How to make a synthetic multicellular computer

Biological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in thi...

Full description

Bibliographic Details
Authors: Macía, Javier, Solé Vicente, Ricard, 1962-
Format: article
Status:Published version
Publication Date:2014
Country:España
Institution:Universitat Pompeu Fabra
Repository:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/23613
Online Access:http://hdl.handle.net/10230/23613
http://dx.doi.org/10.1371/journal.pone.0081248
Access Level:Open access
Keyword:Biologia sintètica
Biologia computacional
id ES_014f1c7380da2e1b9d7e1addb3bef609
oai_identifier_str oai:repositori.upf.edu:10230/23613
network_acronym_str ES
network_name_str España
repository_id_str
spelling How to make a synthetic multicellular computerMacía, JavierSolé Vicente, Ricard, 1962-Biologia sintèticaBiologia computacionalBiological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in this mapping between electronic and wet computational circuits is the wiring problem. Although wires are identical within electronic devices, they must be different when using synthetic biology designs. Moreover, in most cases the designed molecular systems cannot be reused for other functions. A new approximation allows us to simplify the problem by using synthetic cellular consortia where the output of the computation is distributed over multiple engineered cells. By evolving circuits in silico, we can obtain the minimal sets of Boolean units required to solve the given problem at the lowest cost using cellular consortia. Our analysis reveals that the basic set of logic units is typically non-standard. Among the most common units, the so called inverted IMPLIES (N-Implies) appears to be one of the most important elements along with the NOT and AND functions. Although NOR and NAND gates are widely used in electronics, evolved circuits based on combinations of these gates are rare, thus suggesting that the strategy of combining the same basic logic gates might be inappropriate in order to easily implement synthetic computational constructs. The implications for future synthetic designs, the general view of synthetic biology as a standard engineering domain, as well as potencial drawbacks are outlined.This work has been supported by and EU ERC Advanced Grant, the James S. McDonnell Foundation, the Fundaci’on Botin and the Santa Fe InstitutePublic Library of Science (PLoS)201520152014info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/23613http://dx.doi.org/10.1371/journal.pone.0081248reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésPLoS ONE. 2014;9(2):e81248© 2014 Macia, Sole. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedinfo:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/236132026-06-12T07:21:37Z
dc.title.none.fl_str_mv How to make a synthetic multicellular computer
title How to make a synthetic multicellular computer
spellingShingle How to make a synthetic multicellular computer
Macía, Javier
Biologia sintètica
Biologia computacional
title_short How to make a synthetic multicellular computer
title_full How to make a synthetic multicellular computer
title_fullStr How to make a synthetic multicellular computer
title_full_unstemmed How to make a synthetic multicellular computer
title_sort How to make a synthetic multicellular computer
dc.creator.none.fl_str_mv Macía, Javier
Solé Vicente, Ricard, 1962-
author Macía, Javier
author_facet Macía, Javier
Solé Vicente, Ricard, 1962-
author_role author
author2 Solé Vicente, Ricard, 1962-
author2_role author
dc.subject.none.fl_str_mv Biologia sintètica
Biologia computacional
topic Biologia sintètica
Biologia computacional
description Biological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in this mapping between electronic and wet computational circuits is the wiring problem. Although wires are identical within electronic devices, they must be different when using synthetic biology designs. Moreover, in most cases the designed molecular systems cannot be reused for other functions. A new approximation allows us to simplify the problem by using synthetic cellular consortia where the output of the computation is distributed over multiple engineered cells. By evolving circuits in silico, we can obtain the minimal sets of Boolean units required to solve the given problem at the lowest cost using cellular consortia. Our analysis reveals that the basic set of logic units is typically non-standard. Among the most common units, the so called inverted IMPLIES (N-Implies) appears to be one of the most important elements along with the NOT and AND functions. Although NOR and NAND gates are widely used in electronics, evolved circuits based on combinations of these gates are rare, thus suggesting that the strategy of combining the same basic logic gates might be inappropriate in order to easily implement synthetic computational constructs. The implications for future synthetic designs, the general view of synthetic biology as a standard engineering domain, as well as potencial drawbacks are outlined.
publishDate 2014
dc.date.none.fl_str_mv 2014
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/23613
http://dx.doi.org/10.1371/journal.pone.0081248
url http://hdl.handle.net/10230/23613
http://dx.doi.org/10.1371/journal.pone.0081248
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv PLoS ONE. 2014;9(2):e81248
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science (PLoS)
publisher.none.fl_str_mv Public Library of Science (PLoS)
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869402573702692864
score 15,812455

Similar Items