The middle decades of the 20th century saw the rise of molecular biology, and with it an understanding of the chemical nature of genes as sequences of DNA and their relationship, through the genetic code, to protein sequences. At the same time, increasingly powerful techniques for analyzing proteins and sequencing, brought biochemical phenomena into realm of the synthetic theory of evolution. In the early 1960s, biochemists Linus Pauling and Emile Zuckerkandl proposed the molecular clock hypothesis: that sequence differences between homologous proteins could be used to calculate the time since two species diverged. By 1969, Motoo Kimura and others provided a theoretical basis for the molecular clock, arguing that most genetic mutations are neither harmful nor helpful and that genetic drift, rather than natural selection, is responsible for a large portion of genetic change. Studies of protein differences within species also brought molecular data to bear on population genetics by providing estimates of the level of heterozygosity in natural populations.
From the early 1960s, molecular biology was increasingly seen as a threat to the traditional core of evolutionary biology. Established evolutionary biologists were extremely sceptical of molecular approaches, especially when it came to the connection (or lack thereof) to natural selection. The molecular clock hypothesis and the neutral theory were particularly controversial.