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74 of 78 people found the following review helpful
on July 27, 2011
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
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72 of 82 people found the following review helpful
on June 30, 2011
Format: HardcoverVerified 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.
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25 of 28 people found the following review helpful
Format: HardcoverVine Customer Review of Free Product( 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.
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16 of 17 people found the following review helpful
on September 26, 2013
Format: PaperbackVerified Purchase
I got this book mainly to use as a comparison for another book I'm reading, Nei's _Mutation-Driven Evolution_. Koonin's _The Logic of Chance_ also falls in the category of recent books by seasoned researchers whose primary focus is molecular, and who argue that we ought to rethink evolution based on findings of molecular biology or molecular evolution. The 5-word summaries of these books are:
* Engineering, not accident, provides innovation (Shapiro)
* Mutation, not selection, drives evolution (Nei)
* After Darwinism, things get complicated (Koonin)

In the case of Koonin, you have to read the whole book to understand what he means. If you are not familiar with the past 10-20 years of findings from comparative genomics, then it will be educational, and regardless of your familiarity with genomics, it will be entertaining and thought-provoking. In the case of Nei, you can read the whole book and still not understand his thesis because he never defines terms and never actually compares mutation and selection to determine which one drives evolution.

In Shapiro's case, the book explains precisely what is meant by the idea that innovation is the result of engineering, not accident, though he leaves open the question of what are the general implications of this for evolutionary theory.

The argument begins with understanding that heritable variations generally aren't chemical accidents, but programmed responses catalyzed by enzymes acting in complex pathways, sometimes induced by genomic damage or cellular stress.

Shapiro is right about this part. Some kinds of mutations can be seen as accidents, like when a polymerase accidentally inserts a T instead of a C. But other mutations cannot be understood in this way. Most mutation is not an accident like a branch falling on your roof during a storm and leaving a hole. When cells leave unrepaired holes in our DNA, the outcome is genetic death, not mutation. Instead, mutation is like a branch falling on your roof and leaving a hole, followed by a repair-bot auto-detecting the damage and then shingling over both the branch and the hole using the wrong color of shingles. The mutation is not the hole (which has been repaired), but the funny lump in your roof and the patch of differently colored shingles.

The situation gets creepier when we consider that our genomes are chock full of mobile elements. To describe these little zombies as organisms or genomic parasites might be misleading, but their abundance in the most permissive genomes clearly represents the exploitation of a niche: hide out in the genome, get replicated passively for free, and occasionally copy yourself to a new site, facing a risk of losing your free ride (by damaging it) for the benefit of increasing your numbers, which increases your chance of long-term persistence.

Finally, there are cases in which organisms execute specific DNA changes, like switching from one mating type to another in yeast by a stereotyped transposition event.

Shapiro calls all of this "natural genetic engineering". His book includes multiple tables and heavily referenced descriptions of a variety of different processes of heritable change.

In part 3, he lists many cases in which non-infinitesimal changes have played a role in evolution. That is, a great variety of mutations are not infinitesimal modifications, but significant rearrangements, e.g., moving a piece of DNA from one location to another. When we examine the record of evolutionary history, we see that these changes are frequently important in evolution. Change has not occurred entirely by random infinitesimal changes.

The issue of gradualism is a big muddy issue among evolutionists. Darwin clearly said that his theory would break down if a complex organ did not result from numerous successive slight modifications, and his 20th century followers repeatedly doubled down on this bet. When challenged that this theory could not explain the incipient stages of useful structures, they insisted that any slight change in the right direction would be sufficient, and no saltations are needed. A protein or a hox cluster or a genome is clearly a complex organ, and any protein, RNA or genome clearly could have evolved by single-residue changes, i.e., ATGC can change to ATCGTTAGC or any other sequence one residue at a time. If evolution does not occur in this way, then it is not the kind of process that Darwin and his followers imagined. Shapiro is clearly arguing throughout Part III that evolutionary change does not occur in the atomistic way that Darwin's view demands. Sometimes proteins change by blocks being added or deleted. Genomes undergo doublings and fusions as well. We don't understand the details of how innovations are established, and Shapiro's spin on this isn't necessarily the right one, but we at least know this: in molecular evolution, the incipient stages of useful structures often involve a jump.

For Shapiro, the role of non-infinitesmal mutations in molecular evolution clinches the argument that, in evolution, innovation is introduced by natural genetic engineering, and that we should re-think our understanding of evolution on this basis. The idea of a contradiction between science and teleological thinking must be abandoned. Cells carry on goal-directed activities, including mutation. The changes in evolution aren't random, and they aren't infinitesimal. We need a new evolutionary theory that takes into account this new view.

Some of the weak points in this argument are pointed out by Wilkins ([...])-- a friend of Shapiro's who critiques his book in a gentlemanly way.

I don't agree with Shapiro's conclusions, for reasons that I won't explain, except to say that, just as the architects of the Modern Synthesis went way off the deep end characterizing natural selection as an artistic creator-- a writer, composer, or painter working with the variational "raw materials" of words, notes or pigments-- Shapiro has gone off the deep end characterizing the variation-generating process as "natural genetic engineering."

Though Shapiro is wrong, his book is worth reading. What makes the book worth reading is that (1) it is chock full of useful facts that are not familiar to most evolutionists, and (2) it is short, well edited, and well referenced. Kudos to the scientific editor, Kirk Jensen. Shapiro shows excellent form as a writer. He is clear about terms and concepts and provides numerous signposts to the reader. When he makes a logical leap and falls short, you know it. As a reader, you can take what you want from this book.

The problem with the book is the kind of problem you would expect when a molecular biologist delves into evolutionary theory. Shapiro has brought a knife (and not a particularly large one) to a gunfight. If you want to take a seat at the high table of evolutionary theory, and be part of a generation-spanning dialog with evolutionists living and dead, then you need to actually read their work. Shapiro could start by trying to understand West Eberhard, or Kirschner & Gerhardt, because they are all working on a similar angle.

By way of disclosure, I'm a professional researcher, I'm sympathetic to the need for reform in evolutionary theory, and I have published some work relevant to this topic, which anyone may find by searching.
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10 of 11 people found the following review helpful
on July 20, 2011
Format: HardcoverVerified Purchase
As a well read non-scientist I found Shapiro very informative and easy to read. I highly recommend this work for anyone who wants an excellent overview of the current state of our understanding of evolution. He provides a glossary, references and index. He outlines a revolution in our thinking on the subject "It replaces the "invisable hands" of geologically time and natural selection with cognitive networks and cellular functions for self-modification. The emphasis is systemic rather than atomistic and information-based rather than stochastic". pg. 146. I'm going to give this a second reading!
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26 of 33 people found the following review helpful
on June 23, 2011
Format: Hardcover
Shapiro has written an extraordinary well researched and game changing look at the theory of Evolution. the Modern Synthesis defenders will be up in arms.

His research is beyond question. His knowledge of the subject of molecular biology is elucid and clearly obvious.
His conclusions make sense out of a theory of evolution that for so long has been described as "random mutation for fitness and natural selection."
Shapiro explains the developments in molecular biology since the last 40 years of the twentieth century and justifys the need for a new paradigm for evolution.
He describes living cells as cognitive, interacting with purpose to insure survival.
He explains evolutionary novelties arising as a result of active modification and repair made by the cells in a mostly non-random process.
He shows that natural genetic engineering is the driving force of evolution.
He refuses to be caught up in the idealogical stuggle between Modern Synthesis apologists and the Intelligent Design advocates.
He has the courage to set out the new evolutionary theory. A sensory network cell system fueled by cell cognition, an information based system as compared to merely random mutation and natural selection.
this is the most informative, unbiased book on evolultion I have ever read. A must read for anyone wanting to find out how evolution occurs.
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9 of 10 people found the following review helpful
VINE VOICEon August 2, 2011
Format: HardcoverVine Customer Review of Free Product( What's this? )
Altough this volume can be tough going for the lay person, those with a background in the biological sciences and science buffs will find much to interest them. The author, a celebrated bacterial geneticist, has been a leading critic of evolutionary orthodoxy, positing that the genome is read-write memory system as opposed to the write-only model that currently prevails. Evolution occurs on the molecular level, and the author brings together systems-based informational organization, horizontal DNA transfer capabilities and basic updated evolutionary models together to form a new paradigm. Dr. Shapiro's advocacy of natural genetic engineering drives the forward motion of this interesting book. A very helpful glossary of terms and an extensive list of references are included.
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11 of 13 people found the following review helpful
on October 14, 2011
Format: Hardcover
Karl Popper proposed this procedure as falsification in which a central and dominating conceptual framework is shown to contain increasing contradictory assumptions and is therefore replaced by a more appropriate description that can better integrate the available empirical data than the previous one. In this respect, central to Darwinian Evolution is the narrative of the origin of novel organisms or organism functions by variation and selection. With the rise of molecular biology and genetics, the adaption of this narrative to nucleic acid sequences occured, mutations (stochastic damage and copying errors) and their selection is the conceptual basis for Francis Crick's dictum of the central dogma of molecular biology or as he noted too: "The discovery of just one type of present day cell which could carry out any of the three unknown transfers (protein-DNA, protein RNA, protein-protein) would shake the whole intellectual basis of molecular biology". In his book "Evolution: A View from the 21st Century" James Shapiro demonstrates all the current knowledge of the many types of present day cells that carry out the three unknown transfers in great detail. He convincingly proves that the main reason for biological novelty is not random mutations but genetic and genomic change by a variety of natural genetic engineering agents, competent to (re)regulate, alter and invent genomic sequences and formatting, all of them coordinated. From this perspective the neo-darwinian paradigm does not fit into the 21st century view of how evolution occured and still occurs.
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8 of 9 people found the following review helpful
on September 1, 2011
Format: Hardcover
After the much celebrated bicentenary of Charles Darwin, the microbial geneticist J. A. Shapiro from the University of Chicago proposes us a quite invigorating update of evolutionary theory, which he bases on the recent enormous developments in molecular biology, especially in higher organisms.

In doing so, he revisits some conceptual backgrounds characteristic of the last two centuries, such as gradualism in evolution via the occurrence of random mutations and the role given to natural selection. The role of both is of course recognized but has to be put in to perspective with the main claim that the knowledge acquired over the last twenty years of genome sequencing reveals an immense arsenal of tools described collectively under the metaphor of natural genetic engineering and which could play a major role in evolution.

It is a challenge to which Shapiro devotes himself with an impressive pedagogical array of definitions and references for both the specialist and non-specialist reader interested in the evolution of life. In this respect, the glossary of technical terms is remarkable for its effective and informative conciseness. Two levels of reading, one for the specialist (around 1200 references!) and one for the non-specialist reader, are proposed throughout the text, both with their own array of references not to mention a substantial number of web sites and the attention put into the construction of an on-line version. The reader has in his hand a small book which straight away gives a feeling of comfort with its well spaced-out typography and relevant subtitles, the pleasant to the touch quality of the paper and an intriguing front cover: an animal with two large eyes or a butterfly wing?

Of the book's 253 pages, 105 pages are devoted to the glossary, references and index. This also testifies to the personal engagement of the author and his quasi-existential desire to make all the relevant information available to each and every reader and to communicate with her or him (see the striking but discreet use of "you" throughout the text). In 147 pages, J. A. Shapiro describes what knowledge of genomes has taught us about how a cell can sense its environment, rearrange substantial parts of the genome in circumstances that are critical for growth, survival or proliferation of the organism by involving horizontal gene transfer, mobile genetic elements and/or intricate symbiotic associations.

With such a guide (personnally, I especially liked, amongst a plenty of striking, provocative and convincing sentences in the book, the key sentence "The capacity to change is itself adaptive" , we are engaged in a fascinating exploration of a variety of natural genetic engineering mechanisms (some leading to impressive capacities of genome restructuration as a response to external dangers) in the genomes of bacteria, archaea, yeasts, plants, ciliate protozoa, and humans.

At every step, despite the anguishing or forbidding complexity of some subjects, such as the immune response, the genomics of ciliates or epigenetics, they are dealt with in a self-evident, appealing and simple but not simplistic way. The reader is considered here as a real partner and we are offered one of the very first comprehensive panoramas of the teachings provided up to now by deciphering genomes from bacteriophages to man.

Special emphasis is placed on comparative evolution dynamics and the evidence provided by the hundreds of sequenced genomes in all the kingdoms of life and by the tens of millions of genes that have been deciphered, annotated and compared. In addition, straightforward strategies to test the role of natural genetic engineering are proposed as well as propositions for further studies and developments.

When we close this book , through the sheer power of words, we have visited a wonderful interactive museum of life, and we have read a new version of our own history.

Max Mergeay, microbiologist, has studied the adaptation of soil bacteria to the industrial revolution
Hon.professor, Université Libre de Bruxelles, Belgium
Consultant, Belgian Center for Nuclear Energy (SCK*CEN), Mol, Belgium & European Space Agency (ESA)
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49 of 65 people found the following review helpful
on April 8, 2012
Format: HardcoverVerified Purchase
Anthony M. Dean, who works on the molecular evolution of microbes at the University of Minnesota, has bitten the bullet, read Shapiro's book, and reviewed it in the latest issue of Microbe. Unlike Shapiro, Dean doesn't see the edifice of modern evolutionary theory as about to crumble. Dean's take on Shapiro's anti-Darwinian claims:

"It is one thing to establish that certain cellular subsystems do not conform to received dogma. It is quite another to establish that a paradigm shift in thinking is necessary. Every evolutionary biologist knows the field is littered with the corpses of those who once heralded the arrival of the next Kuhnian Messiah. At the end of Part II Shapiro too has failed to convince that the many fascinating molecular phenomena he describes requires a wholesale jettisoning of Darwinian doctrine. Indeed, throwing out basic Darwinian principles (random mutation, heritable variation, and the sieve of natural selection) would seem folly, as they surely predate the evolution of such highly evolved nonconformist subsystems as CRISPR-Cas.

In Part III Shapiro seriously overreaches. He argues that horizontal gene transfer, symbiogenesis, whole genome doubling, and the modular and duplicative nature of protein evolution are non-Darwinian because they do not conform to strict vertical inheritance and Darwin's advocacy of "numerous, successive, slight variations." Shapiro asserts "The data are overwhelmingly in favor of the saltationist school that postulated major genomic changes at key moments in evolution . . . Only by restricting their analyses to certain classes of genomic DNA, such as homologous protein coding sequences, can conventional evolutionists apply their gradualist models."

His (Shapiro) stance is patently unfair. Thomas Huxley famously criticized Darwin for championing too gradualist a view of phenotypic evolution. Today's Darwinists accept Huxley's criticism. Many evolutionary studies focus on gradually evolving homologous coding sequences precisely because these are best for establishing phylogenetic relationships among species-a matter of some importance to biologists. Horizontal gene transfer, symbiotic genome fusions, massive genome restructuring (to remarkably little phenotypic effect in day lilies and muntjac deer), and dramatic phenotypic changes based on only a few amino acid replacements are just some of the supposedly non-Darwinian phenomena routinely studied by Darwinists. Shapiro's implication that gene duplication and functional divergence is somehow non-Darwinian is also wrong. New uses for old parts has long been a staple of the Darwinian diet. In a spectacular example of cognitive dissonance Shapiro first describes, with fanfare, how Woese identified the Archaea as a distinct group of prokaryotes using phylogenetic analyses of rRNA sequences-analyses that assume "the slow accumulation of random gradual changes transmitted by restricted patterns of vertical descent"--only to later assert that "The DNA record definitely does not support the slow accumulation of random gradual changes transmitted by restricted patterns of vertical descent."

I have read the book and I concur with this review.
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