The following list of peer-reviewed scientific publications and 
scholarly sources were cited in DISMANTLED:

​

SCENE 1 – PHILOSOPHY: IS EVOLUTION SCIENCE?

 

1. Our Wild Wild Solar System, National Geographic July, 2013. 

2. Campbell N.A. and Reece J.B., Biology, 7th edition, Pearson Education Inc., publishing as Benjamin Cummings, 2005.

3. Mayr E., Darwin's influence on modern thought, Scientific American November 24, 2009.

SCENE 2 – BIOLOGY: DO ANIMALS EVOLVE?

 

Several Part 2 references listed below are cited in the book Genetic Entropy (available at 

GeneticEntropy.org): Sanford J.C., Genetic Entropy, FMS Publications, 2014.

​

1. Raven P. et al., Biology, 11th edition, McGraw-Hill Education, New York, New York, 2016.

2. Boyko A.R. et al., A Simple Genetic Architecture Underlies Morphological Variation in Dogs, PLoS Biology 8(8): e1000451, 2010.

3. Biggs A. et al., Biology: The Dynamics of Life (Florida Edition), Glencoe/McGraw Hill, New York, 2006, p.399.

4. Tankovic J. et al., Frequent association between alteration of the rdxA gene and metronidazole resistance in French and North African isolates Heliobacter pylori, Antimicrobial Agents and Chemotherapy 45:608-613, 2000.

5. Willmott C.J.R. and A. Maxwell, A single point mutation in the DNA gyrase A protein greatly reduces the binding of fluoroquinolones to the gyrase-DNA complex, Antimicrobial Agents Chemotherapy 37:126–127, 1993.

6. Barnard F.M., and A. Maxwell, Interaction between DNA gyrase and quinolones: effects of alanine mutations at GryA subunit residues Ser83 and Asp87, Antimicrobial Agents and Chemotherapy 45:1994–2000, 2001.

7. Lenski R.E., Bacterial evolution and the cost of antibiotic resistance, International Microbiology 1:265–270, 1998.

8. Crozat, E., N. Philippe, R.E. Lenski, J. Geiselmann, D. Schneider. 2005. Long-Term Experimental Evolution in Escherichia coli. XII. DNA Topology as a Key Target of Selection. Genetics Society of America 169:523-532. 

9. Barrick, J.E., D. Yu, S. Yoon, H. Jeong, T. Oh, D. Schneider, R.E. Lenski, J. Kim. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461:1243-1249. 

10. Philippe, N., L. Pelosi, R. Lenski, D. Schneider. 2009. Evolution of Penicillin-Binding Protein 2 Concentration and Cell Shape during a Long-Term Experiment with Escherichia coli. Journal of Bacteriology 191(3):909-921. 

11. Schneider, D., E. Duperchy, E. Coursange, R.E. Lenski, M. Blot. 2000. Long-Term Experimental Evolution in Escherichia coli. IX. Characterization of Insertion Sequence- Mediated Mutations and Rearrangements. Genetics Society of America 156:477-488. 

12. Barrick, J.E., R.E. Lenski. 2009. Genome-wide Mutational Diversity in an Evolving Population of Escherichia coli. Cold Spring Harbor Symposia on Quantitative Biology LXXIV:119-129. 

13. Woods, R., D. Schneider, C.L. Winkworth, M.A. Riley, R.E. Lenski. 2006. Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proceedings of the National Academy of Sciences 103(24):9107-9112. 

14. Pelosi, L., L. Kuhn, D. Guetta, J. Garin, J. Geiselmann, R.E., Lenski, D. Schneider. 2006. Parallel Changes in Global Protein Profiles During Long-Term Experimental Evolution in Escherichia coli. Genetics Society of America 173:1851-1869.

15. Stanek, M.T., T.F. Cooper, R.E. Lenski. 2009. Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli. BMC Evolutionary Biology 302(9):1-13.

16. Cooper, V.S., D. Schneider, M. Blot, R.E. Lenski. 2001. Mechanisms Causing Rapid and Parallel Loses of Ribose Catabolism in Evolving Populations of Escherichia coli B. Journal of Bacteriology 183(9):2834-2841. 

17. Blount, Z.D., J.E. Barrick, C.J. Davidson, R.E. Lenski. 2012. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489:513-520. 

18. Van Hofwegen, D.J., C.J. Hovde, S.A. 2016. Minnich, Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA. Journal of Bacteriology 198(7):1022-1034.

19. Cooper, T.F., D.E. Rozen, R.E. Lenski. 2003. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proceedings of the National Academy of Sciences 100(3):1072-1077. 

20. Andersson S.G., Kurland C.G. 1998. Reductive evolution of resident genomes. Trends Microbiol 6: 263–268. 

21. Hottes, A.K., P.L. Freddolino, A. Khare, Z.N. Donnell, J.C. Liu, S. Tavazoie. 2013. Bacterial Adaptation through Loss of Function. PLOS Genetics. 9(7):e1003617-e1003617.

22. Koskiniemi, S., S. Sun, O.G. Berg, D.I. Andersson. 2012. Selection-Driven Gene Loss in Bacteria. PLOS Genetics 8(6):1-7.

23. Keightley P. and Lynch M., Toward a Realistic Model of Mutations Affecting Fitness, Evolution 57:683-685, 2003.

24. Gerrish P.J. and Lenski R., The fate of competing beneficial mutations in an asexual population, Genetica 102/203:127-144, 1998.

25. Lenski R.E., Phenotypic and Genomic Evolution during a 20,000-Generation Experiment with Bacterium Escherichia coli, Plant Breeding Reviews 24(2):225-265., 2004.

26. Eyre-Walker A, and Keightley P.D., The distribution of fitness effects of new mutations, Nature Review Genetics 8:610-618. 2007.

27. Ohta T., The nearly neutral theory of molecular evolution, Annual Review Ecological Systems 23:263-286, 1992.

28. Kimura M. and Ohta T., Theoretical Aspects of Population Genetics, Princeton University Press, Princeton, NJ, 26-31, 1971.

29. Gibson P. et al., Can Biological Information be Sustained by Purifying Natural Selection? In: Marks II R.J. et al., (eds) Biological Information – New Perspectives 232-263, 2013.

30. Kondrashov A.S., Contamination of the Genome by Very Slightly Deleterious Mutations: Why Have We Not Died 100 Times Over? Journal of Theoretical Biology 175, 583-594, 1995. 

31. Eyre-Walker A. and Keightley P., High genomic deleterious mutation rates in hominids, Nature 397:344-347, 1999.

32. Loewe L., Quantifying the genomic decay paradox due to Muller’s ratchet in human mitochondria DNA, Genetics Research 87:133-159, 2006.  

33. Muller H.J., The relation of recombination to mutational advance, Mutation Research, 1:2-9, 1964. 

34. Kimura M., Evolutionary rate at the molecular level, Nature 217:624-626, 1968.

35. Kondrashov A.S., Contamination of the Genome by Very Slightly Deleterious Mutations: Why Have We Not Died 100 Times Over? Journal of Theoretical Biology 175, 583-594, 1995.

​

SCENE 3 – PALEOANTHROPOLOGY: WHAT ABOUT "APE-MAN" FOSSILS?

 

Most of the Part 3 references listed below are cited in the book Contested Bones (available at ContestedBones.org): Christopher R. and Sanford J.C., Contested Bones, FMS Publications, 2019.

1. Haile-Selassie Y., Melillo S.M., and Su D.F., The Pliocene hominin diversity conundrum: Do more fossils mean less clarity? Proceedings of the National Academy of Sciences, 113:23, 6364-6371, 2016. 

2. White T., Paleoanthropology. Early hominids–diversity or distortion? Science 299:5615, 1994-1997, 2003.

3. Walker A. and Shipman P., The Wisdom of the Bones: In Search of Human Origins, Alfred A. Knoff Publishing, New York, 1996.

4. Meyer M.R. et al., Lucy's back: Reassessment of fossils associated with the A.L. 288-1 vertebral column, Journal of Human Evolution 85, 174-180, 2015.

5. Johanson D.C. and Taieb M., Plio-Pleistocene hominid discoveries in Hadar, Ethiopia, Nature 260:5549, 293-297, 1976.

6. Johanson D.C., Ethiopia Yields First "Family" of Early Man, National Geographic 770-881, 1976.

7. Johanson D.C. and White T.D., A Systematic Assessment of Early African Hominids, Science 203:4378, 321-30, 1979.

8. Johanson D.C. and Wong K., Lucy’s Legacy: The Quest for Human Origins, Crown Publishing Group, New York, p.145, 2009. "The former group, led by Jack Stern at Stony Brook University, sees A. afarensis as having spent lots of time climbing, whereas the terrestrials’ view, championed by Owen Lovejoy, holds that A. afarensis was essentially a ground-walking biped."

9. Ward C.V., Kimbel W.H., Johanson, D.C., Complete Fourth Metatarsal and Arches in the Foot of  Australopithecus afarensis, Science 331:750-753, 2011.

10. Häusler M. and Schmid P., Comparison of the pelves of Sts 14 and AL 288-1: implications for birth and sexual dimorphism in australopithecines, Journal of Human Evolution 29, 363-383, 1995.

11. Leakey M.D. and Hay R.L., Pliocene footprints in the Laetolil Beds at Laetoli, northern Tanzania, Nature 278:317-323, 1979.

12. Tuttle R.H. and Webb D.M., The Pattern of Little Feet, Am J Phys Anthropol 78(2):316, 1989.

13. Johanson D.C. and Edey M.A., Lucy: The Beginnings of Humankind, Simon & Schuster, New York, p.250, 1981. 

14. Leakey M., Disclosing the Past: An Autobiography, Rainbird Publishing Group Limited, New York, 1984. 

15. Richard G. Klein, Darwin and the recent African origin of modern humans, Proceedings of the National Academy of Sciences, USA 106:38, 2009.

16. Leakey R.E. and Lewin R., Origins Reconsidered: In Search of What Makes Us Human, Anchor Books (Doubleday), New York, p.114-116, 1992.

17. ​Donald C. Johanson & Maurice Taieb, Plio-Pleistocene hominid discoveries in Hadar, Ethiopia, Nature 260:293-297, 1976. 

18. Latimer B.M., Lovejoy C.O., Johanson D.C., and Coppens Y., Hominid Tarsal, Metatarsal, and Phalangeal Bones Recovered from the Hadar Formation: 1974-1977 Collections, American Journal of Physical Anthropology 57, 701-719, 1982.

19. Stern J.T. and Susman R.L., The Locomotor Anatomy of Australopithecus afarensis, American Journal of Physical Anthropology 60, 279-317, 1983. 

20. Susman R.L., Evolution of the Human Foot: Evidence from Plio-Pleistocene Hominids, Foot & Ankle, 3:6, 365-376, 1983.

21. Wong K., Footprints to Fill: Flat feet and doubts about makers of the Laetoli tracks, Scientific American August 1, 2005. 

22. Tuttle R.H., The Pitted Pattern of Laetoli Feet: Who or what walked on the ancient African plain? Natural History 3:90, 61-65, 1990. “We suggest that another species of Australopithecusor an anonymous genus of the Hominidae, with remarkably humanoid feet, walked at Laetoli.” 

23. Tuttle R.H., Webb D.M., and Baksh M., Laetoli Toes and Australopithecus afarensis, Human Evolution 6:3, 193-200, 1991.

24. Tuttle R.H., The Pitted Pattern of Laetoli Feet: Who or what walked on the ancient African plain? Natural History 3:90, p.61, 1990.  “If the G footprints were not known to be so old, we would readily conclude that there had been made by a member of our genus, Homo.”

25. Dalrymple G.B., 40Ar/36Ar Analyses of Historic Lava Flows, Earth and Planetary Science Letters 6:47-55, 1969.

26. Noble C.S. and Naughton J.J., Deep-ocean basalts: inert gas content and uncertainties in age dating, Science 162:265-267, 1968.

27. Dalrymple G.B. and Moore J.G., Argon 40: Excess in submarine pillow basalts from Kilaueau Volcano, Hawaii, Science 161:1132-1135, 1968.

28. Krummenacher D., Isotopic composition of Argon in modern surface volcanic rocks, Earth and Planetary Science Letters 8:109-117, 1970.

29. McDougall I. et al, Excess radiogenic argon in young subaerial basalts from the Auckland volcanic field, New Zealand, Geochemica et Cosmochimica Acta 33:1485-1520, 1969.

30. Esser R.P. et al., Excess Argon in melt inclusions in zero-age Anorthoclase feldspar from Mt Erebus, Antarctica, as revealed by 40Ar/39Ar method, Geochimica et Cosmochimica Acta 61:3789-3801, 1997.

31. Snelling A., The Cause of Anomalous Potassium-Argon "Ages" for Recent Andesite Flows at Mt. Ngauruhoe, New Zealand, and the Implications for Potassium-Argon "Dating". Published in: Proceedings of the Fourth International Conference on Creationism, R.E. Walsh (editor), pp. 503–525.

32. Leakey L.S.B. et al., A new species of the genus Homo from Olduvai Gorge, Nature 202:7-9, 1964.

33. Rightmire G.P., Variation among early Homo crania from Olduvai Gorge and the Koobi Fora Region, American Journal of Physical Anthropology 90:1-33, 1993.

34. Susman R.L., Evolution of the human foot: Evidence from Plio-Pleistocene hominids, Foot and Ankle 3(6):365-376, 1983.

35. Davis P.R., Hominid fossils from Bed I, Olduvai Gorge, Tanganyika: A tibia and fibula, Nature 201: 967-968, 1964.

36. Lewin R., The Earliest "Humans" Were More like Apes, Science 236:1061-1063, May 1987.

37. Wood B., Human evolution: Fifty years after Homo habilis, Nature 508:7494:31-33, 2014.

38. Brown F. et al., Early Homo erectus skeleton from west Lake Turkana, Kenya, Nature 316:788-792, 1985.

39. Tattersall I. and Schwartz J., Extinct Humans, Westview Press, New York, p.132, 2000. 

40. Wolpoff M.H. et al., Modern Homo sapiens Origins: A General Theory of Hominid Evolution Invoking the Fossil Evidence from East Asia; in Smith F.H. and Spencer F. (eds), The Origins of Modern Humans, Alan R. Liss, New York, pp.465-466, 1984.

41. Lasker G.W., Physical Anthropology, Holt, Rinehart and Winston, Inc., New York, 1973.

42. Bednarik R.G., Exograms, Rock Art Research 31(1):47-62, 2014.

43. Norwood M.J. et al., Fission-track ages of stone tools and fossils on the east Indonesian island of Flores, Nature 392:173-176, 1998.

44. Trinkaus E., Pathology and posture of the La Chapelle-aux-Saints Neandertal, American Journal of Physical Anthropology 67:19-41, 1985.

45. Smithsonian National Museum Natural History on La Chapelle-aux-Saints reconstruction, last updated 30 March 2016: http://humanorigins.si.edu/evidence/human-fossils/fossils/la-chapelle-aux-saints

46. Straus W.L. and Cave A.J.E., Pathology and Posture of Neandertal Man, Quarterly Review of Biology 32:348-363, 1957.

47. John R., Missing Links: In Search of Human Origins, Oxford University Press, 2011.

48. Johanson D.C. and Edey M.A., Lucy: The Beginnings of Humankind, Simon & Schuster, New York, p.20, 1981. 

49. Trinkaus E., Hard Times Among the Neandertals, Natural History 87(10):58-63, December, 1978.

50. Conard N.J. et al., Unexpected recent dates for human remains from Vogelherd, Nature 430:198-201, 2004. 

51. Hoffmann D.L. et al., U-Th dating of carbonate crusts reveals Neandertal origin of Iberian cave art, Science 359, 912-915, 2018.

52. Turk M. et al., Neanderthal Flute from Divje Babe I: Old and New Findings, Institute Archaeological Slovenia 251-265, 2011.

53. Rifkin R.F., Processing ochre in the Middle Stone Age: testing the inference of prehistoric behaviours from actualistically derived experimental data, Journal of Anthropological Archaeology 31(2):174-195, 2012. 

54. Radovčić D. et al., Evidence for Neandertal Jewelry: Modified White-Tailed Eagle Claws at Krapina, 

PLoS ONE 10(3):e0119802, 2015

55. Trinkaus E. et al., Comparative morphology and paleobiology of Middle Pleistocene human remains from Bau de l’Aubesier, Vaucluse, France, Proceedings of the National Academy of Sciences, USA 98(20):11097-11102, 2001.

56. Rendu W. et al., Evidence supporting an intentional Neandertal burial at La Chapelle-aux-Saints, 

Proceedings of the National Academy of Sciences 111(1):81-86, 2014.

57. Arsuaga J.L., The Neanderthal’s Necklace: In Search of the First Thinkers, Trans. A. Klat., Four Walls Eight Windows Publishing, New York, 2002.

58. Green R.E. et al., A Draft Sequence of the Neandertal Genome, Science 328(5979):710-722, 2010.

59. Pääbo S., Neanderthal Man: In Search of Lost Genomes, Basic Books, New York, p.237, 2014. “Many would say that a species is a group of organisms that can produce fertile offspring with each other and cannot do so with members of other groups. From that perspective we had shown that Neanderthals and modern humans were the same species.”

60. Small M.F., Human Family Tree Now a Tangled, Messy Bush, 31 August, 2007. http:/​/​www.​livescience.​com/​7376-human-family-tree-tangled-messy-bush.​html

61. Wood B., Origins and evolution of the genus Homo, Nature 355(6363): 783-790, 1992.

62. Wood B., Welcome to the Family, Scientific American 311(3):42-47, 2014.

 

SCENE 4 – GENETICS: EVIDENCE FOR ADAM AND EVE?

 

1. Kronenberg Z.N. et al., High-resolution comparative analysis of great ape genomes, Science 360:6393, 2018.

2.  Hughes J.F.  et al., Chimpanzee and Human Y Chromosomes Are Remarkably Divergent in Structure and Gene Content, Nature 463(7280):536-9, 2010.

3. Cohen J., Relative Differences: The Myth of 1%, Science 316:1836, NewsFocus June 9 2007.

4. Preuss T.M., Human brain evolution: from gene discovery to phenotype discovery, Proceedings of the National Academy of Sciences, USA 109(Suppl 1):10709-10716, 2012.

5. Wildman D.E. et al., Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo, Proceedings of the National Academy of Sciences, USA 100:7181–7188, 2003.

6. Liu G. et al., Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome, Genome Research 13:358–368, 2003.

7. Ebersberger I. et al., Genomewide comparison of DNA sequences between humans and chimpanzees, American Journal of Human Genetics 70:1490–1497, 2002.

8. Nielson R. et al., A scan for positively selected genes in the genomes of humans and chimpanzees, PLOS Biology, 3(6):e170, 2005.

9. Watanabe, A.F. et al., DNA sequence and comparative analysis of chimpanzee chromosome 22, Nature

429:382–388, 2004.

10. Jeffrey T. and J. Bergman, Genomic monkey business—estimates of nearly identical human–chimp DNA similarity re-evaluated using omitted data, Journal of Creation 26(1):94–100, April 2012.

11. The Chimpanzee Sequencing and Analysis Consortium, Initial sequence of the chimpanzee genome and comparison with the human genome, Supplementary Tables S8, S9 Nature 437:69–87, 2005.

12. Tomkins J.P., Comparison of 18,000 De Novo Assembled Chimpanzee Contigs to the Human Genome Yields Average BLASTN Alignment Identities of 84%, Answers Research Journal 11, 205–209, 2018.

13. Buggs R., How Similar Are Human and Chimpanzee Genomes? 2018. http://richardbuggs.com/index. php/2018/07/14/how-similar-are-human-and-chimpanzee-genomes/

14. Sanford J. et al., The Waiting Time Problem in a Model Hominin Population, Theoretical Biology and Medical Modelling 12:18, 2015.

15. Lynch M., Abegg A. The rate of establishment of complex adaptations, Molecular Biology and Evolution 27:6, 1404–14, 2010.

16. Durrett R. and Schmidt D., Waiting for regulatory sequences to appear, The Annals of Applied Probability 17:1, 1–32, 2007. 

17. Cann R.L., Stoneking M., and Wilson A.C., Mitochondrial DNA and human evolution, Nature 325:6099, 31-36, 1987.

18. Hammer M.F. et al., The Geographic Distribution of Human Y Chromosome Variation, Genetics 145:787-805, 1997.

19. Sayres M.A.W. et al., Natural Selection Reduced Diversity on Human Y Chromosomes, PLOS Genetics 10:1, e1004064, 2014. “The human Y chromosome exhibits surprisingly low levels of genetic diversity.”

20. Gibbons A., Y chromosome Shows that Adam was an African, Science Research News 278:5339, 804-805, 1997.

21. Reich D. et al., Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes, PLOS Genetics, 11(11): e1005550, 2015.

22. C. Ewan, DNA clock proves tough to set, Nature, 519:139-140, 12 March 2015. 

23. Pulquério M.J.F. and Nichols R.A., Dates from the molecular clock: how wrong can we be? TRENDS in Ecology and Evolution, 22(4):180-4, 2007.

24. Xue Y. et al., Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree, Current Biology 19:1453-1457, 2009.

25. Madrigal L. et al., High Mitochondrial Mutation Rates Estimated From deep-rooting Costa Rican pedigrees, American Journal of Physical Anthropology 148:327-333, 2012. 

26. Hagelberg E., Recombination or mutation rate heterogeneity? Implications for Mitochondrial Eve, TRENDS in Genetics 19:2, 84-90, 2003.

27. McEvoy B.P. et al., Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs, Genome Research 21:821-829, 2011. 

28.  Stringer C., Lone Survivors: How we came to be the only Humans on Earth, Times Books, Henry Holt and Company LLC, New York, 2013.

29. Kingman, J.F.C., Origins of the coalescent: 1974–1982, Genetics 156:1461–1463, 2000.

30. Harpending H.C. et al., Genetic traces of ancient demography, Proceedings of the National Academy of Sciences, USA 95:1961–1967, 1998.

31. ABC News, One twin’s white, the other’s black—twins’ parents both have white mothers, black fathers, 19 September 2006. https://abcnews.go.com/GMA/story?id=1813509

32. Wolpoff M.H. et al., Multiregional, Not Multiple Origins, American Journal of Physical Anthropology, 112:129–136, 2000.

33. Cameron S.C. and Wycoff, S.M., The destructive nature of the term race: Growing beyond a false paradigm, Journal of Counseling & Development, 76(3):277-285, 1998.

34. Jorde L.B. and Wooding S.P., Genetic variation, classification and ‘race’, Nature Genetics 36(11):528-533, 2004.

35. Rampino M.R., Volcanic winter in the Garden of Eden: The Toba supereruption and the late Pleistocene human population crash, Chapter in Special Paper of the Geological Society of America, 345:71-82, January 2000.

36. O'Brien S.J. et al., The cheetah in genetic peril, Scientific American 254(May):84-92, 1986.

37. Carter R.W. et al., An overview of the independent histories of the human Y chromosome and the human mitochondrial chromosome, In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 133–151, 2018. “The most common Y chromosome haplotype in Africa today (E) apparently arose outside of Africa” (see references below: Karmin et al., 2015; Poznik et al., 2015).

38. Karmin M. et al., A recent bottleneck of Y chromosome diversity coincides with a global change in culture, Genome Research 25:459–466, 2015.

39. Poznik G.D. et al., Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences, Nature Genetics 48:593–599, 2016.

40. DeGiorgio M. et al., Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa, Proceedings of the National Academy of Sciences, USA 106(38):16057-16062, 2009.