Tag Archives: biodiversity loss

From Savior to Villain: Biofuel from Palm Oil

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

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

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

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?

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

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

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