Evolution: A View from the 21st Century (FT Press Science) [Hardcover]

James A. Shapiro (Author)

Book Description

Publication Date: June 22, 2011 | ISBN-10: 0132780933 | ISBN-13: 978-0132780933 | Edition: 1

James A. Shapiro's Evolution: A View from the 21st Century proposes an important new paradigm for understanding biological evolution. Shapiro demonstrates why traditional views of evolution are inadequate to explain the latest evidence, and presents a compelling alternative. His information- and systems-based approach integrates advances in symbiogenesis, epigenetics, and mobile genetic elements, and points toward an emerging synthesis of physical, information, and biological sciences.

Editorial Reviews

From the Author

Most debates about evolution sound like the last fifty years of research in molecular biology had never occurred. Evolution: A View from the 21st Century aims to acquaint the reader with previously "inconceivable" but currently well-documented aspects of cell biology and genomics. This knowledge will prepare the reader for the inevitable surprises in evolutionary science as this new century runs its course. 

The capacity of living organisms to alter their own heredity is undeniable, and our current ideas about evolution have to incorporate this basic fact of life. The genome is no longer the read-only memory (ROM) system subject to accidental changes envisaged by conventional theory. We now understand genomes to be read-write (RW) information storage organelles at all time scales, from the single cell cycle to evolutionary eons. 

The contemporary concept of living organisms as self-modifying beings coincides with the shift in biology from a mechanistic to an information- and systems-based view of vital functions. The life sciences have converged with other disciplines to focus on questions of acquiring, processing and transmitting information to ensure the correct operation of complex adaptive systems.  

Today, we endeavor to understand how new vital capacities arose in the course of evolution during at least 3.5 billion tumultuous years of earth history. Two broad lines of research have made it possible to formulate a new vision of the evolutionary process. One examines how cells regulate the expression, reproduction, transmission and restructuring of their DNA molecules. The other comprises advances in studying interspecific hybridization, symbiogenesis, epigenetics, horizontal DNA transfer and mobile genetic elements. 21st Century evolution science explains abrupt events in the DNA and fossil records. Moreover, this contemporary mode of thinking makes it possible to envisage realistic paths to complex evolutionary innovations.

Additional online material for this book can be found at FTPress.com/shapiro and shapiro.bsd.uchicago.edu/evolution21.shtml.

From the Back Cover

“Shapiro has written a stimulating, innovative manuscript that surely Darwin would have liked.”

—Sidney Altman, Yale University; Nobel Laureate in Chemistry, 1989

 

“Based on a long and highly competent personal experience in science and his novel insights into biological functions, the author has reached views of biological evolution that can reveal to a wide, interested readership how the living world co-evolves with the environment through its intrinsic powers.”

—Werner Arber, Professor Emeritus, University of Basel, Switzerland; Nobel Laureate in Physiology/Medicine, 1978

 

“Professor Shapiro’s offering is the best book on basic modern biology I have ever seen. As far as I can tell, the book is a game changer.”

—Carl Woese, University of Illinois; discoverer of Archaea, the third realm of life; National Medal of Science 2000

 

“‘[N]atural genetic engineering’ explains evolutionary processes that preceded people by at least 3,000 million years. Shapiro’s detailed account of ubiquitous genetic dynamism, DNA machination, repair, and recombination in real life, bacterial to mammalian, destroys myths.... Shapiro’s careful, authoritative narrative is entirely scientific and should interest all of us who care about the evolution of genetic systems.”

—Lynn Margulis, University of Massachusetts, Amherst; National Academy of Sciences, National Medal of Science 1999

 

“[T]his book is a magnificent analysis of the key questions of the origin of variation.... Jim Shapiro has new insights on all the central issues of evolutionary theory. The genome becomes a read-write storage system rather than the sole determinant of heredity. After reading this book, you will find it imperative to see biology as the 21st century is coming to see it.”

—Denis Noble, CBE FRS, Balliol College, Oxford; author of The Music of Life

 

“This book highlights...dynamic systems biology and engineering between the evolving genome, cell, and environmental stresses...affecting the...read-write memory system underlying life’s evolution.”

—Eviatar Nevo, University of Haifa, U.S. National Academy of Sciences; explorer of Evolution Canyon

 

James Shapiro’s Evolution: A View from the 21st Century proposes an important new science-based paradigm for understanding biological evolution. Shapiro explains how conventional evolutionary theory (as elaborated from the neo-Darwinian synthesis) has become outdated, and he marshals new molecular genetics and DNA sequence evidence to reinterpret fundamental evolutionary processes.

 

Shapiro’s new information- and systems-based paradigm integrates important phenomena such as symbiogenesis, epigenetics, and natural genetic engineering. He demonstrates how active cell processes can drive the rapid, large evolutionary changes seen in the DNA that cannot be adequately explained by earlier theories.

 

Evolution: A View from the 21st Century is likely to generate extensive discussion throughout the biological community and might change your own thinking about how life has evolved. Shapiro’s vision also has major implications for evolutionary computation, information science, and the growing synthesis of physical and biological sciences.

 

Living cells: evolution’s not-so-blind watchmakers
How cells acquire and use external information–and what that means for evolution

 

Cellular read-write mechanisms and informatics-based approaches

Cell-mediated genome inscriptions at time scales ranging from days to epochs

 

Nature’s leaps: beyond Linnaeus and Darwin

The growing molecular evidence for rapid, large-scale, evolutionary change

 

A new conceptual basis for 21st century evolutionary research

Discovering how evolutionary innovation is generated, dispersed, and diversified

See all Editorial Reviews

Product Details

• Hardcover: 272 pages
• Publisher: FT Press; 1 edition (June 22, 2011)
• Language: English
• ISBN-10: 0132780933
• ISBN-13: 978-0132780933
• Product Dimensions: 7.7 x 0.9 x 9.2 inches
• Shipping Weight: 1.2 pounds
• Average Customer Review: 4.0 out of 5 stars  See all reviews (28 customer reviews)
• Amazon Best Sellers Rank: #605,757 in Books (See Top 100 in Books)

More About the Author

James A. Shapiro 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). William Hayes was his PhD supervisor, and Sydney Brenner was an unofficial adviser during his time in Cambridge as a Marshall Scholar.
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 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 fusions, Together with Pat Higgins in 1989, he showed that activation of Mu replication and transposition is spatially organized in bacterial colonies. 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 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. Prof. Shapiro has been a leading scientific critic of orthodox evolutionary theory for 20 years.
Following a teaching stint at the University of Havana (1970-1972) and research at Brandeis (1972-1973), Prof. Shapiro moved to a faculty position at the University of Chicago in 1973. He has been there since then with occasional sabbaticals and visting professor appointments at the Institut Pasteur, Tel Aviv University, Cambridge University and the University of Edinburgh, where he was the Darwin Prize Visiting Professor in 1993. He is a fellow of the American Academy of Microbiology, the AAAS and the Linnean Society of London. In 2001, he received an honorary O.B.E. from Queen Elizabeth for services to higher education in the UK and US.

Most Helpful Customer Reviews

56 of 60 people found the following review helpful

5.0 out of 5 stars A provocative view of evolution July 27, 2011

By Frank Harold

Format:Hardcover

The history of life is peppered with novelties, functional and adaptive features never seen before. Eyes to see with come to mind, and wings to fly with; so do the seeds of flowering plants, the intricate cilia that move eukaryotic cells, and a thousand others. How do innovations arise? This is the question addressed in this book, and there can be few issues more crucial to our understanding of evolution.

The conventional answer was formulated seventy years ago as part of the Modern Synthesis, which melded Darwin's insights from natural history with the rising science of population genetics. It invokes a static genome composed of discrete heritable genes that are subject to variation by mutation and other accidents; the variations are then culled by natural selection, with the result that adaptation of the organism improves. Evolution takes place slowly and gradually, by small random steps. The fossil record displays many instances, the classic one being the transformation of horses' toes. But skeptics have questioned this scenario from the beginning, arguing that there cannot have been time enough to bring forth the profusion of biological novelty, and in any event random mutations are more likely to degrade organization than to create it. Such doubts have been reinforced in recent years by our growing knowledge of how genomes are constructed and how they operate. James Shapiro puts himself squarely on the side of the skeptics, and offers an alternative vision that he dubs "natural genetic engineering".

Briefly, the architecture of genomes turned out quite unlike what had been expected. In higher organisms, at least, genes are composed of both coding and non-coding sequences, and must be spliced prior to expression. Classical protein- coding sequences make up an astonishingly small proportion of the genome, just a few percent. The remainder features regions that specify an intricate network of regulatory elements, many based on RNA rather than proteins. These are concerned, not only with the expression of individual genes, but with the fidelity and architecture of the genome as a whole. Genomes also contain numerous stretches, long and short, of repetitious DNA, whose physiological functions are not obvious. Junk DNA? Not necessarily. Some can translocate from one locus to another (or at least did so in the past), with the help of enzymes specified by the genome itself, and thereby reconfigure the instructions laid out in the database. The most conspicuous agents of change are the transposons, "jumping genes", that migrate from one place to another spontaneously or in response to stress. Transposons disrupt genes, but they often carry along genes or fragments of genes, which are thereby transferred from one neighborhood to another. Bacterial genomes are more streamlined than those of animals, but no more static. They are buffeted by a ceaseless rain of foreign genetic material, picked up from the environment or carried by viruses. Cells are forever restructuring their genomes, which proved to be more dynamic than we thought, more malleable and interactive, and therefore more evolvable.

At first sight, the continuous makeover seems merely to supply more variations for selection to winnow, but Shapiro argues that there is much more to it than that. Natural genetic engineering generates different kinds of variation from those produced by classical mutations, one gene at a time. Rearrangements can take place at multiple locations at once and shuffle entire domains from one protein to another, producing novel combinations quickly and abruptly, perhaps even purposefully. Genomes, it seems, are built to evolve ---not at the petty pace of classical genetics, but in leaps that entail rearrangement of the genetic architecture or the import of foreign information. So could this be the way that organisms generate the multiple, coherent variations that seem required to manufacture complex organelles such as eyes or flagella? At the end of the day, that is a question that must be answered by experiment; we are not there yet, but the technology to address such issues is coming to hand.

A book that sets out to break images will raise questions in readers' minds, and hackles too. The central question for me turns on that supple word, "random", which commonly means precisely what the user wants it to mean. When cells sense danger, they restructure their genome by natural genetic engineering; but the variations so generated are still "random" in the sense that they are products of chance, not directed by the needs of the organism. There seem to be no truly adaptive mutations, targeted genetic changes that respond in a specific manner to a particular environmental stress or opportunity. Discovery of such directed variations would really shake the foundations of evolutionary thought! I would hold that to be impossible, but in the context of self-organizing cellular systems the idea no longer sounds as fantastic as it did a decade ago.

So this is a provocative book, one that will make you re-examine what you thought you knew. Candor compels me to add that it does not make for easy reading. Molecular biology comes in endless, mind-numbing detail, much of which the author felt obliged to incorporate. Chapter 2, which alone makes up over a third of the text, is a heavy slog that non-specialists will find discouraging, and so did I. The references number over a thousand; surely, they could have been better selected, and listed alphabetically by author! Yet it would be a big mistake to give way to irritation and fling this book to the winds. Skip along to later and more intelligible chapters, and you may return to the molecular morass in better spirit tomorrow. Dense and demanding as it is, this work may just hold insights needed to make Darwinism work in the real world.

Franklin M. Harold, Department of Microbiology, University of Washington, Seattle.

Address for correspondence: 10525 226th Street, SW, Edmonds, WA, 98020

59 of 67 people found the following review helpful

5.0 out of 5 stars Evolution: The Untold Story June 29, 2011

By Perry Marshall

Format:Hardcover|Amazon Verified Purchase

"Evolution: A View from the 21st Century" is the first book with an accurate depiction of evolutionary processes. To my knowledge, it has not been possible to buy a book that gave you the whole story. Most mechanisms described here were first discovered decades ago. Yet until now, few people knew anything about them.

This book describes:

-"Natural Genetic Engineering" refers to cells' innate ability to re-organize their genomes in response to hundreds of kinds of inputs. This is the star of the show. Not natural selection.

-Horizontal Gene Transfer, cells exchanging segments of DNA to instantly gain new features;

-Inter-species hybridization - new species form when unlikely mates cross from two different species;

-Symbiogenesis, when separate organisms physically merge to form a new species;

-Epigenetics, shaping heredity without altering the DNA sequence;

-Whole Genome Duplication - DNA doubling to expand "hard drive space" and make room for novel features.

Others have grasped at these mysteries with varying degrees of success. "The Plausibility of Life: Resolving Darwin's Dilemma" by Kirschner and Gerhart note how evolution re-uses the same components and processes. But they fall short of recognizing how this is done.

Suzan Mazur's "The Altenberg 16: An Exposé of the Evolution Industry" offers a kaleidoscope of evolutionary ideas but doesn't reach a conclusion. Fodor's "What Darwin Got Wrong" makes good on its title but offers no alternative. Margulis' and Sagan's "Acquiring Genomes" offers a vital puzzle piece, Symbiogenesis, but could have gone much further.

Most popular books and many college textbooks gravely misrepresent the driving forces behind adaptation as random and accidental. This is tragic, because real-world evolution is awe inspiring in its sophistication, elegance and order.

"Evolution: A View from the 21st Century" succeeds where others failed. Shapiro delivers volumes of of evidence for his 'third way' - a tested alternative to both Creationism and Darwinism. This new model is a fundamental revision to evolutionary theory. It answers the questions raised by these other authors. Yet you'll find not a trace of anxiety or polemic.

Interesting insights include the following:

* As cells divide, two separate error detection & correction mechanisms repair DNA copying errors in real time. This reduces the intrinsic error rate of 1 in 100,000 to 1 in 1 billion. Impressive.

* The Hox complex ("Hox Gene") directs growth and body symmetry in fruit flies. Its activity is amplified in mammals and the exact same code directs vastly more complex growth patterns in humans.

* "As evolution proceeds, so does evolvability": As organisms rise in sophistication, their evolutionary feats become more impressive and take less time. Cells re-use and re-combine existing systems in new ways. This is opposite of what we might expect if evolution were random.

* Shapiro shovels dirt on gradual random adaptations. Changes are often rapid and almost never random; the cell militantly guards against copying errors. He says periods of mass extinction are followed by episodes of new developments because organisms must respond fast to changing ecosystems.

* Organisms are intrinsically teleological. They behave much like human engineers. He suggests they may be sentient.

* He notes that physicists and other outsiders bring a level of open-mindedness to evolution that biologists have forbidden for 100 years. (One of my clients is a biotech company in Tel Aviv. The founder says only in the last 5-7 years have large numbers of people from Computer Science begun to pursue genetics. Thankfully, the tide is beginning to turn.)

* 1162 references buttress his case with volumes of published papers.

* Companies and universities commit resources to research programs that do not produce instant gratification. Contrary to those who deny teleology, Shapiro says organisms are similarly forward-looking, having purposes beyond the present. He says viruses appear to play a role in this, generating novelties which other organisms later adopt.

I liked the concluding chapters. They counter prohibitions that have crippled evolutionary research for the last 50 years. He suggests that many fields, from technology to economics, stand to benefit from evolutionary research. He's being modest. We can learn far more from cells than they can learn from us.

Shapiro resists temptation to spar with his opponents. There's not a hint of ad hominem; those who deserve to be ignored are simply not mentioned. Instead of hearing arguments, you witness unswerving commitment to further the aims of science. He's a gentleman through and through.

I do have some cautions. This is not an easy read and the dense material isn't supported by graphics. (The online supplement does include some illustrations). Informed lay people will appreciate this book, but it's squarely aimed at biology professionals. If you're a lay person without a biology background, feel free to skip the hard core technical content.

That said, you'll still get a better understanding of evolution's toolbox from the 50 pages you do read than in almost any other book available. If you're serious about evolution, the whole 150 pages is worth the effort.

No one can accuse Shapiro of operating on the fringe; he himself discovered transposition in bacteria decades ago. All is scrupulously documented. The book is endorsed by several world-class biologists including Lynn Margulis, Sydney Altman and Carl Woese.

Like his mentor Barbara McClintock, Shapiro has made an immense contribution to evolutionary biology. It's hard to imagine that traditional neo-Darwinism can survive the onslaught much longer. James A. Shapiro might someday be regarded as one of the great researchers of our time. May his tribe increase.

18 of 20 people found the following review helpful

5.0 out of 5 stars Excellent summary of our understanding of evolutionary mechanism, and a manifesto for future researchs June 30, 2011

By Michael J. Edelman TOP 100 REVIEWERVINE™ VOICE

Format:Hardcover|Amazon Vine™ Review (What's this?)

There have been four major revolutions in the understanding of inheritance and evolution: First, the Mendelian revolution, which explained how characteristics of organisms might be passed on to successive generations. Second, the Darwinian, which described the process of speciation, and the idea of selection within a gene pool. Third was the discovery of DNA, and unless you're a biologist, that's probably as far as your knowledge goes.

But in the years since Watson's and Crick's description of the double helix of DNA have seen an explosion in the understanding of genetics and evolution that is perhaps even more far reaching than the three previous revolutions combined. The idea of gradual evolution, with natural selection paring away at a set of random mutations has been overthrown in favor of a much more active, one might almost say goal-seeking mechanism, in which organisms play an active role in shaping their evolution.

Consider the case of drug immunity in bacteria. The old story goes something like this: You dose a colony of bacteria with penicillin, killing off 99.99% of them, but then remaining 0.01% carries with it an immunity to penicillin. They replicate and pass this immunity on to their offspring, creating a new colony of penicillin resistant bacteria. You now dose this regrown colony with amoxycillin, killing off 99.99%, and the remaining fraction reproduce, and then you use streptomycin and so on and so on, each time regenerating the community with the new immunity.

There's a serious problem with this story. How can immunity to all possible antibiotics be carried somewhere in the colony? That would imply that every colony of bacteria contains an infinite number of genes that bestow immunity on an infinite number of possible antibiotics- clearly an impossibility. Random mutation is much to slow a mechanism to create these immunities over the times observed. The implication is that some much more active mechanism is at work.

It turns out that a lot of bacteria (and other cells) display what's called natural genetic engineering- the ability to force changes in their genetic structure in order to adapt to change in a single generation. That's kind of astounding. It implies a much greater active role for cells than has ever been imagined. Add to that other recently discovered phenomena, like "horizontal" transfer of genetic fragments between organisms. This is no mere hypothetical; It's been hypothesized that such a mechanism is responsible for the acquisition of immunity to glyphosate weedkillers (i.e., Roundup) in plants that have been exposed to GM crops carrying that gene.

All this is part of what author Shapiro and others see as consequences of the active information-processing properties of cells- the cell not as a mere repository of genetic information (or "read only memory", as Shapiro puts it) but a full blown information processor, storing, manipulating, and creating new information. There are error-correction functions that actually repair strands of DNA in real time during replication, and strands of DNA can actually "double" to increase the amount of information that can be encoded, as new information is acquired by an evolving organism. And there are epigentic factors, information not carried within the DNA, that also contribute to the evolution and genetic transmission of characteristics.

This is not, despite the inviting cover and title, a work of popular science. Rather, it's a summary of current knowledge and a manifesto (if you will) for future research that appears to be aimed at researchers in the field. As such, it's not easy going, even for those with some background in biology and genetics. Nonetheless, this is a very rewarding book for those who have the background and a strong interest in evolution- not just biologists, but researchers and students computer scientists, physicists, and others interested in the mechanics of evolution and evolutionary processes across nature and natural systems.