-/iapu.pavu.com/- on 13 Jul 2000 07:37:43 -0000


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[Nettime-bold] Re: <nettime> Post-Genomics




Eugene Thacker a *crit :

> The Post-Genomic Era Has Already Happened

hello,
we are glad to have this fresh news.

Our laboratories of researche and discovery have searched and discovered the gene
responsible of the Rock and Roll attitude.
This gene is called Gene Vincent and did appear year 1922 in the Auvergne - sunny
day, good mom and strong pop. Today is a good birthday for all attituders around
the world.

thank you for you attention and good R n' R day
spetial thanks to Eu - gene for his cooperation

http://pavu.com
-/ stop it ! before you fall in love ! /-

>
>
> 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>.
>
>
> 
> Eugene Thacker
> e: maldoror@eden.rutgers.edu
> w: http://gsa.rutgers.edu/maldoror/index.html
> Pgrm. in Comparative Literature, Rutgers Univ.
> 
> 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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