[28] Only three months later, "So Much for Destiny: Even Thoughts Can Turn Genes 'On' and 'Off", earned Begley a Front Page Award for Best Column/Editorial from the Newswomen's Club of New York.

[15][23][29] More awards followed for her reporting on a wide variety of topics related to scientific research,[15][23][30][31] including an honorary doctorate of humane letters degree from the University of North Carolina.

[40] Featuring a foreword written by Tenzin Gyatso, the 14th Dalai Lama and a preface by Daniel Goleman, Train Your Mind, Change Your Brain: How a New Science Reveals Our Extraordinary Potential to Transform Ourselves was published in 2007.

[9] This book begins with a description of the visit by scientists from the Mind and Life Institute to the northern Indian town of McLeod Ganj—the home of the 14th Dalai Lama in exile.

The book then explores the ability of various therapeutic treatments to change the functioning of the neural pathways of the brain and the relationship between this research and the traditional meditative practices of Buddhism.

[9] In 2012 Begley again served as a co-author, this time with Richard Davidson, for The Emotional Life of Your Brain: How its Unique Patterns Affect the Way You Think, Feel, and Live — and How You Can Change Them.

[17] "Begley may indeed have a point that too many pap smears are still done after hysterectomy, by simplifying and mocking she completely undermined her point–not to mention showed that she doesn't understand the issues involved.

"[18] This prompted a fresh wave of criticism, such as that expressed by Leslie Becker-Phelps in Psychology Today when she referred to Begley's article as "alarmingly misleading".

[43] Becker-Phelps stressed the intense educational requirements of the field and stated that, "the APA mandates that its member psychologists use their scientific knowledge in their clinical judgments.

"Those skeptics that Begley seems to dismiss have done the hard work for her and other journalists of actually reading the original research, digging down to the salient details, and teasing out the nuances that make all the difference to a proper interpretation of a complex clinical issue.

In a column that appeared in the next issue, Samuelson characterized the article as "'fundamentally misleading' because it focused on the 'peripheral' actions of the 'denial machine' instead of the intractability of man-made warming".