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First Chickens in Americas Were Brought From Polynesia
By JOHN NOBLE WILFORD, The New York Times, June 5, 2007
Why did the chicken cross the Pacific Ocean? To get to the other side, in South America. How? By Polynesian canoes, which apparently arrived at least 100 years before Europeans settled the continent.
That is the conclusion of an international research team, which reported yesterday that it had found “the first unequivocal evidence for a pre-European introduction of chickens to South America,” or presumably anywhere in the New World.
The researchers said that bones buried on the South American coast were from chickens that lived between 1304 and 1424. Pottery at the site was from a similar or earlier time. A DNA analysis linked the bones, which were excavated at El Arenal on the Arauco Peninsula in south central Chile, to chickens from Polynesian islands.
The findings are being published in the Proceedings of the National Academy of Sciences. The lead author is Alice A. Storey, an anthropologist at the University of Auckland, New Zealand, and other team members are from American Samoa, Australia, Canada and the United States.
The research group and other anthropologists said the bones supported the idea that Polynesians in their far-ranging canoes had by then not only populated the Pacific as far east as Hawaii and Easter Island, but also had on occasion reached the Americas.
The presence of the South American sweet potato in pre-European sites in Polynesia indicated some prehistoric contact between America and the islands.
But Dr. Storey’s group said that no firm “archaeological evidence for Polynesian contact with the Americas has been reported before now.”
For more than 30 years, scholars have debated when and how chickens reached the Americas: whether in pre-Columbian times, possibly by Polynesian visitors, or when Portuguese and Spanish settlers arrived in South America after 1500. Most experts had favored the latter hypothesis.
Others thought this unlikely, noting that when the Spanish invaded Peru in 1532, they saw chickens being used in traditional ceremonies. It seemed hard to believe, some scholars pointed out, that chickens would have been so rapidly dispersed from the east coast to the west and already be incorporated in religious events.
From the DNA examination, Dr. Storey and colleagues concluded, the El Arenal bones had a close genetic relationship to chickens from prehistoric sites on several islands, Tonga and American Samoa in particular. Further analysis of prehistoric chicken samples from the islands is expected to discern the specific origin and timing of the Chilean chickens.
Scholars found it disappointing and puzzling that the Polynesians who landed at El Arenal left nothing more than chicken bones. Pottery at the site is in a local style. Perhaps the visitors ate and ran, but not without leaving behind some starter chickens for future plates of arroz con pollo.
Puerto Rico’s AIDS Care in Disarray Over Funds
By ERIK ECKHOLM, The New York Times, June 5, 2007
SAN JUAN, P.R. — His emaciated body advertises the damage wreaked by the AIDS virus. But over the last year, Rolando Warren González, 41, a former steel band member, has faced an extra challenge to his survival.
From the shelter where he lives in Loiza in Puerto Rico’s impoverished northeast, Mr. González travels an hour and a half by bus to reach the government clinic where he receives his “cocktail” of antiviral drugs.
“But sometimes I go, and they just don’t have the medicines,” he said.
Six times in the last year, he said, he has suffered two-week periods with no drugs, undercutting the life-prolonging benefits of modern therapies against H.I.V., the AIDS virus.
Accounts like his — and worse — are repeated across this tropical territory of the United States, where hundreds of H.I.V. and AIDS patients are not receiving vital medical care, say a host of doctors, community groups and patients.
The disarray in treatment reflects a stew of problems. An overstretched health care budget is accentuated by rivalries between the commonwealth and the San Juan city governments, which run separate AIDS programs.
But federal officials and many local doctors say the main culprit is the island’s poor management of the available money provided for AIDS care under the Ryan White Act, amounting to $53 million last year. Clinics have not received drugs on time, and private groups that assist AIDS patients are often reimbursed six months late or more, causing some to cut services or even shut down.
In sharp rebukes to the Puerto Rico Health Department and the City of San Juan, federal officials have put the AIDS grants under unusually tight review and even threatened to halt some federal money. Because of disorganization, the officials say, the island has often failed to spend all its Ryan White aid, losing access to $6.5 million over the last five years.
Adding questions, in December the F.B.I. raided four San Juan Health Department offices, seizing 400 boxes of documents in a criminal investigation into possible misuse of Ryan White grants.
Officials here deny misusing funds. They did have to establish a waiting list for new patients needing drug treatment in the fall, but say that any lapses in care have been brief and that their main worry, in an era when treating a single AIDS patient can cost more than $25,000 a year, is a shortage of money.
At a time when patients live longer and drug costs soar, the challenge is daunting. But doctors and patients here say the government has made poor use of its money. “The state of H.I.V. treatment here is a catastrophe,” said Dr. José Varga Vidot, director of Community Initiative, a private group in San Juan that provides primary care to 1,600 patients including drug addicts, prostitutes and homeless people.
Dr. Varga Vidot said he knew of at least 75 people who were unable to obtain all their drugs from government clinics for up to a month.
In relation to its population of 3.9 million, Puerto Rico has the fifth-highest concentration of AIDS cases of states and territories, with 12,000 patients and estimates that as many more are infected with H.I.V. but are not yet ill.
About half the patients were infected from shared heroin needles, posing special challenges because many are isolated and penniless.
Although no studies have tried to link the spotty care with mortality, according to the latest comparative national data, 580 patients died here in 2003, indicating a mortality rate higher than that in states like New York known for good AIDS care.
A majority of H.I.V. and AIDS patients are covered by the Puerto Rican version of Medicaid, known as Health Reform. That financially struggling program does not cover some crucial drugs. The $53 million provided under the Ryan White law is supposed to fill the gaps.
As a territory, “we don’t get what we need,” said Health Secretary Rosa Pérez-Perdomo.
Federal aid to the Medicaid program here is capped at $240 million, meeting 13 percent of the overall budget, Dr. Pérez-Perdomo said. On the mainland, poorer states receive up to 75 percent of their Medicaid money from Washington, giving them more leeway in treating low-income AIDS patients.
Advocates for AIDS treatment in the United States, where the disease is increasingly concentrated among blacks and Hispanics, juxtapose President Bush’s new call for $30 billion to expand AIDS care abroad, a politically popular cause, with the stagnant financing of the Ryan White program for needy Americans. That has remained around $2.1 billion for four years.
“At a time of rising needs at home, especially among minorities, Puerto Rico and the states all have to compete for flat Ryan White funds,” said Dennis DeLeon, director of the Latino Commission on AIDS in New York.
The advocates say Washington should do more to reshape a dysfunctional care system on the island.
The Health Resources and Services Administration, which administers the Ryan White money, has repeatedly pushed for streamlining the crushing bureaucracy here and sent many advisers, said Dr. Laura Cheever, deputy associate administrator at the agency.
The F.B.I. raid, on Dec. 12, was part of an investigation into the misuse of Ryan White money that San Juan had received for its use and for 30 nearby municipalities, said a spokesman for the agency here, Harry Rodríguez. In 2006, the city received $13 million.
Even patients receiving top-quality care have to struggle with the disease, because H.I.V. can develop resistance, making patients switch to new, costlier drugs.
Gaps in treatment can hasten the development of resistance. Doctors here also say that when they need to switch an ailing patient to a new regimen, approval from the central health department can take months and that the latest drugs are often not available.
Angélica Segarra runs the shelter for homeless AIDS patients where Mr. González stays, a rambling house in Loiza. Ms. Segarra said that she provided medicines to 60 people before recent cuts in financing by San Juan forced her to stop and that many patients have searched in vain for clinics taking new patients.
One patient, Luis Torres, 42, was unable to secure medicines for three months. Another resident, Miguel Vásquez, 44, split his drugs with Mr. Torres because, he said, “it seemed like the right thing to do.”
In March and April, each took half the proper dose until the supply ran out. “Now I’ve had a month with no cocktail and I’m worried,” Mr. Vásquez said.
Cash shortages or errors in drug distribution by the commonwealth Health Department mean that patients sometimes receive five days’ doses at a time or two antivirals instead of the prescribed three, a practice that can do more harm than good.
The main San Juan AIDS clinic, one of the better equipped, serves 2,254 patients. Since late 2006, it has stopped accepting new ones, saying it cannot afford more.
One problem is jurisdictional rivalries. Dr. Héctor Sorentini Méndez, health director of San Juan, said the commonwealth had refused to share its federal grants, $22 million under the AIDS Drug Assistance Program, which pays for otherwise uncovered medicines under the Ryan White law.
Sandra Molinias Rabe, 33, a former heroin addict in the mountains southwest of San Juan, is one of many cases who have slipped through the cracks. Ms. Rabe lives with her partner, Raymond Quiñones, in a squalid shack without running water, reached by an arduous climb up overgrown steps. A neighbor allows them to carry up buckets of water and run an electricity line to power a light bulb.
Her medical condition is poor, and the doctor at Casa Joven del Caribe, an aid group, said she needed new laboratory tests to see whether she should switch medications. The aid group, which is in a dispute with San Juan over late disbursements, can no longer pay for her tests and drugs and sent her to an assigned Medicaid doctor in another town. That doctor said she would have to return in two weeks. In the meantime, she had no medicines.
Antiquated equipment and poor communications have added to the problems. An audit by the comptroller of Puerto Rico published in November found that the Health Department records of drug stocks and deliveries to outlying clinics were grossly deficient, allowing mistakes and medicines to expire. Four of the eight main H.I.V. clinics lacked working bathrooms or computers, another report said in the fall.
Héctor Figueroa, who directs a drug treatment program in Caguas, south of San Juan, said changes in federal priorities and a lack of action by the Puerto Rico government had led to sharp cuts in transportation aid and substance abuse treatment. At the two clinics in his region, Mr. Figueroa said, patients sometimes receive 15 days’ medicines in a month.
The Health Resources and Services Administration, citing problems in administration, patient access, and community participation, put the San Juan government on “restricted drawdown” status in 2005 and did the same for the commonwealth in 2006. The health agencies now have to submit all grant vouchers to Washington for approval before money is disbursed.
Puerto Rico officials say the waiting list for drug assistance has declined, to 36 from 130 in the fall, and will soon be eliminated. A local group, AIDS Patients for a Sane Policy, said that its survey of clinics found 477 patients waiting to start therapy or to make necessary changes in their drug regimens.
For a year, Puerto Rican and mainland groups, including the Congressional Hispanic Caucus, have called on federal authorities to take stronger action here.
In a letter to Michael O. Leavitt, secretary of health and human services, Senator Tom Coburn, Republican of Oklahoma, has said he was “gravely concerned about the ongoing crisis taking place in Puerto Rico.”
In another letter, Senator Hillary Rodham Clinton, Democrat of New York, said mismanagement had “severely curtailed access to life-extending treatment” and called on the health administration to strengthen its oversight of Ryan White programs on Puerto Rico.
Administration officials said that they had proposed transferring San Juan’s Ryan White funds to a separate entity that would manage them, but that Mayor Jorge A. Santini Padilla had refused.
“In the end,” Dr. Cheever of the health administration said, “It’s up to them to do the planning, allocations and administration, and what we can do in terms of sanctions is very limited by legislation.”
Slipstream: First, Cure Malaria. Next, Global Warming
By JASON PONTIN, The New York Times, June 3, 2007
Amyris Biotechnologies has almost finished developing a cheap cure for malaria that could save the lives of millions of the poor. Now, using the same technology, this start-up in Emeryville, Calif., wants to create new biofuels that may help save the planet.
Even in an industry much attached to hyperbole, few companies have excited such high hopes. Investors include the Bill & Melinda Gates Foundation, which granted the Institute for OneWorld Health $42.6 million to finance Amyris’s antimalarial drug, and two princes of Silicon Valley venture capital, John Doerr of Kleiner Perkins Caufield & Byers, and Vinod Khosla of Khosla Ventures, who, with the private equity group of Texas Pacific Group Ventures, invested $20 million.
Explaining his interest in the start-up, Mr. Khosla told me: “Amyris was using a very sexy technology and applying it in a radical way to malarial drugs. When I asked the question, ‘Can you do the same for energy?’ the surprising answer was, ‘Yes, we can.’ ”
Mr. Doerr said he thought that green technologies “could be the largest economic opportunity of the 21st century.” He called Amyris “the best team to do this kind of work.”
Amyris’s technology derives from the research of Jay D. Keasling, a professor of chemical engineering at the University of California, Berkeley, and the director of the synthetic biology department of the Lawrence Berkeley National Laboratory. Mr. Keasling’s lab is widely credited with making commercially practical an emerging technology called metabolic engineering.
Until recently, genetic engineering of the sort associated with traditional biotechnology has been limited to modifying a cell’s processes by inserting, mutating or deleting a single gene or a few significant genes. Genetic engineering has coaxed microorganisms like the common bacterium E. coli to produce drugs like human insulin, but has produced little else besides such protein drugs and a few antibiotics.
Mr. Keasling’s metabolic engineering is farther-reaching and, potentially, much more productive. His lab has invented techniques that rewrite the metabolisms of microorganisms. By modifying the structure of a microorganism’s proteins and adding genes from other organisms, Mr. Keasling has designed microbial factories that can produce a tremendous variety of drugs, biofuels and other chemicals.
Amyris was founded in the summer of 2003 by Mr. Keasling and three young postdoctoral students from his lab: Neil Renninger, Kinkead Reiling and Jack D. Newman. They received the large grant from the Gates Foundation a little more than a year later.
To create an antimalarial drug, Amyris engineered bacteria to excrete a drug called artemisinin. Artemisinin is 100 percent effective against malaria, but it derives from a weed called sweet wormwood that only grows in China and Vietnam and costs $2.40 for a course of treatment — a steep price for the world’s poor.
Every year, 300 million to 500 million people become infected with malaria, according to the World Health Organization; more than 1.5 million of those infected will die, most of them children in Africa and Asia. Amyris’s technique would reduce the cost of artemisinin to less than 25 cents for a course of treatment, according to the company. OneWorld Health, a nonprofit pharmaceutical company, has pledged to give away the drug to poor countries. Amyris says the drug will be ready for mass production in 2008.
It wasn’t until January 2006, when a presentation by Mr. Keasling at the World Economic Forum in Davos caught the attention of Mr. Doerr and Mr. Khosla, that Amyris’s founders began to consider seriously what other compounds their bioengineered bugs might produce. The two venture capitalists encouraged the scientists to think ambitiously.
“At nights and on weekends we’d been working on what our for-profit projects could be at the end of the Gates grant,” Mr. Reiling, the company’s vice president for development, told me. “One of those projects was using our engineering know-how to come up with novel biofuels.”
Mr. Doerr said: “When I met them, it was truly an open question. Should they work on other pharmaceuticals? Chemicals? And while my passion — and theirs — was for fuels and solving global warming, it wasn’t at all obvious that they could make a better fuel.”
Cheap biofuels could eliminate or reduce the use of the fossil fuels whose combustion contributes to climate change. So far, most biofuel ventures have tried to create better ethanol fuels by converting different kinds of “biomass” — everything from corn to sugar cane to switchgrass and jatropha trees — to fermentable sugars. These sugars can then be brewed and distilled into conventional ethanol.
Amyris chose to ask something more basic and more interesting: What would perfect fuels look like if they were designed from scratch? The start-up decided to concentrate on the second stage of creating a biofuel: fermenting sugars into fuel.
The company wanted chemical compounds that could be fermented from sugars derived from any biomass. The fuels had to have an energy content higher than ethanol and be useable in today’s automobile, diesel and jet engines. Finally, the company wanted fuels that were insoluble in water, and hence could be transported through the same pipelines that now move oil.
Over the last year and a half, Amyris has created in its labs microorganisms whose metabolic pathways are yielding alternatives to diesel, jet fuel and gasoline. Now the company is working to make the conversion from sugars to fuel more efficient.
“If you can get above 90 percent efficiency, you’re competitive with ethanol and oil,” Mr. Reiling explained.
Most synthetic biologists familiar with Amyris’s research say that while the company may have created some promising compounds, the real challenge will be achieving these efficiencies of conversion.
Mr. Doerr expresses the economics more bluntly. “If you’re smart enough,” he said, “you can make a better fuel. But to have a business, you have to make it at the right yield and at the right cost.” Mr. Doerr says he believes Amyris’s fuels will need to cost around $30 a barrel (at the moment, less than half the price of crude oil).
Some environmentalists worry that the adoption of biofuels could lead to the diversion of agricultural land from food to biomass production, raising food prices and further despoiling the environment. In March, the British environmental activist George Monbiot warned in The Guardian that government programs to encourage biofuels were “a formula for environmental and humanitarian disaster.” There is some justification for such worries. Earlier this year, increases in the price of maize, caused by swelling demand for corn for ethanol production, led to food riots in Mexico.
But Amyris’s fuels can be fermented from sugars derived from a variety of feed stocks, including switchgrass and jatropha, that are grown on marginal soil that cannot be used for food production. So cultivation of such crops in poorer parts of Africa and Asia might represent an enormous economic opportunity for the regions’ farmers.
Amyris’s new chief executive, John G. Melo, who was previously British Petroleum’s president for fuel operations in the United States, said that Amyris plans to begin selling biodiesel in 2010, and biofuel replacements for jet fuel and gasoline sometime after that.
Mr. Melo would not explain in detail how Amyris planned to sell its products. He says the biogas and biodiesel may be sold, blended with gasoline, in gas stations (as ethanol is sold today). But Mr. Melo said he hoped to sell biofuels through alternative channels like large retail chains like Costco. Richard Chavez, a senior vice president of Costco, confirmed that he and Mr. Melo are discussing using Amryis biofuels as an alternative to ethanol for blended fuels. Most intriguing, Mr. Melo also suggested that the Virgin Group, with which Amyris has been negotiating, might sell the start-up’s biofuels under its own brand.
WHILE it is Mr. Melo’s job to make Amyris into a big business, Mr. Doerr says the company’s scientists are not motivated solely by a desire to enrich themselves; instead, they are excited about Amyris’s innovative science and the importance of curing diseases and developing renewable fuels.
“They haven’t been entrepreneurs before and so there’s a nobleness and commitment they bring to these problems that I find really inspiring,” Mr. Doerr said. “If you told any of them, ‘Guess what? You’ll only make one-tenth of what you might,’ they would continue to do this work.”
Jason Pontin is the editor in chief and publisher of Technology Review, a magazine and Web site owned by M.I.T. E-mail: pontin@nytimes.com.
By JOHN NOBLE WILFORD, The New York Times, June 5, 2007
Why did the chicken cross the Pacific Ocean? To get to the other side, in South America. How? By Polynesian canoes, which apparently arrived at least 100 years before Europeans settled the continent.
That is the conclusion of an international research team, which reported yesterday that it had found “the first unequivocal evidence for a pre-European introduction of chickens to South America,” or presumably anywhere in the New World.
The researchers said that bones buried on the South American coast were from chickens that lived between 1304 and 1424. Pottery at the site was from a similar or earlier time. A DNA analysis linked the bones, which were excavated at El Arenal on the Arauco Peninsula in south central Chile, to chickens from Polynesian islands.
The findings are being published in the Proceedings of the National Academy of Sciences. The lead author is Alice A. Storey, an anthropologist at the University of Auckland, New Zealand, and other team members are from American Samoa, Australia, Canada and the United States.
The research group and other anthropologists said the bones supported the idea that Polynesians in their far-ranging canoes had by then not only populated the Pacific as far east as Hawaii and Easter Island, but also had on occasion reached the Americas.
The presence of the South American sweet potato in pre-European sites in Polynesia indicated some prehistoric contact between America and the islands.
But Dr. Storey’s group said that no firm “archaeological evidence for Polynesian contact with the Americas has been reported before now.”
For more than 30 years, scholars have debated when and how chickens reached the Americas: whether in pre-Columbian times, possibly by Polynesian visitors, or when Portuguese and Spanish settlers arrived in South America after 1500. Most experts had favored the latter hypothesis.
Others thought this unlikely, noting that when the Spanish invaded Peru in 1532, they saw chickens being used in traditional ceremonies. It seemed hard to believe, some scholars pointed out, that chickens would have been so rapidly dispersed from the east coast to the west and already be incorporated in religious events.
From the DNA examination, Dr. Storey and colleagues concluded, the El Arenal bones had a close genetic relationship to chickens from prehistoric sites on several islands, Tonga and American Samoa in particular. Further analysis of prehistoric chicken samples from the islands is expected to discern the specific origin and timing of the Chilean chickens.
Scholars found it disappointing and puzzling that the Polynesians who landed at El Arenal left nothing more than chicken bones. Pottery at the site is in a local style. Perhaps the visitors ate and ran, but not without leaving behind some starter chickens for future plates of arroz con pollo.
Puerto Rico’s AIDS Care in Disarray Over Funds
By ERIK ECKHOLM, The New York Times, June 5, 2007
SAN JUAN, P.R. — His emaciated body advertises the damage wreaked by the AIDS virus. But over the last year, Rolando Warren González, 41, a former steel band member, has faced an extra challenge to his survival.
From the shelter where he lives in Loiza in Puerto Rico’s impoverished northeast, Mr. González travels an hour and a half by bus to reach the government clinic where he receives his “cocktail” of antiviral drugs.
“But sometimes I go, and they just don’t have the medicines,” he said.
Six times in the last year, he said, he has suffered two-week periods with no drugs, undercutting the life-prolonging benefits of modern therapies against H.I.V., the AIDS virus.
Accounts like his — and worse — are repeated across this tropical territory of the United States, where hundreds of H.I.V. and AIDS patients are not receiving vital medical care, say a host of doctors, community groups and patients.
The disarray in treatment reflects a stew of problems. An overstretched health care budget is accentuated by rivalries between the commonwealth and the San Juan city governments, which run separate AIDS programs.
But federal officials and many local doctors say the main culprit is the island’s poor management of the available money provided for AIDS care under the Ryan White Act, amounting to $53 million last year. Clinics have not received drugs on time, and private groups that assist AIDS patients are often reimbursed six months late or more, causing some to cut services or even shut down.
In sharp rebukes to the Puerto Rico Health Department and the City of San Juan, federal officials have put the AIDS grants under unusually tight review and even threatened to halt some federal money. Because of disorganization, the officials say, the island has often failed to spend all its Ryan White aid, losing access to $6.5 million over the last five years.
Adding questions, in December the F.B.I. raided four San Juan Health Department offices, seizing 400 boxes of documents in a criminal investigation into possible misuse of Ryan White grants.
Officials here deny misusing funds. They did have to establish a waiting list for new patients needing drug treatment in the fall, but say that any lapses in care have been brief and that their main worry, in an era when treating a single AIDS patient can cost more than $25,000 a year, is a shortage of money.
At a time when patients live longer and drug costs soar, the challenge is daunting. But doctors and patients here say the government has made poor use of its money. “The state of H.I.V. treatment here is a catastrophe,” said Dr. José Varga Vidot, director of Community Initiative, a private group in San Juan that provides primary care to 1,600 patients including drug addicts, prostitutes and homeless people.
Dr. Varga Vidot said he knew of at least 75 people who were unable to obtain all their drugs from government clinics for up to a month.
In relation to its population of 3.9 million, Puerto Rico has the fifth-highest concentration of AIDS cases of states and territories, with 12,000 patients and estimates that as many more are infected with H.I.V. but are not yet ill.
About half the patients were infected from shared heroin needles, posing special challenges because many are isolated and penniless.
Although no studies have tried to link the spotty care with mortality, according to the latest comparative national data, 580 patients died here in 2003, indicating a mortality rate higher than that in states like New York known for good AIDS care.
A majority of H.I.V. and AIDS patients are covered by the Puerto Rican version of Medicaid, known as Health Reform. That financially struggling program does not cover some crucial drugs. The $53 million provided under the Ryan White law is supposed to fill the gaps.
As a territory, “we don’t get what we need,” said Health Secretary Rosa Pérez-Perdomo.
Federal aid to the Medicaid program here is capped at $240 million, meeting 13 percent of the overall budget, Dr. Pérez-Perdomo said. On the mainland, poorer states receive up to 75 percent of their Medicaid money from Washington, giving them more leeway in treating low-income AIDS patients.
Advocates for AIDS treatment in the United States, where the disease is increasingly concentrated among blacks and Hispanics, juxtapose President Bush’s new call for $30 billion to expand AIDS care abroad, a politically popular cause, with the stagnant financing of the Ryan White program for needy Americans. That has remained around $2.1 billion for four years.
“At a time of rising needs at home, especially among minorities, Puerto Rico and the states all have to compete for flat Ryan White funds,” said Dennis DeLeon, director of the Latino Commission on AIDS in New York.
The advocates say Washington should do more to reshape a dysfunctional care system on the island.
The Health Resources and Services Administration, which administers the Ryan White money, has repeatedly pushed for streamlining the crushing bureaucracy here and sent many advisers, said Dr. Laura Cheever, deputy associate administrator at the agency.
The F.B.I. raid, on Dec. 12, was part of an investigation into the misuse of Ryan White money that San Juan had received for its use and for 30 nearby municipalities, said a spokesman for the agency here, Harry Rodríguez. In 2006, the city received $13 million.
Even patients receiving top-quality care have to struggle with the disease, because H.I.V. can develop resistance, making patients switch to new, costlier drugs.
Gaps in treatment can hasten the development of resistance. Doctors here also say that when they need to switch an ailing patient to a new regimen, approval from the central health department can take months and that the latest drugs are often not available.
Angélica Segarra runs the shelter for homeless AIDS patients where Mr. González stays, a rambling house in Loiza. Ms. Segarra said that she provided medicines to 60 people before recent cuts in financing by San Juan forced her to stop and that many patients have searched in vain for clinics taking new patients.
One patient, Luis Torres, 42, was unable to secure medicines for three months. Another resident, Miguel Vásquez, 44, split his drugs with Mr. Torres because, he said, “it seemed like the right thing to do.”
In March and April, each took half the proper dose until the supply ran out. “Now I’ve had a month with no cocktail and I’m worried,” Mr. Vásquez said.
Cash shortages or errors in drug distribution by the commonwealth Health Department mean that patients sometimes receive five days’ doses at a time or two antivirals instead of the prescribed three, a practice that can do more harm than good.
The main San Juan AIDS clinic, one of the better equipped, serves 2,254 patients. Since late 2006, it has stopped accepting new ones, saying it cannot afford more.
One problem is jurisdictional rivalries. Dr. Héctor Sorentini Méndez, health director of San Juan, said the commonwealth had refused to share its federal grants, $22 million under the AIDS Drug Assistance Program, which pays for otherwise uncovered medicines under the Ryan White law.
Sandra Molinias Rabe, 33, a former heroin addict in the mountains southwest of San Juan, is one of many cases who have slipped through the cracks. Ms. Rabe lives with her partner, Raymond Quiñones, in a squalid shack without running water, reached by an arduous climb up overgrown steps. A neighbor allows them to carry up buckets of water and run an electricity line to power a light bulb.
Her medical condition is poor, and the doctor at Casa Joven del Caribe, an aid group, said she needed new laboratory tests to see whether she should switch medications. The aid group, which is in a dispute with San Juan over late disbursements, can no longer pay for her tests and drugs and sent her to an assigned Medicaid doctor in another town. That doctor said she would have to return in two weeks. In the meantime, she had no medicines.
Antiquated equipment and poor communications have added to the problems. An audit by the comptroller of Puerto Rico published in November found that the Health Department records of drug stocks and deliveries to outlying clinics were grossly deficient, allowing mistakes and medicines to expire. Four of the eight main H.I.V. clinics lacked working bathrooms or computers, another report said in the fall.
Héctor Figueroa, who directs a drug treatment program in Caguas, south of San Juan, said changes in federal priorities and a lack of action by the Puerto Rico government had led to sharp cuts in transportation aid and substance abuse treatment. At the two clinics in his region, Mr. Figueroa said, patients sometimes receive 15 days’ medicines in a month.
The Health Resources and Services Administration, citing problems in administration, patient access, and community participation, put the San Juan government on “restricted drawdown” status in 2005 and did the same for the commonwealth in 2006. The health agencies now have to submit all grant vouchers to Washington for approval before money is disbursed.
Puerto Rico officials say the waiting list for drug assistance has declined, to 36 from 130 in the fall, and will soon be eliminated. A local group, AIDS Patients for a Sane Policy, said that its survey of clinics found 477 patients waiting to start therapy or to make necessary changes in their drug regimens.
For a year, Puerto Rican and mainland groups, including the Congressional Hispanic Caucus, have called on federal authorities to take stronger action here.
In a letter to Michael O. Leavitt, secretary of health and human services, Senator Tom Coburn, Republican of Oklahoma, has said he was “gravely concerned about the ongoing crisis taking place in Puerto Rico.”
In another letter, Senator Hillary Rodham Clinton, Democrat of New York, said mismanagement had “severely curtailed access to life-extending treatment” and called on the health administration to strengthen its oversight of Ryan White programs on Puerto Rico.
Administration officials said that they had proposed transferring San Juan’s Ryan White funds to a separate entity that would manage them, but that Mayor Jorge A. Santini Padilla had refused.
“In the end,” Dr. Cheever of the health administration said, “It’s up to them to do the planning, allocations and administration, and what we can do in terms of sanctions is very limited by legislation.”
Slipstream: First, Cure Malaria. Next, Global Warming
By JASON PONTIN, The New York Times, June 3, 2007
Amyris Biotechnologies has almost finished developing a cheap cure for malaria that could save the lives of millions of the poor. Now, using the same technology, this start-up in Emeryville, Calif., wants to create new biofuels that may help save the planet.
Even in an industry much attached to hyperbole, few companies have excited such high hopes. Investors include the Bill & Melinda Gates Foundation, which granted the Institute for OneWorld Health $42.6 million to finance Amyris’s antimalarial drug, and two princes of Silicon Valley venture capital, John Doerr of Kleiner Perkins Caufield & Byers, and Vinod Khosla of Khosla Ventures, who, with the private equity group of Texas Pacific Group Ventures, invested $20 million.
Explaining his interest in the start-up, Mr. Khosla told me: “Amyris was using a very sexy technology and applying it in a radical way to malarial drugs. When I asked the question, ‘Can you do the same for energy?’ the surprising answer was, ‘Yes, we can.’ ”
Mr. Doerr said he thought that green technologies “could be the largest economic opportunity of the 21st century.” He called Amyris “the best team to do this kind of work.”
Amyris’s technology derives from the research of Jay D. Keasling, a professor of chemical engineering at the University of California, Berkeley, and the director of the synthetic biology department of the Lawrence Berkeley National Laboratory. Mr. Keasling’s lab is widely credited with making commercially practical an emerging technology called metabolic engineering.
Until recently, genetic engineering of the sort associated with traditional biotechnology has been limited to modifying a cell’s processes by inserting, mutating or deleting a single gene or a few significant genes. Genetic engineering has coaxed microorganisms like the common bacterium E. coli to produce drugs like human insulin, but has produced little else besides such protein drugs and a few antibiotics.
Mr. Keasling’s metabolic engineering is farther-reaching and, potentially, much more productive. His lab has invented techniques that rewrite the metabolisms of microorganisms. By modifying the structure of a microorganism’s proteins and adding genes from other organisms, Mr. Keasling has designed microbial factories that can produce a tremendous variety of drugs, biofuels and other chemicals.
Amyris was founded in the summer of 2003 by Mr. Keasling and three young postdoctoral students from his lab: Neil Renninger, Kinkead Reiling and Jack D. Newman. They received the large grant from the Gates Foundation a little more than a year later.
To create an antimalarial drug, Amyris engineered bacteria to excrete a drug called artemisinin. Artemisinin is 100 percent effective against malaria, but it derives from a weed called sweet wormwood that only grows in China and Vietnam and costs $2.40 for a course of treatment — a steep price for the world’s poor.
Every year, 300 million to 500 million people become infected with malaria, according to the World Health Organization; more than 1.5 million of those infected will die, most of them children in Africa and Asia. Amyris’s technique would reduce the cost of artemisinin to less than 25 cents for a course of treatment, according to the company. OneWorld Health, a nonprofit pharmaceutical company, has pledged to give away the drug to poor countries. Amyris says the drug will be ready for mass production in 2008.
It wasn’t until January 2006, when a presentation by Mr. Keasling at the World Economic Forum in Davos caught the attention of Mr. Doerr and Mr. Khosla, that Amyris’s founders began to consider seriously what other compounds their bioengineered bugs might produce. The two venture capitalists encouraged the scientists to think ambitiously.
“At nights and on weekends we’d been working on what our for-profit projects could be at the end of the Gates grant,” Mr. Reiling, the company’s vice president for development, told me. “One of those projects was using our engineering know-how to come up with novel biofuels.”
Mr. Doerr said: “When I met them, it was truly an open question. Should they work on other pharmaceuticals? Chemicals? And while my passion — and theirs — was for fuels and solving global warming, it wasn’t at all obvious that they could make a better fuel.”
Cheap biofuels could eliminate or reduce the use of the fossil fuels whose combustion contributes to climate change. So far, most biofuel ventures have tried to create better ethanol fuels by converting different kinds of “biomass” — everything from corn to sugar cane to switchgrass and jatropha trees — to fermentable sugars. These sugars can then be brewed and distilled into conventional ethanol.
Amyris chose to ask something more basic and more interesting: What would perfect fuels look like if they were designed from scratch? The start-up decided to concentrate on the second stage of creating a biofuel: fermenting sugars into fuel.
The company wanted chemical compounds that could be fermented from sugars derived from any biomass. The fuels had to have an energy content higher than ethanol and be useable in today’s automobile, diesel and jet engines. Finally, the company wanted fuels that were insoluble in water, and hence could be transported through the same pipelines that now move oil.
Over the last year and a half, Amyris has created in its labs microorganisms whose metabolic pathways are yielding alternatives to diesel, jet fuel and gasoline. Now the company is working to make the conversion from sugars to fuel more efficient.
“If you can get above 90 percent efficiency, you’re competitive with ethanol and oil,” Mr. Reiling explained.
Most synthetic biologists familiar with Amyris’s research say that while the company may have created some promising compounds, the real challenge will be achieving these efficiencies of conversion.
Mr. Doerr expresses the economics more bluntly. “If you’re smart enough,” he said, “you can make a better fuel. But to have a business, you have to make it at the right yield and at the right cost.” Mr. Doerr says he believes Amyris’s fuels will need to cost around $30 a barrel (at the moment, less than half the price of crude oil).
Some environmentalists worry that the adoption of biofuels could lead to the diversion of agricultural land from food to biomass production, raising food prices and further despoiling the environment. In March, the British environmental activist George Monbiot warned in The Guardian that government programs to encourage biofuels were “a formula for environmental and humanitarian disaster.” There is some justification for such worries. Earlier this year, increases in the price of maize, caused by swelling demand for corn for ethanol production, led to food riots in Mexico.
But Amyris’s fuels can be fermented from sugars derived from a variety of feed stocks, including switchgrass and jatropha, that are grown on marginal soil that cannot be used for food production. So cultivation of such crops in poorer parts of Africa and Asia might represent an enormous economic opportunity for the regions’ farmers.
Amyris’s new chief executive, John G. Melo, who was previously British Petroleum’s president for fuel operations in the United States, said that Amyris plans to begin selling biodiesel in 2010, and biofuel replacements for jet fuel and gasoline sometime after that.
Mr. Melo would not explain in detail how Amyris planned to sell its products. He says the biogas and biodiesel may be sold, blended with gasoline, in gas stations (as ethanol is sold today). But Mr. Melo said he hoped to sell biofuels through alternative channels like large retail chains like Costco. Richard Chavez, a senior vice president of Costco, confirmed that he and Mr. Melo are discussing using Amryis biofuels as an alternative to ethanol for blended fuels. Most intriguing, Mr. Melo also suggested that the Virgin Group, with which Amyris has been negotiating, might sell the start-up’s biofuels under its own brand.
WHILE it is Mr. Melo’s job to make Amyris into a big business, Mr. Doerr says the company’s scientists are not motivated solely by a desire to enrich themselves; instead, they are excited about Amyris’s innovative science and the importance of curing diseases and developing renewable fuels.
“They haven’t been entrepreneurs before and so there’s a nobleness and commitment they bring to these problems that I find really inspiring,” Mr. Doerr said. “If you told any of them, ‘Guess what? You’ll only make one-tenth of what you might,’ they would continue to do this work.”
Jason Pontin is the editor in chief and publisher of Technology Review, a magazine and Web site owned by M.I.T. E-mail: pontin@nytimes.com.
