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Self Replicating Systems

Self Replicating Systems. Ecoli – division and replication. IL 33 Radiolara, Institut fur Leichte Flachentragwerke,1990. Prof. Joseph Jacobson. MIT Media Laboratory. Goal For Next Decade:. Maximize complexity per unit volume. (6 orders of magnitude left to go in complexity

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Self Replicating Systems

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  1. Self Replicating Systems Ecoli – division and replication IL 33 Radiolara, Institut fur Leichte Flachentragwerke,1990. Prof. Joseph Jacobson MIT Media Laboratory

  2. Goal For Next Decade: • Maximize complexity per unit volume. (6 orders of magnitude left to go in complexity of engineered systems). • To be useful for many applications must be able to manufacture multiple copies. • Self replicating systems may be useful in attaining that goal and it represents a new discipline in engineering.

  3. Nature holds the record in both complexity per unit volume And in the ability to carry out self replication. http://www.ncc.gmu.edu/dna/repanim.htm http://focus.hms.harvard.edu/1997/Apr18_1997/polymerase.JPG

  4. Informationless Replication Prion Replication Autocatalytic Chemistry http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journa l/v411/n6839/full/411810a0_r.html Replicated Parts Lack Complexity

  5. Information Bearing Replication (Non-Protein Biochemical Systems) J. Szostak, Nature,409, Jan. 2001

  6. Information Bearing Replication (Organic Synthetic Systems) Mosley et. Al. ACS Proceedings, July 2002.

  7. Homo sapiens2,900,000,000 Human immunodeficiency virus type 119,750 Mycoplasma genitalium 580,000 Amoeba dubia 670,000,000,000 Amoeba proteus290,000,000,000 How Do We Replicate Complex Systems? Ans. Error Correction http://gnn.tigr.org/articles/02_01/Sizing_genomes.shtml www.nature.com/nsu/010222/images/ mgenetalium_200.jpg

  8. Error Correction in Biological Systems Has Extremely High Fidelity but… Fault Tolerant Translation Codes (Hecht): NTN encodes 5 different nonpolar residues (Met, Leu, Ile, Val and Phe) NAN encodes 6 different polar residues (Lys, His, Glu, Gln, Asp and Asn) Local Error Correction: Ribozyme: 1:103 Error Correcting Polymerase: 1:108 fidelity DNA Repair Systems: MutS System Recombination - retrieval - post replication repair Thymine Dimer bypass. E. Coli Retrieval system - Lewin Error is cumulative.Can We Create An Organism Which Does Not Have Cumulative Error?

  9. Yes Use Error Correcting Codes Basic Idea: M strands of N Bases Result: By carrying out a consensus vote one requires only To replicate with error below some epsilon such that the global replication error is:

  10. Scheme for Self Excising Error Correcting Codes MutS x 1’ 1 DNA Polymerase To transcribe 1’ LoxP Excision of 1 Replacement with 1’ Jacobson ‘02

  11. Combining Error Correcting Polymerase and Error Correcting Codes One Can Replicate a Genome of Arbitrary Complexity For Above Threshold M value Jacobson ‘02

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