If fossil collecting had a theme song, what better than this spiritual? Among vertebrate animals, as the fossil record shows, the thigh bone is connected to the hip bone; the back bone is connected to the neck bone, so to speak.
Paleontologists know about ancient bones. What they don't know about is the soft tissue — the cartilage, the tendons, the muscles — that connected the bones so they could do their work.
Since soft tissue does not fossilize, paleontologists are in the dark about its evolution. "We have no idea. It's like a fishing expedition," Bill Sellers, a biologist at the University of Manchester, said during a recent visit to the Stanford Linear Accelerator Center (SLAC) in Menlo Park.
Mr. Sellers was in town to test a hypothesis: Do fossils have something to say about soft tissue? It might be that an organ or muscle, given a chance to deteriorate in place, leaves trace elements that might show up under X-ray bombardment.
A team of scientists, including Mr. Sellers, gathered for five days in Menlo Park in mid-December at the Stanford Synchrotron Radiation Lightsource at SLAC. They were there to beam X-rays at a fossilized archaeopteryx, a rare fossil of a 145-million-year-old feathered creature widely thought to be a transition species between dinosaurs and birds.
Like the other nine known archaeopteryx fossils, this one, valued at $6 million, was found in a quarry near Solnhofen in western Germany. It is normally on display at the Wyoming Dinosaur Center in Thermopolis, Wyoming.
The remains of the Thermopolis archaeopteryx are captured spread-eagled in a rectangle of tan limestone 22 inches wide, 20 inches tall and a little more than half an inch deep. It's a complete specimen showing spine, teeth, leg and wing bones, bony tail and the outlines of wing and tail feathers as they settled into the soft mud.
The X-ray beam scanned the limestone with an intense beam the diameter of a human hair. Starting at the top front edge of the vertically mounted fossil, the beam traveled horizontally across it, dropped down by a tiny increment, also about the diameter of a hair, and traveled back the other way.
The scientists divided the fossil's surface into a grid of 20 million points, or pixels. The beam paused above each pixel for three thousands of a second, and each pixel emitted its own bit of information based on the reaction to the X-ray beam by any elements present.
A complete scan — there were three done over four and a half days — took 20 hours. The project's intensity led some scientists to stay on the job for 20 hours and snack, University of Manchester paleontologist Phil Manning said.
Beam time, at about $24,000 a day, is a precious commodity, he said. The device sends X-rays around a circular chamber at the speed of light. At the 30 lab stations located around the chamber's perimeter, all of which have waiting lists, scientists sign up to tap into the beam's energy for experiments.
Mr. Manning paid his own passage to and from Menlo Park, as did many of his colleagues, he said. They boarded in a hostel on the Stanford campus.
An ideal result of this experiment would be an image showing never-before-seen shadows among the bones, such as the routes of blood vessels or the location of a kidney or stomach.
The scientists weren't counting on it. "If we're very, very lucky, we'll get information about the organism itself," said Roy Wogelius, a University of Manchester geochemist who is on sabbatical at Stanford University as a visiting professor.
"The most fun about being a geochemist is being surprised," Mr. Wogelius said. What's more likely, he said, are insights into the relationship of various trace elements to fossilized bone, and/or more information about how bones become fossils.
"We're learning as we're going," he said. "Each image teaches us something new that we've never known before. ... For me, it's like a miniature chemistry experiment somebody put in place 150 million years ago."
Indeed, the scientists don't know exactly which elements of the periodic table they should be looking for, and so they meet to talk about it, he said. "It's quite exciting. It's fun. It's a great step into the unknown. We have an analytical problem that involves the whole periodic table," he said.
Experiment leader Uwe Bergmann agreed that a breakthrough about archaeopteryx itself would be an "ambitious" result.
"The funniest thing about science: The simplest questions are the hardest," he said. What, for example, did archaeopteryx eat? he asked. "That's an incredibly difficult question to answer. The real world of science is that your progress is in much tinier steps. Generally, you always find some kind of surprise."
Just as astronomers spend years poring over data acquired from extra-terrestrial probes, so will paleontologists pore over the data from this experiment, Mr. Manning, the paleontologist, said.
The maps, so far, were "far from disappointing," he said. Indeed, they were "utterly gobsmacking, the most insight I could have wished for."
The idea that soft tissue may have left behind a heretofore hidden story is "poetry," he said. Without this X-ray beam, it's locked away and "we need the benefit of X-ray vision."
Asked to comment on his passion for paleontology, Mr. Manning said it's based in his interest in the changes in ecosystems and biodiversity through time, and how biodiversity relates to living organisms.
"We're living in a time of catastrophic environmental change," he said. "Everybody is turning to the scientific community and saying, 'What do we do?' How can we understand the present if we can't understand the past? That's where paleontology fits into the natural world."
This experiment is somewhat timely in that the 200th anniversary of Charles Darwin's birth is in February, and the 150th anniversary of "The Origin of Species" is in October. "This is Darwin's bird," Mr. Manning said, "The archaeopteryx is the most important fossil in the world."
Dinosaurs and birds
The Natural History Museum in London invites Web visitors to "Explore the evidence that helped scientists prove birds are living dinosaurs."
A key exhibit is archaeopteryx, called by staff paleontologist Angela Milner a "halfway house between what we traditionally think of as small theropod dinosaurs and birds."
Theropod dinosaurs were meat eaters and included the monstrous Tyrannosaurus rex and the smaller Velociraptor and other dromaeosaurs, or "raptors." Are birds descended from such small theropod dinosaurs?
"There's absolutely no question that birds evolved from predatory dinosaurs. End of story. The evidence is there now," Mr. Manning told The Almanac.
Mr. Sellers agreed, citing as evidence the similarities in wrist bones and in the genes expressed in the development of a bird's wing and that of a theropod dinosaur's "hand."
Human hands "express" five fingers, or digits. Birds suppress two digits and express three in creating the bone architecture for their wings. Theropod dinosaurs also express three digits and suppress two. Scientists disagree over which digits are suppressed in the two creatures.
Mr. Manning said that genetic studies show both bird and theropod phyla — their categories in the hierarchy of life — using digits 1, 2 and 3.
That genetic connection was rebutted, said Dr. Alan Feduccia, an evolutionary biologist at the University of North Carolina, and the author of two books on the origins of birds and an upcoming third book.
Mr. Feduccia said in an e-mail message that he does not dispute the notion that birds and theropods have a close affinity, but he does question the confident assertion that birds are descended from a highly specialized group of late-occurring smaller theropods.
Archaeopteryx is essentially a modern bird and pre-dates by some 25 million years the theropod fossils that are supposedly ancestral to birds, he said. Bird-as-theropod advocates rely on physical similarities and ignore this timing problem, he added.
Mr. Feduccia said he would accept that birds evolved from theropods if the science was there to prove it, which, so far, it has not been. "The consensus is that birds are dinosaurs. I would argue that whenever you see the word consensus, you're out of (the realm of) science."
The evidence is more compelling that birds and theropods derived from a common ancestor, he said, adding that he expects fossils to be discovered that prove it.
As for the argument over which digits are expressed in the "hands," the "overwhelming evidence" shows birds suppressing digits 1 and 5 and expressing digits 2, 3 and 4, he said, and he has a 2002 photo of a 14-day-old ostrich embryo to prove it.
The idea that birds at some point shifted to the theropod model of digits 1, 2 and 3 is "really a stretch of credulity, frankly," he said in a telephone interview. "Such a fundamental characteristic like the digits of the hand doesn't seem like a thing that would be jumping all over the place."
When asked about Mr. Feduccia, Mr. Manning described him as more or less alone in his dissent.
The Almanac asked Mr. Feduccia about support in the scientific community for his views. He replied that he could spend 10 minutes naming scholars who agree with him.