These are a mix of videos, science papers and web articles and books. The books have been linked as complete downloads wherever possible. Obviously these references make more sense in the context of the book. However, they are informative in their own right and I hope you enjoy and get a better idea of the research regarding Darwinian theory of evolution with all its flaws and a sense of the newer ideas emerging. I will post the references for the other chapters of the book over the next few weeks, but, this should be enough to be going on with for now.
(1). Shapiro, J.A. 1996. “In the detail…What?” University of Chicago, biological sciences, educational resources [PDF doc article] National Review, 63-65.
(2). Koonin, E. “The Origin at 150: is a new evolutionary synthesis in sight?” Trends in Genetics, Volume 25, Issue 11, 473-475, (15 October 2009) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784144/
(3). Dawkins, R. The Selfish Gene, Ebook v1.0.
with prefaces from all additions. Chapter 1. Why are people?http://www.arvindguptatoys.com/arvindgupta/selfishgene-dowkins.pdf
(4). The Project Gutenberg, EBook, “Charles Darwin: His Life in an Autobiographical Chapter, and in a Selected Series of His Published Letters, by Charles Darwin”, Edited by Sir Francis Darwin. Letter from A. R. Wallace to A. Newton. Frith Hill, Godalming, Dec. 3rd, 1887. P. 190
(5). John Lennox (2011), bigquestions.com “Interview with Prof. John Lennox” from Grenville Kent, https://vimeo.com/15789806
(6). David Berlinski (2010 – video interview). ScottyVOR (2010, October 22). “Dr. David Berlinski on evolution, 1/3” [Video file]. (part one)
(7). R. Dawkins. “The Blind Watchmaker” (1986) p. 287, http://uath.org/download/literature/Richard.Dawkins.The.Blind.Watchmaker.pdf
(8). National Geographic (November 2004) “Was Darwin Wrong?”
(9). Richard Attenborough interview “How Darwin won the evolutionary race” by Robin McKie, in The Observer, (Sunday 22 June 2008)
(10). Evolution website at Berkeley
(11). Janusz S. “Adaptive bacteria” (2008) Epigenome Website
(12). Teresi, D. (2011). Interview: Lynn Margulis. Discover Magazine, (April issue 2011), 66-71. (“Q + A”, p. 68)
(13). Casey Luskin (2003). Excerpts from “Evolving Genomes: Acquiring Genomes: The Theory of the Origins of the Species” by Margulis, L. and Dorion Sagan, D. (2003) Basic books, p.29.
(14). Scott Gilbert, John Opitz, and Rudolf Raff, (1996). “Resynthesizing Evolutionary and Developmental Biology”, in Developmental Biology, 173, Article no. 0032, 1996, in evolutionary biology (1996): 357-372.
(15). Linton, A. H. (2001).” Scant Search for the Maker”. Times Higher Education. Posted on timeshighereducation.co.uk (April 20, 2001), Book Section, p. 29
(16). AWF Edwards (2011) “Mathematizing Darwin”, in behavioral ecology and sociobiology 65, 3: (421–430) 5. Published online 2011 January 5. doi: 10.1007/s00265-010-1122-x
(17) Letter from Darwin, C. R. to Hooker, J. D.  Sent from Down on 14 Feb 
(18). Gould, S.J. (1982) “Darwinism and the expansion of evolutionary theory”http://www.bilimfelsefedin.org/blog/wp-content/uploads/2009/04/darwinism-the-expansion-of-the-evolution-theory-stephen-jay-gould.pdf
(19). Koonin, E.V. (2012) “ The Logic of Chance: The Nature and Origin of Biological Evolution” Pearson Education, Inc. Publishing as FT Press Science. pgs. 18 and 19.
(20). Lynch, M. (2007) “The frailty of adaptive hypotheses for the origins of organismal complexity”, [Online Journal], PNAS – Proceedings of the National Academy of Sciences 104:8597–8604.
(21). Wilkins, A. S. (2011) Book review of “Evolution: A View from the 21st Century” by James A. Shapiro. Upper Saddle River, NJ: FT Press, 2011, in Genome Biol Evol (2012) 4 (4): 423-426.doi: 10.1093/gbe/evs008 (First published online: January 24, 2012)
(22) Goldenfeld, N, and Woese, C. (2009) “Life is Physics: Evolution as a Collective Phenomenon Far From Equilibrium” in Cornell University Library online (2010): http://arxiv.org/abs/1011.4125
(23) Raup, D. M. (1979), “Conflicts between Darwin and Paleontology”, in the Field Museum of Natural History Bulletin (Jan. 1979), Vol. 50 No. 1. p. 22-29.
(24). Gould, S. J. (1980) “The Return of Hopeful Monsters,” Natural History 86 (June/July): 22-30; Reprinted with permission from The Panda’s Thumb New York: W. W. Norton & Co., 1980, pp. 186-193. http://www.stephenjaygould.org/library/gould_hopeful-monsters.html
(25). Craig Venter speaking on “The Great Debate – What is Life?” [Video file], The Science Foundation, Published (Mar 7, 2013) http://www.youtube.com/watch?v=xIHMnD2FDeY
(26). Encyclopedia Britannica Website “Mutation Theory” http://www.britannica.com/EBchecked/topic/399746/mutation-theory#ref1191484
(27) De Vries, H. (1914) “The Principles of the Theory of Mutation”, Source: Science, New Series, Vol. 40, No. 1020 (Jul. 17, 1914), pp. 77-84, Pg 80. Published by: American Association for the Advancement of Science. http://www.jstor.org/stable/1640345
(28). Encyclopedia Britannica Website “Hugo De Vries” http://www.britannica.com/EBchecked/topic/633337/Hugo-de-Vries
(29). Mallet, J. (2007) “Hybrid Speciation” Vol 446, (15 March 2007) doi:10.1038/nature05706
(30). Carroll, S. B. (2010) “Hybrids May Thrive Where Parents Fear to Tread” in New York Times, Published: (September 13, 2010) http://www.nytimes.com/2010/09/14/science/14creatures.html?_r=2&
(31). Vega, Y, Marques, I, Castro, S, and Loureiro (2013) “Outcomes of Extensive Hybridization and Introgression in Epidendrum (Orchidaceae): Can We Rely on Species Boundaries?” in PlosOne, Published: November 05, 2013DOI: 10.1371/journal.pone.0080662 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080662
(32 ) Balon, E, K. (2004) “ Evolution by epigenesis: farewell to Darwinism, neo- and otherwise.” In Rivista di biologia 97, No. 2, pp. 269-312. http://www.ncbi.nlm.nih.gov/pubmed/15612191
(33) Saenko, S. V, Marialva, M. S. P, and Beldade, P (2011) “Involvement of the conserved Hox gene Antennapedia in the development and evolution of a novel trait” in EvoDevo. Published online (2011 April 19). doi: 10.1186/2041-9139-2-9
( 34 ). Jablonka, E, and Raz, G, (2009) “Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution” in, The Quarterly Review of Biology , Vol. 84, No. 2 (June 2009) , pp. 131-176, Published by: The University of Chicago Press, Article DOI: 10.1086/598822 http://www.jstor.org/stable/10.1086/598822
(35). Princeton Education website, “August Weismann”.
(36). Charles Darwin. Letter to Sir Joseph Hooker (11 Jan 1844). In Charles Darwin and Francis Darwin (ed.), Charles Darwin: His Life Told in an Autobiographical Chapter, and in a Selected Series of His Published Letters (1892), 173-174.
(37). Wilkins, A. (2011) “Did the modern synthesis give short shrift to soft inheritance?” in, Transformations of Lamarckism: From Subtle Fluids to Molecular Biology, edited by Snait Gissis, Eva Jablonka, Google books pg 30.
(38). Haig, D. (2011) “Lamarck Ascending!” a review of, From Subtle Fluids to Molecular Biology, Transformations of Lamarckism: edited by Snait B. Gissis and Eva Jablonka, MIT Press, (2011), in Philosophy and Theory in Biology http://dx.doi.org/10.3998/ptb.6959004.0003.004
(39). Noble, D. (2011), Professor Noble’s endorsement of book, “Transformations of Lamarckism From Subtle Fluids to Molecular Biology” edited by Snait B. Gissis and Eva Jablonka, MIT press (2011).
(40). Lamarck J. B. (1809) “Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck, On classification and evolution Extracts from: Philosophie zoologique, ou exposition des considérations relatives à l’histoire naturelle des animaux. (Zoological Philosophy). An Exposition with regard to the Natural History of Animals.” Translated by Hugh Elliot, Macmillan, London (1914), reprinted by University of Chicago Press, 1984. http://www.ucl.ac.uk/taxome/jim/Mim/lamarck_contents.html
(41). Lamarck, J. B. (1809), “Zoological Philosophy, Volume One” PARIS, translation by Ian Johnston (September 1999) http://records.viu.ca/~johnstoi/lamarck/tofc.htm
(42). John S. Mattick, J. D. (2012) “Rocking the foundations of molecular genetics” in PNAS (October 9, 2012) vol. 109 no. 41 16400-16401 doi: 10.1073/pnas.1214129109 http://www.pnas.org/content/109/41/16400.full
(43). Bowler, P. J (2003) “Evolution: The History of an Idea”, University of California Press, pg 367
(44). Epigenetics website, “The Genetic versus the Epigenetic Paradigm” http://www.epigenetics.ch/gpage1.html
(45). Medical News Daily website, “What is a gene? What are genes?” Last updated on Monday 2 September (2013) Originally published on Saturday 6 September (2008)
(46). Utah Education website, “A Different Kind of Inheritance” http://learn.genetics.utah.edu/content/epigenetics/rats/
(47). Richard Dawkins in “Homage to Darwin (part 1)” [Video File], Voices from Oxford debate with Dawkins, Margulis, Brasier, Bell, chaired by Denis Noble http://vimeo.com/51768266
(48). Noble, D. 2006. The Music of Life: Biology beyond genes. Oxford University Press
(49). Shapiro, J.A. 2011. Evolution: A View from the 21st Century. FT (Financial Times) Press, U.S.Ahttp://books.google.ie/books/about/Evolution.html?id=t3lcm_4h20QC&redir_esc=y
(50). Mae-Wan Ho and Saunders, P. T. (1979) “Beyond Neo-Darwinism: An Epigenetic Approach to Evolution.” Journal of Theoretical Biology 78 (1979): 573-91.http://www.sciencedirect.com/science/article/pii/0022519379901917
(51). Burkeman, O. (2010) “Why everything you’ve been told about evolution is wrong” in the London Guardian, UK (Friday 19 March 2010) http://www.theguardian.com/science/2010/mar/19/evolution-darwin-natural-selection-genes-wrong
(52). Carey, N. (2013) “The Epigenetics Revolution: How Modern Biology Is Rewriting Our Understanding of Genetics, Disease, and Inheritance”, Columbia university press http://books.google.ie/books/about/The_Epigenetics_Revolution.html?id=2hGUwTlHNH0C&redir_esc=y
(53). Jablonka, E. (2006) “Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life”, MIT press http://books.google.ie/books/about/Evolution_in_Four_Dimensions.html?id=EaCiHFq3MWsC&redir_esc=y
(54). Noble, D. (2013) “Physiology is rocking the foundations of evolutionary biology”, in Exp Physiol expphysiol.2012.071134; published ahead of print April 12, 2013, doi:10.1113/expphysiol.2012.071134
(55). Denis Noble, “Physiology and Evolution Physiology and the revolution in Evolutionary Biology” [Video File], from Voices from Oxfordhttp://vimeo.com/56631836
(56). Shapiro, J. A. (1997) “The Third Way” in the Boston Review: Is Darwin in the Details? A Debate (February/ March 1997 issue) http://shapiro.bsd.uchicago.edu/Shapiro.1997.BostonReview1997.ThirdWay.pdf
More references to follow over the next few weeks
I hope you feel better informed after clicking on the links. As the references refer to Book One the Darwin Delusion, they do make more sense in that context.
Take care for now