Transgene

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In the TRANSGENE project, the main focus has been on the history of genomics, focusing chiefly on the organisation of concerted projects based on DNA sequencing. However, throughout, spin-offs from genomics have been explored. TRANSGENE’s James Lowe began one such exploration with David Ingram of STIS (and formerly Regius Keeper of the Royal Botanic Garden Edinburgh) last year. It has concerned DNA barcoding, an approach to taxonomic research. It was initially motivated by a desire to pursue the idea that genomics  constitutes a natural historical pursuit.

DNA barcoding was developed in the early-2000s by taxonomists as a means of species identification, to meet the challenge of finding and describing the millions of species that are suspected to exist but are as yet unknown to science, before many become extinct. It involves the sequencing of a gene or genes that vary sufficiently across evolutionary time to enable distinct species to be discriminated, and that vary consistently in this respect across different lineages. DNA barcoding does not necessarily constitute genomics in itself, as it focuses on only a few selected small regions of the genome. It does, however, reflect the inspiration of genomic infrastructures and approaches, as well as drawing on the resources produced by it. DNA barcoding itself was an articulation of these by taxonomists themselves. It was not uncontroversial, facing criticism from other taxonomists for being reductive and not offering a solution for actually describing species, as opposed to merely identifying them.

From the start of this investigation of DNA barcoding, James and David's primary focus has been on plant DNA barcoding, but they have also considered the barcoding of animals and the peculiar microscopic photosynthesising planktonic algae known as diatoms. They have surveyed the literature, interviewing taxonomists who have been involved in helping to establish and implement barcoding for the types of organism they work with, and discussed their developing ideas over Zoom calls. More recently, they have taken the opportunity to give form to some of their thoughts that was presented by the organisation of a workshop on the Philosophy of Plant Biology, by Özlem Yılmaz and John Dupré at the University of Exeter. This took place from May 5th to 7th, and involved a stimulating array of talks on topics as varied as plant breeding, phenomics, plant cognition and the philosophy of plants articulated by Theophrastus, who worked with Aristotle.

They presented a paper looking at how the ontological commitments – views of the kinds of entities that exist and, crucially, the relationships between them – of animal, plant and diatom taxonomists have been shaped by DNA barcoding. They take ontological commitments to be intrinsically related to some of the practical difficulties involved in discriminating between species. They found that the transformative potential of DNA barcoding has been tempered by existing ontological commitments held by taxonomists, the practices and institutional framework of taxonomy, but also the working world contexts in which taxonomists perform their work. Here they drew upon the useful concept of working worlds – domains that pose and frame particular problems, which scientists can then approach by constructing abstract representatives – introduced by Jon Agar. Nevertheless, they identify a shift in the way in which taxonomists relate to variation when conducting their work. They intend to further develop the arguments and insights they made in their presentation, with a view to publishing a paper on the topic in a philosophy of biology journal. Furthermore, they believe there is much else to investigate and draw out of the area of DNA barcoding, including a broader narrative of how it relates to taxonomy.