It's the world's greatest detective mystery, a plot billions of years old: How are living things related to one another?

From bats to buzzards, yeast to yaks, salmon to salmonella, all life shares a common ancestry diverging from a long-ago ancestor. This scientific theory, famously expounded in Charles Darwin's "Origin of Species," has been strengthened over the decades with new discoveries.

Not only fossils, but comparative anatomy and molecular biology point to this ancestry. Virtually the same genetic code is shared by all organisms, which makes it possible for a human gene to function when spliced into a bacterium -- the foundation of biotechnology.

But the precise relationship among each of the millions of discovered and extinct species is extremely difficult to determine. That is where an ambitious project funded by the National Science Foundation comes in.

Called "Assembling the Tree of Life," the project is a consortium of 13 universities, including UC San Diego, whose researchers were awarded $4.1 million last month from the foundation.

The project's overall head is Bernard Moret, a computer scientist at the University of New Mexico. At UCSD, the project is directed by Francine Berman, director of the university's San Diego Supercomputer Center.

Scientists say practical benefits from the project could include new drugs and methods to handle extremely large sets of data, such as those used in forecasting weather. There may also be an intellectual satisfaction for one branch of the tree, a certain tailless primate that wonders about how it fits into the history of life.

"We're mapping the history of life on Earth," Berman said. "Another way to think of this is a molecular version of fossil collecting."

Number crunching

At UCSD, Berman's team is developing new methods of analyzing data and will tap into the processing power of supercomputers worldwide to make sense of all the information flowing in. Scientists from many different fields are drawn together for the project.

The emphasis on data and computing is necessary because the days are long past when biologists can make significant discoveries simply by peering through a microscope.

Biologists today are interested in genes, the assemblages of the molecule deoxyribonucleic acid or DNA, which carry the code for life. They are also interested in proteins, which genes code for, and the relationships between sets of genes and proteins.

The Human Genome Project, the much-ballyhooed international effort to map out the entire set of genes in humans, or genome, could not have been possible without high-powered computers.

The genome project started with a lot of traditional biology "wet lab" work, such as collecting and preparing cell specimens to get the genes. However, they were collected in thousands of fragments. The fragmentary gene sequences were fed into supercomputers, which tried to piece them together like a person with a gigantic jigsaw puzzle.

The Tree of Life project is many times more complex, Berman said, because the patterns of millions of species must be compared. Not only genes and proteins, but anatomical features and other identifying markers will be used.

Like the Human Genome Project, the Tree of Life project will also take many years to complete. And Berman cautioned not to expect perfect answers, because in science, there is never perfect information. Gaps will remain even after the work is mainly done, gaps that may be filled in over decades.

Relationships

Biologists accepted evolutionary theory in large part because of its ability to make sense of otherwise unrelated bits of information. "Nothing in biology makes sense except in the light of evolution," wrote the influential 20th century evolutionary biologist Theodosius Dobzhansky.

This need to make sense of facts is even more urgent today because of the huge volumes of data pouring in through genomics and proteomics, the study of genes and proteins. An evolutionary tree, or phylogeny as scientists call it, provides a framework for organizing these facts.

"Once you understand the relationships in an evolutionary sense between these organisms, you can find out an incredible number of things," Berman said, rattling off a series of examples.

"It reflects the history of transmission of life's genetic information, so it tells you a lot about genetics. It provides a way of organizing information about all kinds of diverse organisms and genomes and molecules. It provides a vital role in studies of adaptation. Why do things become extinct? What's the role of environmental phenomena on living things?"

The San Diego Supercomputer Center is working on another project called the Encyclopedia of Life, an attempt to find the proteins produced by every living species and relate their structure to their function. Berman said if that structure/function information is correlated with the creatures' evolutionary history, insights may emerge.

"This could help us to understand in drug design, for example, toxic substances. If they're close to each other on the evolutionary family tree, are there common things that make them toxic?"

Medical researchers are making more extensive use of genetic sequence materials collected from primates, the order of mammals that includes monkeys and apes such as gorillas, chimps and humans, said David Stockwell, an assistant research scientist at the supercomputer center.

Scientists cross-check these gene sequences with similar human gene sequences, Stockwell said, enabling them to "triangulate" their deductions.

"It gives them a better idea about drug effects and drug interactions by having that information from species that are slightly different from humans," Stockwell said.

The big picture

Stockwell is skilled in manipulating large sets of data, and has applied his expertise to biological data. However, he said, some of the techniques developed for handling giga-gobs of information can be applied to other realms of science, such as analyzing weather and even mapping the universe.

"We're talking about writing joint proposals with people you wouldn't necessarily think would benefit from this, but do have connections when it comes to the underlying technology," Stockwell said.

"Science today is a team sport," Berman said." This is a real instance of where you have a very multidisciplinary team, leveraging each others' strengths to attack one of the fundamental problems of science."

Contact staff writer Bradley J. Fikes at (760) 739-6641 or bfikes@nctimes.com.