Biology Reference
In-Depth Information
as the chief of information engineering (a position in which he remains
in 2012).
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In particular, Lipman must have been impressed by Ostell's
vision for integrating and standardizing biological information. As Os-
tell's work and thinking evolved, it became clear to him that the way
data were stored and managed had fundamental signifi cance for bio-
logical practice and knowledge. Developing a new set of tools that he
called a “cyborg software environment,” Ostell attempted to allow the
user to interface directly with the sequence, placing the DNA molecule
at the center of his representation of biological information.
Computer images of DNA sequences have been strongly infl u-
enced by this vision of an isolated object. We sequence a piece
of DNA and read a series of bases as a linear series of bands on
a gel. On paper we represent DNA as a linear series of letters
across a page. Virtually every computer program which oper-
ates on DNA sequences represents a DNA sequence as a linear
series of bytes in memory, just as its representation on a printed
page. However, a typical publication which contains such a lin-
ear series of letters describing a particular DNA always contains
much more information. . . . Most computer programs do not
include any of this information.
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Ostell proposed a new way of representing this extra information that
“tie[d] all annotations to the simple coordinate system of the sequence
itself.”
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The computer now provided a way to order biology and think
about biological problems in which sequences played the central role.
By 1987, as he was fi nishing his thesis, Ostell realized that he had
been involved in “the beginnings of a scientifi c fi eld.”
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Problems that
had been impossibly diffi cult in 1980 were now being solved as a mat-
ter of routine. More importantly, the problems had changed: whereas
Ostell had begun by building individual programs to analyze particular
sequences, by the late 1980s he was tackling the design of “software
environments” that allowed integrated development of tools and large-
scale data sharing that would transcend particular machines and fi le
formats. For the epigraph to the introduction to his thesis, Ostell quoted
Einstein: “Opinions about obviousness are to a certain extent a function
of time.” Given the diffi culties Ostell faced in completing his degree, it is
hard not to read this quotation as a comment on the discipline he had
helped to create: the application of computers to biology had gone from
the “unobvious” to the “obvious.”
But why? What does Ostell's story suggest about the transition?