Is biology Turing Complete?
Ben Haley
Tuesday, 16 December 2008 00:52 UTC
To explore computing in biology we must first identify systems which are capable of the full range of computation. These are known at Turing complete systems.
see http://en.wikipedia.org/wiki/Turing_complete for details
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Replies
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Computation in Ciliates
Stichotrichous Ciliates are a parasitic micro-organism with a unique form of chromosome rearrangement that is supposed to have computational potential.Stichotrichous Cilliates have two sets of nuclei, scrambled micronuclei that have non-coding elements and decoded macronuclei which are used for protein production. Micronuclei are converted to macronuclei through cutting, splicing, rearrangement and excision. Multiple mechanisms have been proposed for the specific cellular operations that produce macronuclei from micronuclei including a template based technique and a more traditional splicing-proposal. Both of these hypothetical mechanisms have been shown by their authors to be computationally complete. It is not clear if other mechanisms would intrinsically be computationally complete.
1. Prescott and Rozenburg, “How ciliates manipulate their own DNA – A splendid example of natural computing” Natural Computing (2002) cited=14
2. Prescott, Ehrenfeucht, and Rozenberg “Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates” – J Theor Biol (2003) cited:24 -
Good News! I’ve found a few relevant sources from the journal of Natural Computing. These are my notes and if you’d like elaboration or citations details, please let me know.
Takashi and Kari prove that splicing systems are Turing complete. Ben-Hur and Sieglemann prove that GNRs are analogous to linear differential equations. Takahara and Yokomori (Japan) show that Insertion/deletion systems equal the set of all enumarable recursive languages. Bouchard and Osbourne (Alberquerque) show that protein networks map to RAM computation models. Balan and Jurgenson use a protein antibody model for computation in 2006.
Various algorithms have been proposed to solve NP complete problems and other fundamental operations using DNA strands in the tradition of Adelman. Oyang (princeton) solves Maximal Clique. Guarnari and Bacroft do addition in 1996. Sakakibara (Japan) solves DNF boolean formulas in 2004 using weighted algorithms to overcome variability. Wu and Seamen (NYU) show multiplication in 2006. Braich and Adelman (USC) solves a 20 var 3-SAT problem in 2002 test tubes, the largest such calculation to date.
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