What had gone wrong? Everyone seemed to have an opinion on Pauling's pratfall. Peter Pauling thought the problem was his father's strictly chemical approach to DNA. "To my father, nucleic acids were just interesting chemicals, just as sodium chloride is an interesting chemical," he wrote. This was not strictly true, however. Thanks to Morgan's influence at Caltech, Pauling had been interested in genes and heredity ever since the early 1930s. In the late 1940s he had predicted that genes would be found to be a complex of two complementary structures, each of which served as the mold for creating the other. He simply got carried away by his pretty structure and figured that the biological facts would fall into place later.

Chargaff concluded simply that Pauling "failed to take account of my results." Wilkins thought Pauling "just didn't try. He can't really have spent five minutes on the problem himself." Verner Schomaker theorized that Pauling did not put enough people onto the problem to gather sufficient hard data. Pauling had his own thoughts about how he had been led astray. At first, he blamed the x-ray photos he had used. Later, he put more emphasis on misreading DNA's density, the error that led to the idea of a three-chain structure. He also cited his lack of detailed knowledge about the DNA subunits. "If we had also done some work on some purines or pyrimidines, I might well have had the background information that would have pushed me in the right direction. But we didn't do any purine or pyrimidine work."