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Bioinformatics Spinning worldwide web of life.

Tim Thwaites reports on plans to dust off the data dinosaurs that lurk in biological collections worldwide.

Using advances in corn purer technology, the information can be made accessible and easier to analyse, broadening the knowledge base upon which decisions about conservation are made.

Students from schools in South Australia's Riverland region are spending time each month clearing insect traps in the nearby Bookmark Biosphere Reserve. They sort their catch into broad groups and send them off to CSIRO Entomology in Canberra for finer identification.

The primary and secondary students are involved in a long-term project to rehabilitate the reserve by planting native species and clearing weeds. By tracking the variation in species and abundance of insects over time, they can monitor the environmental changes they engineer.

It's important work in which a significant part of the students' science curriculum and outdoor education is devoted to renewing part of the Murray Basin. Added to this, the students will be at the forefront of a concerted thrust to gather and open up access to biological data through the use of computers and the World Wide Web.

CSIRO coordinator of the Bookmark project, entomologist Dr Geoff Clarke, says the students will eventually do almost all the insect identification themselves, using information, illustrations and software lodged on the Web. And the results of their work will be freely available. It's all being financed by the Federal Government through its Natural Heritage Trust Fund.

The concept of such a high level of community involvement in gathering biological data and contributing to conservation is so new that some of the computer tools to make it possible have not been developed. But once the project is up and running, Clarke hopes to replicate it across Australia.

`We hope to develop it as a module,' he says. `Then we could transfer the idea to the arid zone or to tropical North Queensland. In this way, scientists and local communities can combine in meaningful conservation. If gathering this sort of data were left to scientists from Canberra, it would be enormously costly.'

The Bookmark project is at the forefront of a revolution known as biological informatics: employing computers to gather, store, combine, search, analyse, present and apply biological information. Advances in computing and the establishment of the Web have made it possible to pull together and analyse information from different disciplines stored in many parts of the globe.

Australia, particularly the CSIRO, is a world leader in providing ways to achieve this. Which is just as well. Because the developed nations of the world have grand plans for biological informatics. And they could well be realised using CSIRO-developed software.

Last June in Paris the Megascience Forum of the Organisation for Economic Cooperation and Development -- the association of the world's rich nations -- gave preliminary endorsement to a US$300 million project to make the more than 350 years worth of biological information stored in the Earth's museums and research institutions available to all via the World Wide Web. (The Megascience Forum is an inter-governmental committee of the OECD which deals with science projects too large for any single nation to handle.)

The project, called the Global Biodiversity Information Facility (GBIF) by the working group which recommended it, is seen as an essential step for studying, conserving and utilising the world's biodiversity. And the task is urgent. According to Dr Peter Raven, Director of the Missouri Botanical Garden and an advisor to the US President on biodiversity, as many as a quarter of the Earth's species of plants, animals, fungi and microorganisms may be extinct by 2025, and three-quarters either extinct or on the way to extinction by the end of next century (see US biologist says sustainability the only path to peace)

This loss is compounded by enormous ignorance. `Imagine in Indonesia trying to convert some wretched, acidic swamp land to rice paddies,' Raven says. `When we do that, we are dealing with (ecological) communities in which we really are aware of the existence of only probably one in 20 of the organisms. These organisms are responsible for the flow of energy through those ecosystems, for regulating the cycling of minerals ... for making them work. It's a very low degree of knowledge.'

The OECD working group views GBIF as a means whereby the rich nations, which hold most of the world's biological information and museum specimens but are home to relatively few of the world's species, can provide useful resources to poorer nations, which are responsible for managing a much greater variety of organisms.

Such `repatriation' of information is already happening. Most type specimens of the birds of Mexico, and the accompanying descriptive and ecological data, are sitting in museums in the US, Canada and Europe. The World Bank is funding a project to transfer that data to Mexico. And the relevant Mexican authorities are using the information to plan conservation areas to secure the future of their birds.

Closer to home, the World Bank is also supporting a team of Australian ecologists, led by Dr Chris Margules of CSIRO Wildlife and Ecology, which is using informatics tools to recommend to the Government of Papua New Guinea which areas of vegetation are important to save from logging to maintain the country's biodiversity.

The backbone of the GBIF plan -- which its proposers intend should be in operation in 2000 -- is a definitive list of the world's 1.5 million named species. (No such list exists, even though named species represent less than one quarter of all organisms.) Eventually, each species name in this electronic `catalogue of life' will lead directly to a description, references in the scientific literature, and information on where museum type-specimens can be found and where the organism is distributed geographically. The catalogue would also act as a gateway to further information on genetics, biochemistry, physiology, ecology, climate, medicine, agriculture -- in fact, to any other scientific data relevant to the species.

CSIRO has a similar project -- the Bioinformatics Initiative. This project is developing software tools that enable researchers to answer questions by gathering and analysing data on species held in CSIRO's plant, insect, wildlife and fish collections, and in other CSIRO databases. Links to the Australian Museum will also be tested. The program is coordinated by Dr John Curran of CSIRO Entomology and is being funded for the next two years by a grant of about $5 million from the Chief Executive Officer's Special Research Fund.

A related project, the Genetic Resource Initiative, will provide access to the latest computer tools for global retrieval and management of genetic data. And a third project, the Bioactive Molecule Discovery Initiative, will use computers to allow better screening and visualisation of data on molecules of interest to agriculture, drug development and nutrition.

Given this background of activity, it is no accident that the director of CSIRO's Australian National Insect Collection, Dr Ebbe Nielsen, was part of the working group which recommended GBIF to the Megascience Forum. This is the only way forward for biodiversity conservation, and it has to be done now, he says. Nielsen chaired the organising committee of the first world conference on Biological Informatics which was held in Canberra within 10 days of the Paris meeting which recommended GBIF.

One of the scientists attracted to that conference was Professor Meredith Lane, of the University of Kansas Natural History Museum. She is an adviser to the US President on biodiversity and ecosystems and another member of the working group which recommended GBIF. `Australia is far and away ahead of the rest of the world in expertise and knowledge in this area,' Lane says. `It has a "just do it" attitude, while the rest of the world dithers. Australians are heavily relied on as the experts in the field.'

Lane says a typical example is eGaz, a program that converts the standard geographic locations written on museum labels -- for example, 10 km north-east of Fiddlers Flat -- into latitude and longitude. Such numerical geographic data can then be processed by computers for several uses, such as automatically mapping the distribution of species and species assemblages for research and management purposes. The eGaz (for electronic gazetteer) program, to be released by CSIRO Publishing next year, was written by Dr Steve Shattuck of CSIRO Entomology. It is the kind of program which will be necessary to convert the world's museum data into a useful electronic form.

`This is incredibly important software,' Lane says. `And Steve produced it without much fanfare. He is an ant taxonomist, not a software person. But he had the support and resources of CSIRO to work beyond the bounds of his discipline to produce a generic program, which was related to the rest of his work.'

In fact, researchers across the breadth of CSIRO have developed or helped to develop a whole suite of software for linking and managing biological data. For instance, DELTA, a computer package to record descriptions of species and produce formal identification systems from them, was first written by Dr Mike Dallwitz, of Entomology, some 25 years ago, which makes it one of the oldest biological informatics programs in the world. A new version has just been released.

Then there is Platypus, a database program that collates, manages and reports taxonomic, bibliographic, geographic and geological information. It links references, type specimens, and distribution maps with species names -- exactly the kind of strategy proposed by GBIF. Platypus was developed by a team led by Dr Keith Houston at the Australian Biological Resources Study (ABRS) -- a federally-funded program of Environment Australia -- and is used by organisations worldwide, including London's Natural History Museum and the Smithsonian Institution at Washington DC. Using Platypus, 25% of Australia's known fauna has been included in the Zoological Catalogue of Australia database, and another 10% is in preparation.

As part of the Bioinformatics Initiative, Steve Shattuck will use Platypus as a key component of BioLink, a new package that covers almost all aspects of biodiversity information management. It will provide links to all relevant information on a particular species in the CSIRO and ABRS databases, and eventually beyond.

The software which will search databases for relevant information and help to forge those links will be developed at CSIRO Mathematical and Information Sciences by a research team led by Dr Kerry Taylor. Her aim is to develop a program which will burrow into the existing data stores and select what is needed. She says it is important not to impose on organisations with a long history of collecting information a whole lot of new rules for organising, recording and displaying data.

Initially, the research team will work at linking collections and databases within CSIRO, but the Australian Museum is interested in cooperating in trials of the system. And the hope is that eventually the project will lead to a capacity to search all the museums in Australia for useful data.

Other kinds of biological data can be linked in too. Under the Genetic Resource Initiative, the Australian National Genomic Information Service (ANGIS), based at Sydney University, has been contracted to develop and provide programs which will allow CSIRO divisions involved in genetic manipulation to manage, display and analyse their data more efficiently. Controlled access to CSIRO databases will become possible through ANGIS.

And the Bioactive Molecule Discovery Initiative aims to develop tools to search databases in the pharmaceutical, agrochemical, food industry and general biology areas with the object of picking out, modelling and evaluating biologically active molecules. For this activity, access to databases in the divisions of Entomology and Marine Science, for instance, becomes just as important as those in Molecular Science or Plant Industry.

What will be the practical outcome of access to this bioinformatics edifice for end users? In the short term, according to ecologist Chris Margules, it will not automatically save time. `Almost everything we do in conservation planning nowadays has large computer databases attached,' he says. `There's a lot of work to do on these datasets before they are of any use to us.'

But the bioinformatics revolution will allow access to data that were never available before informatics began. And the work done by today's pioneering researchers will contribute to developing simpler analytical tools for tomorrow.

Margules is part of a team from the CSIRO and the Centre for Resource and Environmental Studies at the Australian National University which has been given 14 months by the World Bank to advise the Papua New Guinea Government on areas which are important to conserve from logging to maintain biodiversity. The task involves combining data on species distributions, with information on the capacity of different land areas for agriculture, how valuable these areas are for forestry, and how they are being used. There is not enough time for fieldwork, so the research team has had to depend on data already collected.

But all data is biased in various ways, Margules says. For instance, while biologists are good at recording the presence of species, they do not often note the absence of a likely species. Another problem is that the places where museum specimens are collected tend to be close to road or river systems, so geographic distributions based simply on where an organism has been reported are more likely to reflect those systems than reality. One way to compensate for this is to determine under what environmental conditions -- temperature, rainfall, geology, altitude -- an organism tends to live, and use general measures of those conditions to predict the areas where the organism will occur between roads and rivers.

So while Margules thinks the current push to provide greater access to data will be useful, for end-users like himself it is only the beginning of turning such data into information and then knowledge which can be used to make environmental decisions. And we do not have much time. `It's all fairly urgent,' he says. `Decisions are being made day to day. And at present they are often poor decisions. In the absence of information, politicians tend to conserve bits of country no-one else is interested in. Our job is to put everything we can on the table for these decision makers.'

RELATED ARTICLE: US biologist says sustainability the only path to peace

AUSTRALIA'S future security will rely not on increased military expenditure, but on the sharing of scientific and technical infrastructure and information with neighbouring nations, according to leading US environmental scientist Dr Peter Raven.

Raven, director of the Missouri Botanical Garden and a member of the US President's Committee of Advisors on Science and Technology, was delivering the 1998 Australian National Insect Collection Public Lecture at Canberra in July. The address, sponsored by the Australian Academy of Science and CSIRO, underlined the fundamental importance of biodiversity to the future of life on Earth.

Raven said a major obstacle to sustainability was overpopulation, compounded by inequalities in resource use, wealth and education. The world's population had more than doubled from 2.5 billion in 1950 to six billion in 1998. At the same time, the proportion of people living in developed countries such as the US had fallen from 33% to 20%.

Despite this contraction, the `ecological footprint' of the developed world continued extending beyond its borders. `The 135 million people added to the population of the US since 1943 are having the same impact as if four billion people were added to the population of Indonesia,' he said. Developed nations controlled 85% of the economy, burned 80% of industrial energy, and used most of the world's iron, aluminium and steel.

People living in developing countries were paying an enormous price for the West's over-exploitation of resources, Raven said. `We live in a world characterised by massive social injustice and widespread starvation. More than 1.5 billion people live in extreme poverty, on less than one dollar a day. More than 600 million people receive less than 80% of the World Health Organisation minimum calorific intake per day. Fourteen million babies, aged four or younger, die of diseases related to starvation every year.'

Some 80% of people lived in developing nations, mainly in tropical and sub-tropical regions. These countries held 80% of the world's biodiversity, but only 6% of its scientists and engineers: an insufficient knowledge base from which to provide technical advice on biodiversity management.

In contrast, Australia's scientific and technical infrastructure was strong and future security and stability depended on sharing this infrastructure with other countries in the region, Raven said. 'No level of military expenditure can provide a safe environment for Australia. On the other hand, regional sustainability, whereby you improve the capabilities of countries such as Indonesia, Malaysia, Cambodia, Laos and Vietnam, can win both regional security and stability and trading partners for the future.

Raven said the excesses of the industrial revolution, with its dependence on physical science and energy-based progress, must yield to a more sustainable, creative use of biological systems. But just as the technology for building the `age of biology' was being developed, the Earth's biological diversity was in rapid decline. One-quarter of all plant, animal, fungi and microorganism species may be extinct by 2025 and three-quarters may be lost or nearing extinction by the end of next century.

This loss was compounded by enormous ignorance, Raven said. Only 1.6 million of the world's estimated five to seven million plant and animal species were named, and only 5 to 10% were actually known. Bacteria and fungi were the great decomposers of the biosphere, and essential for continued life on Earth, yet only 3000 kinds of bacteria had been fully described. The situation for fungi was even worse, with only 70 species described out of a possible world diversity of 1.5 million species.

Raven said the impact of humanity on Earth had been enormous. Humans used and directly diverted 45% of the planet's total net photosynthetic output on land. In the past 50 years, 25% of topsoil had been lost due to poor farming practices; 20% of agricultural land had been lost to salinisation, erosion, urban sprawl and desertification; atmospheric carbon dioxide levels had risen 15%; the ozone layer had decreased by nearly 8%; and one-third of forests had disappeared.

`We haven't been living off the interest, ecologically speaking, we have been living off the principal,' he said. `That is something that cannot go on.'

Anna Van Dugteren
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Author:Thwaites, Tim
Date:Oct 1, 1998
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