Making computing machines mimic living organisms has captured the imagination of many since the dawn of digital computers. However, today’s artificial intelligence technologies fall short of replicating even the basic autopoietic and cognitive behaviors found in primitive biological systems. According to Charles Darwin, the difference in mind between humans and higher animals, great as it is, certainly is one of degree and not of kind. Autopoiesis refers to the behavior of a system that replicates itself and maintains identity and stability while facing fluctuations caused by external influences. Cognitive behaviors model the system’s state, sense internal and external changes, analyze, predict and take action to mitigate any risk to its functional fulfillment. How did intelligence evolve? what is the relationship between the mind and body? Answers to these questions should guide us to infuse autopoietic and cognitive behaviors into digital machines. In this paper, we show how to use the structural machine to build a cognitive reasoning system that integrates the knowledge from various digital symbolic and sub-symbolic computations. This approach is analogous to how the neocortex repurposed the reptilian brain and paves the path for digital machines to mimic living organisms using an integrated knowledge representation from different sources.

Knowledge processing is an important feature of intelligence in general and artificial intelligence in particular. To develop computing systems working with knowledge, it is necessary to elaborate the means of working with knowledge representations (as opposed to data), because knowledge is an abstract structure. There are different forms of knowledge representations derived from data. One of the basic forms is called a schema, which can belong to one of three classes: operational, descriptive, and representation schemas. The goal of this paper is the development of theoretical and practical tools for processing operational schemas. To achieve this goal, we use schema representations elaborated in the mathematical theory of schemas and use structural machines as a powerful theoretical tool for modeling parallel and concurrent computational processes. We describe the schema of autopoietic machines as physical realizations of structural machines. An autopoietic machine is a technical system capable of regenerating, reproducing, and maintaining itself by production, transformation, and destruction of its components and the networks of processes downstream contained in them. We present the theory and practice of designing and implementing autopoietic machines as information processing structures integrating both symbolic computing and neural networks. Autopoietic machines use knowledge structures containing the behavioral evolution of the system and its interactions with the environment to maintain stability by counteracting fluctuations.

Some researchers suggest that information is a form of matter, calling it the fifth state of matter or the fifth element. Recent results from the general theory of information (GTI) contradict this. This paper aims to explain and prove that the claims of adherents of the physical nature of information are inaccurate due to the confusion between the definitions of information, the matter that represents information, and the matter that is a carrier of information. Our explanations and proofs are based on the GTI because it gives the most comprehensive definition of information, encompassing and clarifying many of the writings in the literature about information. GTI relates information, knowledge, matter, and energy, and unifies the theories of material and mental worlds using the world of structures. According to GTI, information is not physical by itself, although it can have physical and/or mental representations. Consequently, a bit of information does not have mass, but the physical structure that represents the bit indeed has mass. Moreover, the same bit can have multiple representations in the form of a physical substance (e.g., a symbol on a paper or a state of a flip-flop circuit, or an electrical voltage or current pulse.) Naturally, these different physical representations can have different masses, although the information is the same. Thus, our arguments are not against Landauer’s principle or the empirical results of Vopson and other adherents of the physical nature of the information. These arguments are aimed at the clarification of the theoretical and empirical interpretations of these results. As the references in this paper show, recently many publications in which it is claimed that information is a physical essence appeared. That is why it is so important to elucidate the true nature of information and its relation to the physical world eliminating the existing misconceptions in information studies.

All living beings use autopoiesis and cognition to manage their “life” processes from birth through death. Autopoiesis enables them to use the specification in their genomes to instantiate themselves using matter and energy transformations. They reproduce, replicate, and manage their stability. Cognition allows them to process information into knowledge and use it to manage its interactions between various constituent parts within the system and its interaction with the environment. Currently, various attempts are underway to make modern computers mimic the resilience and intelligence of living beings using symbolic and sub-symbolic computing. We discuss here the limitations of classical computer science for implementing autopoietic and cognitive behaviors in digital machines. We propose a new architecture applying the general theory of information (GTI) and pave the path to make digital automata mimic living organisms by exhibiting autopoiesis and cognitive behaviors. The new science, based on GTI, asserts that information is a fundamental constituent of the physical world and that living beings convert information into knowledge using physical structures that use matter and energy. Our proposal uses the tools derived from GTI to provide a common knowledge representation from existing symbolic and sub-symbolic computing structures to implement autopoiesis and cognitive behaviors.

Biological systems have a unique ability inherited through their genome. It allows them to build, operate, and manage a society of cells with complex organizational structures, where autonomous components execute specific tasks and collaborate in groups to fulfill systemic goals with shared knowledge. The system receives information from various senses, makes sense of what is being observed, and acts using its experience while the observations are still in progress. We use the General Theory of Information (GTI) to implement a digital genome, specifying the operational processes that design, deploy, operate, and manage a cloud-agnostic distributed application that is independent of IaaS and PaaS infrastructure, which provides the resources required to execute the software components. The digital genome specifies the functional and non-functional requirements that define the goals and best-practice policies to evolve the system using associative memory and event-driven interaction history to maintain stability and safety while achieving the system’s objectives. We demonstrate a structural machine, cognizing oracles, and knowledge structures derived from GTI used for designing, deploying, operating, and managing a distributed video streaming application with autopoietic self-regulation that maintains structural stability and communication among distributed components with shared knowledge while maintaining expected behaviors dictated by functional requirements.

A special class of complex adaptive systems—biological and social—thrive not by passively accumulating patterns, but by engineering coherence, i.e., the deliberate alignment of prior knowledge, real-time updates, and teleonomic purposes. By contrast, today’s AI stacks—Large Language Models (LLMs) wrapped in agentic toolchains—remain rooted in a Turing-paradigm architecture: statistical world models (opaque weights) bolted onto brittle, imperative workflows. They excel at pattern completion, but they externalize governance, memory, and purpose, thereby accumulating coherence debt—a structural fragility manifested as hallucinations, shallow and siloed memory, ad hoc guardrails, and costly human oversight. The shortcoming of current AI relative to human-like intelligence is therefore less about raw performance or scaling, and more about an architectural limitation: knowledge is treated as an after-the-fact annotation on computation, rather than as an organizing substrate that shapes computation. This paper introduces Mindful Machines, a computational paradigm that operationalizes coherence as an architectural property rather than an emergent afterthought. A Mindful Machine is specified by a Digital Genome (encoding purposes, constraints, and knowledge structures) and orchestrated by an Autopoietic and Meta-Cognitive Operating System (AMOS) that runs a continuous Discover–Reflect–Apply–Share (D-R-A-S) loop. Instead of a static model embedded in a one-shot ML pipeline or deep learning neural network, the architecture separates (1) a structural knowledge layer (Digital Genome and knowledge graphs), (2) an autopoietic control plane (health checks, rollback, and self-repair), and (3) meta-cognitive governance (critique-then-commit gates, audit trails, and policy enforcement). We validate this approach on the classic Credit Default Prediction problem by comparing a traditional, static Logistic Regression pipeline (monolithic training, fixed features, external scripting for deployment) with a distributed Mindful Machine implementation whose components can reconfigure logic, update rules, and migrate workloads at runtime. The Mindful Machine not only matches the predictive task, but also achieves autopoiesis (self-healing services and live schema evolution), explainability (causal, event-driven audit trails), and dynamic adaptation (real-time logic and threshold switching driven by knowledge constraints), thereby reducing the coherence debt that characterizes contemporary ML- and LLM-centric AI architectures. The case study demonstrates “a hybrid, runtime-switchable combination of machine learning and rule-based simulation, orchestrated by AMOS under knowledge and policy constraints”.