue fever, chikungunya, trypanosomiasis and Zika could all be potential targets. So could creatures which harm only humankind’s dominion, not people themselves. Biologists at the University of California, San Diego, have developed a gene-drive system for Drosophila suzukii, an Asian fruitfly which, as an invasive species, damages berry and fruit crops in America and Europe. Island Conservation, an international environmental ngo, thinks gene drives could offer a humane and effective way of reversing the damage done by invasive species such as rats and stoats to native ecosystems in New Zealand and Hawaii.

Such critics fear that the laudable aim of vastly reducing deaths from malaria—which the World Health Organisation puts at 445,000 a year, most of them children—will open the door to the use of gene drives for far less clear-cut benefits in ways that will entrench some interests, such as those of industrial farmers, at the expense of others. They also point to possible military applications: gene drives could in principle make creatures that used not to spread disease more dangerous… The ability to remove species by fiat—in effect, to get them to remove themselves—is, like the prospect of making new species from scratch, a power that goes beyond the past ambit of humankind.

Gene drives based on crispr-Cas9 could easily be engineered to target specific bits of the chromosome and insert themselves seamlessly into the gap, thus ensuring that every gamete gets a copy . By 2016, gene drives had been created in yeast, fruitflies and two species of mosquito. In work published in the journal Nature Biotechnology in September, Andrea Crisanti, Mr Burt and colleagues at Imperial showed that one of their gene drives could drive a small, caged population of the mosquito Anopheles gambiae to extinction—the first time a gene drive had shown itself capable of doing this. The next step is to try this in a larger caged population.

There are also worries about how gene drives might be used to create a weapon. …The need to find ways to guard against such attacks is one of the reasons that the Pentagon’s Defence Advanced Research Projects Agency (darpa) gives for its work on gene drives. Renee Wegrzyn, programme manager for darpa’s “Safe Genes” project, says the work is to prevent “technological surprise”, whether in the form of an unintended consequence or nefarious use. One of the academic teams she funds has made progress in developing anti-crispr enzyme systems that one day might be able to inhibit a drive’s operation.

Oversight needs not just to bring together a range of government agencies; it requires co-operation between governments, too. The Cartagena Protocol on Biosafety, which entered into force under the un Convention on Biological Diversity (cbd) in 2003, provides controls on the transfer of genetically modified organisms. But how it applies to gene drives is unclear—and besides, America has never ratified the convention. An attempt to ban gene-drive research through the cbd, which was backed by the etc Group and other ngos, failed at the convention’s biennial meeting in Cancún in 2016…Like the reintroduction of vanished species advocated by the rewilding movement, gene-drive technology will provide new arenas for the fight between those who wish to defend nature and those who wish to tame it.

Excertps from Gene Drives: Extinction on Demand, Economist, Nov. 10, 2018, at 24

Meddling with Nature: Is it Right? Is it Fair?

Many envisioned environmental applications of newly developed gene-editing techniques such as CRISPR might provide profound benefits for ecosystems and society. But depending on the type and scale of the edit, gene-edited organisms intentionally released into the environment could also deliver off-target mutations, evolutionary resistance, ecological disturbance, and extinctions. Hence, there are ongoing conversations about the responsible application of CRISPR, especially relative to the limitations of current global governance structures to safeguard its use,   Largely missing from these conversations is attention to local communities in decision-making. Most policy discussions are instead occurring at the national or international level even though local communities will be the first to feel the context-dependent impacts of any release. ..

CRISPR gene editing and other related genetic technologies are groundbreaking in their ability to precisely and inexpensively alter the genome of any species. CRISPR-based gene drives hold particular import because they are designed to rapidly spread genetic changes—including detrimental traits such as infertility—through populations of sexually reproducing organisms, to potentially reach every member of a species. Villages in Burkina Faso are weighing the release of gene drive–bearing mosquitoes that could suppress malaria. Nantucket Island residents in the United States are considering the release of genetically engineered white-footed mice to deplete Lyme disease reservoirs. New Zealand communities are discussing the possibility of using genetic methods to eliminate exotic predators.

But what if a gene drive designed to suppress an invasive species escaped its release site and spread to a native population? Or if a coral species gene edited to better adapt to environmental stressors dominated reef ecosystems at the expense of a diversity of naturally evolving coral species and the fish that depend on them ? The gravity of these potential outcomes begs the question: Should humans even be meddling with the DNA of wild organisms? The absence of generally agreed on answers can be used to support calls for moratoria on developing and releasing genetically altered organisms, especially those with gene drives (6).

However, the promising benefits of environmental gene editing cannot be dismissed. Gene drives may provide a long-sought-after tool to control vectors of infectious disease and save millions of human lives. Projects to conserve ecosystems or promote species resilience are often intended to repair human-inflicted environmental damage. Put simply, either using this technology irresponsibly or not using it at all could prove damaging to humans, our welfare, and our planet.

At the international level, the Convention on Biological Diversity (CBD) has enlisted an expert technical panel to, in part, update its Cartagena Protocol (of which the United States is not a party) that oversees transboundary transport of living modified organisms to accommodate gene drive–bearing organisms. The International Union for the Conservation of Nature (IUCN) is also developing policy to address the release of gene-edited organisms. Although the CBD and the IUCN offer fora to engage diverse public feedback, a role largely fulfilled by civil society groups, none of these agencies currently use the broad and open deliberative process we advocate….

Different societal views about the human relationship to nature will therefore shape decision-making. Local community knowledge and perspectives must therefore be engaged to address these context-dependent, value-based considerations.  A special emphasis on local communities is also a matter of justice because the first and most closely affected individuals deserve a strong voice in the decision-making process…Compounding this challenge is that these decisions cannot be made in isolation. Organisms released into local environments may cross regional and even international borders. Hence, respect for and consideration of local knowledge and value systems are necessary, but insufficient, to anticipate the potentially ramifying global implications of environmental release of gene-edited organisms. What is needed is an approach that places great weight on local perspectives within a larger global vision…

The needs of ecosystems could also be given voice to inform deliberative outcomes through custodial human proxies. Inspired by legislative precedent set by New Zealand, in which the Whanganui River was granted legal “personhood,” human representatives, nominated by both an international body like the IUCN and the local community, would be responsible for upholding the health and interests of the ecosystems in question. Proposed gene-editing strategies would be placed in the larger context of alternative approaches to address the public health or environmental issue in question…d

An online registry for all projects intending to release genetically engineered organisms into the environment must be created. Currently, no central database exists for environmental gene-editing applications or for decision-making outcomes associated with their deployment, and this potentially puts the global community at risk…A global coordination task force would be charged with coordinating multiple communities, nations, and regions to ensure successful deliberative outcomes. As a hypothetical example, genetic strategies to eliminate invasive possums from New Zealand must include representatives from Australia, the country likely to be affected should animals be transported outside the intended range. Similarly, the African Union is currently deliberating appropriate governance of gene drive–bearing mosquitoes to combat malaria on a regional scale. 

Excerpts from Natalie Kofl et al.,  Editing nature: Local roots of global governance, Science Magazine, Nov. 2, 2018

De-Extinction: Bring Back the Passenger Pigeon

The Crispr-Cas9 system consists of two main parts: an RNA guide, which scientists program to target specific locations on a genome, and the Cas9 protein, which acts as molecular scissors. The cuts trigger repairs, allowing scientists to edit DNA in the process. Think of Crispr as a cut-and-paste tool that can add or delete genetic information. Crispr can also edit the DNA of sperm, eggs and embryos—implementing changes that will be passed down to future generations. Proponents say it offers unprecedented power to direct the evolution of species.

The technology is widely used in animals. Crispr has produced disease-resistant chickens and hornless dairy cattle. Scientists around the world routinely edit the genes in mice for research, adding mutations for human diseases such as autism and Alzheimer’s in a search of possible cures. Crispr-edited pigs contain kidneys that scientists hope to test as transplants in humans.  Crispr has been discussed as a de-extinction tool since its earliest days. In March 2013 the conservation group Revive & Restore co-organized the first TedXDeExtinction conference in Washington, D.C. Revive & Restore was co-founded by Stewart Brand, the creator of the counterculture Whole Earth Catalog and a vocal advocate for a passenger pigeon revival.

The last known passenger pigeon—a bird named Martha—died in captivity at a Cincinnati zoo in 1914….The first step was to sequence the passenger pigeon genome…Sequencing an extinct species’ genome is no easy task. When an organism dies, the DNA in its cells begins to degrade, leaving scientists with what Shapiro describes as “a soup of trillions of tiny fragments” that require reassembly. For the passenger pigeon project, Shapiro and her team took tissue samples from the toe pads of stuffed birds in museum collections. DNA in the dead tissue left them with tantalizing clues but an incomplete picture. To fill in the gaps, they sequenced the genome of the band-tailed pigeon, the passenger pigeon’s closest living relative.

By comparing the genomes of the two birds, researchers began to understand which traits distinguished the passenger pigeon. In a paper published last year in “Science,” they reported finding 32 genes that made the species unique. Some of these allowed the birds to withstand stress and disease, essential traits for a species that lived in large flocks. They found no genes that might have led to extinction. “Passenger pigeons went extinct because people hunted them to death,” Shapiro says

.Revived passenger pigeons could also face re-extinction. The species thrived in the years before European settlement of North America, when vast forests supported billions of birds. Those forests have since been replaced by cities and farmland. “The habitat the passenger pigeons need to survive is also extinct,” Shapiro says.  But what does it mean to bring an extinct species back? Andre E.R. Soares, a scientist who helped sequence the passenger pigeon genome, says most people will accept a lookalike as proof of de-extinction. “If it looks like a passenger pigeon and flies like a passenger pigeon, if it has the same shape and color, they will consider it a passenger pigeon,” Soares says.

Shapiro says that’s not enough. Eventually, she says, gene-editing tools may be able to create a genetic copy of an extinct species, “but that doesn’t mean you are going to end up with an animal that behaves like a passenger pigeon or a woolly mammoth.” We can understand the nature of an extinct species through its genome, but nurture is another matter. 

After he determines how passenger pigeon DNA manifests in the rock pigeons, Novak hopes to edit the band-tailed pigeon, the passenger pigeon’s closest living relative, with as many of the extinct bird’s defining traits as possible. Eventually, he says, he’ll have a hybrid creature that looks and acts like a passenger pigeon (albeit with no parental training) but still contains band-tailed pigeon DNA. These new-old birds will need a name, which their human creator has already chosen: Patagioenas neoectopistes, or “new wandering pigeon of America.”

Excerpts from Amy Dockser Marcus, Meet the Scientists Bringing Extinct Species Back From the Dead, WSJ, the Future of Everything, Oct. 11, 2018

The Internet Was Never Open

Rarely has a manifesto been so wrong. “A Declaration of the Independence of Cyberspace”, written 20 years ago by John Perry Barlow, a digital civil-libertarian, begins thus: “Governments of the Industrial World, you weary giants of flesh and steel, I come from Cyberspace, the new home of Mind. On behalf of the future, I ask you of the past to leave us alone. You are not welcome among us. You have no sovereignty where we gather.”

At the turn of the century, it seemed as though this techno-Utopian vision of the world could indeed be a reality. It didn’t last… Autocratic governments around the world…have invested in online-surveillance gear. Filtering systems restrict access: to porn in Britain, to Facebook and Google in China, to dissent in Russia.

Competing operating systems and networks offer inducements to keep their users within the fold, consolidating their power. Their algorithms personalise the web so that no two people get the same search results or social media feeds, betraying the idea of a digital commons. Five companies account for nearly two-thirds of revenue from advertising, the dominant business model of the web.

The open internet accounts for barely 20% of the entire web. The rest of it is hidden away in unsearchable “walled gardens” such as Facebook, whose algorithms are opaque, or on the “dark web”, a shady parallel world wide web. Data gathered from the activities of internet users are being concentrated in fewer hands. And big hands they are too. BCG, a consultancy, reckons that the internet will account for 5.3% of GDP of the world’s 20 big economies this year, or $4.2 trillion.

How did this come to pass? The simple reply is that the free, open, democratic internet dreamed up by the optimists of Silicon Valley was never more than a brief interlude. The more nuanced answer is that the open internet never really existed.

[T]e internet, it was developed “by the US military to serve US military purposes”… The decentralised, packet-based system of communication that forms the basis of the internet originated in America’s need to withstand a massive attack on its soil. Even the much-ballyhooed Silicon Valley model of venture capital as a way to place bets on risky new businesses has military origins.

In the 1980s the American military began to lose interest in the internet…. The time had come for the hackers and geeks who had been experimenting with early computers and phone lines.  Today they are the giants. Google, Apple, Facebook, Amazon and Microsoft—together with some telecoms operators—help set policy in Europe and America on everything from privacy rights and copyright law to child protection and national security. As these companies grow more powerful, the state is pushing back…

The other big risk is that the tension between states and companies resolves into a symbiotic relationship. A leaked e-mail shows a Google executive communicating with Hillary Clinton’s state department about an online tool that would be “important in encouraging more [Syrians] to defect and giving confidence to the opposition.”+++ If technology firms with global reach quietly promote the foreign-policy interests of one country, that can only increase suspicion and accelerate the fracturing of the web into regional internets….

Mr Malcomson describes the internet as a “global private marketplace built on a government platform, not unlike the global airport system”.

Excerpts from Evolution of the internet: Growing up, Economist, Mar. 26, 2016

+++The email said Google would be “partnering with Al Jazeera” who would take “primary ownership” of the tool, maintaining it and publicizing it in Syria.  It was eventually published by Al Jazeera in English and Arabic.