Though he was a liberal-arts major, a Republican, and an appointee of an openly creationist president, George W. Bush, Jones ruled against the teaching of intelligent design as science.
His decision is admired by scientists and philosophers of science, not just because they agree with his answer, but also because he left the world with a clear, succinct document that, among other things, helps clarify the nature of science and show why it's not religion.
On Saturday, Jones will speak at Community College of Philadelphia, part of the citywide science festival that began Friday and will continue to April 28. The free talk is being presented by the Philadelphia Association for Critical Thinking.
In light of all this celebration of science, it seemed apropos to devote a column to what qualifies something as science, and why Darwinian evolution makes the grade and intelligent design does not.
I.D. is a brand of creationism that allows living things to evolve, albeit guided by an intelligent designer, the nature of which is never made clear.
The Dover trial was not an obvious battle between scientists and people of the clergy. On the side of I.D. were several Ph.D. biology professors, and on the opposing side was a well-known theologian.
Jones said he wasn't required to rule whether I.D. constituted good science, only whether its promotion in public schools amounted to endorsing a particular religious view. But he realized the two questions were connected. His decision might have been different if I.D. had been a solid, powerful, well-tested, widely accepted theory that just happened to coincide with Christian teachings. But it wasn't.
Jones used several criteria to distinguish science from nonscience, including testability and acceptance in the scientific community. But it was another, less familiar criterion that proved crucial in deciding whether I.D. was science.
That is what is known as "methodological naturalism" - one of the few jargon terms he used in his decision. It's simply a rule for doing science that excludes the invocation of gods or other supernatural entities.
To do good science, scientists don't have to prove supernatural beings don't exist. They can still believe in God or any other supernatural beings if they're so inclined.
But they can't build scientific theories based on supernatural entities any more than an engineer can build a bridge using angels instead of girders.
The world of science came slowly to this conclusion, making a great leap in the Renaissance, when Newton found that heavenly bodies and earthly objects followed the same laws, and Copernicus and Galileo moved the Earth from the center of the universe.
That last part did create friction with the Roman Catholic Church, but as Galileo so poetically summed up his methodological naturalism: "The Bible shows how to go to heaven, not how the heavens go."
By the 1700s, Benjamin Franklin and others continued in the same vein in seeking a natural explanation, rather than a religious one, that unified lightning with other electrical phenomena.
But biologists were slow to adopt methodological naturalism. As late as the 19th century, serious intellectuals were still debating whether God created the "races" of man separately or together.
Jones said his task was made much easier thanks to the witness who spoke out against teaching I.D. as science. "It was like the science class you wish you'd had in school," Jones said. The defense side, however, was not as organized. "They couldn't explain what intelligent design was," he said. Many of their witnesses never showed up.
After his decision, Jones received death threats and was pilloried by conservative television personalities. Ann Coulter tried to paint him as too poorly educated and unsophisticated to grasp the merits of intelligent design.
Most scientists, on the other hand, were relieved and impressed.
Jones was smart to use several criteria to separate science from nonscience, said Massimo Pigliucci, a biologist/philosopher and author of the book Nonsense on Stilts: How to Tell Science From Bunk.
Testability can be a good first-order rule, said Pigliucci, who teaches at the City University of New York and recently spoke for the Philadelphia Association for Critical Thinking, a group of skeptics. But that test sometimes rules out ideas that later become important. Take Copernican astronomy with its sun-centered solar system, he said.
It didn't fit the astronomical data of the time any better than the Earth-centered system did. Despite this, Galileo just knew there was a very important baby in Copernicus' bathwater, and once Kepler figured out that the planets traced elliptical paths rather than circular ones, the sun-centered system worked.
Acceptance in the community is another imperfect measure of science. It's always possible some great idea is simply too revolutionary to be accepted right away, a common claim by pseudoscientists. But over time, the scientific community does tend to weed out the science from the pseudoscience.
Some advocates of intelligent design have tried to argue that God didn't have to be the designer. It could have been space aliens, for example. That still doesn't make it science, says Pigliucci, since there's no mechanism or evidence being proposed. It also leaves open the question of who designed the designers.
Thanks to methodological naturalism, science doesn't require faith, the way religion does. And science is therefore not a religion, but a discipline, a way of thinking, investigating, and testing the nature of the physical universe.
Following the rules allowed scientific fields to become global group projects, where Muslims and Christians, Hindus and atheists could contribute as equal partners without having to give up their faiths.
Philadelphia Science Festival Highlights
Events (including those requiring reservations) are free unless noted. For full details, including reservation forms, go to www.philasciencefestival.org. Phone: 215-448-1128.
Science on Tap presents: Science Quizzo 6 p.m. at National Mechanics, 22 S. Third St.
Here on Earth: A Conversation with Tim Flannery Author and activist charts history of life on Earth. 6:30 p.m. at Academy of Natural Sciences, 1900 Benjamin Franklin Pkwy. Reservation.
Dean Kamen: The Future Belongs to the Innovators 6 p.m. at the Franklin Institute, 222 N. 20th St. $10; reservation.
Astronomy Night Locations around town. See full list.
In the Mouth of a Lion: The Sensory World of Animals Explore the tastes of different species. 6 p.m. at Rembrandt's, 741 N. 23d St. Reservation.
Spring Fling: Party with Your Planet All day at Phila. Zoo, 3400 W. Girard Ave. Regular admission.
Raft Rally Build rafts and explore buoyancy physics. 1 p.m. at Independence Seaport Museum, 211 S. Columbus Blvd.
Critical Decision-Making: Science, Religion, and the Law Judge John E. Jones on his "intelligent design" case. 2 p.m. at Community College of Philadelphia, Student Life building, 1700 Spring Garden St.
From Hops to Stein: The Science of Beer 7 p.m. at Yards Brewery, 901 N. Delaware Ave. $20. Ticket.
No events scheduled.
The Perfect Flower: A Physical Meditation on Beauty and Solitude Contemporary dance bringing botanical sciences to life. 11 a.m. and 7 p.m. at Academy of Natural Sciences. Reservation.
Science Diaries: Cool Jobs in Science and Technology
4 p.m. at Drexel University, Main Auditorium, 32d and Chestnut. Reservation.
Manya: A Visit With Marie Curie Portrayal by storyteller Susan Marie Frontczak. 6 p.m. at the Chemical Heritage Foundation, 315 Chestnut St. Ticket required.
The Hidden Reality with Brian Greene: Parallel Universes and the Deep laws of the Cosmos Noon at the Central Library, 1901 Vine St.
Contact staff writer Faye Flam at 215-854-4977 or email@example.com. Visit her "Planet of the Apes" blog