In flu season, what price for prevention? That's a question the Philadelphia Inquirer is asking as religious and medical leaders discuss the ethics of the handshake. While there is medical debate about avoiding the gesture -- some doctors say a ban is only minimally effective, others carry hand sanitizer in bottles with them -- some people fear a moral contagion.

Philadelphians' concerns on such questions have deep historic roots. Handshaking was once a common form of greeting in Europe, then displaced in the seventeenth and eighteenth centuries by hat doffing and bowing, only to re-emerge as an allegedly English innovation. But it was the Quakers, first settlers of Philadelphia, whose founder George Fox promoted the gesture as a symbol of the equality of believers -- at a time when authorities considered refusing to doff a hat to magistrates something between heresy and treason.
Youtube actually hosts a virtual festival of conspiracy-theory handshake videos like this.
Despite hygienic reservations, the handshake is a Western custom that has made its way around the world. Influenza did not reverse the trend even after the 1918 pandemic, so it's not going to do so now. Some alternative gestures like elbow bumps make as much sense as rituals of safe blood brotherhood. In fact the small risk makes the clasp even more meaningful. So handshakes, perhaps followed by discreet private disinfection, are here for the duration.
from: http://correspondents.theatlantic.com/edward_tenner/2009/10/getting_a_grippe.php

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