Tuesday, November 13, 2007

To Err Is Human, to Forgive...Human

In September, two researchers from Penn State University published about their new way to capture genetic material from extinct animals. I heard about it at the beginning of that month, when the information was released prior to the publication of a paper in Science, and have been talking about it with a friend of mine for two months now.

The thing that's unusual about this new method is that previously, with DNA samples (both nuclear and mitochondrial) from muscle and bone, there was so much cell degradation and genetic interference from bacteria and so on that it was difficult and time-consuming to find a clean enough sample to be able to get a good chunk of sequencing out of it. Sifting through the remains of mammoths and other extinct animals was so complicated and expensive that it would sometimes take six years for a single study of a single bit of mammoth. Think of it: you get this little chunk of animal, and then you have to figure out which of it is that animal and which of it is bacteria, viruses, the drool from the thing that killed and ate it, the bugs and things that broke it down after death, or whatever.

Not only that, but previously the process of saving mitochondrial DNA had been extremely difficult and fragmented, mitochondria being the driver of a number of cellular activities such as cell signaling (which includes communication between an embryo and the uterus), cellular differentiation, and control of a cell's cycles and growth.

Now, however, Stephan C. Schuster and Webb Miller have - nearly by accident - discovered a much faster, cleaner way: they take the DNA from hair.

For a long time it was thought that hair was a poor way to collect DNA because they had to gather from the few cells still clinging to the roots of the hair. The rest of the hair appeared to be dead material. But Mr. Schuster and Mr. Miller found that actually, the core of a hair is, essentially DNA; and that the material surrounding it on the outside of the hair (the keratin) is actually like a natural plastic, in effect laminating that DNA so that it remains quite pure. All they had to do was to wash the hairs very thoroughly, to remove any environmental contaminants, and then essentially crack open the "plastic" protection, and they had an instant cache of genome-building materials - plus a "remarkably enriched [source of] mitochondrial DNA, the special type of DNA frequently used to measure the genetic diversity of a population."

Not only is the DNA cleaner, but this means much, much shorter turnaround times: "In contrast [to previous methods], Miller said, 'Once I get the data from the genome sequencer, it takes only five minutes to assemble the entire mitochondrial genome.' The discovery... demonstrates that hair clippings can give researchers enormous power and efficiency for divining the genetic makeup of ancient species, " says the press release article from Penn State. The pair's work with hairs as old as 50,000 years has already set off a complete genome sequencing for mammoths. There is some discussion in the scientific community of the possibility of cloning a mammoth, which could be gestated by a modern elephant.

This brings up a lot of ideas for my friend and I. If it becomes this easy to sequence a genome for an extinct animal, and insert it into a modern animal's womb, then what's to stop scientists and entrepeneurs from re-creating extinct animals - the dodo, the passenger pigeon - and creating a wild-animal park a la Jurassic park, full of previously extinct animals? What's to stop us from simply fixing our previous mistakes, and putting dodos back on the island where we so gleefully slaughtered them, or re-introducing the many Amazon species which have been lost?

All those museum specimens which have some tiny portion of hair or feathers left - think of how much richness and variety of DNA is now available for us to sequence! We can be gods on our own earth.

Which brings me to the next point, which my obnoxious mind immediately jumped to, beyond the fun and joy my friend was imagining. What is to keep us from saying to ourselves, much as we do about dropping a dish, or about not buying a car with low gas mileage: oh, dear, we've made that species extinct again. Oops! Well, we'll just sequence it and start over. No one will mind...except, well, darn, the funding ran out. We'll do it later. In the meantime, look over there -

It smacks of the Godfather: "Bless me Father, for I have sinned", followed by the inevitable "Say (or compile) three gene sequences and don't forget to say your prayers," and the feeling that we have done our penances so we are all right to go out and kill again.

The thing that is so impressive to my friend is the idea that within his lifetime, he may get to see a wooly mammoth walking around. That right there makes him nearly want to weep, because it's like magic. It's like imaginary things coming to life, like all the things he thought would be the future when he was a kid, and was disappointed by (where's our jet-packs, dammit?). It's all the stuff we've lost, coming back to us - a universe of new exploration, new knowledge. It's a true Wonder, come to us in this time, when we are alive. And he's right; it is. It is really like a miracle. I have to say, the thing, for me, that would make me weep, would be a whole flock of dodos, peacefully minding their own business somewhere. That would be something to see.

But with every marvel comes a warning: the fairies are magic, but they can be dangerous too. Don't trust them too much, or you may fall asleep and wake to find everything you love has gone.

Image: Andy Goldsworthy


D said...

Another problem would be where to introduce that coveted sabretooth tiger without upsetting whatever fragile balance is already in place. Artificial islands? Strictly for the zoo and cirkus?

Would their old genome make them easy prey for every illness that cropped up since they disappeared?

I didn't know this, thank you for the link and the information. Well written, as always.

Anonymous said...

Two things wrong.
First, the researchers are focusing on mitochondrial DNA, which is not the complete genome of an organism. For that you need nuclear DNA. You would not be able to clone an organism using mDNA alone. The nuclear DNA may be present in hair, but the story doesn't specify.
Second, cloning a single organism does not give you a viable population. The lack of genetic diversity would mean that the resulting organisms probably would not be able to maintain a healthy population for long. This is known as the bottleneck effect. Cheetahs, for example, have very low genetic diversity because they went through a population bottleneck, probably due to hunting. They are susceptible to large number of genetic and other diseases as a result. Mutation might eventually be able to increase the diversity of a re-created species, but it would take a long time. More likely is that these animals would never be anything more than zoo specimens.

Heather McDougal said...

Good points.

May I ask if you clicked on the link to the press release? The article there says that they actually are working on nuclear DNA as well, but that the mDNA was of particular interest because it is more present than in other types of tissues. The article also states that for the mammoths, at least, they have hair samples from a number of different animals from different time periods, and that one of the interesting things for them is to compare the mDNA across the different samples.

Unfortunately, since this is a blog not focused on the actual details of scientific method but on the ideas surrounding science, wonder, and other things, I don't want to re-describe what is discussed in detail elsewhere. So I hope you forgive me if I wasn't as clear as I should have been! I'll try to make the link clearer.

Anonymous said...

Another issue is that we can only guess at how much of an extinct animal's behavior is instinct, and how much is learned from its parents and/or social group. Some species are born with all the tools they need to survive, inherent ability to defend themselves, find food, find mates, etc. But others need to learn by observation and practice. This is a problem that we already face when trying to breed and raise endangered species to be released into the wild, and these are animals that we already know quite a bit about. The problem will be multiplied exponentially when we are dealing with a species that have never been observed by modern mankind - we won't know what they should/can eat, or what their proper social behavior is like, or anything like that.

All that said, I deeply hope they can bring a woolly mammoth to life, because it really would be magical.

Anonymous said...

Your point about nuclear DNA is taken, but my point about species diversity still stands. Samples from several dozen animals would be insufficient. Cheetahs have been in dire straits because their population bottlenecked at a few thousand animals. This is why bringing species back from the brink of extinction is so difficult.

Heather McDougal said...

Very true.

In the case of mammoths, it could be that elephants are close enough to the species that any learned behaviors could be taught by its "mother". But who's to say? It could also be that mammoths have completely different needs. And then again, it could end with them simply superimposing elephant sociality onto their own mammoth personalities.

It's a bit like a Pandora's Box, isn't it? Which is exactly why we mustn't get carried away. My friend is an eternal optimist, and I, well, I want there to be magic in the world, so I'm rooting for any wonder that can come out of it. But I'm also a bit wary...so much that is new in science gets put to uses which ultimately don't benefit anyone. And so often science as a profession/community/world view believes too strongly in itself.

However, I always try to refrain from walking down the street with a sandwich board on that says "Beware! The end of the world is Nigh!" It's not very helpful, and doesn't change anything.

Heather McDougal said...

Whoop! Getting out of order here.

About diversity: you're right, of course. I suspect that bringing them back would be nothing more than a scientific curiosity, truly a theme-park exercise.

D said...

Yet such a wonderful theme-park experience it would be. Maybe one extinct species brought back as a helpless specimen with no chance of survival could trult spark some awareness of the species close to extinction now.

Actually, I'm not sure why I want the panda, I just know it would be sad if they disappeared (ok, chances are will be is more appropriate since it seems a certainty).

Marielle said...

I was thinking about the fragile environment issue as well. If you introduce a new species, especially a long-exctinct one, into a thriving environment, there's no telling how it will affect the organisms living there, nor what affect those bacteria, fungi, plants and animals will have on our new (old) species.

But, as an optimist, I believe that thorough research and trial-and-error studies, which may one day be possible, could help scientists get around these issues, at least on a case-by-case basis.

This is the first time I've commented, but I've been a reader for a while and I really enjoy reading your blog. (Don't read mine...it's for a class project and it is terrible).