Understanding Living Systems

1. Life is Not Gene-Centric: Organisms are Active, Self-Organizing Agents.

Living organisms are not their genes, nor are they determined by – or reducible to – their genes.

Challenging orthodoxy. The prevailing gene-centric view, popularized by the Modern Synthesis, fundamentally misunderstands living systems by reducing them to their genetic components. This perspective posits that organisms are passive vehicles for genes, with causation flowing unidirectionally from genes to function. However, this book argues that organisms are active agents, creatively shaping and responding to their environments, with life residing in the purpose and creativity of the whole organism.

Beyond reductionism. The idea that DNA is a "secret code" or blueprint for life, or a central organizer, is false. While genes are essential for making proteins, they are part of a regulatory system, not its directors. The organism itself is the self-regulating director, using its genetic heritage as a diverse range of possible outcomes, and even altering its genes when necessary to cope with environmental stress. This dynamic interplay means that life is more than a code or chemical interactions; it is the continuous operation of complex systems across all levels.

Restoring agency. The book emphasizes that most of what organisms do, especially complex behaviors, does not directly involve genes. For instance, our decisions, emotions, and social interactions are not governed by specific "kindness genes" or "cruelty genes." Genes provide capacities, but the organism makes choices and directs its own functions. Understanding living systems requires acknowledging their agency, recognizing that they are not slaves to their genes but rather active participants in their own existence and evolution.

2. The "Selfish Gene" and Central Dogma are Profound Misconceptions.

The Central Dogma and the Human Genome Project make a fundamental error in attributing purpose to genes.

Debunking myths. The book directly refutes four pillars of the Modern Synthesis: (1) the dogma that acquired changes cannot be passed through the germ line, (2) the belief that organisms cannot alter their genes, (3) the concept of organisms as passive gene vehicles (the "selfish gene"), and (4) the idea of evolution through small, random gene mutations passively selected. Each of these pillars is shown to be incorrect or incomplete, leading to profound misunderstandings about genetics, evolution, and ecology.

Conceptual errors. The "selfish gene" metaphor, while seductive, is a powerful misrepresentation. Genes cannot be selfish because they do not make choices; only purposive entities (organisms) can. Attributing selfishness to genes is like saying paint on a palette creates a picture—it ignores the artist. Similarly, the Central Dogma, stating a one-way flow from DNA to protein, is dogma without sufficient experimental support. It incorrectly assumes cells cannot alter DNA in a directed way, making organisms prisoners of their genes and denying their agency.

Challenging dogma. Francis Crick himself admitted the term "dogma" was used loosely, not implying incontrovertible truth. Evidence now shows that organisms can influence and reorganize their genomes, for example, through:

• Epigenetic changes passed through the germ line.
• Targeted somatic hypermutation in response to stress.
• Large-scale chromosome and genome rearrangements (e.g., Barbara McClintock's "jumping genes").
• Natural genetic engineering, as demonstrated by James Shapiro.
  These processes contradict the idea of a fixed, unalterable genome and a passive organism.

3. Genes are Tools, Not Directors, in a Self-Regulating Organism.

Genes are tools, not masters.

Tools of life. Genes are essential templates for making proteins, which are the building blocks and functional machinery of cells. However, they are not the "secret of life" or a central organizer. The cell itself orchestrates the use and expression of DNA, deciding when and how much of each protein to make. This is evident in processes like the heartbeat, where the rhythm is generated by complex interactions of proteins and membranes, not directly by genes.

Contextual function. The meaning and function of a gene are not inherent but depend entirely on the context of the whole system. Genes are multipurpose; their expression varies with functional context. The "omnigenic theory" suggests that most, if not all, genes are involved in most functions, further undermining the idea of one-to-one gene-to-trait causation. This complexity means that genomics, while useful for identifying probabilistic associations with disease, cannot provide a deterministic "blueprint" for an individual's health or behavior.

Beyond the code. The metaphor of DNA as a "code" or "blueprint" is misleading. DNA is a chemical fact, a template, not a set of instructions that cells "read" like a book. Much of what is necessary for organisms to function is not inherited in genes but develops with the organism through learning and environmental interaction. For example:

• The development of our visual system requires experience.
• Complex brain connections continue developing into adulthood.
• Social functioning relies on interactions, not just genes.
  Genes enable capacities but do not dictate specific actions or outcomes.

4. Evolution is an Active, Purposeful Process, Not Passive Randomness.

Evolution thrives not on immutability but on change.

Beyond passive selection. Darwin's concept of natural selection, often interpreted as a passive filter for random mutations, is incomplete. The book argues that organisms are active agents in evolution, not just passive recipients of environmental changes. The environment itself is largely composed of other active organisms, meaning selection is an iterative ecological process driven by the behavioral and physiological choices of living beings.

Purposeful change. Evolution involves changes in form and function that have a purpose, enhancing fitness and survival. This directionality is evident in how organisms adapt to their habitats, build niches, and interact with other species. Major evolutionary transitions, such as the development of multicellularity or the acquisition of mitochondria, often arise from:

• Cooperation and fusion of existing organisms (symbiogenesis).
• Hybridization between species.
• Rapid genome reorganization, not just slow accumulation of small mutations.
  These processes demonstrate that evolution can occur in "leaps and bounds," driven by active, creative problem-solving by organisms.

Harnessing variability. Reproduction is not merely replication; it is a mechanism of change that creates novelty and variation. This variability is essential for adaptation to continuously changing environments. Life actively manages chance, using stochastic potential to drive dynamic and creative purposeful change. Organisms are constantly "spinning the wheel of invention," adapting their genetic heritage and functional capabilities to enhance fitness, rather than simply preserving immutable genes.

5. More Than Genes is Inherited: Acquired Characteristics and Epigenetics Matter.

It is clear now that selective changes in the organism can be passed on through the germ line.

Challenging Weismann. The "Weismann barrier" dogma, which claimed that changes acquired during an organism's lifetime cannot be passed to offspring through the germ line, is incorrect. This idea, once central to gene-centric thinking, has been disproven by a growing body of evidence. The germ line is not isolated; it can be influenced by somatic changes and environmental factors experienced by the parent.

Epigenetic inheritance. A crucial mechanism for the inheritance of acquired characteristics is epigenetics. These are genetic modifications that impact gene activity without changing the underlying DNA sequence. Examples include:

• Early-life exposures and metabolic adaptations in parents modulating epigenetic regulation in germ cells.
• Such changes influencing offspring health and phenotypes across multiple generations.
• Acquired behaviors passing through non-genetic factors.
  This evidence demonstrates a robust molecular legacy that contributes to intergenerational inheritance of traits and disease risk.

Assimilation into the genome. While epigenetic changes were once thought to be transient, studies of populations adapting to high altitudes show that stress-induced epigenetic changes can be assimilated into the genome over time. This means that adaptations acquired by an organism can become genetically encoded, providing a powerful mechanism for directed evolution. This process highlights that organisms actively orchestrate genetic changes in response to environmental pressures, further reinforcing their agency in evolution.

6. Living Systems are Open, Nested Hierarchies of Interacting Levels.

Organisms are open systems and do not exist apart from their active environment.

Interconnectedness of life. Living systems are not isolated entities but open systems, constantly interacting with their environment and other organisms. This interaction occurs across multiple, nested levels of organization, from molecules to ecosystems. Causation flows in all directions, meaning that higher levels of organization (e.g., social interactions) can influence and constrain lower levels (e.g., gene expression), and vice versa.

Hierarchical constraint. The book illustrates this with a "nesting" principle:

• Molecules are constrained by cell organization.
• Cells are constrained by tissue organization.
• Tissues are constrained by organs.
• Organs are constrained by organ systems and the whole organism.
• Organisms are constrained by social and ecological interactions.
  This hierarchy means that purpose and instruction are often "top-down," with decisions made at higher levels influencing the function of lower levels. For example, the decision to walk uses muscles, but the direction is determined by the organism's purpose, not the muscle cells' molecules.

Variability and integrity. Living systems maintain their integrity not by rigid constancy but through organized change and adaptability. Variability, even at the molecular level, is harnessed to create order and purposive agency. This "jiggling around" of molecules, rather than being a flaw, is fundamental to the flexibility and responsiveness of life. The ability to adapt to changing circumstances, balancing competing imperatives, is a hallmark of life's intelligence and its capacity for creative problem-solving.

7. Ecological and Social Intelligence Drive Adaptation and Evolution.

The interactions between organisms form a powerful functional boundary, influencing the behaviour and physiology of the organisms involved.

Beyond individual action. Organisms possess ecological and social intelligence, enabling them to sense, respond to, and anticipate the actions of others, both within and across species. This intelligence is crucial for survival and reproduction, driving adaptation and conferring directionality on evolution. Examples include:

• Wolves cooperating in hunting and raising young, with a sense of fairness.
• Trees communicating chemical warnings about insect infestations.
• Dodder plants sensing and synchronizing flowering with host plants.
• Ants problem-solving by creating and adapting pheromone trails.
  These interactions highlight that cooperation is as fundamental as competition in nature.

Niche creation. Organisms are not passive occupants of their environment; they actively create and modify their niches. This niche construction, whether building nests, altering landscapes (like beavers), or developing complex social structures, profoundly influences their own evolution and that of other species. Human activity, for instance, has created a "concrete jungle" niche that impacts global climate and habitats, demonstrating our powerful, albeit often destructive, agency.

Cultural transmission. Social intelligence extends to cultural transmission, where learned behaviors, ideas, and problem-solving techniques spread through groups and across generations. This is evident in chimpanzees learning to use tools, birds developing local dialects in their songs, and humans creating complex social norms and technologies. This cultural inheritance, distinct from genetic inheritance, plays a significant role in shaping behavior and evolution, demonstrating that "social logic, rules, ethics and concepts of morality are not found in the gene pool."

8. Purpose, Agency, and Creativity are Defining Features of Life.

Agency and purposeful action is a defining property of all living systems.

Intentional existence. Purpose is not an illusion or an incidental byproduct of mechanistic processes; it is definitively what living things do. Organisms solve the problems of sustaining their existence by acting with intention and creativity. This agency is evident in goal-directed behaviors such as:

• Chimpanzees selecting and shaping stones to crack nuts.
• Birds building nests to rear offspring.
• Plants bending towards the sun for photosynthesis.
• Migrating animals navigating continents to find resources.
  These actions are driven by motivations and intentions, which are integral to biological function.

Situational logic. Organisms use reason and logic to make choices, adapting their behavior to changing circumstances. This "situational logic" is not a fixed algorithm but an iterative, creative process involving trial and error, learning, and anticipation. For example, a chimpanzee's choice of stone for cracking nuts is a dynamic assessment, not a pre-programmed response. This creativity, often involving "unlimited associative learning," is a fundamental facet of life's intelligence.

Beyond mechanism. The mechanistic view of life, inspired by clockwork machines and now by AI, struggles to account for purpose and agency. It reduces explanations to "how" something happens rather than "why." However, the book argues that purpose is created by the fabric of the universe as living entities. This means that intentions do not come from an external source or a separate "mind" but are emergent properties of self-organizing organisms, making them active participants in their own destiny.

9. Mechanistic Metaphors Like AI Misrepresent Life's True Nature.

Ironically, whilst deterministic machine metaphors distort our view of life, we try hard to create lifelike machines with creativity and purpose, for this is the real secret of life, not its DNA.

False comparisons. Artificial intelligence (AI), while powerful for processing algorithms rapidly, fundamentally differs from living intelligence. AI blindly pursues its algorithms and, without explicit programming for randomness, produces predictable outputs. Living organisms, by contrast, create purposes and harness inherent molecular disorder to generate order and agency. The "jiggling around" of water molecules in biological systems provides a natural source of variability that metallic, silicon-based computers lack.

Water-based life. The book highlights the profound difference between silicon-based computers and water-based biological systems. Living cells operate on the edge of disorder, using the stochastic movement of molecules to enable complex, adaptive functions. This "harnessed disorder" is why biological systems don't need artificial random number generators; their very material composition provides it. Replicating this water-based complexity is a challenge that took nature billions of years to solve, making true artificial life a distant prospect.

The real threat. The danger of AI is not that robots will replace humans by achieving true agency, but rather how AI can be maliciously used by humans to undermine our own agency. By processing vast amounts of data, AI can predict and manipulate behavior, potentially limiting freedom of expression and choice. This echoes Orwell's "1984" vision, where technology is used to enslave humanity. AI is a tool, and like nuclear power, its impact depends on human choices and intentions, not on its inherent "life."

10. Consciousness and Unlimited Learning are Key to Life's Intelligence.

Biological research has shown that many animals possess the same skill that Descartes himself, and we, possess – the skill that enables us to be consciously sensitive to and to exercise unlimited forms of choice and behaviour.

The awakening of life. Consciousness, defined as the ability for "unlimited associative learning," is a crucial aspect of life's intelligence. This capacity, which allows organisms to learn new associations without limit, is believed to have emerged around 500 million years ago during the Cambrian explosion, potentially driving the rapid diversification of animal forms. This suggests that conscious choice itself played a significant role in shaping evolution, marking an "awakening of life on earth."

Beyond automata. Descartes' view of animals as mere automata, reserving consciousness for humans, is challenged. Many animals, from apes and birds to octopuses and wood mice, demonstrate conscious choice and unlimited associative learning. This ability allows them to:

• Discriminate against cheats in social groups.
• Choose mates based on complex criteria.
• Develop new problem-solving techniques.
• Engage in creative communication (e.g., whale songs, bird calls).
  These actions are not pre-programmed but reflect genuine intelligence and agency.

Culture as the mind's matrix. The mind is not a separate entity but emerges from the creative evolution of being, materially and culturally. Language, literature, and art are powerful tools for abstract thought, enabling humans to explore ideas, transmit knowledge across generations, and shape their psychosocial niche. This cultural matrix influences our motivations, ethics, and perception of the world, demonstrating that "what accounts for our social and cultural history is not a molecular arrangement, but a cultural one." Recognizing this interdependence and our own conscious agency is vital for addressing global challenges and nurturing life on Earth.

Last updated: January 30, 2026