title: Downward causation by information control in micro-organisms.
abstract: The concepts of functional equivalence classes and information control in living systems are useful to characterize downward (or top-down) causation by feedback information control in synthetic biology. Herein, we re-analyse published experiments of microbiology and synthetic biology that demonstrate the existence of several classes of functional equivalence in microbial organisms. Classes of functional equivalence from the bacterial operating system, which processes and controls the information encoded in the genome, can readily be interpreted as strong evidence, if not demonstration, of top-down causation (TDC) by information control. The proposed biological framework reveals how this type of causality is put in action in the cellular operating system. Considerations on TDC by information control and adaptive selection can be useful for synthetic biology by delineating the irreducible set of properties that characterizes living systems. Through a 'retro-synthetic' biology approach, these considerations could contribute to identifying the constraints behind the emergence of molecular complexity during the evolution of an ancient RNA/peptide world into a modern DNA/RNA/protein world. In conclusion, we propose TDCs by information control and adaptive selection as the two types of downward causality absolutely necessary for life.
authors: Department of Chemistry and Biochemistry ,  University of California ,  Santa Barbara, CA 93106-9510 ,  USA ; Biomolecular Science and Engineering Program ,  University of California ,  Santa Barbara, CA 93106-9510 ,  USA.
authors: Luc
authors: L
authors: Jaeger
authors: Erin R
authors: ER
authors: Calkins
keywords: RNA evolution; RNA world; convergence; convergent evolution; information selection; molecular complexity
references: Curr Opin Struct Biol. 2009 Jun;19(3):251-9
references: 19303767
references: Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):757-61
references: 8290596
references: Bioessays. 2010 Jul;32(7):559-63
references: 20544731
references: Nature. 2010 Mar 18;464(7287):441-4
references: 20154731
references: Nature. 1995 Mar 16;374(6519):227-32
references: 7885442
references: Biochemistry. 1991 Nov 19;30(46):11005-18
references: 1932025
references: Biol Direct. 2011 Jan 03;6:1
references: 21199581
references: Trends Ecol Evol. 2008 Jan;23(1):26-32
references: 18022278
references: Nat Struct Mol Biol. 2008 Feb;15(2):177-82
references: 18204466
references: EMBO Rep. 2006 Apr;7(4):411-7
references: 16470227
references: Curr Opin Microbiol. 2008 Apr;11(2):78-86
references: 18374625
references: Science. 2007 Jun 15;316(5831):1557
references: 17569837
references: Curr Opin Biotechnol. 2010 Oct;21(5):697-703
references: 20638265
references: Science. 2010 Jul 2;329(5987):52-6
references: 20488990
references: EMBO J. 2006 Mar 8;25(5):967-76
references: 16498400
references: Mol Syst Biol. 2006;2:45
references: 16924266
references: Mol Microbiol. 2005 Jul;57(2):357-65
references: 15978070
references: Mol Microbiol. 1998 Sep;29(5):1155-65
references: 9767584
references: Proc Natl Acad Sci U S A. 1989 Oct;86(20):7909-13
references: 2554295
references: Intervirology. 2010;53(5):362-78
references: 20551688
references: J Biomed Biotechnol. 2010;2010:130781
references: 20150964
references: Science. 2008 Feb 29;319(5867):1215-20
references: 18218864
references: Nat Rev Genet. 2004 Feb;5(2):101-13
references: 14735121
references: Nat Rev Genet. 2007 Jun;8(6):450-61
references: 17510665
references: FEBS Lett. 2003 Aug 14;549(1-3):63-6
references: 12914926
references: Nature. 1989 Mar 16;338(6212):217-24
references: 2466202
references: Chaos. 2010 Sep;20(3):037108
references: 20887074
references: J Bacteriol. 2006 Feb;188(3):909-18
references: 16428394
references: J Bacteriol. 2008 Mar;190(6):2217-20
references: 18178736
references: Cold Spring Harb Perspect Biol. 2010 Sep;2(9):a002212
references: 20484387
references: Nature. 2010 Jan 28;463(7280):559-62
references: 20111002
references: Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8774-9
references: 16731630
references: Proc Natl Acad Sci U S A. 2009 May 26;106(21):8477-82
references: 19443689
references: Trends Genet. 2010 Oct;26(10):431-7
references: 20696492
references: Genetics. 2008 Apr;178(4):2389-97
references: 18430956
references: Annu Rev Microbiol. 2010;64:257-75
references: 20825349
references: Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17162-7
references: 15569938
references: Nature. 2008 May 1;453(7191):120-3
references: 18451863
references: BMC Syst Biol. 2008 Feb 26;2:20
references: 18302748
references: Annu Rev Biochem. 2009;78:305-34
references: 19298181
references: Biotechnol J. 2010 Feb;5(2):147-62
references: 20084640
references: Int J Biochem Cell Biol. 2009 Feb;41(2):254-65
references: 18775793
references: J R Soc Interface. 2008 Oct 6;5(27):1159-72
references: 18319208
references: FEMS Microbiol Rev. 2009 Jan;33(1):3-26
references: 19016882
references: Nature. 2001 Jan 18;409(6818):387-90
references: 11201752
references: Syst Synth Biol. 2009 Dec;3(1-4):125-34
references: 19816808
references: ACS Chem Biol. 2008 Jan 18;3(1):64-76
references: 18205292
references: Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21848-53
references: 20007369
references: Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13773-8
references: 16174729
references: J Microbiol. 2004 Jun;42(2):111-6
references: 15357304
references: Curr Opin Biotechnol. 2010 Aug;21(4):498-501
references: 20727733
references: Nat Struct Mol Biol. 2010 Jun;17(6):740-4
references: 20473316
references: J Theor Biol. 2008 Oct 21;254(4):804-6
references: 18694761
references: Nat Chem Biol. 2010 Jun;6(6):464-70
references: 20453864
references: RNA. 2007 Aug;13(8):1141-54
references: 17601995
references: Biol Chem. 2011 Apr;392(4):299-304
references: 21294682
references: Curr Opin Chem Biol. 2007 Dec;11(6):612-9
references: 17967431
references: Orig Life Evol Biosph. 1998 Oct;28(4-6):613-22
references: 9742731
references: Nat Struct Mol Biol. 2008 Oct;15(10):1076-83
references: 18806797
references: Science. 2007 Aug 3;317(5838):632-8
references: 17600181
references: Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):1971-6
references: 10051579
references: Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14351-6
references: 14623972
references: Anat Rec. 2002 Nov 1;268(3):208-14
references: 12382319
references: Bioessays. 2010 Apr;32(4):267-70
references: 20217846
references: J Biol Eng. 2010 Jan 20;4(1):1
references: 20205762
references: Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8742-7
references: 12077305
references: RNA. 2008 Apr;14(4):717-35
references: 18359782
references: Proc Natl Acad Sci U S A. 2006 Jul 11;103(28):10696-701
references: 16818880
references: Nature. 2010 Jul 29;466(7306):642-6
references: 20671709
references: J Eukaryot Microbiol. 2008 Mar-Apr;55(2):59-68
references: 18318857
references: J Am Chem Soc. 2007 May 30;129(21):6807-11
references: 17480075
references: Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15914-9
references: 12451180
references: Nat Rev Genet. 2010 May;11(5):367-79
references: 20395970
references: Nat Struct Biol. 2002 Apr;9(4):257-62
references: 11887185
references: Biogerontology. 2009 Aug;10(4):503-16
references: 18720024
references: RNA. 2009 Nov;15(11):2046-56
references: 19776155