Dataset Information

Time as a consequence of internal coherence.

ABSTRACT: Time has been an elusive concept to grasp. Although we do not yet understand it properly, there have been advances made in regard to how we can explain it. One such advance is the Page-Wootters mechanism. In this mechanism, time is seen as an inaccessible coordinate and the apparent passage of time arises as a consequence of correlations between the subsystems of a global state. Here we propose a measure that captures the relational character of the mechanism, showing that the internal coherence is the necessary ingredient for the emergence of time in the Page-Wootters model. Also, we connect it to results in quantum thermodynamics, showing that it is directly related to the extractable work from quantum coherence.

SUBMITTER: Mendes LRS

PROVIDER: S-EPMC6894544 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Time as a consequence of internal coherence.

Mendes Leandro R S LRS Soares-Pinto Diogo O DO

Proceedings. Mathematical, physical, and engineering sciences 20191113 2231

Time has been an elusive concept to grasp. Although we do not yet understand it properly, there have been advances made in regard to how we can explain it. One such advance is the Page-Wootters mechanism. In this mechanism, time is seen as an inaccessible coordinate and the apparent passage of time arises as a consequence of correlations between the subsystems of a global state. Here we propose a measure that captures the relational character of the mechanism, showing that the internal coherence ...[more]

PMID: 31824220

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Project description:BACKGROUND: Functional profiling methods have been extensively used in the context of high-throughput experiments and, in particular, in microarray data analysis. Such methods use available biological information to define different types of functional gene modules (e.g. gene ontology -GO-, KEGG pathways, etc.) whose representation in a pre-defined list of genes is further studied. In the most popular type of microarray experimental designs (e.g. up- or down-regulated genes, clusters of co-expressing genes, etc.) or in other genomic experiments (e.g. Chip-on-chip, epigenomics, etc.) these lists are composed by genes with a high degree of co-expression. Therefore, an implicit assumption in the application of functional profiling methods within this context is that the genes corresponding to the modules tested are effectively defining sets of co-expressing genes. Nevertheless not all the functional modules are biologically coherent entities in terms of co-expression, which will eventually hinder its detection with conventional methods of functional enrichment. RESULTS: Using a large collection of microarray data we have carried out a detailed survey of internal correlation in GO terms and KEGG pathways, providing a coherence index to be used for measuring functional module co-regulation. An unexpected low level of internal correlation was found among the modules studied. Only around 30% of the modules defined by GO terms and 57% of the modules defined by KEGG pathways display an internal correlation higher than the expected by chance.This information on the internal correlation of the genes within the functional modules can be used in the context of a logistic regression model in a simple way to improve their detection in gene expression experiments. CONCLUSION: For the first time, an exhaustive study on the internal co-expression of the most popular functional categories has been carried out. Interestingly, the real level of coexpression within many of them is lower than expected (or even inexistent), which will preclude its detection by means of most conventional functional profiling methods. If the gene-to-function correlation information is used in functional profiling methods, the results obtained improve the ones obtained by conventional enrichment methods.

Dataset Information

Time as a consequence of internal coherence.

Publications

Time as a consequence of internal coherence.

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