James A. Shapiro

Last updated
James A. Shapiro
NationalityAmerican
Alma mater Churchill College, Cambridge University, England
Known for Natural genetic engineering, first isolation of a gene, cooperative behavior in bacteria, pattern formation
AwardsMarshall Scholarship (1964-1966), [1] Darwin Prize (University of Edinburgh) 1993, [2] AAAS Fellow 1994, [3] Honorary OBE 2001 [2]
Scientific career
Fields Microbiology, Molecular Biology, Genetics, Biochemistry
Institutions University of Chicago; Postdoctoral Fellow at the Institut Pasteur, France; Harvard Medical School; Brandeis University; Visiting Professor at Tel Aviv University and the University of Edinburgh, Scotland; Visiting Fellow at Churchill College, Cambridge University, England

James Alan Shapiro (born May 18, 1943) is an American biologist, an expert in bacterial genetics and a professor in the Department of Biochemistry and Molecular Biology at the University of Chicago. [4]

Contents

Academic biography

Shapiro obtained his Bachelor's degree in English from Harvard College in 1964. [1] [5] Then, inspired by a genetics course he had taken as a senior, [6] he shifted from English to science. He was awarded a Marshall scholarship for postgraduate research at Corpus Christi College, Cambridge from 1964 to 1967, spending his final year at Hammersmith hospital under the supervision of William Hayes, and being awarded a PhD in genetics in 1968. His thesis, The Structure of the Galactose Operon in Escherichia coli K12, contains the first suggestion of transposable elements in bacteria. He confirmed this hypothesis in 1968 during his postdoctoral tenure as a Jane Coffin Childs fellow in the laboratory of François Jacob at the Institut Pasteur in Paris.

As an American Cancer Society fellow in Jon Beckwith’s laboratory at the Harvard Medical School 1968-70, he and his colleagues used in vivo genetic manipulations to clone and purify the lac operon of E. coli.

He was troubled by the potential genetic engineering applications of his research. [6] [7] [8]

He served as Invited Professor in the School of Biological Sciences at the University of Havana, Cuba 1970-1972, before returning to another postdoctorate with Harlyn Halvorson at Brandeis University. [5] Since 1973, he has worked as a professor of microbiology at the University of Chicago.

In 1975 Shapiro attended the ICN-UCLA Squaw Valley Symposium on Bacterial Plasmids, where his interest in DNA restructuring in bacteria was heightened by learning about the movements of antibiotic resistance transposons to new genomic locations. This prompted him to organize, in collaboration with Sankar Adhya and the late Ahmed Bukhari, the first meeting on the topic of DNA insertion elements at Cold Spring Harbour Laboratory in 1976. Although they expected only a few colleagues, the meeting was attended by over 150 scientists from around the world, including Barbara McClintock. McClintock had first identified transposition (horizontal gene transfer) (movement to new genomic location) of DNA "controlling elements" in maize (sweetcorn) in 1948, for which discovery she was awarded a Nobel Prize 1983. Shapiro and McClintock continued their collaboration up until her death in 1992. [9]

He has also been a visiting professor from time to time, including once as a Darwin Prize Visiting Professor at the University of Edinburgh in 1994. [10]

Research

While working with Beckwith at Harvard, Shapiro was lead author of the first team to isolate a single gene from an organism. [5] [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 to clone oppositely oriented copies of the gene inserted into two specialized transducing bacteriophages, then mixing single-stranded DNA from the two phages so that only the bacterial sequences would form a double helix, and finally using a nuclease to degrade the single-stranded phage sequences, leaving only the double-stranded lacZ DNA. [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 detailed molecular mechanism for genetic mobility by transposable elements, such as the Tn3 ampicillin resistance transposon and transposing bacteriophage Mu. In this model, the ends of transposable elements covalently bond to target site DNA sequences to via a process that forms an intermediate structure with replication forks at each end of the transposing element, sometimes called a "Shapiro intermediate". [14]

In other research, Shapiro showed that bacteria organize themselves spatially as they grow in communities on agar surfaces. For instance, he analyzed how each strain of the sometimes pathogenic bacterium Proteus mirabilis forms its own pattern of complex terraced rings by periodic group “swarm" migration, an emergent property that can be explained by mathematical rules derived by a physicist collaborator, Sergei Esipov. Shapiro related this to other complex multicellular behaviors, such as hunting, building protective structures, spreading spores, and individual bacteria sacrificing 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]

Natural genetic engineering

He has proposed the term natural genetic engineering to account for how novelty is created in the course of biological evolution. It has been criticized by some, [19] [20] [21] [22] and Shapiro has responded to points raised by his critics. [23]

Shapiro maintains that many genome changes that occur naturally operate by similar molecular DNA rearrangements to those applied intentionally by scientists using genetic engineering techniques developed over the last few decades. For example, transposable elements may be amplified and moved to different locations in the genome. These DNA changes have been found to result in distributed genomic networks for the execution of a wide range of complex traits in fungi, diatoms, plants and animals, such as flower development, the vertebrate body plan, viviparous reproduction and nervous system development in various mammals. [24]

The Third Way of Evolution

Shapiro and Denis Noble established The Third Way of Evolution (TWE) project in 2014. The TWE which is also known as the "Integrated Synthesis" shares many similarities with the extended evolutionary synthesis but is more extreme in its claims. [25] The TWE consists of a group of researchers who provide a middle path "Third Way" alternative to creationism and the modern synthesis. The TWE predicts that the modern synthesis will be replaced with an entirely new evolutionary framework. [25] In 2023 only a minority of evolutionary biologists currently support the TWE. [25]

Awards and honors

Shapiro was elected to Phi Beta Kappa in 1963 [26] and was a Marshall Scholar from 1964 to 1966. [1] He won the Darwin Prize Visiting Professorship of the University of Edinburgh in 1993. [2] In 1994, he was elected as a fellow of the American Association for the Advancement of Science for "innovative and creative interpretations of bacterial genetics and growth, especially the action of mobile genetic elements and the formation of bacterial colonies." [3] [27] And in 2001, he was made an honorary officer of the Order of the British Empire for his service to the Marshall Scholarship program. [2] In 2014 he was chosen to give the 3rd annual "Nobel Prize Laureate - Robert G. Edwards" lecture [28]

Selected publications

Shapiro edited the books Mobile Genetic Elements (Academic Press, 1983) and, with Martin Dworkin, Bacteria as Multicellular Organisms (Oxford University Press, 1997). He is the author of Evolution: A View from the 21st Century (FT Press Science, 2011, ISBN   978-0-13-278093-3).

In 2022 Shapiro published a greatly expanded and updated second edition of Evolution: A View from the 21st Century (Cognition Press, ISBN   978-1-7374987-0-4).

Shapiro, Denis Noble, Peter A. Corning and Stuart A. Kauffman authored Evolution on "Purpose": Teleonomy in Living Systems in 2023. [29]

Related Research Articles

In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be co-transcribed to define an operon.

<span class="mw-page-title-main">Horizontal gene transfer</span> Transfer of genes from unrelated organisms

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher-order evolution while more significantly shifting perspectives on bacterial evolution.

<span class="mw-page-title-main">François Jacob</span> French biologist

François Jacob was a French biologist who, together with Jacques Monod, originated the idea that control of enzyme levels in all cells occurs through regulation of transcription. He shared the 1965 Nobel Prize in Medicine with Jacques Monod and André Lwoff.

<span class="mw-page-title-main">Evolutionary biology</span> Study of the evolution of life

Evolutionary biology is the subfield of biology that studies the evolutionary processes such as natural selection, common descent, and speciation that produced the diversity of life on Earth. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology.

<span class="mw-page-title-main">Jacques Monod</span> French biologist

Jacques Lucien Monod was a French biochemist who won the Nobel Prize in Physiology or Medicine in 1965, sharing it with François Jacob and André Lwoff "for their discoveries concerning genetic control of enzyme and virus synthesis".

<span class="mw-page-title-main">SOS response</span> Cell response to DNA damage

The SOS response is a global response to DNA damage in which the cell cycle is arrested and DNA repair and mutagenesis are induced. The system involves the RecA protein. The RecA protein, stimulated by single-stranded DNA, is involved in the inactivation of the repressor (LexA) of SOS response genes thereby inducing the response. It is an error-prone repair system that contributes significantly to DNA changes observed in a wide range of species.

Charles Yanofsky was an American geneticist on the faculty of Stanford University who contributed to the establishment of the one gene-one enzyme hypothesis and discovered attenuation, a riboswitch mechanism in which messenger RNA changes shape in response to a small molecule and thus alters its binding ability for the regulatory region of a gene or operon.

<span class="mw-page-title-main">Franklin Stahl</span> American molecular biologist and geneticist

Franklin (Frank) William Stahl is an American molecular biologist and geneticist. With Matthew Meselson, Stahl conducted the famous Meselson-Stahl experiment showing that DNA is replicated by a semiconservative mechanism, meaning that each strand of the DNA serves as a template for production of a new strand.

<span class="mw-page-title-main">Start codon</span> First codon of a messenger RNA translated by a ribosome

The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and archaea and a N-formylmethionine (fMet) in bacteria, mitochondria and plastids.

<span class="mw-page-title-main">Gene</span> Sequence of DNA that determines traits in an organism

In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and non-coding genes. During gene expression, DNA is first copied into RNA. RNA can be directly functional or be the intermediate template for the synthesis of a protein.

<span class="mw-page-title-main">Denis Noble</span> British biologist (born 1936)

Denis Noble is a British physiologist and biologist who held the Burdon Sanderson Chair of Cardiovascular Physiology at the University of Oxford from 1984 to 2004 and was appointed Professor Emeritus and co-Director of Computational Physiology. He is one of the pioneers of systems biology and developed the first viable mathematical model of the working heart in 1960. Noble established The Third Way of Evolution (TWE) project with James A. Shapiro which predicts that the entire framework of the modern synthesis will be replaced.

<span class="mw-page-title-main">Mobile genetic elements</span> DNA sequence whose position in the genome is variable

Mobile genetic elements (MGEs), sometimes called selfish genetic elements, are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In humans, approximately 50% of the genome are thought to be MGEs. MGEs play a distinct role in evolution. Gene duplication events can also happen through the mechanism of MGEs. MGEs can also cause mutations in protein coding regions, which alters the protein functions. These mechanisms can also rearrange genes in the host genome generating variation. These mechanism can increase fitness by gaining new or additional functions. An example of MGEs in evolutionary context are that virulence factors and antibiotic resistance genes of MGEs can be transported to share genetic code with neighboring bacteria. However, MGEs can also decrease fitness by introducing disease-causing alleles or mutations. The set of MGEs in an organism is called a mobilome, which is composed of a large number of plasmids, transposons and viruses.

In molecular cloning, a vector is any particle used as a vehicle to artificially carry a foreign nucleic sequence – usually DNA – into another cell, where it can be replicated and/or expressed. A vector containing foreign DNA is termed recombinant DNA. The four major types of vectors are plasmids, viral vectors, cosmids, and artificial chromosomes. Of these, the most commonly used vectors are plasmids. Common to all engineered vectors are an origin of replication, a multicloning site, and a selectable marker.

<span class="mw-page-title-main">Avery–MacLeod–McCarty experiment</span> 1944 microbiology experiment

The Avery–MacLeod–McCarty experiment was an experimental demonstration by Oswald Avery, Colin MacLeod, and Maclyn McCarty that, in 1944, reported that DNA is the substance that causes bacterial transformation, in an era when it had been widely believed that it was proteins that served the function of carrying genetic information. It was the culmination of research in the 1930s and early 20th century at the Rockefeller Institute for Medical Research to purify and characterize the "transforming principle" responsible for the transformation phenomenon first described in Griffith's experiment of 1928: killed Streptococcus pneumoniae of the virulent strain type III-S, when injected along with living but non-virulent type II-R pneumococci, resulted in a deadly infection of type III-S pneumococci. In their paper "Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III", published in the February 1944 issue of the Journal of Experimental Medicine, Avery and his colleagues suggest that DNA, rather than protein as widely believed at the time, may be the hereditary material of bacteria, and could be analogous to genes and/or viruses in higher organisms.

<span class="mw-page-title-main">Concerted evolution</span>

Concerted evolution is the phenomenon where paralogous genes within one species are more closely related to one another than to members of the same gene family in closely related species. In other terms, when specific members of a family are investigated, a greater amount of similarity is found within a species rather than between species. This is suggesting that members within this family do not in fact evolve independently of one another.

<i>Endless Forms Most Beautiful</i> (book) 2005 evo-devo book by Sean B. Carroll

Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom is a 2005 book by the molecular biologist Sean B. Carroll. It presents a summary of the emerging field of evolutionary developmental biology and the role of toolkit genes. It has won numerous awards for science communication.

Julian Edmund Davies is a British-born microbiologist and Professor Emeritus in the Department of Microbiology and Immunology at the University of British Columbia.

Natural genetic engineering (NGE) is a class of process proposed by molecular biologist James A. Shapiro to account for novelty created in the course of biological evolution. Shapiro developed this work in several peer-reviewed publications from 1992 onwards, and later in his 2011 book Evolution: A View from the 21st Century, which has been updated with a second edition in 2022. He uses NGE to account for several proposed counterexamples to the central dogma of molecular biology. Shapiro drew from work as diverse as the adaptivity of the mammalian immune system, ciliate macronuclei and epigenetics. The work gained some measure of notoriety after being championed by proponents of Intelligent Design, despite Shapiro's explicit repudiation of that movement.

<span class="mw-page-title-main">Jürgen Brosius</span> German molecular geneticist and evolutionary biologist

Jürgen Brosius is a German molecular geneticist and evolutionary biologist. He was professor and director of the Institute of Experimental Pathology at the University of Münster. Some of his scientific contributions involve the first genetic sequencing of a ribosomal RNA operon, the design of plasmids for studying gene expression, expression vectors for high-level production of recombinant proteins and RNA, RNA biology, RNomics as well as the significance of retroposition for plasticity and evolution of genomes, genes and gene modules including regulatory sequences or elements.

References

  1. 1 2 3 "Marshalls Announced", Harvard Crimson , May 5, 1964
  2. 1 2 3 4 "Queen honors Shapiro with OBE", University of Chicago Chronicle, January 10, 2002
  3. 1 2 AAAS Fellow listing
  4. ↑ Faculty profile, Department of Biochemistry and Molecular Biology, University of Chicago, archived from the original on September 21, 2013, retrieved September 20, 2013
  5. 1 2 3 Kolata, Gina (October 13, 1992), "The Biologist Who Saw a Pattern", New York Times
  6. 1 2 Beckwith, Jonathan R. (2002), Making genes, making waves: a social activist in science , Harvard University Press, ISBN   978-0-674-00928-8
  7. ↑ Kolata, Gina (March 5, 1996), "Elusive Genetic Switch At Last Yields Image Of Its 3-D Structure", New York Times
  8. ↑ Knox, Richard (January 20, 1970), "Harvard Geneticist Turns to Social Ills", Boston Globe
  9. ↑ James A. Shapiro. "Perspectives - Letting Escherichia coli Teach Me About Genome Engineering" (PDF). Archived from the original (PDF) on June 12, 2010.
  10. ↑ Curriculum Vitae, James A. Shapiro, University of Chicago
  11. ↑ "Scientists Isolate a Gene; Step in Heredity Control", New York Times , November 23, 1969
  12. ↑ "Playing With Biological Fire", New York Times , December 8, 1969
  13. ↑ Müller-Hill, Benno (1996), The lac Operon: a short history of a genetic paradigm, Walter de Gruyter, p. 42, ISBN   978-3-11-014830-5
  14. ↑ Bushman, Frederic (2002), Lateral DNA transfer: mechanisms and consequences, CSHL Press, p. 46, ISBN   978-0-87969-621-4
  15. ↑ Browne, Malcolm W. (July 5, 1988), "Some Thoughts on Self Sacrifice", New York Times
  16. ↑ Kolata, Gina (October 13, 1992), "Bacteria Are Found to Thrive on a Rich Social Life", New York Times
  17. ↑ Guy, Sandra (December 15, 2004), "Scientist uncovers secret lives of bacteria", Chicago Sun-Times
  18. ↑ Browne, Malcolm W. (April 14, 1992), "Biologists Tally Generosity's Rewards", New York Times
  19. ↑ Bezak, Eva (2011), "(Review) Evolution: A View from the 21st Century", Australasian Physical & Engineering Science in Medicine, 34 (4): 643–645, doi:10.1007/s13246-011-0110-4
  20. ↑ Buratti, Emanuele (2012), "(Review) Evolutionary Lessons for 21st Century Molecular Biotechnologists", Molecular Biotechnology, 52 (1): 89–90, doi:10.1007/s12033-011-9472-9
  21. ↑ Moran, Laurence A (May–June 2011), "(Review) Evolution: A View from the 21st Century" (PDF), Reports of the National Center for Science Education, 32 (3): 10
  22. ↑ Seoighe, Cathal (2012), "(Review) Evolution: A View from the 21st Century", Trends in Evolutionary Biology, 4 (e6): 32–33, doi: 10.4081/eb.2012.e6
  23. ↑ Shapiro, James A. (2012), "Response to Pauline Hogeweg's review of my book, "Evolution: a view from the 21st century"", Evolutionary Intelligence, 5 (3): 211, doi: 10.1007/s12065-012-0074-7
  24. ↑ Distributed genome network innovation attributed to mobile DNA elements
  25. 1 2 3 Svensson, Erik I. (2023), "The Structure of Evolutionary Theory: Beyond Neo-Darwinism, Neo-Lamarckism and Biased Historical Narratives About the Modern Synthesis", in Dickins, T.E.; Dickins, B.J. (eds.), Evolutionary Biology: Contemporary and Historical Reflections Upon Core Theory, Evolutionary Biology – New Perspectives on Its Development, vol. 6, pp. 173–217, doi:10.1007/978-3-031-22028-9_11, ISBN   978-3-031-22027-2
  26. ↑ "16 Elected Phi Beta Kappa At Harvard", Boston Globe , December 8, 1963
  27. ↑ "Four faculty members elected AAAS Fellows", University of Chicago Chronicle, 14 (10), January 19, 1995
  28. ↑ "World Congress Controversies in Obstetrics, Gynecology and Infertility".
  29. ↑ "Evolution on "Purpose". mitpress.mit.edu.

This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.