(postscript version of this figure)

• Ev: the paper
  
  
  • BiBTeX reference:

    @article{Schneider.ev2000,
    author = "T. D. Schneider",
    title = "Evolution of Biological Information",
    journal = "Nucleic Acids Res.",
    volume = "28",
    thenumber = "14",
    pages = "2794--2799",
    pmid = "10908337",
    pmcid = "PMC102656",
    note = "\url{https://doi.org/10.1093/nar/28.14.2794}",
    year = "2000"}
    

  • Evolution of Biological Information at PubMed

  • Evolution of Biological Information at Nucleic Acids Research.

  • Evolution of Biological Information HTML version. This version has active hypertext links in the references.

  • Evolution of Biological Information PDF for NAR version. Reproduced with permission from NAR Online, published by Oxford University Press, http://www.nar.oupjournals.org.

  • Evolution of Biological Information PostScript version

• Ev: the program

  • Ev Java

    Click Here to Start the Evolution! SORRY! I have not set the security properly to allow evj to run on the web. You will need to download. If you would like to be able to run directly from your browser, please send me an email.             Download Java version from here! Unzip the file, and double click on Evj.class inside the evjava directory Have fun running the program! Since it is in Java, it works on any machine. Note: see the special instructions for SeaMonkey Browsers on OSX 10.6 Snow Leopard To learn more, see: Experimenting with Evolution: A Guide to Evj

    Click the yellow link above. Wait for the two new windows to appear. In the second window click on Run. Watch the display. The sequence logo in the box on the top (graph of bits vs binding site positions) shows the information) appearing in the binding sites of the genome below. By 675 generations the amount of information in the sites (Rsequence) has evolved to be the amount of information needed to locate the sites in the genome (Rfrequency). Learn more by clickng on the blue link above. Evj: is a complete rewrite of the Ev program in the language Java by Paul Anagnostopoulos. Note: This program is safe to run on any computer because the Java applet cannot inspect or modify your computer files.

    
    
  • Ev - Pascal: the original program written in the language Pascal.

• Ev: the movie

• Talk materials

  • Ev - pdf version of the talk as of 2012 Mar 14
    I created this talk using PowerDot with my powerdot-zen.sty.
  • Ev - compressed pdf version of the talk as of 2012 Mar 19
    I compressed the talk using Adobe Acrobat Professional, File / Save As / Format / Adobe PDF Files, Optimized.
  • Ev: the Slide Show Talk (old html version) (Abstract, taball for the talk of 2003 Jan 25)
    See below for the corresponding video!

• VIDEO Mathematical Biosciences Institute Workshop, Autumn Quarter 2005, Workshop 2, Aspects of Self-Organization in Evolution (November 14-18, 2005). Ohio State University.
  Abstracts, Lecture Materials, and Video
  The talk, from Ohio State University: Streaming Video: Real Media
  

  Title: Molecular Information Theory: From Clinical Applications To Binding Site Evolution

  Author:

  Molecular Information Theory: From Clinical Applications To Binding

  Abstract:

  Information theory was introduced by Claude Shannon in 1948 to precisely characterize data flows in communications systems. The same mathematics can also be fruitfully applied to molecular biology problems. We start with the problem of understanding how proteins interact with DNA at specific sequences called binding sites. Information theory allows us to make an average picture of the binding sites and this can be shown with a computer graphic called a sequence logo (https://alum.mit.edu/www/toms/glossary.html#sequence_logo).

  Sequence logos show how strongly parts of a binding site are conserved in bits of information. They have been used to study a variety of genetic control systems. More recently the same mathematics has been used to look at individual binding sites using another computer graphic called a sequence walker (https://alum.mit.edu/www/toms/glossary.html#sequence_walker). Sequence walkers are being used to predict whether changes in human genes cause mutations or are neutral polymorphisms. It may be possible to predict the degree of colon cancer by this method.

  How do genetic systems gain information by evolutionary processes? Information theory was used to observe information gain in the binding sites for an artificial `protein' in a computer model of evolution. The model begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. The transition is rapid, demonstrating that information gain can occur by punctuated equilibrium. (https://alum.mit.edu/www/toms/paper/ev).

  as of 2006 Sep 14.

• Ev: history of the program

• Ev: the FAQs of life, Frequently Asked Questions   as of 2005 May 24  

  Replication, mutation and selection are necessary and sufficient for information gain to occur. This process is called evolution.

• Videos about Ev evolution.
  (google search: "Thomas Schneider" youTube evolution)

  • How Evolution Causes an Increase in Information Part II a Youtube video posted February 28, 2007.

• Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2008, 2009, 2010, 2011 and 2012.

• Ev: Pronunciation
  Ev: pronounce it "Eee-Vee"
  Evj: pronounce it "Eee-Vee-Jay"
  The second two letters are not capitalized.

• Ev: Blog Response to the Ev Paper and related events

If you need background information about information theory you can explore my web site. You may find these two resources particularly useful:

• Information Theory Primer, With an Appendix on Logarithms
• A Glossary for Molecular Information Theory and the Delila System.
  A good starting point would be the definition of a bit.

Tom Schneider

Call For Java Programmers The Ev program was written in Pascal, which is a good language for which there is an open source compiler. However, Pascal compilers are not often set up on computers, so this limits experimentation with Ev to the few people willing to download a Pascal compiler and to set up Ev. In contrast, an open source version of Ev written in Java and available from Source Forge could be used in schools all across the world to help educate students in the precise mechanisms of evolution. Paul C. Anagnostopoulos wrote the current Java version, but there is more to do. If you are interested in joining this effort, please contact me.

2004 September 19. Initial announcement. 2005 Jun 16. An alpha version of Evj is now running. 2005 Jul 26. An alpha version of Evj is now public! 2010 Apr 22. A functional version has been available for several years.

Supplementary Analyses

• Effect of Ties on the Evolution of Information by the Ev program - a test of a hypothesis by William Dembski.
• Does the information always increase in Ev runs?
  • Are the Logos Different in Different Runs?
  • Sequence Logos for Different Ev Runs
• Does the information increase if there is no selection?
• Dissecting Dembski's "Specified Complex Information"
• The AND-Multiplication Error 2004 Sep 17
• Refuting Michael Behe's "Irreducible Complexity" with Roman Arches 2004 Sep 23
• Zero Threshold 2005 Sep 20
• The Nitty Gritty Bit 2005 Oct 1
• A Horse Race to Beat Dembski's "Universal Probability Bound" 2005 Oct 13

Scientific Papers Citing Ev

1. Arredondo TV, Neelakanta PS, De Groff D Fuzzy attributes of a DNA complex: Development of a fuzzy inference engine for codon-'junk" codon delineation ARTIF INTELL MED 35 (1-2): 87-105 SEP-OCT 2005
2. Jan't Hoen P, Tuyls K Analyzing multi-agent reinforcement learning using evolutionary dynamics LECT NOTES COMPUT SC 3201: 168-179 2004
3. Tuyls K, Nowe A, Lenaerts T, et al. An evolutionary game theoretic perspective on learning in multi-agent systems SYNTHESE 139 (2): 297-330 MAR 2004
4. Juretic D, Zupanovic P Photosynthetic models with maximum entropy production in irreversible charge transfer steps COMPUT BIOL CHEM 27 (6): 541-553 DEC 2003
5. Tuyls K, Heytens D, Nowe A, et al. Extended replicator dynamics as a key to reinforcement learning in multi-agent systems LECT NOTES ARTIF INT 2837: 421-431 2003
6. Zarrinpar A, Park SH, Lim WA Optimization of specificity in a cellular protein interaction network by negative selection NATURE 426 (6967): 676-680 DEC 11 2003
7. Fraundorf P Heat capacity in bits AM J PHYS 71 (11): 1142-1151 NOV 2003
8. Tuyls K, Verbeeck K, Maes S On a dynamical analysis of reinforcement learning in games: Emergence of Occam's Razor LECT NOTES ARTIF INT 2691: 335-344 2003
9. Ofria C, Adami C, Collier TC Selective pressures on genomes in molecular evolution J THEOR BIOL 222 (4): 477-483 JUN 21 2003
10. Kim JT, Martinetz T, Polani D Bioinformatic principles underlying the information content of transcription factor binding sites? J THEOR BIOL 220 (4): 529-544 FEB 21 2003
11. Sadovsky MG Comparison of real frequencies of strings vs. the expected ones reveals the information capacity of macromoleculae J BIOL PHYS 29 (1): 23-38 2003
12. Lio P Statistical bioinformatic methods in microbial genome analysis BIOESSAYS 25 (3): 266-273 MAR 2003
13. Schneider TD Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation NUCLEIC ACIDS RES 29 (23): 4881-4891 DEC 1 2001
14. Bawden D The shifting terminologies of information ASLIB PROC 53 (3): 93-98 MAR 2001

Related References

• Nature 2002 Mar 28;416(6879):409-13 Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing. Matsumoto M, Saito S, Ohmine I. A non-biological system showing a rapid phase transition.

• Intelligent Design Creationism and Its Critics: Philosophical, Theological, and Scientific Perspectives Robert T. Pennock, Ed. MIT Press, Cambridge, MA, 2001. 825 pp. $110, ISBN 0-262-16204-0. Paper, $45, ISBN 0-262-66124-1. This book contains both creationist writings and very strong rebuttals to those writings. The errors and deceptions of the creationists are laid bare. I strongly recommend this book for anyone who feels swayed by the creationists and for scientists who would like to see the majority of the arguments and facts against their position.

• 2003 April 1: Tyrannosaurus rex Genome Browser. Sorry this link was broken several hundred million years ago :-( in 2003) Fortunately, I found a copy of the Tyrannosaurus rex Genome Browser in my email and have requested permission to post it.

• 2004 Jan 30: Georgia avoids evolution and teaches that DNA is Left Handed .

• 2004 Jan 30: evolution.berkeley.edu, Understanding Evolution, an evolution website for teachers.

• 2004 Sep 5: Bibliography on Genetic Programming

  • Entry for the Ev program

• 2004 Sep 23: evolutionblog.blogspot.com by Jason Rosenhouse.

• 2005 Jan 27: Unnatural Selection, an article about evolutionary algorithms, Sam Williams, Technology Review, February 2005.

• 2005 Mar 7:

  • Artificial Life Links - see Software section

• 2005 May 4: The Fact of Evolution: Implications for Science Education James R. Hofmann and Bruce H. Weber. Science & Education 12: 729-760, 2003.
• 2005 May 4: Evolution as Fact and Theory Stephen Jay Gould, May 1981; from Hen's Teeth and Horse's Toes, New York: W. W. Norton & Company, 1994, pp. 253-262.
• 2005 May 5: Political Challenges to the Teaching of Evolution American Geological Institute. "These efforts [by creationists] fly in the face of science."
• 2005 May 5: National Center for Science Education, Defending the Teaching of Evolution in the Public Schools
• 2005 May 5: list of blogs
• 2005 May 9:

  The Open Scientic Literature on Evolution

  Overwhelming scientific evidence for evolution is now available through the web. Go to the archive of open scientific papers at Pubmed Central (www.pubmedcentral.nih.gov) and search for 'evolution'. There are more than 19000 scientific papers about evolution and roughly three new papers to read every day! Read these papers if you think that there is no evidence supporting the facts and theory of evolution!

  date	number	comment
  2005 May 8	19250
  2005 May 9	19253
  2005 May 18	19309
  2005 May 28	19339	30 papers in 10 days, 3 per day!
  2006 Sep 14	66029

  Note that these are ONLY to the open scientific literature.
• 2005 May 16:

  The Scientic Literature on Evolution

  A larger list of papers on evolution (but still not everything) is found at PubMed (search for 'evolution') but unfortunately most of these are not available to the general public.

  date	number	comment
  2005 May 16	158096
  2005 May 18	158220
  2005 May 28	158739	519 papers in 10 days, 50 per day!
  2005 Sep 28	164527	in 4 months, 48 per day!
  2006 Sep 14	182090	almost a year: in 365-14 days = 351 days, 17563 papers, 50 per day!

• 2005 Jun 20: Evolution Resources From the National Academies
• 2005 Jun 20: Evolution on the Front Line from the American Association for the Advancement of Science (AAAS)
• 2005 Jun 28: Talk Origins Archive FAQ
• 2005 Jul 17: Information Theory and Creationism by Ian Musgrave, Rich Baldwin and others
• 2005 Nov 18: Movie of virus self assembly ... spectacular demonstration that Dembski's computations in No Free Lunch about assembly are completely wrong!
• 2005 Dec 9: Activities, Writings and Resources on Evolution a source from Sigma XI, the Scientific Research Society.
• 2011 Oct 15: http://tinyurl.com/evolutionbiologicalinformation. This is a tiny link that one can use to find this page.
• 2012 Mar 31: Listing in Genetic Programming Bibliography by W.Langdon.

Schneider Lab
origin: 1999 Jul 22
updated: version = 2.32 of ev.html 2024 Jul 09