Biological Ontology

This paper proposes a unified theoretical framework—Causal Life Theory—that reconceptualizes genetic information as a recursive causal field underpinning biological memory, system stability, and evolution. Building on the Causal Conservation Principle, we argue that genes do not merely encode molecular products, but serve as dynamic agents of semantic coherence across time. Through formal models integrating recursion, entropy, and repair dynamics, we reframe development, disease, and speciation as expressions of causal topology and memory stability. The theory culminates in a proposal for causal engineering in synthetic biology, and a philosophical synthesis that interprets life as a semantically persistent system resisting entropic drift through recursive coherence. This work bridges molecular biology, systems theory, and informational ontology to offer a transdisciplinary reconstruction of life and evolution.

The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework—an RNA Ontology (RO)—with a common, dynamic, controlled, and structured vocabulary to describe and characterize RNA sequences, secondary structures, three-dimensional structures, and dynamics pertaining to RNA function. The RO should produce tools for clear communication about RNA structure and function for multiple uses, including the integration of RNA electronic resources into the Semantic Web. These tools should allow the accurate description in computer-interpretable form of the coupling between RNA architecture, function, and evolution. The purposes for creating the RO are, therefore, (1) to integrate sequence and structural databases; (2) to allow different computational tools to interoperate; (3) to create powerful software tools that bring advanced computational methods to the bench scientist; and (4) to facilitate precise searches for all relevant information pertaining to RNA. For...

nigdy osobiście się nie spotkali. Gdy w 1941 roku, krótko przed tym, jak wojska hitlerowskie dokonały agresji na Związek Radziecki, Lorenz pisał w Królewcu obszerny artykuł Kants Lehre vom Apriorischen im Lichte gegenwärtiger Biologie 1 (uważany za symboliczny początek ewolucyjnej teorii poznania 2), to mniej więcej w tym samym czasie Hartmann skrupulatnie pracował w Berlinie nad rękopisem Logiki, który zresztą nigdy nie został wydany 3. "Katastrofy historycznej rzeczywistości-pisał Martin Buber-są częstokroć kryzysami ludzkiego stosunku do rzeczywistości" 4 .

Following Ernst Haeckel and many other fin-de-siecle scientists, Freud conceived mankind's oldest ancestor to be an urmetazoan, or "first animal," a microorganism whose primary organ was its stomach. This primeval organ began as a simple concavity formed by a tensing of cell fibers near the surface of the urganism (this latter term, the present author's coinage, is introduced in place of the less inclusive and more unwieldy urmetazoan; the term also has the advantage of underscoring the first animal's primary activity or urge, which is to eat or otherwise penetrate the membranes of other protists). As the urganism evolved, its primal gastraea developed first into a mouth, next into an anus, and finally, into an armlike or penile appendage that served as a channel or conduit through which food, waste and genetic material passed. Both Freud's ego-libido theory as well as his life instinct-death instinct binary can be interpreted in terms of the Bölschean dividing-melding dichotomy outlined in the essay's opening paragraphs. Divisive love, for Freud, is associated with the maintenance of the organismic boundary or skin by deflecting environmental stimuli and satisfying internal drives that goad the organism into fleeting sexual or consumptive activity; unitive or boundary-dissolving love, on the other hand, Freud saw as an expression of the death instinct, and as such was a denial of the need for a conduit or bridge between self and other.

The diversity of objects and concepts in biological chemistry can be reflected in the number of ways used to describe an ‘elementary’ biochemical event such as enzymatic reaction. The terminology used in publications or biological databases is often a mixture of terms borrowed from widely different or even contradictory classifications. The ever-growing knowledge cannot be processed meaningfully (e.g. efficiently and correctly referenced in biological databases) without organisation, from controlled vocabularies to dictionaries and thesauri to taxonomies and formal ontologies. Ontology of some domain of knowledge is a controlled vocabulary of terms with defined logical relationships to each other. The unique types of relationships between terms have to be included in biochemical ontologies. The relevance of chemical thesauri and ontologies to bioinformatics is illustrated by current resources and projects at the European Bioinformatics Institute, such as IntEnz (Enzyme Nomenclature), COMe (the bioinorganic motif database) and the IUPHAR Receptor Database.