Frank Pastore at Townhall.com extensively cites an article that NRO ran featuring comments from Edward C. Green from Harvard's AIDS Prevention Research Project. (Which makes this a reference to a reference to a reference, I think...)
The most useful paragraph for those who want to defend the pope:
The pope is correct, or put it a better way, the best evidence we
have supports the pope’s comments. He stresses that condoms have been
proven to not be effective at the level of population. There is a
consistent association shown by our best studies, including the
US-funded Demographic Health Surveys, between greater availability and
use of condoms and higher (not lower) HIV-infection rates. This may be
due in part to a phenomenon known as risk compensation, meaning that
when one uses a risk-reduction technology such as condoms, one often
loses the benefit (reduction in risk) by compensating or taking greater
chances than one would take without the risk-reduction technology.
Comments