Fires are increasing in severity and incidence around the globe and affect many different ecosystems; will the new generation of fire science tools help managers retain biodiversity?

From Bob Clark's snug office in Boise, Idaho, where he manages the United States government's Joint Fire Science Program (JFSP), he figures his computer provides fingertip reach to just about everybody who's anybody in wildfire research. This points to a primary need of nations worldwide in combating the scourge of recurrent wildfires: tools and technology suited to the job. It's no small order in places as economically, socially, and ecologically varied as, say, Brazil, South Africa, Australia, Indonesia, and the United States, which are among the countries where wildfire creates the greatest havoc.More than 750,000 acres (303,500 hectares) were burned in southern California alone during last year's wildfires. The 2000 season was one of the country's worst on record, destroying 8.4 million acres (3.4 million hectares), more than double the decade's 10-year average. Australia's summer months around the turn of 2002–2003 brought perhaps the worst drought in a century to the populous southeast and the biggest fire season for two decades. Mountain forests were extensively burned and more than 500 houses were lost. In 2002, Brazil suffered 217,000 wildfires, a number that is almost certainly too low because remote imaging cannot detect many fires under the forest canopy. In Indonesia, wildfires that burned for months during 1997–1998 were later estimated to have released the equivalent to 13%–40% of annual global carbon emissions from fossil fuels, inflicting smoke-related ailments on thousands.Where wildfire is concerned, the many differences between such countries can perhaps be pinned down to two essentials. The first is whether a blaze occurs in temperate or tropical forest, and the second is whether the nation is developed or developing.“The science can be rock solid, but it can only go so far before social, economic, and political pressures take over,” Clark says. “That's what a forest service manager's job is, picking the best option based on all those considerations.”Unfortunately, having science-based options that are applicable to local conditions is largely a luxury for developed countries. Managers there can choose to let a fire burn under hopefully contained conditions, a policy known in the United States as “wildland fire use.” They can set experimental crown fires to study their effects, as was done recently in"journal" Canada ( Figure 1 ). And they can take preemptive measures, such as reducing fuel in the forest to lower fire hazard.The two main fuel-reduction methods are mechanical removal of combustible materials and controlled or “prescribed” burning ( Figure 2 ). During Bill Clinton's administration, prescribed burns were encouraged in protected areas, but thinning was allowed only for trees with trunks of nine inches (22.8 cm) in diameter or less. Under George W. Bush, prescribed burning remains a choice, but the United States Department of Agriculture's (USDA) Forest Service policy is much more focused on mechanical means. The argument runs that there's been too much concern about removing trees, when what counts most is the enhanced fire-resistance of the thinned habitat.Fire hazard reduction methods must be tailored to an understanding of fuel characteristics in a given area, says David Peterson of the Forest Service's Pacific Wildland Fire Sciences Laboratory in Seattle, Washington. “There's no uniform way of doing it, partly because, as scientists, we haven't given the management folks any quantitative guidelines.” Working with other ecologists, social scientists, and economists, he's currently producing just such guidelines for the dry interior forests of the Pacific Northwest. “One thing we don't want to do is take choices out of the hands of field managers working at the local level.”Forecasting Tools: Models and Simulations For those choices to be meaningful, managers need reliable information on the risk of wildfire outbreaks and on the future behavior of existing fires. This requires models and simulations that incorporate climatic conditions, particularly wind ( Figure 3 ). At the Forest Service's Fire Sciences Laboratory in Missoula, Montana, researchers have created a “gridded wind” tool based on the engineering discipline of computational fluid dynamics. The program maps wind speed and direction using a digital elevation model, which is a grid of elevation points every 30–100 feet (9–30.5 meters) over a terrain 10–40 square miles (25.9–103.6 square kilometers) in size. This map forms the floor of a box extending up to five miles (eight kilometers) high, which is subdivided into a million or more cubes. Wind flow from either real observations or estimates can be entered into the software, and the layer of cubes nearest the grid floor is used to create surface wind maps at resolutions of every 100 meters (109 yards) or less. In contrast, the usual resolution of weather forecasts is 12 kilometers (7.5 miles), down to 4 kilometers (2.5 miles) in some urban areas. Figure 3 Shaded Surface Images of Areas in Northwestern Montana That Suffered Wildfires during 2003 The winds are from the west at 20 mph/32 kph. The white lines represent fire perimeters. (Image used by permission of the USDA Forest Service, Fire Sciences Laboratory.) “Two or three years ago, we couldn't have done this simulation on a single-processor laptop,” says one of its developers, physical engineer Bret Butler. “It would have taken two or three days. Now we can do it in a matter of hours.” The ability of these maps to show varying wind flow in valleys, at midslope and on ridgetops, is just the beginning. The next step is to feed these data into models that predict wildfire spread. Butler and colleagues have coupled their gridded wind technology to a fire growth model and tested it against the actual spread of several wildfires, including in Southern California last summer. Maps of actual and predicted surface winds showed strong similarities, encouraging Butler to foresee an ideal scenario in which fire fighting teams enter wind flow data online or by telephone to a central base where gridded wind maps and fire growth simulations are generated within hours, before operational decisions are made. Yet he admits that challenges remain, including the current inability of fire behavior simulation to account for diurnal winds in addition to cold front-driven flow. In mountainous terrain, for example, winds often move up-canyon in the morning and down-canyon in the evening. Moreover, the effect of vegetation on wind is not yet included in such models. Those issues and others are being addressed by researchers working on improvements to the regional weather forecasts of so-called mesoscale models. At the Forest Service's Rocky Mountain Research Center in Fort Collins, Colorado, meteorologist Karl Zeller and colleagues are contributing calculations of biological processes to mesoscale weather models. Their algorithms not only can account for diurnal winds but can predict the effects on local weather when vegetation takes in carbon dioxide and releases water vapor. This process can produce different fluxes of carbon dioxide drawn into the canopy and water vapor coming out, depending largely on the type of vegetation and its canopy density. Zeller's group has analyzed current mesoscale forecasts in the Rocky Mountains and found that in the daytime, they often are too hot in the high country and too cold in the plains. Water vapor estimates are too low in the mountains and too high in the plains, which Zeller thinks is because the models feed off soil moisture estimates, not off vegetation. In coupling his team's new biophysical interface to gridded wind and mesoscale forecast models, Zeller says “point forecasts” are being developed that can focus on a prescribed burn area or even a single house.
Forecasting Tools: Models and Simulations
For those choices to be meaningful, managers need reliable information on the risk of wildfire outbreaks and on the future behavior of existing fires. This requires models and simulations that incorporate climatic conditions, particularly wind ( Figure 3 ). At the Forest Service's Fire Sciences Laboratory in Missoula, Montana, researchers have created a “gridded wind” tool based on the engineering discipline of computational fluid dynamics. The program maps wind speed and direction using a digital elevation model, which is a grid of elevation points every 30–100 feet (9–30.5 meters) over a terrain 10–40 square miles (25.9–103.6 square kilometers) in size. This map forms the floor of a box extending up to five miles (eight kilometers) high, which is subdivided into a million or more cubes. Wind flow from either real observations or estimates can be entered into the software, and the layer of cubes nearest the grid floor is used to create surface wind maps at resolutions of every 100 meters (109 yards) or less. In contrast, the usual resolution of weather forecasts is 12 kilometers (7.5 miles), down to 4 kilometers (2.5 miles) in some urban areas.“Two or three years ago, we couldn't have done this simulation on a single-processor laptop,” says one of its developers, physical engineer Bret Butler. “It would have taken two or three days. Now we can do it in a matter of hours.”The ability of these maps to show varying wind flow in valleys, at midslope and on ridgetops, is just the beginning. The next step is to feed these data into models that predict wildfire spread. Butler and colleagues have coupled their gridded wind technology to a fire growth model and tested it against the actual spread of several wildfires, including in Southern California last summer. Maps of actual and predicted surface winds showed strong similarities, encouraging Butler to foresee an ideal scenario in which fire fighting teams enter wind flow data online or by telephone to a central base where gridded wind maps and fire growth simulations are generated within hours, before operational decisions are made.Yet he admits that challenges remain, including the current inability of fire behavior simulation to account for diurnal winds in addition to cold front-driven flow. In mountainous terrain, for example, winds often move up-canyon in the morning and down-canyon in the evening. Moreover, the effect of vegetation on wind is not yet included in such models.Those issues and others are being addressed by researchers working on improvements to the regional weather forecasts of so-called mesoscale models. At the Forest Service's Rocky Mountain Research Center in Fort Collins, Colorado, meteorologist Karl Zeller and colleagues are contributing calculations of biological processes to mesoscale weather models. Their algorithms not only can account for diurnal winds but can predict the effects on local weather when vegetation takes in carbon dioxide and releases water vapor. This process can produce different fluxes of carbon dioxide drawn into the canopy and water vapor coming out, depending largely on the type of vegetation and its canopy density.Zeller's group has analyzed current mesoscale forecasts in the Rocky Mountains and found that in the daytime, they often are too hot in the high country and too cold in the plains. Water vapor estimates are too low in the mountains and too high in the plains, which Zeller thinks is because the models feed off soil moisture estimates, not off vegetation. In coupling his team's new biophysical interface to gridded wind and mesoscale forecast models, Zeller says “point forecasts” are being developed that can focus on a prescribed burn area or even a single house.Wildfire and Species Diversity Fitting the appropriate mix of strategies to a given situation is an issue that has also received close attention in Australia. After the bushfires of 2002–2003, media commentators called for increased “hazard reduction burning” in national parks, prompting ecologists around the country to distribute a joint statement declaring that such a strategy would not further reduce bushfire risk, but would actually threaten biodiversity. Australian species are often well-adapted to fire, and researchers have learned that different fire regimes—meaning the type of fire, its intensity, severity, extent, season, and frequency—favor different species ( Box 1 ). In the southeast of Australia, prescribed burns of high frequency and low intensity can alter the habitat in ways that therefore threaten survival of numerous plant and animal species. “A generic problem or conundrum seems to be that species which do not prosper under relatively frequent fires can be found in most fire-prone environments,” notes Ross Bradstock, principal research scientist in the New South Wales Department of Environment and Conservation. He says it's very difficult to determine how human interventions in various habitats can foster the coexistence of species that have different fire regime requirements.
Wildfire and Species Diversity
Fitting the appropriate mix of strategies to a given situation is an issue that has also received close attention in Australia. After the bushfires of 2002–2003, media commentators called for increased “hazard reduction burning” in national parks, prompting ecologists around the country to distribute a joint statement declaring that such a strategy would not further reduce bushfire risk, but would actually threaten biodiversity. Australian species are often well-adapted to fire, and researchers have learned that different fire regimes—meaning the type of fire, its intensity, severity, extent, season, and frequency—favor different species ( Box 1 ). In the southeast of Australia, prescribed burns of high frequency and low intensity can alter the habitat in ways that therefore threaten survival of numerous plant and animal species.“A generic problem or conundrum seems to be that species which do not prosper under relatively frequent fires can be found in most fire-prone environments,” notes Ross Bradstock, principal research scientist in the New South Wales Department of Environment and Conservation. He says it's very difficult to determine how human interventions in various habitats can foster the coexistence of species that have different fire regime requirements.Fire Suppression and Tropical Forests As tough as such questions are to answer in developed countries, they pale compared to the problems of tropical forest wildfire researchers and managers in developing countries. In these countries, a destructive cycle of human behavior begins with land-clearing and burning for farming, logging, mining, road-building, and other uses that open gaps in the rainforest's canopy cover. This lets in sunlight and air, reducing the forest's ability to smother fire by trapping moisture, and it encourages the growth of smaller, more fire-prone plants. The first wildfires that occur are bad, but successive ones can eventually transform tropical forest to scrub savanna ( Figure 4 ). Of course, the remaining forest is thereby broken into fragments that continue to suffer incursions at their edges, as the cycle continues. Figure 4 Forest Regeneration (A) Dense understory regeneration three years after a low-intensity fire. (B) The almost total loss of live, above-ground biomass six months after a forest burnt for the third time in 15 years. (Photographs by Jos Barlow; used by permission.) In a recent paper in Science, Michigan State University Amazon expert Mark Cochrane pointed out that prescribed burning is ineffective in tropical forests, because the collateral damage outweighs any benefits. Indeed, tools and technologies employed in temperate conditions can seldom be applied usefully to tropical forests without significant alterations. “One of the main issues in fire science is that the U.S. has no capacity to develop new tools,” charges Ernesto Alvarado, a research scientist at the University of Washington in Seattle. He's been working for several years with United States Forest Service and Brazilian scientists on field studies in Mata Grosso, the southernmost state of the Brazilian Amazon. He says that fire prediction simulations developed decades ago have not yet been replaced by ones that account for tropical wildfire extremes, including either large-scale crown fires or surface fires, which often reach only 10 centimeters (3.9 inches) in height and move slowly but can burn for weeks and kill many trees.  Fire behavior models don't work for tropical surface fires because the physics are different from those in temperate forests, he explains. A slow wind generated from the unburned forest blows toward the fire, forcing the small flames to advance against, rather than with, the wind. Another difference is that the fuel is mostly leaf litter, not conifer needles or sticks. Alvarado and colleagues light experimental fires in clear-cuts to determine factors limiting ignition and spread. Such experimental work is rare in tropical forests, where observation and description still predominate. But the team also monitors surface wildfires, measuring fire length, spread, and heat release. “We're trying to find applications that people can use to control fires or to explain implications of fire policy,” he says. Most wildfires originate from deliberately set burns. For example, many farmers still clear land by the ancient method of slash-and-burn, in which forest is chopped, left to dry, and then burned. These farmers are now banned by Brazilian federal law from burning at the height of the dry season, mid-July to mid-September. They cut in May, but if the rains come early in September, they can't burn after the ban ends and must wait until the next season, with nowhere to grow their crops in the meantime. Alvarado thinks a more flexible burning schedule is a solution. The challenge is to pass on technological understanding to decision-makers. For example, even ranchers in Mata Grosso's economic elite usually haven't heard of fire management techniques, says Amazonian ecologist Carlos Peres at the University of East Anglia in the United Kingdom. Educational projects from nongovernmental organizations have helped to turn some farmers away from heavy reliance on slash-and-burn techniques, but fire suppression information remains to be distributed on the frontiers. “What we really need are very large areas of primary forest that effectively serve as fire breaks,” he says. Conservation plans have been made by the federal government in collaboration with international agencies, but implementation remains a question, particularly given the high level of economic pressure from multinational resource developers eager to enter the Amazon. Major roads through the jungle are also on the drawing board. “Different categories of conservation units can be gazetted on paper, but in practice they're a long way from working. Someone draws lines on a map high in an office in Brasilia, but when you go out to that place in the forest, no one knows it's a conservation zone.”
Fire Suppression and Tropical Forests
As tough as such questions are to answer in developed countries, they pale compared to the problems of tropical forest wildfire researchers and managers in developing countries. In these countries, a destructive cycle of human behavior begins with land-clearing and burning for farming, logging, mining, road-building, and other uses that open gaps in the rainforest's canopy cover. This lets in sunlight and air, reducing the forest's ability to smother fire by trapping moisture, and it encourages the growth of smaller, more fire-prone plants. The first wildfires that occur are bad, but successive ones can eventually transform tropical forest to scrub savanna ( Figure 4 ). Of course, the remaining forest is thereby broken into fragments that continue to suffer incursions at their edges, as the cycle continues.In a recent paper in Science, Michigan State University Amazon expert Mark Cochrane pointed out that prescribed burning is ineffective in tropical forests, because the collateral damage outweighs any benefits. Indeed, tools and technologies employed in temperate conditions can seldom be applied usefully to tropical forests without significant alterations.“One of the main issues in fire science is that the U.S. has no capacity to develop new tools,” charges Ernesto Alvarado, a research scientist at the University of Washington in Seattle. He's been working for several years with United States Forest Service and Brazilian scientists on field studies in Mata Grosso, the southernmost state of the Brazilian Amazon. He says that fire prediction simulations developed decades ago have not yet been replaced by ones that account for tropical wildfire extremes, including either large-scale crown fires or surface fires, which often reach only 10 centimeters (3.9 inches) in height and move slowly but can burn for weeks and kill many trees.Fire behavior models don't work for tropical surface fires because the physics are different from those in temperate forests, he explains. A slow wind generated from the unburned forest blows toward the fire, forcing the small flames to advance against, rather than with, the wind. Another difference is that the fuel is mostly leaf litter, not conifer needles or sticks.Alvarado and colleagues light experimental fires in clear-cuts to determine factors limiting ignition and spread. Such experimental work is rare in tropical forests, where observation and description still predominate. But the team also monitors surface wildfires, measuring fire length, spread, and heat release.“We're trying to find applications that people can use to control fires or to explain implications of fire policy,” he says. Most wildfires originate from deliberately set burns. For example, many farmers still clear land by the ancient method of slash-and-burn, in which forest is chopped, left to dry, and then burned. These farmers are now banned by Brazilian federal law from burning at the height of the dry season, mid-July to mid-September. They cut in May, but if the rains come early in September, they can't burn after the ban ends and must wait until the next season, with nowhere to grow their crops in the meantime. Alvarado thinks a more flexible burning schedule is a solution.The challenge is to pass on technological understanding to decision-makers. For example, even ranchers in Mata Grosso's economic elite usually haven't heard of fire management techniques, says Amazonian ecologist Carlos Peres at the University of East Anglia in the United Kingdom. Educational projects from nongovernmental organizations have helped to turn some farmers away from heavy reliance on slash-and-burn techniques, but fire suppression information remains to be distributed on the frontiers.“What we really need are very large areas of primary forest that effectively serve as fire breaks,” he says. Conservation plans have been made by the federal government in collaboration with international agencies, but implementation remains a question, particularly given the high level of economic pressure from multinational resource developers eager to enter the Amazon. Major roads through the jungle are also on the drawing board. “Different categories of conservation units can be gazetted on paper, but in practice they're a long way from working. Someone draws lines on a map high in an office in Brasilia, but when you go out to that place in the forest, no one knows it's a conservation zone.”Fire Prevention: Developing the Technology Information transfer faces similar barriers in much of Southeast Asia, as Canadian forestry researchers discovered during a five-year project (now winding up) to create a computerized early warning tool for wildfire outbreaks. The program was instigated after the 1997–1998 fires created a regional haze hazard, largely because of peat deposits up to 20 meters (21.8 yards) thick that had become susceptible to burning in swampy forests drained and cleared for development. Michael Brady, who managed the Canadian project in Jakarta, points out that headmen in remote communities are still likely to believe that wildfires start spontaneously, by grasses rubbing together or even by magic. A fire scientist whose doctorate is in tropical forest peat dynamics, Brady sees the project as a medium to strengthen regional fire ecology in general. “In some ways, that's more important to me than the tool itself.” The tool is a variation of the Fire Danger Rating System used in Canada and, with various permutations, in many other countries. The Canadian system has two components, one for indexing fire weather and another predicting fire behavior. The weather component models moisture input and output in fuels generically classed as fine, moderate, and heavy. Brady and Indonesian university scientists grouped grasslands in the fine fuel category, fallen leaves and litter as medium, and peat and woody materials as heavy. They spent three years calibrating these fuels to local weather conditions, examining moisture dynamics and performing ignition tests. In developed countries, fuels are further specified in numerous classes for fire behavior prediction, but that requires decades of field work. Brady's team concentrated instead on helping key agencies in seven Southeast Asian countries, especially Indonesia and Malaysia, to obtain and use the appropriate computing tools. Brady doesn't expect immediate results in terms of reducing acreage burned. “Canada and the U.S. still have huge fire problems after working on it for a century.” But he does hope for a change of thinking, away from a current fascination in the region with satellite imaging of “hot spots” where fires are likely to be occurring. Fire danger rating concentrates on where fires are most likely to begin. “It allows you to add prevention into your management program.”
Fire Prevention: Developing the Technology
Information transfer faces similar barriers in much of Southeast Asia, as Canadian forestry researchers discovered during a five-year project (now winding up) to create a computerized early warning tool for wildfire outbreaks. The program was instigated after the 1997–1998 fires created a regional haze hazard, largely because of peat deposits up to 20 meters (21.8 yards) thick that had become susceptible to burning in swampy forests drained and cleared for development.Michael Brady, who managed the Canadian project in Jakarta, points out that headmen in remote communities are still likely to believe that wildfires start spontaneously, by grasses rubbing together or even by magic. A fire scientist whose doctorate is in tropical forest peat dynamics, Brady sees the project as a medium to strengthen regional fire ecology in general. “In some ways, that's more important to me than the tool itself.”The tool is a variation of the Fire Danger Rating System used in Canada and, with various permutations, in many other countries. The Canadian system has two components, one for indexing fire weather and another predicting fire behavior. The weather component models moisture input and output in fuels generically classed as fine, moderate, and heavy. Brady and Indonesian university scientists grouped grasslands in the fine fuel category, fallen leaves and litter as medium, and peat and woody materials as heavy. They spent three years calibrating these fuels to local weather conditions, examining moisture dynamics and performing ignition tests. In developed countries, fuels are further specified in numerous classes for fire behavior prediction, but that requires decades of field work. Brady's team concentrated instead on helping key agencies in seven Southeast Asian countries, especially Indonesia and Malaysia, to obtain and use the appropriate computing tools.Brady doesn't expect immediate results in terms of reducing acreage burned. “Canada and the U.S. still have huge fire problems after working on it for a century.” But he does hope for a change of thinking, away from a current fascination in the region with satellite imaging of “hot spots” where fires are likely to be occurring. Fire danger rating concentrates on where fires are most likely to begin. “It allows you to add prevention into your management program.”Beyond Prevention In South Africa, “retention” is a conservation buzzword referring to strategies that, in a sense, go beyond prevention of problems. What ecologists hope to retain is biodiversity in the midst of changes that can't be stopped, and their methods are producing major repercussions throughout government. The work is centered on the Cape Floristic Region of Africa's southwestern tip. Almost 90,000 square kilometers (34,750 square miles) in area, it's the world's smallest floral kingdom. A conservation plan was launched in 1998 that has drawn cooperation from tourism, mining, water use, agricultural, and land use planning groups. The project has the ambitious goal of protecting not only the usual biodiversity patterns of conservation areas but also the spatial components of evolutionary processes that enable species to adapt to potentially harmful changes. This entails a complex effort to determine which parts of developed and undeveloped lands are most necessary to such processes, including rivers, sand movement corridors, gradients from uplands to coastal lowlands, and major wilderness areas. University of Port Elizabeth botanist Richard Cowling, one of the scheme's principal architects, estimates that it might require 60%–70% of the region's landscape. As in Australia, fires are important to the Cape's biodiversity, but too-frequent burns are a problem. Cowling thinks that by consolidating mountainous megawilderness under the project's plan and protecting spatial transitions between fire-prone areas and those that resist fire, managers could move toward allowance of natural fire regimes. The current problem, he says, is that protected areas usually stop short of the transition to semidesert areas that are privately owned. When fire spreads from public to private land, the government often gets sued. Under the evolving Cape plan, landowners will sit on governing boards, and property that they contract for conservation will be tax-exempt. The Cape plan has attracted millions of dollars in support from the World Bank and other international sources, but Cowling regards that achievement as much less important than the progress made in gaining support from various interest groups. “The key issue is the extent to which you can get biodiversity concerns mainstreamed to other sectors,” he says. Threats to habitat retention, not least of which is wildfire, endanger every species. “It's about making people realize that biodiversity is the basis upon which all other things will succeed.”
Beyond Prevention
In South Africa, “retention” is a conservation buzzword referring to strategies that, in a sense, go beyond prevention of problems. What ecologists hope to retain is biodiversity in the midst of changes that can't be stopped, and their methods are producing major repercussions throughout government. The work is centered on the Cape Floristic Region of Africa's southwestern tip. Almost 90,000 square kilometers (34,750 square miles) in area, it's the world's smallest floral kingdom. A conservation plan was launched in 1998 that has drawn cooperation from tourism, mining, water use, agricultural, and land use planning groups.The project has the ambitious goal of protecting not only the usual biodiversity patterns of conservation areas but also the spatial components of evolutionary processes that enable species to adapt to potentially harmful changes. This entails a complex effort to determine which parts of developed and undeveloped lands are most necessary to such processes, including rivers, sand movement corridors, gradients from uplands to coastal lowlands, and major wilderness areas. University of Port Elizabeth botanist Richard Cowling, one of the scheme's principal architects, estimates that it might require 60%–70% of the region's landscape.As in Australia, fires are important to the Cape's biodiversity, but too-frequent burns are a problem. Cowling thinks that by consolidating mountainous megawilderness under the project's plan and protecting spatial transitions between fire-prone areas and those that resist fire, managers could move toward allowance of natural fire regimes. The current problem, he says, is that protected areas usually stop short of the transition to semidesert areas that are privately owned. When fire spreads from public to private land, the government often gets sued. Under the evolving Cape plan, landowners will sit on governing boards, and property that they contract for conservation will be tax-exempt.The Cape plan has attracted millions of dollars in support from the World Bank and other international sources, but Cowling regards that achievement as much less important than the progress made in gaining support from various interest groups. “The key issue is the extent to which you can get biodiversity concerns mainstreamed to other sectors,” he says. Threats to habitat retention, not least of which is wildfire, endanger every species. “It's about making people realize that biodiversity is the basis upon which all other things will succeed.”Box 1. Fire-Adapted Species Plants and animals of many countries evolved for millennia with wildfire as a natural occurrence, but when human interventions increase the frequency of fire, species suffer. African fire lilies and Australian “grass trees” are among plants that are stimulated to flower by smoke constituents such as ethylene. Plant seeds in fire-prone landscapes of Australia and South Africa often require fire to stimulate their germination, but it can take more than a decade for new seed banks to mature in some species. If a second fire arrives before then, the species could die out. Animals can be similarly affected. For example, a threatened marsupial called the potoroo is capable of surviving a high-intensity wildfire, but cannot tolerate the habitat changes caused by frequent, low-intensity fires. Likewise, some species of Australian honeyeaters are threatened with extinction because too-frequent fires have changed the proportion of mature and immature nectar plants. On the other hand, ecosystems can also be transformed by fire suppression. In southern Africa, decades of such activity have encouraged forests to replace grasslands. Yet the lovely marsh rose almost disappeared from the Cape before land managers realized that fire suppression was preventing its seeds from germinating. In such ways, biodiversity must find its place among the goals and tradeoffs of human intervention.

Box 1. Fire-Adapted Species
Plants and animals of many countries evolved for millennia with wildfire as a natural occurrence, but when human interventions increase the frequency of fire, species suffer. African fire lilies and Australian “grass trees” are among plants that are stimulated to flower by smoke constituents such as ethylene. Plant seeds in fire-prone landscapes of Australia and South Africa often require fire to stimulate their germination, but it can take more than a decade for new seed banks to mature in some species. If a second fire arrives before then, the species could die out.Animals can be similarly affected. For example, a threatened marsupial called the potoroo is capable of surviving a high-intensity wildfire, but cannot tolerate the habitat changes caused by frequent, low-intensity fires. Likewise, some species of Australian honeyeaters are threatened with extinction because too-frequent fires have changed the proportion of mature and immature nectar plants. On the other hand, ecosystems can also be transformed by fire suppression. In southern Africa, decades of such activity have encouraged forests to replace grasslands. Yet the lovely marsh rose almost disappeared from the Cape before land managers realized that fire suppression was preventing its seeds from germinating. In such ways, biodiversity must find its place among the goals and tradeoffs of human intervention.


Ancel Keys, Ph.D., who died in November, 2004, at the age of 100, was among the first scientists to recognize that human atherosclerosis is not an inevitable consequence of aging, and that a high-fat diet can be a major risk factor for coronary heart disease. During World War II, he and a group of talented co-workers at the University of Minnesota conducted a large-scale study of experimentally-induced human starvation. The data generated by this study – which was immediately recognized to be a classic – continue to be of inestimable value to nutrition scientists. In his later years, Keys spent more time at his home in Naples, Italy, where he had the opportunity to continue his personal study of the beneficial effects on health and longevity of a Mediterranean diet.

Ancel Keys, who died in November, 2004, was an excellent testimonial to the health-promoting effects of his beloved Mediterranean diet. He lived to be 100 and, as the  New York Times  obituary put it, "remained intellectually active through his 97 th  year." His latter years were spent mostly at his home in Naples, ItaIy. I never had the privilege of knowing him well, but encountered him occasionally at scientific meetings where we were both speakers. He was friendly but, I thought, reserved. What struck me about Ancel was his remarkable absence from the counsels of the nutrition establishment. Despite his acknowledged expertise and importance in the field, he was not a member of AMA's Council on Foods & Nutrition (at least not during the many years I served on that organization). I never saw him at any of the NIH advisory committees on which I served. He did not play a role in the deliberations of the Food and Nutrition Board of the National Research Council. He was not involved in the American Society for Clinical Nutrition during its heyday. Why was this? Perhaps the fact that he was a physiologist (later an epidemiologist) and not a physician played some role. Also, I think he preferred to go his own way, and – to some extent – he remained aloof from "academic nutrition." Yet he was willing to lecture to many audiences and was not considered to be a scientific eccentric; to the contrary, his epidemiological work was frequently cited and praised, and his monumental study of experimentally-induced semistarvation in human subjects [ 1 ] was immediately recognized to be a classic.New York TimesKeys and his capable associates conducted careful physiological and psychological studies of 32 initially healthy conscientious objectors (to World War II) through 6 months of experimentally induced semistarvation, followed by a year or more of rehabilitation. These studies generated a cornucopia of data – data that are all the more valuable now because such an experiment would not have a chance of being approved by today's Institutional Review Boards. Protein-calorie malnutrition (PCM) – in effect, famine – remains endemic in many parts of the world; moreover, PCM is the most common nutritional problem encountered in U.S. hospitals and nursing homes. The studies carried out by Keys and his co-workers make it possible for us to distinguish the effects of semistarvation on the body's strength, composition, physiological status, and mood from the confounding effects of such underlying diseases as cancer, intestinal malabsorption, renal insufficiency, emphysema, etc. – illnesses that often give rise to conditioned PCM. The Minnesota group showed clearly that semistarvation can be independently responsible for an array of psychological problems such as anxiety, depression, and hypochondria. From their studies, it is possible to demonstrate a clear relationship between a decline in fat-free mass and PCM-associated morbidity.Keys's major scientific achievements are enumerated in some detail by Jane E. Brody in her  New York Times  obituary, dated November 23, 2004. For those of us who worked for so many years to call attention to the relationship of serum total cholesterol to risk of coronary heart disease (CHD), and to the cholesterol-raising effects of certain saturated fats, Keys will always be one of the major prophets who provided the early evidence that atherosclerosis is not an inevitable concomitant of aging, and that a diet high in saturated fat content can be a major risk factor for CHD. The practical outcome of the work in this field – to which Ancel contributed so much – is the extraordinary decrease in mortality from coronary heart disease that has occurred during the past half-century. Cancer has finally replaced heart disease as America's number one killer. Ancel had his well-deserved reward – a long, productive life unencumbered by an excess of committee meetings, and the opportunity to contemplate the Tyrrhenian sea while enjoying the benefits of a Mediterranean diet.New York Times


On February 11, 2005, the New York City Department of Health and Mental Hygiene announced that a city resident had recently been infected with a multi-drug resistant form of HIV and rapidly progressed to AIDS. The Health Commissioner, Thomas R. Frieden, called for increased vigilance against this new strain. Is this situation an emerging crisis or simply an unusual case report of rapid HIV progression?

On February 11, 2005, New York City (NYC) health officials announced the discovery of a "rare strain of multi-drug resistant HIV that rapidly progresses to AIDS." According to the NYC Department of Health and Mental Hygiene, a man in his mid-40s was diagnosed with HIV infection in December 2004. Shortly after his diagnosis, testing, at the Aaron Diamond AIDS Research Center in Manhattan, revealed that his virus was resistant to almost all anti-HIV therapeutics. Further, despite being infected for only 2–20 months, the man had developed AIDS. NYC Health Commissioner Thomas R. Frieden, MD, MPH, stated, "This case is a wake-up call. First, it's a wake-up call to men who have sex with men, particularly those who may use crystal methamphetamine...now, we've identified this strain of HIV that is difficult or impossible to treat and which appears to progress rapidly to AIDS." Dr. Frieden called on this community to help stop the spread of this and other drug resistant strains of HIV. He also called on NYC doctors and the public health system to improve HIV prevention counseling, to perform HIV drug resistance testing among treatment naïve, HIV +  persons, and to improve anti-HIV drug adherence.At the 12 th  Conference on Retroviruses and Opportunistic Infections (CROI) in Boston, Drs. David Ho and Martin Markowitz of the Aaron Diamond AIDS Research Center in Manhattan presented clinical and laboratory data regarding the NYC resident[ 1 ]. He had tested negatively for HIV-1 antibodies several times before and in May 2003. His total lymphocyte counts during these time points were repeatedly normal. Investigators believe that the NYC resident may have been infected in October 2004, when he, while on crystal methamphetamine, engaged in unprotected, receptive and insertive anal sex with multiple partners. In early November 2004, the NYC resident developed a febrile illness, and then in December 2004, he tested positive for antibodies against HIV. His personal physician, concerned over the possibility of recent acute HIV-1 infection, referred the NYC resident to Dr. Martin Markowitz. At the time of diagnosis, his CD4 +  T-cell count was 80 cells/mm 3  and it has since fallen to less than 50. The NYC resident meets one criterion for the diagnosis of AIDS; his CD4 +  T-cell count is less than 200 cells/mm 3 . His viral load has varied from ~100 K to 650 K/ml. The NYC resident's virus was tested and found to be resistant to all but two anti-HIV drugs, efavirenz (Sustiva ® ) and enfuvirtide (Fuzeon ® ; T20). This high degree of drug resistance existed before the NYC resident was treated with any anti-HIV compound.Is this case a harbinger of a new epidemic with this superbug or is it just an isolated, forme fruste of HIV infection? No one knows the answer to this question yet, but we do have plenty of data to suggest that the latter is the case. In people naïve to drug therapy, bone fide antiviral resistance is uncommon. A recent USA based study of treatment-naïve patients found that the prevalence of mutations associated with drug resistance was 8.8%[ 2 ]. This means 8.8% of the subjects' viruses tested positive by genotyping for 1 or more mutations associated with drug resistance. Having a single mutation associated with resistance does not necessarily make a virus drug resistant. For many drugs, HIV must contain several mutations to become resistant. This fact is true for most protease inhibitors (PIs) and for several nucleoside analogue reverse transcriptase inhibitors (NRTIs). Therefore, the overall level of drug resistance is well less than 8.8% reported in this study. Indeed, in this study, no significant resistance to protease inhibitors was seen. A similar study found the overall prevalence of drug resistance mutations was 8.3%, as also determined by genotyping[ 3 ]. However, when viruses containing these mutations were analyzed by phenotyping, only 39% demonstrated decreased reduced drug susceptibility. In other words, less than 3.5% of all isolates had phenotypic resistance.A commonly held view on why the level of drug resistance is low is that most mutations associated with drug resistance, also decrease viral fitness. Except the K103N reverse transcriptase mutation, which confers resistance to the three approved non-nucleoside inhibitors (NNRTIs), other mutations, associated with high level drug resistance, are thought to significantly decrease viral fitness. Theoretically, in the absence of drug pressure in a newly infected individual, wild-type virus is either selected for during transmission or the transmitted, resistant virus mutates back towards the fitter wild type. The current observation is that the vast majority of viruses in treatment-naïve patients are sensitive to almost all drugs.In addition to CD4, the virus, isolated from the NYC resident, uses CXCR4 or CCR5 to enter cells[ 1 ]. Such viruses, termed dual-tropic, are rarely seen in newly infected individuals. Typically, an R5 virus, which utilize CCR5, is the transmitted type. After years of infection, in approximately 50% of individuals, the viruses' tropism changes from CCR5 to CXCR4[ 4 ]. This phenotypic change is associated with an accelerated disease course. People, who are homozygous for the CCR5, 32-bp deletion, do not express functional CCR5 and have a high relative resistance to infection with HIV. In those Δ32 homozygotes, who have become infected with HIV (8 individuals reported), the disease course appears to be more rapid[ 5 ]. Most of these individuals had CD4 +  T-cell counts less than 300 cells/mm 3  at the time of diagnosis. It is unclear why these individuals became infected, while the vast majority of Δ32 homozygotes remain uninfected. Possibly, these 8 individuals have some other aberration, which allows them to become infected with an X4 virus and, in turn, leads to an accelerated disease course. Perhaps, the NYC resident has a similar abnormality, which has lead to an increased rate of CD4 +  T-cell depletion.Also at CROI this year, Drs. Stephen Gange and Alvarez Muňoz from Johns Hopkins University Bloomberg School of Public Health presented models of rapid HIV progression probability, based on two, large prospective cohorts[ 6 ]. These studies, the MACS and theWIHS, have been on-going for the past 21 and 11 years respectively and have collected longitudinal data on 391 seroconverters. In the pre-HAART era, the median time to AIDS was 8.3 years. Using the cohorts' data, Drs. Gange and Muňoz estimated the probability of clinical AIDS developing within 6–24 months or a low CD4 +  T-cell count existing at the first visit after diagnosis (within the first 9 months of infection). Their model predicts that 7 in 10,000 patients develop clinical AIDS within 6 months of infection. This number increases to 45 in 10,000 after 12 months. Similarly, 10 in 10,000 HIV infected individuals have a CD4 +  T-cell count less than 200 cells/mm 3  after 4.5–9 months of infection.Several reports of rapidly progressing HIV infection have been published. The rapid disease course of the NYC resident is rare, but hardly unique. To date, no cluster of rapid progressors has been described. All rapid progressors have been unrelated, either genetically or virologically. While multi-drug resistant (MDR) viruses may be overall less fit compared with wild-type, drug sensitive strains, MDR HIV still causes steady CD4 +  T-cell depletion. Therefore, it is highly probable that the NYC resident has a genetic predisposition, which led to rapid progression, rather than a new strain of HIV-1, which is simultaneously super-aggressive and multi-drug resistant.Our experience at a large, inner city HIV clinic is in agreement with the above data. We do not see rapidly progressing, newly diagnosed individuals. We also do not see MDR HIV in our treatment-naïve patients. Review of our data does not reveal any evidence of MDR virus in persons, who have never been on therapy.To determine whether this "superbug" has spread to others, the NYC Department of Health is appropriately and aggressively investigating the sexual contacts of the NYC resident. The reason for the NYC Department of Health press release at this early point in the investigation is unclear. In the absence of a documented cluster of patients, should the entire health system react? No, we should wait for more information. I do agree that genotypic resistance testing for treatment-naïve HIV +  patients is prudent, especially when the person is thought to have been infected within the past year. Of course, most patients do not know when they were infected, so we are testing each new patient.Given the availability of free, rapid testing for HIV in New Jersey, we are strongly encouraging any one with current or previous high-risk behavior to get tested and determine his/her HIV status. The best way to fight this disease is with knowledge: knowledge on one's infection status, knowledge on how to avoid becoming infected, and knowledge on how not to infect some one else. HIV is not the common cold. It is transmitted through well-described behaviors, predominantly sex, especially receptive anal intercourse, and intravenous drug use with shared needles. These behaviors can be modified to reduce or eliminate the risk of contracting HIV. Two recent studies conclude that universal testing for HIV is a cost effective way to combat this infection in the USA [ 7 - 9 ]. Outreach prevention education and widespread testing are probably more effective public health strategies than sensational press releases. Dr. Frieden's call for increased vigilance against drug resistant HIV implies that regular, old-fashioned HIV infection is not horrific enough. Any one who has seen this disease up close knows that is not the case. While we have partially effective therapies and we better understand its pathogenesis, HIV infection in this country, not as life threatening as it once was, remains quite life altering.


Regulating metabolism of fat is an important challenge for any animal, from nematodes to humans. Central players in the regulatory network are the nuclear hormone receptors (NHRs), which are transcription factors that turn on or off a set of target genes when bound by specific lipid molecules. NHR genes number 48 in mammals, and a surprising 248 in nematodes. Despite the difference in quantity, there are some structural similarities between NHRs in these two groups, in particular, between the nematode gene  nhr-49  and the mammalian  HNF4 . In this issue, Keith Yamamoto and colleagues show that  nhr-49  controls two different aspects of fat metabolism, which interact to form a feedback system controlling the consumption and composition of fats in the nematode.nhr-49HNF4nhr-49Using RNAi to suppress gene expression, the researchers discovered that when  nhr-49  was absent, the lifespan of the nematode was reduced by more than 50%, and the animal displayed numerous gross abnormalities in the gut and gonad. This was accompanied by unusually high fat content in the larvae. By using quantitative PCR to measure output of fat and glucose metabolism genes, the researchers showed that deletion of  nhr-49  changed expression of 13 of these genes, with the most dramatic effects occurring within two metabolic pathways: mitochondrial lipid oxidation and fatty acid desaturation.nhr-49nhr-49Oxidation degrades lipids to release energy, explaining the build-up of fat in  nhr-49 -suppressed larvae. One of  nhr-49 's normal functions is to increase expression of the mitochondrial acyl–Coenzyme A (CoA) synthetase gene  acs-2 . A principal role for mitochondrial acyl-CoA synthetases is to “activate” free fatty acids for transport into mitochondria, where they are oxidized. This process involves attaching a CoA group to a free fatty acid, and often serves as a rate-limiting step in lipid oxidation. Indeed, the authors found that suppression of  acs-2  alone was sufficient to reproduce the highfat phenotype, while overexpression of  acs-2  rescued the phenotype even in the absence of  nhr-49 .nhr-49nhr-49acs-2acs-2acs-2nhr-49Fatty acid desaturation is the process of converting saturated fats into unsaturated ones, by forming one or more double bonds between adjacent carbons in the tail. This process is catalyzed by fatty acid desaturase enzymes.  nhr-49  increases expression of several desaturases, most importantly  fat-7 , which converts stearic acid to oleic acid; deletion of  nhr-49  more than doubled the proportion of stearic acid compared to oleic acid.nhr-49fat-7nhr-49RNAi interference of  fat-7  alone produced two interesting results. First, it shortened the nematode life span, suggesting this was the primary pathway through which  nhr-49  suppression exerted that same effect. Second, it produced some effects that were opposite those of  nhr-49  suppression: specifically, it reduced rather than increased fat content, and it increased rather than reduced expression of  acs-2 .fat-7nhr-49nhr-49acs-2These results show that in its normal actions,  nhr-49  sets in motion two opposing pathways: it increases  acs-2 , which leads to reduction of fat content, and it increases  fat-7 , which, by reducing  acs-2 , increases fat content. Surprisingly, this behavior links  nhr-49  most closely not to  HNF4 , with which it shares the most structural similarity, but to another type of mammalian NHR, called peroxisome proliferator-activated receptors (PPARs). Further investigation of this link may lead to better understanding of the functions of PPARs, and provide opportunities for altering their function for treatment of fat metabolism disorders such as diabetes and obesity.nhr-49acs-2fat-7acs-2nhr-49HNF4