Tag Archives: biodiversity loss

Miracles Performed by Wild Crops

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Grains that grow year after year without having to be replanted could save money, help the environment, and reduce the need for back-breaking labor. Now, the largest real-world test of such a crop—a perennial rice grown in China—is showing promise. Perennial rice can yield harvests as plentiful as the conventional, annually planted crop while benefiting the soil and saving smallholder farmers considerable labor and expense, researchers have found…

All rice is perennial to some extent. Unlike wheat or corn, rice roots sprout new stems after harvest. The trouble is that this second growth doesn’t yield much grain, which is why farmers plow up the paddies and plant new seedlings. The improved perennial rice, in contrast, grows back vigorously for a second harvest. Researchers developed it by crossing an Asian variety of rice with a wild, perennial relative from Nigeria. Improving the offspring took decades, and in 2018 a variety called Perennial Rice 23 (PR23) became commercially available to Chinese farmers. This was a “scientific breakthrough,” says Koichi Futakuchi, a crop scientist at the Africa Rice Center…

Over 4 years PR23 averaged 6.8 tons of rice per hectare, slightly higher than the annual rice, they report today in Nature Sustainability. As hoped, the perennial crop tended to grow back again and again without sacrificing the size of the harvest. In the fifth year, however, the yields of PR23 declined for some reason, suggesting it needed to be replanted. The perennial rice also improved the soil.

Researchers note potential risks. Because PR23 enables farmers to till less, fungi and other pathogens can build up in the fields. Insects can persist in the stubble after harvest, because it’s not plowed under, then transmit viruses when they feed on the regenerating sprouts in the spring. And without tilling, weeds can flourish; the researchers found that fields with PR23 needed one to two more herbicide treatments than regular rice. They also note that it’s more work to resow the perennial rice when its yield falters, because its larger and deeper roots need to be killed.

Excerpts from ‘Perennial’ rice saves time and money, but comes with risks, Science, Nov. 7, 2022

Reversing Industrialization: the Future of Plants?

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Is it possible that the microbiomes of ancestors of our crops can be used to “rewild” microbiomes of current crops reinstating their diverse microbiota that were lost through domestication and industrialization processes, including including the (over)use of antibiotics, pesticides, and fertilizers?

Similar to reversing industrialization-associated changes in human gut microbiota , plant microbiome rewilding builds on the premise that wild ancestors harbor microbial genera with specific traits that are not found (or are strongly depleted) in the microbiome of modern crops. To date, however, it is unknown for most plant species whether (and which) microbial genera and functions were lost during plant domestication, and to what extent rewilding can enhance the health and sustainability of modern crops. In animal systems, the effectiveness of rewilding approaches is intensely debated , and similar discussions are needed for crop rewilding approaches.

Plant domestication is one of the most important accomplishments in human history, helping drive the transition from a nomadic to a sedentary lifestyle. Through stepwise processes, crop plants acquired a suite of new traits, including larger seeds, determinate growth, photoperiod sensitivity, and reduced levels of bitter substances. Although this led to a more continuous food supply, domestication caused a reduction in plant genetic diversity because only desired alleles were spread, while genomic regions next to the target genes suffered selective sweeps (6). This so-called “domestication syndrome” decreased the ability of crops to withstand pests and diseases

Excerpts from JOS M. RAAIJMAKERS AND E. TOBY KIERM, Microbiota of crop ancestors may offer a way to enhance sustainable food production, Science, Nov. 11, 2022

The Battle for Biodiversity and Human Rights

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From the lush Amazon rainforest to the frigid Arctic Ocean, the world’s landscapes — and all the wildlife they contain — are under threat, and the world needs to set aside a third of all land and sea territories to save them, U.N. experts say.

The call is central to the global agreement being hashed out in December 2022 at the U.N. biodiversity summit in Montreal. If approved, governments would be agreeing to set aside 30% of their land and sea territories for conservation by 2030 – the so-called 30-by-30 goal, doubling the amount of land area and more than tripling the ocean territory currently under conservation…

A June 2022 study in the journal Science found, however, that at least 44% of global land area would be needed to protect areas with a high diversity of species, prevent the loss of intact ecosystems, and optimize the representation of different landscapes and species. But more than 1.8 billion people live in these areas…

One of the key tension points that has emerged in the 30-by-30 debate at COP15 is whether the target should be carried out globally or at a national level…It is an important distinction, scientists and negotiators said. Some countries are small, without much land to set aside for nature. Others are vast and still contain a high degree of biodiversity, such as tropical forest nations like Brazil and Indonesia. Were such countries to protect only 30% of their territories, that could actually result in a significant loss of nature…Currently, just under 50% of the Amazon is under some form of official protection or indigenous stewardship, so a national pledge to conserve 30% would represent a significant downgrade.

The other dispute plaguing 30-by-30 is over what should count as protection. Some countries might allow people to live within protected areas or promote indigenous stewardship of these lands. Some might even allow for extractive industries to operate under permits and regulation. In other cases, conservation areas are off limits to everyone. The European Union has proposed allowing activities like logging, mining and fishing to be carried out under conservation management for 20% of protected areas, while 10% would be held under stricter protections.

The idea caused environmental nonprofit Greenpeace to accused the EU last week of trying to water down language on 30-by-30, which the EU denied.

Excerpts from Gloria Dickie, Protecting 30% of the planet to save nature is not as simple as it sounds, Reuters Dec. 14, 2022

Sins of Environmentalism

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During the opening ceremony of the (Conference of the Parties) COP15 of the Biodiversity Convention taking place in early December 2022,  Canadian Prime Minister Justin Trudeau called for a global agreement to protect 30% of the world’s land and water by 2030. This so-called ’30×30′ plan is opposed by a number of groups that promote the rights of indigenous peoples. According to Survival International, an organization campaigning for Indigenous rights, 30 x 30 will be the biggest land grab in history.

Already in many Protected Areas around the world local people, who have called the land home for generations, are no longer allowed to live on and use the natural environment to feed their families, gather medicinal plants or visit sacred sites.

‘Fortress Conservation’ is one example of a conservation model that excludes Indigenous communities. It began with the formation of Yosemite, the world’s first national park, in North America over 150 years ago.  To preserve the ‘pristine wilderness’ humans needed to be expelled so the native Americans, who had lived in and cared for the region for thousands of years, were evicted.

Only 3 per cent of the world’s land remains ecologically intact, and biodiversity loss continues at an alarming rate.  In 2010, member states of the Convention on Biological Diversity (CBD) committed to placing 17 per cent of the world’s land within protected areas by 2020. Yet during that decade global biodiversity actually declined significantly.

There have also been systemic human rights abuses. Rainforest Foundation UK protects the world’s rainforests by supporting and empowering the Indigenous people and local communities which live in them.  But its research into 34 Protected Areas in the Congo Basin showed that without the presence of Indigenous communities, animal populations dwindled, and extractive activities increased. This was despite large investments having been channeled into them.  It also uncovered widespread disregard for local communities’ rights and livelihoods and conflict between forest peoples and conservationists in this region.

According to Joe Eisen, Executive Director of Rainforest Foundation UK, human rights abuses are commonplace in the Congo Basin. “Our research has shown these human rights abuses are not just the isolated actions of rogue park rangers but are rather part of a system in which displacement, torture, gender-based violence and extrajudicial killings are used to control Indigenous peoples and other local communities who live in, and depend on, areas of high conservation value,” he says.

Protected Areas are often managed by major international conservation organizations, who employ armed guards to evict the local population and prevent their return. These actions have long-term consequences and destroy Indigenous livelihoods and cultures.

There are calls for the development of a community-based conservation model, which empowers Indigenous people, rather than removing them from their ancestral lands.

Excerpts from Plans to protect 30% of the planet by 2030 could be ‘devastating’ for Indigenous people, Euronews, Dec. 8, 2022

Natural Capital and Human Well-Being

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What is the contribution of nature to the economy?… The breathable air, drinkable water and tolerable temperatures that allow humans to do everything they do, and the complex ecosystems that maintain them, tend to be taken for granted. Professor Dasgupta’s review on the Economics of Biodiversity does not seek to play on the heartstrings with tales of starving polar bears. Rather, it makes the hard-headed case that services provided by nature are an indispensable input to economic activity. Some of these services are relatively easy to discern: fish stocks, say, in the open ocean. Others are far less visible: such as the complex ecosystems within soil that recycle nutrients, purify water and absorb atmospheric carbon. These are unfamiliar topics for economists, so the review seeks to provide a “grammar” through which they can be analysed.

The report features its own illustrative production function, which includes nature. The environment appears once as a source of flows of extractable resources (like fish or timber). But it also shows up more broadly as a stock of “natural” capital. The inclusion of natural capital enables an analysis of the sustainability of current rates of economic growth. As people produce GDP, they extract resources from nature and dump waste back into it. If this extraction and dumping exceeds nature’s capacity to repair itself, the stock of natural capital shrinks and with it the flow of valuable environmental services. Between 1992 and 2014, according to a report published by the UN, the value of produced capital (such as machines and buildings) roughly doubled and that of human capital (workers and their skills) rose by 13%, while the estimated value of natural capital declined by nearly 40%. The demands humans currently place on nature, in terms of resource extraction and the dumping of harmful waste, are roughly equivalent to the sustainable output of 1.6 Earths (of which, alas, there is only the one)…Indeed, Professor Dasgupta argues that economists should acknowledge that there are in fact limits to growth. As the efficiency with which we make use of Earth’s finite bounty is bounded (by the laws of physics), there is necessarily some maximum sustainable level of GDP…

Professor Dasgupta hints at this problem by appealing to the “sacredness” of nature, in addition to his mathematical models and analytical arguments.

Excerpts from How should economists think about biodiversity?, Economist, Feb. 6, 2021

Mining the Ocean: the Fate of Sea Pangolin

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A snail that lives near hydrothermal vents on the ocean floor east of Madagascar has become the first deep-sea animal to be declared endangered because of the threat of mining.  The International Union for Conservation of Nature (IUCN) added the scaly-foot snail (Chrysomallon squamiferum) to its Red List of endangered species on 18 July, 2019 — amid a rush of companies applying for exploratory mining licenses…. The scaly-foot snail is found at only three hydrothermal vents in the Indian Ocean.  Two of those three vents are currently under mining exploration licences,…Even one exploratory mining foray into this habitat could destroy a population of these snails by damaging the vents or smothering the animals under clouds of sediment..

Full-scale mining of the deep seabed can’t begin in international waters until the International Seabed Authority (ISA) — a United Nations agency tasked with regulating sea-bed mining — finalizes a code of conduct, which it hopes to do by 2020….The biggest challenge to determining whether the scaly-foot snail warranted inclusion on the Red List was figuring out how to assess the extinction risk for animals that live in one of the weirdest habitats on Earth…

When the IUCN considers whether to include an organism on the Red List, researchers examine several factors that could contribute to its extinction. They include the size of a species’ range and how fragmented its habitat is…The IUCN settled on two criteria to assess the extinction risk for deep-sea species: the number of vents where they’re found, and the threat of mining.   In addition to the scaly-foot snail, the researchers are assessing at least 14 more hydrothermal vent species for possible inclusion on the Red List.

Excerpts from Ocean Snail is First Animal to be Officially Endangered by Deep-Sea Mining, Nature, July 22, 2019

On Sea Pangolins see YouTube video

How to Strengthen the Immune System of Plants: biodiversity

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In the past 150 years, the concentration of carbon dioxide in the atmosphere has risen from 280 parts per million (ppm) to 410 ppm. For farmers this is mixed news. Any change in familiar weather patterns caused by the atmospheric warming this rise is bringing is bound to be disruptive. But more carbon dioxide means more fuel for photosynthesis and therefore enhanced growth—sometimes by as much as 40%. And for those in temperate zones, rising temperatures may bring milder weather and a longer growing season. (In the tropics the effects are not so likely to be benign.) What is not clear, though, and not much investigated, is how rising CO2 levels will affect the relation between crops and the diseases that affect them…

Plant biology is altered substantially by a range of environmental factors. This makes it difficult to predict what effect a changing climate will have on particular bits of agriculture. Carbon dioxide is a case in point. It enhances growth of many plants but,  it also shifts the defences to favour some types of disease over others.

To make matters even more complicated, evidence is mounting that changes in temperature and water availability also shift plant immune responses. André Velásquez and Sheng Yang He, at Michigan State University, wrote an extensive review on the warfare between plants and diseases in Current Biology in 2018. They noted that though some valuable crops, such as potatoes and rice, experience less disease as moisture levels increase, this is not the case for most plants. High humidity, in general, favours the spread of botanical diseases. The same can be said for temperature—with some diseases, like papaya ringspot virus, thriving in rising temperatures while others, for example potato cyst, are weakened.

The problems are daunting, then, but there is a way to try to solve them… Genes which grant resistance to diseases that might become severe in the future need to be tracked down. Modern crops have been streamlined by artificial selection to be excellent at growing today. This means that they have the genes they need to flourish when faced with the challenges expected from current conditions, but nothing more. Such crops are thus vulnerable to changes in their environment.  One way to find genes that may alter this state of affairs is to look to crops’ wild relatives. Uncossetted by farmers, these plants must survive disease by themselves—and have been fitted out by evolution with genes to do so. Borrowing their dna makes sense. But that means collecting and cataloguing them. This is being done, but not fast enough. The International Centre for Tropical Agriculture, a charity which works in the area, reckons that about 30% of the wild relatives of modern crops are unrepresented in gene banks, and almost all of the rest are underrepresented….

[This is becuase] most countries are, rightly, protective of their genetic patrimony. If money is to be made by incorporating genes from their plants into crops, they want to have a share of it. It is therefore incumbent on rich countries to abide by rules that enable poor ones to participate in seed collecting without losing out financially. Poor, plant-rich countries are in any case those whose farmers are most likely to be hurt by global warming. It would be ironic if that were made worse because genes from those countries’ plants were unavailable to future-proof the world’s crops.

Excerpts from Blocking the Road to Rusty Death: Climate Change and Crop Disease, Economist,  Apr. 20, 2019

Biodiversity and Respect for Human Rights

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The instinctive response of many environmentalists  is to to fence off protected areas as rapidly and extensively as possible. That thought certainly dominates discussions of the Convention on Biological Diversity, the main relevant international treaty. An eight-year-old addendum to the pact calls for 17% of the world’s land surface and 10% of the ocean’s water column (that is, the water under 10% of the ocean’s surface) to be protected by 2020. Currently, those figures are 15% and 6%. Campaigners want the next set of targets, now under discussion, to aim for 30% by 2030—and even 50% by 2050. This last goal, biogeographers estimate, would preserve 85% of life’s richness in the long run.  As rallying cries go, “Nature needs half” has a ring to it, but not one that sounds so tuneful in the poor countries where much of the rhetorically required half will have to be found. Many people in such places already feel “Cornered by Protected Areas.” (See also Biodiversity and Human Rights)

James Watson, chief scientist at the Wildlife Conservation Society (wcs), another American charity, has an additional worry about focusing on the fence-it-off approach. If you care about the presence of species rather than the absence of humans, he warns, “‘nature needs half’ could be a catastrophe—if you get the wrong half.” Many terrestrial protected areas are places that are mountainous or desert or both. Expanding them may not translate into saving more species. Moreover, in 2009 Lucas Joppa and Alexander Pfaff, both then at Duke University in North Carolina, showed that protected areas disproportionately occupy land that could well be fine even had it been left unprotected: agriculture-unfriendly slopes, areas remote from transport links or human settlements, and so on. Cordoning off more such places may have little practical effect.

Southern Appalachians, Virginia. image from wikipedia

 In the United States it is the underprotected southern Appalachians, in the south-east of the country, that harbour the main biodiversity hotspots. The largest patches of ring-fenced wilderness, however, sit in the spectacular but barren mountain ranges of the west and north-west. In Brazil, the world’s most speciose country, the principal hotspots are not, as might naively be assumed, in the vast expanse of the Amazon basin, but rather in the few remaining patches of Atlantic rainforest that hug the south-eastern coast.

Deforestation Atlantic Rainforest in Rio de Janeiro. Image from wikipedia

Nor is speciosity the only consideration. So is risk-spreading. A team from the University of Queensland, in Australia, led by Ove Hoegh-Guldberg, has used a piece of financial mathematics called modern portfolio theory to select 50 coral reefs around the world as suitable, collectively, for preservation. Just as asset managers pick uncorrelated stocks and bonds in order to spread risk, Dr Hoegh-Guldberg and his colleagues picked reefs that have different exposures to rising water temperatures, wave damage from cyclones and so on. The resulting portfolio includes reefs in northern Sumatra and the southern Red Sea that have not previously registered on conservationists’ radar screens…

Another common finding—counterintuitive to those who take the “fence-it-all-off” approach—is that a mixed economy of conservation and exploitation can work. For example, rates of deforestation in a partly protected region of Peru, the Alto Mayo, declined by 78% between 2011 and 2017, even as coffee production increased from 20 tonnes a year to 500 tonnes.

Environmental groups can also draw on a growing body of academic research into the effective stewardship of particular species. For too long, says William Sutherland, of Cambridge University, conservationists have relied on gut feelings. Fed up with his fellow practitioners’ confident but unsubstantiated claims about their methods, and inspired by the idea of “evidence-based medicine”, he launched, in 2004, an online repository of relevant peer-reviewed literature called Conservation Evidence.  Today this repository contains more than 5,400 summaries of documented interventions. These are rated for effectiveness, certainty and harms. Want to conserve bird life threatened by farming, for example? The repository lists 27 interventions, ranging from leaving a mixture of seed for wild birds to peck (highly beneficial, based on 41 studies of various species in different countries) to marking bird nests during harvest (likely to be harmful or ineffective, based on a single study of lapwing in the Netherlands). The book version of their compendium, “What Works in Conservation”, runs to 662 pages. It has been downloaded 35,000 times.

Excerpts from How to preserve nature on a tight budget, Economist, Feb. 9, 2919

From Savior to Villain: Biofuel from Palm Oil

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Globally, average palm oil yields have been more or less stagnant for the last 20  years, so the required increase in palm oil production to meet the  growing demand for biofuels  has come from deforestation and peat destruction in Indonesia.  Without fundamental changes in governance, we can expect at least a third of new palm oil  area to require peat drainage, and a half to result in deforestation.

Currently, biofuel policy results in 10.7  million tonnes of palm oil demand.  If the current biofuel policy continues we expect by 2030:
• 67 million tonnes palm oil demand due to biofuel policy.
• 4.5 million hectares deforestation.
• 2.9 million hectares peat loss.
• 7 billion tonnes of CO2 emissions over 20 years, more than total annual U.S. GHG emissions.
It must always be remembered that the primary purpose of biofuel policy in the EU and many  other countries is climate change mitigation. Fuel consumers in the European Union, Norway  and elsewhere cannot be asked to continue indefinitely to pay to support vegetable oil based
alternative fuels that exacerbate rather than mitigate climate change.

The use of palm oil-based biofuel should be  reduced and ideally phased out entirely.  In Europe, the use of biodiesel other than that produced from approved waste or  by-product feedstocks should be reduced or eliminated.
In the United States, palm oil biodiesel should continue to be restricted from generating  advanced RINs under the Renewable Fuel Standard. Indonesia should reassess the relationship between biofuel mandate, and its  international climate commitments, and refocus its biofuel programme on advanced biofuels from wastes and residues. The aviation industry should focus on the development of advanced aviation biofuels  from wastes and residues, rather than hydrotreated fats and oils.

Excerpts from Dr Chris Malins,  Driving deforestation: The impact of expanding palm oil demand through biofuel policy, January 2018

In Feb. 28, 2019, Norway’s $1 trillion sovereign wealth fund, the world’s largest, pulled out of more than 33 palm oil companies over deforestation risks.

Radical New Potatoes

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Potatoes are already a staple for 1.3 billion people… but unlike other major crops, however, the potato has not had a breeding breakthrough of the kind that helped dramatically boost yields during the Green Revolution of the 1950s and 1960s. The reason is that creating a new potato variety is slow and difficult, even by the patient standards of plant breeders…Readying a new potato variety for farm fields can take a decade or more.  Many countries continue to plant popular potato varieties that have remained essentially unchanged for decades. But new approaches, including genetic engineering, promise to add more options. Potato breeders are particularly excited about a radical new way of creating better varieties. This system, called hybrid diploid breeding, could cut the time required by more than half, make it easier to combine traits in one variety, and allow farmers to plant seeds instead of bulky chunks of tuber. 

Solynta Hybrid Potato Seeds

To breed a better potato, it helps to have plenty of genetic raw material on hand. But the world’s gene banks aren’t fully stocked with the richest source of valuable genes: the 107 potato species that grow in the wild. Habitat loss threatens many populations of those plants. In a bid to preserve that wild diversity before it vanishes, collectors have made their biggest push ever, part of a $50 million program coordinated by the Crop Trust, an intergovernmental organization based in Bonn, Germany.

The Crop Trust has provided grants and training to collectors around the world. The effort on wild potatoes, which wraps up this month, has yielded a collection representing 39 species from six nations: Peru, Brazil, Ecuador, Guatemala, Costa Rica, and Chile. Zorrilla’s team alone found 31 species in Peru, including one for which no seeds had ever been collected. They plan to continue to search for four other species still missing from gene banks. “We will not stop,” she says. The plants are being stored in each nation’s gene bank, CIP, and the Millennium Seed Bank at the Royal Botanic Gardens, Kew, in the United Kingdom. The stored seeds will be available to potato breeders worldwide.

THE HARDEST PART comes next: getting desirable genes from wild species into cultivated potatoes….Other researchers are skirting the limitations of traditional breeding by using genetic engineering. CIP’s Marc Ghislain and colleagues, for example, have directly added genes to already successful potato varieties without altering the plants in any other way—an approach not possible with traditional breeding. They took three genes for resistance to late blight from wild relatives and added them to varieties of potato popular in East Africa.

Potato Blight , a disease affecting potatoes

The engineered varieties have proved successful in 3 years of field tests in Uganda and are undergoing final studies for regulators. Transgenic potatoes that resist late blight have already been commercialized in the United States and Canada….

Pim Lindhout has been plotting a revolution that would do away with much of that tedium and complexity. As head of R&D for Solynta, a startup company founded in 2006, he and his colleagues have been developing a new way to breed potatoes….Breeders reduce the complexity either by using species with only two sets of chromosomes (known as diploids) or by manipulating domesticated potatoes to cut the number of chromosomes in half. With persistence, diploid potatoes can be inbred. In 2011, Lindhout published the first report of inbred diploid lines that are vigorous and productive. More recently, Jansky and colleagues also created inbred diploid lines.

Such diploid inbred plants are at the heart of Solynta’s strategy to revolutionize potato breeding. Other firms, including large seed companies, are also working to develop hybrid potatoes. HZPC in Joure, the Netherlands, has begun field trials in Tanzania and in several countries in Asia.

Excerpt from Erik Stokstad, The new potato, Science, Feb. 8, 2019

A Botanical Treasure: Congo

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Situated along the banks of the Congo River, the Yangambi Research Station was in its heyday a booming scientific hub, revered for its invaluable work in the Congo Basin throughout the midcentury.

It wasn’t to last. War, political instability and budget cuts were to hamper the center’s survival after Democratic Republic of Congo (DRC) gained independence from its colonial ruler, Belgium, in 1960. The following decades would see skilled staff numbers dwindle, the jungle reclaim its buildings, and the center’s science work come to a stop.  But inside these crumbling walls lay a botanical treasure-trove. Yangambi’s herbarium holds Central Africa’s largest collection of dried plants. In fact, 15% of its 150,000 specimens are so rare, that they can only be found here….

Efforts from the Congolese Institute for Agronomy Research (INERA) could not keep the center running alone.   It was in 2017 that a ‘game changing’ opportunity arrived. INERA and the Meise Botanic Garden partnered with FORETS, a project coordinated by the Center for International Forestry Research (CIFOR)and financed by the European Union…Now, the herbarium has benefitted from a facelift – including a new roof, windows and doors, and a water cistern – soon its staff will be trained in modern preservation techniques and new technologies…Digitization of specimens will enable access to researchers around the world.

Excerpts from AHTZIRI GONZALEZ, Protecting Congo’s botanical treasures, CIFOR Press Release, Jan 11, 2019

Sequencing All Species: the Earth BioGenome Project

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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

Who Owns the Genes in the Seas?

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It’s an eye-catching statistic: A single company, the multinational chemical giant BASF, owns nearly half of the patents issued on 13,000 DNA sequences from marine organisms. That number is now helping fuel high-stakes global negotiations on a contentious question: how to fairly regulate the growing exploitation of genes collected in the open ocean, beyond any nation’s jurisdiction.

The negotiations that took place at the UN in September 2018 aim, inter alia, to replace today’s free-for-all scramble for marine genetic resources with a more orderly and perhaps more just regime.  Many developed nations and industry groups are adamant that any new rules should not complicate efforts to discover and patent marine genes that may help create better chemicals, cosmetics, and crops. But many developing nations want rules that will ensure they, too, share in any benefits. Scientists are also watching. A regulatory regime that is too burdensome could have “a negative impact” on scientists engaged in “noncommercial ocean research,” warns Robert Blasiak, a marine policy specialist at the Stockholm Resilience Centre.  It is not the first time nations have wrangled over how to share genetic resources. Under another U.N. pact, the 2010 Nagoya Protocol, 105 countries have agreed to rules to prevent so-called biopiracy: the removal of biological resources—such as plant or animal DNA—from a nation’s habitats without proper permission or compensation.

Those rules don’t apply in international waters, which begin 200 nautical miles from shore and are attracting growing interest from researchers and companies searching for valuable genes. The first patent on DNA from a marine organism was granted in 1988 for a sequence from the European eel, which spends part of its life in freshwater. Since then, more than 300 companies, universities, and others have laid claim to sequences from 862 marine species, a team led by Blasiak reported in June in Science Advances. Extremophiles have been especially prized. Genes from worms found in deep-sea hydrothermal vents, for example, encode polymers used in cosmetics. And BASF has patented other worm DNA that the company believes could help improve crop yields. The conglomerate, based in Ludwigshafen, Germany, says it found most of its 5700 sequences in public databases…

It may take years for nations to agree on a marine biodiversity treaty; [A]n “ideological divide” between developing and developed countries has, so far, “led to stalemate” on how to handle marine genetic resources, says Harriet Harden-Davies, a policy expert at the University of Wollongong in Australia.

Most developing nations want to expand the “common heritage” philosophy embedded in the 1982 United Nations Convention on the Law of the Sea, which declares that resources found on or under the seabed, such as minerals, are the “common heritage of mankind.” Applying that principle to genetic resources would promote “solidarity in the preservation and conservation of a good we all share,” South Africa’s negotiating team said in a recent statement. Under such an approach, those who profit from marine genes could, for example, pay into a global fund that would be used to compensate other nations for the use of shared resources, possibly supporting scientific training or conservation.

But developed nations including the United States, Russia, and Japan oppose extending the “common heritage” language, fearing burdensome and unworkable regulations. They argue access to high seas genes should be guaranteed to all nations under the principle of the “freedom of the high seas,” also enshrined in the Law of the Sea. That approach essentially amounts to finders keepers, although countries traditionally have balanced unfettered access with other principles, such as the value of conservation, in developing rules for shipping, fishing, and research in international waters.

The European Union and other parties want to sidestep the debate and seek a middle ground. One influential proposal would allow nations to prospect for high seas genes, but require that they publish the sequences they uncover. Companies could also choose to keep sequences private temporarily, in order to be able to patent them, if they contribute to an international fund that would support marine research by poorer nations. “Researchers all around the world should be put all on a level playing field,” says Arianna Broggiato, a Brussels-based legal adviser for the consultancy eCoast, who co-authored a paper on the concept this year in The International Journal of Marine and Coastal Law.

Exceprts from Eli Kintisch U.N. tackles gene prospecting on the high seas, Science, Sept. 7, 2018

An Earth Bank of Codes: who owns what in the biological world

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A project with the scale and sweep of the original Human Genome Project…should be to gather DNA sequences from specimens of all complex life on Earth. They decided to call it the Earth BioGenome Project (EBP).

At around the same time as this meeting, a Peruvian entrepreneur living in São Paulo, Brazil, was formulating an audacious plan of his own. Juan Carlos Castilla Rubio wanted to shift the economy of the Amazon basin away from industries such as mining, logging and ranching, and towards one based on exploiting the region’s living organisms and the biological information they embody. At least twice in the past—with the businesses of rubber-tree plantations, and of blood-pressure drugs called ACE inhibitors, which are derived from snake venom—Amazonian organisms have helped create industries worth billions of dollars. ….

For the shift he had in mind to happen, though, he reasoned that both those who live in the Amazon basin and those who govern it would have to share in the profits of this putative new economy. And one part of ensuring this happened would be to devise a way to stop a repetition of what occurred with rubber and ACE inhibitors—namely, their appropriation by foreign firms, without royalties or tax revenues accruing to the locals.

Such thinking is not unique to Mr Castilla. An international agreement called the Nagoya protocol already gives legal rights to the country of origin of exploited biological material. What is unique, or at least unusual, about Mr Castilla’s approach, though, is that he also understands how regulations intended to enforce such rights can get in the way of the research needed to turn knowledge into profit. To that end he has been putting his mind to the question of how to create an open library of the Amazon’s biological data (particularly DNA sequences) in a way that can also track who does what with those data, and automatically distribute part of any commercial value that results from such activities to the country of origin. He calls his idea the Amazon Bank of Codes.

Now, under the auspices of the World Economic Forum’s annual meeting at Davos, a Swiss ski resort, these two ideas have come together. On January 23, 2018 it was announced that the EBP will help collect the data to be stored in the code bank. The EBP’s stated goal is to sequence, within a decade, the genomes of all 1.5m known species of eukaryotes. ..That is an ambitious timetable. The first part would require deciphering more than eight genomes a day; the second almost 140; the third, about 1,000. For comparison, the number of eukaryotic genomes sequenced so far is about 2,500…

Big sequencing centres like BGI in China, the Rockefeller University’s Genomic Resource Centre in America, and the Sanger Institute in Britain, as well as a host of smaller operations, are all eager for their share of this pot. For the later, cruder, stages of the project Complete Genomics, a Californian startup bought by BGI, thinks it can bring the cost of a rough-and-ready sequence down to $100. A hand-held sequencer made by Oxford Nanopore, a British company, may be able to match that and also make the technology portable…..It is an effort in danger of running into the Nagoya protocol. Permission will have to be sought from every government whose territory is sampled. That will be a bureaucratic nightmare. Indeed, John Kress of the Smithsonian, another of the EBP’s founders, says many previous sequencing ventures have foundered on the rock of such permission. And that is why those running the EBP are so keen to recruit Mr Castilla and his code bank.

The idea of the code bank is to build a database of biological information using a blockchain. Though blockchains are best known as the technology that underpins bitcoin and other crypto-currencies, they have other uses. In particular, they can be employed to create “smart contracts” that monitor and execute themselves. To obtain access to Mr Castilla’s code bank would mean entering into such a contract, which would track how the knowledge thus tapped was subsequently used. If such use was commercial, a payment would be transferred automatically to the designated owners of the downloaded data. Mr Castilla hopes for a proof-of-principle demonstration of his platform to be ready within a few months.

In theory, smart contracts of this sort would give governments wary of biopiracy peace of mind, while also encouraging people to experiment with the data. And genomic data are, in Mr Castilla’s vision, just the start. He sees the Amazon Bank of Codes eventually encompassing all manner of biological compounds—snake venoms of the sort used to create ACE inhibitors, for example—or even behavioural characteristics like the congestion-free movement of army-ant colonies, which has inspired algorithms for co-ordinating fleets of self-driving cars. His eventual goal is to venture beyond the Amazon itself, and combine his planned repository with similar ones in other parts of the world, creating an Earth Bank of Codes.

[I]f the EBP succeeds, be able to use the evolutionary connections between genomes to devise a definitive version of the tree of eukaryotic life. That would offer biologists what the periodic table offers chemists, namely a clear framework within which to operate. Mr Castilla, for his part, would have rewritten the rules of international trade by bringing the raw material of biotechnology into an orderly pattern of ownership. If, as many suspect, biology proves to be to future industries what physics and chemistry have been to industries past, that would be a feat of lasting value.

Excerpts from Genomics, Sequencing the World, Economist, Jan. 27, 2018

Unjustifiable Extinctions

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The world’s botanic gardens contain at least 30% of all known plant species, including 41% of all those classed as ‘threatened’, according to the most comprehensive analysis to date of diversity in ‘ex situ’ collections: those plants conserved outside natural habitats.

The study, in September 2017 in the journal Nature Plants, found that the global network of botanic gardens conserves living plants representing almost two-thirds of plant genera and over 90% of plant families.  However, researchers from the University of Cambridge discovered a significant imbalance between temperate and tropical regions. The vast majority of all plants species grown ex situ are held in the northern hemisphere. Consequently, some 60% of temperate plant species were represented in botanic gardens but only 25% of tropical species, despite the fact that the majority of plant species are tropical.

For the study, researchers analysed datasets compiled by the Botanic Gardens Conservation International (BGCI)….

“The global network of botanic gardens is our best hope for saving some of the world’s most endangered plants,” said senior author Dr Samuel Brockington, a researcher at Cambridge’s Department of Plant Sciences as well as a curator at the University’s own Botanic Garden….“Currently, an estimated one fifth of plant diversity is under threat, yet there is no technical reason why any plant species should become extinct.   “If we do not conserve our plant diversity, humanity will struggle to solve the global challenges of food and fuel security, environmental degradation, and climate change.”

The plants not currently grown in botanic gardens are often more interesting than those that are, say the researchers. Hydrostachys polymorpha, for example, an African aquatic plant that only grows in fast flowing streams and waterfalls, or the tiny parasitic plant Pilostyles thurberi – only a few millimetres long, it lives completely within the stem tissue of desert shrubs.  Species from the most ancient plant lineages, termed ‘non-vascular’ plants, are currently almost undocumented in botanic gardens – with as few as 5% of all species stored in the global network. These include plants such as the liverworts and mosses.

“Non-vascular species are the living representatives of the first plants to colonise the land,” said Brockington. “Within these plants are captured key moments in the early evolutionary history of life on Earth, and they are essential for understanding the evolution of plants”

Excerpts from World’s botanic gardens contain a third of all known plant species, and help protect the most threatened, Press Release of Botanic Gardens Conservation International, Sept. 25, 2016

Biodiversity in the Lawless Seas

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The United Nations General Assembly adopted a resolution on May 2015 (reissued on June 2015) aimed at drafting a legally binding international treaty for the conservation of marine biodiversity and to govern the mostly lawless high seas beyond national jurisdiction.The resolution was the result of more than nine years of negotiations by an Ad Hoc Informal Working Group, which first met in 2006.

If and when the treaty is adopted, it will be the first global treaty to include conservation measures such as marine protected areas and reserves, environmental impact assessments, access to marine genetic resources and benefit sharing, capacity building and the transfer of marine technology.

The High Seas Alliance (HSA), a coalition of some 27 non-governmental organisations (NGOs), played a significant role in pushing for negotiations on the proposed treaty and has been campaigning for this resolution since 2011…The General Assembly will decide by September of 2018 on the convening of an intergovernmental conference to finalise the text of the agreement and set a start date for the conference….

A new treaty would help to organise and coordinate conservation and management [in the high seas].  That includes the ability to create fully protected marine reserves that are closed off to harmful activities. Right now there is no way to arrange for such legally binding protections, she added….In a statement released Friday, the HSA said the resolution follows the Rio+20 conference in 2012 where Heads of State committed to address high seas protection.The conference came close to agreeing to a new treaty then, but was prevented from doing so by a few governments which have remained in opposition to a Treaty ever since.

The U.N. Convention on the Law of the Sea (UNCLOS), which is recognised as the “constitution” for global ocean governance, has a broad scope and does not contain the detailed provisions necessary to address specific activities, nor does it establish a management mechanism and rules for biodiversity protection in the high seas.  Since the adoption of UNCLOS in 1982, there have been two subsequent implementing agreements to address gaps and other areas that were not sufficiently covered under UNCLOS, one related to seabed mining and the other related to straddling and highly migratory fish stocks, she added. This new agreement will be the third implementing agreement developed under UNCLOS….

The “high seas” is the ocean beyond any country’s exclusive economic zone (EEZ) ‑ amounting to 64 percent of the ocean…

Excerpts from Thalif Deen, U.N. Takes First Step Towards Treaty to Curb Lawlessness in High Seas, IPS, June 19 2015

Demand for Gold Causes Deforestation

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The global gold rush, driven by increasing consumption in developing countries and uncertainty in financial markets, is an increasing threat for tropical ecosystems. Gold mining causes significant alteration to the environment, yet mining is often overlooked in deforestation analyses because it occupies relatively small areas. As a result, we lack a comprehensive assessment of the spatial extent of gold mining impacts on tropical forests.

The study Global demand for gold is another threat for tropical forests published in Environmental Research Letters provides a regional assessment of gold mining deforestation in the tropical moist forest biome of South America. Specifically, we analyzed the patterns of forest change in gold mining sites between 2001 and 2013, and evaluated the proximity of gold mining deforestation to protected areas (PAs)….Approximately 1680 km2 of tropical moist forest was lost in these mining sites between 2001 and 2013. Deforestation was significantly higher during the 2007–2013 period, and this was associated with the increase in global demand for gold after the international financial crisis….In addition, some of the more active zones of gold mining deforestation occurred inside or within 10 km of ~32 PAs. There is an urgent need to understand the ecological and social impacts of gold mining because it is an important cause of deforestation in the most remote forests in South America, and the impacts, particularly in aquatic systems, spread well beyond the actual mining sites.

Excerpt from Abstract, Global demand for gold is another threat for tropical forests

Amazon Protected Areas: 215 Million Fund

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Brazil’s government, the World Wildlife Fund and various partners are expected to unveil an agreement that would establish a $215 million fund for conservation of protected jungle in the Amazon rainforest.  The fund, which seeks to ensure conservation of over 90 protected areas in the Amazon, comes as renewed developmental pressures mount in the region, resulting last year in an uptick in deforestation figures after years of record lows.

Under the terms of the agreement, partners in the fund will make annual contributions to help Brazil meet financing needs for the protected lands, whose combined area totals more than 60 million hectares, or an area 20 percent larger than Spain.  Contributions, partners said, will be contingent upon conditions required of Brazil, including audits of the government body that will administer the fund and continued staffing and financing of government offices required to administer the rainforest areas.

Money from the fund would be used for a range of basic conservation measures, including fences and signs to delineate protected areas and to pay for vehicles used to patrol them…

Brazil’s government through 2012 made large inroads against deforestation, largely through strict environmental enforcement and financial measures that blocked credit for companies and individuals caught doing business with loggers, ranchers, farmers or others known to exploit illegally cleared land.

In recent years, however, the government has made changes to environmental agencies and regulations that critics say make it easier for would-be developers to target protected areas. The government has also altered borders of some parkland to make way for infrastructure projects, including hydroelectric dams on various Amazon tributaries.

Financing for the new fund, expected to pay out over 25 years, was secured from private and public sources including the German government, the Inter-American Development Bank, the World Bank, philanthropists and the Amazon Fund, an existing facility financed mostly by the Norwegian government and administered by Brazil’s national development bank.

Together, the forest zones targeted by the fund are known as the Amazon Region Protected Areas, or ARPA, a program established in 2002 to coordinate financing and conservation strategy in the region.

Whereas previous financing for the effort relied on cumulative fundraising efforts, partners this time agreed to an all-or-nothing approach, borrowed from private-sector financing practices, to build momentum toward a target total. The $215 million is the amount calculated as necessary to help the Brazilian government, over the 25 years, become self-sufficient in terms of financing the rainforest areas.

Excerpts from  PAULO PRADA, Donors commit $215 million for Amazon conservation in Brazil, Reuters, May 21, 2014