[Nettime-bold] Post-Genomics

[Eugene Thacker <maldoror@eden.rutgers.edu>]

The Post-Genomic Era Has Already Happened

Eugene Thacker

[originally posted at The Thing Reviews http://bbs.thing.net]


"What the Web browser is to the Internet, DoubleTwist.com is to the
human genome."
Greg Papadopoulos, Sun Microsystems


The End of the Genome

Months before the Human Genome Project-Celera announcement of the
"completion" of the human genome, a small bioinformatics company named
DoubleTwist announced that it had analyzed all of the human genome data
produced to date. By utilizing proprietary bioinformatics software
tools, developed in collaboration with Sun Microsystems, DoubleTwist
claimed it had provided the first overall analysis of the human genome,
including potential gene targets, novel and previously characterized
genes, analysis and examination of gene structure, identification of
splice variants, exon, intron, and promoter regions, and the prediction
of protein structures. DoubleTwist is not in the business of genome
sequencing (as is Celera), it is not a technology provider (as
Perkin-Elmer is), and it is not in the business of gene discovery and
patenting (as is Human Genome Sciences). It calls itself an ASP or
"applications service provider." DoubleTwist takes pre-existing
information and figures out a way to make it the most efficient and
generative information possible. As a business, its goal is to make
medical-genetic value and e-commerce/e-service value coincide.

To understand the importance of DoubleTwist's analysis of the human
genome, we need to remember that the mapping of the human genome is
actually a long three-step process: The first step is sequencing, in
which the letters of the genome are spelled out in bits and pieces (this
is what both Celera and the HGP have claimed to have finished); the
second step involves assembling those bits and pieces into the right
order on the chromosomes (Celera claims to be nearing completion of this
phase); finally there is the last phase of annotation, in which
researchers analyze what the genomes does, how it operates, and what all
those As, Ts, Cs, and Gs mean.

It goes without saying that it is this final phase of annotation or
analysis that will provide the most potentially meaningful information
for medical research, with the first two steps being the equivalent of
no-brainer recitative tasks. For the biotech and pharmaceutical
industries, the hope here is that by understanding how the genome works,
a revolution in genetic medicine will occur, allowing fields such as
pharmacogenomics, gene therapy, and regenerative medicine to be fully
integrated into mainstream health care.

But, with only the sequencing phase done, there is still no guarantee
that the genome will "mean" anything, let alone provide long-sought
after secrets to complex diseases such as cancer or AIDS. The HGP-Celera
announcement can be understood as being indicative of a deep-rooted
crisis in biotech and biomedicine: At a moment when biotech, at one of
its high-points hegemonically and economically, is thriving totally on
the basis of futuristic scenarios, the sequencing of the human genome
provides the reassurance of something done, something completed, as if
to serve as an alibi for all of the hype biotech has received in the
past few years. In other words, we have long seen how biotech and
biomedicine has been able to survive with a combination of futuristic
promises and a lack of substantial, concerete results (gene therapy is a
prime example here). With the human genome sequence, biotech at least
has something to show for all the risk-investment and media-hype it has
generated; metaphorically speaking, biotech now has the beginnings of a
map, with which to perform more articulate advances into the frontiers
of molecular life. Scientifically speaking, the primary advantage of the
human genome sequence is that it will offer a navigation tool for
researchers, enabling an era of "post-genomic" research in fields such
as proteomics (the study of proteins), pharmaceogenomics (genetic
drugs), functional genomics (what genes do), and bioinformatics (the
computerization of biotech).

Subroutines

This era of "post-genomic" science continues the linear, causal
narrative initially put forth by the public consortium in the late
1980s: that privileged DNA sequences called genes form the central
component, if not the primary agency, for the production of proteins
which form the foundation for the body's stucture and function. Though
researchers and critics have pointed to other, more complex approaches
(systems biology, autopoiesis, networked/distributive approaches), two
things still remain central to the ideology of genetics and biotech:

First, that DNA - and more specifically genes - are the privileged and
central element to understanding life, health, and disease, at the
molecular level. Even when researchers attempt to bypass DNA for more
efficient discovery approaches (focusing on mRNA, RFLPs, BACs) the
underlying methodology still preserves the centrality of DNA, as opposed
to DNA in the mitrochondria, cytoplasmic elements, intra- and
extra-cellular elements, context and environmental conditions,
biochemical pathways, and so on. Watson and Crick's rhetorical move in
the early 1950s was to demonstrate the structural centrality of DNA in
hereditary mechanisms, and this remains a "central dogma" to this day,
as the HGP-Celera announcement shows.

Second, DNA is information, or a genetic "code," and not simply like a
code. Although recent critical work on the tropes of genetics has shown
how molecular genetics often mistakes metaphors for things-in-themselves
(for instance, taking a DNA molecule as a written text), contemporary
biotech demands the abolition of metaphor. The rise of new computing and
networking technologies has propelled molecular genetics and biotech
into a new arena in which DNA is, functionally and structurally,
information. The resultant effect is that discovery science (novel
genes, genetically-designed drugs) takes place almost exclusively on the
level of data, and only reaches physical bodies during clinical trials
or at the consumer-health end.

The DoubleTwist/Sun announcement is not exactly about the fusion of the
biological with the informatic, or about human-machine interfaces, but
rather about the translation of the entire science of biotech and
molecular biology into the level of informatics. Bioinformatics is a key
field here, because it mediates the gaps between the organism and the
database, genetic information and computer information. Automated
database management, gene discovery data mining software, genetic
screening software, gene assembly algorithms, and protein prediction
software, all provide means of working on the molecular body through the
lens of informatics. What DoubleTwist has done is to accelerate the
transformation of biotech into an integrated infotech-biotech apparatus,
whereby the body can be seamlessly encoded and decoded through the
bioinformatic medical practices of gene therapy, drug development,
disease profiling, and so on.

Data Made Flesh

In this sense it is helpful to characterize biotech according to three
generations of human-computer, biology-technology, relationships:

First generation relationships between biology and technology occur at a
predominantly discursive level, with the emergence of a language of
"codes," "models," and "scripts." Physicist Erwin Schrodinger's comments
in the mid-1940s concerning genes as operating like a morse code and
"executive law code" provided one source of influence for researchers
such as Francis Crick, who, with Watson, began to discuss DNA as
information-transmission. The then-concurrent research into cybernetics
(Wiener), information theory (Shannon), and mainframe computers (von
Neumann) provided a parallel discourse from lifescience researchers
approaching the body on the molecular level. Here we are still dealing
with the wet biology lab, gradually incorporating and integrating this
language of information into actual research questions. Metaphor.

Second generation relationships take off with the emergence of a biotech
industry in the late 1970s and 1980s. While recombinant DNA and PCR
techniques provide early uses of innovative techniques and technologies
for manipulating and replicating genetic material, it is mainly with
large-scale genome projects (Celera, Incyte, HGP) that an actual science
of bio-informatics comes of age. Simultaneous advances into lab-based
computing technologies, as well as the growth of the Internet and Web,
significantly contribute to a new set of techniques for manipulating
genetic code, in the computer. Here we move to the suggestion that DNA
and the genome is all about information systems, not unlike advanced
network computers. What becomes more important is not wet lab research,
but developing advanced, "intelligent" sequencing computers. Data feeds
into data.

Third generation relationships- our current situation - move further
away from the sequencing of the second generation, and operates
exclusively on the level of information technology. However this is not
so much a recuperation of the biological-genetic into the informatic, as
it is a reconstitution of the biological-material domain on the level of
a "molecular informatics." The life sciences themselves have become
information sciences, both theoretically (e.g., systems biology
approaches) and technically (e.g., bioinformatics). Database management,
data mining, algorithmic approaches, molecular prediction and modeling,
and other practices become more than just technical details; they become
the new foundation of a life science which operates almost exclusively
through informatics. Data processing.

What this suggests is something more than technological determinism, or
the incorporation of the "human" into the machine. Biotech is both more
diversified and less reductive than an exclusive dependence on simple
human-machine binaries. Once some kind of a point of translation is
effected, however weak a link it is, between genetic information and
computer information, the management of the gap between them becomes a
matter of data transfers. But this management of data is not simply
self-referential, or rather it is only partly so. The desires embedded
within biotech research, and the true promises held by new lab
technologies, is to both work on the molecular body at the level of
informatics, as well as enabling informatics to phenotypically (that is,
materially and physically) affect the biological body. 

The imaginary of bioinformatics is that life is computational (that is,
it is discovered that "life" is fundamentally an issue of informatics,
DNA, and biochemical patterning), and that the genome is a computer. So,
what we are facing, philosophically, technically, and politically, with
an event such as DoubleTwist's annotated genome, is not the
incorporation of the body into technology, and it is not a process of
disembodiment - despite the far-reaching tendency towards informatics.
Instead, we are seeing steps in a long, complex process of the creation
of the conditions for an informatics-based approach to the body, where
data not only encodes the molecular body, but it also preceeds and
constitutes the body. 

Molecular Biopolitics

While it would seem that all the hype concerning the "completion" of the
human genome map would be the official announcement that the "biotech
century" had finally arrived, the DoubleTwist announcement shows us
something more radical. In short, DoubleTwist had skipped over the
excitement regarding the completion of the sequencing phase of the human
genome, even before it had been completed. Thus, as soon as genome
sequence data is output, DoubleTwist is there to analyze that data,
adding another modular component to the giant software application that
the genome project has now become. DoubleTwist had brought the life
science of genomics to another level of informational abstraction; while
genome sequencing endeavors, as well as gene patenting and medical
genetics, are based at some point on sampling and encoding DNA from
human subjects (most often through blood samples or tissue banks, for
instance), DoubleTwist in effect announced the secondary importance of
"wet" biological samples for biotech research. That is, DoubleTwist's
emphasis on database streamlining, data mining, and computational gene
discovery shows the extent to which contemporary biotech is as much
information technology as it is molecular biology. As Celera's CEO Craig
Venter stated to the U.S. Congress recently, "We are both a bio-tech and
a high-tech company."

DoubleTwist is an example of the new directions in which both
governments and corporations are able to establish articulate,
sophisticated means of regulation, management, and knowledge-production
over individualized and collective bodies. In this combination of the
earlier techniques of demography, population genetics, and political
economy, the new "molecular biopolitics" can be seen as a way of
utilizing imperatives in healthcare and medicine towards a database
management of the population. As the DoubleTwist.com website states, "If
genes are cities in the vast landscape of the human genome, annotations
are pieces of information about those cities - their location, their
population, and so on."

To be sure, a major question brought up by efforts to map the human
genome has had to do with database management. Whether government-owned
(e.g., GenBank) or privately owned (e.g., Celera), this is a political
approach based in molecular biotechnology and information technology.
Current bioethical debates concern the threats of genetic discrimination
(for example, in health insurance and employment), disease profiling
(should one know one's disease predispositions ahead of time?) and
privacy (one's supposed natural rights to one's own genetic code). While
these are indeed crucial issues that need to be made public, what also
needs to be considered is the general process of bio-informatic
translation which enables genetic discrimination, disease profiling, and
genetic privacy to exist at all. The genome project serves as both an
example and a test-bed for a medical approach to the body on the level
of information; it demonstrates that the biological organism can indeed
be textualized, encoded, uploaded, and analyzed, not through Galenic
humoral medicine, anatomical medicine, germ theory, or through
holistic/alternative approaches, but through software. 

Genethnicities

Biopolitically speaking, the "race" to map the genome was also a race in
another sense. Celera's samples consisted of an egalitarian group
representing various ethnicities and genders, and it plans to continue
its diversifying of genetic polymorphisms by concentrating on targeted
groups: isolated ethnic populations, disease groups, and non-phenotypic
polymorphisms (genetic differences which are not expressed in the
organism). The claim for a genetic basis to ethnicity is a combination
of sociobiology (explaining social phenomenon through biology) and
population genetics (analyzing population migration, settlement, and
drift through genetics). The Human Genome Diversity Project (HGDP) was a
first major, government-sponsored project to take genetic samples from
some 600 geographically-stable ethnic populations (some of which patents
were sought for, but were subsequently dropped due to interventions by
RAFI). 

But the HGP-Celera announcement was different. While the HGDP assumed a
Western, white standard, against which it could map out the differences
from "other" cultures on the genetic level, the HGP-Celera announcement,
by contrast, is all about the use of the rhetoric of multiculturalism
and diversity towards social and cultural problems. This incorporation
of issues concerning ethnicity and the biologisation of race into
informatics can only mean that "difference" becomes a matter of errors
in code, noise in information patterns, or a means of multi-levelled
database classification. With fields such as pharmacogenomics (custom
drug design), SNP mapping (minute genetic differences from individual to
individual), and genetic screening (disease susceptbility profiles), the
ideology of the genome project makes a two-fold political statement:
First, we are all genetically different in our own ways - the assurance
that we are unique as individual subjects, that, genetically speaking,
difference can indeed exist within collectivity. Second, because those
differences only account for 1 to .1% of the entire genome (that is, the
genetic difference between you and I ranges from 1 to .1% of our 100,000
or so genes), this also means that we are more alike than different. As
President Clinton's statement iterated:

"After all, I believe one of the great truths to emerge from this
triumphant expedition inside the human genome is that in genetic terms
all human beings, regardless of race, are more than 99.9 percent the
same. What that means is that modern science has confirmed what we first
learned from ancient faiths. The most important fact of life on this
earth is our common humanity."

The genome project is thus a technically-produced political dream, the
desire to be able to have it both ways: It can state genetic difference,
but it can also use a statistical argument to reiterate that the "human"
genome project is about us all collectively. As the prime example of
democratic science, the genome project lets you have your own voice
while also feeling the solidarity of the collective. The HGP-Celera
announcement is a prime example, not only of a new molecular
biopolitics, but of the ways in which unassuming objects such as
databases, genes, and lab-technologies are all interwoven with political bodies.


References

Celera Genomics <http://www.celera.com>.

DoubleTwist <http://www.doubletwist.com>.

----. "DoubleTwist Completes the First Analysis of the Human Genome."
DoubleTwist.com Press Release (8 May 2000): <http://www.doubletwist.com>.

Human Genome Diversity Project: <http://www.stanford.edu/group/morrinst>.

Human Genome Project (NIH Division):
<http://www.ornl.gov/TechResources/Human_Genome/home.html>.

Kay, Lily. Who Wrote the Book of Life? A History of the Genetic Code
(Stanford: Stanford UP, 2000).

Wade, Nicholas. "Genetic Code of Human Life is Cracked by Scientists."
New York Times online (26 June 2000): <http://www.nytimes.com>.


 
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Eugene Thacker
e: maldoror@eden.rutgers.edu
w: http://gsa.rutgers.edu/maldoror/index.html
Pgrm. in Comparative Literature, Rutgers Univ.
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CURRENT:
"The Post-Genomic Era Has Already Happened"
@ The Thing Reviews <http://bbs.thing.net>

"Point-and-Click Biology: Why Programming is
the Future of Biotech" @ MUTE (Issue 17 - archives
at http://www.metamute.com)

"Performing the Technoscientific Body: RealVideo 
Surgery & the Anatomy Theater" @ Body Modification,
ed. Mike Featherstone (London: Sage, 2000; 
http://www.sagepub.co.uk)

"Fakeshop: Science Fiction, Future Memory & the 
Technoscientific Imaginary" @ CTHEORY
<http://www.ctheory.com>

"Database/Body: Bioinformatics, Biopolitics, and 
Totally Connected Media Systems" @ Switch 
<http://switch.sjsu.edu>
¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬¬
also:
FAKESHOP <http://www.fakeshop.com>
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