Learning to do incorrect research

In the latest issue of EPW, there is a perspective piece by Donald W Attwood titled How I Learned to do Incorrect Research which might be worth your while (and, pray tell me, how do you NOT READ an essay titled thus?)

On a different note, Yes; I know. But, I am not able to figure out how to get the link for the pdf of the article at the EPW site.  Anyway, hurry before the piece disappears from the front page.

What is SRI — System of Rice Intensification?

This NYTimes profile of Norma T Upoff explains:

Rejecting old customs as well as the modern reliance on genetic engineering, Dr. Uphoff, 67, an emeritus professor of government and international agriculture with a trim white beard and a tidy office, advocates a management revolt.

Harvests typically double, he says, if farmers plant early, give seedlings more room to grow and stop flooding fields. That cuts water and seed costs while promoting root and leaf growth.

The method, called the System of Rice Intensification, or S.R.I., emphasizes the quality of individual plants over the quantity. It applies a less-is-more ethic to rice cultivation.

In a decade, it has gone from obscure theory to global trend — and encountered fierce resistance from established rice scientists. Yet a million rice farmers have adopted the system, Dr. Uphoff says. The rural army, he predicts, will swell to 10 million farmers in the next few years, increasing rice harvests, filling empty bellies and saving untold lives.

By the way, the Tamilnadu agriculture minister also gets quoted in the piece:

Dr. Uphoff’s improbable journey involves a Wisconsin dairy farm, a billionaire philanthropist, the jungles of Madagascar, a Jesuit priest, ranks of eager volunteers and, increasingly, the developing world. He lists top S.R.I. users as India, China, Indonesia, Cambodia and Vietnam among 28 countries on three continents.

In Tamil Nadu, a state in southern India, Veerapandi S. Arumugam, the agriculture minister, recently hailed the system as “revolutionizing” paddy farming while spreading to “a staggering” million acres.

And, apparently, internet also has played a crucial role in SRI:

His computers link him to a global network of S.R.I. activists and backers, like Oxfam, the British charity. Dr. Uphoff is S.R.I.’s global advocate, and his Web site (ciifad.cornell.edu/sri/) serves as the main showcase for its principles and successes.

“It couldn’t have happened without the Internet,” he says. Outside his door is a sign, “Alfalfa Room,” with a large arrow pointing down the hall, seemingly to a pre-electronic age.

Though the method does not seem to be without its critics, the piece also gives details of the method:

Dr. Uphoff grew up on a Wisconsin farm milking cows and doing chores. In 1966, he graduated from Princeton with a master’s degree in public affairs and in 1970 from the University of California, Berkeley, with a doctorate in political science.

At Cornell, he threw himself into rural development, irrigation management and credit programs for small farmers in the developing world.

In 1990, a secret philanthropist (eventually revealed to be Charles F. Feeney, a Cornell alumnus who made billions in duty-free shops) gave the university $15 million to start a program on world hunger. Dr. Uphoff was the institute’s director for 15 years.

The directorship took him in late 1993 to Madagascar. Slash-and-burn rice farming was destroying the rain forest, and Dr. Uphoff sought alternatives.

He heard that a French Jesuit priest, Father Henri de Laulanié, had developed a high-yield rice cultivation method on Madagascar that he called the System of Rice Intensification.

Dr. Uphoff was skeptical. Rice farmers there typically harvested two tons per hectare (an area 100 by 100 meters, or 2.47 acres). The group claimed 5 to 15 tons.

“I remember thinking, ‘Do they think they can scam me?’ ” Dr. Uphoff recalled. “I told them, ‘Don’t talk 10 or 15 tons. No one at Cornell will believe it. Let’s shoot for three or four.’ ”

Dr. Uphoff oversaw field trials for three years, and the farmers averaged eight tons per hectare. Impressed, he featured S.R.I. on the cover of his institute’s annual reports for 1996 and 1997.

Dr. Uphoff never met the priest, who died in 1995. But the success prompted him to scrutinize the method and its origins.

One clear advantage was root vigor. The priest, during a drought, had noticed that rice plants and especially roots seemed much stronger. That led to the goal of keeping fields damp but not flooded, which improved soil aeration and root growth.

Moreover, wide spacing let individual plants soak up more sunlight and send out more tillers — the shoots that branch to the side. Plants would send out upwards of 100 tillers. And each tiller, instead of bearing the usual 100 or so grains, would puff up with 200 to 500 grains.

One drawback was weeds. The halt to flooding let invaders take root, and that called for more weeding. A simple solution was a rotating, hand-pushed hoe, which also aided soil aeration and crop production.

But that meant more labor, at least at first. It seemed that as farmers gained skill, and yields rose, the overall system became labor saving compared with usual methods.

Dr. Uphoff knew the no-frills approach went against the culture of modern agribusiness but decided it was too good to ignore. In 1998, he began promoting it beyond Madagascar, traveling the world, “sticking my neck out,” as he put it.

Slowly, it caught on, but visibility brought critics. They dismissed the claims as based on wishful thinking and poor record keeping, and did field trials that showed results similar to conventional methods.

In 2006, three of Dr. Uphoff’s colleagues at Cornell wrote a scathing analysis based on global data. “We find no evidence,” they wrote, “that S.R.I. fundamentally changes the physiological yield potential of rice.”

While less categorical, Dr. Dobermann of the rice research institute called the methods a step backward socially because they increased drudgery in rice farming, especially among poor women.

An interesting piece; take a look!

Asexual and sexual reproduction in plants!

D Balasubramanian, in his latest (fortnightly) column in the Hindu, Speaking of Science, describes some of the recent research carried out at CCMB, Hyderabad (and is getting published in Nature next week a couple of weeks ago) on the genetic altering of the sexual life of plants that can lead to sustained production of high yielding plants.

The issue?

Just as we would (if we could) choose our mates with desired qualities and traits, we choose, while farming, to cross plants with desired qualities in their offspring.

These qualities are high yield, pest resistance, better fruits, more beautiful flowers and so on. In agriculture and major food crops, such well-chosen crosses lead to high yielding hybrids. The Green Revolution is the result of such an exercise.

But farmers face a problem. Once they have a good hybrid, they wish to keep its genes and propagate them by self-fertilizing the hybrid, so that the cultivars have superior yields than the parental inbred lines

Sadly though, this hybrid vigour decreases with each generation of hybrid self crossing. The copies of the different genes in the hybrid separate from each other during germ cell production, and get reshuffled in each succeeding generation. As a result we need to cross the parental lines anew each time — not a satisfactory situation.

And, is there a way out? Seems to be, and that is precisely where the CCMB researchers lead by Dr. Imran Siddiqi come in:

But there is way out. This comes from a peculiar property of many plants (and some animals such as insects and fish). Some plants such as dandelion, some berries and grasses side-step the meiosis process altogether and their seeds reproduce clonally, asexually.

The entire gene pool of the mother is passed on straight to the daughter seed. This curious, but exciting, property is referred to as apomixis, the first step of which is called apomeiosis (the apo-referring to the missing of a component).

While berries and grasses do this, major crop plants do not; they reproduce sexually. If only they could be made apomictic, we could retain hybrid vigour forever, since no reshuffling of genes as in sexual reproduction kind would occur.

If we understand the genetic and cell biological basis behind apomeiosis, we could perhaps send wheat, rice and corn along the apomixis path and produce high yielding hybrid seeds.

What are the genes controlling apomixis? It is this important issue that has been elegantly addressed and identified by Dr. Imran Siddiqi and co-workers, using the sexually reproducing plant Arabidopsis.

They show that alteration in the gene called DYAD leads to apomeiosis, sending the plant into the asexual mode. The DYAD gene normally regulates the organisation of chromosomes during meosis. Plants with mutation in DYAD, however, give rise to seeds that contain the full set of genes from the parent.

A single gene, whose function is known, can lead to a plant becoming apomictic, when its function is tampered with! This is truly a path-finding discovery and we should applaud the group for this breakthrough.

A nice piece; take a look!

Couple of anthropology resources online

One of the things that Ram Guha in his India after Gandhi touches upon, albeit very briefly, is the effect of green revolution on the Indian rural population. Anthropologi.info informs us that the archives of the Anthropological papers of the American Museum of Natural History have been given open access; among other things, I understand, a paper on green revolution and its role in agricultural and social change in an north Indian village is available for download. Anthropolgi.info also links to a site called AfricaWrites where you can watch several videos of African rural life. Have fun!

Freeman Dyson on our biotech future

Freeman Dyson writes about our biotech future in New York Review of Books; via /.

Dyson begins with the domestication of biotechnology, i.e., genetic engineering that is accessible to people so that they may breed their own varieties of pets, for example, and goes on to ask

If domestication of biotechnology is the wave of the future, five important questions need to be answered. First, can it be stopped? Second, ought it to be stopped? Third, if stopping it is either impossible or undesirable, what are the appropriate limits that our society must impose on it? Fourth, how should the limits be decided? Fifth, how should the limits be enforced, nationally and internationally?

And, he does not answer these questions, but leaves it to the future generations.

He then proceeds to discuss evolution,  in the context of which talks about an Open Source approach to biology:

We are moving rapidly into the post-Darwinian era, when species other than our own will no longer exist, and the rules of Open Source sharing will be extended from the exchange of software to the exchange of genes. Then the evolution of life will once again be communal, as it was in the good old days before separate species and intellectual property were invented.

Dyson then talks about rural poverty and how domestication of genetic engineering might help achieve green technologies that can alleviate such poverty, in which context he talks about India:

In a country like India with a large rural population, bringing wealth to the villages means bringing jobs other than farming. Most of the villagers must cease to be subsistence farmers and become shopkeepers or schoolteachers or bankers or engineers or poets. In the end the villages must become gentrified, as they are today in England, with the old farm workers’ cottages converted into garages, and the few remaining farmers converted into highly skilled professionals. It is fortunate that sunlight is most abundant in tropical countries, where a large fraction of the world’s people live and where rural poverty is most acute. Since sunlight is distributed more equitably than coal and oil, green technology can be a great equalizer, helping to narrow the gap between rich and poor countries.

Take a look!

A forerunner of pulses revolution in India

I can not imagine a proper south Indian meal without pigeon pea (toor, tuvaram, togari, kandi,…), which is the main ingredient of sambar and rasam, not to mention bisibelabath which is half rice and half pigeon pea.

This article in the recent issue of Science which profiles K B Saxena,  an Indian agricultural scientist who specialises on pigeon peas, has some good news:

During a 30-year career at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Patancheru, India, Saxena helped create nearly a dozen kinds of pigeon pea that mature sooner and resist diseases better than do traditional varieties. Yet the big prize–high-yielding hybrids–never seemed within reach. “People had lost hope that yield could improve,” says Saxena, who narrowly escaped being laid off a decade ago and barely managed to keep his program going during hard times at ICRISAT.

Now, hope is back. Two years ago, Saxena’s group finally succeeded in creating the first commercially viable system in the world for producing hybrid legume seed. It couldn’t have come at a better time: India faces a pigeon pea shortage severe enough that the government banned exports of it and other so-called pulses last year. Last month, ICRISAT announced that one of its most promising hybrids can achieve yields nearly 50% higher than those of a popular variety. “This will become the forerunner of a pulses revolution in India,” predicts M. S. Swaminathan, a plant breeder considered one of the chief architects of the original green revolution. The first seeds should reach farmers next year, and Swaminathan himself is working on a project to make sure even the poorest can afford them.

The profile also gives some measures taken by the agricultural scientists in India in making sure that the seeds reach the needy farmers:

There is, however, a downside: Unlike traditional varieties, hybrid seed must be bought every year, because only the first generation has the hybrid vigor. Most of those seeds will come from companies, which makes some observers worry that small farmers won’t be able to afford them. ICRISAT has provided the male sterile system, which is in the public domain, to a consortium of 15 Indian seed companies so that they can create their own hybrid pigeon pea varieties. Several companies are also preparing to sell ICPH 2671, and Saxena estimates that the seed will cost about $3.25 a kilo, about 50% more than standard cultivars. He says it’s likely that some government agencies will sell the seed at half price to poor farmers.

Swaminathan isn’t taking any chances, however. His foundation, based in Chennai, is beginning a project to train women to produce the hybrid seed themselves from ICRISAT seeds. Beginning in June, agronomists will go to villages about 180 km south of Chennai and teach some 100 women, mostly the wives of subsistence farmers. The goal is for them eventually to sell hybrid seed in their neighborhoods. “The principle is social inclusion and technology access for all,” Swaminathan says. “You can keep the cost of seed low and increase employment in villages.”

Take a look!