standOff, and the article is at its publisher via the link below. When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.| relation to other work | claim_relations | how this paper stands to another: agrees, contradicts, extends, qualifies |
| claim type | claim_type | the shape of the claim: existence, mechanism, method, critique, prediction, null |
| concept edge | concept_edges | an asserted relation between two concepts, with the sentence asserting it |
| concept | concepts | an idea the paper works with, quoted where the paper uses it |
| content tag | content_tags | a finding, definition, quantity, statistic or variable named in the paper |
| contribution | contribution | what the paper claims to add |
| limitation | limitations | what the paper says its evidence cannot support |
| mechanism | mechanisms | how the reported effect is said to come about |
| method | method | how the paper produced its evidence |
| object of study | object_of_study | what the paper is about — the thing it investigates |
| phenomenon | phenomenon | the effect or regularity under study |
| research question | research_question | the question the paper sets itself |
| sense | senses | a distinct use of a term, quoted where the paper fixes it |
| unrecordable relation | unhoused_relations | a relation the paper asserts that this vocabulary cannot express, with the reason |
Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; 4 of 4 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.
This record holds no controls. A layer is empty when the tagger recorded nothing in it — which is not the same as the paper having nothing to record.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | 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 — this record is not cleared for redistribution. The sentence is in the paper at the link above. | object_of_study | the paper's words | |
| research_question | 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 — this record is not cleared for redistribution. The sentence is in the paper at the link above. | research_question | the paper's words | |
| contribution | 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 — this record is not cleared for redistribution. The sentence is in the paper at the link above. | contribution | the paper's words | |
| claim_type | critique Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_type | the paper's words | |
| phenomenon | 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 — this record is not cleared for redistribution. The sentence is in the paper at the link above. | phenomenon | the paper's words | |
| method | conceptual-analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: conceptual-analysis | method | the paper's words | |
| mechanisms | 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. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: reading the score produces music | mechanisms[0] | 0.9 | the tagger's words |
| mechanisms | 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. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: law of projection | mechanisms[1] | 0.9 | the tagger's words |
| mechanisms | 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. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: major transition | mechanisms[2] | 0.92 | the tagger's words |
| mechanisms | 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. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: generational representation | mechanisms[3] | 0.9 | the tagger's words |
| mechanisms | 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). Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: half-thinking, half-seeing | mechanisms[4] | 0.9 | the tagger's words |
| limitations | 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 — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[0] | 0.9 | the tagger's words |
| limitations | Following Wittgenstein, the meaning of the word 'life' can only be shown, not understood, and consequently cannot be clearly expressed in propositions. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[1] | 0.9 | the tagger's words |
| limitations | In the absence of correct interpretation, a music score cannot be differentiated from a random sequence of notes. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[2] | 0.88 | the tagger's words |
| limitations | 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 — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[3] | 0.9 | the tagger's words |
| limitations | Validating models by comparing them with 'reality' may be a circular problem, since 'reality' can only be defined by models. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[4] | 0.9 | the tagger's words |
| concepts | intelligibility Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: intelligibility | concepts[0] | 0.95 | the paper's words |
| concepts | complex systems Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: complex systems | concepts[1] | 0.92 | the paper's words |
| concepts | representation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: representation | concepts[2] | 0.95 | the paper's words |
| concepts | score of life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: score of life | concepts[3] | 0.93 | the paper's words |
| concepts | book of life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: book of life | concepts[4] | 0.92 | the paper's words |
| concepts | music score Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: music score | concepts[5] | 0.92 | the paper's words |
| concepts | musical score Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: musical score | concepts[6] | 0.9 | the paper's words |
| concepts | score Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: score | concepts[7] | 0.9 | the paper's words |
| concepts | music Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: music | concepts[8] | 0.92 | the paper's words |
| concepts | life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: life | concepts[9] | 0.93 | the paper's words |
| concepts | genome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: genome | concepts[10] | 0.92 | the paper's words |
| concepts | genomic sequences Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: genomic sequences | concepts[11] | 0.9 | the paper's words |
| concepts | metaphor Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: metaphor | concepts[12] | 0.9 | the paper's words |
| concepts | epistemology Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: epistemology | concepts[13] | 0.88 | the paper's words |
| concepts | family resemblances Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: family resemblances | concepts[14] | 0.9 | the paper's words |
| concepts | experience of meaning Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: experience of meaning | concepts[15] | 0.9 | the paper's words |
| concepts | half-thinking, half-seeing Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: half-thinking, half-seeing | concepts[16] | 0.9 | the paper's words |
| concepts | legibility Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: legibility | concepts[17] | 0.88 | the paper's words |
| concepts | imageability Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: imageability | concepts[18] | 0.88 | the paper's words |
| concepts | major transition Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: major transition | concepts[19] | 0.9 | the paper's words |
| concepts | law of projection Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: law of projection | concepts[20] | 0.9 | the paper's words |
| concepts | Chinese room Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Chinese room | concepts[21] | 0.88 | the paper's words |
| concepts | proposition Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: proposition | concepts[22] | 0.88 | the paper's words |
| concepts | the will of life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: the will of life | concepts[23] | 0.85 | the paper's words |
| concepts | reductionism Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: reductionism | concepts[24] | 0.88 | the paper's words |
| concepts | systems biology Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: systems biology | concepts[25] | 0.88 | the paper's words |
| concepts | internal similarity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: internal similarity | concepts[26] | 0.9 | the paper's words |
| concepts | facts Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: facts | concepts[27] | 0.88 | the paper's words |
| concepts | world Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: world | concepts[28] | 0.85 | the paper's words |
| unhoused_relations | representation → reproduction Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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. | unhoused_relations[0] | 0.9 | the tagger's words |
| unhoused_relations | music → the will of life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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. | unhoused_relations[1] | 0.85 | the tagger's words |
| unhoused_relations | genome → life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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. | unhoused_relations[2] | 0.9 | the tagger's words |
| unhoused_relations | lower levels → higher levels Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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. | unhoused_relations[3] | 0.85 | the tagger's words |
| unhoused_relations | score → genetic language Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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. | unhoused_relations[4] | 0.88 | the tagger's words |
| senses | reading - human/sequential sense: a text read in one way only, sequentially, involving all characters Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[0] | 0.92 | the tagger's words |
| senses | 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 — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[1] | 0.92 | the tagger's words |
| senses | intelligibility - linguistic-theory sense: the trade-off between hierarchical levels in a shared world (Komarova and Niyogi) Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[2] | 0.9 | the tagger's words |
| senses | intelligibility - the authors' epistemological sense: the construction of meaningful (thinkable) models reflecting complex natural systems Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[3] | 0.9 | the tagger's words |
| senses | representation - Wittgenstein's picture sense: a proposition/picture sharing a logical form with the fact it represents Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[4] | 0.9 | the tagger's words |
| senses | representation - Schopenhauer's sense: music as a copy of the will itself, resembling an original reality that cannot be copied Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[5] | 0.88 | the tagger's words |
| senses | representation - biological sense: genomic sequences representing life, meaningful only when a living system is present Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[6] | 0.9 | the tagger's words |
| senses | score - musical sense: the notation from which a symphony can be reconstructed by a general rule (Tractatus 4.0141) Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[7] | 0.9 | the tagger's words |
| senses | score - 'score of life' sense: the genomic language, proposed as a better image than the book of life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[8] | 0.9 | the tagger's words |
| senses | will - Schopenhauer's metaphysical sense: the will itself, of which music is a copy and the Ideas its objectivity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[9] | 0.85 | the tagger's words |
| senses | 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 — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[10] | 0.85 | the tagger's words |
| claim_relations | builds-on → Wittgenstein's Tractatus logico-philosophicus (theorem 4.0141 and the picture theory of representation) Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. note: The essay takes the Tractatus as its main post-Kantian framework for the limits of knowledge of the natural world. | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | builds-on → Schopenhauer's account of music as a copy of the will (The World as Will and Representation) Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. note: The will represented in music is read as a representation of the will of life. | claim_relations[1] | 0.9 | the tagger's words |
| claim_relations | extends → Dennis Noble's 'music of life' metaphor Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. note: The essay extends Noble's music-of-life idea to the intelligibility of microbial life. | claim_relations[2] | 0.92 | the tagger's words |
| claim_relations | builds-on → Maynard Smith and Szathmary's theory of major evolutionary transitions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. note: Major transitions between hierarchical levels frame the score-to-music and genes-to-life passages. | claim_relations[3] | 0.9 | the tagger's words |
| claim_relations | contrasts-with → the classic 'book of life' metaphor for the genome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. note: The 'score of life' is proposed as a better image of the genomic language. | claim_relations[4] | 0.92 | the tagger's words |
| claim_relations | recommends → developing complex models of complex systems through convergent, multidisciplinary 'Big Science' Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. note: The half-seeing part needs more powerful model tools integrating all the -omics data. | claim_relations[5] | 0.88 | the tagger's words |
| concept_edges | life —is-a→ music Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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. | concept_edges[0] | 0.8 | the tagger's words |
| concept_edges | music score —causes→ music Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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. also in: music score · music | concept_edges[1] | 0.85 | the tagger's words |
| concept_edges | facts —part-of→ world Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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. | concept_edges[2] | 0.9 | the tagger's words |
| concept_edges | score of life —contrasted-with→ book of life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. 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. also in: score of life · book of life | concept_edges[3] | 0.85 | the tagger's words |
| content_tags | Increasing diversification and complexity in microbiology paradoxically results in a strong reduction of the intelligibility of microbial life. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[0] | 0.9 | the tagger's words |
| content_tags | 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 — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[1] | 0.9 | the tagger's words |
| content_tags | Both life and music can be shown but not thought; genomic sequences and musical scores are mere representations of these obscure realities. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[2] | 0.9 | the tagger's words |
| content_tags | A strategy of half-thinking and half-seeing is needed to expand knowledge of complex systems such as life and music. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[3] | 0.9 | the tagger's words |
| content_tags | The epistemological process for complex biological systems has three phases: legibility, imageability, and intelligibility. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[4] | 0.9 | the tagger's words |
| content_tags | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: intelligibility | content_tags.definitions[0] | 0.92 | the tagger's words |
| content_tags | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: score | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | the descriptive level of anatomy and physiology - the composition of Wittgensteinian atomic facts and propositions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: legibility | content_tags.definitions[2] | 0.88 | the tagger's words |
| content_tags | the stage at which a holistic, physiognomically comparable image of a living structure can be seen or shown Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: imageability | content_tags.definitions[3] | 0.88 | the tagger's words |
| content_tags | a half-thinking perception of fine shades of meaning - a kinship between seeing an aspect and understanding that enables connections and comparisons Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: experience of meaning | content_tags.definitions[4] | 0.9 | the tagger's words |
Tags that could not be placed in the text:
What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.