Intelligibility in microbial complex systems: Wittgenstein and the score of life

Intelligibility in microbial complex systems: Wittgenstein and the score of life Fernando Baquero Andrés Moya

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Intelligibility in microbial complex systems: Wittgenstein and the score of life 2012 10.3389/fcimb.2012.00088 intelligibility-in-microbial-complex-systems intelligibility-in-microbial-complex-systems.txt, the project's staged copy 8fb8e92c9740dd92c5d0db299a74e12311e530f6 cc-by philosophy-of-art

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0 spans located by searching the stored text for the quote's exact words, allowing any whitespace between them the intelligibility of microbial (and biological) life: the epistemology of representing complex living systems, reframed through the metaphor of the genome as a 'score of life' rather than a 'book of life' Quotation withheld because this record is not cleared for redistribution. how to cross the epistemological gaps between the successive hierarchical levels of the complex system of life, and whether life can be rendered intelligible by reducing it to the genetic-genomic language Quotation withheld because this record is not cleared for redistribution. a 'half-thinking, half-seeing' (HT-HS) strategy for complex biological systems: combining analysis of representations (genomes, scores) with a non-propositional experience of meaning, to move through legibility and imageability toward higher intelligibility Quotation withheld because this record is not cleared for redistribution. critique Quotation withheld because this record is not cleared for redistribution. life and music can be shown but not thought: their representations (genomes, musical scores) are mere representations of obscure realities, and diversification of knowledge paradoxically reduces intelligibility Quotation withheld because this record is not cleared for redistribution. conceptual-analysis conceptual-analysis Quotation withheld because this record is not cleared for redistribution. A general rule (the law of projection) lets an interpreter read a symphony out of a static score, and the same rule inverts to reconstruct the score from the sound on a gramophone record - the internal similarity that makes these transitions possible. reading the score produces music Quotation withheld because this record is not cleared for redistribution. Wittgenstein's rule of translation projects the symphony into the language of the musical score and translates that language into the gramophone record, and runs in reverse. law of projection Quotation withheld because this record is not cleared for redistribution. A collection of small parts assembles to produce a qualitatively different larger whole - groove-pattern to music, genes to a bacterial cell, cells to an ecological community. major transition Quotation withheld because this record is not cleared for redistribution. Reproduction of a bacterial organism or a string quartet depends entirely on its representation (genome or score), while the higher living level leads by selecting the representation. generational representation Quotation withheld because this record is not cleared for redistribution. Understanding a complex system combines analysis of its representation (half-thinking) with a non-propositional experience of meaning that can only be seen or shown (half-seeing). half-thinking, half-seeing Quotation withheld because this record is not cleared for redistribution. Analysis of scores and genomic sequences yields mechanistic, phylogenetic and evolutionary insight, but not the real dynamics or nature of music and life, which remain unthinkable. Quotation withheld because this record is not cleared for redistribution. Following Wittgenstein, the meaning of the word 'life' can only be shown, not understood, and consequently cannot be clearly expressed in propositions. Quotation withheld because this record is not cleared for redistribution. In the absence of correct interpretation, a music score cannot be differentiated from a random sequence of notes. Quotation withheld because this record is not cleared for redistribution. Systems Biology models are insufficient by themselves for full intelligibility, because deducing models of function from a complex system's behaviour is an inverse problem that is impossible to solve. Quotation withheld because this record is not cleared for redistribution. Validating models by comparing them with 'reality' may be a circular problem, since 'reality' can only be defined by models. Quotation withheld because this record is not cleared for redistribution. intelligibility intelligibility Quotation withheld because this record is not cleared for redistribution. complex systems complex systems Quotation withheld because this record is not cleared for redistribution. representation representation Quotation withheld because this record is not cleared for redistribution. score of life score of life Quotation withheld because this record is not cleared for redistribution. book of life book of life Quotation withheld because this record is not cleared for redistribution. music score music score Quotation withheld because this record is not cleared for redistribution. musical score musical score Quotation withheld because this record is not cleared for redistribution. score score Quotation withheld because this record is not cleared for redistribution. music music Quotation withheld because this record is not cleared for redistribution. life life Quotation withheld because this record is not cleared for redistribution. genome genome Quotation withheld because this record is not cleared for redistribution. genomic sequences genomic sequences Quotation withheld because this record is not cleared for redistribution. metaphor metaphor Quotation withheld because this record is not cleared for redistribution. epistemology epistemology Quotation withheld because this record is not cleared for redistribution. family resemblances family resemblances Quotation withheld because this record is not cleared for redistribution. experience of meaning experience of meaning Quotation withheld because this record is not cleared for redistribution. half-thinking, half-seeing half-thinking, half-seeing Quotation withheld because this record is not cleared for redistribution. legibility legibility Quotation withheld because this record is not cleared for redistribution. imageability imageability Quotation withheld because this record is not cleared for redistribution. major transition major transition Quotation withheld because this record is not cleared for redistribution. law of projection law of projection Quotation withheld because this record is not cleared for redistribution. Chinese room Chinese room Quotation withheld because this record is not cleared for redistribution. proposition proposition Quotation withheld because this record is not cleared for redistribution. the will of life the will of life Quotation withheld because this record is not cleared for redistribution. reductionism reductionism Quotation withheld because this record is not cleared for redistribution. systems biology systems biology Quotation withheld because this record is not cleared for redistribution. internal similarity internal similarity Quotation withheld because this record is not cleared for redistribution. facts facts Quotation withheld because this record is not cleared for redistribution. world world Quotation withheld because this record is not cleared for redistribution. representation → reproduction A trans-hierarchical cyclic correlation ties representation to reproduction, produced blindly in both senses. — the relation stated: Representation and reproduction stand in a cyclic, blind, trans-hierarchical correlation. Quotation withheld because this record is not cleared for redistribution. music → the will of life Reinterpreting Schopenhauer, the will represented in music is a representation of the will of life; a common will is independently perceived in both. — the relation stated: Music represents the will of life; a common will is shown in both. Quotation withheld because this record is not cleared for redistribution. genome → life The life of a particular bacterial organism is, to a certain extent, represented in the organization of its genome, as a Mozart quartet is represented in its score. — the relation stated: The genome represents the life of the organism, but subordinate to what is represented. Quotation withheld because this record is not cleared for redistribution. lower levels → higher levels It is tempting to propose that the lower levels of the hierarchy blindly 'represent' the higher levels, though the higher levels categorically impose organisations on the lower. — the relation stated: Lower hierarchical levels blindly represent higher ones. Quotation withheld because this record is not cleared for redistribution. score → genetic language In the central analogy, reading the score corresponds to reading the genetic language, producing music as reading the genome produces life. — the relation stated: The music score is the analogue of the genetic language. Quotation withheld because this record is not cleared for redistribution. reading - human/sequential sense: a text read in one way only, sequentially, involving all characters Quotation withheld because this record is not cleared for redistribution. reading - cellular/genomic sense: genetic texts 'read' by cellular mechanisms in several different ways, each using a different selection of characters while skipping others Quotation withheld because this record is not cleared for redistribution. intelligibility - linguistic-theory sense: the trade-off between hierarchical levels in a shared world (Komarova and Niyogi) Quotation withheld because this record is not cleared for redistribution. intelligibility - the authors' epistemological sense: the construction of meaningful (thinkable) models reflecting complex natural systems Quotation withheld because this record is not cleared for redistribution. representation - Wittgenstein's picture sense: a proposition/picture sharing a logical form with the fact it represents Quotation withheld because this record is not cleared for redistribution. representation - Schopenhauer's sense: music as a copy of the will itself, resembling an original reality that cannot be copied Quotation withheld because this record is not cleared for redistribution. representation - biological sense: genomic sequences representing life, meaningful only when a living system is present Quotation withheld because this record is not cleared for redistribution. score - musical sense: the notation from which a symphony can be reconstructed by a general rule (Tractatus 4.0141) Quotation withheld because this record is not cleared for redistribution. score - 'score of life' sense: the genomic language, proposed as a better image than the book of life Quotation withheld because this record is not cleared for redistribution. will - Schopenhauer's metaphysical sense: the will itself, of which music is a copy and the Ideas its objectivity Quotation withheld because this record is not cleared for redistribution. harmony - sensibility-relative sense: an ordered score follows rules of harmony, yet that harmony may be totally useless for a different sensibility and out of any aesthetic possibility Quotation withheld because this record is not cleared for redistribution. builds-on → Wittgenstein's Tractatus logico-philosophicus (theorem 4.0141 and the picture theory of representation) note: The essay takes the Tractatus as its main post-Kantian framework for the limits of knowledge of the natural world. Quotation withheld because this record is not cleared for redistribution. builds-on → Schopenhauer's account of music as a copy of the will (The World as Will and Representation) note: The will represented in music is read as a representation of the will of life. Quotation withheld because this record is not cleared for redistribution. extends → Dennis Noble's 'music of life' metaphor note: The essay extends Noble's music-of-life idea to the intelligibility of microbial life. Quotation withheld because this record is not cleared for redistribution. builds-on → Maynard Smith and Szathmary's theory of major evolutionary transitions note: Major transitions between hierarchical levels frame the score-to-music and genes-to-life passages. Quotation withheld because this record is not cleared for redistribution. contrasts-with → the classic 'book of life' metaphor for the genome note: The 'score of life' is proposed as a better image of the genomic language. Quotation withheld because this record is not cleared for redistribution. recommends → developing complex models of complex systems through convergent, multidisciplinary 'Big Science' note: The half-seeing part needs more powerful model tools integrating all the -omics data. Quotation withheld because this record is not cleared for redistribution. life —is-a→ music life music the relation itself is separately evidenced · strength of the relation: 0.6 — the record marks this weak · note: Figurative is-a via Noble's metaphor ('a kind of music'); low weight marks the hedge. · the relation stated: Quoting Noble, life is figuratively cast as a kind of music - a symphonic interplay between genes, cells, organs, body and environment. Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span quotes a metaphor ('a kind of music'); is-a states it literally. Quotation withheld because this record is not cleared for redistribution. music score —causes→ music music score music the relation itself is separately evidenced · strength of the relation: 0.85 · note: Positive production ('gives rise to'); conditional on interpretation, hence not fully flat. · the relation stated: The music score gives rise to music, but only when an interpreter is available to read the notation and convert it into sounds. Audit 2026-09-28: RESTORED AND DOUBTFUL - the full span was re-read; kept, but the full span says 'the music score gives rise to music only if interpreters are available' - the relation is stated but only on that condition, which the edge drops; the withdrawal said the span does not say a score causes music. The earlier withdrawal is kept in the record. Quotation withheld because this record is not cleared for redistribution. facts —part-of→ world facts world the relation itself is separately evidenced · strength of the relation: 1 · note: Flat categorical composition stated as a Tractatus theorem (the world constituted by the totality of facts). · the relation stated: On Wittgenstein's theorem 1.1 Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span is about propositions; part-of 'world' is loose. Quotation withheld because this record is not cleared for redistribution. score of life —contrasted-with→ book of life score of life book of life the relation itself is separately evidenced · strength of the relation: 0.85 · note: Differentiator stated: sequential single reading versus multiple simultaneous cellular readings. · the relation stated: The 'score of life' is contrasted with the classic 'book of life': human texts are read one way only and sequentially, whereas genetic texts are read by cellular mechanisms in several different ways. Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the 'score of life' 'could be a better image'; hedged. Quotation withheld because this record is not cleared for redistribution. Increasing diversification and complexity in microbiology paradoxically results in a strong reduction of the intelligibility of microbial life. Quotation withheld because this record is not cleared for redistribution. The 'score of life' is a better image of the genomic language than the classic 'book of life', because genetic texts are read by cellular mechanisms in several different ways rather than sequentially. Quotation withheld because this record is not cleared for redistribution. Both life and music can be shown but not thought; genomic sequences and musical scores are mere representations of these obscure realities. Quotation withheld because this record is not cleared for redistribution. A strategy of half-thinking and half-seeing is needed to expand knowledge of complex systems such as life and music. Quotation withheld because this record is not cleared for redistribution. The epistemological process for complex biological systems has three phases: legibility, imageability, and intelligibility. Quotation withheld because this record is not cleared for redistribution. the construction of meaningful (thinkable) models in response to the assimilation of knowledge, able to reflect to some extent the reality of complex natural systems intelligibility Quotation withheld because this record is not cleared for redistribution. a series of staves on which all the instrumental and/or vocal parts of a musical work are written in vertical alignment so the parts may be read simultaneously score Quotation withheld because this record is not cleared for redistribution. the descriptive level of anatomy and physiology - the composition of Wittgensteinian atomic facts and propositions legibility Quotation withheld because this record is not cleared for redistribution. the stage at which a holistic, physiognomically comparable image of a living structure can be seen or shown imageability Quotation withheld because this record is not cleared for redistribution. a half-thinking perception of fine shades of meaning - a kinship between seeing an aspect and understanding that enables connections and comparisons experience of meaning Quotation withheld because this record is not cleared for redistribution.

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