Editing Self-replication (section)

==Overview==

===Theory===
{{See also|Von Neumann universal constructor}}

Early research by [[John von Neumann]]<ref name=Hixon_vonNeumann>{{cite book|last=von Neumann|first=John|title=The Hixon Symposium|year=1948|location=Pasadena, California|pages=1–36}}</ref> established that replicators have several parts:

*A coded representation of the replicator
*A mechanism to copy the coded representation
*A mechanism for effecting construction within the host environment of the replicator

Exceptions to this pattern may be possible, although almost all known examples adhere to it. Scientists have come close to  constructing [https://arstechnica.com/science/2011/04/investigations-into-the-ancient-rna-world/ RNA that can be copied] in an "environment" that is a solution of RNA monomers and transcriptase, but such systems are more accurately characterized as "assisted replication" than "self-replication". In 2021 researchers succeeded in constructing a system with sixteen specially designed DNA sequences. Four of these can be linked together (through base pairing) in a certain order following a template of four already-linked sequences, by changing the temperature up and down. The number of template copies is thus increased in each cycle. No external agent such as an enzyme is needed, but the system must be supplied with a reservoir of the sixteen DNA sequences.<ref name="EL-20210302">{{cite journal |last1=Kühnlein |first1=Alexandra |last2=Lanzmich |first2=Simon A. |last3=Brun |first3=Dieter |title=tRNA sequences can assemble into a replicator |doi=10.7554/eLife.63431 |pmc=7924937 |date=2 March 2021 |journal=[[eLife]] |volume=10 |pages=e63431 |pmid=33648631 |doi-access=free }} For an interpretation in terms of the origin of life, see {{cite news |last=Maximilian |first=Ludwig |title=Solving the Chicken-and-the-Egg Problem – "A Step Closer to the Reconstruction of the Origin of Life" |url=https://scitechdaily.com/solving-the-chicken-and-the-egg-problem-a-step-closer-to-the-reconstruction-of-the-origin-of-life/ |date=3 April 2021 |work=[[SciTech (magazine)|SciTechDaily]] |accessdate=3 April 2021 }}</ref>

The simplest possible case is that only a genome exists.  Without some specification of the self-reproducing steps, a genome-only system is probably better characterized as something like a [[crystal]].

===Origin of life===

Self-replication is a fundamental feature of life.  It was proposed that self-replication emerged in the evolution of life when a molecule similar to a double-stranded [[polynucleotide]] (possibly like [[RNA]]) dissociated into single-stranded polynucleotides and each of these acted as a template for synthesis of a complementary strand producing two double stranded copies.<ref name = Quastler1964>HenryQuastler (1964) Emergence of Biological Organization, Yale University Press, New Haven Connecticut ASIN: B0000CMHJ2</ref>  In a system such as this, individual duplex replicators with different nucleotide sequences could compete with each other for available mononucleotide resources, thus initiating natural selection for the most “fit” sequences.<ref name = Quastler1964/>   Replication of these early forms of life was likely highly inaccurate producing mutations that influenced the folding state of the polynucleotides, thus affecting the propensities for strand association (promoting stability) and disassociation (allowing genome replication).  The evolution of order in living systems has been proposed to be an example of a fundamental order generating principle that also applies to physical systems.<ref>Bernstein, Harris; Byerly, Henry C.; Hopf, Frederick A.; et al. (June 1983). "The Darwinian Dynamic". The Quarterly Review of Biology. 58 (2): 185–207. doi:10.1086/413216. JSTOR 2828805. S2CID 83956410</ref>

===Classes of self-replication===
Recent research<ref>{{cite web|url = https://www.MolecularAssembler.com/KSRM/5.1.htm | date = 2004 | access-date = 29 June 2013 | last1 = Freitas | first1 = Robert | last2 = Merkle | first2 = Ralph | title = Kinematic Self-Replicating Machines - General Taxonomy of Replicators}}</ref> has begun to categorize replicators, often based on the amount of support they require.

*Natural replicators have all or most of their design from nonhuman sources. Such systems include natural life forms.
*[[Autotroph]]ic replicators can reproduce themselves "in the wild".  They mine their own materials. It is conjectured that non-biological autotrophic replicators could be designed by humans, and could easily accept specifications for human products.
*Self-reproductive systems are conjectured systems which would produce copies of themselves from industrial feedstocks such as metal bar and wire.
*[[Self-assembly|Self-assembling]] systems assemble copies of themselves from finished, delivered parts. Simple examples of such systems have been demonstrated at the macro scale.

The design space for machine replicators is very broad. A comprehensive study<ref>{{cite web|url = https://www.MolecularAssembler.com/KSRM/5.1.9.htm | date = 2004 | access-date = 29 June 2013 | last1 = Freitas | first1 = Robert | last2 = Merkle | first2 = Ralph | title = Kinematic Self-Replicating Machines - Freitas-Merkle Map of the Kinematic Replicator Design Space (2003–2004)}}</ref> to date by [[Robert Freitas]] and [[Ralph Merkle]] has identified 137 design dimensions grouped into a dozen separate categories, including: (1) Replication Control, (2) Replication Information, (3) Replication Substrate, (4) Replicator Structure, (5) Passive Parts, (6) Active Subunits, (7) Replicator Energetics, (8) Replicator Kinematics, (9) Replication Process, (10) Replicator Performance, (11) Product Structure, and (12) Evolvability.

===A self-replicating computer program===
{{Main|Quine (computing)}}

In [[computer science]] a [[Quine (computing)|quine]] is a self-reproducing computer program that, when executed, outputs its own code. For example, a quine in the [[Python (programming language)|Python programming language]] is:

:{{code|1=a='a=%r;print(a%%a)';print(a%a)|2=python}}

A more trivial approach is to write a program that will make a copy of any stream of data that it is directed to, and then direct it at itself. In this case the program is treated as both executable code, and as data to be manipulated. This approach is common in most self-replicating systems, including biological life, and is simpler as it does not require the program to contain a complete description of itself.

In many programming languages an empty program is legal, and executes without producing errors or other output. The output is thus the same as the source code, so the program is trivially self-reproducing.

===Self-replicating tiling===
{{See also|Self-similarity}}

In [[geometry]] a self-replicating tiling is a tiling pattern in which several [[congruence (geometry)|congruent]] tiles may be joined together to form a larger tile that is similar to the original.  This is an aspect of the field of study known as [[tessellation]].  The "[[sphinx tiling|sphinx]]" [[hexiamond]] is the only known self-replicating [[pentagon]].<ref>For an image that does not show how this replicates, see: Eric W. Weisstein. "Sphinx." From MathWorld--A Wolfram Web Resource. [https://mathworld.wolfram.com/Sphinx.html https://mathworld.wolfram.com/Sphinx.html]</ref>  For example, four such [[concave polygon|concave]] pentagons can be joined together to make one with twice the dimensions.<ref>For further illustrations, see [http://www.geoaustralia.com/italian/Sphinx/Guide.html Teaching TILINGS / TESSELLATIONS with Geo Sphinx] {{Webarchive|url=https://web.archive.org/web/20160308171305/http://www.geoaustralia.com/italian/Sphinx/Guide.html |date=2016-03-08  }}</ref> [[Solomon W. Golomb]] coined the term [[rep-tiles]] for self-replicating tilings.

In 2012, [[Lee Sallows]] identified rep-tiles as a special instance of a [[self-tiling tile set]] or setiset. A setiset of order ''n'' is a set of ''n'' shapes that can be assembled in ''n'' different ways so as to form larger replicas of themselves. Setisets in which every shape is distinct are called 'perfect'.  A rep-''n'' rep-tile is just a setiset composed of ''n'' identical pieces.
{|
|- style="vertical-align:bottom;"
|[[File:Self-replication of sphynx hexidiamonds.svg|thumb|left|text-bottom|260px|Four '[[Sphinx tiling|sphinx]]' hexiamonds can be put together to form another sphinx.]]
[[File:A rep-tile-based setiset of order 4.png|thumb|right|text-bottom|290px|A perfect [[Self-tiling tile set|setiset]] of order 4]]
|}
{{clear}}

===Self replicating clay crystals===
One form of natural self-replication that is not based on DNA or RNA occurs in [[clay]] crystals.<ref>{{cite web|url=http://www.bbc.com/earth/story/20160823-the-idea-that-life-began-as-clay-crystals-is-50-years-old |title=The idea that life began as clay crystals is 50 years old |publisher=bbc.com |date=2016-08-24 |archive-url=https://web.archive.org/web/20160824164754/http://www.bbc.com/earth/story/20160823-the-idea-that-life-began-as-clay-crystals-is-50-years-old |access-date=2019-11-10|archive-date=24 August 2016 }}</ref> Clay consists of a large number of small crystals, and clay is an environment that promotes [[crystal growth]]. Crystals consist of a regular [[lattice (group)|lattice of atoms]] and are able to grow if e.g. placed in a [[water solution]] containing the crystal components; automatically arranging atoms at the crystal boundary into the crystalline form. Crystals may have irregularities where the regular atomic structure is broken, and when crystals grow, these irregularities may propagate, creating a form of self-replication of [[Crystallographic defect|crystal irregularities]]. Because these irregularities may affect the probability of a crystal breaking apart to form new crystals, crystals with such irregularities could even be considered to undergo evolutionary development.

===Applications===
It is a long-term goal of some engineering sciences to achieve a [[clanking replicator]], a material device that can self-replicate.  The usual reason is to achieve a low cost per item while retaining the utility of a manufactured good.  Many authorities say that in the limit, the cost of self-replicating items should approach the cost-per-weight of wood or other biological substances, because self-replication avoids the costs of [[labour (economics)|labor]], [[Capital (economics)|capital]] and [[distribution (business)|distribution]] in conventional [[factory|manufactured goods]].

A fully novel artificial replicator is a reasonable near-term goal.
A [[NASA]] study recently placed the complexity of a [[clanking replicator]] at approximately that of [[Intel]]'s [[Pentium (brand)|Pentium]] 4 CPU.<ref>{{cite web|url=https://www.niac.usra.edu/files/studies/final_report/883Toth-Fejel.pdf |title=Modeling Kinematic Cellular Automata Final Report |date=April 30, 2004 |access-date=2013-10-22}}</ref>  That is, the technology is achievable with a relatively small engineering group in a reasonable commercial time-scale at a reasonable cost.

Given the currently keen interest in biotechnology and the high levels of funding in that field, attempts to exploit the replicative ability of existing cells are timely, and may easily lead to significant insights and advances.

A variation of self replication is of practical relevance in [[compiler]] construction, where a similar [[bootstrapping]] problem occurs as in natural self replication. A compiler ([[phenotype]]) can be applied on the compiler's own [[source code]] ([[genotype]]) producing the compiler itself. During compiler development, a modified ([[Mutation|mutated]]) source is used to create the next generation of the compiler. This process differs from natural self-replication in that the process is directed by an engineer, not by the subject itself.