In the late-1960s, she married philosopher and author David Berlinski and had two children, daughter Claire (born 1968) and son Mischa (born 1973), both of whom are published authors.
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In May 2010, the Discovery Institute released a free 105 page eBook titled Signature of Controversy: Responses to Critics of Signature in the Cell edited by Klinghoffer with chapters by Discovery Institute fellows David Berlinski, Casey Luskin, Stephen C. Meyer, Paul Nelson, Jay Richards and Richard Sternberg.