This webpage contains recommended reading materials in support of the article HASARD ET DÉGÉNÉRESCENCE (Chance and Degeneracy) by Sergei P. Atamas. The initial title of this paper was LA SURVIVANCE DU DÉGÉNÉRÉ (Survival of the degenerate). Please suggest additional references for this list by e-mailing the author. Books mentioned below are written for a general reader, although most of the mentioned articles are from professional research journals and therefore may be difficult for an unprepared reader.

1. A model of self-organization in computer-simulated selective systems based on degeneracy of repertoires:
   - Atamas SP. Self-organization in computer simulated selective systems. Biosystems 1996;39(2):143-51.
   [Abstract] This might be a diffcult to understand due to technicalities, but a more basic descripiton of the model presented in LA SURVIVANCE DU DÉGÉNÉRÉ. You will not miss much by not reading it. You are welcome to request a reprint of this paper (the paper is in English) from the author by e-mailing me. Also, the very first paper on this model was published in Russian, in a journal called Dopovidi Akademii Nauk Ukraini, in 1992. If you can read Russian, you can enjoy this very simple article by downloading the full paper in PDF.
   
   Competition in degenerate repertoires can be applied to realistic systems such as polymerase chain reaction:
   - Atamas SP, Luzina IG, Handwerger BS, White B. 5'-degenerate 3'-dideoxy-terminated competitors of PCR primers increase specificity of amplification. Biotechniques 1998 Mar;24(3):445-50.
   [Abstract] Proof for the theoretical considerations in the paper above.
   An interesting update by Atamas SP, Luzina IG, Thaler DS to this paper can be found in a book
   - Expression Genetics: Differential Display. A.B. Pardee, M. McClelland, Eds., Eaton Publishing, pp. 257-266, 1999.
   
   Akira Sasaki, was not as much interested in degenerate repertoires, but in a spatially distributed Lotka-Volterra model. This model is classical in ecology, and describes predator-prey relationships. Sasaki updated Lotka-Volterra's model by assuming that individuals in the predator and prey populations "diffuse randomly," and analyzed mathematically what would happen in such a case. His assumption is obvious, because animals and even plants (not individual plants, but plant offspring) do move from place to place. For our purposes, "random diffusion" in space is just "spatial degeneracy." Sasaki's model is purely analytical (based on formulas rather than cellular automata), but this model behaves very similarly to our cellular automata model above! See:
   - Sasaki A. Clumped distribution by neighborhood competition. J Theor Biol 1997 Jun 21; 186 (4): 415-30
   This article may be diffult to understand for those who are not very strong at mathematics (I surely had problems understanding the details of this model), but the outcome confirms our modeling (compare Figure 11 in Sasaki's paper and Figure 3D from our model)
   
   
2. Selective (adaptive) systems as degenerate repertoires:
   Niels Kaj Jerne made crucial contributions to immunology, one of which was suggesting that the adaptive immune system works selectively rather than instructively. For a review, see
   - Silverstein AM. The History of Immunology. In: Fundamental Immunology. W.E. Paul, Ed., Lippincott-Raven Publishers, pp. 19-35, 1999.
   
   Jerne also speculated that human mind is also a selective system. An excellent article, which may be difficult to find, was
   - Jerne NK. Antibodies and learning: selection versus instruction. In: The Neurosciences. G.C. Quarton, T. Melnechuk, F.O. Schmitt, Eds., The Rockefeller University Press, pp. 200-205, 1967.
   
   Jerne's idea on the brain as a selective system were taken to a new level by Gerald M. Edelman, who made a particular emphasis on the central role of degeneracy in the functioning of selective systems, and published numerous research articles and popular books on the subject, particularly in an attempt to apply understanding of degenerate repertoires to how the brain, mind, and consciousness work:
   - The Mindful Brain: Cortical Organization and the Group-Selective Theory of Higher Brain Function. G. M. Edelmann, V. B. Mountcastle, Eds., MIT Press, 1978. This book contains two large parts, one of them written by Edelman. It may be difficult for understanding by an unprepared reader, but investing time and effort into working on it really pays off.
   - Edelman GM, Gally JA. Degeneracy and complexity in biological systems. Proc Natl Acad Sci U S A 2001 Nov 20;98(24):13763-8.
   [Abstract] This is a great review. Find and read it.
   - Edelman GM. Naturalizing consciousness: A theoretical framework. Proc Natl Acad Sci U S A 2003 Apr 29;100(9):5520-4.
   [Abstract]
   - Tononi G, Sporns O, Edelman GM. Measures of degeneracy and redundancy in biological networks. Proc Natl Acad Sci U S A 1999 Mar 16;96(6):3257-62.
   [Abstract]
   - Edelman, GM. Neural Darwinism: the theory of neuronal group selection. Basic Books, New York, 1987.
   - You will find plenty of books by this author by searching amazon.com database
   
   Excellent discussions of degenerate repertoires as adaptive systems can be found in
   - Frank S.A. The design of natural and artificial adaptive systems. In: Adaptation. M.R. Rose, G.V. Lauder, Eds., Academic Press, pp. 451-505, 1996.
   - Ohno, S. The significance of gene duplication in immunoglobulin evolution (Epimethean natural selection and Prometean evolution). In: Inmunoglobulins. G.W. Litman, R.A. Good, Eds., Plenum Medical Book, pp. 197-215, 1978.
   
   
3. Stuart Kauffman wrote several popular books on selection and self-organization as propelling forces of evolution:
   - Kauffman S. At Home in the Universe: The Search for the Laws of Self-Organization and Complexity. Oxford University Press, 1995.
   - Kauffman S. The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, 1993.
   
   
4. In cellular biology, degeneracy raises from stochastic gene expression and creates the basis for structural and functional differentiation of cells through selection. Stochastic gene expression is currently studied very actively (abstracts of selected research papers can be seen by clicking here). Although this idea appears obvious to many now days, it was very challenging to promote it initially. Jean-Jacques Kupiec was one of the pioneers of this idea, see two of his articles:
   
   - Kupiec JJ. Gene regulation and DNA C-value paradox: a model based on diffusion of regulatory molecules. Med Hypotheses 1989 Jan;28(1):7-10.
   [Abstract]
   - Kupiec JJ. A Darwinian theory for the origin of cellular differentiation. Mol Gen Genet 1997 Jun;255(2):201-8.
   [Abstract]
   
   Other similar papers on the subject, selected arbitrarily from a large body of literature, supporting the concept of living creatures' (cell, organisms, species) fate being defined by both genetic and stochastic mechanisms:
   - Herndon LA, Schmeissner PJ, Dudaronek JM, Brown PA, Listner KM, Sakano Y, Paupard MC, Hall DH, Driscoll M. Stochastic and genetic factors influence tissue-specific decline in ageing C. elegans. Nature. 2002 Oct 24;419(6909):808-14.
   [Abstract]
   - Blake WJ, KAErn M, Cantor CR, Collins JJ. Noise in eukaryotic gene expression. Nature. 2003 Apr 10;422(6932):633-7.
   [Abstract]
   - Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science. 2002 Aug 16;297(5584):1183-6.
   [Abstract]
   - Kuznetsov VA, Knott GD, Bonner RF. General statistics of stochastic process of gene expression in eukaryotic cells. Genetics. 2002 Jul;161(3):1321-32.
   [Abstract]
   - Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat Genet. 2002 May;31(1):69-73.
   [Abstract]
   - McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):814-9.
   [Abstract]
   - McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 1999 Feb;15(2):65-9.
   [Abstract]
   
   
5. How degeneracy works in real biological system. Keep in mind that the list below is a tiny representation of the welth of available literature. The author will be thankful for any suggestions as to upgrading this list with new references (e-mail the author).
   
   Metabolism:
   - D'Ari R, Casadesus J. Underground metabolism. Bioessays. 1998 Feb;20(2):181-6.
   [Abstract]
   - Nishida H. Evolution of amino acid biosynthesis and enzymes with broad substrate specificity. Bioinformatics. 2001 Dec;17(12):1224-5.
   [Abstract]
   - Lazcano A, Diaz-Villagomez E, Mills T, Oro J. On the levels of enzymatic substrate specificity: implications for the early evolution of metabolic pathways. Adv Space Res. 1995 Mar;15(3):345-56.
   [Abstract]
   
   Olfactory receptors:
   - Kajiya K, Inaki K, Tanaka M, Haga T, Kataoka H, Touhara K. Molecular bases of odor discrimination: Reconstitution of olfactory receptors that recognize overlapping sets of odorants. J Neurosci. 2001 Aug 15;21(16):6018-25.
   [Abstract]
   - Duchamp-Viret P, Duchamp A, Chaput MA. Peripheral odor coding in the rat and frog: quality and intensity specification. J Neurosci. 2000 Mar 15;20(6):2383-90.
   [Abstract]
   - Duchamp-Viret P, Chaput MA, Duchamp A. Odor response properties of rat olfactory receptor neurons. Science. 1999 Jun 25;284(5423):2171-4.
   [Abstract]
   - Lancet D, Sadovsky E, Seidemann E. Probability model for molecular recognition in biological receptor repertoires: significance to the olfactory system. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3715-9.
   [Abstract] Dr. Lancet has been exceptionally prolific on the subject. His other interesting paper is
   - Rosenwald S, Kafri R, Lancet D. Test of a statistical model for molecular recognition in biological repertoires. J Theor Biol. 2002 Jun 7;216(3):327-36.
   [Abstract]
   - Malnic B, Hirono J, Sato T, Buck LB. Combinatorial receptor codes for odors. Cell. 1999 Mar 5;96(5):713-23.
   [Abstract]
   
   Cytochrome P450:
   - Negishi M, Uno T, Darden TA, Sueyoshi T, Pedersen LG. Structural flexibility and functional versatility of mammalian P450 enzymes. FASEB J. 1996 May;10(7):683-9.
   [Abstract]
   
   Scavenger receptors and other multiligand receptors:
   - Krieger M, Stern DM. Series introduction: multiligand receptors and human disease. J Clin Invest. 2001 Sep;108(5):645-7.
   [Text]
   - Krieger M. The other side of scavenger receptors: pattern recognition for host defense. Curr Opin Lipidol. 1997 Oct;8(5):275-80.
   [Abstract]
   - Platt N, Gordon S. Scavenger receptors: diverse activities and promiscuous binding of polyanionic ligands. Chem Biol. 1998 Aug;5(8):R193-203.
   [Abstract]
   - Yamada Y, Doi T, Hamakubo T, Kodama T. Scavenger receptor family proteins: roles for atherosclerosis, host defence and disorders of the central nervous system. Cell Mol Life Sci. 1998 Jul;54(7):628-40.
   [Abstract]
   
   Immunology:
   The degeneracy of T and B cell receptors ensures that new unpredictable antigens are recognized and dealt with; it also defines the composition of T and B cell populations. However, it also leads to such a dreadful failure as molecular mimicry between foreign and own antigens, with subsequent autoimmunity, and to a phenomenon of "primary antigenic sin," analysis of which I leave to the interested reader.
   - Maverakis E, van den Elzen P, Sercarz EE. Self-reactive T cells and degeneracy of T cell recognition: evolving concepts-from sequence homology to shape mimicry and TCR flexibility. J Autoimmun. 2001 May;16(3):201-9.
   [Abstract]
   - Hafler DA. Degeneracy, as opposed to specificity, in immunotherapy. J Clin Invest. 2002 Mar;109(5):581-4.
   [Abstract]
   - Jacobsen M, Cepok S, Oertel WH, Sommer N, Hemmer B. New approaches to dissect degeneracy and specificity in T cell antigen recognition. J Mol Med. 2001 Jul;79(7):358-67.
   [Abstract]
   - Klenerman P, Zinkernagel RM. Original antigenic sin impairs cytotoxic T lymphocyte responses to viruses bearing variant epitopes. Nature. 1998 Jul 30;394(6692):482-5.
   [Abstract]
   - Amrani A, Serra P, Yamanouchi J, Trudeau JD, Tan R, Elliott JF, Santamaria P. Expansion of the antigenic repertoire of a single T cell receptor upon T cell activation. J Immunol. 2001 Jul 15;167(2):655-66.
   [Abstract]
   
   
6. Compare panels A and B in Figure 3 to Figure 31 in
   - Simson, GG. Tempo and Mode in Evolution. Hafner Publishing Company, New York, 1944. This classic work has been reprinted several times since the original.