From Empedocles to Symbiogenetics: Lynn Margulis's revolutionary influence on evolutionary biology

Scientific novelty beyond the experiment

Practical experiments drive important scientific discoveries in biology, but theory-based research studies also contribute novel-sometimes paradigm-changing-findings. Here, we appraise the roles of theory-based approaches focusing on the experiment-dominated wet-biology research areas of microbial growth and survival, cell physiology, host-pathogen interactions, and competitive or symbiotic interactions. Additional examples relate to analyses of genome-sequence data, climate change and planetary health, habitability, and astrobiology. We assess the importance of thought at each step of the research process; the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most-direct and most-scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork. We highlight the intrinsic need for human engagement in scientific innovation, an issue pertinent to the ongoing controversy over papers authored using/authored by artificial intelligence (such as the large language model/chatbot ChatGPT). Other issues discussed are the way in which aspects of language can bias thinking towards the spatial rather than the temporal (and how this biased thinking can lead to skewed scientific terminology); receptivity to research that is non-mainstream; and the importance of theory-based science in education and epistemology. Whereas we briefly highlight classic works (those by Oakes Ames, Francis H.C. Crick and James D. Watson, Charles R. Darwin, Albert Einstein, James E. Lovelock, Lynn Margulis, Gilbert Ryle, Erwin R.J.A. Schrödinger, Alan M. Turing, and others), the focus is on microbiology studies that are more-recent, discussing these in the context of the scientific process and the types of scientific novelty that they represent. These include several studies carried out during the 2020 to 2022 lockdowns of the COVID-19 pandemic when access to research laboratories was disallowed (or limited). We interviewed the authors of some of the featured microbiology-related papers and-although we ourselves are involved in laboratory experiments and practical fieldwork-also drew from our own research experiences showing that such studies can not only produce new scientific findings but can also transcend barriers between disciplines, act counter to scientific reductionism, integrate biological data across different timescales and levels of complexity, and circumvent constraints imposed by practical techniques. In relation to urgent research needs, we believe that climate change and other global challenges may require approaches beyond the experiment.

Choices by organisms: on the role of freedom in behaviour and evolution

Neo-Darwinian biology has demonstrated that it is possible to construct a theory of life that excludes the role of organisms’ free choice. In a richer theory, the latter as a possibility needs to be taken into account. For that purpose, it is necessary to introduce the biological concept of choice, analyse its structure and roles, and consider some implications for biological theory. It is argued here that the conditions for free choice emerge together with umwelt—the space of synchronous options. Basically, choice does not require purpose. This leads to the conclusion that freedom is an attribute of life.

The role of self-maintaining resilient reaction networks in the origin and evolution of life

We characterize living systems as resilient "chemical organizations", i.e. self-maintaining networks of reactions that are able to resist a wide range of perturbations. Dissipative structures, such as flames or convection cells, are also self-maintaining, but much less resilient. We try to understand how life could have originated from such self-organized structures, and evolved further, by acquiring various mechanisms to increase resilience. General mechanisms include negative feedback, buffering of resources, and degeneracy (producing the same resources via different pathways). Specific mechanisms use catalysts, such as enzymes, to enable reactions that deal with specific perturbations. This activity can be regulated by "memory" molecules, such as DNA, which selectively produce catalysts when needed. We suggest that major evolutionary transitions take place when living cells of different types or species form a higher-order organization by specializing in different functions and thus minimizing interference between their reactions.

Climate Science as Counterculture

This article investigates climate science as a cultural object. By pursuing the “logic of its aporias”, it is shown that climate science emerged at the confluence of the objective development of the means of production (constituting a “planetary general intellect”) and the countercultural movement of the 60s, which put ecology at its center, but was broader than mere “environmentalism”. This resulted in the emergence of new forms of sensibility and a qualitative transformation of the natural sciences, which recognized the autonomy and complexity of nature. The constitution of climate science is reconstructed by taking the IGBP’s Amsterdam Declaration as historical archive, and by discussing biographical aspects of representative scientists, in mediation with their work and their world-historical context. Yet, the limits of climate science are those of counterculture. Climate science and its institutions preserve aspects of the previous mechanistic science as well as remaining traces of commodity fetishism