soft computing lab. dept. computer science yonsei univ. korea self-replication from random parts 30...

Soft Computing Lab.Dept. Computer Science

Yonsei Univ. Korea

Self-replication from random parts30 Mar. 2010, Keunhyun Oh

Saul Griffith, Dan Goldwater, and Joseph M. JacobsonMIT Media Lab

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Nature, vol. 437, pp. 636, 2005.

ContentsContents

• Overview

• Related works– Key feature of biological replication– Previous studies

• Proposed methods

• Experiments

• Summary and future works

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The autonomous self-replicationThe autonomous self-replication

• Autonomously self-replication machines– not yet to acquire the sophistication of biological systems, which assemble

structures from disordered building blocks

• The autonomous replication of complex systems from random inputs

– A replication of a reconfigurable string of parts– Randomly positioned input components

• Components– Suitable Miniaturized and mass-produced– Constituting self-fabricating systems whose assembly is brought about by the

parts themselves

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Key feature of biological replicationKey feature of biological replication

• Selecting the appropriate building blocks(nucleotides) from parts (ex. DNA)

– Parts• randomly and continuously distributed in its environment

• Correcting errors made during copying

• The efficiency– Enabling biological systems to generate exponential numbers of accurate

copies of themselves as a function of time

• To create these properties– Autonomous acquisition of randomly distributed building blocks– Carrying out error correction during the copying process

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Previous studiesPrevious studies

• A scheme for the autonomous self-replication– A simple 2-bit mechanical string outlined almost half a century ago

• Using structured inputs has since been achieved

• Including a self-reproducing machine that relies on a well-or-dered supply of its building blocks

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The complexity of a given structureThe complexity of a given structure

• The bit length describing the configuration of parts – in this case, a 5-bit string

• Ɛ– the error per addition(arising from random input) of each new building block

in the copied string

• (1- Ɛ)n

– The yield for replicating an n-bit string– Exponentially small for complex (large n) systems

(Ɛ = 0.5, n=5; the yield is about 3% in the case described here)

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Error correctionError correction

• For complex structures to be copied accurately from random in-puts

• A process in which a linear increase in resource leads to an ex-ponential decrease in error rate

• DNA replication– the polymerase enzymes responsible for copying may also check each re-

cruited nucleotide base for correct complementary base-pairing with the DNA template strand

– if the incoming base does not fit, it is removed by the enzyme’s exonuclease domain.

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To implement error-correcting repli-cation

To implement error-correcting repli-cation• A set of programmable electromechanical components

– Run as a 7-state, finite-state machine– the components can be reversibly latched and unlatched in response to near-

est neighbor communications– These parts interact by floating on a two-dimensional air table on which mo-

tion is random

• Self-replication of this sequence– A result of a random part latching on to the seed string– the part is queried for self-similarity and proper position in the growing repli-

cant– subsequently it is either permanently latched or released according to an

embedded rule

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Growing MachinesGrowing Machines

• S. Griffith, 2004

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6-state machine6-state machine

• S. Griffith, 2004

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Electromechanical unitsElectromechanical units

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An example of latching each otherAn example of latching each other

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Self-replication of a 5-bit stringSelf-replication of a 5-bit string

• Figure 1 shows a series of frame shots that start with a single-seed string (coloured in a green, green, yellow, yellow, green se-quence).

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ResultResult

• The kinetics of these processes are exponential until they be-come limited by the supply of parts(Fig. 2).

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Another formationAnother formation

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Summary and future worksSummary and future works

• Summary– The autonomous replication of complex systems the ability of the DNA tem-

plate to select the right building blocks • A set of randomly scattered parts• The ability to correct copying errors

– developing machines for the autonomous self-replication of a reconfigurable string of parts from randomly positioned components.

• Future works– Machines will be more miniaturized – Possible to create a general system

• self-replicating and programmed to self-fabricate into complex structures that run with exponential kinetics.

Thank you

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