Overview

Refuting abiogenesis / chemical evolution / material origin of life
  1. Abel, D.L.  (2012). Is life unique?. Life, Vol. 2, pp. 106-134.
  2. Kuhn, J.A. (2012). Dissecting Darwinism. Baylor University Medical Center Proceedings, Vol. 25(1), pp. 41-47.
  3. Meyer, S.C. and Nelson, P.A. (2011). Can the origin of the genetic code be explained by direct RNA templating?. BIO-Complexity, Vol. 2011(2).
  4. Shapiro, R. (2011). Astrobiology: Life’s beginnings. Nature, Vol. 476, pp. 30-31.
  5. Singh, T.D. (2011). Ethics and human value – a direct challenge to chemical evolution. The Harmonizer, Newsletter, Bhakti Vedanta Institute, Vol. June, pp. 2-3.
  6. Shanta, B.N. (2011). Sorry, Darwin: Chemistry never made the transition to Biology. Darwin Under Siege.
  7. Abel, D.L. (2010). The GS (genetic selection) principle. Frontiers in Bioscience, Vol. 14, pp. 2959-2969.
  8. Kelley, D. (February 7, 2010). Is it time to throw out 'primordial soup' theory?. NPR.
  9. McIntosh, A.C. (2009). Information and entropy – Top-Down or Bottom-Up development in living systems. International Journal of Design & Nature and Ecodynamics, Vol. 4(4), pp. 351-385.
  10. Abel, D.L. (2009). The capabilities of chaos and complexity. International Journal of Molecular Sciences, Vol. 10, pp. 247-291.
  11. Puri, B.M. (2008). The logic of lifeScience and Scientist – Inquiring into the Origin of Matter and Life, Newsletter Issue: January – March, Bhakti Vedata Institute.
  12. Mazzocchi, F. (2008). Complexity in biology. Exceeding the limits of reductionism and determinism using complexity theory. EMBO Rep., Vol. 9(1), pp. 10-14.
  13. Zimmer, C. (2005). How and where did life on Earth arise?. Science, Vol. 309, p. 89.
  14. Shapiro, R. (2000). A replicator was not involved in the origin of life. IUBMB Life, Vol. 49, pp. 173–176.
  15. Schwartz, A.W. and de Graaf, R.M. (1993). The prebiotic syntheses of carbohydrates: A reassessment. J. Mol. Evol., Vol. 36, pp. 101-106.
  16. Joyce, G.F., and Orgel, L.E. (1993). Prospects for understanding the origin of the RNA World. The RNA World, eds. Gesteland R.F., and Atkins, I.E. New York, Cold Spring Harbor Laboratory Press, pp. I-25.
  17. Benner, S.A. (1993). Catalysis: Design versus selection. Science, Vol. 261, p. 1403.
  18. Kasting, J.F. (1993). Earth’s early atmosphere . Science, Vol. 259, pp. 920-926.
  19. National Research Council Space Studies Board. (1990). The search for life’s origins (suggested that origin of life scientists should undertake a “reexamination of biological monomer synthesis under primitive Earthlike environments, as revealed in current models of the early Earth.”). National Academy Press, Washington D.C.
  20. Waldrop, M.M. (1990). Goodbye to the warm little pond?. Science, Vol. 250, pp. 1078-1080.
  21. Maher, K.A., and Stevenson, D.J. (1988). Impact frustration of the origin of life. Nature, Vol. 331, pp. 612-614.
  22. Shapiro, R. (1988). Prebiotic ribose synthesis: A critical analysis. Origins Life and Evol. Biosphere, Vol. 18, pp. 71-85.
  23. Shapiro, R. (1984). The improbability of prebiotic nucleic acid synthesis. Origins Life, Vol. 14, pp. 565-570.
  24. Hulett, H.R. (1969). Limitations on prebiological synthesis. Journal of Theoretical Biology, Vol. 24, pp. 56-72.

 

Refuting Darwinism / neo-Darwinism / Evolution Theory
Disproving Darwin's 'Tree of Life'
  1. Koonin, E.V. (2011). The logic of chance: The nature and origin of biological evolution. FT Press.
  2. O’Malley, M.A. and Koonin, E.V. (2011). How stands the Tree of Life a century and a half after The Origin? Biology Direct, 6:32.
  3. Lawton, G. (21 January, 2009). Why Darwin was wrong about the tree of life. New Scientist Magazine, Issue 2692, pp. 34-39.
  4. Bapteste, E. et. al. (2009). Prokaryotic evolution and the tree of life are two different things. Biol Direct, Vol. 4:34.
  5. Kunin, E.V., Goldovsky, L., Darzentas, N. and Ouzounis, C.A. (2005). The net of life: reconstructing the microbial phylogenetic network. Genome Res., Vol. 15(7), pp. 954-959.
  6. Bapteste, E., Susko, E., Leigh, J., MacLeod, D., Charlebois, R.L. and Doolittle, W.F. (2005). Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol., Vol. 5:33.
  7. Doolittle, W.F. (2000). Uprooting tree of life. Scientific American, Vol. 282(2), pp. 90-95.
  8. Woese, C. (1998). The universal ancestor. PNAS, Vol. 95(12),  pp. 6854-6859.

Disproving 'Natural Selection'

  1. Kuhn, J.A. (2012). Dissecting Darwinism. Baylor University Medical Center Proceedings, Vol. 25(1), pp. 41-47.
  2. Lynch, M. (2010). Rate, molecular spectrum, and consequences of human mutation. PNAS, Vol. 107(3), pp. 961-968.
  3. Clune, J., Misevic, D., Ofria, C., Lenski, R.E., Elena, S.F. and Sanjuán, R. (2008). Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Comput Biol, Vol. 4(9): e1000187.
  4. Nei, M. (2005). Selectionism and neutralism in molecular evolution. Mol Biol Evol, Vol. 22(12), pp. 2318-2342.
  5. Sanford, J.C. (2005). Genetic entropy & the mystery of the genome, ILN.

Disproving 'Random Mutation'
  1. Shapiro, J.A. (2011). Evolution: A view from the 21st century, FT Press.
  2. Bohne, A., Brunet, F., Galiana-Arnoux, D., Schultheis, C. and Volff, J.N. (2008). Transposable elements as drivers of genomic and biological diversity in vertebratesChromosome Res., Vol. 16, pp. 203-215.
  3. Arguello, J.R., Fan, C., Wang, W. and Long, M. (2007). Origination of chimeric genes through DNA-level recombination. Genome Dyn, Vol. 3, pp. 131-146.
  4. Shapiro, J.A. and Sternberg, R.v. (2005). Why repetitive DNA is essential to genome function. Biol Rev Camb Philos Soc., Vol. 80, pp. 227-250.
  5. Biemont, C. and Vieira, C. (2005). What transposable elements tell us about genome organization and evolution: the case of Drosophila. Cytogenet Genome Res., Vol. 110, pp. 25-34.
  6. Kazazian, H.H., Jr. (2004). Mobile elements: drivers of genome evolution. Science, Vol. 303, pp. 1626-1632.

Disproving 'Central Dogma'
  1. Shapiro, J.A. (2009). Revisiting the Central Dogma in the 21st Century. Annals of the New York Academy of Sciences, Vol. 1178, pp. 6-28.
  2. Shapiro, J.A. (2006). Genome informatics: The role of DNA in cellular computations. Biological Theory, Vol. 1(3), pp. 288-301.
  3. Sapp, J. (1987). Beyond the gene: Cytoplasmic inheritance and the struggle for authority in genetics. Oxford University Press, New York.

Disproving 'Chronology of Geological Column'/'Fossil Dating'

  1. Shanta, B.N. (2013). A scientific basis for vedantic view of biodiversity. Science and Scientist.
  2. Schieber, J. (2011). Shifting paradigms in shale sedimentology – The implications of recent flume studies for interpreting shale fabrics and depositional environmentsProc. Recovery – CSPG CSEG CWLS Convention, pp. 1-4.
  3. Schieber, J., Southard, J.B. and Schimmelmann, A. (2010). Lenticular shale fabrics resulting from intermittent erosion of muddy sediments - Comparing observations from flume experiments to the rock record. Journal of Sedimentary Research, Vol. 80, 119-128.
  4. Schieber, J. and Southard, J.B. (2009). Bedload transport of mud by floccule ripples – Direct observation of ripple migration processes and their implicationsGeology, Vol. 37, pp. 483-486.
  5. Schieber, J. and Yawar, Z. (2009). A new twist on mud deposition - Mud ripples in experiment and rock record. The sedimentary record, Vol. 7/2, pp. 4-8.
  6. Schieber, J., Southard, J.B. and Thaisen, K.G. (2007). Accretion of mudstone beds from migrating floccule ripples. Science, Vol. 318, pp. 1760-1763.
  7. Macquaker, J.H.S., Bohacs, K.M. (2007). Geology: On the accumulation of mud. Science, Vol. 318(5857), Vol. 1734–1735.
  8. Berthault, G. (2002). Analysis of the main principles of stratigraphy on the basis of experimental data. Lithology and Mineral Resources, Vol. 37(5), pp. 442-446.
  9. Makse, H.A., Havlin, S., King, P.R. and Stanley, H.E. (1997). Spontaneous stratification in granular mixtures. Nature, Vol. 386, pp. 379-382.
  10. Fineberg, J. (1997). From cinderella’s dilemma to rock slides. Nature, Vol. 386, pp. 323-324.
  11. Julien, P.Y., Lan, Y. and Berthault, G. (1993). Experiments on stratification of heterogeneous sand mixtures. Bulletin Géologique de France, Vol. 164(5), pp. 649-660.
  12. Julien, P.Y., and Berthault, G. (1993). Fundamental experiments on stratification. Video, Sarong Ltd., Monaco.

Ontogeny Refutes Phylogeny (Theory of Evolution)
  1. Muni, B.V. (February, 2013). Ontological wholism and soul is the concept of developmental biology: A review of the experiments and scientific conclusions of Hans Adolf Eduard DrieschThe Harmonizer.
  2. Kalinka, A.T. et. al. (2010). Gene expression divergence recapitulates the developmental hourglass modelNature,  Vol 468, pp. 811-814.
  3. Müller, G.B. (2010). Epigenetic innovation. In: Evolution - The extended synthesis. Pigliucci M. and G.B. Müller eds., MIT Press.
  4. Pigliucci, M. (2009). An extended synthesis for evolutionary biologyAnn. N.Y. Acad. Sci., Vol. 1168, pp. 218-228.
  5. Moczek, A.P. (2008). On the origins of novelty in development and evolutionBioEssays, Vol. 30, pp. 432-447.
  6. Grossberg, R.K. and Strahmann, R.R. (2007). The Evolution of multicellularity: A minor major transition? Ann. Rev Eco. and Evo. Syst., Vol. 38, pp. 621-654.
  7. Goldbeter, A., Gonze, D. and Pourquié, O. (2007). Sharp developmental thresholds defined through bistability by antagonistic gradients of retinoic acid and FGF signalingDev. Dyn., Vol. 236, pp. 1495-1508.
  8. Newman, S.A. and Bhat, R. (2007). Activator–inhibitor dynamics of vertebrate limb pattern formation. Birth Def Res., Vol. C81, pp. 305-319.
  9. Salazar-Ciudad, I. and Jernvall, J. (2005). Graduality and innovation in the evolution of complex henotypes: Insights from developmentJ. Expt Zool., Vol. 304B, pp. 619-631.
  10. Minelli, A. and Fusco, G. (2005). Conserved versus innovative features in animal body organizationJ. Expt Zool., Vol. 304B, pp. 520-525.
  11. Melen, G.J., Levy, S., Barkai, N. and Shilo, B.Z. (2005). Threshold responses to morphogen gradients by zero-order ultrasensitivityMol. Sys Bio., doi:10.1038/msb4100036.
  12. Newman, S.A. (2005). The pre-Mendelian, pre-Darwinian world: Shifting relations between genetic and epigenetic mechanisms in early multicellular evolutionJ. Biosci., Vol. 30, pp. 75-85.
  13. Love, A.C. (2005). Explaining evolutionary innovation and novelty: A historical and philosophical study of biological conceptsDoctoral dissertation, University of Pittsburgh.
  14. Newman, S., (2005). The pre-Mendelian, pre-Darwinian world: Shifting relations between genetic and epigenetic mechanisms in early multicellular evolutionJ. Biosci., Vol. 30(1), pp. 75-85.
  15. Grantham, T.A. (2004). The role of fossils in phylogeny reconstruction: why is it so difficult to integrate paleontological and neontological evolutionary biology? Biology and Philosophy, Vol. 19(5), pp. 687-720.
  16. Schmidt, K. and Starck, J.M. (2004). Developmental variability during early embryonic development of zebra fishJ. Expt. Zoology Part B: Mol. Dev. Evo., Vol. 302, 446-457.
  17. Poe, S. and Wake, M.H. (2004). Quantitative tests of general models for the evolution of developmentAm. Nat., Vol. 164, pp. 415-422.
  18. Hentschel, H.G.E., Glimm, T., Glazier, J.A. and Newman, S.A. (2004). Dynamical mechanisms for skeletal pattern formation in the vertebrate limbProc. Royal Soc., London, Vol. B271, pp. 1713-1722.
  19. Wells, J. (2002). Icons of evolution: Science or Myth? Why much of what we teach about evolution is wrong, Regnery Publishing.
  20. Hall, B.K. (1997). Phylotypic stage or phantom, is there a highly conserved embryonic stage in vertebrates? Trends Ecol. Evol., Vol. 12, pp. 461-463.
  21. Richardson, M.K. et al. (1997). There is no highly conserved embryonic stage in the vertebrates: Implications for current theories of evolution and developmentAnat. Embryol. (Springer-Verlag), Vol. 196, pp. 91-106.
  22. Raff, R.A. (1996). The Shape of Life: Genes, development and the evolution of animal form, Univ. Chicago Press.
  23. Slack, J.M.W. (1994). Inducing factors in Xenopus early embryosCurr. Biol., Vol. 4, pp. 116-126.
  24. Gould, S.J. and Vrba, E.S. (1982). Exaptation: A missing term in the science of form. Paleobiology, Vol. 8, pp. 4-15.
  25. Blechschmidt, E. (1978). The beginnings of human life, Springer-Verlag, New York.
  26. Eldredge, N. and Gould, S.J. (1972). Punctuated equilibria: An alternative to phyletic gradualism. In: Models in paleobiology. T.J.M Schopf, ed., San Francisco: Freeman, Cooper, pp. 82-115.
  27. Mayr, E. (1960). The emergence of evolutionary novelties. In: Evolution after Darwin. S Tax, ed., Cambridge, MA: Harvard University Press, pp. 349-380.
  28. Waddington, C.H. (1942). Canalization of development and the inheritance of acquired charactersNature, Vol. 150, pp. 563-565.
  29. Waddington, C.H. (1940). Organisers and genes, Cambridge Univ. Press, Uk.

Disproving Darwin
  1. Kuhn, J.A. (2012). Dissecting Darwinism. Baylor University Medical Center Proceedings, Vol. 25(1), pp. 41-47.
  2. Axe, D.D., Lu, P. and Flatau, S. (2011). A stylus-generated artificial genome with analogy to minimal bacterial genomes. BIO-Complexity, Vol. 2011(3).
  3. Shapiro, J.A. (2011). Evolution: A view from the 21st century, FT Press.
  4. Meyer, S.C. (2010). Signature in the Cell: DNA and the evidence for intelligent design. HarperOne.
  5. Behe, M.J. (2010). Experimental evolution, loss-of-function mutations, and "the first rule of adaptive evolution". The Quarterly Review of Biology, Vol. 85(4), pp. 1-27.
  6. Lönnig, W.E. (2010). Mutagenesis in Physalis pubescens L. ssp. floridana: Some further research on Dollo’s law and the law of recurrent variation. Floriculture and Ornamental Biotechnology, pp. 1-21.
  7. Axe, D.D. (2010). The case against a Darwinian origin of protein folds. BIO-Complexity, Vol. 2010 (1).
  8. Axe, D.D. (2010). The limits of complex adaptation: An analysis based on a simple model of structured bacterial populations. BIO-Complexity, Vol. 2010(4).
  9. Gauger, A.K., Ebnet, S., Fahey, P.F. and Seelke, R. (2010). Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness. BIO-Complexity, Vol. 2010(2).
  10. Behe, M.J. (2007). The edge of Evolution: The search for the limits of Darwinism, Free Press.
  11. Meyer, S.C. (2007). Explore evolution: The arguments for and against neo-Darwinism, Hill House Publishers.
  12. Behe, M.J. (2006). Darwin's black box: The biochemical challenge to evolution.  Free Press.
  13. Wells, J. (2002). Icons of evolution: Science or Myth? Why much of what we teach about evolution is wrong, Regnery Publishing.
  14. Darwin’s Dilemma: The mystery of the cambrian fossil record (DVD).
  15. Denton, M. (1986). Evolution: A theory in crisis, Adler & Adler.

Cognitive Biology
  1. Shapiro, J.A. (2011). Evolution: A view from the 21st century, FT Press.
  2. Lanza, R. (2010). Biocentrism: How life and consciousness are the keys to understanding the true nature of the universe, BenBella Books.
  3. Shapiro, J.A. (2007). Bacteria are small but not stupid: Cognition, natural genetic engineering and socio-bacteriology. Stud. Hist. Phil. Biol. & Biomed. Sci., Vol. 38, pp. 807-819.
  4. Ben-Jacob, E., Shapira, Y., and Tauber, A.I. (2006). Seeking the foundations of cognition in bacteria. from Schrödinger’s negative entropy to latent information. Physica A, Vol. 359, pp. 495-524.
  5. Sridhar, B.R. (1989). Subjective evolution of consciousness – The play of the sweet Absolute. Published by Sri Chaitanya Saraswat Math.


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