An open book
head of Tyrannosaurus Rex
©1998 Christopher Srnka
and Jeff Poling
ev: Evolution of Biological Information

I never satisfy myself until I can make a mechanical model of a thing. If I can make a mechanical model I can understand it. As long as I cannot make a mechanical model all the way through I cannot understand ...
--- Lord Kelvin ( 1 , 2 )
... adaptation has been achieved by the process, already mentioned, which hinges on the gaining of information by means of genetic change and natural selection, as well as on the storing of knowledge in the code of the chain molecules in the genome.
-- Konrad Lorenz, Nobel Prize lecture, 1973
"The Evolution of Molecules -- A Minute-by-Minute Account"
-- Stacy Gilbert
Figure 2 of the paper Evolution of Biological
Information showing information (bits per site) ranging
from -1.0 to 6.0 bits versus Generation running from0 to
2000.  A dashed line at 4.0 bits is Rfrequency.  The
evolution of the binding sites is shown by a green curve
that starts near zero bits and evolves to around 4.0 bits
by 1000 generations and then oscillates there around 4
bits.  Selection covers this entire range.  A second red
curve starts again at 1000 without selection.  The red
curve decays exponenentially to near zero bits.

(postscript version of this figure)
Summary: This paper and the corresponding Evj computer program show how information, measured in bits as Claude Shannon did, appears in DNA by Charles Darwin's natural selection.

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

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.

Wooden Roman Arch

Supplementary Analyses

Scientific Papers Citing Ev

As of 2005 Nov 1.
  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

color bar Small icon for Theory of Molecular Machines: physics,
chemistry, biology, molecular biology, evolutionary theory,
genetic engineering, sequence logos, information theory,
electrical engineering, thermodynamics, statistical
mechanics, hypersphere packing, gumball machines, Maxwell's
Daemon, limits of computers

Schneider Lab

origin: 1999 Jul 22
updated: version = 2.31 of ev.html 2024 Jan 04

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