From Riboswitches to the Cosmos: Biological Decision Making and the Stoic Logos COSP
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Issue 78
A publication of the College of Stoic Philosophers
July 2026
From Riboswitches to the Cosmos:
Biological Decision Making
and the Stoic Logos
Walter N. Moss
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
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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.
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Issue 78
A publication of the College of Stoic Philosophers
July 2026
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
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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
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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.
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Issue 78
A publication of the College of Stoic Philosophers
July 2026
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
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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
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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
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Issue 78
A publication of the College of Stoic Philosophers
July 2026
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
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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
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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
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Issue 78
A publication of the College of Stoic Philosophers
July 2026
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