In this project, we examine the ways in which contemporary molecular biology is influencing the understanding of some of the key concepts in evolutionary biology. The influence in question can be traced not only in ‘big-science’ projects, most notably, the Human Genome Project (HGP) and its follow-ups, e.g., the Encyclopedia of DNA Elements (ENCODE), but also in many ‘small-science’ research projects. We focus on the exchange between these two major biological domains as an underexplored layer in philosophy of biology. Accordingly, our project is structured as follows.
In Part 1 of the ThUMB project, we examine how discoveries of intricate workings within eukaryotic genomes, in particular, the human genome, have clear implications for reconsideration of our understanding of the genome structure and for an upgrade of the corresponding more theoretical notions of a gene, biological function and natural selection. Namely, the discoveries concerned with (1) the mechanisms of gene duplication and gene sharing, (2) extremely large portions of mobile DNA elements within eukaryotic genomes and (3) new functional genes arising from non-coding regions, all call for significant accommodations at the corresponding conceptual level. Namely, mechanisms of gene duplication, extensively studied, are the main source of functional novelty, but at the same time, a cause of ‘bloated’ architectures of eukaryotic genomes. In that sense, it is interesting to examine what is the role of selection in maintaining genetic redundancy at the genome level, especially, in bringing about novel functions. Scientists’ conjectures about new genes are laden with theoretical considerations regarding what constitutes a (new) function, and whether positive Darwinian selection is necessary for producing them. For instance, in cases of new genes arising after gene duplication, it is supposed that it is sufficient that purifying selection acts on the sequences, while in case of de novo genes from non-coding regions, it appears that working of positive Darwinian selection is necessary. These examples illustrate how the concept of gene is closely associated with the understanding of biological function, which, depending on the account endorsed, can be defined with reference to natural selection, thereby making these concepts theoretically intertwined in interesting ways. Additionally, discoveries of large proportions of mobile DNA, predominantly non-functional, open questions regarding distinct levels of selection, since such elements can be proliferated for their ‘selfish’ reasons. In this Part, our research activities are directed towards the following two Objectives in Section (d) of the Proposal: (1) to address the conceptual puzzles emerging from the scientific reasoning concerned with functional ascriptions to ‘evolutionary conserved regions’ in eukaryotic genomes and, accordingly, to assess the role of natural selection in grounding biological functions; and (2) to unravel the intricate relationship between the notions of gene, biological function, and natural selection.
In Part 2, ThUMB singles out distinct types of explanatory practices in the area of genome evolution, referring in particular to the abovementioned mechanisms of gene duplication, sharing and de novo genes from non-coding regions. We claim that, in this regard, we should go beyond the standard view of mechanisticexplanation (i) by taking into consideration rival general accounts of scientific explanation, namely, the unificationist account, (ii) addressing some important internal issues within the mechanistic approach itself, and (iii) by working out an appropriate level of explanatory integration between the structural and etiological types of scientific explanation.
Finally, in Part 3, through some recent case studies, the ThUMB project explores how scientific decision-making and dissemination of research results relate to the public understanding of the life sciences. We address two potential problems with the organization of scientific work into big-science projects: (1) large funds cause extra pressure to produce extraordinary outputs, and (2) research that is basically data-driven, or hypothesis-free, and delivered directly to the public, may be unachievable.