Subject: Tierra V3.11: Evolution of Digital Organisms FollowupTo: talk.origins sys,alt.cyb

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From: Thomas Ray Subject: Tierra V3.11: Evolution of Digital Organisms Organization: University of Delaware From: ray@chopin.udel.edu (Thomas Ray) Message-ID: 19756@chopin.udel.edu Followup-To: talk.origins Newsgroups: alt.brother-jed,alt.buddha.short.fat.guy,alt.cyb- sys,alt.cyberspace,alt.cyberpunk,alt.cyberpunk.tech,alt.ketchup,alt.mcdonalds. mut,alt.religion.computers,talk.origins TIERRA UPDATE: (Version 3.11 now available, FTP site reorganized, New Tools, Bug Fixes, Genebank Verification, Garbage Collection, New Genomes, Mneumonics Shortened, Virtual Extraction, DEC Grant, Sex) This message contains: 1) Availability of Tierra V3.11 source code a) by ftp b) by snail mail on disk 2) FTP Site Reorganized 2) New Tools 3) Bug Fixes 4) Genebank Verification 5) Garbage Collection 6) New genomes distributed 7) Opcode mneumonics limited to six characters 8) Virtual Extraction 9) Grant from Digital Equipment Corporation 10) Future Sex 11) Abstract Describing Tierra 1) Availability of Tierra V3.11 source code a) by ftp The V3.11 source code, the source code, and DOS executables of all tools is available now. If you use the software, be sure to pick up new versions soon from the ftp site. The source in the ftp site will be replace on a roughly monthly or bi-monthly basis. The complete source code and DOS executables are available by anonymous ftp at: tierra.slhs.udel.edu [128.175.41.34] and life.slhs.udel.edu [128.175.41.33] in the directories: DOS/, almond/, beagle/, doc/, and tierra/. To get it, ftp to tierra or life, log in as user "anonymous" and give your email address (eg. tom@udel.edu) as a password. Be sure to transfer binaries in binary mode (it is safe to transfer everything in binary mode). Each directory contains a compressed tar file (filename.tar.Z) and a SRC directory that contains all the files in raw ascii format. You can just pick up the .tar.Z files, and they will expand into the complete directory strucutre with the following commands: uncompress tierra.tar.Z tar oxvf tierra.tar b) by snail mail on disk If you do not have ftp access you may obtain everything on DOS disks by making a check for $65 (US dollars drawn on a US bank) payable to Virtual Life. Specify 3.5" or 5.25" disks. Send the check to one of the following addresses: Tom Ray (January through August) Santa Fe Institute 1660 Old Pecos Trail Suite A Santa Fe, NM 87501 Virtual Life (September through December) P.O. Box 625 Newark, Delaware 19715 The DOS disks contain everything but ALmond. They include DOS executables, source code and documentation. The DOS disks include an easy installation program. This is the same source and executables available in the ftp site. If you have ftp access, there is no need to buy the disks. 2) New Tools Several new (and some old) tools, developed by Dan Pirone and Tom Ray, are now fully documented and available in the ftp site: rnd_inst - A tool for altering the physics of the system by randomly mapping opcodes to instructions, with some optional restrictions on hamming distances between pairs of instructions. The output is an opcode.map file. probe - A tool for surveying the genebank, with various optional selection criteria (a new tool, but proving very useful). tieout - A tool for generating x,y data from the tierra.log file. This is used on a regular basis to generate graphics of size of creatures over time during a run. diverse - A tool that reads the birth and death records (break.X files) output by Tierra and transforms them into various measures of diversity, for graphical or other analysis. beagle - A DOS only tool which provides a variety of graphical displays of the output from the Tierra simulator. It is used after a run, and is highly recommended as a tool for analyzing the results of a run. run_info - A function of the beagle program, also available as a stand-alone, due to its hunger for memory. fragment - A function of the beagle program, also available as a stand-alone, due to its hunger for memory. ALmond - A UNIX only tool which runs as a separate process on the same or a different machine. ALmond establishes socket communications with a running Tierra, and provides a color display of the spatial distribution of the creatures in the soup, showing all births and deaths. This tool has some new functions: you can view the positions of the instruction pointers, or the activity of the moviab instruction. 3) Bug Fixes histograms - Version 3.1 included some obvious errors in the histogram display. These have been corrected. moviab - This instruction allows creatures to alter their own genome by writing on themselves. Before V3.11, the genebanker did not watch for genetic changes occurring in this manner. This created observational errors comparable to the ploidy bug corrected in V3.1. The genebanker now catalogs genetic change by this mechanism. It is believed that the genebanker is now fully reliable (see below). chmod - The chmod function was supposed to return a value, but did not. This had the consequence that a flag was set every time a creature allocated space for a daughter, and these were recorded with the demography data associated with each creature. This has been corrected. arg r option - The arg r option (replace or add) was not working, but is now. 4) Genebank Verification Error checking code has been added which completely verifies that the distribution of genotypes in the soup matches that reflected in the genebank, and that various counts are internally consistent within the genebank. 5) Garbage Collection Routines have been added which clean-up the genebank once per million exectued instructions. Among other things, once a size class is extinct, all genomes of that size are eliminated from RAM. Permanent genomes are first saved to disk. 6) New genomes distributed Many new genomes were first distributed with V3.1, but they were not mentioned in the announcement. These are the genomes of most of the creatures described in the publications and videos: parasites, hyper-parasites, social creatures, cheaters, etc. 7) Opcode mneumonics limited to six characters To facilitate their display by the Beagle tools, the opcode mneumonics have been limited to six characters. This affects push_ax, push_bx, push_cx, push_dx, and mov_iab. These have been changed to pushax, pushbx, pushcx, pushdx and moviab. This means that old ascii genome files can not be read by the new tools. It does not affect binary genome files. Old binary files will be mapped to the new names when they are converted to ascii by the new software. All the ascii .tie files are redistributed in the new format. 8) Virtual Extraction When a new genotype crosses one of the thresholds (SavThrMem or SavThrPop) its name becomes permanent and it is ``extracted'' (written to disk). This event is noted in the user interface and in the tierra.log file like: ex = 0079aaa @ 13 The new feature is that when a genotype goes extinct, then reappears and crosses the thresholds again, it experiences a ``virtual extraction'', which means that it is not written to disk (since it is already there), but the extraction event is written to the interface and the tierra.log file like: ex = 0079aaa @ 13 v This was done to facilitate the use of the tieout tool with cumulative genebanks, but it results in nicer extraction data in other senses as well. 9) Grant from Digital Equipment Corporation The Semiconductor Engineering Group of Digital Equipment Corporation has donated two fully loaded DS5000 workstations to the Santa Fe Institute as a part of a grant to Tom Ray titled: ``Computer Architectures for the Natural Evolution of Machine Codes''. These two machines will be the primary platform for Tierra research and development in the near future. 10) Future Sex Walter Tackett (tackett@ipld01.hac.com or tackett@priam.usc.edu) has implemented haploid sex based on cross-over (a random cross-over point used by the moviab instruction) in his private copy of Tierra V3.0. The methodology used by Tackett has been implemented in the Santa Fe verison of Tierra. It will be released when it has undergone more testing to verify its functions. 11) Abstract Describing Tierra Synthetic organisms have been created based on a computer metaphor of organic life in which CPU time is the ``energy'' resource and memory is the ``material'' resource. Memory is organized into informational patterns that exploit CPU time for self-replication. Mutation generates new forms, and evolution proceeds by natural selection as different genotypes compete for CPU time and memory space. Observation of nature shows that evolution by natural selection is capable of both optimization and creativity. Artificial models of evolution have demonstrated the optimizing ability of evolution, as exemplified by the field of genetic algorithms. The creative aspects of evolution have been more elusive to model. The difficulty derives in part from a tendency of models to specify the meaning of the ``genome'' of the evolving entities, precluding new meanings from emerging. I will present a natural model of evolution demonstrating both optimization and creativity, in which the genome consists of sequences of executable machine code. From a single rudimentary ancestral ``creature'', very quickly there evolve parasites, which are not able to replicate in isolation because they lack a large portion of the genome. However, these parasites search for the missing information, and if they locate it in a nearby creature, parasitize the information from the neighboring genome, thereby effecting their own replication. In some runs, hosts evolve immunity to attack by parasites. When immune hosts appear, they often increase in frequency, devastating the parasite populations. In some runs where the community comes to be dominated by immune hosts, parasites evolve that are resistant to immunity. Hosts sometimes evolve a response to parasites that goes beyond immunity, to actual (facultative) hyper-parasitism. The hyper-parasite deceives the parasite causing the parasite to devote its energetic resources to replication of the hyper-parastie genome. This drives the parasites to extinction. Evolving in the absence of parasites, hyper-parasites completely dominate the community, resulting in a relatively uniform community characterize by a high degree of relationship between individuals. Under these circumstances, sociality evolves, in the form of creatures which can only replicate in aggregations. The cooperative behavior of the social hyper-parasites makes them vulnerable to a new class of parasites. These cheaters, hyper-hyper-parasites, insert themselves between cooperating social individuals, deceiving the social creatures, causing them to replicate the genomes of the cheaters. The only genetic change imposed on the simulator is random bit flips in the machine code of the creatures. However, it turns out that parasites are very sloppy replicators. They cause significant recombination and rearrangement of the genomes. This spontaneous sexuality is a powerful force for evolutionary change in the system. One of the most interesting aspects of this instance of life is that the bulk of the evolution is based on adaptation to the biotic environment rather than the physical environment. It is co-evolution that drives the system. --- Squish v1.01 * Origin: Universal Electronics Inc [714 939-6401] HST/DS (1:103/208)

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