In 1971, he became the initial editor of the Journal of Molecular Evolution, and in the late 1970s became President of the Linus Pauling Institute (then in 1992 of its successor, the Institute of Molecular Medical Sciences).
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Emanuel Margoliash's first publication of sequence data for cytochrome c allowed comparison of the rates of molecular evolution for different proteins (cytochrome c seemed to evolve faster than hemoglobin), which Zuckerkandl discussed at a 1964 conference in Bruges.
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The notion of the existence of a so-called "molecular clock" was first attributed to Emile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin between different lineages changes roughly linearly with time, as estimated from fossil evidence.