Bioinformatics and Bio-logics http://0-muse.jhu.edu.opac.sfsu.edu/journals/postmodern_culture/v013/13....

Eugene Thacker
© 2003
PMC 13.2

Point-and-Click Biology

1. It is often noted that progress in biotechnology research is as

much a technological feat as a medical one. The field of
"bioinformatics" is exemplary here, since it is playing a significant
role in the various genome projects, the study of stem cells, gene
targeting and drug development, medical diagnostics, and genetic
medicine generally. Bioinformatics may simply be described as the
application of computer science to molecular biology research. The
development of biological databases (many of them online), gene
sequencing computers, computer languages (such as XML-based
standards), and a wide array of software tools (from pattern-
matching algorithms to data mining agents), are all examples of
innovations by means of which bioinformatics is transforming the
traditional molecular biology laboratory. Some especially optimistic
reports on these developments have suggested that the "wet" lab of
traditional biology is being replaced by the "dry" lab of "point-
and-click biology."1

Figure 1: Production Sequencing Facility

at Department of Energy's Joint Genome Institute in Walnut Creek, CA

2. While current uses of bioinformatics are mostly pragmatic

(technology-as-tool) and instrumental (forms of intellectual
property and patenting), the issues which bioinformatics raises are
simultaneously philosophical and technical. These issues have

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already begun to be explored in a growing body of critical work

that approaches genetics and biotechnology from the perspective of
language, textuality, and the various scripting tropes within
molecular biology. The approach taken here, however, will be
different. While critiques of molecular biology-as-text can
effectively illustrate the ways in which bodies, texts, and contexts
are always intertwined, I aim to interrogate the philosophical claims
made by the techniques and technologies that molecular biotech
designs for itself. Such an approach requires an inquiry into the
materialist ontology that "informs" fields such as bioinformatics,
managing as it does the relationships between the in vivo, the in
vitro, and the in silico.

3. Such questions have to do with how the intersection of genetic

and computer codes is transforming the very definition of "the
biological"--not only within bioinformatics but within molecular
biotechnology as a whole. Thus, when we speak of the intersections
of genetic and computer codes, we are not discussing the
relationships between body and text, or material and semiotic
registers, for this belies the complex ways in which "the body" has
been enframed by genetics and biotechnology in recent years.

4. What follows is a critical analysis of several types of

bioinformatics systems, emphasizing how the technical details of
software and programming are indissociable from these larger
philosophical questions of biological "life." The argument that will
be made is that bioinformatics is much more than simply the
"computerization" of genetics and molecular biology; it forms a set
of practices that instantiate ontological claims about the ways in
which the relationships between materiality and data, genetic and
computer codes, are being transformed through biotech research.

Bioinformatics in a Nutshell

5. The first computer databases used for biological research were

closely aligned with the first attempts to analyze and sequence
proteins.2 In the mid-1950s, the then-emerging field of molecular
biology saw the first published research articles on DNA and
protein sequences from a range of model organisms, including
yeast, the roundworm, and the Drosophila fruit fly.3 From a
bioinformatics perspective, this research can be said to have been
instrumental in identifying a unique type of practice in biology: the
"databasing" of living organisms at the molecular level. Though
these examples do not involve computers, they do adopt an
informatic approach in which, using wet lab procedures, the
organism is transformed into an organization of sequence data, a set
of strings of DNA or amino acids.

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6. Because most of this sequence data was related to protein

molecules (structural data derived from X-ray crystallography), the
first computer databases for molecular biology were built in the
1970s (Protein Data Bank) and 1980s (SWISS-PROT database).4
Bioinformatics was, however, given its greatest boost from the
Human Genome Project (HGP) in its originary conception, a joint
Department of Energy (DoE) and National Institutes of Health
(NIH) sponsored endeavor based in the U.S. and initiated in
1989-90.5 The HGP went beyond the single-study sequencing of a
bacteria, or the derivation of structural data of a single protein. It
redefined the field, not only positing a universality to the genome,
but also implying that a knowledge of the genome could occur only
at this particular moment, when computing technologies reached a
level at which large amounts of data could be dynamically archived
and analyzed. Automated gene sequencing computers, advanced
robotics, high-capacity computer database arrays, computer
networking, and (often proprietary) genome analysis software were
just some of the computing technologies employed in the human
genome project. In a sense, the HGP put to itself the problem of
both regarding the organism itself as a database and porting that
database from one medium (the living cell) into another (the
computer database).6

Figure 2: Commercial bioinformatics application by Celera Genomics

7. At this juncture it is important to make a brief historical aside,

and that is that bioinformatics is unthinkable without a discourse
concerning DNA-as-information. As Lily Kay has effectively
shown, the notion of the "genetic code"--and indeed of molecular
genetics itself--emerges through a cross-pollination with the
discourses of cybernetics, information theory, and early computer
science during the post-war era, long before computing technology
was thought of as being useful to molecular biology research.7

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Though there was no definitive formulation of what exactly genetic

"information" was (and is), the very possibility of an
interdisciplinary influence itself conditions bioinformatics'
possibility of later technically materializing the genome itself as a
database.

8. Against this discursive backdrop, we can make several points in

extending Kay's historiography in relation to contemporary
bioinformatics. One is that, while earlier paradigms in molecular
biology were, according to Kay, largely concerned with defining
and deciphering DNA as a "code," contemporary molecular
genetics and biotech research is predominantly concerned with the
functionality of living cells and genomes as computers in their own
right.8 What this means is that contemporary biotech is constituted
by both a "control principle" and a "storage principle," which are
seen to inhere functionally within biological organization itself. If
the control principle derives from genetic engineering and
recombinant DNA techniques, the storage principle is derived from
the human genome project. Both can be seen to operate within
bioinformatics and biotech research today.9

Figure 3: The genetic code.

Triplet codons each code for a particular amino acid.

9. To give an idea of what contemporary bioinformatics

researchers do, we can briefly consider one technique. Among the

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most common techniques employed in current bioinformatics

research is the sequence alignment, a technique which can lead to
the identification and characterization of specific molecules (e.g.,
gene targeting for drug development), and even the prediction of
the production and interaction of molecules (e.g., gene prediction
for studying protein synthesis).10 Also referred to as "pairwise
sequence alignment," this simply involves comparing one sequence
(DNA or protein code) against a database for possible matches or
near-matches (called "homologs"). Doing this involves an
interactive pattern-matching routine, compared against several
"reading frames" (depending on where one starts the comparison
along the sequence), a task to which computer systems are well
attuned. Bioinformatics tools perform such pattern-matching
analyses through algorithms which accept an input sequence, and
then access one or more databases to search for close matches.11
What should be noted, however, is that despite this breadth of
expandability and application, bioinformatics tools are often geared
toward a limited number of ends: the isolation of candidate genes or
proteins for medical-genetic diagnostics, drug development, or
gene-based therapies.

Bio-logic

10. However, if bioinformatics is simply the use of computer

technologies to analyze strings, access online databases, and
perform computational predictions, one question may beg asking:
aren't we simply dealing with data, data that has very little to do
with the "body itself"? In many senses we are dealing with data,
and it is precisely the relation of that data to particularized bodies
which bioinformatics materializes through its practices. We can
begin to address this question of "just data" by asking another
question: when we hear talk about "biological data" in relation to
bioinformatics and related fields, what exactly is meant by this?

11. On one level, biological data is indeed nothing but computer

code. The majority of biological databases store not biological
nucleic acids, amino acids, enzymes, or entire cells, but rather
strings of data which, depending on one's perspective, are either
abstractions, representations, or indices of actual biomolecules and
cells. In computer programming terminology, "strings" are simply
any linear sequence of characters, which may be numbers, letters,
symbols, or combinations thereof. Programs that perform various
string manipulations can carry out a wide array of operations based
on combinatorial principles applied to the same string. The most
familiar type of string manipulation takes place when we edit text.
In writing email, for instance, the text we type into the computer
must be encoded into a format that can be transmitted across a

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network. The phrase "in writing email, for instance" must be

translated into a lower-level computer language of numbers, each
group of numbers representing letters in the sequence of the
sentence. At an even more fundamental level, those numbers must
themselves be represented by a binary code of zeros and ones,
which are themselves translated as pulses of light along a fiber optic
cable (in the case of email) or within the micro-circuitry of a
computer processor (in the case of word processing).

12. In text manipulations such as writing email or word processing, a

common encoding standard is known as ASCII, or the American
Standard Code for Information Interchange. ASCII was established
by the American Standards Association in the 1960s, along with the
development of the Internet and the business mainframe computer,
as a means of standardizing the translation of English-language
characters on computers. ASCII is an "8-bit" code, in that a group
of eight ones and zeros represents a certain number (such as "112"),
which itself represents a letter (such as lower case "p"). Therefore,
in the phrase "in writing email, for instance" each character--letters,
punctuation, and spaces--is coded for by a number designated by
the ASCII standard.12

13. How does this relate to molecular biotechnology and the

biomolecular body? As we've noted, most biological databases,
such as those housing the human genome, are really just files which
contain long strings of letters: As, Ts, Cs, and Gs, in the case of a
nucleotide database. When news reports talk about the "race to
map the human genome," what they are actually referring to is the
endeavor to convert the order of the sequence of DNA molecules in
the chromosomes in the cell to a database of digital strings in a
computer. Although the structural properties of DNA are
understood to play an important part in the processes of
transcription and translation in the cell, for a number of years the
main area of focus in genetics and biotech has, of course, been on
DNA and "genes." In this focus, of primary concern is how the
specific order of the string of DNA sequence plays a part in the
production of certain proteins, or in the regulation of other genes.
Because sequence is the center of attention, this also means that,
for analytical purposes, the densely coiled, three-dimensional,
"wet" DNA in the cell must be converted into a linear string of
data. Since nucleotide sequences have traditionally been
represented by the letter of their bases (Adenine, Cytosine,
Guanine, Thymine), ASCII provides a suitable encoding scheme for
long strings of letters. To make this relationship clearer, we can use
a table:

DNA A T C G

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ASCII 65 84 67 71

Binary 01000001 01010100 01000011 01000111

14. In the same way that English-language characters are encoded

by ASCII, the representational schemes of molecular biology are
here also encoded as ASCII numbers, which are themselves binary
digits. At the level of binary digits, the level of "machine language,"
the genetic code is therefore a string of ones and zeros like any
other type of data. Similarly, a database file containing a genetic
sequence is read from ASCII numbers and presented as long linear
strings of four letters (and can even be opened in a word processing
application). Therefore, when, in genetics textbooks, we see DNA
diagrammed as a string of beads marked "A-T" or "C-G," what we
are looking at is both a representation of a biomolecule and a
schematic of a string of data in a computer database.

15. Is that all that biological data is? If we take this approach--that
is, that biological data is a quantitative abstraction of a "real" thing,
a mode of textuality similar to language itself--then we are indeed
left with the conclusion that biological data, and bioinformatics, is
nothing more than an abstraction of the real by the digital, a kind of
linguistic system in which letters-molecules signify the biological
phenotype. While this may be the case from a purely technical--and
textual--perspective, we should also consider the kinds of
philosophical questions which this technical configurations elicits.
That is, if we leave, for a moment, the epistemological and
linguistic debate of the real vs. the digital, the thing-itself vs. its
representation, and consider not "objects" but rather relationships,
we can see that "biological data" is more than a binary sign-system.
Many of the techniques within bioinformatics research appear to be
more concerned with function than with essence; the question a
bioinformatician asks is not "what it is," but rather "how it works."
Take, for example, a comment from the Bioinformatics.org website,
which is exemplary of a certain perspective on biological data:
It is a mathematically interesting property
of most large biological molecules that they
are polymers; ordered chains of simpler
molecular modules called monomers....Many
monomer molecules can be joined together to
form a single, far larger, macromolecule
which has exquisitely specific informational
content and/or chemical properties.
According to this scheme, the monomers in a
given macromolecule of DNA or protein can be
treated computationally as letters of an
alphabet, put together in pre-programmed
arrangements to carry messages or do work in
a cell. 13

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16. What is interesting about such perspectives is that they suggest

that the notion of biological data is not about the ways in which a
real (biological) object may be abstracted and represented
(digitally), but instead is about the ways in which certain "patterns
of relationships" can be identified across different material
substrates, or across different platforms. We still have the code
conversion from the biological to the digital, but rather than the
abstraction and representation of a "real" object, what we have is
the cross-platform conservation of specified patterns of
relationships. These patterns of relationships may, from the
perspective of molecular biology, be elements of genetic sequence
(such as base pair binding in DNA), molecular processes (such as
translation of RNA into amino acid chains), or structural behaviors
(such as secondary structure folding in proteins). The material
substrate may change (from a cell to a computer database), and the
distinction between the wet lab and the dry lab may remain (wet
DNA, dry DNA), but what is important for the bioinformatician is
how "biological data" is more than just abstraction, signification, or
representation. This is because the biological data in computer
databases are not merely there for archival purposes, but as data to
be worked on, data which, it is hoped, will reveal important
patterns that may have something to say about the genetic
mechanisms of disease.

17. While a simulation of DNA transcription and translation may be

constructed on a number of software platforms, it is noteworthy
that the main tools utilized for bioinformatics begin as database
applications (such as Unix-based administration tools). What these
particular types of computer technologies provide is not a more
perfect representational semblance, but a medium-specific context,
in which the "logic" of DNA can be conserved and extended in
various experimental conditions. What enables the practices of
gene or protein prediction to occur at all is a complex integration of
computer and genetic codes as functional codes. From the
perspective of bioinformatics, what must be conserved is the
pattern of relationships that is identified in wet DNA (even though
the materiality of the medium has altered). A bioinformatician
performing a multiple sequence alignment on an unknown DNA
sample is interacting not just with a computer, but with a "bio-logic"
that has been conserved in the transition from the wet lab to the dry
lab, from DNA in the cell to DNA in the database.

18. In this sense, biological data can be described more accurately

than as a sign system with material effects. Biological data can be
defined as the consistency of a "bio-logic" across material
substrates or varying media. This involves the use of computer
technologies that conserve the bio-logic of DNA (e.g., base pair
complementarity, codon-amino acid relationships, restriction

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enzyme splice sites) by developing a technical context in which that

bio-logic can be recontextualized in novel ways (e.g., gene
predictions, homology modeling). Bioinformatics is, in this way,
constituted by a challenge, one that is as much technical as it is
theoretical: it must manage the difference between genetic and
computer codes (and it is this question of the "difference" of
bioinformatics that we will return to later).

19. On a general level, biotech's regulation of the relationship

between genetic codes and computer codes would seem to be
mediated by the notion of "information"--a principle that is capable
of accommodating differences across media. This "translatability"
between media--in our case between genetic codes and computer
codes--must then also work against certain transformations that
might occur in translation. Thus the condition of translatability
(from genetic to computer code) is not only that linkages of
equivalency are formed between heterogeneous phenomena, but
also that other kinds of (non-numerical, qualitative) relationships
are prevented from forming, in the setting-up of conditions whereby
a specific kind of translation can take place.14

20. Thus, for bioinformatics approaches, the technical challenge is

to effect a "translation without transformation," to preserve the
integrity of genetic data, irrespective of the media through which
that information moves. Such a process is centrally concerned with
a denial of the transformative capacities of different media and
informational contexts themselves. For bioinformatics, the medium
is not the message; rather, the message--a genome, a DNA sample,
a gene--exists in a privileged site of mobile abstraction that must be
protected from the heterogeneous specificities of different media
platforms in order to enable the consistency of a bio-logic.

BLASTing the Body

21. We can take a closer look at how the bio-logic of bioinformatics

operates by considering the use of an online software tool called
"BLAST," and the technique of pairwise sequence alignment
referred to earlier. Again, it is important to reiterate the approach
being taken here. We want to concentrate on the technical details to
the extent that those details reveal assumptions that are extra-
technical, which are, at their basis, ontological claims about
biological "information." This will therefore require--in the case of
BLAST--a consideration of software design, usability, and
application.

22. BLAST is one of the most commonly used bioinformatics tools.

It stands for "Basic Local Alignment Search Tool" and was
developed in the 1990s at the National Center for Biotechnology

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Information (NCBI).15 BLAST, as its full name indicates, is a set of

algorithms for conducting analyses on sequence alignments. The
sequences can be nucleotide or amino acid sequences, and the
degree of specificity of the search and analysis can be honed by
BLAST's search parameters. The BLAST algorithm takes an input
sequence and then compares that sequence to a database of known
sequences (for instance, GenBank, EST databases, restriction
enzyme databases, protein databases, etc.). Depending on its search
parameters, BLAST will then return output data of the most likely
matches. A researcher working with an unknown DNA sequence
can use BLAST in order to find out if the sequence has already
been studied (BLAST includes references to research articles and
journals) or, if there is not a perfect match, what "homologs" or
close relatives a given sequence might have. Either kind of output
will tell a researcher something about the probable biochemical
characteristics and even function of the test sequence. In some
cases, such searches may lead to the discovery of novel sequences,
genes, or gene-protein relationships.

23. Currently, the NCBI holds a number of different sequence

databases, all of which can be accessed using different versions of
BLAST.16 When BLAST first appeared, it functioned as a
stand-alone Unix-based application. With the introduction of the
Web into the scientific research community in the early 1990s,
however, BLAST was ported to a Web-ready interface front-end
and a database-intensive back-end.17

Figure 4: Sequence search interface for BLAST.

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24. BLAST has become somewhat of a standard in bioinformatics

because it generates a large amount of data from a relatively
straightforward task. Though sequence alignments can sometimes
be computationally intensive, the basic principle is simple:
comparison of strings. First, a "search domain" is defined for
BLAST, which may be the selection of or within a particular
database. This constrains BLAST's domain of activity, so that it
doesn't waste time searching for matches in irrelevant data sets.
Then an input sequence is "threaded" through the search domain.
The BLAST algorithm searches for closest matches based on a
scoring principle. When the search is complete, the highest scoring
hits are kept and ranked. Since the hits are known sequences from
the database, all of their relevant characterization data can be easily
accessed. Finally, for each hit, the relevant bibliographical data is
also retrieved. A closer look at the BLAST algorithm shows how it
works with biological data:

Figure 5: The BLAST search algorithm.

25. In considering the BLAST algorithm, it is important to keep in

mind the imperative of "bio-logic" in bioinformatics research.
BLAST unites two crucial aspects of bioinformatics: the ability to
flexibly archive and store biological data in a computer database,
and the development of diversified tools for accessing and
interacting with that database (the control and storage principles
mentioned earlier). Without a database of biological data--or rather,
a database of bio-logics--bioinformatics tools are nothing more than
simulation. Conversely, without applications to act on the biological
data in the database, the database is nothing more than a static
archive. Bioinformatics may be regarded as this ongoing attempt to
integrate seamlessly the control and storage principles across
media, whether in genetically engineered biomolecules or in online
biological databases.

26. Though databases are not, of course, exclusive to

bioinformatics, the BLAST algorithm is tailored to the bio-logic of

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nucleotide and protein sequence.18 The bio-logic of base pair

complementarity among sequential combinations of four
nucleotides (A-T; C-G) is but one dimension of the BLAST
algorithm. Other, more complex aspects, such as the identification
of repeat sequences, promoter and repressor regions, and
transcription sites, are also implicated in BLAST's biological
algorithm. What BLAST's algorithm conserves is this pattern of
relationships, this bio-logic which is seen to inhere in both the
chromosomes and the database.

27. BLAST not only translates the biomolecular body by conserving

this bio-logic across material substrates; in this move from one
medium to another, it also extends the control principle to enable
novel formulations of biomolecules not applicable to the former,
"wet" medium of the cell's chromosomes. One way in which
BLAST does this is through the technique of the "search query."
The "query" function is perhaps most familiar to the kinds of
searches carried out on the Web using one of many "search
engines," each of which employs different algorithms for gathering,
selecting, and ordering data from the Web.19 BLAST does not
search the Web but rather performs user-specified queries on
biological databases, bringing together the control and storage
principles of bioinformatics. At the NCBI website, the BLAST
interface contains multiple input options (text fields for pasting a
sequence or buttons for loading a local sequence file) which make
use of special scripts to deliver the input data to the NCBI server,
where the query is carried out. These scripts, known as "CGI" or
"Common Gateway Interface" scripts, are among the most
commonly used scripts on the Web for input data on web pages.
CGI scripts run on top of HTML web pages and form a liason for
transmitting specific input data between a server computer and a
client's computer.20 A BLAST query will take the input sequence
data and send it, along with instructions for the search, to the
server. The BLAST module on the NCBI server will then accept the
data and run its alignments as specified in the CGI script. When the
analysis is finished, the output data is collected, ordered, and
formatted (as a plain-text email or as HTML).

28. BLAST queries involve an incorporation of "raw" biological

data that is ported through the medium (in this case, computer
network code) so that it can be processed in a medium-specific
context in which it "makes sense." The output is more than mere
bits, signs, or letters; the output is a configured bio-logic that is
assumed to exist above the domain of specific substance (carbon or
silicon). From a philosophical-technical perspective, BLAST is not
so much a sequence alignment tool as an exemplary case of the
way bioinformatics translates a relationship between discrete

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entities (DNA, RNA, and synthesis of amino acids in the cell)

across material substrates, with an emphasis on the ways in which
the control principle may extend the dimensions of the biological
data.

Translation without Transformation

29. In different ways, tools such as BLAST constantly attempt to

manage the difference between genetic and computer codes
through modes of regulating the contexts in which code conversions
across varying media take place.

30. BLAST also aims for a transparent translation of code across

different contexts; such software systems are primarily concerned
with providing bio-logical conversions between output data that can
be utilized for analysis and further molecular biology research.
Presenting an output file that establishes relationships between a
DNA sequence, a multiple pairwise alignment, and other related
biomolecular information, is a mode of translating between data
types by establishing relations between them that are also biological
relations (e.g., base pair complementarity, gene expression). The
way in which this is done is, of course, via a strictly
"non-biological" operation which is the correlation of data as data
(as string manipulation, as in pairwise alignments). In order to
enable this technical and biological translation, BLAST must
operate as a search tool in a highly articulated manner. A
"structured query language" in this case means much more than
simply looking up a journal author, title of a book, or subject
heading. It implies a whole epistemology, from the molecular
biological research point of view. What can be known and what
kinds of queries can take place are intimately connected with tools
such as BLAST. For this reason, such tools are excellent as "gene
finders," but they are poor at searching and analyzing nested,
highly-distributed biopathways in a cell. The instability in such
processes as cell regulation and metabolism is here stabilized by
aligning the functionalities of the materiality of the medium (in this
case, computer database query software) with the constrained
organization of biological data along two lines: first in a database,
and secondly as biological components and processes (DNA, RNA,
ESTs, amino acids, etc.).

31. In the example of BLAST, the interplay of genetic and computer

codes is worked upon so that their relationship to each other is
transparent. In other words, when looked at as "biomedia"--that is,
as the technical recontextualiztion of the biological
domain--BLAST reinforces the notion of media as transparent.21
The workings of a BLAST search query disappear into the
"back-end," so that the bio-logic of DNA sequence and structure

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may be brought forth as genetic data in itself. However, as we've

seen, this requires a fair amount of work in recontextualizing and
reconfiguring the relations between genetic and computer codes;
the regulatory practices pertaining to the fluid translation of types
of biological data all work toward this end.

32. The amount of recontextualizing that is required, the amount of

technical reconfiguration needed, is therefore proportionately
related to the way the bio-logic of DNA sequence and structure is
presented. In a BLAST query and analysis, the structure and
functionalities of computer technology are incorporated as part of
the "ontology" of the software, and the main reason this happens is
so that novel types of bio-logic can become increasingly
self-apparent: characteristics that are "biological" but that could
also never occur in the wet lab (e.g., multiple pairwise alignments,
gene prediction, multiple-database queries).

33. This generates a number of tensions in how the biomolecular

body is reconceptualized in bioinformatics. One such tension is in
how translation without transformation becomes instrumentalized in
bioinformatics practices. On the one hand, a majority of
bioinformatics software tools make use of computer and
networking technology to extend the practices of the molecular
biology lab. In this, the implication is that computer code
transparently brings forth the biological body in novel contexts,
thereby producing novel means of extracting data from the body.
Within this infrastructure is also a statement about the ability of
computer technology to bring forth, in ever greater detail, the
bio-logic inherent in the genome, just as it is in the biological cell.
The code can be changed, and the body remains the same; the same
bio-logic of a DNA sequence in a cell in a petri dish is conserved in
an online genome database.

34. On the other hand, there is a great difference in the fact that
bioinformatics doesn't simply reproduce the wet biology lab as a
perfect simulation. Techniques such as gene predictions, database
comparisons, and multiple sequence analysis generate biomolecular
bodies that are specific to the medium of the computer.22 The
newfound ability to perform string manipulations, database queries,
modeling of data, and to standardize markup languages also means
that the question of "what a body can do" is extended in ways
specific to the medium.23 When we consider bioinformatics
practices that directly relate (back) to the wet lab (e.g., rational
drug design, primer design, genetic diagnostics), this
instrumentalization of the biomolecular body becomes
re-materialized in significant ways. Change the code, and you
change the body. A change in the coding of a DNA sequence in an
online database can directly affect the synthesis of novel

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compounds in the lab.

35. As a way of elaborating on this tension, we can further elaborate

the bio-logics of bioinformatics along four main axes.

36. The first formulation is that of equivalency between genetic and

computer codes. As mentioned previously, the basis for this
formulation has a history that extends back to the post-war period,
in which the discourses of molecular biology and cybernetics
intersect, culminating in what Francis Crick termed "the coding
problem." 24 In particular, gene sequencing (such as Celera's
"whole genome shotgun sequencing" technique) offers to us a
paradigmatic example of how bioinformatics technically establishes
a condition of equivalency between genetic and computer codes.25
If, so the logic goes, there is a "code" inherent in DNA--that is, a
pattern of relationships which is more than DNA's substance--then
it follows that that code can be identified, isolated, and converted
across different media. While the primary goal of this procedure is
to sequence an unknown sample, what genome sequencing must
also accomplish is the setting up of the conditions through which an
equivalency can be established between the wet, sample DNA, and
the re-assembled genome sequence that is output by the computer.
That is, before any of the more sophisticated techniques of
bioinformatics or genomics or proteomics can be carried out, the
principles for the technical equivalency between genetic and
computer codes must be articulated.

37. Building upon this, the second formulation is that of a

back-and-forth mobility between genetic and computer codes. That
is, once the parameters for an equivalency can be established, the
conditions are set for enabling conversions between genetic and
computer codes, or for facilitating their transport across different
media. Bioinformatics practices, while recognizing the difference
between substance and process, also privilege another view of
genetic and computer codes, one based on identified patterns of
relationships between components--for instance, the bio-logic of
DNA's base pair binding scheme (A-T; C-G), or the identification of
certain polypeptide chains with folding behaviors (amino acid
chains that make alpha-helical folds). These well-documented
characteristics of the biomolecular body become, for
bioinformatics, more than some "thing" defined by its substance;
they become a certain manner of relating components and
processes.

38. The mobility between genetic and computer codes is more than
the mere digitization of the former by the latter. What makes DNA
in a plasmid and DNA in a database the "same"? A definition of
what constitutes the biological in the term "biological data." Once

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the biological domain is approached as this bio-logic, as these

identified and selected patterns of relationships, then, from the
perspective of bioinformatics--in principle at least--it matters little
whether that DNA sample resides in a test tube or a database. Of
course, there is a similar equivalency in the living cell itself, since
biomolecules such as proteins can be seen as being isomorphic with
each other (differing only in their "folds"), just as a given segment
of DNA can be seen as being isomorphic in its function within two
different biopathways (same gene, different function). Thus the
mobility between genetic and computer codes not only means that
the "essential data" or patterns can be translated from wet to dry
DNA. It also means that bioinformatics practices such as database
queries are simultaneously algorithmic and biological.

39. Beyond these two first formulations are others that develop
functionalities based on them. One is a situation in which data
accounts for the body. In examples relating to genetic diagnostics,
data does not displace or replace the body, but rather forms a kind
of index to the informatic muteness of the biological body--DNA
chips in medical genetics, disease profiling, pre-implantation
screening for IVF, as well as other, non-biological uses, all depend
to some extent of bioinformatics techniques and technologies. The
examples of DNA chips in medical contexts redefine the ways in
which accountability takes place in relation to the physically-
present, embodied subject. While its use in medicine is far from
being common, genetic testing and the use of DNA chips are, at
least in concept integrating themselves into the fabric of medicine,
where an overall genetic model of disease is often the dominant
approach to a range of genetic-related conditions, from Alzheimer's
to diabetes to forms of cancer.26 However, beneath these issues is
another set of questions that pertain to the ways in which a mixture
of genetic and computer codes gives testimony to the body, and
through its data-output, accounts for the body in medical terms
(genetic patterns, identifiable disease genes, "disease
predispositions").27 Again, as with the establishing of an
equivalency, and the effecting of a mobility, the complex of genetic
and computer codes must always remain biological, even though its
very existence is in part materialized through the informatic
protocols of computer technology. In a situation where data
accounts for the body, we can also say that a complex of genetic
and computer codes makes use of the mobility between genetic and
computer codes, to form an indexical description of the biological
domain, as one might form an index in a database. But, it should be
reiterated that this data is not just data, but a conservation of a
bio-logic, a pattern of relationships carried over from the patient's
body to the DNA chip to the computer system. It is in this sense
that data not only accounts for the body, but that the data (a

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complex of genetic and computer codes) also identifies itself as

biological.

40. Finally, not only can data account for the body, but the body can
be generated through data. We can see this type of formulation
occurring in practices that make use of biological data to effect
changes in the wet lab, or even in the patient's body. Here we can
cite the field known as "pharmacogenomics," which involves the
use of genomic data to design custom-tailored gene-based and
molecular therapies.28 Pharmacogenomics moves beyond the
synthesis of drugs in the lab and relies on data from genomics in its
design of novel compounds. It is based not on the diagnostic model
of traditional pharmaceuticals (ameliorating symptoms), but rather
on the model of "preventive medicine" (using predictive methods
and genetic testing to prevent disease occurrence or onset). This not
only means that pharmacogenomic therapies will be custom-
designed to each individual patient's genome, but also that the
therapies will operate for the long-term, and in periods of health as
well as of disease.

41. What this means is that "drugs" are replaced by "therapies," and
the synthetic is replaced by the biological, but a biological that is
preventive and not simply curative. The image of the immune
system that this evokes is based on more than the correction of
"error" in the body. Rather, it is based on the principles of
biomolecular and biochemical design, as applied to the optimization
of the biomolecular body of the patient. At an even more specific
level, what is really being "treated" is not so much the patient but
the genome. At the core of pharmacogenomics is the notion that a
reprogramming of the "software" of the genome is the best route to
preventing the potential onset of disease in the biological body. If
the traditional approaches of immunology and the use of vaccines
are based on synthesizing compounds to counter certain proteins,
the approach of pharmacogenomics is to create a context in which
a reprogramming will enable the body biologically to produce the
needed antibodies itself, making the "medium" totally transparent.
The aim of pharmacogenomics is, in a sense, not to make any drugs
at all, but to enable the patient's own genome to do so.29

Virtual Biology?

42. To summarize: the equivalency, the back-and-forth mobility, the

accountability, and the generativity of code in relation to the body
are four ways in which the bio-logic of the biomolecular body is
regulated. As we've seen, the tensions inherent in this notion of
biological information are that sometimes the difference between
genetic and computer codes is effaced (enabling code and file

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conversions), and at other times this difference is referred back to

familiar dichotomies (where flesh is enabled by data, biology by
technology). We might abbreviate by saying that, in relation to the
biomolecular body, bioinformatics aims to realize the possibility of
the body as "biomedia."

43. The intersection of biotech and infotech goes by many names--

bioinformatics, computational biology, virtual biology. This last
term is especially noteworthy, for it is indicative of the kinds of
philosophical assumptions within bioinformatics that we have been
querying. A question, then: is biology "virtual"? Certainly from the
perspective of the computer industry, biology is indeed virtual, in
the sense of "virtual reality," a computer-generated space within
which the work of biology may be continued, extended, and
simulated. Tools such as BLAST, molecular modeling software, and
genome sequencing computers are examples of this emerging
virtual biology. From this perspective, a great deal of biotech
research--most notably the various genome efforts--is thoroughly
virtual, meaning that it has become increasingly dependent upon
and integrated with computing technologies.

44. But if we ask the question again, this time from the philosophical
standpoint, the question changes. Asking whether or not biology is
philosophically virtual entails a consideration of how specific fields
such as bioinformatics conceptualize their objects of study in
relation to processes of change, difference, and transformation. If,
as we've suggested, bioinformatics aims for the technical condition
(with ontological implications) of "translation without
transformation," then what is meant by "transformation"? As we've
seen above, transformation is related technically to the procedures
of encoding, recoding, and decoding genetic information that
constitute a bio-logic. What makes this possible technically is a
twofold conceptual articulation: there is something in both genetic
and computer codes that enables their equivalency and therefore
their back-and-forth mobility (DNA sampling, analysis, databasing).
This technical-conceptual articulation further enables the
instrumentalization of genetic and computer codes as being
mutually accountable (genetic disease predisposition profiling) and
potentially generative or productive (genetically based drug design
or gene therapies).

45. Thus, the transformation in this scenario, whose negation forms

the measure of success for bioinformatics, is related to a certain
notion of change and difference. To use Henri Bergson's distinction,
the prevention of transformation in bioinformatics is the prevention
of a difference that is characterized as quantitative (or "numerical")
and extensive (or spatialized).30 What bioinformatics developers
want to prevent is any difference (distortion, error, noise) between

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what is deemed to be information as one moves from an in vitro

sample to a computer database to a human clinical trial for a
gene-based therapy. This means preserving information as a
quantifiable, static unit (DNA, RNA, protein code) across variable
media and material substrates.

46. However, difference in this sense--numerical, extensive

difference--is not the only kind of difference. Bergson also points to
a difference that is, by contrast, qualitative ("non-numerical") and
intensive (grounded in the transformative dynamics of
temporalization, or "duration"). Gilles Deleuze has elaborated
Bergson's distinction by referring to the two differences as external
and internal differences, and has emphasized the capacity of the
second, qualitative, intensive difference continually to generate
difference internally--a difference from itself, through itself.31

47. How would such an internal--perhaps self-organizing--difference

occur? A key concept in understanding the two kinds of differences
is the notion of "the virtual," but taken in its philosophical and not
technical sense. For Bergson (and Deleuze), the virtual and actual
form one pair, contrasted to the pair of the possible and the real.
The virtual/actual is not the converse of the possible/real; they are
two different processes by which material-energetic systems are
organized. As Deleuze states:
From a certain point of view, in fact, the
possible is the opposite of the real, it is
opposed to the real; but, in quite a
different opposition, the virtual is opposed
to the actual. The possible has no reality
(although it may have an actuality);
conversely, the virtual is not actual, but
as such possesses a reality. (Bergsonism 96)

48. We might add another variant: the possible is negated by the real
(what is real is no longer possible because it is real), and the virtual
endures in the actual (what is actual is not predetermined in the
virtual, but the virtual as a process is immanent to the actual). As
Deleuze notes, the possible is that which manages the first type of
difference, through resemblance and limitation (out of a certain
number of possible situations, one is realized). By contrast, the
virtual is itself this second type of difference, operating through
divergence and proliferation.

49. With this in mind, it would appear that bioinformatics--as a

technical and conceptual management of the material and
informatic orders--prevents one type of difference (as possible
transformation) from being realized. This difference is couched in
terms derived from information theory and computer science and is
thus weighted toward a more quantitative, measurable notion of

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information (the first type of quantitative, extensive difference).

But does bioinformatics--as well as molecular genetics and
biology--also prevent the second type of qualitative, intensive,
difference? In a sense it does not, because any analysis of
qualitative changes in biological information must always be
preceded in bioinformatics by an analysis of quantitative changes,
just as genotype may be taken as causally prior to phenotype in
molecular genetics. But in another sense the question cannot be
asked, for before we inquire into whether or not bioinformatics
includes this second type of difference in its aims (of translation
without transformation), we must ask whether or not such a notion
of qualitative, intensive difference exists in bioinformatics to begin
with.

50. This is why we might question again the notion of a "virtual

biology." For, though bioinformatics has been developing at a rapid
rate in the past five to ten years (in part bolstered by advances in
computer technology), there are still a number of extremely
difficult challenges in biotech research which bioinformatics faces.
Many of these challenges have to do with biological regulation: cell
metabolism, gene expression, and intra- and inter-cellular
signaling.32 Such areas of research require more than discrete
databases of sequence data, they require thinking in terms of
distributed networks of processes which, in many cases, may
change over time (gene expression, cell signaling, and point
mutations are examples).

51. In its current state, bioinformatics is predominantly geared

toward the study of discrete, quantifiable systems that enable the
identification of something called genetic information (via the
four-fold process of bio-logic). In this sense bioinformatics works
against the intervention of one type of difference, a notion of
difference that is closely aligned to the traditions of information
theory and cybernetics. But, as Bergson reminds us, there is also a
second type of difference which, while being amenable to
quantitative analysis, is equally qualitative (its changes are not of
degree, but of kind) and intensive (in time, as opposed to the
extensive in space). It would be difficult to find this second kind of
difference within bioinformatics as it currently stands. However,
many of the challenges facing bioinformatics--and biotech
generally--imply the kinds of transformations and dynamics
embodied in this Bergsonian-Deleuzian notion of difference-
as-virtual.

52. It is in this sense that a "virtual biology" is not a conceptual

impossibility, given certain contingencies. If bioinformatics is to
accommodate the challenges put to it by the biological processes of
regulation (metabolism, gene expression, signaling), then it will

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have to consider a significant re-working of what counts as

"biological information." As we've pointed out, this reconsideration
of information will have to take place on at least two fronts: that of
the assumptions concerning the division between the material and
informatic orders (genetic and computer codes, biology and
technology, etc.), and that of the assumptions concerning material-
informatic orders as having prior existence in space, and secondary
existence in duration (molecules first, then interactions; objects
first, then relations; matter first, then force).33 The biophilosophy
of Bergson (and of Deleuze's reading of Bergson) serves as a
reminder that, although contemporary biology and biotech are
incorporating advanced computing technologies as part of their
research, this does not necessarily mean that the informatic is
"virtual."

School of Literature, Communication, and Culture

Georgia Institute of Technology
[email protected]

Copyright © 2003 Eugene Thacker NOTE: Readers

may use portions of this work in accordance with the Fair Use provisions
of U.S. copyright law. In addition, subscribers and members of
subscribed institutions may use the entire work for any internal
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fax to one person at another location for that individual's personal use,
distribution of this article outside of a subscribed institution without
express written permission from either the author or the Johns Hopkins
University Press is expressly forbidden.

1. For non-technical summaries of bioinformatics see the

articles by Howard, Goodman, Palsson, and Emmett. As one
researcher states, bioinformatics is specifically "the
mathematical, statistical and computing methods that aim to
solve biological problems using DNA and amino acid
sequences and related information" (from
bioinformatics.org).

2.The use of computers in biology and life science research is

certainly nothing new, and, indeed, an informatic approach to
studying biological life may be seen to extend back to the
development of statistics, demographics, and the
systematization of health records during the eighteenth and
nineteenth centuries. This proto-informatic approach to the
biological/medical body can be seen in Foucault's work, as
well as in medical-sociological analyses inspired by him.
Foucault's analysis of the medical "gaze" and nosology's use
of elaborate taxonomic and tabulating systems are seen to

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emerge alongside the modern clinic's management and

conceptualization of public health. Such technologies are, in
the later Foucault, constitutive of the biopolitical view, in
which power no longer rules over death, but rather impels
life, through the institutional practices of the hospital, health
insurances, demographics, and medical practice generally.
For more see Foucault's The Birth of the Clinic, as well as
"The Birth of Biopolitics."

3. Molecular biochemist Fred Sanger published a report on

the protein sequence for bovine insulin, the first publication
of sequencing research of this kind. This was accompanied a
decade later by the first published paper on a nucleotide
sequence, a type of RNA from yeast. See Sanger, "The
Structure of Insulin," and Holley, et al., "The Base Sequence
of Yeast Alanine Transfer RNA." A number of researchers
also began to study the genes and proteins of model
organisms (often bacteria, roundworms, or the Drosophila
fruit fly) not so much from the perspective of biochemical
action, but from the point of view of information storage. For
an important example of an early database-approach, see
Dayhoff et al., "A Model for Evolutionary Change in
Proteins."

4.This, of course, was made possible by the corresponding

advancements in computer technology, most notably in the
PC market. See Abola, et al., "Protein Data Bank," and
Bairoch, et al. "The SWISS-PROT Protein Sequence Data
Bank."

5. Initially the HGP was funded by the U.S. Department of

Energy and National Institute of Health, and had already
begun forming alliances with European research institutes in
the late 1980s (which would result in HUGO, or the Human
Genome Organization). As sequencing endeavors began to
become increasingly distributed to selected research centers
and/or universities in the U.S. and Europe, the DoE's
involvement lessened, and the NIH formed a broader
alliance, the International Human Genome Sequencing
Effort, with the main players being MIT's Whitehead
Institute, the Welcome Trust (UK), Stanford Human Genome
Center, and the Joint Genome Institute, among many others.
This broad alliance was challenged when the biotech
company Celera (then The Institute for Genome Research)
proposed its own genome project funded by the corporate
sector. For a classic anthology on the genome project, see the
anthology The Code of Codes, edited by Kevles and Hood.
For a popular account see Matt Ridley's Genome.

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6. In this context it should also be stated that bioinformatics

is also a business, with a software sector that alone has been
estimated to be worth $60 million, and many pharmaceutical
companies outsourcing more than a quarter of their R&D to
bioinformatics start-ups. See the Silico Research Limited
report "Bioinformatics Platforms," at: <http://www.silico-
research.com>.

7. See Kay's book Who Wrote the Book of Life? A History of

the Genetic Code, as well as her essay "Cybernetics,
Information, Life: The Emergence of Scriptural
Representations of Heredity."

8. Kay provides roughly three discontinuous, overlapping

periods in the history of the genetic code--a first phase
marked by the trope of "specificity" during the early part of
the twentieth century (where proteins were thought to
contain the genetic material), a second "formalistic" phase
marked by the appropriation of "information" and "code"
from other fields (especially Francis Crick's formulation of
"the coding problem"), and a third, "biochemical" phase
during the 1950s and 60s, in which the informatic trope is
extended, such that DNA is not only a code but a fully-
fledged "language" (genetics becomes cryptography, as in
Marshall Nirenberg and Heinrich Matthai's work on
"cracking the code" of life).

9. Herbert Boyer and Stanley Cohen's recombinant DNA

research had demonstrated that DNA could not only be
studied, but be rendered as a technology. The synthesis of
insulin--and the patenting of its techniques--provides an
important proof-of-concept for biotechnology's control
principle in this period. For an historical overview of the
science and politics of recombinant DNA, see Aldridge, The
Thread of Life. For a popular critical assessment, see Ho,
Genetic Engineering. On recombinant DNA, see the
research articles by Cohen, et al. and Chang, et al. The work
of Cohen and Boyer's teams resulted in a U.S. patent,
"Process For Producing Biologically Functional Molecular
Chimeras" (#4237224), as well as the launching of one of the
first biotech start-ups, Genentech, in 1980. By comparison,
the key players in the race to map the human genome were
not scientists, but supercomputers, databases, and software.
During its inception in the late 1980s, the DoE's Human
Genome Project signaled a shift from a control principle to a
"storage principle." This bioinformatic phase is increasingly
suggesting that biotech and genetics research is non-existent
without some level of data storage technology. Documents on

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the history and development of the U.S. Human Genome

Project can be accessed through its website, at
<http://www.ornl.gov/hgmis>.

10. At the time of this writing, molecular biologists can

perform five basic types of research using bioinformatics
tools: digitization (encoding biological samples),
identification (of an unknown sample), analysis (generating
data on a sample), prediction (using data to discover novel
molecules), and visualization (modeling and graphical display
of data).

11. Bioinformatics tools can be as specific or as general as a

development team wishes. Techniques include sequence
assembly (matching fragments of sequence), sequence
annotation (notes on what the sequence means), data storage
(in dynamically updated databases), sequence and structure
prediction (using data on identified molecules), microarray
analysis (using biochips to analyze test samples), and whole
genome sequencing (such as those on the human genome).
For more on the technique of pairwise sequence alignment
see Gibas and Gambeck's technical manual, Developing
Bioinformatics Computers Skills, and Baxevanis, et al., eds.,
Bioinformatics: A Practical Guide to the Analysis of Genes
and Proteins. For a hacker-hero's narrative, see Lincoln
Stein's paper "How PERL Saved the Human Genome
Project."

12. See MacKenzie, Coded Character Sets.

13. At <http://www.bioinformatics.org>.

14. "Translation" is used here in several senses. First, in a

molecular biological sense, found in any biology textbook, in
which DNA "transcribes" RNA, and RNA "translates" a
protein. Secondly, in a linguistic sense, in which some content
is presumably conserved in the translation from one language
to another (a process which is partially automated in online
translation tools). Third, in a computer science sense, in
which translation is akin to "portability," or the ability for a
software application to operate across different platforms
(Mac, PC, Unix, SGI). This last meaning has been elaborated
upon by media theorists such as Friedrich Kittler, in his
notion of "totally connected media systems." In this essay it
is the correlation of the first (genetic) and third
(computational) meanings which are of the most interest.

15. See Altschul, et al., "Basic Local Alignment Search Tool."

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16. For instance, "blastn" is the default version, searching

only the nucleotide database of GenBank. Other versions
perform the same basic alignment functions, but with
different relationships between the data: "blastp" is used for
amino acid and protein searches, "blastx" will first translate
the nucleotide sequence into amino acid sequence, and then
search blastp, "tblastn" will compare a protein sequence
against a nucleotide database after translating the nucleotides
into amino acids, and "tblastx" will compare a nucleotide
sequence to a nucleotide database after translating both into
amino acid code.

17. Other bioinformatics tools websites, such as University of

California San Diego's Biology Workbench, will also offer
portals to BLAST searches, oftentimes with their own
front-end. To access the Web-version of BLAST, go to
<http://0-www.ncbi.nlm.nih.gov.opac.sfsu.edu/BLAST>. To
access the UCSD Biology Workbench, go to
<http://workbench.sdsc.edu>.

18. A key differentiation in bioinformatics as a field is

between research on "sequence" and research on "structure."
The former focuses on relationships between linear code,
whether nucleic acids/DNA or amino acids/proteins. The
latter focuses on relationships between sequence and their
molecular-physical organization. If a researcher wants to
simply identify a test sample of DNA, the sequence approach
may be used; if a researcher wants to know how a particular
amino acid sequence folds into a three-dimensional protein,
the structure approach will be used.

19. A query is a request for information sent to a database.

Generally queries are of three kinds: parameter-based (fill-
in-the-blank type searches), query-by-example (user-defined
fields and values), and query languages (queries in a specific
query language). A common query language used on the
Internet is SQL, or structured query language, which makes
use of "tables" and "select" statements to retrieve data from a
database.

20. CGI stands for Common Gateway Interface, and it is

often used as part of websites to facilitate the dynamic
communication between a user's computer ("client") and the
computer on which the website resides ("server"). Websites
which have forms and menus for user input (e.g., email
address, name, platform) utilize CGI programs to process the
data so that the server can act on it, either returning data
based on the input (such as an updated, refreshed splash

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page), or further processing the input data (such as adding an

email address to a mailing list).

21. For more on the concept of "biomedia" see my "Data

Made Flesh: Biotechnology and the Discourse of the
Posthuman."

22. Though wet biological components such as the genome

can be looked at metaphorically as "programs," the
difference here is that in bioinformatics the genome is
actually implemented as a database, and hence the
intermingling of genetic and computer codes mentioned
above.

23. The phrase "what a body can do" refers to Deleuze's

reading of Spinoza's theory of affects in the Ethics. Deleuze
shows how Spinoza's ethics focuses on bodies not as discrete,
static anatomies or Cartesian extensions in space, but as
differences of speed/slowness and as the capacity to affect
and to be affected. For Deleuze, Spinoza, more than any
other Continental philosopher, does not ask the metaphysical
question ("what is a body?") but rather an ethical one ("what
can a body do?"). This forms the basis for considering ethics
in Spinoza as an "ethology." See Deleuze, Spinoza: Practical
Philosophy, 122-30.

25. Crick's coding problem had to do with how DNA, the

extremely constrained and finite genetic "code," produced a
wide array of proteins. Among Crick's numerous essays on
the genetic "code," see "The Recent Excitement in the
Coding Problem." Also see Kay, Who Wrote the Book of
Life?, 128-63.

25. For an example of this technique in action, see Celera's

human genome report, Venter, et al., "The Sequence of the
Human Genome."

26. For a broad account of the promises of molecular

medicine, see Clark, The New Healers.

27. While genetic testing and the use of DNA chips are
highly probabilistic and not deterministic, the way they
configure the relationship between genetic and computer
codes is likely to have a significant impact in medicine.
Genetic testing can, in the best cases, tell patients their
general likelihood for potentially developing conditions in
which a particular disease may or may not manifest itself,
given the variable influences of environment and patient
health and lifestyle. In a significant number of cases this

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amounts to "leaving things to chance," and one of the biggest

issues with genetic testing is the decision about the "right to
know."

28. See Evans, et al., "Pharmacogenomics: Translating

Functional Genomics into Rational Therapeutics." For a
perspective from the U.S. government-funded genome
project, see Collins, "Implications of the Human Genome
Project for Medical Science."

29. This is, broadly speaking, the approach of "regenerative

medicine." See Petit-Zeman, "Regenerative Medicine."
Pharmacogenomics relies on bioinformatics to query,
analyze, and run comparisons against genome and proteome
databases. The data gathered from this work are what sets the
parameters of the context in which the patient genome may
undergo gene-based or cell therapies. The procedure may be
as concise as prior gene therapy human clinical trials--the
insertion of a needed gene into a bacterial plasmid, which is
then injected into the patient. Or, the procedure may be as
complex as the introduction of a number of inhibitors that
will collectively act at different locations along a
chromosome, working to effectuate a desired pattern of gene
expression to promote or inhibit the synthesis of certain
proteins. In either instance, the dry data of the genome
database extend outward and directly rub up against the wet
data of the patient's cells, molecules, and genome. In this
sense data generate the body, or, the complex of genetic and
computer codes establishes a context for recoding the
biological domain.

30. Bergson discusses the concepts of the virtual and the

possible in several places, most notably in Time and Free
Will, where he advances an early formulation of "duration,"
and in The Creative Mind, where he questions the priority of
the possible over the real. Though Bergson does not theorize
difference in its post-structuralist vein, Deleuze's reading of
Bergson teases out the distinctions Bergson makes between
the qualitative and quantitative in duration as laying the
groundwork for a non-negative (which for Deleuze means
non-Hegelian) notion of difference as generative, positive,
proliferative. See Deleuze's book Bergsonism, 91-103.

31. Deleuze's theory of difference owes much to Bergson's

thoughts on duration, multiplicity, and the virtual. In
Bergsonism, Deleuze essentially re-casts Bergson's major
concepts (duration, memory, the "élan vital") along the lines
of difference as positive, qualitative, intensive, and

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internally-enabled.

32. There are a number of efforts underway to assemble

bioinformatics databases centered on these processes of
regulation. BIND (Biomolecular Interaction Network
Database) and ACS (Association for Cellular Signaling) are
two recent examples. However, these databases must convert
what are essentially time-based processes into discrete image
or diagram files connected by hyperlinks, and, because the
feasibility of dynamic databases is not an option for such
endeavors, the results end up being similar to sequence
databases.

33. As Susan Oyama has noted, more often than not, genetic
codes are assumed to remain relatively static, while the
environment is seen to be constantly changing. As Oyama
states, "if information . . . is developmentally contingent in
ways that are orderly but not preordained, and if its meaning
is dependent on its actual functioning, then many of our ways
of thinking about the phenomena of life must be altered"
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