Robustness and Evolvability in Living Systems: (Princeton Studies in Complexity)

Book Description

All living things are remarkably complex, yet their DNA is unstable, undergoing countless random mutations over generations. Despite this instability, most animals do not grow two heads or die, plants continue to thrive, and bacteria continue to divide. Robustness and Evolvability in Living Systems tackles this perplexing paradox. The book explores why genetic changes do not cause organisms to fail catastrophically and how evolution shapes organisms' robustness. Andreas Wagner looks at this problem from the ground up, starting with the alphabet of DNA, the genetic code, RNA, and protein molecules, moving on to genetic networks and embryonic development, and working his way up to whole organisms. He then develops an evolutionary explanation for robustness.

Wagner shows how evolution by natural selection preferentially finds and favors robust solutions to the problems organisms face in surviving and reproducing. Such robustness, he argues, also enhances the potential for future evolutionary innovation. Wagner also argues that robustness has less to do with organisms having plenty of spare parts (the redundancy theory that has been popular) and more to do with the reality that mutations can change organisms in ways that do not substantively affect their fitness.

Unparalleled in its field, this book offers the most detailed analysis available of all facets of robustness within organisms. It will appeal not only to biologists but also to engineers interested in the design of robust systems and to social scientists concerned with robustness in human communities and populations.

Directed Evolution Library Creation: Methods and Protocols (Methods in Molecular Biology)

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Directed Evolution Library Creation: Methods and Protocols (Methods in Molecular Biology)

Manufacturer: Humana Press
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Directed Enzyme Evolution: Screening and Selection Methods (Methods in Molecular Biology)

ASIN: 1588292851

Book Description

A comprehensive compendium of cutting-edge protocols for the generation of molecular diversity. Described in step-by-step detail to ensure experimental success, these protocols include readily reproducible methods for random mutagenesis of entire genes or segments of genes, for homologous and nonhomologus recombination, and for constructing in vivo libraries in bacteria and yeast. In addition to the various protocols for creating libraries, this volume also describes ways to analyze libraries, particularly those made by recombination. An accompanying volume, Directed Enzyme Evolution: Screening and Selection Methods (ISBN: 1-58829-286-X), is devoted entirely to selection and screening methods that can be applied to the directed evolution of enzymes.

Copy for Both Volumes

Directed Evolution Library Creation: Methods and Protocols and Directed Enzyme Evolution: Screening and Selection Methods constitute an extraordinary collection of all the key methods used today for directed evolution research. Described in step-by-step detail to ensure robust experimental results, these methods will enable both newcomers and more experienced investigators to design and implement directed evolution strategies for the engineering of novel proteins. The first volume describes methods for the creation of mutated DNA molecules, or DNA libraries, encoding variants of desired proteins. The second volume describes methods for screening DNA libraries to isolate mutant proteins that exhibit a specified function.

Sudden Origins: Fossils, Genes, and the Emergence of Species

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Hoxgenes to the rescue?
Sits atop an important trend, but maybe too history-heavy
Hox genes, and the new origin of the species
A New Take on an Old Theory -- But Watch Out!
A Courageous Scientist and His Flawed Theory

Sudden Origins: Fossils, Genes, and the Emergence of Species
Jeffrey H. Schwartz
Manufacturer: Wiley
ProductGroup: Book
Binding: Paperback

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ASIN: 0471379123

Amazon.com

Despite the title, Darwin's Origin of Species doesn't really explain how new species are born. Scientists have been struggling with that thorny problem ever since its publication, and the recent revolution in molecular biology has turned up great piles of new evidence. Anthropologist Jeffrey H. Schwartz takes a close look at this evidence, as well as the more traditional paleontological material, in Sudden Origins: Fossils, Genes, and the Emergence of Species. He claims that the tide is turning in favor of "punctuated equilibrium"--the theory that species typically remain static for great lengths of time and then experience brief spurts of accelerated change--thanks in no small part to the discovery of homeobox genes.

These remarkable structures are the genetic equivalent of the proverbial butterfly wings that cause hurricanes halfway around the world--small changes can produce enormous effects. Homeobox genes regulate development and are remarkable similar between species and even between phyla--you share some with fruit flies, for example. By turning our attention toward embryology and development, Schwartz shows us that fossils can't tell the whole story, since much of it lies within the womb. He covers a lot of ground and stretches the reader's intellectual muscles; the scope of Sudden Origins and the greater understanding of Darwin's problem make the challenge well worth it. --Rob Lightner

Book Description

"Fascinating."-Nature
Finally a compelling answer to the question that has plagued scientists for centuries . . .
"A detailed and informative historical account."-Nature
"This is an intriguing and significant work."-Library Journal
"A provocative new theory to explain how species arise."-Scientific American
"A worthwhile attempt at bridging the new developments in how species may change and the evidence for the patterns of those changes."-American Scientist
Darwin may have argued that new species emerge through a slow, gradual accumulation of tiny mutations, but the fossil record reveals a very different scenario-the sudden emergence of whole new species, with no apparent immediate ancestors.
In this provocative and timely book, Jeffrey Schwartz presents a groundbreaking and radical new theory that explains exactly how evolution works. Turning to the marvels of genetics, paleontology, embryology, and anatomy, and introducing the recent discovery of an extraordinary type of gene, known as homeobox genes, Schwartz provides an evocative answer to the long-standing question: How do species emerge?
Writing with the expert knowledge only an insider can bring, Schwartz tells the intriguing history of the study of evolution, from the initial breakthrough discoveries to the famous Piltdown controversy up through the genetics revolution. Sudden Origins is a monumental book that ties together all the threads of evolutionary theory while providing a compelling answer to one of life's most enduring conundrums. This book is crucial reading for anyone who has ever pondered the mysteries of our evolutionary heritage.

Customer Reviews:

Hoxgenes to the rescue?.......2001-05-14

The first ten chapters is merely a historical survey of evolutionary discourse, and I shall not comment on them. It is the two final chapters that are supposed to offer a hopeful alternative to the beleaguered neo-Darwinian approach to evolution. Here the author relies on the role of homeobox genes, and highlights their effects on changes in morphology. His argument can be briefly summarised by referring to two of the examples he gives: the Rx gene in eye development, and the Manx gene in the development of the notochord during the larval stage of a species of tunicate.

Experiments with mice showed that individuals which carry a mutated (and therefore non-functioning) Rx gene failed to develop either an eye or its bony socket if the condition is homozygous, but individuals that are heterozygous in Rx undergo normal eye development. Schwartz argues that the reverse situation must have occurred in the past, i.e., a precusor mutated into the Rx gene. This was initially in the recessive state, as mutated genes generally are. This then spread widely through the population via heteroxygotes, until eventually homozygotes were produced in sufficient numbers to mate with each other. The mutant gene, i.e. Rx, was then expressed in the homozygotes, which developed eyes.

It is helpful to juxtapose the facts that the author appeals to, and the inferences he draws from them. The facts are that mutations in functioning genes render them non-functional - a loss of information. Schwartz turns this on its head and hypothesises that a mutation in a non-functioning DNA segment could render it functional - the emergence of novel information by natural processes.

One can get any complex multi-functioning mechanism, make a random change to one of its components, and render a part of the mechanism non-functional. It does not follow from this fact that the faulty component could have come about by chance, waiting for a random change to put it into working order. This is the kind of inverted logic employed above. The real world abounds in examples of natural processes producing degeneration, and causing malfunction in previously functioning mechanisms. The reverse process, however, has no basis in fact.

The case of the tunicate illustrates the importance Schwartz attaches to embryonic development in evolution. The homeobox gene, Manx, is responsible for the development of the notochord during the tunicate's larval stage. At a later stage the gene is deactivated and the adult tunicate does not possess a notochord. Schwartz hypothesises that at some point in the tunicate's evolution a mutation in some regulatory gene extended the duration of activation of the Manx gene, resulting in an adult with a notochord. This is a case of heterochrony, specifically paedomorphosis. Such a discrete change would be consistent with what one finds in the fossil record.

The author argues convincingly for the discrete nature of the fossil record, as many others have done before him. In doing so he poses an effective challenge to the neo-Darwinian model. But the substitute he offers is hardly able to provide the solution. Schwartz hypothesises on the possible discrete evolutionary changes that could be brought about by changes in the control genes, given a fully functioning genetic apparatus to start with. The real problem for evolution, however, is to explain how that fully functioning apparatus got there in the first place. Deactivation of a homeobox gene may possibly explain the reduction of a three-toed horse into a one-toed horse, as Schwaltz suggests, but it can hardly account for the origin of horses.

Since mutant genes are useless or lethal, it is hardly surprising that they are recessive rather than dominant. It is most reasonable to infer that this is part of life's defense mechanism, designed to protect the organism from potential damage from mutations.

Sits atop an important trend, but maybe too history-heavy.......2000-12-28

This is an excellent book that provides a reasonable introduction and much historical context to the concepts behind a class of theories of speciation that are gradually becoming less controversial.

The notion of cumulative gradual change in allele frequencies as the only source of variety has been a thorn in the side of serious biology for some time. Not least because it leaves the door open to claims that speciation itself is "improbable" in higher species. Richard Dawkins' brave attempts to rescue biology from "Mount Improbable" may very well turn out to be partly an exercise in futility.

Schwartz joins a number of recent authors and researchers to face head on the challenge of improving our understanding of evolutionary biology by recognizing that it makes perfect sense of much otherwise confusing data to allow for sudden "saltational" changes in species. As hard as it remains for many to swallow, S.J. Gould was probably right about much of this, and deserves credit for bucking the "received" view of Darwinism.

This book is disappointing however, in that it seems to revel in telling the history rather than describing the new concepts. There's just so much politics behind this issue that authors can't seem to avoid the temptation to add their own spin to the history in every book. But that part has been done already. Sterlny and Griffiths' "Sex and Death" does a great job of discussing all of the various chinks in the armor of the received view of how evolution works, without spending so much time interpreting intellectual history yet again.

The new part that is most exciting is the details of how regulatory genes work, their duplications and mutations, and the role they play in speciation. There is sadly relatively little of that in Schwartz's otherwise useful presentation.

A very recent release in the U.K. by Mark Ridley, "Mendel's Demon," looks like it handles similar deep questions but goes far more deeply into the genetics that forms the foundation for theories of sudden origins and other alternatives to simple cumulative gradual interpretations of Darwinism.

One point I wanted to make as a comment to a previous review. It was claimed at one point that this kind of theory is more congenial to the way many people view creation by God. That's something I think is a welcome sign. But they also commented that "creationists" is a meaningless label, and it seems to me that claim is simply nonsense. "Creationists" deny that speciation occurs at all, at least in the origin of humans. They don't argue that it could only occur suddenly. Whatever else they may accept or reject from evolutionary biology or genetics or paleoscience, it seems to me that they cannot accept that humans were not special creations of God separate from other animals. The United States is divided into those who find the close relationship of humans and apes ridiculous and those who pretty much take it for granted. That's not an easy line to cross, much less pretend it doesn't exist.

It would be very heartwarming and reaffirming to my faith in human reason of some people who consider themselves "creationists" were to find the theory of sudden origins in this book an acceptable version of evolutionary theory, but I'm not going to hold my breath waiting for it to happen.

The difference is critically important scientifically because the power of evolutionary thinking is not in whether we happen to be related to apes, but in the value of being able to apply adaptational thinking to species characteristics and describe and predict how characteristics relate to environments. Creationist interpretations deny the central concept of evolutionary thinking, that natural selection explains adaptation. The details of how it works and where other explanations supercede adaptational ones is what is left to ongoing research to discover.

That's where Schwartz contributes best to the literature, by placing "sudden origins" into its rightful historical context, (though I don't agree with some of his intellectual history in the medieval period). This is not something that creationists can honestly take any credit for, or honestly use in support of their agenda it is a theory of speciation not a denial of speciation.

Hox genes, and the new origin of the species.......2000-12-24

This is a very important source of information both as to the history of the Neo-Darwinian Synthesis and the recent discoveries of regulatory hox genes and the light they throw on the riddles of speciation and large scale evolutionary change. The realization that major morphological changes do not in fact occur in the fashion of microevolution (as presented by traditional Darwinists), due to the effect of homeobox genes, is a revolutionary discovery and confirmation of the importance of the developmental tradition moving in parallel to standard Darwinism. This data creates a foundation for the various theories of macroevolution and punctuated equilibrium proposed almost a generation ago but still sidelined by the Darwinian mainline. The book contains an invaluable review of paleoanthropological theories, issues of neotonous evolution, and the various genetical theories of Mendelism, from de Vries and Bateson, to Haldane, Wright, and Fisher. The views of Goldschmidt, and his near miss of this new perspective, is also treated. This confusing history of Mendelism sorted out is invaluable, and shows how cogent (in part) where the intimations of Bateson and Morgan. The new perspective both confirms the concept of 'macroevolution' while suggesting this can be seen as a microevolution of regulatory genes, a point open to debate perhaps. The next mystery is the evolution of these complex sequences of development. But that does not distract from the great usefulness of this account. One can dispense with much of the erroneous literature on evolution, a great saving in brain space. The endless debate over the slow evolution of the eye, etc, that went on and on and drove all parties batty is hopefully over if we know the right combination of homeobox genes will control the development of this and other organs. Times are changing in Darwin land. Highly recommended.

A New Take on an Old Theory -- But Watch Out!.......2000-03-29

Evolution, let's face it, is a creation myth for a post-industrial age. At the time Darwin (and Wallace) re-created the theory, which itself was old as time, PROGRESS was idolized by a Victorian society with many manners and little religion. The Industrial Revolution had proved that progress was not only beneficial, but necessary, and so Darwin's myth was taken to people's hearts. He believed in gradual progression, and was certain the fossil record would bear him out.

In fact, it doesn't. Part of that is the nature of fossils. To become a fossil a plant or animal must get itself stuck in a tarpit or a mudslide, and then stay there a few million years until done. By their nature, fossils cannot provide a record without gaps. And with the recent "winged dinosaur" fossil proven a hoax or forgery, there remains little trace of progression.

To cling to evolution as a philosophical framework, one must move to what the fossil record does show: saltation! New species appear in spurts and jumps. And this is, in fact, what Jeffrey Schwartz attempts to accomodate in this interesting new book. It's clear he knows his stuff.

But it isn't clear he knows his history. My own field is mediaeval scholastic thought rather than natural sciences. It's amazing how little scientists know about their own history, regurgitating long-exploded myths to show how dumb mediaeval thinkers were. I suppose part of this is because evolutionists frankly don't know and don't care about the difference between Creationists and people who believe in creation, but lump them all together. Creation is a belief that G-d Created the Universe. He did so in millions of years (look at the jumps, like the jump in the fossil record, between Gen. 1:1 and Gen 1:2). "Creationism" is an attempt to sneak Creation by the p.c. thought police who are terrified that G-d might be mentioned in a public place, especially when it might open the eyes of schoolchildren to alternative possibilities.

But Schwartz, possibly in an attempt to keep himself from being written off as a "Creationist" but to salvage his reputation as a legitimate scientist who does have a very valid take on evolution, not only makes this confusion, but he himself shows an utter lack of grasp on the development of science.

For instance, he writes that the church had a "stranglehold" on learning, which is a myth or at best a misconstruction. Ancient learning was preserved from antiquity, from barbarian marauders who destroyed everything in their path, in monasteries. When the barbarians and later the Vikings were calmed by their own acceptance of Christ, a flowering of intellectual activity resulted, particularly in the twelfth century, where Cathedral schools welcomed an amazingly wide variety of thought (even the development of the mode of thought now called humanism). Oxford, Cambridge, etc. through Europe were fostered by the scholastics, who wanted the propagation of education.

True, there was no universal literacy, but before the invention of printing. There is the illusion that "the church" controlled learning, because that's where the books were -- not only ancient works but the burgeoning numbers of books on all subjects, including natural sciences, such as they were able to study with the instruments at their disposal. One took orders to join in the intellecutal advancement because the monasteries and cathedral schools were where books were painstakingly copied by hand, and usually where they resided as they weren't appreciated elsewhere.

Today, PhDs are rewarded by bright young persons spending ten years writing and defending a micro-study dissertation, usually hammered out between the student and a master professor. Some are very interesting and shed new light; others are relegated to minor publications or even see no more light than the stacks of the university library. These days Universities, invented by the scholastics, represent just the same sort of "stranglehold" as Schwartz purports the church to have had. A bright amateur, say an obscure German railway clerk, might produce a paper that gains some acceptance, but it's increasingly unlikely.

Schwartz also mentions, as does everyone, that before Copernicus it was thought the earth was the center of the universe. What he fails to follow up with was that after Copernicus and into the 20th century a science long divorced from the church taught that the SUN was the center of the universe.

Indeed, it's important to study our historical roots. Scientists may find the subject uninteresting, and one can't expect a natural scientist to understand scholasticism, just as some, seeing a mediaevalist writing on evolution may be dismissed as ignorant.

He even has the temerity to say Augustine believed the earth was flat. He didn't, nor did his great mentor, St. Ambrose. There never was any such teaching, because no one believed it except a few oddballs who had no schools in the west and no following. What Augustine did say was that the earth may be round, but it was irrelevant to him.

One more problem with his historical presentation: somehow he manages to present an absolutely opposite case from the fact. He presents Creation as somehow racist, when it proves, as Thomas Jefferson wrote, "all men are created equal." Where he got the idea he floats about anyone who believes in Creation -- or ever did -- thinks there was more than one Creation, I can't say. There's only one in my Bible, although it is reiterated. His take seems to be that if someone writes a biography of Napoleon and they refer more than once to some aspect of Napoleon's life, that aspect must have repeated itself like a fugue from Toulouse to St. Helena! The fact is, evolution is the theory that can be construed as racist, and that was another reason Victorians adopted it. It not only confirmed their belief in progress, but their belief in the superiority of the white race, which was the "most progressed".

I was fascinated by Schwartz's presentation of his exciting new take on evolution. A natural scientist is more qualified to discuss it than I, and I hope Schwartz knows it better than he does the history of his discipline! His is a beautiful addition to the evolutionary myth and I would hate to see it dismissed by his peers.

A Courageous Scientist and His Flawed Theory.......2000-03-29

Saltations have always been a problem for evolutionary theorists, and supporters of saltations have generally been dismissed highhandedly. So has anyone who has questioned the dogmas of evolution. Authors of any books or articles questioning the status quo, for whatever reason, are branded "creationists", though most of those who dismiss them don't seem to understand the difference in those who believe in Creation, and the small coterie who cover themselves with the flimsy and meaningless term "creationist", and who do not represent believers in Creation. Creation cannot be proven in a laboratory -- but unfortunately, neither can evolution. And though for more than a century the fossil record has been scrutinized for proof, the evidence, if it proves any evolutionary theory, tends to support saltation. Since most evolutionary scientists, by their attitude, seem to live in terror under the misapprehension that by admitting their own theories are somehow incorrect means yeilding to the tiny but vocal "creationists", any suggestion that the holy writ of evolution can be questions on the slightest jot or tittle brings the scorn of the establishment on the questioner's head.

With this threat in mind, the author of SUDDEN ORIGINS has risks his reputation to propose a sweeping new theory in evolution that would account for the fossil record's evidence of saltations.

The major plus in the book is the history of evolutionary squabbles past. Frankly, this is something that evolutionary scientists need to heed. I've read too many scientific books where the author, usually some respected PhD at a prestigious institution, seems to have no grasp at all of the history of his topic. Certainly this is the case in astronomy, where myths of medieval cosmology and compete misunderstandings and misconstructions of astronomical development (not to mention outright lies taken as gospel) find their way into print as truth. Scientists ignore their history at their peril (cf: George Santayana). And perhaps examinations of the bickerings of evolutionary scientists within "the family" can help them to stop being so rigid.

If the book remained a history of evolutionary problems, it would be a five-star book -- such a book, from a scientific perspective, is necessary, but scientists seem too timid to do it themselves (what they need is a Teilhard in their ranks who will risk excommunication by the scientific elite) and leave it to the "creationists", who, like some scientists (and Teilhard) and unlike most genuine Christians, are not above fudging facts to reach their conclusions.

But he goes on with his theory, which is very specialized and interesting, but rather rough going for the lay reader. I eagerly await the author's forthcoming book, which promises to build on the history presented here. Unfortunately, his theory, like the double-sun theory for our solar system presented a few years ago in a book called NEMESIS, will most likely prove an interesting but ultimately futile study.

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A conversation that revealed nothing

A top pick for both public and school holdings.

Surprisingly Good Science for Such Plain English

Enjoyable read, though limited in depth

More like 3 and a half stars

Creatures of Accident: The Rise of the Animal Kingdom
Wallace Arthur
Manufacturer: Hill and Wang
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Binding: Hardcover

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The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution

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The Tinkerer's Accomplice: How Design Emerges from Life Itself

ASIN: 0809043211
Release Date: 2006-09-05

Book Description

The most important aspect of evolution, from a philosophical viewpoint, is the rise of complex, advanced creatures from simple, primitive ones. This “vertical” dimension of evolution has been downplayed in both the specialist and popular literature on evolution, in large part because it was in the past associated with unsavory political views. The avoidance of evolution’s vertical dimension has, however, left evolutionary biology open to the perception, from outside, that it deals merely with the diversification of rather similar creatures, all at the same level of “advancedness” from a common ancestor—for example, the classic case studies of finches with different beaks or moths of different colors.

The latest incarnation of creationism, dubbed intelligent design (or ID), has taken advantage of this situation. It portrays an evolutionary process that is constantly guided—especially in its upward direction—by the hand of an unseen Creator, who is able to ensure that it ends up producing humans. Creatures of Accident attacks the antiscience ID worldview, mainly by building a persuasive picture of how “unaided” evolution produces advanced creatures from simple ones by an essentially accidental process. Having built this picture, in the final chapter the book reflects on its religious implications.

Customer Reviews:

A conversation that revealed nothing.......2007-01-14

I was excited to read this book. I believe that we are "creatures of accident". The author failed at his goal to "demonstrate... that the rise of complex creatures can be explained with ease".

Evolution has a few simple concepts:
- Natural selection
- Survival of the fittest which allows inheritance of acquired characteristics. (Genes)
- Mutations, divergence of species (bad genes)

I am not a scientist, but I've been interested in creationism and evolution since 7th grade. I am now 43, and othen read literature on both subjects. This book failed because the author did not maintain his point of view. His thoughts turned into a litany of digressions; that made it difficult to get a concise understanding of evolution.

The first chapter titled "Hand Luggage Only" directed the reader to leave bias and preconceived notions behind and to read the book with an open mind. I'm not sure he made a point in the first chapter that set the course of the book or gave good reason to have an open mind. He continues the discussion with an explanation of life's lawn and life's ladder that became so confusing I considered whether it was worth reading more.

I found the last chapter on "Big Questions" most interesting. It showed that the author has his own baggage and failed to check it before attempting to explain a concept as intriguing and enlightening as evolution.

I do not agree with this author that atheism constitutes a system of faith. He seems angry at religion and seems to have a biased view of any opinion not his own. This is what constitutes a belief system; the notion that your understanding is correct and that everyone should/must agree with you. It is such dogmatic views that allow others to murder and slaughter their fellow human brothers and sister.

This book did not add to my understanding or appreciation of evolution, it revealed nothing.

A top pick for both public and school holdings........2006-12-14

Creatures of Accident: The Rise of the Animal Kingdom comes from a renowned professor of zoology in Ireland who delves into the weighty-sounding science of 'evolutionary developmental biology' - and while it may seem like this book is for college-level holdings, it will appeal equally well to general public library collections with its easy introduction to evolutionary theory. From analyses of the structure of life forms and the complex methods of evolution which are neither predictable nor straightforward to conflicts between creationism and evolutionary theory, this book provides both general reader and science readers with an easily-understood set of explanations, making it a top pick for both public and school holdings.

Diane C. Donovan
California Bookwatch

Surprisingly Good Science for Such Plain English.......2006-11-08

I read a lot of magazine and Internet articles about science and written in plain English for general readers. The science is usually vague and often inaccurate. Wallace Arthur manages to get across real science while avoiding jargon. For example, the old biology cliché "ontogeny recapitulates phylogeny" is rendered as "development repeats evolution". This is followed by a few paragraphs of explanation. And he covers a number of topics which are important for understanding evolution that aren't generally included id beginners' books.

The most important of these is gene duplication. The machinery that manages our DNA sometimes makes extra copies of one or more genes. The duplicate copies may then undergo mutation and take on new functions while the old ones remain unchanged. A LOT of evolution involves gene duplication. Arthur doesn't say how gene duplication happens - that requires biochemistry - but it is important to know that it happens.

Another topic is development, from egg to adult. This is critical for understanding the evolution of complexity. Some genes involved in development, such as the Hox genes that Arthur mentions, are important in evolution. Copying of Hox genes is a major factor in the increasing complexity of animals; some more advanced books have charts showing the parallel between Hox gene duplication and increasing complexity. The interaction of genes and proteins is another important topic. And there are other topics, too much for me to cover in a short review.

Arthur frequently pauses to relate a current topic to what came earlier in the book, or to suggest what is to come. People who read a lot of science books are used to doing this for themselves and might be annoyed by Arthur's doing it. But for true beginners, this will probably be helpful.

Creatures of Accident provides only a beginning look at the natural processes that give rise to complexity. A number of other books - all more advanced - go into the subject in more depth. I have reviewed several of these and I recommend them. Click above on "See all my reviews" for more. There is also a brief summary in my Listmania list "Natural Processes That Promote Evolution". To find it, click on my name, above, and scroll down my profile page to that title. I will mention here that Sean B. Carroll's The Making of the Fittest is an excellent next book for someone who has read Creatures of Accident; a reader who has had a decent HS biology course might want to start with that book. Carroll's Endless Forms Most Beautiful would be suitable for a college course, but is suitable for readers who are not bio students. Darwin in the Genome by Lynn Caporale looks at the evolution of those natural processes themselves. There are a number of very good books ranging from elementary to some suitable for graduate bio majors.

Creatures of Accident won't convince anybody that the ID claim is false; there's not enough detail for that. But it will give beginners a start to learning what evolution is really about. And that means the prospect of a lot of exciting reading ahead.

Enjoyable read, though limited in depth.......2006-10-31

Arthur Wallace's book is an informal account of how biological complexity has arisen in the evolutionary history of life. The book is written in a conversational style and the individual chapters are short, giving the reader the satisfying feeling that he is `getting somewhere'. It is clear that Wallace, a professor of zoology, knows his subject well. While I agree with the author's thesis that the evolution of complexity can be largely explained through Darwinian evolution by natural selection (that is, without invoking additional mechanisms or anything supernatural or mysterious like an `intelligent designer'), I found the book generally disappointing in its lack of detail concerning the evidence supporting the account he proposes (which I feel could have been encapsulated in a brief essay instead of a full-length book). Wallace notes that a basic strategy for creating novelty and for building biological complexity can be expressed in just a few words: Duplication, Diversification, and Co-option- old genetic tools and morphological elements doing new tricks. Co-option (or `exaptation') is the process by which a structure or system with an original function adds or changes to a new function, a process which is enabled by redundancy and duplication. These ideas are not new, having been discussed in greater depth by a number of other evolutionary biologists and geneticists. While it is good to see them summarized succinctly in this book, there is a frustrating paucity of detail concerning specific examples of this evolutionary process. Wallace stresses the important role of alterations in developmental pathways as engines of evolutionary novelty, an idea which is also not new and embodied in the field of "Evo-Devo" (the study of evolution from a developmental perspective). However, discussion of Evo-Devo in the book is frustratingly limited (for readers seeking greater depth, I recommend Sean Carroll's book, Endless Forms Most Beautiful).

Wallace concludes that evolutionary history, at least in its broad strokes, is probably more predictable than has been acknowledged by other scientists stressing evolutionary contingency and divergence (e.g., S.J. Gould). Replaying the tape of life on Earth or on other Earth-like planets would probably yield similar (though certainly not identical) biological designs and would likely display similar evolutionary trajectories, at least on a coarse-grained scale. The fact of evolutionary convergence is often cited as evidence in support of this prediction (see Simon Conway-Morris's work for a rich account of evolutionary convergence). While I generally agree with Wallace's assessment, I found Wallace's case for evolutionary repeatability to be unsatisfying (for readers seeking a more persuasive and detailed argument for the repeatability and predictability of biological evolution see David Darling's book, Life Everywhere).

The author rightly dismisses so-called intelligent design (ID) as an explanation for life, biological complexity, and adaptation, claiming that the processes of divergence, duplication, and co-option occurring within a framework of Darwinian natural selection are sufficient to account for the evolution of biological complexity. While this may very well be the case (and I tend to agree), Wallace devotes little attention to how specific biological structures claimed by ID supporters to be "irreducibly complex" could have evolved via the strategies he mentions. Instead, he simply dismisses ID as "crass nonsense", without detailing precisely why it is so. In my opinion, it behooves the author to provide a much deeper critique of ID than he offers (for some excellent critiques of ID, see Young and Edis's Why Intelligent Design Fails, Perakh's Unintelligent Design, and Shanks' God, the Devil and Darwin: A Critique of Intelligent Design Theory).

Finally, Wallace describes himself as "a committed agnostic" with regard to God's existence and asserts that "committed atheism" is just as much of a faith position as is "committed theism". He cites Richard Dawkins as an example of a "convinced atheist". Dawkins may be "convinced", but he is not "committed", however. At least according to his most recent book, The God Delusion, Dawkins admits that he would give up his atheism if there were powerful evidence in support of theism. But Dawkins's atheism is hardly a dogmatic position- rather it is an intellectually honest and sensible one, which derives from following reason and evidence wherever they may lead. Wallace suggests that there is no evidence either for or against God's existence and that therefore the appropriate position is that of agnosticism. However, there is indeed evidence, both direct and background, which counts against the God hypothesis, thereby rendering the existence of God more improbable than not (for instance, one piece of evidence against the God hypothesis is that minds and intelligence are the derivative result of biological evolution- not primary- and that thought requires a physical substrate, e.g., a physical brain, in order to occur). How Wallace's "committed agnosticism" is not itself an example of "faith-based" dogmatism is beyond this reviewer's capacity to comprehend. Is there no evidence that in principle could sway him either way on the question of God's existence? Is Wallace a "committed agnostic" concerning the existence of fairies, ghosts, goblins, a host of pagan gods, and the "Flying Spaghetti Monster"? Does Wallace truly evaluate the probability that these extraordinary entities exist to be at 50 percent? If not, then what is the warrant for Wallace's "committed agnosticism" concerning the existence of God?

Wallace also blames Stalinist atrocities on the "faith of atheism". Overlooking Wallace's mistaken view that atheism (at least that which is the outcome of careful reasoning and an honest consideration of evidence) is "faith-based", Wallace's suggestion that Stalin's acts were done in the name of atheism is uncritical at best and misleading at worst. Arguably, the massacres of Stalin's reign were committed in the name of Socialist ideology, not atheism. His atheism (if indeed he was an atheist) appeared to be largely incidental, and not an essential motivation for his barbarous acts. At least Wallace's condemnation of atheism as the cause of Stalin's atrocities deserves a far more critical analysis than is offered in his book. And even if atheism was the primary motivation behind Stalin's acts (which is debatable), this does not thereby make theism or agnosticism any more intellectually defensible.

More like 3 and a half stars.......2006-10-20

I just finished this book yesterday. I completed it in two days, not necesarily because it was so exciting, but more so because it was written in a very easy to read, conversational tone--and I do mean a conversational tone, not an informal tone. The author frequently and intentionally repeats himself, refers to material that will come later, and interjects personal experiences--it all reminded me of a folksy college professor giving a lecture. Along with this non-scholarly approach, the book includes a glossary, but no foot or endnotes. On the other hand, the reader needs some background in at least popular magazine biology to be able to follow the book.

The putative point of the book is to explain how complexity in living organisms arises through evolution. The author gives a good explanation, but takes awhile getting there, due to his conversational tone. Basically, the explanation is that mutations lead to extra but unused body parts, which evolution can then experiment with, possibly producing greater complexity in the lineage. I had never read this explanation before, or at least not remembered I had, so I learned something. I might mention that the author makes a point that lineages can also de-evolve to lower complexity in this manner (de-evolve is my word, not the author's). He also makes the point that, say, birds differing only in beak types are of the same level of complexity, so are therefore not an example of evolution leading to greater complexity. (In fact, I suspect he would say that all extant bird species birds are at essentially the same level of complexity.) Thus the book makes a big point of the difference between micro- and macro-evolution.

The author states that he is an agnostic, not having much truck with either atheism or religious fundamentalism. He tells of visiting creationist websites as background before writing the book, and being appalled at how the websites mistate evolutionary theory. Interestingly, at one point toward the end of the book, the author says that some concept or other is no longer "just a theory", using the term as non-scientists and creationists do. I'm sure "hypothesis" would have been the preferred term, and was surprised to see the author's use of "theory" since he seems very cognizant of using terminology correctly in the rest of the book--for example being quite emphatic about the difference between agnostcism and atheism.

So all in all not a bad book, but one I suspect whose main point about how complexity in living organisms can arise through natural processes could have been dealt with in an article a few pages long in any number of popular scientific magazines.

Evolutionary Algorithms: The Role of Mutation and Recombination (Natural Computing Series)

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Interesting. Very academic
Essential Reading on Evolutionary Algorithms

Evolutionary Algorithms: The Role of Mutation and Recombination (Natural Computing Series)
William M. Spears
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 3540669507

Book Description

Despite decades of work in evolutionary algorithms, there remains a lot of uncertainty as to when it is beneficial or detrimental to use recombination or mutation. This book provides a characterization of the roles that recombination and mutation play in evolutionary algorithms. It integrates prior theoretical work and introduces new theoretical techniques for studying evolutionary algorithms. An aggregation algorithm for Markov chains is introduced which is useful for studying not only evolutionary algorithms specifically, but also complex systems in general. Practical consequences of the theory are explored and a novel method for comparing search and optimization algorithms is introduced. A focus on discrete rather than real-valued representations allows the book to bridge multiple communities, including evolutionary biologists and population geneticists.

Customer Reviews:

Interesting. Very academic.......2001-06-13

This book is based on the author's PhD dissertation and it shows (you can download the dissertation from the web). There is page after page of mind numbing step-by-step derivations that do not add too much to the discussion. I would have enjoyed the book more if Spears had shortened some of his derivations. I found the results interesting. Although some of the conclusions seem fairly obvious after reading the book, I think it is important that someone took the time to come up with the mathematical models to formalize things.

The empirical approach is very interesting, and I wish more people would follow and improve on Spears' ideas. Empirical studies of evolutionary algorithms are justly critized for being too limited to a few "standard" functions that do not show much about the capabilities and limitations of the algorithms. Spears took a good step in emulating the machine learning comunity and using test problem generators. With these generators, the experimenters can play around with parameters such as the multimodality or noise in a problem and make systematic empirical studies of the algorithms. Unfortunately, it is difficult to translate from those systematic studies to real life. For example, how much noise or how many peaks are in real-life problems?

Still, I would recommend to go and read this book (or the free dissertation). Skip the equations, though, and get to the point.

BTW, Dr Gordon (the first reviewer) is married to Spears, which may explain some of the excitement in her review...

Essential Reading on Evolutionary Algorithms.......2000-12-25

This book is an essential resource for anyone studying the theoretical underpinnings of evolutionary algorithms (EAs). The book very carefully analyzes the effects of two fundamental evolutionary operators, recombination and mutation, and their interaction with evolutionary selection. This analysis significantly enhanced my understanding of EAs because of the fundamental role that these operators play. The book begins with the more traditional static analysis approach, but soon it transitions to a very exciting dynamic analysis. Just as neurophysiologists have discovered that when studying the brain it helps to view it as a dynamic process, Spears illustrates how much better we can understand EAs when using dynamic models, such as the popular Markov chain model approach. One of the best parts of the book was the creative use of problem generators for empirically testing the theory and for characterizing the classes of problems for which each EA operator is more effective. This was exciting for two reasons. For one, it encourages EA researchers to break away from myopic use of the same old test suites. Secondly, the problem characterization has tremendous potential value for practical applications of EAs.

Another of my favorite parts of the book was Spears' novel algorithm for compressing Markov chains. I particularly liked the mathematical analysis, which was both elegant and clear. Because Markov chains are widely used, e.g., in operations research, control theory, and artificial intelligence, this compression algorithm has wide-reaching implications for reducing the complexity of modeling a variety of systems.

The intended audience for Spears' book is computer scientists, mathematicians, and biologists, as well as students of evolutionary processes. To make the book accessible to such a diverse audience, the presentation is exceptionally clear and devoid of excessive jargon and obscure mathematics. Only an undergraduate level math background is required. One thing that I found mildly distracting was the repetition between chapters. The reason for the repetition was to make the chapters as self-sufficient as possible. Nevertheless, I read the book as a continuous whole and for anyone who does this I recommend skimming or skipping over the redunant portions. If this is done, the reader can maintain a high level of interest.

Book Description

As an introduction to principles of evolution, this inexpensive paperback text is ideally suited as a main text for general evolution or as a supplement for general biology, genetics, zoology, botany, anthropology or any life science course that utilizes evolution as the underlying theme of all life.

Genetics and the Search for Modern Human Origins

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Within and Between: Evolution of the Study of Human Origins
Lucid and Engaging
.

Genetics and the Search for Modern Human Origins
John H. Relethford
Manufacturer: Wiley-Liss
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471384135

Book Description

A major debate in anthropology concerns the relationship between anatomically modern humans and earlier "archaic" humans including the Neandertals. What was the origin of modern humans? Did we arise as a new species in Africa 200,000 years ago and then replace archaic human populations outside of Africa, or are our origins part of a single evolving lineage extending back over the past two million years? In addition to fossil and archaeological evidence, anthropologists have increasingly turned to using genetic data on living populations to address this question. Patterns of genetic variation within and between living human populations are felt to contain clues as to our species' evolutionary history, and provide a reflection of the past.

This book reviews the modern human origins debate focusing on the genetic evidence relating to our origins, including genetic variation in living humans and recent discoveries of ancient DNA from fossil specimens. Following a brief introduction to the problem and a review of evolutionary genetics, the book focuses on gene trees and the search for a common ancestor, genetic diversity within populations, genetic distances between populations, the use of genetic data to reconstruct ancient demography, and Neandertal DNA. The main point of the text is that although the genetic data are often compatible with a replacement model, they are also compatible with some multiregional models. The concluding chapter makes the case that modern human origins are mostly, but not exclusively, out of Africa.

Customer Reviews:

Within and Between: Evolution of the Study of Human Origins.......2005-04-05

Coming from a perspective outside the field of biological anthropology I am always struck by a certain level of hesitation upon embarking on a document written by someone from within this technical field. While evolutionary theory is the main tenant of both this field as well as my field of study, evolutionary psychology, the approaches, suppositions, and terminologies are often perceived as being different and very distinctive. Likewise, the conflict within the field itself, the various approaches, and contrasting interpretations utilizing the same evidence can easily leave an outsider (not to mention insiders!) feeling overwhelmed and confused. After reading Relethford's Genetics and the Search for Modern Human Origins, some of this hesitation, and some of the seeming non-overlap between scientific groups, has been lifted.

Relethford offers a clear, well-constructed argument on the modern human origins debate that has been volleyed back and forth between (and within!) the different areas of anthropology. He presents a basic background in the area of evolutionary theory, genetics, and the archeological evidence; an in-depth review of the various genetic studies and a strong argument for the application for the various computer-modeling techniques currently used. What is especially refreshing is that rather than relying on one technique (i.e. computer models or archeological evidence) and by not taking a definitive stance on one model alone to explain the time and place of human origins, he presents the perspectives of the central models of human evolution as a moderator, rather than a competitor. This manner allows the evidence itself to engage the reader into developing their own interpretation, rather than forcing them to accept the authors' own biases.

The evidence presented throughout the book is used mainly to pit the African replacement model and the Multiregional evolution model against each other, in what Chamberlin (1897) called "the method of multiple working hypotheses" and Platt (1964) called "strong inference". By comparing the evidence to each model, rather than trying to fit it all within one chosen framework, Relethford arrives at the conclusion that modern humans arose from a "Mostly Out of Africa" scenario. This suggests that humans did indeed first arise in Africa, with subsequent evolutionary forces (mutation, natural selection, genetic drift, gene flow, and the interaction of) mediated by inter and intra-continental migrations, affecting their evolution both within this continent of origin and throughout the world. Overall, the genetic patterns elucidated by human DNA studies (mtDNA, Y-chromosome, and nuclear) suggest that Africa was the point of origin, with an initial migration toward the Middle East, branching off to Europe, Asia and Oceania, with a smaller (yet still substantial) return migration back home to Africa.

Likewise, Relethford examines some of the controversy surrounding the placement of Neandertal's in relation to human lineage's. Were Neandertal's a distinct sub-species of archaic human which contributed genetic material to modern humans, or are we completely free of Neandertal genes? This issue is explored within the context of the archeological evidence which suggests that there are certain Neandertal characteristics in human bone structure, and the genetic evidence which supports the latter proposition. Again by careful expression he explains the evidence in the light of each model, and suggests that the best fit is still up in the air.

Overall, the issues this book explores are well articulated and are examined in a style that doesn't necessitate substantial background knowledge in the study of human genetic variation or modeling formulas. However, Relethford also doesn't ignore those who are well-versed in such areas. Genetics are discussed in a technical manner and mathematics are explained at the end of the book in "Chapter Notes".

A few notes of caution must be expressed upon opening this book. First, this book should be read while attempting to leave your preconceived biases behind. This book is aimed at giving an unbiased presentation of the current evidence for the origins of modern humans. As such, it should be read with an open mind. Second, there are some minor editorial, and factual mistakes made within the book. These mistakes are, for the most part, unnoticed by individuals without a background in either genetics or genetic theory as applied to modern human origins. For individuals who wish to use this book as a tool for learning the basics of genetics this may be a detriment. Third, because new evidence within this and other fields utilizing evolutionary theory are changing daily, some of the evidence offered here may quickly become dated. However, the main approach of this book, the overarching perspective, and the engaging manner in which it is written, should make it a must read for anyone interested in gaining at least a rudimentary understanding of this area of scientific scrutiny.

By assimilation of bones and stones, genes, memes, and models, Relethford sifts through the various forms of evidence for the emergence and subsequent existence of Homo sapiens. He accomplishes this feat in a calming integrated manner that makes sense to those who may think that the techniques and approaches common within the field are inherently different from their own. As such he has showed, at least to this reader, that once again the within group variation may be more prevalent than between group variation.

Lucid and Engaging.......2002-07-02

"Relethford writes...in a lucid and engaging manner. He dispassionately examines the major controversies surrounding modern human origins and clearly identifies the ways in which the genetic data impinge on the predictions of the explanatory models....[T]his book will appeal to the general science reader, as well as being suitable for upper-level undergraduate and graduate courses in Biological Anthropology." (American Journal of Human Biology)

........2001-06-12

The modern human origins debate is finally illuminated with the first clear and understandable discussion of the genetic arguments on both sides. Relethford is a key player in this debate, and he brings to it a sorely needed perspective, placing the exciting laboratory results in the theoretical frame that explains them, and doing it in manner that the rest of us can grasp. It's good writing, because it's good thinking, and Relethford is to be congratulated for his efforts in clarifying and explaining the complex issues that underlie the conflict between Multiregional evolution and the Eve Theory. --Milford H. Wolpoff, Paleoanthropology Laboratory, University of Michigan

The Mathematical Theory of Selection, Recombination, and Mutation (Wiley Series in Mathematical & Computational Biology)

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WORLD OF MATHEMATICAL GENETICS.... EKREM AYNA

The Mathematical Theory of Selection, Recombination, and Mutation (Wiley Series in Mathematical & Computational Biology)
R. Bürger
Manufacturer: Wiley
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471986534

Book Description

"It is close to being a masterpiece...could well be the classic presentation of the area." Warren J. Ewens, University of Pennsylvania, USA
Population genetics is concerned with the study of the genetic, ecological, and evolutionary factors that influence and change the genetic composition of populations. The emphasis here is on models that have a direct bearing on evolutionary quantitative genetics. Applications concerning the maintenance of genetic variation in quantitative traits and their dynamics under selection are treated in detail.
* Provides a unified, self-contained and in-depth study of the theory of multilocus systems
* Introduces the basic population-genetic models
* Explores the dynamical and equilibrium properties of the distribution of quantitative traits under selection
* Summarizes important results from more demanding sections in a comprehensible way
* Employs a clear and logical presentation style
Following an introduction to elementary population genetics and discussion of the general theory of selection at two or more loci, the author considers a number of mutation-selection models, and derives the dynamical equations for polygenic traits under general selective regimes. The final chapters are concerned with the maintenance of quantitative-genetic variation, the response to directional selection, the evolutionary role of deleterious mutations, and other topics.
Graduate students and researchers in population genetics, evolutionary theory, and biomathematics will benefit from the in-depth coverage. This text will make an excellent reference volume for the fields of quantitative genetics, population and theoretical biology.

Customer Reviews:

WORLD OF MATHEMATICAL GENETICS.... EKREM AYNA .......2005-06-13

Well It is different than quantitative genetics, forget about the statistical work,forget the statistical rules. Now a new subject exists. Mathematical genetics (NOT QUANTITATIVE GENETICS). This book is a must for every one who is interested in genetics and who is planning a life for it. The book its self is not highly related with diagnosis genetics but IF YOU WANT TO UNDERSTAND THE THEORY OF GENETICS GET THIS BOOK WELL IT MAYBE EXPENSIVE BUT DO NOT FORGET THAT YOU WÝLL BUY ONCE NOT TWICE :) BUY IT DO NOT THINK MUCH AS I DID

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For fans of Richard Dawkins...

The Intelligent Genome
Adolf Heschl
Manufacturer: Springer
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Binding: Hardcover

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ASIN: 3540671668

Book Description

Do our genes determine our behavior? Do education and environment have any influence at all? Do humans occupy a unique position in evolution? To clarify these provoking questions, the author takes the reader on an ambitious and entertaining journey through a variety of scientific disciplines. In doing so, he creates an image of human evolution that says that our entire individual knowledge is determined - to the smallest detail - by phylogeny. " ... before shocked humanists discard such radical theses as mere nonsense, they should not completely close their minds to the explanations of a biologist who says that we still know very little about the genetic determination of human behavior and that the invariance of many forms of behavior present in all cultures nourish the suspicion that the determining role of genes is probably far more comprehensive than we have ever dreamed."
Wolfgang Wieser, translated from his review in "Merkur" (Sept./Oct. 1999)

Customer Reviews:

For fans of Richard Dawkins..........2004-06-02

I have just begun to read this book and am delighted to find it extends the logical implications I found so right in Richard Dawkins' work.

If you're interested in a little extraordinary illumination about the phenomenon of the genome in the cosmos, then please have a look at what's presented here.

I will update this review upon further investigation, but I didn't want to leave this page without some well-deserved positive feedback.

Book Description

Lewontin is undoubtedly one of the most distinguished evolutionary biologists of our time. He has contributed to science not only by his own work on evolutionary theory and molecular variation and by his influence on the many young scientists who have worked with him, but also by asking us to think about the relationships between the science we do and the world we do it in. This collection of essays is produced in honor of Lewontin's 65th birthday. This unique volume offers comprehensive coverage of modern evolutionary genetics from molecules to morphology by a group of star authors, including his students and colleagues. Sciences in general, and the life sciences in particular, need their own critic, and Lewontin has been an untiring critic of science and its relevance to society. This volume brings out the central role of evolutionary genetics in all aspects of its connection to evolutionary biology and is a must for all graduate students and researchers in evolutionary biology.

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