IT IS TEMPTING TO BELIEVE THAT THE PRINCIPLES, METHODS, AND TOOLS USED
FOR COMPUTATIONAL BIOLOGY THAT WE TAKE FOR GRANTED ARE AS MODERN
AS THE COMPUTERS THAT WE USE THEM ON. BUT THEIR ORIGIN CAN BE TRACED
BACK TO ONE PARTICULAR WOMAN WHO PIONEERED BIOINFORMATICS.
Writers Anthony Nguyen, Cam McMenamie
Originally published 9 March 2021.
1925 - 1983
#ChooseToChallenge this year reminds us that we can choose to seek out and celebrate the achievements of women. In 1965, the very first database for protein sequences was compiled and printed by American physical chemist Dr. Margaret Oakley Dayhoff. Fast forward half a century and you are very likely to find databases based on her work being used day-to-day by both bioinformaticians and scientists alike.
Dayhoff, arguably the pioneer of the bioinformatics field, was responsible for interlacing biochemistry with the rapid advances in computing present during the Cold War. In doing so, she paved the way for new methods and technologies to be developed in order to tackle tough biological puzzles -- methods that have evolved into the modern bioinformatics tools that we are familiar with today.
Born in Philadelphia in 1925, Dayhoff
gained an education in mathematics while
attending the Washington Square College in
New York, and after three years of study,
would go on to also pursue a doctorate in
quantum chemistry at Columbia University.
This would place her at the very forefront of
computing at the time, particularly IBM’s
Watson Scientific Computer Laboratory. The
Watson Lab played an important role in the
development of aerospace defence
technology, and would later be involved with
nuclear missile systems and used by NASA in
the Apollo missions.
Driven by an interest in using computers to improve the speed and accuracy of the scientific calculations in her work, Dayhoff began an uphill journey to lay the seeds for the tools and techniques that we all recognise today in bioinformatics. In her position at the National Biomedical Research Foundation, Dayhoff addressed the problem of comparing and piecing together small peptide sequences to form a complete protein. Using IBM’s new 7090 data processing machine, six times more powerful than previous models, she developed the first protein sequence alignment program named “COMPROTEIN”, which she published in 1962.
Dayhoff also created the one-letter code used
to describe amino acids as they appear in
protein sequences. In the era of punch-cards
and bulky vacuum-tube computers, the
hardware used for piecing together these
protein sequences was limited, and any
opportunity to increase efficiency was
valuable. In an effort to reduce file size out of
necessity, Dayhoff developed the one-letter
code to which biochemists still refer to this
very day.
It is important to note that digital computing and statistics have not always been appreciated in biology. Dayhoff’s work with her colleague, Robert Ledley, at the National Biomedical Research Foundation challenged many scientific “purists” to speak out against the move to incorporate new computer-basedCome along and answer all your burning questions about where your degree can take you whilst gaining insightful advice from industry leaders. Note: no experience studying bioinformatics required, everyone is welcome. speakers on next page > #ChooseToChallenge this year reminds us that we can choose to seek out and celebrate the achievements of women. In 1965, the very first database for protein sequences was compiled and printed by American physical chemist Dr. Margaret Oakley Dayhoff. Fast forward half a century and you are very likely to find databases based on her work being used day-to-day by both bioinformaticians and scientists alike. Dayhoff, arguably the pioneer of the bioinformatics field, was responsible for interlacing biochemistry with the rapid advances in computing present during the Cold War. In doing so, she paved the way for new methods and technologies to be developed in order to tackle tough biological puzzles -- methods that have evolved into the modern bioinformatics tools that we are familiar with today. Born in Philadelphia in 1925, Dayhoff gained an education in mathematics while attending the Washington Square College in New York, and after three years of study, would go on to also pursue a doctorate in quantum chemistry at Columbia University. This would place her at the very forefront of computing at the time, particularly IBM’s Watson Scientific Computer Laboratory. The Watson Lab played an important role in the development of aerospace defence technology, and would later be involved with nuclear missile systems and used by NASA in the Apollo missions. Driven by an interest in using computers to improve the speed and accuracy of the scientific calculations in her work, Dayhoff began an uphill journey to lay the seeds for the tools and techniques that we all recognise today in bioinformatics. In her position at the National Biomedical Research Foundation, Dayhoff addressed the problem of comparing and piecing together small peptide sequences to form a complete protein. Using IBM’s new 7090 data processing machine, six times more powerful than previous models, she developed the first protein sequence alignment program named “COMPROTEIN”, which she published in 1962. Dayhoff also created the one-letter code used to describe amino acids as they appear in protein sequences. In the era of punch-cards and bulky vacuum-tube computers, the hardware used for piecing together these protein sequences was limited, and any opportunity to increase efficiency was valuable. In an effort to reduce file size out of necessity, Dayhoff developed the one-letter code to which biochemists still refer to this very day. It is important to note that digital computing and statistics have not always been appreciated in biology. Dayhoff’s work with her colleague, Robert Ledley, at the National Biomedical Research Foundation challenged many scientific “purists” to speak out against the move to incorporate new computer-based methods into the realm of biology. Despite being an outsider to the challenging culture surrounding her, Dayhoff continued her push to show the true potential of computerised models in answering questions within the life sciences.
Her next step was compiling a list of all known protein sequences at the time, and documenting their variations across species. This work would be published in her “Atlas of Protein Sequence and Structure” in 1965. Later editions were moved to magnetic tape, and the legacy she started would continue through projects including the Protein Data Bank and GenBank. Notably, the reconstruction of phylogenetic trees to describe evolutionary history was made possible through her method of comutational sequence comparison.
Dayhoff’s approach to computing and biology has allowed the expansion of biomedical research to where it is today. Her contributions to bioinformatics are humbling, and are responsible for giving us the tools and methods to continue asking computational questions to answer biological questions -- from the proteins in our blood, peptide sequences in our atmosphere, and the origin of life itself.