Scott studied at the University of Missouri - Columbia where she obtained a Ph.D. in anthropology. She served as president of the American Association of Physical Anthropologists from 2000 to 2002. She was elected as a Fellow of the American Association for the Advancement of Science and awarded an honorary D.Sc. by McGill University in 2003 and by Ohio State University in 2005. She is also a fellow of the Committee for the Scientific Investigation of Claims of the Paranormal.
Scott is a secular humanist and in 2003 was one of the signers of Humanism and Its Aspirations, the third humanist manifesto. The NCSE is religiously neutral and has members who hold a variety of faith-based beliefs or no beliefs at all. She and the NCSE are nevertheless criticized for being "atheist" by creationist groups.
In 2004, the National Center for Science Education was represented by Dr. Scott on Penn and Teller's Showtime television show %¤#&!§-! on the episode "Creationism." Dr. Scott offered scientific views about the creationist and intelligent design movements. She noted "it would be unfair to tell students that there is a serious dispute going on among scientists whether evolution took place" because there is no such debate between scientists. She further noted that "a lot of the time the creationists... they'll search through scientific journals and try to pull out something they think demonstrates evolution doesn't work and there is a kind of interesting rationale behind it. Their theology is such that if one thing is wrong with the Bible you have to throw it all out so that's why Genesis has to be interpreted literally. They look at science the same way. If one little piece of the evolutionary puzzle doesn't fit the whole thing has to go." Scott then explained "that's not the way science is done."
Scott is widely considered to be a leading expert on creationism (including intelligent design), as well as one of its strongest opponents. Her book Evolution vs. Creationism: An Introduction was published by Greenwood Press in 2004 and then in paperback by the University of California Press in 2005. It has a foreword by Niles Eldredge.
Scott has taken part in numerous interviews on MSNBC and the Fox News Channel, debating various creationist and Intelligent Design advocates. On May 6, 2005 Scott debated Stephen C. Meyer of the Discovery Institute, on The Big Story with John Gibson. On 29 November 2004, Scott debated astrophysicist Jason Lisle of Answers in Genesis on CNN.
In 2005, Scott was a consultant for the plantiffs in the monumental case Kitzmiller v. Dover Area School District, which originated in Dover, PA. Judge John Jones ruled strongly against teaching intelligent design or creationism in the public schools.