Literature DB >> 26449352

The relativity of biological function.

Manfred D Laubichler1,2,3, Peter F Stadler4,5,6,7,8,9, Sonja J Prohaska10, Katja Nowick11.   

Abstract

Function is a central concept in biological theories and explanations. Yet discussions about function are often based on a narrow understanding of biological systems and processes, such as idealized molecular systems or simple evolutionary, i.e., selective, dynamics. Conflicting conceptions of function continue to be used in the scientific literature to support certain claims, for instance about the fraction of "functional DNA" in the human genome. Here we argue that all biologically meaningful interpretations of function are necessarily context dependent. This implies that they derive their meaning as well as their range of applicability only within a specific theoretical and measurement context. We use this framework to shed light on the current debate about functional DNA and argue that without considering explicitly the theoretical and measurement contexts all attempts to integrate biological theories are prone to fail.

Entities:  

Keywords:  Biological function; Biological theory; Coarse graining; ENCODE; Theory integration

Mesh:

Substances:

Year:  2015        PMID: 26449352     DOI: 10.1007/s12064-015-0215-5

Source DB:  PubMed          Journal:  Theory Biosci        ISSN: 1431-7613            Impact factor:   1.919


  26 in total

Review 1.  What is a gene, post-ENCODE? History and updated definition.

Authors:  Mark B Gerstein; Can Bruce; Joel S Rozowsky; Deyou Zheng; Jiang Du; Jan O Korbel; Olof Emanuelsson; Zhengdong D Zhang; Sherman Weissman; Michael Snyder
Journal:  Genome Res       Date:  2007-06       Impact factor: 9.043

Review 2.  Origin of phenotypes: genes and transcripts.

Authors:  Thomas R Gingeras
Journal:  Genome Res       Date:  2007-06       Impact factor: 9.043

Review 3.  Measurement and meaning in biology.

Authors:  David Houle; Christophe Pélabon; Günter P Wagner; Thomas F Hansen
Journal:  Q Rev Biol       Date:  2011-03       Impact factor: 4.875

Review 4.  The evolutionary origin of orphan genes.

Authors:  Diethard Tautz; Tomislav Domazet-Lošo
Journal:  Nat Rev Genet       Date:  2011-08-31       Impact factor: 53.242

5.  Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies.

Authors:  Wolfgang Otto; Peter F Stadler; Francesc López-Giraldéz; Jeffrey P Townsend; Vincent J Lynch; Günter P Wagner
Journal:  Genome Biol Evol       Date:  2009-05-25       Impact factor: 3.416

6.  Cocaine as a naturally occurring insecticide.

Authors:  J A Nathanson; E J Hunnicutt; L Kantham; C Scavone
Journal:  Proc Natl Acad Sci U S A       Date:  1993-10-15       Impact factor: 11.205

7.  Birth and expression evolution of mammalian microRNA genes.

Authors:  Julien Meunier; Frédéric Lemoine; Magali Soumillon; Angélica Liechti; Manuela Weier; Katerina Guschanski; Haiyang Hu; Philipp Khaitovich; Henrik Kaessmann
Journal:  Genome Res       Date:  2012-10-03       Impact factor: 9.043

8.  Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution.

Authors:  Rafik Neme; Diethard Tautz
Journal:  BMC Genomics       Date:  2013-02-21       Impact factor: 3.969

9.  An integrated encyclopedia of DNA elements in the human genome.

Authors: 
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

10.  The expansion of the metazoan microRNA repertoire.

Authors:  Jana Hertel; Manuela Lindemeyer; Kristin Missal; Claudia Fried; Andrea Tanzer; Christoph Flamm; Ivo L Hofacker; Peter F Stadler
Journal:  BMC Genomics       Date:  2006-02-15       Impact factor: 3.969

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  4 in total

1.  The meanings of 'function' in biology and the problematic case of de novo gene emergence.

Authors:  Diane Marie Keeling; Patricia Garza; Charisse Michelle Nartey; Anne-Ruxandra Carvunis
Journal:  Elife       Date:  2019-11-01       Impact factor: 8.140

Review 2.  DNA methylation: conducting the orchestra from exposure to phenotype?

Authors:  Fleur A D Leenen; Claude P Muller; Jonathan D Turner
Journal:  Clin Epigenetics       Date:  2016-09-06       Impact factor: 6.551

3.  Functions of consciousness: conceptual clarification.

Authors:  Takuya Niikawa; Katsunori Miyahara; Hiro Taiyo Hamada; Satoshi Nishida
Journal:  Neurosci Conscious       Date:  2022-03-29

Review 4.  Seq'ing identity and function in a repeat-derived noncoding RNA world.

Authors:  Rachel J O'Neill
Journal:  Chromosome Res       Date:  2020-03-07       Impact factor: 5.239

  4 in total

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