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James A. Shapiro
James A. Shapiro, author of the 2011 book Evolution: A View from the 21st Century, is Professor of Microbiology at the University of Chicago. He has a BA in English Literature from Harvard (1964) and a PhD in Genetics from Cambridge (1968).

Shapiro’s thesis, The Structure of the Galactose Operon in Escherichia coli K12, written under the supervision of William Hayes, 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 Francois Jacob at the Institut Pasteur in Paris. The following year, as an American Cancer Society fellow in Jonathan Beckwith's laboratory at Harvard Medical School, he and his colleagues used in vivo genetic manipulations to clone and purify the lac operon of E. coli, an accomplishment that received international attention. In 1979, Prof. Shapiro formulated the first precise molecular model for transposition and replication of phage Mu and other transposons. In 1984, he published the first case study of what is now called "adaptive mutation." He found that selection stress triggers a tremendous increase in the frequency of Mu-mediated coding sequence fusions. Since 1992, he has been writing about the importance of biologically regulated natural genetic engineering as a fundamental new concept in evolution science. Together with the late Ahmed Bukhari and Sankhar Adhya, Prof. Shapiro organized the first conference on DNA insertion elements in May, 1976, at Cold Spring Harbor laboratory. He is editor of DNA Insertion Elements, Episomes and Plasmids (1977 with Bukhari and Adhya), Mobile Genetic Elements (1983), and Bacteria as Multicellular Organisms (1997 with Martin Dworkin). From 1980 until her death in 1992, Prof. Shapiro maintained a close scientific and personal friendship with Barbara McClintock, whom he credits with opening his eyes to new ways of thinking about science in general and evolution in particular.

Entries by James A. Shapiro

The Gibbon Genome and Natural Genetic Engineering in Primate Evolution

(1) Comments | Posted September 23, 2014 | 11:39 AM

Last week Nature published the draft genome of a Gibbon species (Nomascus leucogenys) in an important article, "Gibbon genome and the fast karyotype evolution of small apes." Gibbons are near relatives. They are intermediate between Old World Monkeys and the Great Apes, to which we belong. The four...

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Misquoting Science in the Texas Textbook Battles

(134) Comments | Posted December 5, 2013 | 2:56 PM

December 4th brought a striking concurrence of events revealing how the opponents of science education operate.

I had just participated in a Union of Concerned Scientists webinar about "Getting Science Right in the Media: Rapid response to the good, the bad, and the provocative." The point of the...

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Roger Ebert and Evolution - What Does the DNA Tell Us?

(35) Comments | Posted April 5, 2013 | 3:40 PM

The famous and distinguished film critic Roger Ebert passed away yesterday, after a heroic battle against throat cancer that left him voiceless but hardly wordless the last seven years of his life. The news about the death of such an influential and heroic man was all over the airwaves, especially...

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Life and Death Decisions by Cells, Investigated Under Life-threatening Conditions During WWII

(66) Comments | Posted March 14, 2013 | 3:34 PM

I am using this posting to call attention to a moving and important blog about Nobel Laureate Rita Levi-Montalcini's life and research (A Tale of Centenarians, posted February 25, 2013).

My fellow student from the mid-1960s at the Cambridge University Genetics Department, Claudio Scazzocchio, originally...

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What Natural Genetic Engineering Does and Does Not Mean

(288) Comments | Posted February 28, 2013 | 5:17 PM

In correspondence and comments on some of my blogs, there have been confusions or questions as to what I mean by "natural genetic engineering" (NGE). I will use this blog to spell out what my understanding of NGE is. Then I will discuss some implications of our knowledge of NGE...

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In Memorium Carl Woese (1928-2012), the Most Important Evolutionary Biologist of the 20th Century

(66) Comments | Posted January 28, 2013 | 2:09 PM

Shortly before New Year's Day, we lost Carl Woese, one of the 20th Century's greatest scientists. It is fitting to use the first blog of 2013 to pay homage to this creative and determined pioneer of molecular phylogenomics.

Carl put our picture of living organisms on a solid empirical basis...

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Inconvenient Truths: Why Are Self-Styled Defenders of Evolution so Resistant to Lessons From Molecular Genetics?

(726) Comments | Posted December 4, 2012 | 11:32 AM

Last week, on his very popular blog,, Jerry Coyne ridiculed Nicholas Wade's NYT article discussing the negative consequences resulting from the anti-religious tone of most orthodox defenses of evolution.

Wade's article was far from ideal. He failed to distinguish clearly between the overwhelming empirical evidence...

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Why the 'Gene' Concept Holds Back Evolutionary Thinking

(83) Comments | Posted November 30, 2012 | 1:12 PM

Wendell Read just sent me notice of a new paper in Genome Biology linking transposable elements, long intergenic non-coding RNAs, and cell type. This paper highlights difficulties in understanding genome evolution using the conventional idea of "genes."

In the early days of genetics, following the rediscovery of Mendel's...

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Inter-Kingdom Horizontal DNA Transfer in All Directions: Infectious Bacteria Evolve by Acquiring Protein Domains From Eukaryotic Hosts

(24) Comments | Posted November 6, 2012 | 5:54 AM

Earlier blogs have covered horizontal DNA transfer between bacteria and from bacteria and fungi to animals. This blog will present some of the evidence for horizontal transfer in the reverse direction: DNA acquisition by infectious bacteria from eukaryotic hosts.

Bacteria pick up eukaryotic sequences encoding different...

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Evelyn Witkin, Jean Weigle, the SOS Response and How E. Coli Generates Mutations in Response to UV Irradiation

(92) Comments | Posted October 20, 2012 | 3:32 PM

Last week, PLOS Genetics published a delightful interview with National Medal of Science winner Evelyn Witkin. The interview rewards the time it takes to read.

From the 1940s to the 1980s, Evelyn (born 1921) was a key pioneer in understanding how E. coli and other bacteria respond to...

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Sociobacteriology: Small Cells Talking And Listening -- And How It May Affect You If You Go Under the Knife

(28) Comments | Posted October 16, 2012 | 8:32 AM

A couple of weeks ago, Sdf Dsfds asked me to write something about my work on bacteria as multicellular organisms. I promised to do so after posting the blog about horizontal DNA transfer in animal evolution. The announcement of the UCS Center for Science and Democracy...

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Union of Concerned Scientists Launches a New Center for Science and Democracy

(19) Comments | Posted October 7, 2012 | 4:27 PM

In commenting on a recent blog, James Ballard admonished me: "Might I suggest you not wait around in the protective wings of academia..."

Part of my response to James' useful admonition is to serve as a member of the National Advisory Board of the Union of Concerned...

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The Evolutionary Importance of Horizontal DNA Transfer into Animal Germ Lines

(143) Comments | Posted October 3, 2012 | 12:03 PM

In a recent blog, I discussed symbiogenesis, one way that sudden large changes have occurred in evolution. Symbiogenetic events included the origin of the eukaryotic cell. This major step enabled all the following evolution leading up to multicellular organisms, including us.

Let me repeat that last point...

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Could Bill Nye Have Done More to Keep Creationism out of the Classroom?

(165) Comments | Posted September 27, 2012 | 11:48 AM

On a number of occasions over the past month, my frequent commentator John Kwok has chided me to be more like "Science Guy" Bill Nye in defending evolution and science in general against Creationists (Bill Nye: Creationism Is Not Appropriate For Children).

I agree with John that...

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Mobile DNA Repeats and Transcriptional Formatting of the Mammalian Genome in Evolution

(9) Comments | Posted September 22, 2012 | 3:21 PM

I previously mentioned attending the European Molecular Biology Organization meeting on "Evolution in the Time of Genomics" this past May in Venice. There were several interesting talks about the functional and evolutionary roles of mobile DNA repeats. They provided good evidence that many of these repeats have helped establish genome...

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Further Thoughts on the ENCODE/Junk DNA Debates

(102) Comments | Posted September 18, 2012 | 1:12 PM

Last week, there were two HuffPost blogs on the release of the ENCODE (Encyclopedia of DNA Elements) project data: mine and one by colleague Michael White. We took opposing positions on the question of whether the ENCODE results are compatible with the "junk DNA" explanation for...

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Dan Hartl, Sewall Wright, and the Role of "Ecological Opportunity" in Evolution

(17) Comments | Posted September 12, 2012 | 5:18 PM

As I wrote in a previous blog, I attended the EMBO conference "Evolution in the Time of Genomics" in Venice this past May. At that conference, after my presentation (visible on YouTube), I had an exchange with Dan Hartl, a Harvard evolutionary biologist who studies...

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Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin'

(124) Comments | Posted September 12, 2012 | 5:01 PM

"And don't criticize
What you can't understand"

Last week, the ENCODE project (ENCyclopedia Of Dna Elements) released a tremendous amount of new information about our genomes. The results of literally hundreds of millions of experiments using the most current "high throughput" technologies provided the data for over a dozen...

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The Distinct Roles of Selection, Horizontal Transfer and Natural Genetic Engineering in Dangerous Superbug Evolution

(258) Comments | Posted August 29, 2012 | 11:57 PM

An August 25, 2012 Washington Post article talked about a superbug outbreak at the NIH. The article highlighted the problem that we are running out of useful antibiotics. Antibiotic resistance is an evolutionary question of great practical importance. I have recently been asked and agreed to sign on...

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Cell Mergers and the Evolution of New Life Forms: Symbiogenesis Rather Than Selection

(256) Comments | Posted August 21, 2012 | 5:13 PM

In the last blog, I questioned the creative role of natural selection in evolutionary innovation. To clarify further what I had in mind, this blog will look at one of the truly creative processes of tremendous importance in evolutionary history: symbiotic mergers of two distinct organisms to generate...

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