In undergoing the heating and cooling steps over and over again, the target stretch of DNA keeps being duplicated, the total growing in a geometric progression—2, 4, 8, 16, 32, 64, 128. In a couple of hours more than a million copies can be made of a target gene. Making so many copies provides enough DNA to be sequenced, that is, to have the code read. Computer power allows the information gathered through biochemical reactions to be processed to determine the sequence of nucleotides in the gene.
Woodward used this process to amplify DNA from his fossil bone samples. He concluded that the DNA had not come from modern birds, mammals, or reptiles. Nor, he claimed, were they the result of bacterial or human contamination. He concluded that he had likely recovered DNA from Cretaceous era dinosaur bones. Or, as he put it in the cautious conclusion to his scientific report, “The recovery of DNA from well-preserved Cretaceous period bone may be possible.”
The response was the scientific equivalent of bench clearing when the opposing pitcher plunks someone on your team. Several critiques were published by the same journal that had published his initial report. The authors had reanalyzed the data that Woodward had presented, in particular the claims that the fragments of DNA were not mammalian. Mary wrote one of the responses along with Blair Hedges at Penn State, and other responses came from researchers in the United States, Germany, and the Netherlands. All the critics concluded, and they convinced me, that the samples of DNA Woodward had amplified could well be mammalian, and if any mammalian DNA were present, that would mean contamination, either ancient or contemporary. By far the most plausible explanation for his results, the critics argued, was that the handling of the samples had allowed contamination with human DNA. Nobody has repeated his findings, and nobody has found DNA in fossils of that age since.
DNA has, however, been retrieved from extinct animals, such as mammoths frozen in permafrost and, arguably, from Neanderthals. But tissue frozen in ice, or at most a few tens of thousands of years old as in the case of the Neanderthals, is nothing like an eighty-million-year-old fossil. Contamination is a particularly sticky problem in attempting to sequence the DNA of Neanderthals, since they were so close to us. They belonged to the genus
Homo
and were either a different species or a subspecies, meaning that their DNA would be very hard to distinguish from that of modern humans. Consider that the chimpanzee genome is 98 percent the same as the human genome, at least. The Neanderthal genome, presumably, is much, much closer. So tracking down the ever-present possibility of contamination is extremely difficult. And with chimps, at least we have some idea of the differences. With Neanderthals we don’t even know where the differences in DNA lie.
Just as this book was going to press, the sequencing of the complete mammoth genome was announced. Reconstruction of the mammoth genome was possible because of the frozen tissue that had been preserved and advances in sequencing technology. DNA from ancient sources is recovered in fragments that can be fed into new sequencing machines developed only in the last decade that allow the amplification and sequencing of shorter fragments of DNA than were useful before. These machines are expected to improve rapidly, since computer power grows ever better and cheaper. With future generations of such technology the cost of sequencing the whole genome of an individual will drop precipitously. As it is, James Watson’s genome was sequenced at a cost of only $2 million, compared to the $3 billion cost to complete the Human Genome Project, which produced the first sequence of a human genome. The cost of sequencing genes is dropping rapidly. It was offered at $350,000 in 2008 and one company had two takers. Scientists and, perhaps even more eagerly, entrepreneurs are looking forward to the day when anyone can get his or her genome sequenced for $1,000.
Once the cheap, or rather, affordable genome mapping becomes available, many people will have their entire genome sequenced. No doubt most of them will be disappointed by how little can be done about what a genome tells us, and by how little it will tell. Traits like intelligence and athletic ability have not been pinned down to any set of genes that prospective parents might want to provide their children. That may be just as well. Eugenics, selecting for only particular human traits, inevitably diminishes those not selected for. The movie
Gattaca
that came out a few years ago, starring Ethan Hawke, is a nice tour through some of these issues. It presents a world where everyone is healthy, and no one has “defects,” at least no one with a good job. The natural-born children, whose genes are the result of the old-fashioned parental roll of the dice when sperm meets egg, are restricted to menial jobs.
The ability to sequence genomes is a powerful tool, and its future uses are unknown. So far, however, it has challenged, but not conquered, the tyranny of time, which still ravages the biochemistry of fossils. The farther back one goes in time, the less DNA is available. A common rule of thumb had been that a hundred thousand years was a limit for recovery of DNA, with the length of DNA molecules being gradually eroded through a variety of chemical processes as bones were fossilized.
If fragments of DNA are ever recovered from fossils that have come down to us from deep time, they would be valuable even if they were only hints and snippets. A few years ago, Mary wrote an article about the future possibilities for paleontology, concentrating on pursuing molecular fossils. She wrote that “if a two-hundred-base-pair fragment of DNA (e.g., the hemoglobin gene) with forty informative sites could be recovered from exceptionally preserved bone tissues of a
Velociraptor,
it would be possible to align the dinosaur gene region with the comparable region of extant crocodiles and birds.”
This could help track the course of evolution. Small sections of a gene in a dinosaur could be compared with small sections of a gene in a bird or crocodile. The pace at which genetic change occurs during evolution could be determined definitively by the amount of change in that fragment.
The DNA Woodward found may not have been dinosaur DNA, and in fact, finding truly ancient DNA, more than a million years old, may be a tantalizing but unreachable goal. But he was on the right track in the sense that many researchers have been finding that biological molecules can last longer than had been thought and open a new window on the past. They haven’t found DNA from dinosaurs, but they have used new technology to find other molecules that have survived the eons.
DISCOVERING FOSSIL MOLECULES
It was only in the past half century that scientists really began looking for ancient biochemicals. Philip Abelson was one of the first. A physicist who contributed his ideas on the enrichment of uranium to the scientists working on the Manhattan Project, Abelson switched to biology after the war, entering the field of biophysics, a new branch of research. He was in the Department of Terrestrial Magnetism at the Carnegie Institution when he started this work and became director of the institution’s Geophysical Laboratory. “Until recently,” he wrote in a 1965 issue of
Scientific American
, “it was thought that the hard parts could tell us little or nothing about the chemistry of extinct organisms.” But he reported finding “organic material in fossils as old as three hundred million years.” In the 150-million-year-old fossil vertebrae of a
Stegosaurus
he found a half-dozen different amino acids. He also reported work to assess the potential longevity of different amino acids. After testing the rapid degradation of alanine at 450 degrees centigrade, he wrote, a projection of that information based on a well-known and often-used formula suggested that at room temperature alanine would survive for billions of years. He found amino acids in fossilized remains of horses, scallops, snails, dinosaurs, and fish.
That 1965 article was a call for more work in this new field of research. Progress, however, turned out to be slow. In the late 1950s and the 1960s all biology was in the shadow of the explosion of work on DNA prompted by Watson and Crick’s discovery of the structure of DNA in 1953. Progress in DNA research was so rapid that by the early 1970s researchers were beginning to fiddle with the genes of existing life-forms, and the prospect of what was then called recombinant DNA, and is now referred to as genetic engineering, became science fact rather than science fiction.
Today disputes still rage over genetically modified food and over what sort of prenatal genetic selection or even modification of embryos might be ethical. Scientists saw the new age coming and decided to tackle the ethical problems posed by molecular genetics themselves rather than wait for Congress. Molecular biologists held a landmark meeting at the Asilomar Conference on Recombinant DNA in Monterey, California, in 1974 to begin to talk about the possible dangers of combining DNA from different organisms. The biologists and other professionals agreed on a variety of safety measures, such as physical containment when risk was high, and the use of laboratory organisms like bacteria that were effectively prevented from existence in the wild by being dependent on specific laboratory conditions.
With the future of humanity and the planet being discussed by those at the frontiers of biology, dinosaur scientists and other paleontologists largely stuck to rock and bone collecting, with some progress in extracting ancient chemicals. In 1974 proteins were found in seventy-million-year-old mollusk shells. Amino acids were found later in fossil bones. New techniques were developed, using the reactive nature of immune-system chemistry to identify biological materials in fossils. Collagen was identified, and albumin and other proteins. Hemoglobin was found with archaeological materials, old bones and old tools. As I described earlier, Mary reported in 1999 on the possible presence of hemoglobin in that first dinosaur bone she worked on. Even though creationists have said that she found actual red blood cells, what she and I reported in that paper was the presence of features that looked like they could be fossilized red blood cells. And chemical evidence of hemoglobin that was not definitive.
It became clear to some of us in paleontology that it was time for a change in the way we did our work. We didn’t need to give up the satisfying summer fieldwork, the digging up of the past, but we did need to add new tools. And we needed to go beyond the dissecting microscope, through which we could see fine details of bone structure. We needed to get down to the level of molecules in fossils—and in living things. By the 1980s molecular biologists were already using differences in genes in living creatures to calculate rates of evolution and to date events in evolution. They had developed a new stream of evidence to compete with or supplement the fossils weathering out of the earth.
Clearly there was a vast amount of evolutionary information in the molecules, and paleontology had to adapt to the new world if it was to stay valid. Abelson made his pitch in 1965. Twenty years later, in 1985, Bruce Runnegar of UCLA made a similar call for paleontology to change in an address to a meeting of the Palaeontological Association, which is based in the United Kingdom. And after another twenty years— actually, twenty-seven—three scientists, Kevin J. Peterson of Dartmouth, Roger E. Summons of MIT, and Philip C. Donoghue of the University of Bristol, made another call for change, citing Runnegar’s earlier address.
Each time, of course, the emphasis was different. The emphasis now is heavily on the importance of connecting embryonic development with evolutionary patterns, the essence of evo-devo, which I described briefly in the introduction.
But they also wrote about the possibility of finding ancient DNA and using it to help track evolution. They limited the realistic prospects of DNA recovery to thousands of years, however, with deep time essentially unreachable because of the instability of DNA. They did acknowledge a realistic way of reaching into deep time that doesn’t involve DNA: that is, to search for preserved proteins from tens of millions of years ago. In this they paid explicit tribute to the work done by Mary and her colleagues on ancient collagen.
In the last chapter, I described Mary and her lab tech, Jennifer Wittmeyer, noticing the springiness of the microscopic remnants of sixty-eight-million-year-old fossil bone left after mild acid had been used to leach out the minerals. They thought of collagen. It had been reported in ancient fossils and so seemed a possibility. With nothing left of the rock in which the fossil had been embedded and none of the minerals that had seeped into the bone itself, what was left could be bent and twisted by delicate tweezers under a dissecting microscope.
Collagen injections are now a staple of cosmetic plastic surgery. In reading advertisements and promises for the benefits of one or the other of the several collagen treatments, you can almost hear the subliminal whisper that here is a miracle substance. Well, it may not be a miracle but collagen is certainly a marvel. It is the most common animal protein. Twenty to twenty-five percent of all protein in mammals is collagen. It is a major component in bone and the main component in connective tissue in vertebrates. It is, quite literally, what holds our skeletons together.
It is hard to overstate the importance of proteins in living animals. Collagen, for example, has a structural role. Other proteins transport nutrients, oxygen, and metabolic waste throughout the body. They also promote all sorts of biochemical reactions, regulate growth and other processes, and are important immune-system chemicals. Antibodies are proteins. Proteins are made up of smaller molecules—amino acids—which in turn are made up of atoms of carbon, nitrogen, hydrogen, oxygen. Sulfur is also part of some amino acids.
Not only are proteins so important in the metabolism of the animal body, they offer a coded record of parts of an animal’s DNA. And we know the code—it is the one in which genes are written. The genetic code contained in DNA is usually represented as the four letters
GATC
. The letters refer to guanine, adenine, thymine, and cytosine, chemicals called bases. Each DNA strand is a string of bases that fits together with another string in the famous double helix shape, because the bases link to each other. They do so in a predictable way: G pairs with C and A with T.