How to Build a Dinosaur (10 page)

Jen came back to tell Mary what was going on. “She said to me, ‘You’re not going to believe this, but I think we have blood vessels.’ I said, ‘You’re right. I don’t believe this.Nobody’s going to believe this. We can’t talk about this.’ I don’t think either one of us slept for three weeks. We kept repeating and repeating and repeating our experiments. We actually hardly talked to each other.”

Further demineralization and washing showed that the flexible vessels were transparent. Jen continued working to compare the
T. rex
material with demineralized ostrich bone. Ostriches and emus are among the most primitive of living birds and presumably marginally more closely related to nonavian dinosaurs. The ostrich bone yielded the same kind of vessels. Furthermore, both the dinosaur and ostrich vessels contained small round red structures. And in the dinosaur, some of those round structures had dark centers that looked a lot like cell nuclei.

Using a scanning electron microscope to get a closer view, similarities between dinosaur and ostrich bone were just as strong. And between fibers in the bone matrix of the dinosaur, Jen and Mary found something even more surprising, the unmistakable outline of the cells that make bones grow—osteocytes.

These cells secrete the minerals that make up the hard scaffolding, or matrix, that makes bone rigid and strong. As builders, however, they strand themselves inside the structure they are producing. How, then, to get the energy needed to keep working and to get rid of waste material? The cells have unmistakable tendrils called filipodia that extend far out from the central body of each osteocyte and connect to filipodia of other osteocytes. They are strung out in a network that transports nutrients in and waste out. “It’s like a bucket brigade,” says Mary.

When Mary was first working on this material, she called me up to say she had found osteocytes. I assumed she meant the spaces where the osteocytes would have been, which is what I suggested.

“No, Jack, actually we have the cells and they have filipodia and they have nuclei.”

“Mary, the freaking creationists are just going to love you.”

“Jack, it’s your dinosaur.”

To continue to check these results Mary used the same methods of demineralization and light and electron microscopy on two other tyrannosaurs and a hadrosaur, or duckbilled dinosaur. She and Jen found vessels and structures that looked like osteocytes in all of them. But not all the vessels were flexible and transparent. Some of them were hard, crystalline shapes and some were just the same as the vessels in B. rex. It was hard to imagine that these microscopic remnants of vessels could be preserved, perhaps as some kind of flexible fossil with chemical substitutions for the original material of the vessel. But it was even harder to imagine what else the apparent vessels might be.

The findings on the presence of the transparent vessels and the gender of B. rex were published in two papers in
Science
in 2005, March 25 and June 3, just two months apart. Mary, her technician, and I were among the coauthors. One question that was not answered in these papers was exactly how you could end up with a blood vessel still flexible after so many millions of years. How was it preserved? We don’t know. Research to answer that question is going on now. Certainly, these are not untouched and unchanged blood vessels. They have been fossilized but remained flexible. Or so it seems so far.

Nothing in science is ever accepted until it has been replicated by other scientists, and so far this has not happened with Mary’s discoveries. She is the first to say that although these may seem to be blood vessels with everything we know now, contrary evidence may be forthcoming. In fact, she has admitted that she doubted her findings and that consequently, she and Jen set out to see if they could find similar materials in other bone and fossil bone.

“We started with a chicken that we went and got at the grocery store. And we worked our way back to Triassic bone.” What they found was that the flexible material that seemed like blood vessels was “amazingly prevalent.” That, she said, “makes me really nervous.” Why would it be so common? The question is still unanswered, but alternative explanations are no more persuasive, she says.

At the 2006 meeting of the Society of Vertebrate Paleontology an independent dinosaur researcher, Tom Kay, presented a poster that argued that she had found biofilms.

“So what Tom proposes is that they’re microbial biofilms. But I’m not sure I buy that, because we have looked at material that crosses taxa, that crosses continents, that crosses depositional environments, that crosses temporal ranges, and the vessels all look the same.

“There are a million reasons why this stuff is not consistent with biofilms. For one thing, Tom hasn’t shown that biofilm will grow in bone, or that it will form flexible tubes. If it is modern biofilm then it is defined by the presence of cell bodies, which he didn’t demonstrate. Biofilms are rather thin and grow kind of patchy because they get nutrient limited. No one has shown that they will form interconnected hollow tubes to the extent that we have observed. And, biofilms are rather homogeneous in texture, whereas we show textural differences between the osteocyte filipodia and the matrix they extend into.

“So he’s challenging our hypothesis, which is great and I applaud it, but he hasn’t produced any data to support his alternative hypothesis that’s any more valid than mine.” Further challenges have been made, but so far, neither Mary nor I see any effective criticism that undermines the idea that these are remnants of blood vessels. The next step in her research was a much larger one, and that was to tackle the apparent presence of collagen. In some ways this was more important than either of the previous findings, because of the nature of proteins, and what they can tell us about different species and their evolution. This was to take the second excavation of B. rex a level deeper, and move further in the complex discipline of molecular paleobiology.

BIOLOGICAL SECRETS IN ANCIENT BONES

Miracles from molecules are dawning every day,
Discoveries for happiness in a fab-u-lous array!
A never-ending search is on by men who dare and plan:
Making modern miracles from molecules for man!

—“Miracles from Molecules,” theme song of
Adventure Thru Inner Space,
an attraction at Disneyland from 1967 to 1985

 

 

J
urassic Park
was released in 1993 and was an immediate success. It grossed more than any previous movie, taking in more than $900 million worldwide. The film was an adaptation of Michael Crichton’s novel of the same name, published in 1990. In the book and movie dinosaurs are cloned through the recovery of ancient dinosaur DNA. It was a classic piece of science fiction. Crichton started out with real science and stretched it beyond current boundaries, into the realm of myth and fairy tale, producing a story of universal appeal. Monsters of the unimaginable past brought back to vivid and dangerous life.

Crichton imagined that a mosquito that fed on the blood of dinosaurs was trapped in amber and preserved. Not only was the insect preserved in amber, but so was the dinosaur DNA in its gut. Scientists implanted the ancient DNA into a frog’s egg. In 1993 frogs had been cloned at the tadpole stage, but no other vertebrates. So the technique made sense. In the story the dinosaur genes take over and the egg grows into a full-blown dinosaur.

In some ways the book and the movie were prescient. In 1997 a mammal was cloned for the first time, a sheep named Dolly. Since then a number of mammals have been cloned and one species of fish, a carp, but no reptiles or birds as of this writing. I don’t think Crichton saw the cloning explosion coming; few scientists did. But cloning was and is a favorite science fiction topic.

In other ways the book was very much of its time, reflecting a stage of the revolution in molecular biology and computer science. The human genome project was started in 1990, at the time
Jurassic Park
was published. This was an attempt to map all of the genes that go into the making of a human being. It was an obvious project, given the state of the science. But it was breathtaking in its ambition, and the notion that one could compile the set of instructions that would form a human being was, and is, shocking. Certainly no scientist would say that genes alone make a human. Genes are always affected by environment. And there were and are long stretches of DNA with no known function. Furthermore, since then, the question of how genes are regulated has become ever more important. But the dominance of the gene was at its height then.

The first genome of a multicellular organism, the millimeter-long roundworm
C. elegans,
was completed in 1998. The fruit fly genome was decoded in 2000. A draft of the human genome was released that year, and a finished, although not really complete, genome was released in 2003. None of this could have been done without the discovery of DNA and the development of chemical techniques to take it apart and determine the sequence, and computer power to massage and understand the information gained from the biochemistry.

The ability to read stretches of DNA, to compare them to other stretches of DNA, to fish out genes and identifying markers of different species, changed the way all biology was done, and not just the biology of living animals. It also began to change the study of the history of life, both in raising the value of finding traces of biological molecules in fossil bones, and in promising a new treasure trove of information about the past in the genomes of living organisms. A genome does not tell you everything about an organism. Much DNA doesn’t fall into the categories of genes as we define them, self-contained lengths of DNA that contain the code and starting and stopping instructions for making RNA that in turn is translated into protein molecules.

But a genome tells you a great amount and it made complete sense, given the state of molecular biology when he was writing, for Crichton to pick the method he did for re-creating a dinosaur. Ancient DNA seemed like a good bet, at least for a novel. And sometimes science imitates science fiction. In 1994, four years after
Jurassic Park
was published, and a year after the
Jurassic Park
movie was released, Scott Woodward at Brigham Young University reported the recovery of DNA from eighty-million-year-old fragments of dinosaur bone found in a Utah coal mine. The report was quite a surprise. Crichton put the preserved dinosaur DNA in
Jurassic Park
in the gut of a mosquito safely encased in fossilized tree resin because that was far more believable than dinosaur DNA being recovered from a fossil bone buried for tens of millions of years.

Somehow, Woodward argued, the fossils he found in the mine had been protected from biochemical reactions and other forces that would have caused the DNA to fall apart. There was some infiltration of minerals to replace biological chemicals. But when the bone was examined under a light microscope, Woodward reported, bone cells and possible cell nuclei were visible.

Taking care to preserve sterility and not to contaminate the bone with human DNA (which, as we all know from watching
CSI,
can be found on cups and cigarette butts), he and his colleagues took very small pieces of bone, turned them in powder, and then turned to what may be the most important technique in the molecular biology revolution, the polymerase chain reaction, known affectionately to scientists as PCR. The process, by which stretches of DNA can be multiplied by the hundreds of thousands, enables scientists to identify traces of DNA. A scientist named Kary Mullis won a Nobel Prize for discovering the enzyme that makes the process possible. Mullis, who lives in southern California, may be the only Nobel laureate who takes surfing at least as seriously as science. Indeed, Mullis is as unconventional as his technique is irreplaceable. He has written about his own experimentation with drugs, about possible experiences with space aliens, and has said that he does not believe the human immunodeficiency virus, HIV, causes AIDS. I’m not sure he actually believes everything he says. I know him, and I think he likes to provoke discussion. But he does say some outrageous things.

PCR relies on an enzyme Mullis discovered in bacteria in warm springs in Yellowstone National Park. The bacteria is called
Thermus aquaticus
and its enzyme is Taq polymerase. It is valuable because it comes from an organism that evolved to tolerate high temperatures. Consequently Taq (short for
Thermus aquaticus
) polymerase stays stable at high temperatures.

In preparation for initiating the polymerase chain reaction DNA is heated so that the two strands that make up each molecule separate. Molecules called primers target a stretch of DNA for which they have been designed, and serve as a marker, to tell the polymerase enzyme where to start copying. So the marked section of DNA is duplicated, and each single strand becomes a double helix again. This solution is again heated so the two helixes will separate into four strands, which the polymerase turns into four double helixes and the next heating turns into eight single strands.