What is a genome, and what is genomics?

James Lowe, University of Edinburgh

Definitions are fraught with implications because what they include and exclude incorporates assumptions as to what the thing being defined is and does. The genome is often defined as the complete set of genetic material possessed by an organism, and genomics the science organised around cataloguing and understanding the genome. What, though, do we mean by “complete set”, “genetic material” or “organism”?

“Organism” could mean the individual, the sort of thing that has a name. ‘Bob’, for example. But it could be the species or sub-species Bob belongs to.

Genetic material could be DNA sequences, understood as extensive strings of the nucleotide bases that make it up: As, Ts, Cs and Gs. It could include the chemicals bound to the DNA that affect how it is expressed: epigenetic modifications. It could also incorporate different species of RNA that affect gene expression, some of which are directly inherited from one or both parents.

“Complete set” is even trickier. Is it just the DNA in the nucleus of a cell, contained in the chromosomes? Or does it include the DNA contained in mitochondria, or freely circulating in the body? Does it include all DNA in all cells of the body? DNA is never copied perfectly with every cell division, so all cells in our bodies all have subtly different DNA sequences. Additionally, there are other organisms living in and with us, countless microbes that contribute to our everyday functioning. Should their DNA count?

These are the problems with even an inclusive definition of genome that does not presume what kind of parts or functions of the genome might be relevant, as some definitions that cite genetic ‘information’ or ‘instructions’ may do. It is not possible to get around all of these issues, even if you wanted to scrap the term altogether. The Russian-American geneticist Theodosius Dobzhansky wanted to do just that in the era before DNA was found to be the crucial material basis of heredity. In 1937’s Genetics and the Origin of Species, he preferred “set of chromosomes”. Which and whose set is still not specified by this. Any definition must steer between the twin poles of being overdetermined and importing too many assumptions about the object and its functioning, and being too underdetermined and therefore vague.

In defining the term genome, one inevitably tangles up the descriptive content with a prescription: that this is the proper object of study. The term ‘genomics’ has a similar problem.

‘Genomics’ was coined by the geneticist Thomas H. Roderick of the Jackson Laboratory in the USA, in a debate that by his own recollection was well-fuelled by beer drinking. It was conceived as a title for a journal concerning the science of genomes. The formation of journals is a crucial part of the formation and definition of a scientific field. Part of this is a demarcation of what activity and objects of study constitute part of that field, and what are not. To be able to define genomics would be to shape where and how the billions of dollars of funding coming the way of this new venture would be spent. It would affect what it was for, and how it was conducted.

For example, Maynard Olson, who worked on the human genome project at the University of Washington in the USA, stated in 1988 that “projects should be considered genome research only if they promised to increase scale factors threefold to tenfold”. In other words, genomics was about a process of production of sequence data, which implies a certain mode of organising the sequencing focusing on efficiency. Scaling-up in this fashion meant a centralisation of sequencing activity in a smaller number of large-scale production facilities. This model was counter-posed to a vision of genomics derided by James Watson as a “cottage-industry”, in which smaller-scale operations focused on parts of the genome that were relevant to more specific research goals, finding genes relating to particular diseases for example.

The likes of Olson and Watson were successful in framing genomics in terms of large-scale efforts to sequence the ‘complete’ sets of DNA in organisms, with increasing speed and productivity. However, other ways of understanding and doing genomics persisted alongside this, in hospitals, universities and private laboratories.

Genomics research after the ‘completion’ of the sequencing of the human genome in 2003 has often labelled ‘post-genomics’. This term is a reflection of the success of Olson’s perspective, but it can mislead us. Rather than being in an era succeeding genomics, we instead see a flowering of whole genome projects on different species or even environments, and more specific and targeted genomic research that resembles the  previously disdained ‘cottage-industry’ approach.

We should be attentive to the power of definitions, and what prescriptions and norms are built into them. In the case of ‘genome’, definitions can smuggle in all kinds of assumptions about the role of genes in the development and operations of an organism, units of analysis in biology, which parts of the genome have functional significance and the nature and salience of genetic variation. Framing what constitutes ‘genomics’ has been a powerful way of supporting particular visions of genomic research, and attempting to marginalise others.

 

Supporting bibliography and further reading

Robert Cook-Deegan (1994) The Gene Wars: Science, Politics and the Human Genome. Norton.

Aaron David Goldman and Laura F. Landweber (2016) What Is a Genome?. PLOS Genetics, Volume 12 Number 7, e1006181. This paper is an argument that turns definitions like the US National Institutes of Health one (“An organism’s complete set of DNA, including all of the genes, makes up the genome. Each genome contains all of the information needed to build and maintain that organism”) on its head. Noting that not “all of the information needed to build and maintain that organism” is contained in “[a]n organism’s complete set of DNA”, they propose instead to define genome in terms of “all of the information needed”, which would include much else beyond DNA. Alternatively, one can abandon the informational criterion and just focus on the DNA. Each approach has its benefits and limitations.

Stephan Guttinger and John Dupré (2016) Genomics and Postgenomics. In The Stanford Encyclopedia of Philosophy, edited by Edward N. Zalta.

‘Beer, Bethesda, and Biology: How “Genomics” Came Into Being’. Interview of Thomas H. Roderick by Bob Kuska, Journal of the National Cancer Institute, Volume 90 Number 2, January 21st 1998.

Joshua Lederberg (2001) ‘Ome Sweet ‘Omics – A Genealogical Treasury of Words. The Scientist, April 2001.


Published online: September 2019

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