In 1981, Doolittle received some level of notoriety for his article in The CoEvolution Quarterly entitled "Is Nature Really Motherly?". This was a sharp rebuttal of J. E. Lovelock's formulation of the Gaia Theory. Doolittle's article is often cited by Lovelock's critics.
Because of his philosophical musings on the non-existence of an all-encompassing Tree of life, Doolittle has occasionally been cited on Intelligent Design blogs. However, though Doolittle argues that a bifurcating tree is not an adequate metaphor for the evolution of life on earth, he is not a supporter of Intelligent Design. A single common ancestor and tree relating all of life on earth is not a necessary component of the theory of descent with modification, the essence of evolution.
Doolittle is currently involved in a debate about the proper use of function (biology) within evolutionary biology sparked by controversy over the results of the ENCODE consortium stating that 80% of the genome is "functional".[6] He is a supporter of the concept of junk DNA.