Shapiro, J.A. 1967. The structure of the galactose operon in Escherichia coli K-12. Doctoral dissertation, University of Cambridge.

Bukhari, A.I., J.A. Shapiro, and S.L. Adhya (eds.) 1977. DNA Insertion Elements, Plasmids and Episomes, Cold Spring Harbor Laboratory.

Shapiro, J.A. (ed.) 1983. Mobile Genetic Elements, Academic Press.

Shapiro, J.A. and M. Dworkin (eds.). 1997. Bacteria as Multicellular Organisms, Oxford University Press.

Shapiro, J.A. 2011. Evolution: A View from the 21st Century. FT Press Science (ISBN-10: 0-13-278093-3; ISBN-13: 978- 0-13-278093-3)

Shapiro, James A. 2022d. Evolution: A View from the 21st Century. Fortified. (2nd Edition). Chicago IL, USA: Cognition Press

Complete list of published articles:

Shapiro, J.A. 1966. The chromosomal location of the gene determining uridine diphosphoglucose formation in Escherichia coli K-12. J. Bacteriol. 92, 518.

Adhya, S. and J.A. Shapiro. 1969. The galactose operon of E. coli K-12. I. Structural and pleiotropic mutants of the operon. Genetics 62, 231-248. (Reprinted in Beckwith J and Silhavy TJ. The Power of Bacterial Genetics: A Literature-Based Course. Cold Spring Harbor Laboratory, 1992)

Shapiro, J.A. and S. Adhya. 1969. The galactose operon of E. coli K-12. II. A deletion analysis of operon structure and polarity. Genetics 62, 249.

Shapiro, J.A. 1969. Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli. J. Mol. Biol. 40, 93-105. (Reprinted in Beckwith J and Silhavy TJ. The Power of Bacterial Genetics: A Literature-Based Course. Cold Spring Harbor Laboratory, 1992)

Shapiro, J., L. MacHattie, L. Eron, G. Ihler, K. Ippen, J. Beckwith, R. Arditti, W. Reznikoff and R. MacGillivray. 1969. The isolation of pure lac operon DNA. Nature (London) 224, 768.

Ippen, K., J.A. Shapiro and J.R. Beckwith. 1971. Transposition of the lac region to the gal region of the Escherichia coli chromosome: Isolation of llac transducing bacteriophages. J. Bacteriol. 108, 5.

Shapiro, J., D. Dean and H.O. Halvorson. 1974. Low frequency specialized transduction with Bacillus subtilis bacteriophage F105. Virology62, 393-403.

Nieder, M. and J. Shapiro. 1975. Physiological function of the Pseudomonas putida PpG6 (Pseudomonas oleovorans) alkane hydroxylase: monoterminal oxidation of alkanes and fatty acids. J. Bacteriol. 122, 93-98.

Grund, A., J. Shapiro, M. Fennewald, P. Bacha, J. Leahy, K. Markbreiter, M.Nieder and M. Toepfer. 1975. Regulation of alkane oxidation in Pseudomonas putida. J. Bacteriol. 123, 546-556.

Benson, S. and J. Shapiro. 1975. Induction of alkane hydroxylase protein by unoxidized alkane in Pseudomonas putida. J. Bacteriol. 123, 759-760.

Benson, S. and J. Shapiro. 1976. Plasmid-determined alcohol dehydrogenase in alkane-utilizing strains of Pseudomonas putida. J. Bacteriol. 126, 794-798.

Shapiro, J.A., S. Benson, M. Fennewald, A. Grund and M. Nieder. 1976. Genetics of alkane utilization. In Microbiology 1976 (D. Schlessinger,ed.), American Society for Microbiology, pp. 568-571.

Shapiro, J.A. 1976. Observations on lysogeny in the glutamic acid bacteria. Appl. Environ. Microbiol. 32, 179-182.

Benedik, M., M. Fennewald and J. Shapiro. 1977. Transposition of a beta -lactamase locus from RP1 in P. putida degradative plasmids. J. Bacteriol. 129, 809-814.

Shapiro, J. and P. Sporn. 1977. Tn402: A new transposable element determining trimethoprim resistance that inserts in bacteriophage l. J. Bacteriol. 129, 1632-1635.

Shapiro, J.A. 1977. DNA insertion elements and the evolution of chromosome primary structure. Trends in Biochem. Sci. 2, 622-627.

Benson, S., M. Fennewald, J. Shapiro and C. Huettner. 1977. Fractionation of inducible alkane hydroxylase activity in P. putida and characterization of hydroxylase- negative plasmid mutations. J. Bacteriol. 132, 614-621.

Fennwald, M. and J. Shapiro. 1977. Regulatory mutations of the Pseudomonas plasmid alk regulon. J. Bacteriol. 132, 622-627.

Contributions to DNA Insertion Elements, Plasmids and Episomes (1977):

Fennewald, M., S. Benson and J. Shapiro. 1978. Plasmid-chromosome interactions in the
Pseudomonas alkane system. In Microbiology 1978 (D. Schlessinger, ed.) American Society for Microbiology, pp. 170-173.

Fennwald, M., W. Prevatt, R. Meyer and J. Shapiro. 1978. Isolation of IncP-2 plasmid DNA from Pseudomonas aeruginosa. Plasmid 1, 164-173.

MacHattie, L. and J. Shapiro. 1978. Chromosomal integration of bacteriophage lambda by means of a DNA insertion element. Proc. Nat. Acad. Sci. U.S.A. 75, 1490-1494.

Benson, S. and J. Shapiro. 1978. TOL is a broad host-range plasmid. J. Bacteriol. 135, 278-280.

Shapiro, J. and L. MacHattie. 1979. Integration and excision of lambda prophage mediated by the IS1 element. Cold Spr. Harb. Symp. Quant. Biol. 43, 1135-1142.

Meyer, R., G. Boch, and J. Shapiro. 1979. Transposition of DNA inserted into deletions of the Tn5 kanamycin resistance element. Molec. Gen. Genet. 171, 7-13.

Shapiro, J. 1979. A molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc. Nat. Acad. Sci. U.S.A. 76, 1933-1937. (Reprinted in Beckwith J and Silhavy TJ., 1992, The Power of Bacterial Genetics: A Literature-Based Course, Cold Spring Harbor Laboratory, and in Miller, JH, 1996, Discovering Molecular Genetics: A case study course with problems and scenarios, Cold Spring Harbor Laboratory)

Shapiro, J., M. Fennewald and S. Benson. 1979. Plasmid-determined alkane oxidation in Pseudomonas. In Genetics of Industrial Microorganisms (O. Sebek, ed.), American Society for Microbiology, pp. 147-153.

Fennewald, M. and J. Shapiro. 1979. Transposition of Tn7 in P. aeruginosa and isolation of alk::Tn7 mutations. J. Bacteriol. 136, 264-269.

Fennewald, M., S. Benson, M. Oppici and J. Shapiro. 1979. Insertion element analysis and mapping of the Pseudomonas plasmid alk regulon. J. Bacteriol. 139, 940-952.

Benson, S., M. Oppici, J. Shapiro and M. Fennewald. 1979. Regulation of membrane peptides by the Pseudomonas plasmid alk regulon. J. Bacteriol. 140, 754-762.

Shapiro, J., S. Benson and M. Fennewald. 1980. Genetics of plasmid-determined hydrocarbon oxidation. In Plasmids and Transposons: Environmental Effects and Maintenance Mechanisms (C. Stuttard and K. Rozee, eds.), Academic Press, New York, pp. 1-19.

Shapiro, J. 1980. A model for the genetic activity of transposable elements involving DNA replication. In Plasmids and Transposons: Environmental Effects and Maintenance Mechanisms (C. Stuttard and K. Rozee, eds.), Academic Press, New York, pp. 229-247.

Meyer, R. and J. Shapiro. 1980. Genetic organization of the broad host-range IncP-1 plasmid R751. J. Bacteriol. 143, 1362-1373.

Cohen, S.N. and J.A. Shapiro. 1980. Transposable genetic elements. Sci. American 242 (2), 40-49.

Krylov, V.N., V.G. Bogush and J.A. Shapiro. 1980. Pseudomonas aeruginosa phages whose DNA structure is similar to Mu1 phage DNA. I. General description, localization of endonuclease-sensitive sites in DNA, and the structure of D3112 phage homoduplexes. Genetika 16, 824-832 (in Russian).

Muster, C.J. and J.A. Shapiro. 1981. Recombination involving transposable elements: On replicon fusion. Cold. Spr. Harb. Symp. Quant. Biol. 45, 239-242.

Shapiro, J.A., A. Charbit, S. Benson, M. Caruso, R. Laux, R. Meyer and F. Banuett. 1981. Perspectives for genetic engineering of hydrocarbon oxidizing bacteria. In Trends in the Biology of Fermentations for Fuels and Chemicals (A. Hollaender et al, eds.), Plenum Press, New York, pp. 243-272.

Muster, C.J., L.A. MacHattie and J.A. Shapiro. 1981. Transposition and rearrangements in plasmid evolution. In Molecular Biology, Pathogenicity and Ecology of Bacterial Plasmids (S.B. Levy, R.C. Clowes and E.L. Koenig, eds.), Plenum Press, New York, pp. 349-358.

Meyer, R., R. Laux, G. Boch, M. Hinds, R. Bayly and J.A. Shapiro. 1982. Broad host-range IncP-4 plasmid R1162: Effects of deletions and insertions on plasmid maintenance and host range. J. Bacteriol. 152, 140-150.

Caruso, M. and J.A. Shapiro. 1982. Interactions of Tn7 and temperate phage F116L of Pseudomonas aeruginosa. Mol. Gen. Genet. 188, 292-298.

Shapiro, J.A. 1982. Changes in gene order and gene expression. Natl. Cancer Inst. Monograph 60, 87-110.

Shapiro, J.A. and B. Cordell. 1982. Eukaryotic mobile and repeated genetic elements. Biol. Cell. 43, 31-54.

Shapiro, J.A. 1982. Mobile genetic elements and reorganization of prokaryotic genomes. In Genetics of Industrial Microorganisms, 1982 (Y. Ikeda and T. Beppu, eds.), Kodansha, Tokyo, pp. 9-32.

Shapiro, J.A. 1983. Variation as a genetic engineering process. In Evolution from Molecules to Men (D.S. Bendall, ed.), Cambridge University Press, Cambridge, pp. 253-270.

Shapiro, J.A. 1983. Letter to Nature Vol 303 19 May 1983 p.196

Muster, C.J., L.A. MacHattie and J.A. Shapiro. 1983. The plCM system: Observations on the roles of transposable elements in the formation and breakdown of plasmids derived from bacteriophage l replicons. J. Bacteriol. 153, 976-990.

Muster, C.J., J.A. Shapiro and L.A. MacHattie. 1983. Recombination involving transposable elements: The role of target molecule replication in Tn1DAp-mediated replicon fusion. Proc. Nat. Acad. Sci. U.S.A. 80, 2314-2317.

Shapiro, J.A., D.J. Owen, M. Kok, and G. Eggink. 1983. Pseudomonas hydrocarbon oxidation. In Genetic Control of Environmental Pollutants (G. Omenn and A. Hollaender, eds.), Plenum Press, New York.

Rehmat, S. and J.A. Shapiro. 1983. Insertion and replication of the Pseudomonas aeruginosa mutator phage D3112. Molec. Gen. Genet. 192, 416-423.

Hauer, B., and J.A. Shapiro. 1984. Control of Tn7 transposition. Molec. Gen. Genet. 194, 149-158.

Burck, C.J., J.A. Shapiro and B. Hauer. 1984. The plambdaCM system: Phage immunity-specific incompatibility with IncP-1 plasmids. Mol. Gen.Genet. 194, 340-342.

Shapiro, J.A.1984a. Observations on the formation of clones containing araB-lacZ cistron fusions. Molec. Gen. Genet. 194, 79-90.

Shapiro, J.A. 1984b. Transposable elements, genome reorganization and cellular differentiation in Gram-negative bacteria. Symp. Soc. Gen. Microbiol. 36 (Part 2), 169-193.

Shapiro, J.A. 1984c. The use of Mudlac transposons as tools for vital staining to visualize clonal and non-clonal patterns of organization in bacterial growth on agar surfaces. J. Gen. Microbiol. 130, 1169-1181.

Shapiro, J.A. and P. Brinkley. 1984. Programming of DNA rearrangements involving Mu prophages. Cold Spr. Harb. Symp. Quant. Biol. 49, 313-320.

Owen, D.J., G. Eggink, B. Hauer, M. Kok, D.L. McBeth, Y.L. Yang and J.A. Shapiro. 1984.Physical structure, genetic content and expression of the alkBAC operon. Molec. Gen. Genet. 197, 373-383.

McBeth, D.L. and J.A. Shapiro. 1984. Reversal by DNA amplifications of an unusual mutation blocking alkane and alcohol utilization in Pseudomonas putida. Molec. Gen. Genet. 197, 384-391.

Shapiro, J.A. 1985a. Photographing bacterial colonies. A.S.M. News 51, 62-69. (Reprinted in Miller JH. A Short Course in Bacterial Genetics. Cold Spring Harbor Laboratory, 1992).

Shapiro, J.A. 1985b. Mechanisms of DNA reorganization in bacteria. Int. Rev. Cytol. 93, 25-56.

Shapiro, J.A. 1985c. Intercellular communication and genetic change in bacteria. In Halvorson, H.O., D. Pramer & M. Rogul (eds.), Engineered Organisms in the Environment: Scientific Issues, American Society for Microbiology, pp. 63-69.

Shapiro, J.A. 1985d. Scanning electron microscope study of Pseudomonas putida colonies. J. Bacteriol. 164, 1171-1181.

Shapiro, J.A. 1986. Control of Pseudomonas putida growth on agar surfaces. In The Bacteria, vol. X (J.R. Sokatch, ed.), Academic Press, New York, pp. 27-69.

Shapiro, J.A. 1987a. Organization of Developing E. coli colonies viewed by scanning electron microscopy. J. Bacteriol. 197, 142-156.

Shapiro, J.A. 1987b. Some lessons of phage Mu. In The Bacteriophage Mu (N. Symonds, A. Toussaint, P van de Putte and M. Howe, eds.), Cold Spring Harbor Laboratory, pp. 251-258.

Shapiro, J.A. 1987c. Eukaryotic transposable elements as mutagenic agents: a meeting review. Genes and Development 1, 747-749.

Shapiro, J.A. 1988a. What transposable elements do in bacteria. In Eukaryotic Transposable Elements as Mutagenic Agents, Banbury Report 30, 3-16.

Shapiro, J.A. and N.P. Higgins. 1988. Variation of s -galactosidase expression from Mudlac elements during the development of E. coli colonies. Annales de l'Institut Pasteur 139, 79-103.

Shapiro, J.A. 1988b. Bacteria as multicellular organisms. Scientific American 256 (6), 82-89.

Shapiro, J.A. and N.P. Higgins. 1989. Differential activity of a transposable element in E. coli colonies. J. Bacteriol. 171, 5975-5986.

Shapiro, J.A. and C. Hsu. 1989. E. coli K-12 cell-cell interactions seen by time-lapse video. J. Bacteriol. 171, 5963-5974.

Shapiro, J.A. and D. Leach. 1990. Action of a transposable element in coding sequence fusions. Genetics 126, 293-299.

Shapiro, J.A. and D. Trubatch. 1991. Sequential events in bacterial colony morphogenesis. Physica D 49, 214-223.

Shapiro, J.A. 1991a. Multicellular behavior of bacteria. ASM News57, 247-253 (meeting report).

Shapiro, J.A. 1991b. Genomes as smart systems. Genetica 84, 3-4.

Shapiro, J.A. 1992a. Concentric rings in Escherichia coli colonies. In Oscillations and Morphogenesis, L. Rensing (ed.), Marcell Dekker, pp 297 - 310.

Shapiro, J.A. 1992b. Natural genetic engineering in evolution. Genetica86, 99-111(reprinted in J.F. McDonald (ed.), 1993, Transposable Elements and Evolution, Kluwer, Dordrecht).

Shapiro, J.A. 1992c. Kernels and colonies: The challenge of pattern. In The Dynamic Genome, N. Federoff and D. Botstein (eds), Cold Spring Harbor Press, pp. 213-221.

Shapiro, J.A. 1992d. Differential action and differential expression of E. coli DNA polymerase I during colony development. J. Bacteriol. 174, 7262-7272.

Shapiro, J.A. 1992e. Barbara McClintock, 1902-1992. BioEssays14, 791-792.

Shapiro, J.A. 1992f. Pattern and control in bacterial colonies. Science Progress 76, 399-424.

Shapiro, J.A. 1993a. A role for the Clp protease in activating Mu-mediated DNA rearrangements. J. Bacteriol. 175, 2625-2631.

Shapiro, J.A. 1993b. Natural genetic engineering of the bacterial genome. Curr. Opin. Genet. Devel. 3, 845-848.

Shapiro, J.A. 1994b. The smallest cells have important lessons to teach. In Cosmic Beginnings and Human Ends, C. Matthews, R. Varghese and D. Steele (eds), Open Court Publishing, pp. 205-224.

Maenhaut-Michel, G. & Shapiro, J.A. 1994c. The roles of starvation and selective substrates in the emergence of araB-lacZ fusion clones. EMBO J. 13, 5229-5239.

Shapiro, J.A. 1994d. Adaptive mutation. Science 265, 94 (letter).

Shapiro, J.A. 1995a. The discovery and significance of mobile genetic elements. In Mobile Genetic Elements - Frontiers in Molecular Biology, D.J. Sherratt (ed.), IRL Press, Oxford, pp. 1-17.

Shapiro, J.A. 1995b. Adaptive mutation: Who's really in the garden? Science 268, 373-4.

Shapiro, J.A. 1995c. The significances of bacterial colony patterns. Bioessays 17, 597-607.

Shapiro, J.A. 1995d. Adaptive mutation: The debate goes on. Science 269, 286-288 (letter).

Rauprich,O., M. Matsushita, K. Weijer, F. Siegert, S. Esipov, and J.A. Shapiro. 1996. Periodic phenomena in Proteus mirabilis swarm colony development. J. Bacteriol. 178, 6525-6538.

James A. Shapiro. 1996. "Darwin's Black Box: The Biochemical Challenge to Evolution."  (book review) National Review, Sep 16, 1996 v48 n17 p62(4)

Shapiro, J.A. 1997a. Multicellularity is the rule, not the exception: Lessons from E. coli colonies. In Shapiro, J.A. and Dworkin, M. (eds.). Bacteria as Multicellular Organisms, Oxford University Press, pp. 14-49.

Shapiro, J.A. 1997. A third way [alternative to Darwinism & Creationism]. Boston Review 22 (1), 32-33.

Shapiro, J.A. 1997b. Genome organization, natural genetic engineering, and adaptive mutation. Trends in Genetics 13, 98-104.

Maenhaut-Michel, G., C.E. Blake, D.R.F. Leach and J.A. Shapiro. 1997. Different structures of selected and unselected araB-lacZ fusions. Molec. Micro. 23, 1133-1146.

Esipov, S. and J.A.Shapiro. 1998. Kinetic model of Proteus mirabilis swarm colony development. J. Math. Biol. 36, 249-268.

Shapiro, J.A. 1998. Thinking about bacterial populations as multicellular organisms. Ann. Rev. Microbiol. 52, 81-104.

Shapiro, J.A. 1999. Natural genetic engineering, adaptive mutation & bacterial evolution, in Microbial Ecology and Infectious Disease, E. Rosenberg (ed.), ASM Press, Washington, pp. 259-275.

Shapiro, J.A. 1999. Genome system architecture and natural genetic engineering in evolution. In Molecular Strategies for Biological Evolution, L. Caporale, ed., Annal. NY Acad. Sci. 870, 23-35.

Shapiro, J.A. 1999. Views about evolution are evolving. ASM News 65 (4) (meeting report).

Lamrani. S., C. Ranquet, M.-J. Gama, H. Nakai, J.A. Shapiro, A. Toussaint and G. Maenhaut-Michel. 1999. Starvation-induced Mucts62-mediated Coding Sequence Fusion: Roles for ClpXP, Lon, RpoS and Crp. Molec. Microbiol. 32, 327-343.

Newman, D.L. and J.A. Shapiro. 1999. Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development. Molec. Microbiol. 33, 18-32.

Shapiro, J.A. 1999. Transposable elements as the key to a 21st Century view of evolution. Genetica 107 (1/3):171-179. (reprinted in Georgia Genetics Review I: Transposable Elements & Genome Evolution, edited by John F. McDonald, Kluwer, 2000)

Shapiro, J.A. 2002. "Genome system architecture and natural genetic engineering." In Evolution as Computation, L.F. Landweber and E. Winfree (eds.), Springer, Berlin, pp 1-14.

Shapiro, J.A. 2002. Peering into the Natural Genetic Engineering Toolbox (book review). Cell 111(4) 464-465.

Shapiro, J.A. 2002. A 21st Century View of Evolution. J. Biol. Phys. 28: 1-20. (PROCEEDINGS of the 4th International Conference on Biological Physics, Kyoto, Japan, July 30 - August 3, 2001)

Shapiro, J.A. 2002. Genome Organization and Reorganization in Evolution: Formatting for Computation and Function. In From Epigenesis to Epigenetics: The Genome in Context, L.Van Speybroack, G. Van de Vijver, and D. de Waele (eds.), Ann. NY Acad Sci 981, 111-134.

Shapiro JA. 2002. Repetitive DNA, genome system architecture and genome reorganization. Res Microbiol. 153:447-53.

Shapiro JA and Sternberg Rv. 2005. Why repetitive DNA is essential to genome function. Biol. Revs. 80: 227-50.

Sternberg, R.v. and Shapiro, J.A. 2005. How repeated retroelements format genome function. Cytogenet. Genome Res., 110:108-116.

Shapiro, JA. 2005. A 21st Century View Of Evolution: Genome System Architecture, Repetitive DNA, And Natural Genetic Engineering. Gene 345: 91-100 (special issue on "Structural approaches to sequence evolution: Molecules, networks, populations").

Shapiro JA. 2005. Retrotransposons and regulatory suites. BioEssays 27, 122-125.

Shapiro JA. 2005. Thinking about evolution in terms of cellular computing. Natural Computing, 4, 297-324.

Shapiro JA. 2006. Genome informatics: The role of DNA in cellular computations. Biological Theory 1(3): 288-301.

Shapiro JA. 2007. Bacteria are small but not stupid: cognition, natural genetic engineering and sociobacteriology. Studies in History and Philosophy of Biological and Biomedical Sciences 38 (2007) 807–819.

Shapiro JA. 2009. Letting E. coli teach me about genome engineering, Genetics 183: 1205–1214

Shapiro JA. 2009. Revisiting the central dogma in the 21st Century. Ann NY Acad Sci 1178: 6-28. Paper presented at a symposium on Natural Genetic Engineering – Natural Genome Editing, July 2-6, 2008, organized by Guenther Witzany.

Shapiro JA. 2010. Mobile DNA and evolution in the 21st Century. Mobile DNA, 1:4.

Shapiro JA. 2012. Reply to Larry Moran’s RNCSE review of Evolution: A View from the 21st Century. Reports of the National Center for Science Education, in press.

Shapiro JA. 2013. Rethinking the (Im)Possible in Evolution. Progress in Biophysics and Molecular Biology 111 (2–3), Pages 92–96, April 2013,

special issue on “Conceptual Foundations of Systems Biology."

Shapiro JA. 2013. How Life Changes Itself: The Read-Write (RW) Genome. Physics of Life Reviews 10:287-323.

Figures and fully referenced tables at

Shapiro JA 2013. Implications of the RW Genome view (responses to published comments).
Physics of Life Reviews 10:347-350.

Partner ID: 1376 Partner ID: 1376

Shapiro JA. 2014. The Special Character of Barbara McClintock's Nobel Prize Address. In Kass, Lee B. (Ed.) Perspectives on Nobel Laureate Barbara McClintock’s publications (1926-1984): A Companion Volume [The Internet-First University Press]

Shapiro JA 2014. Constraint and Opportunity in Genome Innovation. RNA Biology 11(3):1-11 (March 1, 2014, special issue dedicated to Carl Woese) 

Shapiro JA. 2014. The Physiology of the Read-Write (RW) Genome.

2014 Jun 1;592(Pt 11):2319-41. doi: 10.1113/jphysiol.2014.271130

(Focus issue of Journal of Physiology on “The integration of evolutionary biology with physiological science.”).


Shapiro JA. 2014. Epigenetic control of mobile DNA as an interface between experience and genome change. Frontiers in Genetics 25, Focus Topic on “Epigenetics as a deep intimate dialogue between host and symbionts,”

Shapiro JA 2014. Bringing Cell Action into Evolution
, in "Earth, Life & System" (Fordham University Press), in press (lecture to the "Earth, Life & System" Interdisciplinary Symposium on Environment and Evolution in Honor of Lynn Margulis, Texas Tech University, September 13-14, 2012).

Shapiro, J. A. (2014). The RW Genome, Epigenetics, Evolution and Pregnancy. 20th WORLD CONGRESS ON CONTROVERSIES IN OBSTETRICS, GYNECOLOGY & INFERTILITY (COGI), Paris, Monduzzi Editoriale (Milan).

Shapiro, J.A. (2016). The Basic Concept of the Read-Write Genome: Mini-Review on Cell-Mediated DNA Modification
. Biosystems 
Volume 140, February 2016, Pages 35–37 doi:10.1016/j.biosystems.2015.11.003.

Shapiro JA 2016. Nothing in Evolution Makes Sense Except in the Light of Genomics. Biology 5(2), 27; doi:10.3390/biology5020027 (Special Issue "Beyond the Modern Evolutionary Synthesis- what have we missed?").


Shapiro, J. A. (2017). "Exploring the read-write genome: mobile DNA and mammalian adaptation." Crit Rev Biochem Mol Biol 52(1): 1-17.

Shapiro, J.A. (2017). Biological Action in Read-Write Genome Evolution. Interface Focus (Royal Society), 7(5):20160115. doi: 10.1098/rsfs.2016.0115


Shapiro, J.A. (2017), Living Organisms Author Their Read-Write Genomes in Evolution. Biology (Basel)6(4).,

Shapiro, J. A. (2019). "No genome is an island: toward a 21st century agenda for evolution." Ann N Y Acad Sci 1447(1): 21-52.

Sciamanna, I., A. Serafino, et al. (2019). "The active role of spermatozoa in transgenerational inheritance." Proc Biol Sci 286(1909): 20191263.

Shapiro, J. A. (2021). "All living cells are cognitive." Biochem Biophys Res Commun.

        • Cognitive behaviors in single-celled eukaryotes
        • Cognition in plants

Shapiro, J., A. (2021). How Should We Think About Evolution in the Age of Genomics? In New Horizons in Evolution. S. P. Wasser and M. Frenkel-Morgenstern (eds.), Elsevier.

Shapiro, J. and D. Noble. 2021. "What Prevents Mainstream Evolutionists Teaching the Whole Truth About How Genomes Evolve?" Prog Biophys Mol Biol. 

Shapiro, J. A. 2021b. "What Can Evolutionary Biology Learn from Cancer Biology?" Prog Biophys Mol Biol.

Shapiro, J. A. 2021c. "How Chaotic Is Genome Chaos?" Cancers (Basel) 13(6).

Shapiro, J. A. 2022a. "What We Have Learned About Evolutionary Genome Change in the Past 7 Decades." Biosystems 115-116:104669.

Shapiro, J. A. 2022b. "Evolutionary Change Is Naturally Biological and Purposeful." in Evolution ‘on Purpose’: Teleonomy in Living Systems, edited by Peter A. Corning and Richard Vane-Wright. Cambridge MA: MIT Press.

Shapiro, J.A. 2021d. "Response to Denis Noble’s Article “the Illusions of the Modern Synthesis,”." Biosemiotics (March 14, 5051):1-6.

Shapiro, James A. 2022c. "Engines of Innovation: Biological Origins of Genome Evolution." Biological Journal of the Linnean Society XX:1-16.



More Evidence on the Real Nature of Evolutionary DNA Change

Posted: 1/6/12 11:15 AM ET


Evolutionary Lessons From Superbugs

Posted January 8, 2012

Living Cells, Complex Systems and the Economy Posted: 1/13/12 02:34 PM ET


"Is James Shapiro a Design Theorist?": James Shapiro Replies


DNA as Poetry: Multiple Messages in a Single Sequence

Posted: 01/24/2012 6:05 pm


The Wall Street Journal and Climate Change: Where Are the Facts?

Posted January 30, 2012


Purposeful, Targeted Genetic Engineering in Immune System Evolution

Posted: February 6, 2012


What Is the Key to a Realistic Theory of Evolution?

Posted February 16, 2012

Response to Jerry Coyne, Posted February 19, 2012


Further Comments on 'What Is the Key to a Realistic Theory of Evolution?'

Posted: February 23, 2012


Theory of evolution

Submitted by Jim Shapiro on February 24, 2012


Barbara McClintock, X-Rays, and Self-Aware, Self-Healing Cells

Posted March 8, 2012


Barbara McClintock, Genome Self-Repair and Cell Cognition: A Revolutionary Vision for the Future of Biology

Posted March 19, 2012


Your Life Depends on Immune Cells Doing the 'Impossible': Purposeful, Targeted DNA Engineering (Part 2)  

Posted April 3, 2012 | 1:36 PM


Jerry Coyne Fails to Understand Yet Again

Posted April 10, 2012


What Is the Best Way to Deal With Supernaturalists in Science and Evolution?

Posted April 16, 2012


Natural Genetic Engineering and Natural Selection: Perplexing Delusions of Certain Neo-Darwinist Advocates

Posted April 23, 2012


Natural Genetic Engineering and Vitalism: What's the Difference?

Posted: 05/15/2012


Variation and Selection: What's the Difference? What Are the Issues?

Posted: 05/17/2012


How Natural Genetic Engineering Solves Problems in Protein Evolution

Posted: 05/24/2012


Interspecific Hybridization and Introgression in Animal Evolution

Posted: 05/27/2012 

Cells Executing Sophisticated Search Strategies (and How Our Physicist Friends Helped Us Learn About It)  Posted May 31, 2012


Can Cells Bias Natural Genetic Engineering Toward Useful Evolutionary Outcomes?  Posted: 06/06/2012

Network Evolution: How Natural Genetic Engineering Builds Circuits in the Genome Posted: 06/14/2012


Experimental Evolution: How Can We Watch Natural Genetic Engineering in Real Time? Posted: 06/25/2012


Experimental Evolution II: More Ways to Watch Natural Genetic Engineering in Real Time  Posted: 07/02/2012

Epigenetics I: Turning a DNA Packaging Problem Into a Developmental Control System Posted: 07/09/2012


Epigenetics II: Cellular Memory, Imprinting, and Targeting Genome Configuration With RNA