It isn't what you have, it's what you don't have--resistance.
Perhaps the recovered virus DNA researchers are looking at is similar to the modern Yersinia pestis because it is the same critter--just somewhat removed in ancestry. It doesn't take many changes in our own biological functions to acquire a resistance to Yersinia pestis. That alone can explain the difference in symptoms between the Black Plague victims and victims of the virus today. There is good evidence that such a thing occurs. Syphilis is a good example.
Syphilis existed in the Old World, before contact with the Americas, but only in a relatively mild form--it was more of a skin condition then anything else. It wasn't until European contact with the area now know as The Guianas, in South America, that the Old World was re-exposed to syphilis--only this time it was a long-lost cousin of syphilis that had changed over the course of time, the time it took for humanity to spread around the globe and carry it into the New World. Europeans had not developed a resistance to this long-lost cousin and suffered horribly. The symptoms were very different from the syphilis they were used to back home--bone deformities that crushed organs and brains and swiftly killed the host. Killing the host is not always a good evolutionary tactic for long-term survival of a species. Not long after this cousin virus was "brought home", Europeans began to develop resistances to this cousin eventually leading to what we have today--a sexually-transmitted disease that rarely kills it's host, and based on past symptoms, is relatively benign. Jared Diamond wrote extensively on the subject.
There is the distinct possibility that it was not merely a matter of us developing a resistance, but rather the syphilis evolving is such a way as to not kill it's host and thereby increase the chance for survival. Maybe that is all that has happened with Yersinia pestis--it stopped killing it's meal-ticket. A trillion trillion syphilis virii can't ALL be wrong.
All of that being said, I think the researchers are trying to find the specific changes in genes that changed the symptoms of the virus--if they can determine that, they can then take that knowledge and attempt to force such changes in other modern virii and possibly lessen, or end altogether, the symptoms of said virii. It is a little like taking two images of a piece of the night sky, a month apart, and looking for what changed--the changes are more apparent when scaled differently in terms of time. These guys are literally digging up past "images" of Yersinia pestis.
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