Literature DB >> 20534598

The evolvability of programmable hardware.

Karthik Raman1, Andreas Wagner.   

Abstract

In biological systems, individual phenotypes are typically adopted by multiple genotypes. Examples include protein structure phenotypes, where each structure can be adopted by a myriad individual amino acid sequence genotypes. These genotypes form vast connected 'neutral networks' in genotype space. The size of such neutral networks endows biological systems not only with robustness to genetic change, but also with the ability to evolve a vast number of novel phenotypes that occur near any one neutral network. Whether technological systems can be designed to have similar properties is poorly understood. Here we ask this question for a class of programmable electronic circuits that compute digital logic functions. The functional flexibility of such circuits is important in many applications, including applications of evolutionary principles to circuit design. The functions they compute are at the heart of all digital computation. We explore a vast space of 10(45) logic circuits ('genotypes') and 10(19) logic functions ('phenotypes'). We demonstrate that circuits that compute the same logic function are connected in large neutral networks that span circuit space. Their robustness or fault-tolerance varies very widely. The vicinity of each neutral network contains circuits with a broad range of novel functions. Two circuits computing different functions can usually be converted into one another via few changes in their architecture. These observations show that properties important for the evolvability of biological systems exist in a commercially important class of electronic circuitry. They also point to generic ways to generate fault-tolerant, adaptable and evolvable electronic circuitry.

Mesh:

Year:  2010        PMID: 20534598      PMCID: PMC3033018          DOI: 10.1098/rsif.2010.0212

Source DB:  PubMed          Journal:  J R Soc Interface        ISSN: 1742-5662            Impact factor:   4.118


  19 in total

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Authors:  E van Nimwegen; J P Crutchfield; M Huynen
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-17       Impact factor: 11.205

2.  Distributed robustness versus redundancy as causes of mutational robustness.

Authors:  Andreas Wagner
Journal:  Bioessays       Date:  2005-02       Impact factor: 4.345

3.  Thermodynamic prediction of protein neutrality.

Authors:  Jesse D Bloom; Jonathan J Silberg; Claus O Wilke; D Allan Drummond; Christoph Adami; Frances H Arnold
Journal:  Proc Natl Acad Sci U S A       Date:  2005-01-11       Impact factor: 11.205

4.  Modelling neutral and selective evolution of protein folding.

Authors:  D J Lipman; W J Wilbur
Journal:  Proc Biol Sci       Date:  1991-07-22       Impact factor: 5.349

5.  Neutral fitness landscapes in signalling networks.

Authors:  Pau Fernández; Ricard V Solé
Journal:  J R Soc Interface       Date:  2007-02-22       Impact factor: 4.118

6.  From sequences to shapes and back: a case study in RNA secondary structures.

Authors:  P Schuster; W Fontana; P F Stadler; I L Hofacker
Journal:  Proc Biol Sci       Date:  1994-03-22       Impact factor: 5.349

7.  Exploring phenotype space through neutral evolution.

Authors:  M A Huynen
Journal:  J Mol Evol       Date:  1996-09       Impact factor: 2.395

8.  Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force.

Authors:  A Babajide; I L Hofacker; M J Sippl; P F Stadler
Journal:  Fold Des       Date:  1997

9.  Neutrality and robustness in evo-devo: emergence of lateral inhibition.

Authors:  Andreea Munteanu; Ricard V Solé
Journal:  PLoS Comput Biol       Date:  2008-11-21       Impact factor: 4.475

10.  Evolutionary plasticity and innovations in complex metabolic reaction networks.

Authors:  João F Matias Rodrigues; Andreas Wagner
Journal:  PLoS Comput Biol       Date:  2009-12-18       Impact factor: 4.475

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  12 in total

1.  Zipf's Law, unbounded complexity and open-ended evolution.

Authors:  Bernat Corominas-Murtra; Luís F Seoane; Ricard Solé
Journal:  J R Soc Interface       Date:  2018-12-21       Impact factor: 4.118

Review 2.  Spaces of the possible: universal Darwinism and the wall between technological and biological innovation.

Authors:  Andreas Wagner; William Rosen
Journal:  J R Soc Interface       Date:  2014-08-06       Impact factor: 4.118

3.  Biological conservation law as an emerging functionality in dynamical neuronal networks.

Authors:  Boris Podobnik; Marko Jusup; Zoran Tiganj; Wen-Xu Wang; Javier M Buldú; H Eugene Stanley
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-24       Impact factor: 11.205

4.  A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure.

Authors:  Sam F Greenbury; Iain G Johnston; Ard A Louis; Sebastian E Ahnert
Journal:  J R Soc Interface       Date:  2014-04-09       Impact factor: 4.118

5.  Genonets server-a web server for the construction, analysis and visualization of genotype networks.

Authors:  Fahad Khalid; José Aguilar-Rodríguez; Andreas Wagner; Joshua L Payne
Journal:  Nucleic Acids Res       Date:  2016-04-22       Impact factor: 16.971

6.  Robustness to Faults Promotes Evolvability: Insights from Evolving Digital Circuits.

Authors:  Nicola Milano; Stefano Nolfi
Journal:  PLoS One       Date:  2016-07-13       Impact factor: 3.240

7.  Crosstalk and the evolvability of intracellular communication.

Authors:  Michael A Rowland; Joseph M Greenbaum; Eric J Deeds
Journal:  Nat Commun       Date:  2017-07-10       Impact factor: 14.919

8.  The architecture of an empirical genotype-phenotype map.

Authors:  José Aguilar-Rodríguez; Leto Peel; Massimo Stella; Andreas Wagner; Joshua L Payne
Journal:  Evolution       Date:  2018-05-25       Impact factor: 3.694

9.  Insertions and deletions in the RNA sequence-structure map.

Authors:  Nora S Martin; Sebastian E Ahnert
Journal:  J R Soc Interface       Date:  2021-10-06       Impact factor: 4.118

10.  Latent phenotypes pervade gene regulatory circuits.

Authors:  Joshua L Payne; Andreas Wagner
Journal:  BMC Syst Biol       Date:  2014-05-30
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