International Society for History, Philosophy, and Social Studies of Biology

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TUESDAY, JULY 7  /  09:00 - 10:30  /  DS-R520
Organized session / standard talks
The use and abuse of function concepts in genomics

Stefan Linquist (University of Guelph, Canada)

The field of genomics is actively engaged in a philosophical debate over the appropriate use of function concepts. The catalyst for this debate was a widely publicized finding by the ENCODE research consortium. In 2012, ENCODE announced that over 80% of the human genome has a biochemical function. The popular media quickly seized on this finding, claiming that the “myth” of junk DNA had been overturned. Almost immediately, these claims drew fierce criticism from some of the world’s leading molecular biologists. They challenged ENCODE’s definition of “function” and accused them of exploiting an ambiguity in this term in order to exaggerate the significance of their research. This session will explore three dimensions of this debate. Dr Gregory will place the recent ENCODE controversy into historical context, arguing that there is a long tradition of abuse surrounding the function/junk distinction . Dr Doolittle will provide an play-by-play account of the ENCODE controversy, identifying what he takes to be at issue in this debate. Dr Linquist will discuss some of the philosophical implications of this debate, focusing on whether causal role functions are overly permissive.

Junk and the genome

T. Ryan Gregory (University of Guelph, Canada)

It has been known for more than 60 years that the amount of DNA in the genome bears no relation to the complexity of the organism in which it is found or the number of protein-coding genes which it contains. Once considered paradoxical, this discrepancy between genome size and gene number is explained by the massive quantity of non-coding DNA in most animal and plant genomes. If media reports, anti-evolutionists, and the authors of many scientific papers are to be believed, this non-coding majority has long been dismissed as useless “junk”, and only now is its potential biological significance being considered. But is this characterization accurate? And what is the current state of knowledge regarding so-called “junk DNA”? In this seminar, I will present historical and conceptual background to this topic and will address the most common misconceptions about the biology of “junk DNA”. In broader terms, this seminar will examine the importance of properly acknowledging the history of scientific research, the dangers of scientific hype, and the standards of evidence necessary for ascribing “function” to biological features.

The ENCODE kerfuffle

W. Ford Doolittle (Dalhousie University, Canada)

The publication in Nature, in September 2012, of a flurry of papers describing results form the well-funded ENCODE (Encyclopedia of DNA Elements) megaproject drew much attention in the popular press and scientific/philosophical literature. The upset was caused by ENCODE’s claim to have debunked the notion that much of our DNA is “junk” (that is, not expressed in phenotype, or at least not in phenotype within the purview of natural selection.) Two philosophical issues, not often seen as such by practicing molecular and genomic biologists, are at stake. The first is adapationism – the common belief that every base in DNA is somehow accountable to selection. The second is conflation of causal role and selected effect conceptions of biological “function”. Although the history of debate around these is long and rich, ENCODE investigators seem ignorant of it. Some simple thought experiments involving C-value (DNA content per haploid genome) tell us that unless we humans are very special, not only in the eyes of God but of Natural Selection, our genomes must be very “junky.” An alternative is to regard “function” as diffusible, spreading to engage all of its potential genomic determinants. I will discuss both, and possible reasons for the apparent obtuseness of the ENCODE consortium and Nature magazine, a principle supporter.

How best to reform function-talk in genomics?

Stefan Linquist (University of Guelph, Canada)

Until recently, debates about the nature of biological function have transpired primarily across the pages of philosophical journals. The near-consensus in philosophy is a form of pluralism: both selected effect (SE) and causal role (CR) function-concepts are employed in biological explanation. However, the recent controversy surrounding the ENCODE project has drawn molecular biologists into the function debate. Interestingly, many of them do not recognize the CR concept as legitimate. The problem is that CR functions are too permissive, allowing for “bizarre outcomes” as one molecular biologist recently put it. This retreat to the perceived legitimacy of SE functions is motivated by ENCODE’s abuse of the CR concept. Does it go too far? This paper will assess three alternative proposals for reforming function-talk in genomics. One option is to abandon CR functions altogether and use “function” exclusively for elements with selected effects. A second strategy limits the kinds of investigator-interests that can legitimately motivate a CR functional analysis. A third strategy (most preferable, I think) is to restrict CR functional analysis to certain types of system. I argue that highly cohesive systems, in which the functional components are proper parts of the systems whose capacities they explain, are most conducive to CR analysis. The further one gets from this ideal, the less useful CR analysis becomes. Recent developments in whole genome biology suggest that the majority of DNA in the genome is indeed far from this ideal.