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Genetic resources


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Special publication on livestock genetic resources
Agricultural Biodiversity | Weblog 19 08 2008 Livestock Science has a special issue on animal genetic resources. Or it will have, it doesn’t seem to be out yet, although some corrected proofs are available. You can get a flavour of the thing with the introduction. Here are some of the highlights:Animal genetic resource trade flows: Economic assessmentGenebank development for the conservation of [...]

Ethiopia - Access to Genetic Resources and Community Knowledge, and Community Rights Proclamation No. 482/2006
GRAIN | News 13 08 2008

'Seed Wars: Controversies and Cases on Plant Genetic Resources and Intellectual Property'
EurekAlert! | Technology, Engineering and Computer Science | News 12 08 2008 (University of California - Davis) Book examines intellectual property rights issues related to plant genetic resources.

'Seed Wars: Controversies and Cases on Plant Genetic Resources and Intellectual Property'
EurekAlert! | Agriculture | News 12 08 2008 (University of California - Davis) Book examines intellectual property rights issues related to plant genetic resources.

New agreement helps permanently protect the world’s thousands of rice varieties �' the planet’s most important food source
IRRI | News 09 08 2008 Los Baños, Philippines �' An unprecedented new agreement �' that will involve the annual dispersal in perpetuity of US$600,000 - was unveiled today in the Philippines to help fund the protection and management of the world’s thousands of unique rice varieties. IRRI and the Rome-based Global Crop Diversity Trust unveiled the historic new agreement at a special dedication ceremony at IRRI’s Genetic Resources Center which houses more than 100,000 samples of rice, the biggest and most important such collection in the world.

New era of biodiversity access
IRRI | News 09 08 2008 On World Food Day, Monday 16 October 2006, at a signing ceremony in FAO jointly with all other CGIAR centres, IRRI concluded an agreement with the Governing Body of the International Treaty on Plant Genetic Resources for Food and Agriculture. The Treaty introduces a new multilateral system for the safe conservation and fair use of plant genetic resources. It brings to an end over two decades of doubt and suspicion about the use and misuse of plant genetic resources for food and agriculture, by ensuring that a fair share of the benefits arising from their use flow equitably to where they are most needed and most deserved - conservation of genetic resources primarily in developing countries.

IRRI introduces its new Strategic Plan, 2007-2015
IRRI | News 09 08 2008 The world has changed enormously since IRRI developed its last strategic plan a decade ago. Recent scientific discoveries�'particularly in genetics and genomics�'now open up new opportunities to achieve impact that would have been difficult if not impossible as recently as the turn of the century. A reduction in poverty and sustainability of the rice production environment, through the use of modern technology and the latest communication tools, are at the heart of IRRI’s exciting and innovative plan. Rice remains the most important staple food on the planet since it feeds roughly half the population on a daily basis. Approximately 750 million of the world’s poorest people depend on it to survive. So, an agenda for continued research on this vital crop is still very relevant. IRRI’s plan (1) brings the best rice technologies to all regions of the world that need it, including East and southern Africa where demand is increasing; (2) focuses on health and nutrition; and (3) is committed to the long-term conservation and use of rice genetic resources. Five strategic goals and seven programs embodied in the plan are described as are three Frontier Projects being designed to continue beyond the life of the plan in research areas that have the potential to make an enormous impact on the lives of poor rice farmers and consumers. The new plan endeavors to take IRRI over a modest 9 years so that it can join colleagues and partners from around the world to reach the Millennium Development Goals by 2015. Nevertheless, much of the work will obviously extend well beyond that date.

Common variable immunodeficiency: a new look at an old disease
The Lancet | Headlines 08 08 2008 Primary immunodeficiencies comprise many diseases caused by genetic defects primarily affecting the immune system. About 150 such diseases have been identified with more than 120 associated genetic defects. Although primary immunodeficiencies are quite rare in incidence, the prevalence can range from one in 500 to one in 500 000 in the general population, depending on the diagnostic skills and medical resources available in different countries. Common variable immunodeficiency (CVID) is the primary immunodeficiency most commonly encountered in clinical practice, and appropriate diagnosis and management of patients will have a significant effect on morbidity and mortality as well as financial aspects of health care. Advances in diagnostic laboratory methods, including B-cell subset analysis and genetic testing, coupled with new insights into the molecular basis of immune dysfunction in some patients with CVID, have enabled advances in the clinical classification of this heterogeneous disease.

Nibbles: Dog genetics, ITPGRFA, Mapping, Neolithic, Insects, Markers, Soybeans, Milk
Agricultural Biodiversity | Weblog 08 08 2008 Man’s best friend helps out again.Intellectual Property Watch looks at the International Treaty on Plant Genetic Resources for Food and Agriculture. And they found that it was good. Well, kinda.More on predicting the results of climate change on species distributions.A nice summary of what agriculture has meant for human genetics. I vote we go back [...]

Nibbles: Dog genetics, ITPGRFA, Mapping, Neolithic, Insects, Markers, Soybeans
Agricultural Biodiversity | Weblog 08 08 2008 Man’s best friend helps out again.Intellectual Property Watch looks at the International Treaty on Plant Genetic Resources for Food and Agriculture. And they found that it was good. Well, kinda.More on predicting the results of climate change on species distributions.A nice summary of what agriculture has meant for human genetics. I vote we go back [...]

Improved varieties in West Africa
Agricultural Biodiversity | Weblog 08 08 2008 This just in from FAO’s Seed and Plant Genetic Resources Service (AGPS).Please find below links to the West African Catalogue of Plant Species and Varieties (COAFEV). This document was prepared in the framework of the West African Seed Regulation Harmonization, which was supported by AGP. This process involved 17 West and [...]

Tanzania's livestock sector faces stiff challenges
African Agriculture | Web log 08 08 2008 Experts in anzania's livestock sector have been challenged to offset the barriers that frustrate livestock trade at home and abroad. Last year, the then Minister for Livestock Development, Mr Anthony Diallo, said with an 18.8 million-strong herd of cattle Tanzania came third in Africa in respect of cattle population after Ethiopia and Sudan. “However, despite having such a huge herd Tanzania did not perform well in exports of cattle and their products.
He also gave the example of Botswana, a southern Africa nation that had a much smaller herd but featured more prominently on the world market for cattle and their products. He also said that Tanzania had huge pastureland but pastoralists kept migrating.

He said 98 per cent of Tanzanian cattle were predominantly the traditional small-value zebu or boran stock, which is raised by peasants who are also small-scale subsistence farmers. Most of them have no skills in improved animal husbandry, he said. Diallo said the best high-value variety of cattle was the brick red Mpwapwa. Unfortunately, although Mpwapwa cattle had higher nutritional value, their multiplication remained difficult and largely unpopular.

Other improved stocks of cattle include Ufipa (which are raised on ranches in Rukwa Region); Iringa Red (in Iringa Region); Mbulu (in Arusha and Manyara Regions) and Ankole (in Kagera Region).

The government will also distribute 85 hybrid Mpwapwa bulls to Iramba, Igunga, Mvomero and Simanjiro districts. Livestock research institutes at Mpwapwa, Uyole and Tanga will be financed to boost their effort on raising better diary cattle breeds.

Mr Diallo called upon researchers in livestock development to ensure that barriers that impinge upon the sector are brought down. The meeting had brought together university professors, expert livestock development researchers and prominent cattle keepers.

An official from the Department of Livestock Research, Training and Extension Services in the Ministry of Livestock Development, Dr David Sendalo, said conservation and use of indigenous cattle breeds were vital in the quest to respond to the changing production environment. Adapted livestock, he added, are more resistant to diseases and environmental challenges.

“They can maintain productivity without the need for higher value inputs,” he observed. They also increase farm income and contribute to poverty alleviation. He said interactions between genetic traits need to be addressed in order to promote resistance to parasites.

According to Dr Sendalo, infections and parasitic diseases among livestock herds remain formidable constraints that frustrate profits in the livestock trade. “Diseases reduce incomes directly by causing considerable livestock losses,” he pointed out.

He told the meeting that it was envisaged that the growth rates for processed products “would probably be higher than the growth rates for meat and milk production in the near future. Important technological developments have already taken place in research institutions, he said.

“The presence of dairy plants and slaughter houses in producing areas is likely to play an important role in stimulating market oriented production,” he observed. Trading of vacuum packed meat and pasteurized milk over long distances needs high-tech tools, he noted.

The current Minister for Livestock and Fisheries, Mr John Magufuli, told the National Assembly early this month that the country has a shortage of 13,469 extension workers in the livestock sector �' mainly at village level. He, however, informed the House that 1,006 livestock management diploma course students would graduate this year. Tengeru Institute trains 402 students; Mpwapwa (232); Morogoro (231); Madaba (69); Temeke 43 and Buhuri 29.

The institutes would enroll a total of 1, 185 livestock management trainees next financial year, the minister said. Current statistics show that Tanzania has more than 18.8 million head of cattle; 13.5 million goats, 3.6 million sheep and 1.4 million pigs.

Tanzania is also home to 33 million indigenous chickens and 20 million modern breed ones. The average annual consumption of meat for every Tanzanian stands at 11 kilos.The consumption of milk stands at 41 litres and that of eggs has been pegged at 64. Consumption of fish is estimated at 6.9 kilos per person.

The Food and Agriculture Organisation (FAO) recommends that annual average consumption of meat per person be 50 kilos; 200 litres of milk; 300 eggs and 10.96 kilos of fish.

The Livestock Training Institute (LTI) in Mpwapwa continues to investigate the prevalence of cattle diseases including Rift Valley Fever, Tuberculosis and miscarriages among cattle (Brucellosis) in ranches especially at Kongwa in the Central Zone.

The Officer In-charge at LITI, Dr Deogratius Mukangi, told President Jakaya Kikwete last year, that his institute faced a serious shortage of workers. He said there were only five veterinary doctors, three livestock field officers and two technicians.He said these workers had an unmanageable workload and needed support. He also told the president, who was visiting, that the institute was also short of reagents, chemicals and other laboratory paraphernalia.

Mukangi said workstations were constantly short of funds. He reported that in 2006, the institute diagnosed 1,638 cattle in Mpwapwa and Kongwa ranches and discovered that 293 of them carried Brucellosis fever, an ailment that is easily passed over to humans. The institute also diagnosed 210 residents for Brucellosis in Mpwapwa District and detected infections in 17 people. Dr Mukangi said all the affected people were treated successfully.

Meanwhile, the government is working on the Grazing Land and Animal Feed Resources Act, a new law that would envisage protection of pasturelands, encourage improved cattle breeding and safeguard against production of harmful, poor quality animal feeds.

Stakeholders in the livestock sector have already met and polished the contents of a Bill for the Grazing Land and Animal Feed Resources Act which seeks better management and control of grazing lands, animal feeds, production of feed additives and trade.

The then Deputy Minister for Livestock Development, Dr Charles Mlingwa, reported at a seminar last year that the new law would take livestock development to greater heights.

He was confident that improvement of livestock quality would trigger the need to improve the quality of pastures and other forms of animal feeds. Statistics indicate that as the human population increases, pastureland diminishes due to expanding human activity, he noted.

“It is this stark reality that has prompted the need to have a Grazing Land and Animal Feed Resources Act,” the deputy minister said. At that moment, there were 40 private farmers who produced and sold hay for feeding livestock.

“These pastoral farmers produce about 200 bales of hay per hectare. They also produce 50 kilos of hay seeds and 100 kilos of legumes per hectare,” Dr Mlingwa informed his audience. He added that production of hay, seeds and legumes was still insignificant.

The hay farmers are in Dar es Salaam, Coast, Morogoro, Tanga and Kilimanjaro regions. Tanzania had 60 small-scale animal feed canning factories that commanded a collective production of between 10 and 60 tonnes a day.

He pointed out the need to increase the number of animal feed factories to attain a production of 700,000 tonnes a year. “The animal feed market would expand gradually once livestock keepers adopt commercial breeding,” the deputy minister said.

The Grazing Land and Animal Feed Resources Act is tailored to protect both the health of livestock (hybrid cows, pigs, sheep, goats and chicken) and human consumers of livestock products such as meat, milk and eggs.

The former PS opined that the new law would challenge livestock keepers to take up improved methods of commercial breeding “which targeted market requirements and was more profitable.” He stressed that this would require higher quality feeds and adequate supplies of water.

He noted that improved livestock breeding was environment friendly because most cattle are normally penned. He insisted, however, that traditional cattle keepers (who mainly rear zebu or Ankole cattle) should be allocated pasturelands to avoid conflicts with farmers.

Until October, 2006, a total of 256,414 cows, 5345 goats, 14,659 sheep, 601 donkeys and 120 dogs had been moved out of Ihefu valley -- a water catchment area in Mbarali District -- as an environment conservation effort.

Pastureland for the cattle keepers evicted from Ihefu and a few other areas has been setaside in 155 villages in 24 Mainland districts. The pastureland covers about 930,276 hectares, he said.

The new pasturelands are in Mbeya, Iringa, Coast, Lindi, Morogoro, Singida, Dodoma, Kagera, Tabora and Kigoma regions. Unfortunately, not every region accepts migratory pastoralists with open hands.

Rukwa Regional Commissioner (RC) Daniel Ole Njoolay is resentful that the migrant pastoralists keep herds that are too large. “A family of migrants keeps between 100 and 300 head of cattle.

“This has pushed the cattle population in Rukwa to an estimated 512,000, ” he lamented recently. In Rukwa, indigenous residents raise a maximum of eight head of cattle. The RC said areas suitable for grazing in Rukwa Region cover 1,536,894 hectares.

“Unfortunately some 339, 952 hectares, which are suitable for both grazing and agriculture, are heavily infested with tsetse flies and are completely inhospitable,” he lamented. The total area for agriculture is 2,357,028 hectares.

The Capital Development Authority (CDA) in Dodoma has in the same vein, surveyed 54 plots of land out of the envisaged 300 in Michese, Zuzu and Nala villages for feedlots on which high-quality cattle would be raised.

Smallholder pastoralists would use the feedlots to fatten cattle for slaughter. When complete, the feedlots would cover 2,000 hectares of pastureland. The scheme would produce 250 high-value cattle daily for Dodoma Modern Abattoir.

The CDA Director for Planning, Mr Emson Adamson Mwanamtwa, said recently that the
abattoir, an ultra-modern facility with capacity to slaughter 250 head of cattle daily, handles only 80 bulls a day at the moment.

The cattle the abattoir slaughters are mainly for municipal consumption, however, the bulls are mostly lean, underfed and low-weight. When successful, the scheme would see smallholder cattle breeders raising small herds of high-quality bulls in the feedlots.

The 300 or more feedlots would have a bull population running into several thousands. The scheme would also establish a cattle feed mill, high-quality pasture farms and a bull centre with an artificial insemination department.

Daily News TZ

Biodiversity and Plant Genetic Resources
DG | Food Security 07 08 2008

CGIAR: Biodiversity and Plant Genetic Resources
DG | Knowledge Economy 07 08 2008

Canada-China partnership aims to increase oil yield of canola
Checkbiotech | Biofuels | News 06 08 2008 SASKATOON, SASKATCHEWAN, Canada - The National Research Council Canada (NRC) and the Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences have signed an agreement to collaborate on genetic research to improve the production of canola. Over the next five years, the Oil Crops Research Institute will contribute $300,000 in cash and the NRC Plant Biotechnology Institute (NRC-PBI) will contribute $210,000 worth of facilities and analytical resources to complete the first project under this agreement.

Building on Gender, Agrobiodiversity and Local Knowledge - a Training Manual
Siyanda | Gender Mainstreaming Resources 01 08 2008 What are the linkages between local knowledge systems, gender roles and relationships, the conservation and management of agrobiodiversity, plant and animal genetic resources, and food security? This training manual aims to promote a holistic understanding of these components.
Author: The Food and Agriculture Organization of the United Nation (FAO)

An economist's eye view
Gristmill | Environmental news and commentry | Web log 30 07 2008 By Jason D Scorse The agricultural industry is one of the biggest users of water, energy, and chemicals on the planet. Overall it poses one of the biggest threats to global biodiversity, which is why it deserves significant attention from the environmental community. But when it comes to defining what is meant by "sustainable agriculture," there is a lot of confusion. Many people think "organic," or "local," or "non-GMO," or even "biodynamic." It will come as little surprise that economists don't think of the issue in this way; they primarily examine the basic conditions for the efficient use of resources in the agricultural sector. The following outline is the beginning of what a move toward a sustainable agricultural system would entail: 1. Ending the full range of agricultural subsidies It is impossible to even begin to work on a sustainable agricultural system when prices for agricultural goods are severely distorted by counterproductive government policies. The system of agricultural subsidies that exists in (mostly) the developed world is an anachronism that is an affront to any notion of sustainability. Farmers in rich countries are provided with a price floor for their products which leads them to produce more than they otherwise would; this leads them to farm marginal land and convert an excess of natural systems to food systems. The combined effect lowers the world price, thereby hurting farmers whose governments do not subsidize them (while helping the poor consumers of the world; more on this later). Most of these farmers are wealthy, making the current agricultural subsidy system inherently regressive, which runs counter to the social dimension of sustainability. Eliminating agricultural subsidies should be a primary goal of all environmentalists, but the opposition to subsidies should not end there. Farmers receive many other types of subsidies in the forms of lower-priced water and energy. The water subsidies are particularly egregious in many parts of the country where water is a relatively scarce commodity and the value of water for environmental, industrial, and residential purposes is much greater than that for agriculture. For example, in any reasonable and rational water allocation scheme, water would not be used to grow alfalfa in the desert of California at a time when many of California's rivers go dry, leading to the decimation of wildlife populations. We all receive the energy subsidies that farmers do; mostly in the form of under-priced fossil fuels, which act as a passive subsidy. Since the price of carbon is not included the price of oil and natural gas these energy sources are cheaper than they should be in a well-functioning market that takes into account external costs. If we phased out all of the direct payments to farmers and the water subsidies, and we accurately priced fossil fuels, the agricultural landscape would change dramatically, and in a much more sustainable direction. Farmers would be forced to use resources much more efficiently. The prices of resource-intensive products would also rise significantly, which would also lead to large shifts in consumer behavior (e.g. meat and dairy would be a lot more expensive relative to legumes, grains, and vegetables). In addition, the issue of food miles would be at least partially solved by the fact that food would cost a lot more to ship, and thereby, demand would likely decrease for long-distance imports, causing a shift to more locally-grown foods. One downside to this is that countries that rely on food exports for foreign exchange might be harmed; this could partially be minimized by a move to high-value and specialty crops for which consumers would be willing to pay a premium. 2. Supporting the World Trade Organization The WTO plays an extremely constructive role in moving toward agricultural sustainability. Its mission is to move the world toward a system free of subsidies, as well tariffs on agricultural goods, which provide another layer of price distortion. Unfortunately, the Doha Round is currently in its last throes because of the inability to agree on cuts in agricultural subsidies and tariffs. The power of the farm lobbies and large agribusiness throughout the world is disproportionate to its economic power, and until that can be curbed, it will continue to hamper efforts to move toward a sustainable agricultural system. 3. Providing access to food As Amartya Sen brilliantly demonstrated in his landmark work Poverty and Famines: An Essay on Entitlement and Deprivation (and subsequent work), access to food is essentially an issue of access to money and resources that can be traded for food, not the absolute quantity of food produced in society. Put simply, in our international system, those with money have access to food. This means that for those who are undernourished, the best option is to provide them with economic opportunities so that they can earn income or provide them with land and resources to grow their own food. While the latter course is attractive since it promotes a degree of self-sufficiently, it may limit people's ability to climb the economic ladder; those who spend a large portion of their time engaged in subsistence work may not have the time to engage in economic activities that provide them with surplus and a route to a middle-class life. 4. Additional thoughts

The excellent international system of seed banks aids the cause of agricultural sustainability since all nations have access to the world's shared genetic inheritance. Seed banks also provide an insurance system against the loss of agricultural biodiversity.
The issue as to whether GMOs are moving agricultural systems toward or away from sustainability is quite contentious. If, as the evidence appears to indicate, the overwhelming majority of GMO varieties are safe and do not present serious ecological or health risks, it seems that their potential to make plants more draught-resistant, productive, or nutritious makes them an asset for sustainability rather than a liability.
The issue of agricultural pesticides remains a serious concern, especially for consumers and vulnerable populations such as farm workers, pregnant mothers, and children. Much more research is needed to understand and evaluate both the individual and synergistic effects of these chemicals to which we are all exposed at increasing rates. Those that are the most toxic should be banned or severely curtailed while more benign substitutes should be developed for even those that pose less risk. This is one area where a more "command and control" approach is warranted, as opposed to "market-based" mechanisms, due to the uncertainty and our poor state of knowledge with respect to the effects of prolonged exposure to these compounds.

Al-Hawshabi calls Arab efforts to develop genetic resources - Yemen News Agency
Google News | Biodiversity 28 07 2008

Al-Hawshabi calls Arab efforts to develop genetic resources
Yemen News Agency, Yemen - 9 hours ago
For his part, the regional official of Natural Resources Program Ahmed Ghusn briefed that the Arab world has a big wealth of biodiversity and natural ...

Al-Hawshabi calls Arab efforts to develop genetic resources - Yemen News Agency
Google News | Biodiversity 28 07 2008

Al-Hawshabi calls Arab efforts to develop genetic resources
Yemen News Agency, Yemen - 7 hours ago
For his part, the regional official of Natural Resources Program Ahmed Ghusn briefed that the Arab world has a big wealth of biodiversity and natural ...

Al-Hawshabi calls Arab efforts to develop genetic resources - Yemen News Agency
Google News | Biodiversity 28 07 2008

Al-Hawshabi calls Arab efforts to develop genetic resources
Yemen News Agency, Yemen - 5 hours ago
For his part, the regional official of Natural Resources Program Ahmed Ghusn briefed that the Arab world has a big wealth of biodiversity and natural ...

Al-Hawshabi calls Arab efforts to develop genetic resources - Yemen News Agency
Google News | Biodiversity 27 07 2008

Al-Hawshabi calls Arab efforts to develop genetic resources
Yemen News Agency, Yemen - 1 hour ago
For his part, the regional official of Natural Resources Program Ahmed Ghusn briefed that the Arab world has a big wealth of biodiversity and natural ...

How the Personal Genome Project Could Unlock the Mysteries of Life
Wired magazine | Top Stories 27 07 2008 George Church is dyslexic, narcoleptic, and a vegan. He is married with one daughter, weighs about 210 pounds, and has worn a pioneer-style bushy beard for decades. He has elevated levels of creatine kinase in his blood, the consequence of a heart attack. He enjoys waterskiing, photography, rock climbing, and singing in his church choir. His mother's maiden name is Strong. He was born on August 28, 1954. If this all seems like too much information, well, blame Church himself. As the director of the Lipper Center for Computational Genetics at Harvard Medical School, he has a thing about openness, and this information (and plenty more, down to his signature) is posted online at arep.med.harvard.edu/gmc/pers.html. By putting it out there for everyone to see, Church isn't just baiting identity thieves. He's hoping to demonstrate that all this personal information — even though we consider it private and somehow sacred — is actually fairly meaningless, little more than trivia. "The average person shouldn't be interested in this stuff," he says. "It's a philosophical exercise in what identity is and why we should care about that." As Church sees it, the only real utility to his personal information is as data that reflects his phenotype — his physical traits and characteristics. If your genome is the blueprint of your genetic potential written across 6 billion base pairs of DNA, your phenome is the resulting edifice, how you actually turn out after the environment has had its say, influencing which genes get expressed and which traits repressed. Imagine that we could collect complete sets of data — genotype and phenotype — for a whole population. You would very quickly begin to see meaningful and powerful correlations between particular genetic sequences and particular physical characteristics, from height and hair color to disease risk and personality. Church has done more than imagine such an undertaking; he has launched it: The Personal Genome Project, an effort to make those correlations on an unprecedented scale, began last year with 10 volunteers and will soon expand to 100,000 participants. It will generate a massive database of genomes, phenomes, and even some omes in between. The first step is to sequence 1 percent of each volunteer's genome, focusing on the so-called exome — the protein-coding regions that, Church suspects, do 90 percent of the work in our DNA. It's a long way from sequencing all 6 billion nucleotides — the As, Ts, Gs, and Cs — of the human genome, but even so, cataloging 60 million bits multiplied by 100,000 individuals is an audacious goal. The PGP stands as the tent pole of what Church calls his "year of convergence," the moment when his 30 years as a geneticist, a technologist, and a synthetic biologist all come together. The project is a proof of concept for the Polonator G.007, the genetic-sequencing instrument developed in Church's lab that hit the market this spring. And the PGP will also put Church's expertise in synthetic biology to use, reverse engineering volunteers' skin cells into stem cells that could help diagnose and treat disease. If the convergence comes off as planned, the PGP will bring personal genomics to fruition and our genomes will unfold before us like road maps: We will peruse our DNA like we plan a trip, scanning it for possible detours (a predisposition for disease) or historical markers (a compelling ancestry). Bringing the genome into the light, Church says, is the great project of our day. "We need to inspire our current youth in a way that outer space exploration inspired us in 1960," he says. "We're seeing signs that knowing about our inner space is very compelling." To Church, who built his first computer at age 9 and taught himself three programming languages by 15, all of this is unfolding according to the same laws of exponential progress that have propelled digital technologies, from computer memory to the Internet itself, over the past 40 years: Moore's law for circuits and Metcalfe's law for networks. These principles are now at play in genetics, he argues, particularly in DNA sequencing and DNA synthesis. Exponentials don't just happen. In Church's work, they proceed from two axioms. The first is automation, the idea that by automating human tasks, letting a computer or a machine replicate a manual process, technology becomes faster, easier to use, and more popular. The second is openness, the notion that sharing technologies by distributing them as widely as possible with minimal restrictions on use encourages both the adoption and the impact of a technology.

Inside the Personal Genome Project

The project will turn information from 100,000 subjects into a huge database thath can reveal the connections between our genes and our physical selves. Here's how. — Thomas Goetz


1. Entrance Exam Volunteers take a quiz to show genetic literacy. One question: How many chromosomes do unfertilized human egg cells contain? a) 11, b) 22, c) 23, d) 46, or e) 92? (Answer: c.) Only those with a perfect score proceed, but retests are allowed.	2. Data Collection Volunteers sign an "open consent" form acknowledging that their information, though anonymized, will be accessible by others. They fill out their phenotype traits, listing everything from waist size to diet habits. Suitable respondents go on to the next step.	3. Sample Collection Volunteers hit the medical center, where they are interviewed by an MD. Then a technician draws some blood, gathers a saliva sample, and takes a punch of skin. Don't worry: It hurts about as much as a bee sting.

4. Lab Work The tissues are sent to a biobank, where DNA is extracted from the blood. One percent of it — the exome — is sequenced. Meanwhile, bacteria DNA is extracted from the saliva and sequenced to reveal the volunteer's microbiome.	5. Research Now the fun part: Crunching the numbers. PGP scientists and other researchers start working with the data assembled from 100,000 individuals to investigate potential links between phenotypes and genotypes. The team will look for patterns and statistically significant anomalies.	6. Sharing The volunteers get access to not only the raw data from their genome, but anything the research team gleans from their information. Insights — a newly discovered cancer risk, for example — are posted in a volunteer's file, which they'll be free to share with other PGP participants.

"I always tell people, your biggest problem in life is not going to be hiding your stuff so nobody steals it," Church says. "It's going to be getting anybody to ever use it. Start hiding it and that decreases the probability to almost zero." For most of his career, Church has been known as a brilliant technologist, more behind-the-scenes tinkerer than scientific visionary. Though he was part of the group that kicked off the Human Genome Project, he's far less known than scientists like Francis Collins or J. Craig Venter, who took the stage at the end. His obscurity is due partly to his style. He talks about his accomplishments with a certain detachment that one might mistake for ambivalence. "He's not without ego; it's just a different sort of ego," says entrepreneur Esther Dyson, a friend and one of the first 10 PGP volunteers. "Everything is a subject of his intellectual curiosity, including himself." His low profile may be the result of his tendency to get too far ahead of the curve, working a decade or two ahead of his field — so far that even the experts don't always get what he's talking about. "Lots of George's work is so advanced it's not ready to become standard," says Drew Endy, a professor of bioengineering at Stanford and cofounder with Church of Codon Devices, a synthetic-biology startup. "He's perfectly happy to spin out tons of ideas and see what might stick. It's high-throughput screening for technology and science. That's not the way most people work." But thanks to the PGP, the Polonator, and the fact that the rest of the world is finally starting to understand what he's been talking about, Church's obscurity is coming to an end. He sits on the advisory board of more than 14 biotech companies, including personal genomics startup 23andMe and genetic testing pioneer DNA Direct. He has also cofounded four companies in the past four years: Codon Devices, Knome, LS9, and Joule Biosciences, which makes biofuels from engineered algae. Newsweek recently tagged him as one of the 10 Hottest Nerds ("whatever that means," Church laughs). For someone who has spent his whole career ahead of his time, he is suddenly very much a man of the moment. Most historians would cite Prague or Paris or Berkeley as the intellectual hub of the 1960s, but for people interested in computers, there was no place so significant as Hanover, New Hampshire. There, at Dartmouth College, an experiment in time-share computing was flourishing. Developed by professors John Kemeny and Thomas Kurtz, the Dartmouth Time-Sharing System let students remotely access the power of a mainframe computer to do calculations for mathematics or science assignments or to play a simulated game of college football. It ran on an easy-to-learn, intuitive program that Kemeny and Kurtz called Basic. In 1967, the DTSS transitioned to a more-powerful GE-635 machine and offered remote terminals to 33 secondary schools and colleges, including Phillips Academy, a prep school in nearby Andover, Massachusetts. The terminal — not much more than a teletype machine, really — sat in the basement of the school's math building, forgotten until the next fall, when a young George Church showed up for his freshman year and began asking whether there was a computer on campus. Someone pointed Church to the basement. "There wasn't even a chair in the room. I had used a typewriter before, but never a teletype. And so I just started pressing keys," Church recalls. "Eventually I hit Return, and it came back with 'What?' And so I started typing in stuff like crazy and hitting Return. And it kept coming back with 'What?' At that point, I was pretty convinced it wasn't a human, but it was actually talking in words. So I just hadn't asked the right question or given the right answer." Soon, Church found a book on Basic. "I was just sailing," he says. He spent endless hours in that basement — he eventually borrowed a chair — and taught himself the intricacies of coding, learning to program in Basic, Lisp, and Fortran. Indeed, thinking in code came so naturally to Church that he stopped going to his classes (a habit that would later get him kicked out of graduate school at Duke) and taught the computer linear algebra instead. It turns out that learning how to write code — change it, hit Return, see what it will do — was ideal training for Church's eventual career in computational biology. "That's how we reverse engineer things like E. coli — you change something, and you see how it behaves," he says. "Little did I know that 30 years later, we would use almost exactly the same operations to optimize metabolic networks." Church first hit on the power of computation to automate biology in the mid-'70s when he was in graduate school at Harvard. At the time, he was working on recombinant DNA, a then-new technique to splice a gene from one organism into another. Identifying a sequence of 80 or so base pairs of genetic code was a slow, tedious process. "You had to literally read off the bases and write them on a piece of paper, one by one," Church says. "So I wrote a sequence-reading program that would crunch it out. When the senior graduate student heard I had automated that, he said, 'What do you want to do that for? That's the only fun part.'" By 1980, when Church's adviser, Wally Gilbert, won the Nobel Prize for DNA sequencing techniques, the process was still slow and expensive, executing one DNA strand at a time. So Church began working on one of his earlier targets for automation. His idea was to sequence several strands together by combining them into a single sample mixture. He called it multiplexing, drawing an analogy to signal multiplexing in electronics, in which more than one signal flows through a current at the same time. Church thought most of the work could even be integrated into one device rather than numerous machines. It was a provocative idea, not just because he was substituting several human tasks for machine-driven ones, but also because he didn't make the usual false promise that technology would simplify the process. On the contrary, multiplexing would be complicated, Church maintained. But technology was up to the task. Four years later, Church was invited to present his work on multiplexing at a small meeting in Alta, Utah. The Department of Energy had gathered about 20 scientists to mull over one question for five days: How might recent advances in genetics be used to measure an increase in genetic mutations arising from radiation exposure, as in Hiroshima? The group quickly reached the conclusion that technology circa 1984 couldn't answer that question. Meanwhile, they still had several more days in the mountains. "There were a bunch of us there who could talk about genomics as if it were an engineering exercise. And then we said, well, as a kind of booby prize, we could think of other things you could do," Church recalls, "like, say, sequencing the human genome." Though Church was almost entirely unknown before the meeting, his presentation on multiplex sequencing methods stole the show. When he fell into a huge snow drift during a break one afternoon, one participant worried that the future of sequencing had disappeared with him. That Alta brainstorm would become the Human Genome Project — the effort, adopted by the National Institutes of Health, to sequence one human genome for $3 billion within 15 years. However audacious the HGP seemed, Church was disappointed by it almost from the start. "We could have said our goal was to get everybody's genome for some affordable price," he says, "and one genome would be a milestone" on the way toward that goal. The HGP also played it safe with its choice of technology. Despite the promise of Church's multiplexing system, the HGP instead used a more established instrument manufactured by Applied Biosystems, based on a technique developed by biochemist Frederick Sanger. As Church saw it, this meant that the project had failed to put its $3 billion toward improving the state of the art. Even worse, the HGP consumed so many of the resources available to the field of genetics that it effectively locked that state of the art into 1980s technology. The result was nearly two decades of inertia. It wasn't until 2005, when the Human Genome Project was complete and new goals were put forth, that Church finally perfected the multiplexing approach he had presented 20 years earlier at Alta. In a paper published in Science, Church demonstrated a technique that could analyze millions of sequences in one run (Sanger's method could handle just 96 strands of DNA at a time). And Church's method not only accelerated the process, it made it far cheaper, too, elegantly demonstrating the power of automation to drive exponential advances and bring down costs. Church's approach, and a competing innovation developed by 454 Life Sciences that same year, inaugurated the second generation of sequencing, now in full swing. In the past three years, more companies have joined the marketplace with their own instruments, all of them driving toward the same goal: speeding up the process of sequencing DNA and cutting the cost. Most of the second-generation machines are priced at around $500,000. This spring, Church's lab undercut them all with the Polonator G.007 — offered at the low, low price of $150,000. The instrument, designed and fine-tuned by Church and his team, is manufactured and sold by Danaher, an $11 billion scientific-equipment company. The Polonator is already sequencing DNA from the first 10 PGP volunteers. What's more, both the software and hardware in the Polonator are open source. In other words, any competitor is free to buy a Polonator for $150,000 and copy it. The result, Church hopes, will be akin to how IBM's open-architecture approach in the early '80s fueled the PC revolution. In the sequencing game, though, the cost of the machine is only half the equation. The more telling expense is the operating cost, particularly the cost of sequencing entire human genomes. Executives at 454 estimate that their latest machine can pull off a whole genome sequence for $200,000. Applied Biosystems claims its instrument has completed a genome for just $60,000. Church maintains that, while the Polonator isn't up to whole-genome reads, it is clocking in at about one-third the cost of Applied Biosystems' estimate. A whole sequence from Knome, the retail genomics firm cofounded by Church, goes for $350,000. (It's worth noting that these figures are only roughly comparable, since each company uses slightly different quality measures and specifications.) As these numbers continue to drop, the mythical $1,000 genome comes ever closer. Sequencing a human genome for $1,000 is the somewhat arbitrary benchmark for true personalized genomics — when the science could become a component of standard medical care. An important catalyst in achieving that point is the Archon X Prize for Genomics, which is offering $10 million to the team that can sequence 100 complete genomes in 10 days for less than $10,000 each. As of June, seven teams, including Church's lab, had entered the competition. Church, who served for a time on the advisory board of the contest, says that the prize will drive costs down further and help publicize the potential of personalized whole-genome sequencing. That's important because Church hopes the Polonator and other next-generation instruments will inspire a new generation of smaller labs to begin work in personal genomics, as well as other genetic sciences. Already, the onslaught of technology has jump-started new projects, like sequencing part of the Neanderthal genome, examining extremophile microbes in old California iron mines, and studying the regenerative properties of the salamander. In medicine, cheaper sequencing has enabled research into drug-resistant tuberculosis; the genetics of breast, lung, and other cancers; and the DNA architecture of schizophrenics. But if the Polonator is going to lead that charge, it has to work — and work on a massive scale. And that means passing a major test: successfully sequencing the 100,000 exomes in the PGP.

Photo: Lloyd Ziff

All of us know our height, weight, and eye color. Fewer of us know our arm span or resting blood pressure. But who among us knows the direction of our hair whorls or the Gell-Coombs type of our allergies? This is the level of detail that the PGP requires the 100,000 volunteers to reveal about themselves, a list staggering in its exhaustiveness. The PGP will tally head circumferences, injuries, chin clefts and cheek dimples, whether volunteers can roll their tongues or hyperflex their joints, whether they dislike hot climates or are hot tempered, if they've often been exposed to power lines or wood dust or diesel exhaust or textile fibers. The project questionnaire asks how many meals they eat a day and whether they prefer their food fried, broiled, or barbecued. It even demands to know how much television they watch. And, of course, PGP volunteers will hand over most aspects of their medical history, from vaccines to prescriptions. This phenotype data will be integrated with a volunteer's genomic information, then combined with statistics from all the other subjects to create a potent database ripe for interrogation. In contrast to the heavy lifting that genetic research requires now — each study starts from scratch with a new hypothesis and a fresh crop of subjects, consent forms, and tissue samples — the PGP will automate the research process. Scientists will simply choose a category of phenotype and a possible genetic correlation, and statistically significant associations should flow out of the data like honey from a hive. A genetic predisposition for colon cancer, for instance, might be found to lead to disease only in connection with a diet high in barbecued foods, or a certain form of heart disease might be associated with a particular gene and exposure to a particular virus. Genomic discovery won't be a research problem anymore. It'll be a search function. (This helps explain why Google, among others, has donated to the project). The process began last year, and each of the first 10 volunteers has a background in medicine or genetics. They include John Halamka, CIO of Harvard Medical School and a physician; Rosalynn Gill, chief science officer at Sciona (a personalized genetics nutrition company); and Steven Pinker, the noted psychologist and author. The other 99,990 participants won't be expected to be so elite, though they will have to pass a genetics-literacy quiz to demonstrate informed consent. The general selection process, which starts with registration at personalgenomes.org, is scheduled to begin later this year. Besides offering up their genomes, subjects will have to part with some spit and a bit of skin. The saliva contains their microbiome — the trillions of microbes that exist, mostly symbiotically, on and in our bodies. If phenotype is a combination of genotype plus environment, the microbiome is the first wash of that environment over our bodies. By measuring some fraction of it, the PGP should offer a first look at how the genome-to-microbiome-to-phenome chain plays out. The skin sample goes into storage, creating what would be one of the world's largest biobanks. Members of Church's lab have devised a way to automate turning the skin cells into stem cells, and they hope to publish the technique later this year. (Similar work has been done at the University of Wisconsin and Kyoto University.) By reprogramming the skin cells using synthetically engineered adenoviruses, Church's team can transform the skin cells into many sorts of tissue — lungs, liver, heart. These tissues could be used as a diagnostic baseline to detect predisposition for various diseases. What's more, the reprogrammed cells could be used to treat disease, replacing damaged or failing tissue. It's an intriguing hint of how Church's work with synthetic biology complements genomic sequencing. If the PGP were simply an exercise in breaking down 100,000 individuals into data streams, it would be ambitious enough. But the project takes one further, truly radical step: In accordance with Church's principle of openness, all the material will be accessible to any researcher (or lurker) who wants to plunder thousands of details from people's lives. Even the tissue banks will be largely accessible. After Church's lab transforms the skin into stem cells, those new cell lines — which have been in notoriously short supply despite their scientific promise — will be open to outside researchers. This is a significant divergence from most biobanks, which typically guard their materials like holy relics and severely restrict access. For the PGP volunteers, this means they will have to sign on to a principle Church calls open consent, which acknowledges that, even though subjects' names will be removed to make the data anonymous, there's no promise of absolute confidentiality. As Church sees it, any guarantee of privacy is false; there is no way to ensure that a bad actor won't tap into a system and, once there, manage to extract bits of personal information. After all, even de-identified data is subject to misuse: Latanya Sweeney, a computer scientist at Carnegie Mellon University, demonstrated the ease of "re-identification" by cross-referencing anonymized health-insurance records with voter registration rolls. (She found former Massachusetts governor William Weld's medical files by cross-referencing his birth date, zip code, and sex.) To Church, open consent isn't just a philosophical consideration; it's also a practical one. If the PGP were locked down, it would be far less valuable as a data source for research — and the pace of research would accordingly be much slower. By making the information open and available, Church hopes to draw curious scientists to the data to pursue their own questions and reach their own insights. The potential fields of inquiry range from medicine to genealogy, forensics, and general biology. And the openness doesn't serve just researchers alone. PGP members will be seen as not only subjects, but as participants. So, for instance, if a researcher uses a volunteer's information to establish a link between some genetic sequence and a risk of disease, the volunteer would have that information communicated to them. This is precisely what makes the PGP controversial in genetics circles. Though Church talks about it as the logical successor to the Human Genome Project, other geneticists see it as a risky proposition, not for its privacy policy but for its presumption that the emerging science of genomics already has implications for individual cases. The National Human Genome Research Institute, for example, has cautioned that the burgeoning personal-genomics industry, which includes research-oriented projects like the PGP as well as straight-to-consumer companies like Navigenics and 23andMe and whole-genome-sequencing shops like Knome, puts the sales pitch ahead of the science. "A lot of people would like to rapidly capitalize on this science," says Gregory Feero, a senior adviser at the NHGRI. "But for an individual venturing into this now, it's a risk to start making any judgments or decisions based on current knowledge. At some point, we'll cross over into a time when that's more sensible." Church cautions, however, that keeping clinicians and patients in the dark about specific genetic information — essentially pretending the data or the technology behind it don't exist — is a farce. Even worse, it violates the principle of openness that leads to the fastest progress. "The ground is changing right underneath them," he says of the medical establishment. "Right now, there's a wall between clinical research and clinical practice. The science isn't jumping over. The PGP is what clinical practice would be like if the research actually made it to the patient." In the not-too-distant future, Church says, hospitals and clinics could be outfitted with a genome sequencer much the way they now have x-ray machines or microscopes. "In the old books," Church says, "almost every scientist was sitting there with a microscope on their table. Whether they're a physical scientist or a biological scientist, they've got that microscope there. And that inspires me." Wired deputy editor Thomas Goetz (thomas@wired.com) wrote about personal genomics in issue 15.12.

How the Personal Genome Project Could Unlock the Mysteries of Life
Wired Magazine | Science | News 27 07 2008 George Church is dyslexic, narcoleptic, and a vegan. He is married with one daughter, weighs about 210 pounds, and has worn a pioneer-style bushy beard for decades. He has elevated levels of creatine kinase in his blood, the consequence of a heart attack. He enjoys waterskiing, photography, rock climbing, and singing in his church choir. His mother's maiden name is Strong. He was born on August 28, 1954. If this all seems like too much information, well, blame Church himself. As the director of the Lipper Center for Computational Genetics at Harvard Medical School, he has a thing about openness, and this information (and plenty more, down to his signature) is posted online at arep.med.harvard.edu/gmc/pers.html. By putting it out there for everyone to see, Church isn't just baiting identity thieves. He's hoping to demonstrate that all this personal information — even though we consider it private and somehow sacred — is actually fairly meaningless, little more than trivia. "The average person shouldn't be interested in this stuff," he says. "It's a philosophical exercise in what identity is and why we should care about that." As Church sees it, the only real utility to his personal information is as data that reflects his phenotype — his physical traits and characteristics. If your genome is the blueprint of your genetic potential written across 6 billion base pairs of DNA, your phenome is the resulting edifice, how you actually turn out after the environment has had its say, influencing which genes get expressed and which traits repressed. Imagine that we could collect complete sets of data — genotype and phenotype — for a whole population. You would very quickly begin to see meaningful and powerful correlations between particular genetic sequences and particular physical characteristics, from height and hair color to disease risk and personality. Church has done more than imagine such an undertaking; he has launched it: The Personal Genome Project, an effort to make those correlations on an unprecedented scale, began last year with 10 volunteers and will soon expand to 100,000 participants. It will generate a massive database of genomes, phenomes, and even some omes in between. The first step is to sequence 1 percent of each volunteer's genome, focusing on the so-called exome — the protein-coding regions that, Church suspects, do 90 percent of the work in our DNA. It's a long way from sequencing all 6 billion nucleotides — the As, Ts, Gs, and Cs — of the human genome, but even so, cataloging 60 million bits multiplied by 100,000 individuals is an audacious goal. The PGP stands as the tent pole of what Church calls his "year of convergence," the moment when his 30 years as a geneticist, a technologist, and a synthetic biologist all come together. The project is a proof of concept for the Polonator G.007, the genetic-sequencing instrument developed in Church's lab that hit the market this spring. And the PGP will also put Church's expertise in synthetic biology to use, reverse engineering volunteers' skin cells into stem cells that could help diagnose and treat disease. If the convergence comes off as planned, the PGP will bring personal genomics to fruition and our genomes will unfold before us like road maps: We will peruse our DNA like we plan a trip, scanning it for possible detours (a predisposition for disease) or historical markers (a compelling ancestry). Bringing the genome into the light, Church says, is the great project of our day. "We need to inspire our current youth in a way that outer space exploration inspired us in 1960," he says. "We're seeing signs that knowing about our inner space is very compelling." To Church, who built his first computer at age 9 and taught himself three programming languages by 15, all of this is unfolding according to the same laws of exponential progress that have propelled digital technologies, from computer memory to the Internet itself, over the past 40 years: Moore's law for circuits and Metcalfe's law for networks. These principles are now at play in genetics, he argues, particularly in DNA sequencing and DNA synthesis. Exponentials don't just happen. In Church's work, they proceed from two axioms. The first is automation, the idea that by automating human tasks, letting a computer or a machine replicate a manual process, technology becomes faster, easier to use, and more popular. The second is openness, the notion that sharing technologies by distributing them as widely as possible with minimal restrictions on use encourages both the adoption and the impact of a technology.

Inside the Personal Genome Project

The project will turn information from 100,000 subjects into a huge database thath can reveal the connections between our genes and our physical selves. Here's how. — Thomas Goetz


1. Entrance Exam Volunteers take a quiz to show genetic literacy. One question: How many chromosomes do unfertilized human egg cells contain? a) 11, b) 22, c) 23, d) 46, or e) 92? (Answer: c.) Only those with a perfect score proceed, but retests are allowed.	2. Data Collection Volunteers sign an "open consent" form acknowledging that their information, though anonymized, will be accessible by others. They fill out their phenotype traits, listing everything from waist size to diet habits. Suitable respondents go on to the next step.	3. Sample Collection Volunteers hit the medical center, where they are interviewed by an MD. Then a technician draws some blood, gathers a saliva sample, and takes a punch of skin. Don't worry: It hurts about as much as a bee sting.

4. Lab Work The tissues are sent to a biobank, where DNA is extracted from the blood. One percent of it — the exome — is sequenced. Meanwhile, bacteria DNA is extracted from the saliva and sequenced to reveal the volunteer's microbiome.	5. Research Now the fun part: Crunching the numbers. PGP scientists and other researchers start working with the data assembled from 100,000 individuals to investigate potential links between phenotypes and genotypes. The team will look for patterns and statistically significant anomalies.	6. Sharing The volunteers get access to not only the raw data from their genome, but anything the research team gleans from their information. Insights — a newly discovered cancer risk, for example — are posted in a volunteer's file, which they'll be free to share with other PGP participants.

Photo: Lloyd Ziff