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.

4. Informationless Replication
Autocatalytic Chemistry
Prion Replication
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. How Do We Replicate Complex Systems?
Amoeba dubia 670,000,000,000
Amoeba proteus 290,000,000,000
               
Homo sapiens 2,900,000,000
Human immunodeficiency virus type 1 19,750
Mycoplasma genitalium
580,000
Ans. Error Correction
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