Literature DB >> 31674305

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

Diane Marie Keeling1, Patricia Garza2, Charisse Michelle Nartey3, Anne-Ruxandra Carvunis4,5.   

Abstract

The word function has many different meanings in molecular biology. Here we explore the use of this word (and derivatives like functional) in research papers about de novo gene birth. Based on an analysis of 20 abstracts we propose a simple lexicon that, we believe, will help scientists and philosophers discuss the meaning of function more clearly.
© 2019, Keeling et al.

Entities:  

Keywords:  de novo gene birth; evolutionary biology; function; genetics; genomics; none; philosophy of biology; philosophy of science; rhetoric

Mesh：

Substances：

Year:  2019        PMID： 31674305      PMCID： PMC6824840          DOI： 10.7554/eLife.47014

Source DB:  PubMed          Journal:  Elife        ISSN： 2050-084X            Impact factor:   8.140


  22 in total

1.  GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.

Authors:  C Friedman; P Kra; H Yu; M Krauthammer; A Rzhetsky
Journal:  Bioinformatics       Date:  2001       Impact factor: 6.937

2.  The relativity of biological function.

Authors:  Manfred D Laubichler; Peter F Stadler; Sonja J Prohaska; Katja Nowick
Journal:  Theory Biosci       Date:  2015-10-08       Impact factor: 1.919

3.  In what sense does 'nothing make sense except in the light of evolution'?

Authors:  Paul Edmund Griffiths
Journal:  Acta Biotheor       Date:  2008-09-06       Impact factor: 1.774

Review 4.  More than just orphans: are taxonomically-restricted genes important in evolution?

Authors:  Konstantin Khalturin; Georg Hemmrich; Sebastian Fraune; René Augustin; Thomas C G Bosch
Journal:  Trends Genet       Date:  2009-08-27       Impact factor: 11.639

Review 5.  The evolutionary origin of orphan genes.

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

Review 6.  Open questions in the study of de novo genes: what, how and why.

Authors:  Aoife McLysaght; Laurence D Hurst
Journal:  Nat Rev Genet       Date:  2016-07-25       Impact factor: 53.242

7.  Of mice, men and immunity: a case for evolutionary systems biology.

Authors:  Peter B Ernst; Anne-Ruxandra Carvunis
Journal:  Nat Immunol       Date:  2018-05       Impact factor: 25.606

8.  On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE.

Authors:  Dan Graur; Yichen Zheng; Nicholas Price; Ricardo B R Azevedo; Rebecca A Zufall; Eran Elhaik
Journal:  Genome Biol Evol       Date:  2013       Impact factor: 3.416

Review 9.  An evolutionary classification of genomic function.

Authors:  Dan Graur; Yichen Zheng; Ricardo B R Azevedo
Journal:  Genome Biol Evol       Date:  2015-01-28       Impact factor: 3.416

10.  We simply cannot go on being so vague about 'function'.

Authors:  W Ford Doolittle
Journal:  Genome Biol       Date:  2018-12-18       Impact factor: 13.583
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  17 in total

1.  Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes.

Authors:  Neel Prabh; Christian Rödelsperger
Journal:  Genome Res       Date:  2022-05-26       Impact factor: 9.438

2.  Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons.

Authors:  Marina Athanasouli; Christian Rödelsperger
Journal:  BMC Genomics       Date:  2022-07-19       Impact factor: 4.547

Review 3.  The Origins and Functions of De Novo Genes: Against All Odds?

Authors:  Caroline M Weisman
Journal:  J Mol Evol       Date:  2022-04-22       Impact factor: 3.973

4.  Pervasive translation in Mycobacterium tuberculosis.

Authors:  Carol Smith; Jill G Canestrari; Archer J Wang; Matthew M Champion; Keith M Derbyshire; Todd A Gray; Joseph T Wade
Journal:  Elife       Date:  2022-03-28       Impact factor: 8.713

5.  Identification of novel translated small ORFs in Escherichia coli using complementary ribosome profiling approaches.

Authors:  Anne Stringer; Carol Smith; Kyle Mangano; Joseph T Wade
Journal:  J Bacteriol       Date:  2021-10-18       Impact factor: 3.476

6.  A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants.

Authors:  Igor Fesenko; Svetlana A Shabalina; Anna Mamaeva; Andrey Knyazev; Anna Glushkevich; Irina Lyapina; Rustam Ziganshin; Sergey Kovalchuk; Daria Kharlampieva; Vassili Lazarev; Michael Taliansky; Eugene V Koonin
Journal:  Nucleic Acids Res       Date:  2021-10-11       Impact factor: 16.971

7.  A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster.

Authors:  Emily L Rivard; Andrew G Ludwig; Prajal H Patel; Anna Grandchamp; Sarah E Arnold; Alina Berger; Emilie M Scott; Brendan J Kelly; Grace C Mascha; Erich Bornberg-Bauer; Geoffrey D Findlay
Journal:  PLoS Genet       Date:  2021-09-03       Impact factor: 5.917

8.  The analysis of living systems can generate both knowledge and illusions.

Authors:  Antony M Jose
Journal:  Elife       Date:  2020-06-18       Impact factor: 8.140

9.  Structural and functional characterization of a putative de novo gene in Drosophila.

Authors:  Andreas Lange; Prajal H Patel; Brennen Heames; Adam M Damry; Thorsten Saenger; Colin J Jackson; Geoffrey D Findlay; Erich Bornberg-Bauer
Journal:  Nat Commun       Date:  2021-03-12       Impact factor: 14.919

10.  Phosphorylation of a Human Microprotein Promotes Dissociation of Biomolecular Condensates.

Authors:  Zhenkun Na; Yang Luo; Danica S Cui; Alexandra Khitun; Stephanie Smelyansky; J Patrick Loria; Sarah A Slavoff
Journal:  J Am Chem Soc       Date:  2021-08-04       Impact factor: 16.383
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