I posted the following as a response to his article, but thought it would be useful to re-post here for posterity.
Tom, thanks for the link. I'm not going to attempt to address all of your assertions in the article, but I'll say that your summary idea that human morality can be easily explained as an evolved survival instinct suffers in the light of others' claims that humanity's war-like nature can be easily explained as an evolved survival instinct. So which is it, are humans moral because it promotes survival of the fittest, or is that why they're war-like? You can't have it both ways. The "hard-core atheists" were much more consistent in the application of their faith by acknowledging that it leads to nihilism.
In regards to whether or not athiesm/naturalism qualifies as a faith, let's look at the surprising discovery of red blood cells and still-flexible blood vessels in dinosaur fossils a few years ago. Why was this surprising? Because the hemoglobin in the red blood cells should have broken down within thousands of years, but it was found in bones claimeded to be millions of years old. But what was the scientists reaction to this discovery? Did they question the evolutionary dogma that dinosaurs died out 65 million years ago? No, by a leap of blind faith, they assumed there must be some way to preserve hemoglobin for millions of years. These scientists demonstrated an amazing knack for ignoring the evidence against millions of years due to their creedal assertion that evolution requires those millions of years. And gives the lie to your claim that "Naturalists’ commitment to science in this regard isn’t a matter of faith, it’s based on experience – the widely shared experience that beliefs about the world based in science are generally more reliable than those that aren’t."
For more on the dinosaur red blood cells story, read this follow-up article that refutes claims that what was found was not actual hemoglobin and red blood cells.
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