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Publications
Books:
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:
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. 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., 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.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):
- J. Shapiro, A.I. Bukhari and S. Adhya. New Pathways in the evolution of chromosome structure, pp. 3-13.
- J. Shapiro. Bacterial plasmids: Introduction, pp. 601-606.
- A.E. Jacob, J. Shapiro, L. Yamamoto, D.I. Smith, S.N. Cohen and D. Berg. Plasmids studied in Escherichia coli and other enteric bacteria, pp. 607-638.
- G.A. Jacoby and J. Shapiro. Plasmids studied in Pseudomonas aeruginosa and other Pseudomonads, pp. 639-656.
- R.P. Novick, S. Cohen, L. Yamamoto and J. Shapiro. Plasmids of Staphylococcus aureus, pp. 657-662.
- A.E. Jacob, J.A. Shapiro and L. Yamamoto. Plasmids of other Gram-positive bacteria, pp. 663-664.
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.
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., 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.
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.
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
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. 1984b. Transposable elements, genome
reorganization and cellular differentiation in
Gram-negative bacteria. Symp. Soc. Gen. Microbiol. 36
(Part 2), 169-193.
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. 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. 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 
-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 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. 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. 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.
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).
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. 1997b. Genome
organization, natural genetic engineering, and adaptive
mutation. Trends in Genetics 13,
98-104.
Shapiro, J.A.
1998. Thinking about bacterial populations as
multicellular organisms. Ann. Rev. Microbiol. 52,
81-104. http://micro.annualreviews.org/cgi/content/full/52/1/81
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).
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. 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. 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." http://www.sciencedirect.com/science/article/pii/S0079610712000909
Shapiro JA. 2013. How Life Changes Itself: The Read-Write (RW) Genome. Physics of Life Reviews 10:287-323.
http://www.sciencedirect.com/science/article/pii/S1571064513000869
Shapiro JA 2013.
Implications of the RW Genome view (responses to
published comments). Physics
of Life Reviews 10:347-350. http://www.sciencedirect.com/science/article/pii/S1571064513000985
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] http://ecommons.library.cornell.edu/handle/1813/34897.
Shapiro JA 2014. Constraint and
Opportunity in Genome Innovation. RNA Biology 11(3):1-11
(March 1, 2014, special issue dedicated to Carl Woese) https://www.landesbioscience.com/journals/rnabiology/article/27506/
Shapiro JA. 2014. The Physiology of the Read-Write (RW) Genome.
J
Physiol. 2014 Jun 1;592(Pt 11):2319-41.
doi: 10.1113/jphysiol.2014.271130
http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2014.271130/abstract
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,” http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00087/full
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?"). http://www.mdpi.com/2079-7737/5/2/27/html
Shapiro, J. A. (2017). "Exploring the
read-write genome: mobile DNA and mammalian adaptation." Crit
Rev Biochem Mol Biol 52(1): 1-17. http://www.ncbi.nlm.nih.gov/pubmed/27599542.
Shapiro, J.A. (2017).
Biological Action in Read-Write Genome Evolution. Interface
Focus (Royal Society), 7(5):20160115.
doi: 10.1098/rsfs.2016.0115 http://www.ncbi.nlm.nih.gov/pubmed/28839913
Shapiro,
J.A. (2017), Living Organisms Author Their Read-Write
Genomes in Evolution. Biology (Basel)6(4). http://www.ncbi.nlm.nih.gov/pubmed/29211049,
http://www.mdpi.com/2079-7737/6/4/42/htm.
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. http://www.ncbi.nlm.nih.gov/pubmed/30900279
Sciamanna, I., A. Serafino, et al. (2019). "The active role of spermatozoa in transgenerational inheritance." Proc Biol Sci 286(1909): 20191263. http://www.ncbi.nlm.nih.gov/pubmed/31455195.
Shapiro, J. A. (2021). "All living cells are cognitive." Biochem Biophys Res Commun. http://www.ncbi.nlm.nih.gov/pubmed/32972747.
• 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. https://pubmed.ncbi.nlm.nih.gov/33933502/
Shapiro,
J. A. 2021b. "What Can Evolutionary Biology Learn from
Cancer
Biology?" Prog
Biophys Mol Biol.
https://pubmed.ncbi.nlm.nih.gov/33930405/
Shapiro,
J. A. 2021c. "How Chaotic Is Genome Chaos?" Cancers (Basel) 13(6). https://pubmed.ncbi.nlm.nih.gov/33802828/
Shapiro,
J. A. 2022a. "What We Have Learned About Evolutionary Genome
Change in the
Past 7 Decades." Biosystems
115-116:104669. https://pubmed.ncbi.nlm.nih.gov/35358607/
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. https://doi.org/10.1093/biolinnean/blac041
BLOGS
More Evidence on the Real Nature of
Evolutionary DNA Change
Posted: 1/6/12 11:15 AM ET http://www.huffingtonpost.com/james-a-shapiro/more-evidence-on-the-real_b_1158228.html
Evolutionary
Lessons
From Superbugs
Posted
January 8, 2012 http://www.huffingtonpost.com/james-a-shapiro/bacterial-antibiotic-resistance_b_1192507.html
Living Cells, Complex Systems and
the Economy
Posted: 1/13/12 02:34 PM ET http://www.huffingtonpost.com/james-a-shapiro/living-cells-complex-syst_b_1204827.html
"Is James Shapiro a Design Theorist?": James
Shapiro Replies http://www.evolutionnews.org/2012/01/is_james_shapir_1055151.html
DNA as Poetry: Multiple Messages in
a Single Sequence
Posted: 01/24/2012 6:05 pm http://www.huffingtonpost.com/james-a-shapiro/dna-as-poetry-multiple-me_b_1229190.html
The
Wall
Street Journal
and Climate Change: Where
Are the Facts?
Posted January 30, 2012 http://www.huffingtonpost.com/james-a-shapiro/the-wall-street-journal-a_6_b_1239203.html
Purposeful, Targeted Genetic
Engineering in Immune System Evolution
Posted: February 6, 2012 http://www.huffingtonpost.com/james-a-shapiro/genetic-engineering-immune-system-evolution_b_1255771.html
What
Is
the Key to a Realistic Theory of Evolution?
Posted
February
16, 2012 http://www.huffingtonpost.com/james-a-shapiro/what-is-the-key-to-a-real_b_1280685.html
Response to Jerry Coyne, Posted
February
19, 2012 http://whyevolutionistrue.wordpress.com/2012/02/18/a-colleague-wrongfully-disses-modern-evolutionary-theory/#comment-186010
Further Comments on 'What Is the
Key to a Realistic Theory of Evolution?'
Posted: February 23, 2012 http://www.huffingtonpost.com/james-a-shapiro/theory-of-evolution_b_1294315.html
Submitted by Jim Shapiro
on February 24, 2012 http://www.psychologytoday.com/blog/explananda/201202/is-evolution-just-theory/comments
Barbara McClintock, X-Rays,
and Self-Aware, Self-Healing Cells
Posted March 8, 2012 http://www.huffingtonpost.com/james-a-shapiro/barbara-mcclintock-x-rays_b_1322879.html
Barbara
McClintock,
Genome Self-Repair and Cell Cognition: A Revolutionary
Vision for the Future of Biology
Posted March 19, 2012 http://www.huffingtonpost.com/james-a-shapiro/cell-cognition_b_1354889.html
Your Life Depends on Immune Cells Doing the 'Impossible': Purposeful, Targeted DNA Engineering (Part 2)
Posted April 3, 2012 | 1:36 PM http://www.huffingtonpost.com/james-a-shapiro/immune-cells-dna-engineering_b_1395040.html
Jerry Coyne Fails to Understand Yet Again
Posted April 10, 2012 http://www.huffingtonpost.com/james-a-shapiro/jerry-coyne-fails-to-unde_b_1411144.html
What Is the Best Way to Deal With Supernaturalists in Science and Evolution?
Posted April 16, 2012 http://www.huffingtonpost.com/james-a-shapiro/evolution-debate_b_1425133.html
Natural Genetic Engineering and Natural Selection: Perplexing Delusions of Certain Neo-Darwinist Advocates
Posted April 23, 2012 http://www.huffingtonpost.com/james-a-shapiro/natural-genetic-engineeri_b_1442309.html
Natural
Genetic
Engineering and Vitalism: What's the Difference?
Posted:
05/15/2012 http://www.huffingtonpost.com/james-a-shapiro/natural-genetic-engineering_b_1511451.html
Variation
and
Selection: What's the Difference? What Are the Issues?
Posted:
05/17/2012 http://www.huffingtonpost.com/james-a-shapiro/variation-and-selection-w_b_1522314.html
How
Natural Genetic Engineering Solves Problems in Protein
Evolution
Posted:
05/24/2012 http://www.huffingtonpost.com/james-a-shapiro/genetic-engineering_b_1541180.html
Interspecific Hybridization and
Introgression in Animal Evolution
Posted:
05/27/2012 http://www.huffingtonpost.com/james-a-shapiro/interspecific-hybridizati_b_1549324.html
Cells
Executing Sophisticated Search Strategies (and How Our
Physicist Friends Helped Us Learn About It) Posted May 31, 2012 http://www.huffingtonpost.com/james-a-shapiro/cell-research_b_1559647.html
Can Cells Bias Natural Genetic Engineering Toward Useful Evolutionary Outcomes? Posted: 06/06/2012 http://www.huffingtonpost.com/james-a-shapiro/natural-genetic-engineering-evolutionary-outcomes_b_1572730.html
Network
Evolution:
How Natural Genetic Engineering Builds Circuits in the
Genome Posted:
06/14/2012 http://www.huffingtonpost.com/james-a-shapiro/network-evolution-genetics_b_1594000.html
Experimental
Evolution:
How Can We Watch Natural Genetic Engineering in Real Time? Posted:
06/25/2012 http://www.huffingtonpost.com/james-a-shapiro/experimental-evolution-ho_b_1619171.html
Experimental
Evolution
II: More Ways to Watch Natural Genetic Engineering in Real
Time Posted:
07/02/2012 http://www.huffingtonpost.com/james-a-shapiro/natural-genetic-engineering_b_1638823.html
Epigenetics
I:
Turning a DNA Packaging Problem Into a Developmental Control
System Posted:
07/09/2012 http://www.huffingtonpost.com/james-a-shapiro/epigenetics-i-turning-a-d_b_1654549.html
Epigenetics
II: Cellular Memory, Imprinting, and Targeting Genome
Configuration With RNA Posted: 07/13/2012 http://www.huffingtonpost.com/james-a-shapiro/epigenetics-ii-cellular-m_b_1668820.html
Epigenetics
III:
Epigenetic Control of Natural Genetic Engineering and
Environmental Inputs into Evolutionary Change Posted:
07/18/2012 http://www.huffingtonpost.com/james-a-shapiro/epigenetics-iii-epigeneti_b_1683713.html
Legitimate
and
Illegitimate Recombination: Targeting Homologous Exchange
for Multiple Adaptive Purposes Posted:
08/02/2012 http://www.huffingtonpost.com/james-a-shapiro/legitimate-and-illegitima_b_1728003.html
Take 2: Why Genetic Recombination Is Not Random, and How Cells Take Advantage of Non-randomness Posted: 08/07/2012 http://www.huffingtonpost.com/james-a-shapiro/genetic-recombination-not-random_b_1743647.html
Does Natural Selection Really
Explain What Makes Evolution Succeed? Posted:
08/12/2012 http://www.huffingtonpost.com/james-a-shapiro/does-natural-selection-evolution_b_1769524.html
Cell Mergers and the
Evolution of New Life Forms: Symbiogenesis Rather Than
Selection Posted:
08/21/2012
The Distinct Roles of Selection,
Horizontal Transfer and Natural Genetic Engineering in
Dangerous Superbug Evolution Posted:
08/29/2012
http://www.huffingtonpost.com/james-a-shapiro/the-distinct-roles-of-sel_b_1831996.html
Dan Hartl, Sewall Wright, and the
Role of "Ecological Opportunity" in Evolution Posted:
09/12/2012 http://www.huffingtonpost.com/james-a-shapiro/dan-hartl-sewall-wright-a_b_1863672.html
Bob Dylan, ENCODE and Evolutionary
Theory: The Times They Are A-Changin' Posted:
09/12/2012
http://www.huffingtonpost.com/james-a-shapiro/bob-dylan-encode-and-evol_b_1873935.html
Further Thoughts on the
ENCODE/Junk DNA Debates Posted:
09/18/2012
http://www.huffingtonpost.com/james-a-shapiro/further-thoughts-on-the-e_b_1893984.html
Mobile DNA Repeats and
Transcriptional Formatting of the Mammalian Genome in
Evolution
Posted: 09/22/2012
http://www.huffingtonpost.com/james-a-shapiro/mobile-dna-repeats-and-tr_b_1906135.html
Could Bill Nye Have Done More to
Keep Creationism out of the Classroom?
Posted: 09/27/2012
http://www.huffingtonpost.com/james-a-shapiro/could-bill-nye-have-done-_b_1919558.html
The Evolutionary Importance of
Horizontal DNA Transfer into Animal Germ Lines
Posted: 10/03/2012
http://www.huffingtonpost.com/james-a-shapiro/the-evolutionary-importan_b_1936059.html
Union of Concerned Scientists
Launches a New Center for Science and Democracy
Posted: 10/07/2012
http://www.huffingtonpost.com/james-a-shapiro/union-of-concerned-scient_b_1946734.html
Sociobacteriology: Small Cells
Talking And Listening -- And How It May Affect You If You Go
Under the Knife
Posted: 10/16/2012
http://www.huffingtonpost.com/james-a-shapiro/sociobacteriology-small-c_b_1963701.html
Evelyn Witkin, Jean Weigle, the
SOS Response and How E. Coli Generates Mutations in Response
to UV Irradiation
Posted: 10/20/2012
http://www.huffingtonpost.com/james-a-shapiro/evelyn-witkin-jean-weigle_b_1992789.html
Inter-Kingdom
Horizontal
DNA Transfer in all directions: Infectious bacteria evolve
by acquiring protein domains from eukaryotic hosts
Posted: 11/06/2012
http://www.huffingtonpost.com/james-a-shapiro/interkingdom-horizontal-d_b_2081420.html
Why the 'Gene' Concept Holds Back
Evolutionary Thinking
Posted: 11/30/2012 http://www.huffingtonpost.com/james-a-shapiro/why-the-gene-concept-hold_b_2207245.html
Inconvenient Truths: Why Are
Self-Styled Defenders of Evolution so Resistant to Lessons
From Molecular Genetics?
Posted: 12/04/2012 http://www.huffingtonpost.com/james-a-shapiro/inconvenient-truths-why-a_b_2228277.html
In Memorium Carl Woese
(1928-2012), the Most Important Evolutionary Biologist of
the 20th Century
Posted: 01/28/2013 http://www.huffingtonpost.com/james-a-shapiro/in-memorium-carl-woese-19_b_2558605.html
What Natural Genetic
Engineering Does and Does Not Mean Posted:
02/28/2013 http://www.huffingtonpost.com/james-a-shapiro/what-natural-genetic-engi_b_2783419.html
Life and Death Decisions by
Cells, Investigated Under Life-threatening Conditions During
WWII
Posted: 03/14/2013 http://www.huffingtonpost.com/james-a-shapiro/important-work-on-cell-co_b_2871689.html
