Synthetic biology and the search for alternative genetic systems: Taking how-possibly models seriously

Abstract

Many scientific models in biology are how-possibly models. These models depict things as they could be, but do not necessarily capture actual states of affairs in the biological world. In contemporary philosophy of science, it is customary to treat how-possibly models as second-rate theoretical tools. Although possibly important in the early stages of theorizing, they do not constitute the main aim of modelling, namely, to discover the actual mechanism responsible for the phenomenon under study. In the paper it is argued that this prevailing picture does not do justice to the synthetic strategy that is commonly used in biological engineering. In synthetic biology, howpossibly models are not simply speculations or eliminable scaffolds towards a single how-actually model, but indispensable design hypotheses for a field whose ultimate goal is to build novel biological systems. The paper explicates this by providing an example from the study of alternative genetic systems by synthetic biologist Steven Benner and his group. The case will also highlight how the method of synthesis, even when it fails, provides an effective way to limit the space of possible models for biological systems.

Multiple Realization in Systems Biology

“…Systems biology is a thriving new discipline that enjoys both an engineering and biological perspective, in which general design principles (called 'network motifs') that recur in 4 Koskinen (2017) and Chirimuuta (2018) recently have also argued for the common existence of MR in biological systems. Koskinen approaches this issue from the perspective of synthetic biology, where scientists not only create novel functional realizations that are not true of the actual biological world, but also streamline functional realizations that could otherwise come to be true in the actual biological world.…”

“…Multiple realization (MR) is the thesis that, roughly speaking, a higher-level scientific kind can be multiply realized (or is at least multiple realizable) by more basic scientific kinds (Shapiro 2000). 1 The thesis was initially proposed to describe the relationship between psychological and neuroscientific kinds (Putnam 1967;Block and Fodor 1972;Fodor 1974), but was later extended to fields such as philosophy of biology (Kitcher 1984;Sober 1999;Koskinen 2017;Fang 2018). For many participants in the debate (e.g., Polger and Shapiro 2016), MR is essentially an empirical thesis concerning a particular type of phenomenon happening in the real world and, as such, claims for (or against) it must be supported by empirical evidence.…”

Multiple Realizability as a design heuristic in biological engineering

“…Engineers typically do not aim for just one all-purpose solution, but assesses alternatives based on pragmatic criteria, like efficiency, reliability, or even aesthetics (Kroes 2012). Biological engineering is no exception here (Koskinen 2017).…”

“…In the engineering of novel biological systems, this fixing of a shared function has a number of beneficial features. First, it imposes an effective constraint that limits the search space for novel designs (see Koskinen 2017). To be sure, there may in theory be a myriad of different ways to implement even a single function.…”

Could We Really Be Made of Swiss Cheese? Xenobiology as an Engineering Epistemology for Biological Realization

“…[14] The best proof of a possibility is to make it real. [29] Combing these results with more general theories about the world, synthetic knowledge can be generalized beyond single instances of tinkering, making it an indispensable tool for generating new perspectives, [30,31] and even helping to tackle questions in the philosophy of biology. [32,33]…”