Biological computation: Difference between revisions
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In the most literal interpretation of the term, <b>biological computation</b> refers to | In the most literal interpretation of the term, <b>biological computation</b> refers to computation by means of biological systems — specifically, biological systems/processes that imbed mathematical/computational operations — hence, its application to the emerging subdiscipline of biology that explores and exploits the use of biological systems to perform mathematical/computational operations and achieve solutions to mathematical/computational problems — for example, computing with DNA molecules<ref name=Kari/> — and that studies computational processes in biological and living systems.<ref name=Bray/><ref name=Landweber/><ref name=Simeonov/> | ||
==Parallel computing== | |||
The prospect of using molecules and chemistry to undertake massively parallel computation has been raised.<ref name=Reif/> The notion is based upon simultaneous analysis of an assembly of molecules like DNA that are "trial" solutions and use of various chemical tricks to decide in parallel which ones fit the problem criteria. A description of one such approach is provided by Maley.<ref name=Maley/> A practical problem has proved to be a high error rate that requires careful study. | |||
==Embedded controllers== | |||
One different kind of application for biological computation is the administration of [[chemotherapy]]. The underlying idea is that bacteria are arranged to invade a tumor to selectively produce a drug that kills the tumor. Within the injected bacteria is an embedded controller that executes the logical computation "If ''X'' is present, produce ''Y''" or possibly, "If the rate of change of ''X'' is within certain bounds, produce ''Y''", thereby conditionally activating the bacteria only where a tumor is present.<ref name=Anderson/> | |||
== References == | == References == | ||
{{Reflist|refs= | {{Reflist|refs= | ||
<ref name=Anderson> | |||
{{cite journal |title=Environmentally controlled invasion of cancer cells by engineered bacteria |journal =Journal of Molecular Biology, |author=JC Anderson, EJ Clarke, AP Arkin, CA Voigt |url=http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.161.6839&rep=rep1&type=pdf |date= 2005 |doi=10.1016/j.jmb.2005.10.076 |pages=pp. 619 ''ff'' }} | |||
</ref> | |||
<ref name=Bray> | <ref name=Bray> | ||
{{cite book |author=Bray D. |year=2009 |title=Wetware: A Computer in Every Living Cell |publisher=Yale University Press |isbn= 9780300141733 |url= http://books.google.com/books?id=UL7xW_FL_hMC&dq=WETWARE&source=gbs_navlinks_s}} Google Books preview.</ref> | {{cite book |author=Bray D. |year=2009 |title=Wetware: A Computer in Every Living Cell |publisher=Yale University Press |isbn= 9780300141733 |url= http://books.google.com/books?id=UL7xW_FL_hMC&dq=WETWARE&source=gbs_navlinks_s}} Google Books preview. | ||
</ref> | |||
<ref name=Kari> | <ref name=Kari> | ||
{{cite journal|author=Kari L, Landweber LF. |year=2000 |title= Computing with DNA |journal=Methods Molecular Biology: Bioinformatics methods and protocols |volume=132 |pages=pp. 413-430 |url=http://www.csd.uwo.ca/faculty/lila/pdfs/Computing%20with%20DNA.pdf}} | {{cite journal|author=Kari L, Landweber LF. |year=2000 |title= Computing with DNA |journal=Methods in Molecular Biology: Bioinformatics methods and protocols |volume=132 |pages=pp. 413-430 |url=http://www.csd.uwo.ca/faculty/lila/pdfs/Computing%20with%20DNA.pdf}} | ||
</ref> | </ref> | ||
<ref name=Landweber> | <ref name=Landweber> | ||
{{cite journal |author=Landweber LF, Kari L. |year=1999 |url=http://dx.doi.org/10.1016/S0303-2647(99)00027-1 |title=The evolution of cellular computing: nature’s solution to a computational problem |journal=Biosystems |volume=52|pages=pp. 3-13}} | {{cite journal |author=Landweber LF, Kari L. |year=1999 |url=http://dx.doi.org/10.1016/S0303-2647(99)00027-1 |title=The evolution of cellular computing: nature’s solution to a computational problem |journal=Biosystems |volume=52|pages=pp. 3-13}} | ||
</ref> | |||
<ref name=Maley> | |||
{{cite journal |title=DNA Computation: Theory, Practice, and Prospects |author=Carlo C. Maley |url=http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.35.8235&rep=rep1&type=pdf |journal=Evolutionary computation |volume=6 |pages=pp. 201-229 |year=1998}} | |||
</ref> | |||
<ref name=Reif> | |||
{{cite journal |author=John H Reif |title=Parallel biomolecular computation: models and simulations |url=http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.47.3260&rep=rep1&type=pdf |journal =Algorithmica |year=1999 |volume=25 |pages=pp. 142-175 |doi=10.1007/PL00008272 }} | |||
</ref> | </ref> | ||
<ref name=Simeonov> | <ref name=Simeonov> | ||
{{cite journal |author=Simeonov PL |year=2010 |url=http:// | {{cite journal |author=Simeonov PL |year=2010 |url=http://www.simeio.org/pages/details/papers/papers_pool/intbiomath.pdf |title=Integral biomathics: A post-Newtonian view into the logos of bios |journal=Progress in Biophysics and Molecular Biology |pages=pp. 85-121 |doi=10.1016/j.pbiomolbio.2010.01.005}} Proof of article as published online. | ||
</ref> | </ref> | ||
}} | }}[[Category:Suggestion Bot Tag]] | ||
Latest revision as of 16:01, 18 July 2024
In the most literal interpretation of the term, biological computation refers to computation by means of biological systems — specifically, biological systems/processes that imbed mathematical/computational operations — hence, its application to the emerging subdiscipline of biology that explores and exploits the use of biological systems to perform mathematical/computational operations and achieve solutions to mathematical/computational problems — for example, computing with DNA molecules[1] — and that studies computational processes in biological and living systems.[2][3][4]
Parallel computing
The prospect of using molecules and chemistry to undertake massively parallel computation has been raised.[5] The notion is based upon simultaneous analysis of an assembly of molecules like DNA that are "trial" solutions and use of various chemical tricks to decide in parallel which ones fit the problem criteria. A description of one such approach is provided by Maley.[6] A practical problem has proved to be a high error rate that requires careful study.
Embedded controllers
One different kind of application for biological computation is the administration of chemotherapy. The underlying idea is that bacteria are arranged to invade a tumor to selectively produce a drug that kills the tumor. Within the injected bacteria is an embedded controller that executes the logical computation "If X is present, produce Y" or possibly, "If the rate of change of X is within certain bounds, produce Y", thereby conditionally activating the bacteria only where a tumor is present.[7]
References
- ↑ Kari L, Landweber LF. (2000). "Computing with DNA". Methods in Molecular Biology: Bioinformatics methods and protocols 132: pp. 413-430.
- ↑ Bray D. (2009). Wetware: A Computer in Every Living Cell. Yale University Press. ISBN 9780300141733. Google Books preview.
- ↑ Landweber LF, Kari L. (1999). "The evolution of cellular computing: nature’s solution to a computational problem". Biosystems 52: pp. 3-13.
- ↑ Simeonov PL (2010). "Integral biomathics: A post-Newtonian view into the logos of bios". Progress in Biophysics and Molecular Biology: pp. 85-121. DOI:10.1016/j.pbiomolbio.2010.01.005. Research Blogging. Proof of article as published online.
- ↑ John H Reif (1999). "Parallel biomolecular computation: models and simulations". Algorithmica 25: pp. 142-175. DOI:10.1007/PL00008272. Research Blogging.
- ↑ Carlo C. Maley (1998). "DNA Computation: Theory, Practice, and Prospects". Evolutionary computation 6: pp. 201-229.
- ↑ JC Anderson, EJ Clarke, AP Arkin, CA Voigt (2005). "Environmentally controlled invasion of cancer cells by engineered bacteria". Journal of Molecular Biology,: pp. 619 ff. DOI:10.1016/j.jmb.2005.10.076. Research Blogging.