Monday, September 19, 2011

Our most intimate inmates

kw: book reviews, nonfiction, viruses, evolution

Either physician and researcher Frank Ryan and the colleagues he interviewed while writing Virolution are on the brilliant forefront of evolutionary discoveries, or they are stark, staring mad. I tend to believe the former is true. But consider what the book claims:
  • Viruses are primarily beneficial, even necessary for our existence, and that of all life.
  • Viruses that reside in our genome mediate the development of our bodily organs.
  • While "vertebrate DNA" makes up 1.5% of the total human genome, ready-to-activate viruses make up 6-7%, and partial viruses make up another 35-40% (more are being determined all the time).
  • These partial viruses are experts at moving about, and such "jumping genes" are huge agents of genetic change, greatly increasing the variation that natural selection depends upon to produce new species.
  • Viral symbiosis and mutualism are responsible for our continued health and longevity.
  • Virus infections and diseases are an unfortunate side effect of the ages-long interplay of viral and animal (and plant) DNA.
I don't know about you, but I find some of these ideas rather unsettling. I remember predicting, nearly twenty years ago, that within a few generations, ever person still living on Earth would be either immune to or tolerant of HIV infection. It seems Dr. Ryan would agree, and moreover, he would further predict that HIV-1 and -2 would become integrated into our genome, as at least 98,000 other retroviruses have done in past ages, going back to the first cells. And that figure is actually a tip-of-the-iceberg amount; each virus has infected numerous times. The number of complete virus genomes and genome fragments in the DNA of every creature is several million.

Well, I hope I got all that correct. The book is fascinating reading. It points to HIV and to a virus that is currently decimating koalas as examples of early stages in the integration of a new virus into the genome. This ruthless culling made me recall something else I read in an article many years ago.

I don't recall author or title, but the premise was this: Viruses descend from a toolbox of small, initially non-living DNA "machines", created to facilitate regulation of DNA in multi-cellular creatures. They became the original "Frankenstein monsters", having attained great powers to modify DNA and create copies of themselves. Achieving a kind of quasi-life, they did what life does, and began to reproduce selfishly. They have become the prototype of the "gray goo" that some researchers fear will result if we produce self-reproducing nanomachines. The fact that we have not become a world of gray goo, AKA virus fodder, is that, in self-defense, early control mechanisms evolved just quickly enough into a more robust and active immune system. This virus-versus-immune system arms race has now gone on for about two billion years.

Whichever way viruses arose, Frank Ryan's claim is that they are primarily symbiotic with us and with all plants, animals and fungi. In a late chapter in the book, he outlines epigenetics, the subject of a book I reviewed two weeks ago. I saw no obvious connection between epigenetics and virology, but if I understood right, the various mechanisms of DNA control that we lump under epigenetics also activate and deactivate retroviral genomes that are so intimately involved in our development from a fertilized ovum to a grown adult, and throughout our lives.

Dr. Ryan's interest is not only academic. He is a physician, with a doctor's practicality. Pathological cases and other problems help researchers figure out the difference between things working right and working wrong, or not working at all. Diseases highlight areas that need to be understood. Pathologies that were once thought to be this or that "bad gene" are now often shown to be problems of development, or or epigenetic mistakes, or of a DNA-virus interaction gone wrong. Once they are better understood, therapies that attack the proper cause can be developed. Because epigenetics is so variable from person to person, because of our differing experiences, this will inevitably lead to very personalized medicine, almost the way my eyeglasses will only work with my eyes, and you need your own pair with different parameters, if you need any at all. If future DNA-HERV-epigenetic medicine can be done at acceptable cost, the possibilities are breathtaking.

The book is written at a bit higher level than many popularizations, but I didn't find the reading itself to be difficult. The concepts, however, are so mind-blowing that I'll have to set the book aside a while and re-read it later to be sure my impressions are in any way accurate.

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