Tuesday, June 23, 2015

What We're Reading: How to Clone A Mammoth

How to Clone a Mammoth: The Science of De-Extinction, by Beth Shapiro

With the resurrected creatures of Jurassic World poised to devour the summer’s box office, we have, it so happens, just received a book that will help readers understand what is possible and what is improbable in the science of “de-extinction.” It seems fair to address the reader’s interest in resurrected dinosaurs first, since that’s probably what got you to read this review.

Michael Crichton said that his inspiration for Jurassic Park in 1990 came from his learning about the Extinct DNA Study Group at the University of California, a group of scientists pioneering the development of protocols to recover fragments of DNA from dead organisms. Shortly after his book appeared, several scientific groups reported sequencing ancient DNA from insects that had been preserved in amber (much like the premise of Crichton’s book). As it turns out, however, no one has been able to replicate these initial much-publicized results, and it appears that the source of any “recovered” DNA was most likely the result of contamination from living sources.

We have since learned a lot about the speed at which DNA degrades, and the likely effectiveness of amber as a preservative, and Shapiro tells us that “the weight of evidence suggests that ancient DNA is not preserved in amber.” A complete intact genome of a creature that lived 65 million years ago is probably not going to be found, and it is unlikely that any fragments of that DNA are going to be found either. If “dinosaurs” are ever to be resurrected, they will come to exist only as genetically engineered speculations about what we think the phenotype, biology, and behavior of such a creature might have been, not because we were able to “clone” one from DNA derived from a once living animal. And we are not capable of  a genetic engineering project of that sort at this time. So sorry.
Experiments at the University of
Manchester in 2013 offered strong evidence
that DNA is not preserved in amber.
Yes, you can reconstruct the motorbike, but good luck
resurrecting these dinosaur buddies for your raptor pack.

Shapiro uses recent research on the mammoth genome as a way to explain to us the field of paleogenomics (the study of the DNA of extinct animals). We learn how this science works and what it is currently capable of doing.

Beth Shapiro is associate professor of ecology and evolutionary biology at the University of California, Santa Cruz. She is a distinguished scientist, not a natural history journalist, yet she displays here an extraordinary gift for making her field comprehensible to the lay reader. This is some of the finest popular science writing you are likely to encounter. We learn here that the journey from genotype to phenotype (the physical expression of what genes encode) to a viable living organism is something much more complicated than we might suppose. In popular culture, we have come to think of living organisms as the direct result of a DNA “code,” a kind of recipe that, in a mathematical and computational sense, results in the animal we know. If we have the code we have the animal. But the expression of genes is controlled by other genes in an organism’s genome (the epigenome) as well as by its biological and physical environment, and beyond the problem of properly sequencing or engineering a genome and getting a resurrected or reconstructed genome into the nucleus of a cell that can reproduce, there is the problem of finding a suitable surrogate in which that embryo can live and develop.

The issue of setting that animal free into the environment and having it survive and thrive involves yet another set of hurdles that must be faced (in connection with this topic she discusses some of the recent experiments in “re-wilding” that have been done---reintroducing, or introducing for the first time, living species into environments in which they have not recently lived). And with a resurrected species, if we are able to produce a viable “offspring,” there is also the problem of finding some substitute, at least initially, for the vital social and behavioral learning that an animal needs in order to survive, something that would have come from the missing others of his or her species.

We learn in How to Clone a Mammoth, through the example of efforts to resurrect the mammoth, that our resurrection or “de-extinction” of extinct species is not likely to come from cloning cells with the intact genome of an extinct animal (this is unlikely to be found) or from back breeding (trying to breed domesticated cattle back to something like the extinct aurochs of their genetic past) but rather by genomic engineering. For example, in the case of the mammoth, some of the recovered fragmented sections of its genome, may be spliced into the genome of its nearest extant living relative, the Asian elephant, to produce the characteristic physical and adaptive traits of the mammoth. It may look like a mammoth and walk like a mammoth but...no, it’s not exactly a mammoth.

Dolly the sheep, born July 5, 1996, was the first animal to be cloned from an
adult somatic cell using the process of nuclear transfer. Here members of Green-
peace protest against patents on life at the Office of European Patents. The author
discusses briefly some of the moral and legal issues involved in genetic engineering.

The Asian elephant is the closest surviving relative

of the mammoth, and would be the likely surrogate
parent (and major genetic donor) for a genetically
engineered mammoth genome.
Drawing by Kazuhiko Sano.
Of course you may be wondering why, in any event, we would seek to “de-extinct” a species. A discussion of this matter is what begins and ends Shapiro’s How to Clone a Mammoth. She argues that de-extinctions should not be done merely to assuage our guilt at having been the cause of some species' extinction, or to satisfy our curiosity (or to create a theme park!). The reason (and justification) for bringing back to life creatures like the mega-fauna mammoth is because of how that species might revive and restore a vulnerable ecosystem. The value of selective de-extinction is in its use as a tool for preserving and increasing diversity, as a weapon in the war against contemporary extinctions. And with that as the objective, it doesn’t matter that we cannot in a strict sense recreate the particular species, only that we can come up with an facsimile of that species which acts the way the extinct species did and fills its role in the ecosystem.

Shapiro believes this is a viable goal of her work, something essential to conservation of our natural environment, and although she carefully lays out all the many challenges and problems, both scientific and political, that must be faced in order for significant “de-extinctions” to occur, what will impress readers as much as the clarity of her explications is her confidence that these obstacles will be overcome, that significant “de-extinctions” will be possible. In the not-too-distant future, resurrected species will be introduced into contemporary ecological environments. How to Clone a Mammoth shows us that, when it comes to our own species, our great gift may lie not so much in what we are able to imagine, but rather in the unimagined ways in which we are able to make what we imagined become the possible.

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