1. MAS.961 How To Make Something That Makes (Almost) Anything jacobson@media.mit.edu Complexity, Self Replication and all that…

2. Itanium Quad Tukwila Transistor Count: 2B Cost: ~$100 Si Wafer with Area sufficient for 2 Billion Transistors Cost: ~$0.50 Flash Memory Transistor Count: 2B Cost: ~$3 NetBook Cost: ~$200 Sand (Chips and Screen) Cost: ~$0 Plastic Resin / Metal Ore Cost: ~$4 What governs the cost of placing atoms where we want them? What are the limits?

3. Fabricational Complexity Fabricational Complexity Per Unit Cost AGTCGCAAT N Fabricational Complexity for N-mer or M Types = Fabricational Cost for N-mer = Where is the yield per fabricational step Complexity Per Unit Cost Complexity Per Unit Time*Energy

4. Fabricational Complexity Application: Why Are There 20 Amino Acids in Biology? (What is the right balance between Codon code redundancy and diversity?) Question: Given N monomeric building blocks of Q different types, what is the optimal number of different types of building blocks Q which maximizes the complexity of the ensemble of all possible constructs? The complexion for the total number of different ways to arrange N blocks of Q different types (where each type has the same number) is given by: And the complexity is: N Blocks of Q Types For a given polymer length N we can ask which Q* achieves the half max for complexity such that:.

5. …Can we use this map as a guide towards future directions in fabrication ? Fabricational Complexity Application: Identifying New Manufacturing Approach for Semiconductors

6. Printed Electronics ~Minutes ~ 3Weeks of 7x24 Processing LithographyPrinted Electronics + Liquid Inorganic Semiconductors [1] [1] Ridley et al., Science, 286, 746 (1999) Science 297,416 (2000) High Speed Printing

7. …Can we use this map as a guide towards future directions in fabrication ? Fabricational Complexity

8. DNA Synthesis Chemical Synthesis (Open Loop Protection Group) Biological Synthesis (Error Correcting Polymerase) Error Rate: 1:10 2 Throughput: 300 S per Base Addition http://www.med.upenn.edu/naf/services/catalog99.pdf Error Rate: 1:10 6 Throughput: 10 mS per Base Addition Beese et al. (1993), Science, 260, 352-355. http://www.biochem.ucl.ac.uk/bsm/xtal/teach/repl/klenow.html Throughput Error Rate Product Differential: ~10 8 template dependant 5'-3' primer extension 5'-3' error-correcting exonuclease 3'-5' proofreading exonuclease Example: [A] Synthesize 1500 Nucleotide Base Gene. Error Rate = 0.99 (0.99) 1500 ~ 10 -7. [B] 3000 Nucleotide Base Gene. (0.99) 3000 ~ 10 -13.

9. Fabricational Complexity Per Unit Cost 2 Ply Error Correction Non Error Correcting: 2Ply Error Correcting: AGTC AGTC AGTC p=0.99

10. Fabricational Complexity Per Unit Cost 3 Ply Error Correction Non Error Correcting: 3Ply Error Correcting: AGTC AGTC AGTC AGTC (a)(b) (c) For values of, and R increases exponentially with N.

11. 1] Error Correcting Fabrication 2] Fault Tolerant Hardware Architectures 3] Fault Tolerant Software or Codes 4] Quantum Phase Space Resources which increase the complexity of a system exponentially with a linear addition of resources Resources for Exponential Scaling

12. Self-Replicating Systems Advanced_Automation_for_Space_Missions_figure_5-29.gif

13. Information Poor Replication Autocatalytic Chemistry Replicated Parts Lack Complexity

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

15. Threshold for Life What is the Threshold for Self Replicating Systems? Measurement Theory ++ + ++ Step 1 Step 2 Step 3 + Parts Template Machine Replication Cycle http://en.wikipedia.org/wiki/File:Stem-loop.svg Error Correcting Exonuclease (Ruler) DNA Number of Nucleotides Probability of Self Replication Watson Crick.18 nm How Well Can N Molecules Measure Distance? /sandwalk.blogspot.com/2007/12/dna- denaturation-and-renaturation-and.html

16. Threshold for Life Generalized Theory Measurement Theory Machine of N Blocks at Temperature T Measures the Correctness of the new added block. Energy: Energy consumption per replication (dominated by measurement just like in Szilard Maxwell’s Demon): Must Determine size (position) to within 1 atom: Heisenberg limit: lambda / number of photons 0.1 nm = 5000 * 500nm photons ~ 5 Kev per addition Number of Building Blocks: N Block machine must serve as a stable reference point to make measurement on the new added block.

17. Autonomous self replicating machines from random building blocks

21. Mechrep Emthingy Rep5mer In Presentations/Saul

22. Lipson et. al.

23. Exponential Fabrication

25. Mean-Green von Neumann Machine X Prize Rules Prize Awarded to First Team to construct multiple copies of a machine that: 1.Consumes readly available raw materials (garbage,rocks, soil, air, water) 2. Produces renewable energy at reasonable area/power (concentrated solar,photovoltaic cells, wind) 3. Manufactures every part required to replicate itself