Constructive Neutral Evolution is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic and molecular structures (...) or processes, such as retained gene duplications, the spliceosome, and RNA editing. Here we aim to expand the scope of such explanation beyond the molecular level, integrating CNE with Multi-Level Selection theory, and arguing that several popular higher-level selection scenarios are in fact instances of CNE. Suitably contextualized, CNE occurs at any level in the biological hierarchy at which natural selection as normally construed occurs. As examples, we focus on modularity in protein–protein interaction networks or “interactomes,” the origin of eukaryotic cells and the evolution of co-dependence in microbial communities—a variant of the “Black Queen Hypothesis” which we call the “Gray Queen Hypothesis”. (shrink)

Microbiologists are transitioning from the study and characterization of individual strains or species to the profiling of whole microbiomes and microbial ecology. Equipped with high-throughput methods for studying the taxonomic and functional characteristics of diverse samples, they are just beginning to encounter the conceptual, theoretical, and experimental problems of comparing taxonomy to function, and extracting useful measures from such comparisons. Although still unresolved, these problems are well studied in macro-ecology and are reiterated here as an historical precautionary for microbial ecologists. (...) Beyond expected and unresolved terminological vagueness, we argue that assessments and comparisons of taxonomic and functional profiles in micro-ecology suffer from theoretically unresolvable arbitrariness and ambiguities. We divide these into problems of scale, individuation, and commensurability. We argue that there is no technically/theoretically “correct” scale, individuation, or comparison of taxonomy and function, but there are nonetheless better and worse methodologies for profiling. (shrink)

Recent debates about the biological and evolutionary conditions for sentience have generated a renewed interest in fine-grained functionalism. According to one such account advanced by Peter Godfrey-Smith, sentience depends on the fine-grained activities characteristic of living organisms. Specifically, the scale, context and stochasticity of these fine-grained activities. One implication of this view is that contemporary artificial intelligence is a poor candidate for sentience. Insofar as current AI lacks the ability to engage in such living activities it will lack sentience, no (...) matter what its coarse-grained functions. In this paper, we review the case for fine-grained functionalism and show that there are contemporary machines that fulfil the fine-grained functional criteria identified by Godfrey-Smith, and thus are candidates for sentience. Molecular machines such as Brownian computers are analogous to metabolic activity in their scale, context and stochasticity, and can serve as the basis of AI. Molecular computation is a promising candidate for artificial sentience according to contemporary philosophical accounts of sentience. (shrink)

In the 1970s, R.D. MacElroy coined the term ‘extremophile’ to describe microorganisms that thrive under extreme conditions (MacElroy 1974). This hybrid word transliterates to ‘love of extremes’ and has been studied as a straightforward concept for the past 40 years. In this paper, we discuss several ways the term has been understood in the scientific literature, each of which has different consequences for the distribution and importance of extremophiles. They are, briefly, Human-Centric, at the Edge of life’s habitation of Morphospace, (...) by appeal to Statistical Rarity, described by Objective Limits, and at the Limits of Impossibility for metabolic processes. Importantly, these concepts have co-existed, unacknowledged and conflated, for decades. Confusion and equivocation threaten to follow from the wildly varied inclusion or exclusion of organisms as extremophiles depending on the concept used. Under some conceptions, entire kinds of extremophiles become meaningless. Since our understanding of how life works is shaped by what we take to be its extremes, clarifying extremophily is key for many large-scale projects in biology, ecology, biotechnology and astrobiology. In what follows, we proceed as if a noncontroversial account of life is possible and that it is possible to find complex chemistry in the Universe that is similar enough to Life on Earth such that both may be considered instances of ‘life’ (but see Mariscal & Doolittle 2018). We raise, but do not address, the questions of whether the distribution of Life on Earth is representative of what we may find elsewhere in the Universe, whether the same kinds of extremophiles would exist given a replay of the tape of life. Additionally, each of these concepts assumes life based on some sort of biochemistry in this universe, effectively setting aside claims made by some artificial life proponents that their digital organisms are genuine examples of life (Langton 1989, Ray 1995). On the distinction between extremophilic and extremotolerant, we note that all accounts accept the latter as a broader category than the former, since ‘phily’ means love and tolerance is a prerequisite for love under any conception. Indeed, there will be many extremely impoverished environments where tolerance is the only option and thriving is precluded, e.g. Bacillus marismortui was extracted and grown from 250-million-year-old salt crystals in the Permian Salado Formation in an inactive yet persistent state (Vreeland et al., 2000). We also note that extremophily, as a functional category, is potentially applicable at many levels of the biological hierarchy. Extremophily at one level does not necessarily extend to higher and lower levels. For instance, a microorganism in isolation might be quite intolerant to certain environmental conditions yet flourish when subjected to the same conditions as a community or natural biofilm. Alternatively, a protein molecule might be quite stable or active under certain conditions even if the optimal environment for the organism containing it is far more mesophilic. There is an industry of artificially selecting organisms and proteins to adapt to extreme environments (see van den Burg & Eijsink 2002), providing some justification to consider ‘functioning at extremes’ as a worthwhile category of investigation. Finally, we also note certain physico-chemical ranges are rarely considered with respect to extremophily – timespan, size, nutrient availability (Hoehler & Jørgensen 2013), etc. – as well as some biological parameters – abundance, isolation, competition, etc. Perhaps scientific interest must also come into play as to the reason these criteria are not considered relevant. We return to this issue later. In the next section, we give five definitions of extremophily, show their benefits, drawbacks, and unintended yet unavoidable consequences. These arguments are summarized in Table 1 and represented visually in Figures 1 and 2. Given research on polyextremophiles, it seems Figure 2 is a more plausible representation of the state of current knowledge than Figure 1 (Harrison et al. 2013). Life is patchily distributed across various dimensions, which may reflect its contingent history, poor sampling, or (perhaps) fundamental limits. Figure 3 shows the conceptual flowchart for all of these views. In the following section, we take a step back to ask whether we should choose between these definitions and how such a judgment could be made. We argue for a limited pluralism, in which some, but not all, of the concepts are acceptable relative to certain practical and theoretical aims. (shrink)

Constructive Neutral Evolution theory provides selectively neutral explanations of the origin and maintenance of biological complexity. This essay provides an analysis of CNE as an explanatory strategy defined by a tripartite set of conditions, and shows how this applies to cases of the evolution of complexity at higher-levels of the biological hierarchy. CNE was initially deployed to help explain a variety of complex molecular structures and processes, including spliceosomal splicing, trypansomal pan-editing, scrambled genes in ciliates, duplicate gene retention and fungal (...) ATP synthetase structure. CNE has also been generalized to apply to phenomena at the cellular level, including protein-protein interaction network modularity, obligate microbial symbioses, eukaryogenesis and microbial unculturability. This essay further extends CNE to cases of complexity at levels of organization higher than the molecular and cellular. These are multicellular phenotypic complexity, multicellular ecological complexity and, some cases of cultural complexity. (shrink)

We begin with the idea that lines of reasoning are continuous mental processes and develop a notion of continuity in proof. This requires abstracting the notion of a proof as a set of sentences ordered by provability. We can then distinguish between discrete steps of a proof and possibly continuous stages, defining indexing functions to pick these out. Proof stages can be associated with the application of continuously variable rules, connecting continuity in lines of reasoning with continuously variable reasons. Some (...) examples of continuous proofs are provided. We conclude by presenting some fundamental facts about continuous proofs, analogous to continuous structural rules and composition. We take this to be a development on its own, as well as lending support to non-finitistic constructionism. (shrink)