Tuesday, August 15, 2006

Ice Age DNA

JURASSIC PARK here we come? Not quite, but we might now be able to sequence the genomes of mammoths and even Neanderthals, thanks to a new way to correct the errors in sequencing ancient DNA that are made because it degrades over time.
When Svante Pääbo's group at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, analysed DNA from 50 to 50,000-year-old bone samples from wolves, a single error stood out: one of DNA's "letters", cytosine, had degraded in such a way that sequencing machines misinterpreted it as the letter thymine. Comparison of ancient DNA with a closely related modern species could allow such errors to be identified and corrected (Proceedings of the National Academy of Sciences, DOI: 10.1073 pnas.0605327103).
This opens the way for sequencing species that died out during the last ice age, says Pääbo.


At 6:56 PM, Blogger Seamus said...

This is a really interesting topic. It would be awe-inspiring to see ancient creatures alive again, especially creatures that have long been extinct.

The problem here is that multiple assumptions have to be made in order to accomplish this. Not only that, but these assumptions are certainly based on further assumptions which takes us from any hope of certainty into the realm of nearly pure speculation.

For starters, our knowledge of DNA's structure and function within an organism is so limited that it amounts to nothing but observational commentary. We can look at DNA and compare it with other DNA but we lack any ability to meaningfully manipulate or control it. The most we can do is tamper with it and watch to see what happens.

For example, do we know the exact genotype-phenotype relationship of either modern or extinct wolves? No. Can we take an extinct wolf skeleton and precisely recreate its DNA sequence? HA! We're not even close enough to dignify the phrase "we're not even close". In fact, we don't possess enough knowledge to explain this relationship for any creature on this planet. So much for our knowledge of DNA.

Even with this limitation, we can make some meaningful observations, but we're ultimately comparing things that we don't fully understand.

How do we know that the "only error" was the cytosine-thymine translation/degredation? Until we understand the genome completely, how can we make such a bold conclusion? We could take the DNA of a wolf and, once it does, compare the results some time later, but this doesn't help us with reference to 50,000 year old wolves.

On that note, we are also assuming that we know the exact age of dead or fossilized specimens. This is another area where we simply can not make conclusive judgments. Unless we possessed comprehensive knowledge of earth's entire history, which we do not, we can not objectively state any age beyond what we directly observe and record. We can theorize, maybe even using reliable methods, but these theories remain subjective.

Also, how do we know what DNA is degraded and what DNA is not? Unless we possess the original uncorrupted sample, how do we really know?

How do we know if our old sample is from a wolf that even provided any ancestors? How do we know that this wolf wasn't a hopelessly diseased creature with horribly disfigured DNA?

We don't know any of these things, we can only guess. On top of that, our guesses take place within a larger scheme of assumptions like the assumption of evolution through common descent and random mutation. It can be guaranteed that Paabo plans to both create his questions and validate his answers using this larger assumption.

All we can really say is this:

We are now able to examine DNA from old specimens (though of an age not determinable by objective means). This DNA can be compared to modern specimens (though both the relationship between the specimens and their correlating DNA distinctions only provide more cause for speculation). Essentially all we know is that wolves died and that they had DNA.

Does this mean that we can not take old DNA, implant it into a living wolf, and witness the rebirth of an ancient creature? No, I bet we probably could. But we wouldn't be any better off in our understand of what we had done; we would not be able to determine whether our DNA specimen was accurate or not; and we would not be able to determine whether the birth of this creature was the result of our hard scientific work or the result of sheer dumb luck.


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