In the same issue Asara, along with Mary and three other researchers, reported actual protein sequences, the sort of information than can provide valuable evolutionary connections, in mastodon and
T. rex
fossils. The sequences showed the predicted similarity to bird collagen.
Mary also used material in old dinosaur and mammoth fossils to create antibodies, a reverse process. You inject material from a dinosaur bone into a rabbit, to see if it is in good enough shape to prompt creation of an antibody. Then you see what components these antibodies find and latch on to in modern bone. If, for instance, the dinosaur antibodies recognize collagen in a chicken, that is pretty suggestive that the dinosaur bone of sixty-five million years ago retains collagen that is an awful lot like chicken collagen.
That finding hasn’t gone unchallenged. Mike Buckley from the University of York, in England, and about two dozen other scientists, including Peggy Ostrom, criticized the findings in January 2008. In particular they argued that the evidence for
T. rex
wasn’t sufficient to conclude that surviving collagen had been sequenced. The evidence was, however, convincing for the mastodon tests, they said. One of the reasons was that, in their reading of the results, it appeared that more change had occurred to the mastodon fossil over a relatively short time than had occurred in the
T. rex
fossil over sixty-eight million years. And they thought the fragmented sequences claimed for
T. rex
showed a similarity to amphibian proteins that didn’t make sense.
Asara and Mary replied in the same issue including the technical comment. They cited the many supporting lines of evidence that collagen had survived, and the extreme unlikelihood of amphibian contamination, since amphibians are not native to the Hell Creek area and weren’t present in the labs where the substances were tested.
In answering the challenges to their work, Asara and Mary noted that the samples were not tested at other labs because few exist. They do plan to offer material to other labs in the future if they have enough material. But they defend the validity of their tests and the evidence for collagen survival.
Such challenges are essential in science. Mary is convinced, and I am too, that she has the goods on collagen from B. rex, but I would be disappointed and worried if there were no strong critiques.
In April 2008 Chris Organ at Harvard and several other authors, including Mary and Asara, followed up the initial papers by analyzing the sequence data of
T. rex
and mastodon collagen. Chris is a former student of mine. As an outgoing and outstanding graduate student in Bozeman, he had done his dissertation on the biomechanics of dinosaur tails—how they affected movement. He did the research on collagen as a postdoctoral student at Harvard, where he has moved more into molecular biology. That research on collagen found that, as expected,
T. rex
is closely related to the chicken, and a distant cousin of an alligator.
These conclusions are much muddier than they sound, because the evidence is seldom simple and straightforward. It would be wonderful if we could simply pull a chunk of collagen out of a fossil bone and say, “There we have it.” Instead we run many tests on a fossil bone, tests that can rule out the existence of a protein, or tests that show direct evidence of collagen. And we interpret the results of the tests, interpretations that are always up for revision and discussion. What we can say, after all our tests, is this: The best explanation of our results, as of now, is that bits of protein have survived for tens of millions of years. It’s kind of an opening salvo in a scientific discussion. And, if we’re lucky, it will result in more experiments by other people and either the confirmation of our finding, or the development of solid contradictory evidence that tells us we were wrong.
A good question is one that will push our understanding forward when we try to answer it. Can protein molecules survive in original form, in good enough condition to be sequenced over sixty-eight million years? Let’s find out. A good question is not always the most profound. It is one that we have the ability to answer. Why is there something rather than nothing? I couldn’t tell you and I don’t know how to go about pursuing an answer. Whether protein molecules can survive sixty-eight million years is a good question, and we have our provisional answer, which brings up many more questions. How much of the protein can we read? How can we find more fossils like this? How does a molecule survive so long? Why proteins and not DNA? Can we find other proteins? Can we find them from many extinct animals?
“I think the more we study this bone matrix—and eventually the blood vessels and cells, which is where I want to go next—the more information we’re going to get on the process of fossilization, the process of degradation, the process of molecular aging, which has a lot of side implications that I think are very intriguing.”
Mary’s findings have changed how we do field paleontology and I think will have a bigger effect in the future on how everyone does paleontology. We used to collect only the bones and were conscious of the shape and structure of those bones, the gross morphology of animals from the past. In order to prevent disintegration we would immediately coat everything with a preservative.
This was a bit like varnishing the bones, the way you might varnish the wood on a boat to protect it from the elements. It works well to keep old fossils from further disintegrating. But, like varnish, the preservative seeps into the dry fossils, which absorb the chemicals. There is no point in looking for traces of biochemicals from tens of millions of years ago in a fossil bone that has been absorbing new chemicals.
Each summer field season teams from the Museum of the Rockies will now be looking for fossils that have been buried in rock deep enough to make preservation of biomolecules more likely. And we will be making sure Mary gets them right away.
Last year when we excavated the leg of a
Brachylophosaurus
(a duckbill dinosaur), and sent the samples to Mary, it was discovered that there had been some degradation of the sample, even in the short time it took to get the sample to North Carolina. So, to reduce the degradation time, we have taken the lab to the site.
Mary’s mobile lab is the trailer part of a tractor-trailer, or eighteen-wheeler. But instead of being filled with freight, the trailer is outfitted as a laboratory. The geology department at North Carolina State University purchased the lab, which was built by the army to be used on a Superfund site, and paid for its transportation to Montana. It has a diesel generator, fuel tanks, water tanks, office space, and a bathroom. It originally cost $500,000 for the army to create the lab. We had it pulled to Bozeman and the museum, then put about $25,000 more into renovations to create a clean-lab where we could extract soft tissues. The lab has a fume hood, a couple of microscopes, a pure-water system, and other analytical equipment. We hope to get a scanning electron microscope in there eventually.
The lab provided some terrific results this past summer. Mary has some nice material from the Judith River Formation, dating to the Upper Cretaceous, a few million years older than the material in the Hell Creek Formation.
Mary is particularly excited about some of the new material. “We got a lot of great specimens,” she says. “We’re just learning so much about how we treat the bone in the field. For the first time we started looking at teeth, and those are pretty exciting.”
What causes fossil degradation over time and what makes it happen faster or slower are important questions. Mary points out that learning how molecules age could give us new insight into the process of aging in living animals. And there is nothing of more interest to most of us than our own aging. The nature of molecular aging also has implications for our search for evidence of life on other planets. If we know how molecules fall apart, at what rate, under what conditions, we will have a better idea of what we’re looking for on Mars or Titan, or beyond.
There is a potential treasure trove of information on evolution. Currently, rates of evolutionary change and the points in the history of life where a lineage diverges have been estimated by the structure of bones—the gross morphology—and by comparing the genes of living creatures to see the degree of difference from one species or genus to another. With that information the pace of evolution can be estimated and evolutionary events backdated. With evidence of protein sequences from ancient creatures, we may be able to dip directly into deep time to test our ideas about evolution.
But there is only so deep you can dig into a dinosaur bone, only so far you can go with the bits of collagen and other biomolecules that may be left. We may not be there yet, but at a certain point we are left with dust in our hands, wondering where to dig next. The answer is: the genes of living animals, because a record of evolution is to be found there. For our purposes the most important record is in the genes of the only remaining dinosaurs—the birds.
4
DINOSAURS AMONG US
CHICKENS AND OTHER COUSINS OF
T. REX
According to our leading scientists, I am not yet extinct, and they ought to know. Well, there’s no use crying about it.
—Will Cuppy,
How to Become Extinct
E
very morning, the dinosaurs make such a racket. I can hear them outside my bedroom window, singing the dawn chorus. When I leave the house they are everywhere. I see them in parks, patrolling the parking lots of shopping malls, on the prairie, along rivers, at the sea, and in New York City, where they live in astonishing numbers. I often find them on my plate at fine and fast-food restaurants.
I’m talking about avian dinosaurs, of course, warblers, starlings , catbirds, cowbirds, robins, orioles, gulls, vultures, king-fishers, sandpipers, falcons, pigeons, and chickens, billions of chickens. I’ve been saying for most of the book that the dinosaurs never did go extinct, that birds are dinosaurs, descended from theropod dinosaurs, related to
T. rex
, and with a great library of dinosaur genes in their genome.
This is the consensus of scientists now, but it has not always been so, and since the connection of birds to dinosaurs—both in what we have found so far and in what we hope to find—is at the center of the story I want to tell, it is worth stepping back from the digging and pause, before we dive into laboratory work, to do a little evolutionary bird-watching. Our understanding of the relationship of the blue jay to
Velociraptor,
of the chicken to
T. rex
, has itself evolved. It’s a good story within a story, the evolution of birds and how we have uncovered it.
We have always known that there was a connection between dinosaurs and birds. Dinosaurs are reptiles and birds clearly descended from reptiles, but exactly which reptiles, and how and when that descent occurred, has been an intriguing puzzle. Modern birds are as magical as any creatures on earth. They are beautiful and clever and they live right in our midst. Unlike almost all other wildlife that we might want to observe, birds do not hide from us. Robins hop across our lawns, gulls chase our boats and congregate at beaches, dumps, and the parking lots of fast food restaurants. Red-tailed hawks sit, unconcerned about the traffic, by roadsides. Hunted birds grow wary, but so many others are so much with us that they have become like the trees and flowers and sunlight. And they fly. That is the single most impressive and intoxicating fact about birds. They fly.
They straddle the winds and stroll the updrafts as if air were solid ground or ocean swells. Intuitively, that puts such a vast distance between them and nonavian dinosaurs that it seems odd to connect them to ancient animals we imagine often as thundering through Cretaceous swamps and coursing across the ancient plains.
How did it occur to us that they might be dinosaurs? How did we know they are reptiles? How did we find out about their evolutionary heritage? In short, where do birds come from?
The answers won’t be found in the Hell Creek deposits. By the time B. rex was prowling the Cretaceous delta in the shadow of the Rocky Mountains, the sky, land, and sea were well colonized by birds. Some would seem strange to us now. Diving birds up to four or five feet long with teeth, tiny forelimbs, and short tails fished in the inland sea. They had, for company, the recognizable ancestors of modern birds, including shorebirds, parrots, and flying and diving birds like petrels. Amid these birds and the dinosaurs were the Alvarezsaurids, initially thought to be very primitive birds, now thought by many to be birdlike dinosaurs. No doubt this difficulty we have in pinning down what category we want to put the Alvarezsaurids in did not bother them as they ran about, catching small mammals or other prey. Another bird present in the late Cretaceous was
Ichthyornis
, about a foot long, a diver, with teeth, but with wings long enough to fly.
The great radiation of birds into the many and varied creatures we know today took another ten million years to begin, after the nonavian dinosaurs disappeared. But the birds were already ancient by the time the tyrannosaurs appeared. For their origins we need to delve much deeper.
The proposed ancestors of birds have been many, including turtles, pterosaurs, and other ancient reptiles. In the later nineteenth century, according to Luis Chiappe in
Glorified Dinosaurs: The Origin and Early Evolution of Birds
, several scientists, starting with Karl Gegenbaur in Germany and including Thomas Huxley in England and Edwin Drinker Cope in America, argued for a bird descent from dinosaurs.
Then other reptiles became more popular candidates for bird ancestry. Birds, after all, seemed so different from dinosaurs. Dinosaurs were cold-blooded, sluggish, small-brained, plodding reptiles. Birds are vibrant, quick, and generally have their wits about them. They are engines of heat. Birds live in some of the coldest environments on earth, precisely because their internal temperature regulation is so sophisticated. Owls and falcons populate the Arctic. Skuas and penguins thrive in the Antarctic. Small terns migrate from pole to pole each year in one of the planet’s great marathons. Bernd Heinrich, who has studied ravens in the Maine woods, has written eloquently of the gold-crowned kinglet, which lives on the very edge of disaster in terms of energy management. In the North American conifer forests the tiny bird survives the fierce winters by eating constantly during the day, just to gain enough calories to stay alive through the night. At that it has to drop into a torpor of some sort to conserve energy. The gold-crowned kinglet just does not fit the idea of dinosaurs as sluggish and cold-blooded, which predominated for decades until the 1970s.