From Riboswitches to the Cosmos: Biological Decision Making and the Stoic Logos

In the modern scientific conception, intelligence is generally treated as a localized phenomenon and the proprietary feature of the brain. We view the rest of the natural world as a collection of “blind” mechanisms devoid of genuine agency: enzymes randomly encountering substrates and molecules folding under a buffeting of “thermal noise.” But as a scientist who also practices Stoic philosophy, I find that this reductionist view creates a potential limitation to our understanding of intelligence – here expressed through “biological decision making.”

To bridge this gap, we can look to the Stoic concept of the Logos. This word originally had a variety of commonplace meanings in Ancient Greek, such as “word”, “idea”, “reason”, “explanation”, or “subject matter.” Thus, one could talk of the logos of a profession, person, or situation, among others. In this sense, the logos of carpentry or painting, for example, would consist of the set of rules that describe the field. Etymologically, the word “logos” lives on in modern English words like “logic”, “biology”, “physiology”, and many other -ologies that define different scientific disciplines.

This original definition of logos was expanded upon by the pre-Socratic philosopher Heraclitus of Ephesus, who conceived of the Logos (capital “L” added here for emphasis) as the universal, divine principle of reason and order that governs the cosmos (Geldard, 2000). This Heraclitean concept of a Universal Logos was taken up by the Stoics, notably Zeno and Chrysippus, who emphasized the rationality of the Logos, which orders, animates, and permeates everything. This may be familiar to some through the Bible’s description of the Logos/Word of God (Britannica Editors, 2024).

The Stoics proposed a sophisticated physical model for how the Logos was able to manifest this rational principle within the cosmos. This manifestation was accomplished via pneuma, which they conceptualized as a “fiery breath” that completely penetrates passive/inert matter giving it structure (via tonos or tension) and defining its properties (Sellars, 2006). Different levels of tonos within the pneuma gave rise to the scala naturae, a hierarchy of four distinct scales of complexity. At the base sits hexis (cohesion), the lowest level of tension, which provides the physical properties and structural form of inanimate matter. Next is physis (organic growth) found in living things, followed by psyche (soul/perception) which animates animal life. Finally, Logos (rationality) governs both rational beings and the Cosmic whole. Importantly, this architecture is nested, where each higher level encompasses and regulates the lower levels.

Modern science has evolved from these early philosophical models—based on speculation grounded in reason—to embrace a more quantitative picture of reality based on observable/measurable properties, (generally) testable/falsifiable hypotheses, and mathematical models. Despite these divergent approaches, there is a remarkable correspondence between the role of Logos in Stoicism and the scientific understanding of information flow. In this essay, I explore this correspondence through the specific lens of biological decision making to see how ancient philosophical ideas were not only prescient of modern scientific ones, but may also help to inform/expand our understanding.

Molecular logic gates – riboswitches

RNA (ribonucleic acid) is a biopolymer that is chemically similar to DNA but structurally quite distinct. Unlike DNA, which exists almost exclusively as double-stranded (Watson-Crick) helixes, RNA exists as a single strand that can “fold” back onto itself to form complex molecular shapes. Significantly, these shapes (or folds) dictate the diverse functions of RNAs in the cell by mediating important interactions with other biomolecules or altering intrinsic properties of the RNA molecule itself. To highlight the logos (lower case l) of RNA structure/function relationships, we can focus on a large and diverse class of RNAs known as riboswitches.

Riboswitches are short segments of highly-structured RNA embedded within longer RNA sequences that “carry” genetic information within the cell acting as “messenger” RNAs. Specifically, these messenger RNAs carry the information to make proteins for the cell via the process of “translation,” where a huge molecular engine known as the ribosome reads out the messenger RNA like a tape. The role of the riboswitch here is to regulate this translation process to control the flow of genetic information. They do this through a fascinating process that involves the “sensing” of a biological state (such as metabolite concentration) and a structural alteration that affects the expression of the associated gene (Edwards & Batey, 2010).

Riboswitch functions are exemplified by the classic example of the thiamine pyrophosphate (TPP) riboswitch, which is found embedded within the genes of a wide variety of microbes. The role of this riboswitch is to sense the concentration of TPP (a biologically active form of vitamin B1). This “sensing” takes the form of the direct binding of the TPP molecule by the riboswitch, which induces a dramatic structural rearrangement in the riboswitch. It is this structural rearrangement that transmits the binding information to the messenger RNA that results in the inactivation of gene expression through mechanisms like transcription termination or inhibition of protein translation (Kavita & Breaker, 2023).

This system forms a molecular logic gate that Nature repeatedly uses in important biological feedback loops. For example, TPP riboswitches can be found in genes used in the biosynthesis of TPP. Thus, a negative feedback loop is formed, where the accumulation of the end-product of the regulated gene “loops back” to reduce its expression. This encoded information acts as a plan for managing the metabolic demands of the cell. The logos (logic) of the riboswitch is the structural and functional information encoded within its sequence, which itself arises from the chemical and physical laws that dictate how RNAs form and fold. In this sense, the “knowledge” to build a regulatory loop via a riboswitch is present within the material itself. This manifests the Stoic concept of hexis – the base level of the scala naturae where pneumatic tension (tonos) imparts cohesion, form, and unique physical properties to matter. Viewed through this lens, the riboswitch is an expression of Nature’s ability to manifest systems to process information. With this concept in mind, it is interesting to note that the TPP, and other riboswitches, have convergently evolved multiple times in a variety of organisms across evolution. While the mutational processes that drive molecular evolution occur through seemingly stochastic processes, the sequence/structure solution spaces funnel RNAs toward near-identical solutions.

Allosteric regulation of enzymes – glycogen synthase

The metabolic processes of life require the coordinated activity of multiple enzymes. An enzyme is a type of specialized protein with a functional structure that includes an “active site” for catalyzing a chemical change or reaction. Enzymes are typically chained together in coordinated pathways where the products of one enzyme are fed to additional enzymes in a pathway to yield a desired final product. Particularly important enzymes in these pathways are typically the sites of intense regulation. This is illustrated very nicely using the example of glycogen synthase, one of the key enzymes involved in the synthesis of glycogen: the polymeric form of glucose that is used to store energy in animals (Berg et al., 2023). Glycogen synthase catalyzes the growth of glycogen chains, effectively removing free glucose from the cell and storing it in glycogen particles. This is a key process not only for the cell but for maintaining homeostasis (metabolic balance) across the entire organism.

A regulatory paradigm used in many enzymes, including glycogen synthase, is allostery. Allostery is the chemically induced conformational change in a protein that affects its activity. In the case of glycogen synthase, the molecule G6P plays a key role in allosteric regulation. G6P (glucose-6-phosphate) is a signal of glucose abundance in the cell; when glucose is high, G6P concentration is high. G6P binds to a specialized site on glycogen synthase called an allosteric regulatory site. When bound at this site, G6P alters the shape of the enzyme through global structural rearrangements that convert it from an inactive “tense” conformation (where the active site is constrained) to an active “relaxed” conformation (where the active site is accessible). In this relaxed state where tension has been relieved, the enzyme has increased activity, making it better able to convert glucose into glycogen. In Stoic physics pneuma exists in different levels of tonos (tension) to imbue objects with various properties. In the allosteric regulation of enzymes like glycogen synthase, we see an interesting case where a molecule’s tension literally affects its function.

As glucose is removed from the cell by this activated enzyme, G6P levels drop, and fewer allosteric sites are bound. Naturally, the unbound glycogen synthase returns to a state of increased tonos (tension) so that activity drops with its glucose substrate: as need for the enzyme is reduced, so is its activity. This process of modulating tension/activity through allosteric regulation links a highly local process, the activity of an enzyme, to the global state of the cell and, indeed the whole organism—as high levels of glucose in the cell are ultimately linked to blood glucose levels. In this sense the logos of glycogen synthase is to “sense” glucose levels and respond accordingly to store for energy and to maintain healthy levels of glucose for not only the cell, but the organism as a whole (by sequestering excess glucose as glycogen). The local logos of the enzyme is also a participant in the greater logos of the whole organism.

Information processing in the plant root-shoot axis

Moving beyond the logos of individual molecules, let’s look at a fascinating macroscopic system found in plants: the root-shoot axis, which forms a complex communications network (Stassen et al. 2021). While it may seem that plants are simple, static, “vegetative,” organisms, their lives are in fact extremely dynamic and driven by the need to make rapid and complex decisions in response to changes across a variety of external/environmental, internal/physiological, and temporal states (Brenner et al., 2006). In mediating this complex decision-making, the root-shoot axis plays key roles; but what precisely is the root shoot axis? The root-shoot axis establishes the plant’s basic body plan and defines the polarity between the aboveground portion (the shoot) and the belowground portion (the root), which are connected through a central stem. It also provides a key conduit for the flow of nutrients and information throughout the plant. This manifests the next level on the scala naturae, the physis (organic growth) that governs vegetative life. 

Plants are connected to the soil through their root system. Roots play a structural role in anchoring the plant in place and in bringing nutrients from the soil, such as water, minerals, and various molecules into the plant. Indeed, roots play a fascinating role in cultivating their own “microbiomes” of beneficial microorganisms. This includes nitrogen-fixing bacteria (in some plants) that shelter within the roots to provide chemical fertilizer by fixing atmospheric nitrogen, as well as mycorrhizal fungi that form extensive networks to extend the plant’s ability to absorb nutrients. Nutrient-rich water flows through the roots of the plant into the stem and then the shoots and is dispersed throughout the stems and leaves, where it collects the metabolic products of photosynthesis, such as energy in the form of sugars, then returns through the shoots back to the roots. Like in animals, this circulation facilitates the transport of signaling molecules, such as hormones, to effect physiological changes. However, this “biological conversation” extends beyond the plant’s own cells; it includes molecules from the root microbiome, which themselves are receiving chemical signals from their host plant. In this way there is a constant flow of information from the plant microbiome to the roots, stem, shoots, leaves, and back again—from the plant to the environment and back again.

Ultimately, the root-shoot axis, grounded in the root apex, forms a decentralized command center (Baluška et al., 2004), or what the ancient Stoics would call the hegemonikon. Notably, the root apex was originally (and controversially) hypothesized to be the “plant brain” by Charles Darwin in 1880 (Darwin, 1880) for its ability to integrate data and make decisions. This hegemonikon of the plant is constantly receiving and integrating data about soil nitrogen levels, temperature, the microbiome, etc. to make key biological decisions. For example, the root apex can sense low levels of soil nitrogen, trigger rapid root elongation and “call” for more nitrogen-fixing bacteria. In this sense, the Darwinian “root brain” is not a specific organ like the human brain, but a distributed information processing system whose logos provides the immobile plant the ability to navigate an ever-changing and dynamic world..

The gut-brain axis and our distributed intelligence

It may be surprising to learn that your gut contains more neurons than your spinal column. This huge number of gut neurons forms what is called the enteric nervous system, which represents the next step up on the scala naturae – psyche, which encompasses animal perception. This enteric nervous system is considered by some to be “the second brain” because it is the only major component of the peripheral nervous system that can operate independently of the brain (Ruder, 2017). It can make its own independent decisions, without input from the brain, when faced with biological inputs. The gut is faced with a variety of inputs from the digestion of food, its own gut microbiome (analogous to the root microbiome in plants), and from pathogens. It then makes decisions on how to best respond to these signals: for example, to absorb additional nutrients, to send signals to the microbiome, or to initiate an immune response against pathogenic infection. In this sense, the gut forms its very own hegemonikon or command center for making rapid local decisions.

Despite being able to operate independently, the gut is also highly integrated within the larger context of the human body. Significantly, the gut is connected with the brain via the vagus nerve—a dense collection of nerve fibers that forms a physical axis connecting the brain to the gut (analogous to the plant stalk in the root-shoot axis). While the vagus nerve serves as an information “highway” allowing the brain to send information to the gut, approximately 80% of the nerve fibers carry information from the gut to the brain! This “express highway” carries important information to the brain about fullness and satiety (helping the brain know when to eat and how much). Indeed, this process is leveraged by weight-loss drugs like Ozempic that “fool” this system to dampen the urge to eat by sending false signals of fullness to the brain.

As mentioned above, the gut hosts a massive array of microbes that form the gut microbiome (Cryan and Dinan, 2012). This dynamic assembly of microorganisms not only plays a major role in health, by providing key metabolites, but also in one’s mood. Notably, these microbes are responsible for producing important neurotransmitters: 50% of our dopamine and 95% of our serotonin are made within the gut microbiome. These neurotransmitters do not only stimulate effects within the gut but circulate throughout the body and signal the brain through the vagus nerve or by providing the chemical precursors that cross the blood-brain barrier to influence mood. In profound ways your mood is being defined by the bacteria in your gut. This emerging picture of the gut-brain axis as a sort of distributed decision-making system has important implications to how we think about mind and rationality.

The Stoics viewed the hegemonikon (our “ruling part”) as the center of a web. Some Stoics thus placed the hegemonikon, the seat of consciousness, in the heart because this organ was seen as the literal and metaphorical hub of the “breath” (pneuma) that radiated throughout the body. Some modern commentators use this fact to dismiss Stoic physical models as naïve or primitive, because now we “know” that intelligence/consciousness lies within the brain. However, contemporary research findings, such as the distributed “intelligence” of the gut-brain axis, challenge this brain-centered view of intelligence/consciousness. Even at the physiological level, our conscious selves are so much more than simply a brain phenomenon. Perhaps the ancients were less naïve than some would have it. While they may have been off by identifying the heart as the hegemonikon, their intuition that the ‘seat of the soul’ was a systemic phenomenon rather than a brain-centered one is increasingly supported by contemporary science. In modern biology, for example, we can view the gut-brain axis as a sort of decentralized hegemonikon: a distributed regulator that helps to make important local decisions and relay information to the other parts of the nervous system.

Our connection to the ecosystem through the cycles of matter

Our earlier discussion of glycogen synthase focused on how the logos of this glucose-storing enzyme is connected to the greater logos of homeostatic maintenance in the organism. We can extend this connection even further, transcending the boundary of the individual, to encompass the global ecosystem through the carbon cycle (National Ocean Service, 2026). An important thing to highlight about the glucose molecules processed by glycogen synthase is that one of their major constituents is carbon. Each of the carbon atoms in glucose originated as the gas carbon dioxide, which was “fixed” as sugar through the process of photosynthesis. As part of the food webs that make up our world’s ecosystem, we acquire these carbon atoms from the plants and animals that we eat. Conversely, we shed carbon with each breath (in the form of exhaled carbon dioxide) as well as with our dead cells. When we die our bodies decompose, primarily returning carbon back to the Earth’s atmosphere as the carbon dioxide gas that is emitted by the decomposers that eat us. This gas can then be fixed again during photosynthesis as part of the carbon cycle.

In this sense, the tiny enzyme glycogen synthase forms an important linkage not only to the movement of carbon within our own bodies, but to the movement of carbon through our entire ecosystem. Through the carbon cycle we are intimately connected to all other living things that are caught up in it through the ecosystem, as we are constantly being made and unmade into each other. We are also connected to the Earth’s atmosphere—breathing ourselves out to be fixed again by plants and other photosynthetic organisms. This continuous exchange and flow is highly responsive to an array of environmental, ecological, and biological inputs. Decisions are constantly being made by the ecosystem to partition carbon between the atmosphere and the biosphere, ensuring a global “homeostasis” analogous to the internal regulation of a single cell. This brings us to the apex of the scala naturae, the Logos, where each of the lower levels are contained: e.g., the Logos of the ecosystem contains the hexis of enzymes, the physis of growing plants, and the psyche of animal sensation.

This interconnectedness of biological processes and decision making underpins Marcus Aurelius’ reflection that “All things are interwoven with one another, and the bond is holy; scarcely is anything alien to another. For they have been coordinated and together order the same world.” (Meditations, 7.9). It highlights how the local logos of a single enzyme, organ, or organism is a hierarchical level within a much larger Logos that can be expanded outwards. The ancient Stoics used the word sympatheia to refer to the causal connections that bind the World into one unified, rational whole. Viewed through the lens of the carbon cycle, for example, the decision of an enzyme to store sugar is not only a local metabolic event but an expression of a huge and ancient interconnected process: a world-spanning feedback loop.

Conclusion

While the concept of the Logos could be dismissed as an outdated artifact of a pre-scientific society, contemporary research challenges this dismissal. Throughout this essay, I have outlined how biological decision-making occurs across molecular and organismal levels and how these systems are nested within even larger ecological frameworks. We have seen how the logos of an individual molecule, such as glycogen synthase, is a manifestation of the logos of the organism’s homeostasis, which in turn is a portion of the planetary logos expressed through the carbon cycle.

A consideration of the Stoic Logos in Science, particularly in biological decision making, helps us to transcend the limitations of reductionist thinking. By moving towards a more holistic and integrative view of Science we can see how individual systems, such as riboswitches and enzymes, function within interconnected systems. Viewing Nature as a nested hierarchy of information helps to bridge the gap between how the isolated parts of life work and “what” life is: a unified, rational, and interconnected expression of natural laws: what the ancient Stoics would call the Logos. By this definition, intelligence can be seen as an emergent property of the Cosmos. Whether expressed through a riboswitch, the gut-brain axis, or the global carbon cycle, it is the signature of matter being organized by Logos. Where a strictly reductionist lens sees a riboswitch as a series of stochastic collisions governed by thermodynamics, viewing biological decision-making through the Logos illuminates a grander reality. Ultimately, this framework emphasizes the profound interconnectedness of Nature. 

Acknowledgements

I would like to thank Dr. Eric Brenner for his helpful reading of this manuscript and for discussions of the field of “plant neurobiology.”