Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s Atlas of Protein Sequence and Structure, 1954–1965

Abstract

Collecting, comparing, and computing molecular sequences are among the most prevalent practices in contemporary biological research. They represent a specific way of producing knowledge. This paper explores the historical development of these practices, focusing on the work of Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley, who produced the first computer-based collection of protein sequences, published in book format in 1965 as the Atlas of Protein Sequence and Structure. While these practices are generally associated with the rise of molecular evolution in the 1960s, this paper shows that they grew out of research agendas from the previous decade, including the biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code. It also shows how computers became essential for the handling and analysis of sequence data. Finally, this paper reflects on the relationships between experimenting and collecting as two distinct "ways of knowing" that were essential for the transformation of the life sciences in the twentieth century.

A Tale of Two Crocoducks: Creationist Misuses of Molecular Evolution

“…The ubiquitous presence of closely related cytochromes c in virtually all forms of life and their relatively short sequences of approximately 100-120 amino acids would eventually make comparisons possible between almost any pair of species. Hans Tuppy began sequencing the active site of cytochrome c proteins during the 1950s and in 1961 he collaborated with Emanuel Margoliash, Emil Smith, and Gunther Kreil to publish the full amino acid sequence for horse cytochrome c (Margoliash et al 1961;Strasser 2010). Other complete cytochrome c sequences soon were available for comparisons.…”

“…Primarily due to the efforts of Margaret Dayhoff and Richard Eck, the 1965 Atlas included all protein amino acid sequences available at that time (Strasser 2010). For cytochrome c these included human, chicken, horse, pig, tuna fish, silkworm moth and rattlesnake as well as cytochrome c-551 for the bacterium Pseudomonas and cytochrome c 2 for the partially sequenced purple photosynthetic bacterium Rhodospirillum rubrum.…”

Bioinformatic resources for the investigation of proteins and proteomes

“…Protein three-dimensional structures, together with amino acid and nucleotide sequences, suggested scientists to collect such information within ordered archives, and to generate software able to manage the data and elaborate new information. Scientists of the protein world are indebted to the pioneering work of Margaret Dayhoff in this field [1]. Computers, fifty years ago were only present in few laboratories.…”

Inscribing a discipline: tensions in the field of bioinformatics

“…Others identify pioneering work in protein research in the 1960s as a starting point (Smith 1990). In particular, the protein sequencing work of Margaret Dayhoff is celebrated as the first attempt to use computers to solve biological problems (Dayhoff 1969;Persidis 1999;Strasser 2010). The late 1960s and 1970s also saw significant developments in the Advanced Research Projects Agency Network (ARPAnet) project -the precursor to the Internet.…”