INTRODUCTION: Taking a fresh look at the basics of evolution in the new century

Evolutionary Reconceptualization

(Driesch 1908; Weiss 1973; Stebbins and Ayala 1981; McClintock 1984; Gould 2002; Zuckerkandl 2002; Carroll 2005; Ho and Ulanowicz 2005; Jablonka 2005; Kurakin 2005; Jablonka and Lamb 2007; Koonin 2007; Pigliucci 2007; Sapp 2007; Zuckerkandl and Cavalli 2007; Carroll 2008; Depew 2008; Pigliucci 2008; Stern and Orgogozo 2008; Caporale 2009; Koonin 2009; Koonin 2009; Koonin and Wolf 2009; Mattick 2009; Penzlin 2009; Pigliucci 2009; Ryan 2009; Ryan 2009; Ayala 2010; Cloud 2010; Fusco and Minelli 2010; Hunter 2010; Kupiec 2010; Kurakin 2010; Lewens 2010; Mattick, Taft et al. 2010; Moczek 2010; Pigliucci 2010; Ruiz-Mirazo, Pereto et al. 2010; Talbott 2010; Badyaev 2011; Barham 2011; Chen and Lin 2011; Depew and Weber 2011; Kurakin 2011; Talbott 2011)

Non-DNA inheritance

(Weiss 1969; Weiss 1971; Weiss 1972; Sathananthan 1997; Iftode and Fleury-Aubusson 2003; Roberts and Wickner 2003; Terada 2004; Satpute-Krishnan and Serio 2005; Satpute-Krishnan, Langseth et al. 2007; Boulinier and Staszewski 2008; Evsikov and Marin de Evsikova 2009; Knight and Pinney 2009; Wei and Seemann 2009; Azimzadeh and Marshall 2010; Derdowski, Sindi et al. 2010; Fujimoto, Saito et al. 2010; Tuite and Serio 2010; van Breugel, Hirono et al. 2011)

            Ciliate cortex and cell structural templating: (Sonneborn 1943; Sonneborn 1948; Sonneborn 1948; Sonneborn 1948; Sonneborn and Lesuer 1948; Sonneborn 1949; Sonneborn 1950; Sonneborn 1950; Sonneborn 1950; Sonneborn 1951; Sonneborn 1955; Beisson and Sonneborn 1965; Nanney 1966; Sonneborn 1967; Sonneborn 1970; Tamm, Sonneborn et al. 1975; Ng and Frankel 1977; Sonneborn 1977; Sonneborn 1978; Aufderheide, Frankel et al. 1980; Harold 1990; Lwoff 1990; Sapp 1991; Elias 2010; Fletcher and Mullins 2010; Lacomble, Vaughan et al. 2010; Vaughan 2010; Gluenz, Povelones et al. 2011; Marshall 2011)

            Centrioles/centrosomes: (Sathananthan, Ratnam et al. 1996; Sapp 1998; Chapman, Dolan et al. 2000; Iftode and Fleury-Aubusson 2003; Tsou and Stearns 2006; Feldman, Geimer et al. 2007; Nakazawa, Hiraki et al. 2007; Salisbury 2007; Uetake, Loncarek et al. 2007; Dobbelaere, Josue et al. 2008; Rodrigues-Martins, Riparbelli et al. 2008; Song, Miliaras et al. 2008; Strnad and Gonczy 2008; Wilson 2008; Bettencourt-Dias and Glover 2009; Cunha-Ferreira, Bento et al. 2009; Loncarek and Khodjakov 2009; Marshall 2009; Riparbelli, Dallai et al. 2009; Azimzadeh and Marshall 2010; Carvalho-Santos, Machado et al. 2010; Debec, Sullivan et al. 2010; Dzhindzhev, Yu et al. 2010; Hatch and Stearns 2010; Hodges, Scheumann et al. 2010; Kitagawa, Fluckiger et al. 2011; Kobayashi and Dynlacht 2011; Lampert and Westermann 2011; Nigg and Stearns 2011; Pagan and Pagano 2011; Puklowski, Homsi et al. 2011; Song, Liu et al. 2011; van Breugel, Hirono et al. 2011; Wang, Soni et al. 2011; Azimzadeh, Wong et al. 2012)

            Other cell organelles: (Wei and Seemann 2009)

            Prions: (Prusiner 1984; Prusiner 1998; Wickner, Taylor et al. 1999; True and Lindquist 2000; Tompa, Tusnady et al. 2001; Osherovich and Weissman 2002; Weissmann, Enari et al. 2002; Roberts and Wickner 2003; Si, Lindquist et al. 2003; Chien, Weissman et al. 2004; King and Diaz-Avalos 2004; Roberts and Wickner 2004; Wickner, Edskes et al. 2004; Meredith 2005; Satpute-Krishnan and Serio 2005; Benkemoun and Saupe 2006; Hunter 2006; Soto, Estrada et al. 2006; Baskakov and Breydo 2007; Inge-Vechtomov, Zhouravleva et al. 2007; Kushnirov, Vishnevskaya et al. 2007; Maddelein 2007; Pastor, Esteras-Chopo et al. 2007; Pezza and Serio 2007; Sabate, Baxa et al. 2007; Satpute-Krishnan, Langseth et al. 2007; Saupe 2007; Wickner, Edskes et al. 2007; Wickner, Edskes et al. 2007; Margittai and Langen 2008; True, Kalastavadi et al. 2008; Tyedmers, Madariaga et al. 2008; Wickner, Shewmaker et al. 2008; Glover and Lum 2009; Inoue 2009; Maji, Wang et al. 2009; Patel, Gavin-Smyth et al. 2009; Polano, Bek et al. 2009; Sindi and Serio 2009; Tuite and Cox 2009; Vitagliano, Stanzione et al. 2009; Alberti, Halfmann et al. 2010; Benetti, Geschwind et al. 2010; Chen, Bruce et al. 2010; Derdowski, Sindi et al. 2010; Edgeworth, Gros et al. 2010; Greenwald and Riek 2010; Halfmann and Lindquist 2010; Mathur, Taneja et al. 2010; Rincon-Limas, Casas-Tinto et al. 2010; Si, Choi et al. 2010; Taguchi and Kawai-Noma 2010; Tuite and Serio 2010; Villar-Pique, Sabate et al. 2010; Wickner, Shewmaker et al. 2010; Afanasieva, Kushnirov et al. 2011; Benkemoun, Ness et al. 2011; Colby and Prusiner 2011; Halfmann, Alberti et al. 2011; Heinrich and Lindquist 2011; Hines, Li et al. 2011; Hou, Sun et al. 2011; Manogaran, Hong et al. 2011; Mathur, Seuring et al. 2011; McGlinchey, Kryndushkin et al. 2011; Saupe 2011; Toombs, Liss et al. 2011; Verges, Smith et al. 2011; Wickner, Edskes et al. 2011; Beringue, Herzog et al. 2012)

                        Prion domains and prion/amyloid nucleation: (Kushnirov, Vishnevskaya et al. 2007; Maddelein 2007; Maji, Wang et al. 2009; Sabate, Castillo et al. 2009; Tompa 2009; Wasmer, Schutz et al. 2009; Greenwald, Buhtz et al. 2010; Greenwald and Riek 2010; Wasmer, Zimmer et al. 2010; Baiesi, Seno et al. 2011; Gendoo and Harrison 2011)

                        Chaperones and prions: (Malato, Dos Reis et al. 2007; Nenninger, Robinson et al. 2009; Romanova and Chernoff 2009; Hines, Li et al. 2011)

                        Prokaryotic amyloids: (de Groot, Sabate et al. 2009; Nenninger, Robinson et al. 2009; Romero, Aguilar et al. 2010; Garcia-Fruitos, Sabate et al. 2011; Lotti 2011; Shewmaker 2011)

The “gene” concept

(Keller 2002 ; Griffiths and Stotz 2006; Keller and Harel 2007; Buchanan, Sholtis et al. 2009)

Cell and organism decision-making

(Miklos 1993; Nakagaki, Yamada et al. 2000; Nakagaki 2001; Heit, Tavener et al. 2002; Jamshidi 2003; Trewavas 2003; Dueber, Yeh et al. 2004; Glimcher and Rustichini 2004; Griffin and Speck 2004; Nakagaki, Kobayashi et al. 2004; Nakagaki, Yamada et al. 2004; Seth, Baars et al. 2005; Patnaik 2006; Adamatzky 2007; Bebber, Hynes et al. 2007; Nakagaki, Iima et al. 2007; Strome and Lehmann 2007; Helikar, Konvalina et al. 2008; Saigusa, Tero et al. 2008; Scherbaum, Dshemuchadse et al. 2008; St-Pierre and Endy 2008; Stephens 2008; Tagkopoulos, Liu et al. 2008; Tero, Yumiki et al. 2008; Brembs 2009; Carlson 2009; Cortes and Londono 2009; Grasso and Basil 2009; Halley, Burden et al. 2009; Zhang, Liu et al. 2009; Ambravaneswaran, Wong et al. 2010; Avlund, Krishna et al. 2010; Clark 2010; Clark 2010; Dussutour, Latty et al. 2010; Gilbert 2010; Karpinski and Szechynska-Hebda 2010; Kobayashi 2010; Maki 2010; Morris, Saez-Rodriguez et al. 2010; Ngalim, Magenau et al. 2010; O'Malley 2010; Sanges and Cosma 2010; Tero, Takagi et al. 2010; Waltermann and Klipp 2010; Wu, Tschumper et al. 2010; Zhang, Liu et al. 2010; Avraham and Yarden 2011; Balazsi, van Oudenaarden et al. 2011; Bandyopadhyay, Parua et al. 2011; Bateson, Desire et al. 2011; Bendesky, Tsunozaki et al. 2011; Brembs 2011; Chittka and Skorupski 2011; Cretel, Touchard et al. 2011; Hines, Li et al. 2011; Joh and Weitz 2011; Kalenscher and van Wingerden 2011; Latty and Beekman 2011; Latty and Beekman 2011; Li, Rosenbaum et al. 2011; Mendl, Paul et al. 2011; Mitra, Das et al. 2011; Morris 2011; Neal and Meek 2011; Paddock, Bauman et al. 2011; Watanabe, Tero et al. 2011; Zhou and Huang 2011)

Cognition and Decision in Non-Human Biological Organisms edited by Steven Shaviro

http://www.livingbooksaboutlife.org/books/Cognition_and_Decision

            Neuronal computation: (Pitts and Mc 1947; Blomfield 1974; McCulloch and Pitts 1990; Herz, Gollisch et al. 2006; Marder and Goaillard 2006; Schnupp and Carr 2009; Parker 2010; Prinz 2010; Branco 2011; Godil, Shamim et al. 2011)

Computer Evolution, Control and Cognition

(Barricelli 1957; Simon 1962; Fogel, Owens et al. 1966; Kauffman 1969; Simon 1969 (1996 edition); Manoilenko and Khakhina 1974; Kauffman and Levin 1987; Holland 1992; Yamakawa 1992; Angeline and Pollack 1993; Kosko and Isaka 1993; Koza 1994; Potter and De Jong 1994; Bull and Fogarty 1995; Levin 1995; Floreano and Mondada 1996; Koza and Andre 1996; Beyer 1997; Bull 1999; Fogel 1999; Sadegh-Zadeh 1999; Cheong and Lai 2000; Holland 2000; Parasuraman, Masalonis et al. 2000; Potter and De Jong 2000; Gero and Kazakov 2001; Rosenberg 2001; Tomlinson and Bull 2001; Zadeh 2001; De Jong 2002; Lipson, Pollack et al. 2002; Watson 2002; Bedau and Packard 2003; Eiben and Smith 2003; Jamshidi 2003; Koza, Keane et al. 2003; Pepper 2003; Poole, Phillips et al. 2003; Ravasz and Barabasi 2003; Shin and Iba 2003; Watson and Pollack 2003; Adriaenssens, De Baets et al. 2004; Earl and Deem 2004; Honda and Kobayashi 2004; Reinkensmeyer, Emken et al. 2004; Ashwin and Timme 2005; Harvey, Di Paolo et al. 2005; Keller 2005; Banzhaf, Beslon et al. 2006; Bongard, Zykov et al. 2006; Dwight Kuo, Banzhaf et al. 2006; Eguchi, Hirasawa et al. 2006; Griswold 2006; Marder and Goaillard 2006; Patnaik 2006; Toussaint 2006; Watson 2006; Wu and Tan 2006; Ciesielski, Udupa et al. 2007; Ho, Hsieh et al. 2007; Toussaint and von Seelen 2007; Bull, Budd et al. 2008; Collier 2008; Di Paolo and Iizuka 2008; Elena and Sanjuan 2008; Fang, Wang et al. 2008; Garduno and Herman 2008; Hsiao, Xu et al. 2008; Kampis and Gulyas 2008; Minku and Ludermir 2008; Parter, Kashtan et al. 2008; Salazar-Ciudad 2008; Sole and Valverde 2008; Ziemke 2008; Alavandar and Nigam 2009; Kashtan, Mayo et al. 2009; Macia and Sole 2009; Marbach, Mattiussi et al. 2009; Marchal-Crespo and Reinkensmeyer 2009; Meltzoff, Kuhl et al. 2009; Rubenstein, Sai et al. 2009; Schnupp and Carr 2009; Ali 2010; Azar 2010; Correia 2010; Espinosa-Soto and Wagner 2010; Floreano and Keller 2010; Grigorie 2010; Harding, Miller et al. 2010; Hong and Song 2010; Korosec 2010; Koza 2010; Molina 2010; Parker 2010; Perusich 2010; Prinz 2010; Tero, Takagi et al. 2010; Usmani 2010; Wang, Liao et al. 2010; Bongard 2011; Kita 2011; Maeda, Fukano et al. 2011; Mitra, Das et al. 2011; Momeni, Chen et al. 2011; Paperin, Green et al. 2011; Pavlicev, Cheverud et al. 2011; Pavlicev, Norgard et al. 2011; Wagner and Zhang 2011)

            Jörg Heitkötter & David Beasley, 2001, The Hitch-Hiker's Guide to Evolutionary Computation (http://www.aip.de/~ast/EvolCompFAQ/top.htm ); Jason Brownlee, Evolutionary Programming (http://www.cleveralgorithms.com/nature-inspired/evolution/evolutionary_programming.html )

Fuzzy logic: (Parasuraman, Masalonis et al. 2000; Leng and Bentwich 2002; Walsh, Luhrs et al. 2003; Adriaenssens, De Baets et al. 2004)

Language and cultural evolution, linguistic approaches to genome analysis

(Pietrokovski and Trifonov 1992; Popov, Segal et al. 1996; Searls 1997; Nowak, Komarova et al. 2002; Steels 2003; Gheorghe and Mitrana 2004; Smith 2004; Emery 2006; Steels 2006; Kirby, Dowman et al. 2007; Griffiths, Kalish et al. 2008; Zlatev 2008; Kandler 2009; Vogt 2009; Fitch, Huber et al. 2010; Reali and Griffiths 2010; Dunn, Greenhill et al. 2011; Fitch 2011; Loreto and Tria 2011; Perlovsky 2011; Smith 2011)

Practical innovation (inventions, patents, product engineering)

(Christensen 1997; Chakravorti 2004; Bongard, Zykov et al. 2006; Abbott 2007; Meltzoff, Kuhl et al. 2009; Rubenstein, Sai et al. 2009; Koza 2010)

http://innovationzen.com/blog/2006/10/14/innovation-management-theory-round-up/

            TRIZ/TIPS (= Theory of Inventive Problem Solving): (Altshuller 1984; Altshuller 1996; Terninko, Zusman et al. 1998; Altshuller 1999; Kim and Cochran 2000; Mann 2003; Cascini and Rissone 2004; Cascini and D. 2007; Akay, Demıray et al. 2008; Cascini 2009; Sheng and Kok-Soo 2010)

The Altshuler Institute for TRIZ Studies http://www.aitriz.org/index.php

Barry, Katie; Domb, Ellen and Slocum, Michael S. What Is TRIZ? The TRIZ journal.  http://www.triz-journal.com/archives/what_is_triz/

Hipple, J. Introduction to The TRIZ Inventive Problem Solving Process. Available online at: http://www.innovation-triz.com/papers/understandingtriz.ppt

            QFD (Quality Function Deployment) and Taguchi Methods, Philosophy of Robust Design: (Taguchi 1995; Johansson and Timpka 1996; Smith 1998; Terninko, Zusman et al. 1998; Abdul-Rahman and Berawi 2001; Leysi-Derilou and Antony 2001; Bogaerts and Vande Wouwer 2003; Grimm, Revilla et al. 2005; Marsot 2005; Breitling, Gilbert et al. 2008; Daun, Rubin et al. 2008; Ng, Ng et al. 2008; Rahman and Qureshi 2008; Rao, Kumar et al. 2008; Hunt, Ropella et al. 2009; Kuijt-Evers, Morel et al. 2009)

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