Why do people deny evolution?

To equate that side with the side of the "religious nutters" makes almost no sense.

You are a bit delusional

I have argued with the 'nutters' over the impossibility of the Bible being literally true and can really see a resemblance between both sides.

Maybe the self-appointed scientists should admit to some of the holes in it, and maybe the religious nutters should admit it is fairly solid science and the Bible couldnt possibly be the literal word of God . Unfortunately, the unintelligent on both sides need their doctrine .

The recent reviews in your columns of books by Dennett, Dawkins, and Behe are testimony to the unflagging interest in controversies about evolution. Although such purists as Dennett and Dawkins repeatedly assert that the scientific issues surrounding evolution are basically solved by conventional neo-Darwinism, the ongoing public fascination reveals a deeper wisdom. There are far more unresolved questions than answers about evolutionary processes, and contemporary science continues to provide us with new conceptual possibilities.... the debate about evolution continues to assume the quality of an abstract and philosophical "dialogue of the deaf" between Creationists and Darwinists....

What significance does an emerging interface between biology and information science hold for thinking about evolution? It opens up the possibility of addressing scientifically rather than ideologically the central issue so hotly contested by fundamentalists on both sides of the Creationist-Darwinist debate...However, the potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise. This is to be expected from the Creationists, who naturally refuse to recognize science's remarkable record of making more and more seemingly miraculous aspects of our world comprehensible to our understanding and accessible to our technology. But the neo-Darwinian advocates claim to be scientists, and we can legitimately expect of them a more open spirit of inquiry. Instead, they assume a defensive posture of outraged orthodoxy and assert an unassailable claim to truth, which only serves to validate the Creationists' criticism that Darwinism has become more of a faith than a science.

“Darwin modeled natural selection on artificial selection by humans. He ignored the inconvenient fact that human selection for altered traits has never generated a truly new organismal feature (e.g., a limb or an organ) or formed a new species. Selection only modifies existing characters. When humans wish to create new species, they use other means.”

Ive always admitted to "holes " in evolution.

What do you personally understand of the Bible?

for as it goes the world will end with or without the fossil fuels

Bullshit . You may say that now, but years ago when I first started arguing with you that evolution was not perfect, that whilst I believed it to be true, the difference between scientific proof and theory is a sizable gap . And you would always answer like the good clone you are that there was nothing wrong with Evolutionary Theory . Shall I go back and find them ? Then will you admit you are wrong like I am waiting for you to admit you were wrong over the facts on the T'Rex article .

You have a habit of being a self declared scientist with a very average ability to understand anything but belligerence . If you aint lernt it, den it aint tru . You are past learning . Admit you were wrong on the T'Rex article .

His argument has always been that evolution "doesnt create any new forms"> SO, in one sweep of ignorance he avoids consulting the fossil record and Lenski's work on creating new forms and genes.

Darwin modeled natural selection on artificial selection by humans. He ignored the inconvenient fact that human selection for altered traits has never generated a truly new organismal feature (e.g., a limb or an organ) or formed a new species. Selection only modifies existing characters. When humans wish to create new species, they use other means. [Here he embeds a link to research done by Joseph H. Hulse & David Spurgeon].

Have we learned since 1859 about processes that can lead to organism change "independently of natural selection?" The answer is overwhelmingly positive. In combination, cytogenetics and molecular genetics have taught us about many processes that lead to biological novelties "independently of natural selection" -- hybridization, genome duplication, symbiogenesis, chromosome restructuring, horizontal DNA transfer, mobile genetic elements, epigenetic switches, and natural genetic engineering (the ability of all cells to cut, splice, copy, and modify their DNA in non-random ways).

Shapiro has failed to ever satifactorily comment on one of Dennets' own comments that"Evidence seems to support the conclusion that entirely new orders seem to congregate at times in the fossil record that just post date major environmental changes. (not only cataclysmic events but large scale climate changes and glaciation).

Darwin was correct in believing that natural selection could only play a creative role if variation was continual and small. Based on the "Uniformitarian" idea that change had to occur in the small steps we observe under normal conditions, he originally insisted that evolutionary innovation had to be gradual...

[quoting Darwin] "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case" (Origin of Species, Chapter 6). [At the time this was written, Darwin could find "no such case," BUT]...

Unlike most followers, Darwin acknowledged later that significant, sudden changes could occur in a fundamentally different way. He wrote about "... variations which seem to us in our ignorance to arise spontaneously. It appears that I formerly underrated the frequency and value of these latter forms of variation, as leading to permanent modifications of structure independently of natural selection" (Origin of Species, 6th edition, Chapter XV, p. 395, emphasis added).

Shapiro seems to write much of his deeper thought on evolution for the Huffington Post rather than for the scientific literature that is peer reviewed and open to fair comment. WHY'x this

While working with Beckwith at Harvard, Shapiro was part of the first team to isolate a single gene from an organism.[6][11][12] The gene they isolated was lacZ, which codes for the β-galactosidase enzyme used by E. coli bacteria to digest the sugars in milk. Their technique involved transduction of two complementary copies of the gene into two different bacteriophages, then mixing the genetic material from the two phages, and finally using a nuclease to degrade the single-stranded phage genome, leaving only the double-stranded DNA formed by the two copies.[13]

In a paper published in the Proceedings of the National Academy of Sciences in 1979, Shapiro was the first to propose replicative transposition as a mechanism for gene mobility. In this model, genes such as retrotransposons are copied from one DNA sequence to another via a process in which the two sequences combine to form an intermediate "theta" shape, sometimes called a "Shapiro intermediate".[14]

Later, Shapiro showed that bacteria cooperate in communities that exhibit complex behavior such as hunting, building protective structures, and spreading spores, and in which individual bacteria may sacrifice themselves for the benefit of the larger community.[15][16][17] Based on this work, Shapiro believes that cooperative behavior is a fundamental organizing concept for biological activity at all levels of complexity.[18]

Shapiro has also studied pattern formation in bacteria, an area where he feels that there are new mathematical principles to be discovered that also underlie the growth of crystals and the shape of cosmological structures.[6] For instance, he found that the gut bacterium proteus mirabilis forms complex terraced rings, an emergent property of simple rules that the bacterium uses to avoid neighboring cells He is the author of "Evolution: A View from the 21st Century" (FT Press Science, 2011, ISBN 978-0-13-278093-3).

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)

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):
•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.

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.

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. 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).
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. 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." 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
Figures and fully referenced tables at http://shapiro.bsd.uchicago.edu/PLREV.RWGenome.html

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. Focus issue of Journal of Physiology on “The integration of evolutionary biology with physiological science,” in press.



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

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).

Wed 10 Mar, 2010 02:04 pm
@farmerman,
I hope we can put this in the past, and the next time we discuss something I would prefer not to be insulted. You most certainly wouldnt do it without the safety of several thousand miles separation. I have appreciated your expert opinion in the past and will continue to do so. If I defer to your knowledge, I do not expect it to rebound in a later discussion on a different but broadly related matter.

"Where the Hell did we get T rex DNA??"

Thinking about it, who says they are extinct ? Ever eaten a chicken ? It seems the T-Rex's closest living relative (based on DNA) is the chicken.

"The analysis shows that T-rex collagen makeup is almost identical to that of a modern chicken - this corroborates a huge body of evidence from the fossil record that demonstrates birds are descended from meat-eating dinosaurs," said Angela Milner, the associate keeper of palaeontology at the Natural History Museum in London. "So, it is very satisfying that the molecules have provided a positive test for the morphology."

"The fact that protein sequences from collagen of a T-rex have been recovered does not mean that we will be able to clone dinosaurs, despite what the makers of Jurassic Park suggest. Cloning any organism needs its DNA which carries the instructions to make a copy. DNA is not a protein, it is not a very stable molecule and it has never been recovered from any organism more than 30,000 years old."

remember, DArwin had no idea about how old the earth really was. The concept of a "Cambrian Explosion" was unknown to him...

The seemingly rapid appearance of fossils in the “Primordial Strata” was noted as early as the 1840s,[14] and in 1859 Charles Darwin discussed it as one of the main objections that could be made against the theory of evolution by natural selection.

Shapiro seems to reveal his ignorance of how interdisciplinary and multidisciplinary studies of evolution really are .