Caltech Physicist Sean Carroll has a level-headed response to the Templeton Foundation, and scientists who take money directly from it.
And that’s the real reason why I don’t want to be involved directly with Templeton. It’s not a matter of ethical compromise; it’s simply a matter of sending the wrong message. Any time respectable scientists take money from Templeton, they lend their respectability — even if only implicitly — to the idea that science and religion are just different paths to the same ultimate truth. That’s not something I want to do. If other people feel differently, that’s for them and their consciences, not something that is going to cause me to shun them.
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It’s [shift in perspective from theism to atheism] the one piece of scientific/philosophical knowledge that could really change people’s lives. So in my view, we have a responsibility to get the word out — to not be wishy-washy on the question of religion as a way of knowing, but to be clear and direct and loud about how reality really works. And when we blur the lines between science and religion, or seem to contribute to their blurring or even just not minding very much when other people blur them, we do the world a grave disservice.
Interesting comments, including some from the evolutionary biologist, Jerry Coyne, author of “Why Evolution is True”

A small sideline to this issue, I’m on Carroll’s side (not as purist as Coyne), but another thing in the mix: even if you are a believer (and I’m not), “religion” is not one undifferentiated mass of work. Different religions believe profoundly different things about the nature of reality (means and ends). Just as Templeton, to me, is off-base to believe in the potential synthesis of scientific and religious ways of thinking, the “all religions are streams heading to the same sea,” idea, although romantically appealing, is also flawed.