Mooney continued this line of inquiry into a fourth book published in 2012. "The Republican Brain" generated some controversy, with his argument compared to eugenics, and Mooney was on "Up with Chris Hayes", "Hardball with Chris Matthews", and "Now with Alex Wagner". From 2010 to 2013, Mooney served as one of the hosts of the Center for Inquiry podcast Point of Inquiry. In June 2013, due to disagreement with Center for Inquiry president Ronald Lindsay over his remarks at a conference focused on women in secularism, Mooney, co-host Indre Viskontas, and producer Adam Isaak announced their resignation from the Point of Inquiry podcast. Mooney, Viskontas, and Isaak started a new podcast at "Mother Jones", titled "Inquiring Minds", and the first episode of the new podcast was released in September 2013. On October 10, 2014, Mooney announced his departure from the Inquiring Minds podcast, in order to pursue a new assignment with the Washington Post. In 2009, he joined the "Center for Collaborative History" at Princeton University for the Spring semester as a visiting associate. From 2009 to 2010, Mooney was a Knight Science Journalism Fellow at the Massachusetts Institute of Technology. In February 2010, Mooney was named a Templeton-Cambridge Journalism Fellow at the Templeton Foundation. In 2007 Mooney and co-author Matthew Nisbet wrote a paper for Science on the topic of "Framing Science". They advocated that scientists and science communicators tailor their messages to account for how the general public filters information based on pre-existing beliefs. Practical examples of this filtering include the impact of fundamental religious beliefs on the topic of evolution and conservative political beliefs on the topic of climate change. Mooney and Nesbit called out popular biologist and author Richard Dawkins, noting his criticism of religion was unlikely to change religious fundamentalist minds and in fact more likely to strengthen their doubt of the scientific data. The framing science proposal created a large, often contentious debate within the online scientific blogging community, though research continues to study the influence of framing. In the book "Unscientific America", Mooney and co-author Sheril Kirshenbaum expressed the concern that some science communicators were pressing the view that one must make a choice between accepting science or accepting religion. Critics of Mooney labelled him as an "accommodationist", or one who seeks to find compatibility between religious and scientific beliefs. Mooney defended his position in a number of publications and podcasts by citing that ongoing scientific studies continues to support the hypothesis that people integrate new information based on their pre-existing worldviews, and that failure to account for this fact will lead to continued failures in science communication.