SA: So far there is no empirical evidence to support the hyperdisease hypothesis. What are the chances that you¿re going to find a smoking gun¿a microbe¿in ancient megafaunal remains?

RM: I do not expect to be successful in the short term. There are both practical and theoretical reasons for that. The very practical one is that we¿re working with ancient DNA, which has a very poor reputation scientifically because of the enormous claims that were once made for retrieving DNA from dinosaurs and from inclusions in amber early in the '90s. None of these results could be replicated independently, and there¿s therefore a prevalent belief that most work in ancient DNA is so riddled with error and the possibility of contamination that it¿s not worth doing. Unfortunately it¿s one of the few approaches we can take in respect to trying to find evidence of pathogens, so we¿re going to continue doing it. But what that means is that every experiment we do has to be cleaner than clean. We have to be able to stand behind every result that we think is good, which means endlessly redoing experiments and sending samples to independent labs to see whether they can replicate our results. As a result it¿s a slow operation, but there¿s no other way of doing it¿we want to be right.

Image: CLARE FLEMMING IN THE LAB. Alex Greenwood prepares extractions from the mammoth bone tissue for ancient DNA studies.

In principle (and here¿s the theoretical part) there is no reason, if pathogenic material is present in a well-preserved bone, that we shouldn¿t be able to visualize what¿s there by PCR [the polymerase chain reaction]. Because the technique is so sensitive, anything that is in your sample will be replicated. If you have the right fishing tools, in terms of primers, you should be able to get a good length of sequence and determine whether it¿s one that you¿re interested in dealing with, which in our case would be a sequence from an existing virus, for example. The troubling detail is copy number. People have an easy time doing mitochondrial DNA, from the point of view of getting results, because whereas in the average cell you have only one nucleus and therefore only one copy of the complete nuclear genome, in any such cell you might have a thousand mitochondria. So just from a statistical point of view, the chances are that if anything gets replicated it¿ll be mitochondrial DNA. For a long time people didn¿t think it would be possible to get nuclear DNA from fossil material, but my colleague Alex Greenwood [at the American Museum of Natural History], who works with me on the disease hypothesis, was able to do exactly that with mammoth material a couple of years ago, and we have now consistently done it with mammoth specimens that we¿re working on for the hyperdisease work. This means that our techniques are at least good enough to go out and get material of infectious organisms that might be there in very low copy number. In principle we think we should be able to do it. The techniques exist, at least primitively, and we have expectations that there will be great improvements in what we can do with ancient DNA in the next decade or so.

One of the difficulties we¿ve had with PCR work is that in order to be successful you¿ve got to know what you¿re after before you do it, because it¿s all in the primer design. And we don¿t know for a verifiable fact what kinds of pathogens we¿re even dealing with, so it¿s a real needle in a haystack kind of problem. To deal with this situation we are trying some other approaches that would help us prior to the actual PCR-ing. One of these would be to use immunological approaches, which are used diagnostically all the time in the case of human diseases. If you want to know whether someone has sleeping sickness, or syphilis, for example, there are immunological tests that you can utilize that will give you a very clear yes/no answer because of the specificity of what¿s known as antibody/antigen reactions. If you get a positive result, it is meaningful because of the specificity of these reactions. Or if you get nothing, that is also meaningful¿it means that the antigen [and therefore probably the microbe] you are probing for is simply not there.

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