From: "Tom S. Ray" Subject: ALIFE: Tierra Update: V3.13 Date: Wed, 8 Jul 92 22:49:46 GMT [Co-mod (Mark): I've chopped this message so that interested parties can get to the Tierra ftp site to find out more information.] TIERRA UPDATE: Version V3.13 Now Available; Unified License Agreement; FTP Site Reorganized; Bug Fixes; Virtual Debugger; Instruction Set Documented; Genome Injector; Genebank Hash Function; Haploid Sex; Resolution Toggle; Diversity Tool Improved; Chris Stephenson, Kurt Thearling and Walter Tackett visit SFI; Future Phylogeny; Tierra in the News; Tierra Publications; Mailing Lists; What Tierra Is; This message contains: 1) Availability of Tierra V3.13 Source Code a) by ftp b) by snail mail on disk 2) Unified License Agreement 3) FTP Site Reorganized 4) Bug Fixes 19) What Tierra Is (If you don't know what Tierra is, read this first) 1) Availability of Tierra V3.13 Source Code The Tierra V3.13 source code; and the source code, and DOS executables of all tools is available now. Please note that the source code in the ftp site and the source code provided on disk will each compile and run on either DOS or UNIX platforms. It is exactly the same source code in either case. The DOS executables are available only on disk, and can not be freely distributed. If you purchase this program on disk, thank you for your support. If you obtain the source code through the net or friends, we invite you to contribute an amount that represents the program's worth to you. You may make a check in US dollars payable to Virtual Life, and mail the check to one of the two addresses listed below. a) by ftp If you use the software, be sure to pick up new versions from the ftp site. The source in the ftp site will be replaced on a roughly monthly or bi-monthly basis. The complete source code and documentation is 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: 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 structure with the following commands (Unix only): uncompress tierra.tar.Z tar oxvf tierra.tar b) by snail mail on disk The source code, documentation and the beagle.exe file can be distributed freely, however, the executables (the .exe files in DOS) are for sale and cannot be freely distributed (with the exeception of beagle.exe). 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 (ALmond can be provided on disk by request, but it only runs on a Unix platform). The disks include DOS executables, source code and documentation. The DOS disks include an easy installation program. This is the same source code available in the ftp site. If you have ftp access, there is no need to buy the disks. 2) Unified License Agreement If you have seen the earlier versions (pre V3.12), you may have noticed that there were different license agreements for the DOS and Unix versions. There is now a single and perhaps more coherent license agreement. 3) FTP Site Reorganized With Version 3.11 the ftp site was reorganized. The files are no longer distributed in shar format. They are in both raw form, and in compressed tar files. All the documentation has been moved to the doc/ directory. The doc/ directory also includes manuscripts on Tierra in LaTeX and Postscript formats. 4) Bug Fixes new in V3.13: adr() - the parse function for the adr instruction, previous to V3.13, set is.iip = 0, which meant that the instruction pointer would not increment. This means that if ever the adr instruction were executed, the virtual cpu would hang on this instruction. This has been fixed in V3.13. GarbageCollectGB() - previous to V3.13, this function (in bookeep.c) caused some empty .gen files to be created, which would clutter up the genebank directory. This has been fixed. genotype histogram - there were some problems with the genotype histogram display in V3.12, these have been fixed. new in V3.12: template search - Version 3.11 and earlier had a bug in the bi-directional template search algorithm. God intended that the search should move outward at equal rates in both directions. However, some situations caused one direction to get ahead of the other. This does not matter to the creatures or evolution; evolution makes due with whatever physics or chemistry it has at hand. However, it makes it difficult for the observer reading the genome files to tell what the outcome of a bi-directional template search might be. Another problem with the same algorithm is that the limit on the distance of the template search was not properly implemented, they tend to search farther than the intended limit. Both these bugs are fixed in V3.12. [ Much of message deleted... ---Mark] 19) What Tierra Is The C source code creates a virtual computer and its operating system, whose architecture has been designed in such a way that the executable machine codes are evolvable. This means that the machine code can be mutated (by flipping bits at random) or recombined (by swapping segments of code between algorithms), and the resulting code remains functional enough of the time for natural (or presumably artificial) selection to be able to improve the code over time. Along with the C source code which generates the virtual computer, we provide several programs written in the assembler code of the virtual computer. One of these was written by a human and does nothing more than make copies of itself in the RAM of the virtual computer. The others evolved from the first, and are included to illustrate the power of natural selection. The operating system of the virtual computer provides memory management and timesharing services. It also provides control for a variety of factors that affect the course of evolution: three kinds of mutation rates, disturbances, the allocation of CPU time to each creature, the size of the soup, etc. In addition, the operating system provides a very elaborate observational system that keeps a record of births and deaths, sequences the code of every creature, and maintains a genebank of successful genomes. The operating system also provides facilities for automating the ecological analysis, that is, for recording the kinds of interactions taking place between creatures. This system results in the production of synthetic organisms 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. Diverse ecological communities have emerged. These digital communities have been used to experimentally examine ecological and evolutionary processes: e.g., competitive exclusion and coexistence, host/parasite density dependent population regulation, the effect of parasites in enhancing community diversity, evolutionary arms race, punctuated equilibrium, and the role of chance and historical factors in evolution. This evolution in a bottle may prove to be a valuable tool for the study of evolution and ecology.