1. ESRC Genomics Network (archive)
  2. Gengage
  3. The Human Genre Project

Cesagen · Research

Transcending the Genome: The paradigm shift to proteomics

Peter Glasner

Start date

2002-04-01

Affiliated staff

Ruth McNally

Background

For most of the 20th century, the gene occupied a privileged position in Western culture, culminating in the Human Genome Project (HGP). Completed at the beginning of the 21st century, the legacy of the HGP is more than maps and sequences. It is credited with leaving an imprint on the goals, methods and organisation of biological and biomedical research. Referred to as the ‘omic’ revolution, the objective of this 21st century research trajectory is to compile complete data sets for numerous biomolecules, and then to model biological systems in silico by linking various omic databases together. Moreover, omics and the new systems biology are presented as constituting a paradigm shift from the genetic reductionism of the past. A new term – ‘post-genomics’ – has been coined to describe biological research after the completion of the HGP. But what is post-genomics? Does the term imply that the genome and the gene have been transcended? And if so, what has, or might, take their place? In other words, how are the fields of biology and biomedicine and their knowledges and social relations being constituted beyond the HGP? And what might be the role(s) of science and technology studies in these scientific-social worlds? This project was an exploration of the transformation of knowledge production beyond the HGP through the study of the emergent field of ‘proteomics’. Proteomics is a key example of the new omics. Its object of analysis is the proteome, an entity which is typically defined as the protein equivalent of the genome, but in practice the proteome has multiple definitions and proteomics has contested boundaries.

Aims

The overarching aim was to explore whether, and in what ways, proteomics constitutes, or is part of, a paradigm shift in the production of knowledge in the biosciences. This involved the following objectives:

  • To locate proteomics as a research field by mapping the locations and identities of key actants (people, artifacts, organizations), and monitoring their relations over time
  • To compare and contrast different visions of what proteomics is – its origins, boundaries and future trajectories - in particular in relation to protein biochemistry, genomics and systems biology
  • To analyse how the production of knowledge in proteomics is accomplished
  • To enrol proteomics actants in our research and engage in collaborative research with them
  • To identify, experiment with and critically evaluate new research methods



Methods

  • Using IssueCrawler/ReseauLu software to locate, map and monitor proteomics networks on the WWW
  • Observation and participation in proteomics meetings, workshops, congresses and core facilities
  • Interviews with key figures in the global, national and local organisation of proteomics
  • Qualitative data analysis


Findings

  • Proteomics is a ‘discovery’ science (unlike hypothesis driven genomics) characterised by high-throughput production of large-scale data sets to form reference databases and public repositories. It is an expensive ‘big science’ enterprise requiring substantial sustainable funding if it is to succeed.
  • Following the failure of the Human Genome Project to deliver significant downstream therapeutic interventions, Proteomics promises to fill the gap in identifying therapies and diagnoses for human illnesses.
  • The Human Genome Project is however presented as an exemplar for the unfolding ‘omic’ scientific revolution. There is an ongoing ‘turf war’ to enrol allies among several competing visions for its outcome including genomics, proteomics, and the ‘new biology’.
  • Proteomics is characterised by multi-disciplinarity, including physicists, chemists and statisticians as well as biologists, which is increasing engineered by the development of core facilities through performative architecture (eg QB3 Building at UCSF or Newcastle’s Centre for Life).
  • Laboratory life has changed to become more virtual, and the experiment has become redefined to rely increasingly on the construction, curation and mining of large scale databases, rather than using conventional ‘wet’ laboratories.
  • The requisite standardisation protocols for evaluating large scale data sets have yet to be agreed, and dissemination therefore rests with gatekeepers such as scientific journals who set the standards. The Human Proteome Organisation is currently developing its own standards through the PSI (Protein Standards Initiative).
  • The proteomics community recognises that their results are, in practice, irreproducible, and so uses surrogates: statistics using bioinformatics; and wet lab platforms (a return to genomics?) to validate function biologically.
  • The division of labour has been significantly altered with the emergence of an increasingly male, fulltime, and relatively unskilled workforce combined with a shift toward the ‘grey’ labour market, and personnel located in the new growth economies such as India and Singapore.
  • There are no ELSI (Ethical, Legal, and Social Implications) research initiatives in the Human Proteome Organisation (HUPO) as there were in Human Genome Organisation (HUGO). Proteomics is not an activist in, for example, the agendas of Non-governmental Organisations (NGOs). In effect, proteins do not have a ‘social life’ in the way that genes still do


Publications

McNally, R. and Glasner, P. (2006) 'Transcending the genome? Studying life in the proteomic bioscape', in Peter Glasner and Paul Atkinson (eds) New Genetics, New Social Formations, London: Routledge.

McNally R. (2005) 'Sociomics! Using the "IssueCrawler" to map, monitor and engage with the global proteomics research network'. Proteomics 5: 12 pp. 1-7. Available here (external website)

Glasner P. 2002 'Beyond the genome: Reconstituting the new genetics'. New Genetics and Society 21(3): 267-277 

Further information

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