Category Archives: agriculture

Deforestation Tolerance: Amazon

Guianan savanna. Image from wikipedia

Amazon generates approximately half of its own rainfall by recycling moisture 5 to 6 times as airmasses move from the Atlantic across the basin to the west.  From the start, the demonstration of the hydrological cycle of the Amazon raised the question of how much deforestation would be required to cause this hydrolological cycle to degrade to the point of being unable to support rain forest ecosystems.

High levels of evaporation and transpiration that forests produce throughout the year contribute to a wetter atmospheric boundary layer than would be the case with non-forest.This surface-atmosphere coupling is more important where large-scale factors for rainfall formation are weaker, such as in central and eastern Amazonia. Near the Andes, the impact of at least modest deforestation is less dramatic because the general ascending motion of airmasses in this area induces high levels of rainfall in addition to that expected from local evaporation and transpiration.

Where might the tipping point be for deforestation-generated degradation of the hydrological cycle? The very first model to examine this question  showed that at about 40% deforestation, central, southern and eastern Amazonia would experience diminished rainfall and a lengthier dry season, predicting a shift to savanna vegetation to the east.

Moisture from the Amazon is important to rainfall and human wellbeing because it contributes to winter rainfall for parts of the La Plata basin, especially southern Paraguay, southern Brazil, Uruguay and central-eastern Argentina; in other regions, the moisture passes over the area, but does not precipitate out. Although the amount contributing to rainfall in southeastern Brazil is smaller than in other areas, even small amounts can be a welcome addition to urban reservoirs…

In recent decades, new forcing factors have impinged on the hydrological cycle: climate change and widespread use of fire to eliminate felled trees and clear weedy vegetation. Many studies show that in the absence of other contributing factors, 4° Celsius of global warming would be the tipping point to degraded savannas in most of the central, southern, and eastern Amazon. Widespread use of fire leads to drying of surrounding forest and greater vulnerability to fire in the subsequent year.

We believe that negative synergies between deforestation, climate change, and widespread use of fire indicate a tipping point for the Amazon system to flip to non-forest ecosystems in eastern, southern and central Amazonia at 20-25% deforestation.

We believe that the sensible course is not only to strictly curb further deforestation, but also to build back a margin of safety against the Amazon tipping point, by reducing the deforested area to less than 20%, for the commonsense reason that there is no point in discovering the precise tipping point by tipping it. At the 2015 Paris Conference of the Parties, Brazil committed to 12 million ha of reforestation by 2030. Much or most of this reforestation should be in southern and eastern Amazonia.

Excerpts from Amazon Tipping Point  by Thomas E. Lovejoy and Carlos Nobre, Sciences Advances,  Feb. 21, 2018

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

image from wikipedia

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

Islands of Paradise, Sewage and Garbage

Cesspools—holes in the ground where untreated human waste is deposited—have become a crisis in Hawaii, threatening the state’s drinking water, its coral reefs and the famous beaches that are the lifeblood of its tourist economy.  Sewage from cesspools is seeping into some of Hawaii’s ocean waters, where it has been blamed for infections suffered by surfers and snorkelers. It is also entering the drinking water in part of the state, pushing nitrate levels close to the legal limit.

Hawaii has 88,000 cesspools across its eight major islands, more than any other state. Collectively, they deposit 53 million gallons of raw sewage into the ground every day, according to the state health department. More than 90% of the state’s drinking water comes from groundwater wells…

Replacing all of the state’s cesspools with alternate sewage systems would cost at least $1.75 billion, according to the health department…At one groundwater well, nitrate levels are already at 8.7 milligrams a liter; the legal limit is 10, and the Department of Health estimated that some parts of the aquifer are already over that limit. Environmentalists say they are worried about the potential effect of the water on infants, who can be killed by high levels on nitrates, which are chemicals found in fertilizer and sewage.

Many bathrooms in homes outside Honolulu still pump sewage into nearby holes in the ground.  Yet, some residents resist plans to replace cesspools, worried about expense. In January 2018, Upcountry Maui residents overwhelmed a Department of Public Health meeting, complaining about potential costs.

Excerpt from Hawaii’s Big Headache: Cesspools, Wall Street Journal, Feb. 12, 2018

The Maritime Environment Protection Authority’s (MEPA) of Sri Lanka spent millions of rupees on coastal cleanups last year — a reflection of “spending public money for public waste,” as the MEPA’s General Manager and CEO, Dr. Terney Pradeep Kumara, puts it.

A large proportion of the problem is attributable to inland waste, he notes. “It is not merely what is dumped directly on the beaches, but all that flows through canals and rivers,” he says, pointing out that other triggers, including the fisheries and the tourism sector, are only secondary to inland waste which ends up on the coast. Added to the burden is the garbage which flows from India, Indonesia and Thailand, he says. The MEPA’s role in controlling pollution covers Sri Lanka’s 1640 km coastal belt and extends up to 200 nautical miles to the deep sea, the area, which, according to Dr. Pradeep Kumara, is eight times the size of Sri Lanka’s land area.

The garbage dumped in the coastal vegetation is contributing to the dengue problem…especially the fishing craft, both in use and abandoned, in which water is stagnated.”   Mitigating inland pollution is seen by MEPA authorities as the first step in realising cleaner beaches. They moot a site-specific garbage disposal system, as opposed to a ‘blanket system’. “What works for Colombo will not work for other areas,” says Dr. Pradeep Kumara.

Excerpt Sea of trash: Inland and overseas garbage washes up on Lanka’s beaches, Sunday Times (Sri Lanka), Feb. 11, 2018

Turning Oceans into Muck

image from http://recon.sccf.org/events

Oxygen is critical to the health of the planet. It affects the cycles of carbon, nitrogen and other key elements, and is a fundamental requirement for marine life from the seashore to the greatest depths of the ocean. Nevertheless, deoxygenation is worsening in the coastal and open ocean. This is mainly the result of human activities that are increasing global temperatures (CO2-induced warming) and increasing loads of nutrients from agriculture, sewage, and industrial waste, including pollution from power generation from fossil fuels and biomass.

Facts: During the past 50 years the area of low oxygen water in the open ocean has increased by 4.5 million km2. The world’ oceans are now losing approximately  1 gigaton of oxygen each year.

The Millennium Ecosystem Assessment released by the UN in 2005 reported that nitrogen containing compounds (e.g. sewage, fertilizers) release into the oceans grew 80 percent from 1860 to 1990.

Increasing temperatures will reduce the capacity of the ocean to hold oxygen in the future;
Oxygen deficiency is predicted to worsen in estuaries, coastal areas and oxygen minimum zones in the open ocean;
The ocean’s capacity to produce oxygen will be reduced in the future.
Habitat loss is expected to worsen, leading to vertical and horizontal migration of species;
Oxygen deficiency will alter biogeochemical cycles and food webs;
Lower oxygen concentrations are projected to result in a decrease in reproductive capacity and biodiversity loss;
There are important local decreases of commercially important species and aquaculture production;
Harmful Algal Blooms will be exacerbated from nutrients released in bottom waters due to hypoxia (e.g. in the Baltic Sea);
Reduced ocean oxygen concentrations will lead to an increase in greenhouse gas emissions, thereby initiating feedbacks on climate change;

Excerpts from UNESCO, Jan. 2018

View Extensive Abstract

Background paper (pdf)

Global Ocean Oxygen Network: Through the participation of high level scientists from across the world, the IOC expert group, the Global Ocean Oxygen Network GO2NE, established in 2016, is committed to providing a global and multidisciplinary view of deoxygenation, with a focus on understanding its multiple aspects and impacts.

Old Continents, New Trees

In the 1920s, when Ireland became independent, it was thought to have just 220,000 acres (90,000 hectares) of woods, covering about 1% of the land. Once-extensive forests had been shrinking for centuries…In 2017, though, almost 11% of Ireland is covered with forest, and an unknown additional amount by small woods and scattered trees. The government’s target is to cover 18% of the land area with forests by 2046. Ireland is behind schedule. Still, about 6,000 hectares of new forest ought to be planted this year, while almost none will be lost. It is part of a broad trend: the foresting of the West.

Trees are spreading in almost every European country. Because many of these forests are young, the quantity of wood in them is growing faster than their extent. Europe’s planted forests put on a little more than 1.1m cubic metres of wood per day. For comparison, the iron in the Eiffel Tower is about 930 cubic metres. Russia’s forests spread more slowly in percentage terms between 2005 and 2015, but, because Russia is so big, more than in the entire European Union in absolute terms. Forests now occupy a third of America’s land, having grown by 2% in the past decade. They are even expanding in Australia, following a long decline.

Deforestation in South America and Africa rightly gets most of conservationists’ attention. That loss is huge—equivalent to about 4.8m hectares a year, which far outweighs gains elsewhere. Yet the foresting of rich countries is still one of the world’s great land-use changes. It seems just as unstoppable as the deforestation of poorer places. It has plenty of critics, too.

The growth of forests is partly a result of changes to food markets. As the best farming areas have become more productive, and as rich countries have imported more of their food, marginal land has become unusable for ordinary agriculture…Forests are also growing because governments have favored them through laws and subsidies….Since the 1990s environmental considerations have weighed more heavily. Forests are increasingly valued as sponges for heavy rain, as wildlife habitats and as carbon sinks…

Planted forests are far from universally popular, though. Between June and October 2017, forest fires in Spain and Portugal killed more than 100 people and darkened Europe’s skies. The fires were partly blamed on the spread of non-native trees, especially eucalyptus. That Australian import, which was planted with support from the World Bank, among others, grows so quickly that trees can be harvested for pulp when less than ten years old. It also burns readily, scattering embers far afield. Portugal’s government has begun to restrict planting, in an effort to prevent the country from turning into what one green group calls “Eucalyptugal”.

The eucalyptus tree is a scapegoat for a bigger problem, argues Marc Castellnou, a fire analyst in Spain. The real trouble is that forests in Portugal and Spain have expanded quickly, with little thought for the consequences. Well-managed eucalyptus plantations are not the biggest danger—much worse are ill-managed ones with lots of underbrush and fallen wood, and the impromptu forests that grow on abandoned farms. The fires that get going in such forests jump to the treetops and burn so energetically that they cannot be stopped.

In Ireland, the criticisms are different. The country’s default tree is the sitka spruce, a fast-growing, damp-tolerant conifer from America’s Pacific Northwest. Spruce plantations are said to be devoid of life—vertical deserts of dark green. They are accused of wrecking rural communities and driving farmers off the land….

The first charge is false. Mark Wilson of the British Trust for Ornithology says that conifer plantations support more bird life per hectare than farmland, largely because they harbour more insects. Inevitably, some birds benefit more than others. The march of conifers across Britain and Ireland has increased the numbers of pine-loving birds such as siskins and crossbills. Conifers are also loved by crows—which is less obviously good, because crows raid the nests of rare birds such as curlews.

The second accusation, that trees push out other kinds of agriculture, is only partly true. Forestry subsidies and regulations have indeed distorted Ireland’s land market.

Excerpts from The Foresting of the West, Economist, Dec. 2, 2017,at 51

Red-Dead: water crisis in the Middle East

The Dead Sea is dying. Half a century ago its hyper-salty, super-pungent waters stretched 80km from north to south. That has shrunk to just 48km at its longest point. The water level is falling by more than a meter per year. All but a trickle from its source, the Jordan River, is now used up before it reaches the sea. “It will never disappear, because it has underground supplies, but it will be like a small pond in a very big hole,” says Munqeth Mehyar of EcoPeace, an NGO.

Until the summer of 2017 Israel and Jordan, which share the sea, were trying to slow the decline. The “Red-Dead project”, as it is called, would desalinate seawater at the Jordanian port of Aqaba and pump 200m cubic metres of leftover brine into the Dead Sea each year. That would not be enough to stabilise the sea, which needs at least 800m cubic metres to stay at current levels. Still, it would help—and the project has a much more important benefit.

The World Bank defines water scarcity as less than 1,000 cubic metres per person annually. Jordan can provide less than 15% of that. The Aqaba plant would send fresh water to southern towns in both Jordan and Israel. In return for its share, Israel agreed to pump an equal amount to parched northern Jordan, where most of the population lives.

But the project was now on hold due a dispute between Jordan and Israel. On July 23rd, 2017 a Jordanian teenager delivering furniture to the Israeli embassy stabbed a security guard. The guard opened fire, killing both his assailant and an innocent bystander….

Jordan is already one of the world’s most arid countries. Climate change will make matters worse. By the end of the century, say scientists from Stanford University, Jordan could be 4°C hotter, with about a third less rain. It needs to rationalise water consumption. And Israel, which wants a stable neighbour to its east, has an interest in getting water projects back on track.

Excerpts from Jordan’s Water Crisis: Diplomatic Drought: Economist, Dec. 2, 2017

The Silent Environmentalists

Serendipity Berry. Image from wikipedia

Elephant ears are leafy vegetables. African locusts are tree-borne legumes. All are standard fare in various parts of Africa. What they also have in common is that they are, from the point of view of plant breeders, orphans. They are neglected by breeders because they are not cash crops. Conversely, they are not cash crops because they are neglected by breeders.

That neglect matters. The cereals which dominate human diets—rice, wheat and maize—have had their yields and nutritional values boosted over the years by scientific breeding programmes. In the modern era of genomics, they have had their DNA scrutinised down to the level of individual base pairs, the molecular letters in which genetic information is written. They are as far removed, nutritionally, from their ancestors of as little as two centuries ago as those ancestors were from the wild plants which begat them. Orphan crops have yet to undergo such a genetic revolution.

Even for adults, a lack of calories and essential nutrients is harmful. For children it can be devastating. Poor childhood nutrition leads to stunting—inadequate bodily development, including the development of the brain. A report published by the World Health Organisation on November 16th, 2017 suggests that almost a third of Africa’s children, nearly 60m of them, are stunted. And stunted children grow into adults unable to achieve their potential. Researchers at the World Bank reckon the effects of stunting have reduced Africa’s GDP by 9-10% from what it would otherwise be.

One way to reduce stunting would be to improve the crops that Africans, particularly those in the countryside, actually eat—in other words, orphan crops. Such improvement is the purpose of two recent, interrelated projects that are now getting into their strides. Both are based in Nairobi and are conducted under the auspices of the World Agroforestry Centre, an international non-governmental research organisation. One is the African Orphan Crops Consortium (AOCC). The other is the African Plant Breeding Academy. The AOCC’s task is to obtain complete sequences of the DNA of 101 neglected food crops

Breeding and disseminating new crops is a long-winded business, but a DNA-based approach has already shown promise. One scientist who is embracing it is Robert Mwanga of the International Potato Centre. Dr Mwanga was an early proponent of the scientific improvement of African crops. His own work, for which he was awarded the World Food prize in 2016, is on sweet potatoes. The varieties of these root-tubers that were popular in Uganda, his native land, and other parts of Africa in the mid-1980s, when he began his studies, are deficient in vitamin A. A lack of this vitamin damages children’s eyesight and opens them to infection by such things as measles. This is a disease that can kill, and, if it does not, it can cause brain damage.  Starting with Asian varieties that had more vitamin A in them, Dr Mwanga bred a dozen strains that are vitamin-A rich and have more dry matter (and thus more calorific value) than African landraces. He then led a campaign to encourage local farmers to adopt his novelties—which they did…

Julia Sibiya of the University of KwaZulu Natal, in Durban, meanwhile, is working on sorghum, another under-studied African crop. She is also working with Dr Achigan-Dako to set up MoBreed, a pan-African collaboration with the self-appointed task of improving ten orphan crops, including Kersting’s groundnut, the African custard apple and fonio, a type of millet.

Happiness Oselebe… is even more ambitious. Dr Oselebe works at Ebonyi State University in Nigeria. Not content with improving existing crops, she wants to create a new one by domesticating serendipity berries. These are wild vines that produce a protein 3,000 times as sweet as table sugar. That, she thinks, could be the starting-point not merely for something grown for local consumption, but of an industrial-scale cash crop.

Excerpts from Nutrition and Genetics in Africa, Economist, Nov 25, 2017