Science and the giant rubber duck… He's watching..
This article was originally published in Scientific American.
We are in the small town of Clarkia, Idaho. It’s an ordinary middle-class town by anyone’s standards. I say a ‘town’… just 97 people live here, so as you can imagine the nightlife is usually a little wanting, but other than that it’s pretty normal. Kids go to school; people go to work, mostly civil service jobs, just another place in the Northwest. To most of the people here it’s a pretty unexceptional place to live, but to a certain group of fossil hunters, it is among the most important sites in the world…
Deep within the mudstones of Clarkia reside some of the most awe inspiring fossils of the Miocene period. The fossilised plants and insects here are simply incredible. Hidden for 18 million years, it is not uncommon for leaves to come out of the ground as vibrant a green as the day they fell, before turning black in the oxygen rich air. As early as 1975 Clarkia was put on the map due to its exceptional preservation of cellular and subcellular structures, but we are here for its potential to preserve a particular molecule. The one that controls heredity: DNA.
Fast forward twenty years. It is the early 1990’s. The Reagan years have come to an end, MC Hammer is (unfortunately) still in the charts and the World Wide Web is taking its first tentative steps into existence. This was to be an incredible time for science. These few short years were to see the cloning of Dolly the sheep, the beginnings of the digital revolution and the launch of the Hubble telescope. The advent of Polymerase chain reaction (PCR) was revolutionising the way we do genetics and for the first time it allowed minute amounts of DNA to be increased and analysed in the lab. The world of palaeontology was going through changes of its own and in the 90’s, the next big thing was use PCR to find and amplify the minute quantities of ancient DNA (aDNA) present in fossils.
The potential for ancient DNA (aDNA) preserved in fossils had long fascinated palaeontologists. The oldest DNA sample so far reported was that of a 13,000 year old sloth but up now the field was moving about as slowly as that sloth. The publication of the 1990 novel Jurassic Park changed all that. In the story, scientists use DNA recovered from insects in amber to clone dinosaurs that then run amok on an island off the coast of Costa Rica. It was a smash hit and galvanised public interest in fossils in a way that few works of science fiction have before or since. With it the race for ancient DNA fired its starting pistol.
15 million year old plant leaf found at Clarkia. Similar to the ones Golenberg and his team used for the aDNA extraction.
Back at Clarkia, and a team of scientists headed by Edward M. Golenberg had been interested in using PCR on aDNA for some time. Their aims were of course much more modest than in Jurassic Park, the prize was to use aDNA to track genetic changes throughout evolutionary history and PCR was to bring that within reach. In 1990, Golenberg and his team set about extracting DNA from the 20 million year old Miocene plant fossils. They were ground up, the DNA extracted out. It was a delicate job; PCR is famous for amplifying contaminants, but they managed it. A 770-base pair (bp) DNA fragment had been found. It belonged to Magnolia latahensis, an extinct tree of the Miocene period. The gene was the chloroplast gene rbcL, a gene commonly used in establishing plant lineages, and it was found to differ from living relatives by just 17 base pairs.
This was huge, if it was authentic. It would mean that this DNA had survived intact for nearly 20 million years and come out ready to be used in measuring the genetic differences between extinct and living species. Golenberg seemed to have found an elegant, yet clear cut way to decipher the evolutionary relationships between organisms through evolutionary time.
Soon after, a paper outlined DNA extraction from 25-30 million years old fossilised termite in Oligo-Miocene amber (Mastotermes electrodominicus). The DNA was sequenced, and it too was analysed and found to differ from living species, this time by 10%. It was followed by Chrysomelid beetles in Dominican amber that went through a similar procedure. Both were released around the time Jurassic park was published and the idea exploded. Suddenly reviewed and un-reviewed reports of DNA from ancient fossils were all appearing over the scientific literature. Insects in amber were more popular than ever.
Not everyone was happy. The extractions from amber had resulted in the complete destruction of the specimens and many in the fossil community were uneasy at damaging these ancient fossils. Nevertheless, the extractions continued, and eyes soon turned to a priceless and unique 125 million year old weevil specimen in Lebanese amber. Surely this would be going too far?
Then came a sceptic. Tomas Lindahl, a Swedish born scientist with a background in cancer research entered the picture. He knew a thing or two about DNA preservation and had been keeping a close eye on the race for aDNA. He was doubtful that DNA could have stood the hydrolytic and oxidative forces acting on it for the millions of years boasted. Even under ideal conditions DNA is unlikely to last much longer than 100,000 years, and the sloppy nature of the PCRs being done meant that the ancient DNA samples were more likely just recent contaminants. In 1993 he published a major critical review of the reports outlining the problems associated with aDNA preservation in fossils. Suddenly it was a race against time to prevent more fossils being destroyed for worthless DNA.
Some of the experiments were put to an immediate halt, for others it was too late. On the same day Jurassic Park the movie debuted, a publication was released in Nature; the same journal Lindahl published his warning just two months before. It outlined how the priceless 125 Mya weevil specimen had been cracked open and its DNA sequenced. It was a unique specimen that had been destroyed for nothing.
After Jurassic Park came another brief burst of popularity in amber, but after the Lebanese weevil extraction, the damage was done. Scepticism grew. Attempts to repeat the experiments with the Clarkia and beetle samples found the results were unreplicable and even Golenberg was sceptical of his earlier findings. Lindahl was right. The millions of years old aDNA samples were just contaminants. By the end of the craze around 1996, reports of ancient DNA from fossils were met with widespread scepticism.
This phase in palaeontology’s history is extremely controversial. We lost some incredible fossils for little benefit. Perhaps one thing we can take consolation from is that for all the specimens we lost to these experiments, the aDNA rush increased our understanding not only of amber fossils but the preservation of molecular structures in general. Recent aDNA (<100,000 years) has proven useful in our understanding of evolutionary relationships between species, and without these early tests we may perhaps have not realised how useful these samples could be. The aDNA rush of the 90’s is at an end, but the deciphering of evolutionary history at Clarkia has not.