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

["-/iapu.pavu.com/-" <ctgr@free.fr>]

Eugene Thacker a *crit :

> The Post-Genomic Era Has Already Happened

hello,
we are glad to have this fresh news.

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This gene is called Gene Vincent and did appear year 1922 in the Auvergne - sunny
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spetial thanks to Eu - gene for his cooperation

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>
>
> 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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