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61. The Triune Brain in Evolution:
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62. Biological Sequence Analysis :
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63. 3D Math Primer for Graphics and
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64. Introduction to Population Genetics
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65. Earth : An Intimate History
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66. What Evolution Is
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67. The Journey of Man : A Genetic
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68. Our Family Tree: An Evolution
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69. The Phylogenetic Handbook : A
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71. Fundamentals of Queueing Theory
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72. How Humans Evolved, Third Edition
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73. Data Analysis Tools for DNA Microarrays
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74. Introduction to Computational
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75. The Cartoon Guide to Genetics
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76. What Makes Biology Unique? : Considerations
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77. Beginning Perl for Bioinformatics
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78. Finding Darwin's God: A Scientist's
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79. Bioinformatics: A Practical Guide
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80. Games of Strategy

61. The Triune Brain in Evolution: Role in Paleocerebral Functions
by Paul D. MacLean
list price: $204.00
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Asin: 0306431688
Catlog: Book (1990-02-01)
Publisher: Kluwer Academic Publishers
Sales Rank: 318720
Average Customer Review: 5 out of 5 stars
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Reviews (1)

5-0 out of 5 stars

The Triune Brain...A Provocative Theory Goes Unchallenged

Paul D. MacLean has distinguished himself as a foremost figure in neuroscience. His early contributions to the understanding of the brain lie most notably in the area that he has named the limbic system. For the past thirty years, he has dedicated his research efforts at the NIMH Laboratory of Brain Evolution and Behavior, which he heads, to the promotion of his theory of the triune nature of the modern mammalian brain. His latest work, _The Triune Brain in Evolution: Role in Paleocerebral Functions_, is the paramount testament to that effort. The book is an impressive volume incorporating research from evolutionary biology, neuroscience, physiology, animal behavior, ethology, etc., into an insightful framework from which he draws many interesting, provocative conclusions, implications, and suppositions.

The triune theory has gained wide recognition, attention, and application in fields as diverse as psychiatry, education, and theology. However, neuroscientists have made little comment on the theory, pro or con, and, for the most part, have ignored it. Although chapters dedicated to the topic have appeared in a number of symposia, MacLean is usually the author. Since MacLean's peers, professional neuroscientists, have almost unequivocally declined comment, it thus becomes quite difficult for a novice to gain a critical view of the theory. In fact, since MacLean's review of the field is seemingly so complete, he is free to present the established thought on the evolution of the brain as he wishes. The novice is left only with his own efforts to sort things out. ... Read more

62. Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids
by Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison
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Asin: 0521629713
Catlog: Book (1999-07-01)
Publisher: Cambridge University Press
Sales Rank: 62111
Average Customer Review: 4.73 out of 5 stars
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Book Description

Probablistic models are becoming increasingly important in analyzing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project.For example, hidden Markov models are used for analyzing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it is accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time presents the state of the art in this new and important field. ... Read more

Reviews (11)

5-0 out of 5 stars Excellent overview of probabilistic computational biology
This book is a very well written overview to hidden Markov models and context-free grammar methods in computational biology. The authors have written a book that is useful to both biologists and mathematicians. Biologists with a background in probability theory equivalent to a senior-level course should be able to follow along without any trouble. The approach the author's take in the book is very intuitive and they motivate the concepts with elementary examples before moving on to the more abstract definitions. Exercises also abound in the book, and they are straightforward enough to work out, and should be if one desires an in-depth understanding of the main text. In addition, there is a software package called HMMER, developed by one of the authors (Eddy) that is in the public domain and can be downloaded from the Internet. The package specifically uses hidden Markov models to perform sequence analysis using the methods outlined in the book.

Probabilistic modeling has been applied to many different areas, including speech recognition, network performance analysis, and computational radiology. An overview of probabilistic modeling is given in the first chapter, and the authors effectively introduce the concepts without heavy abstract formalism, which for completeness they delegate to the last chapter of the book. Bayesian parameter estimation is introduced as well as maximum likelihood estimation. The authors take a pragmatic attitude in the utility of these different approaches, with both being developed in the book.

This is followed by a treatment of pairwise alignment in Chapter Two, which begins with substitution matrices. They point out, via some exercises, the role of physics in influencing particular alignments (hydrophobicity for example). Global alignment via the Gotoh algorithm and local alignment via the Smith-Waterman algorithm, are both discussed very effectively. Finite state machines with accompanying diagrams are used to discuss dynamic programming approaches to sequence alignment. The BLAST and FASTA packages are briefly discussed, along with the PAM and BLOSUM matrices.

Hidden Markov models are treated thoroughly in the next chapter with the Viterbi and Baum-Welch algorithms playing the central role. HIdden Markov models are then used in Chapter 4 for pairwise alignment. State diagrams are again used very effectively to illustrate the relevant ideas. Profile hidden Markov models which, according to the authors are the most popular application of hidden Markov models, are treated in detail in the next chapter. A very surprising application of Voronoi diagrams from computational geometry to weighting training sequences is given.

Several different approaches, such as Barton-Sternberg, CLUSTALW, Feng-Doolittle, MSA, simulated annealing, and Gibbs sampling are applied to multiple sequence alignment methods in Chapter 6. It is very well written, with the only disappointment being that only one exercise is given in the entire chapter. Phylogenetic trees are covered in Chapter 7, with emphasis placed on tree building algorithms using parsimony. The next chapter discusses the same topic from a probabilistic perspective. This to me was the most interesting part of the book as it connects the sequence alignment algorithms with evolutionary models.

The authors switch gears starting with the next chapter on transformational grammars. It is intriguing to see how concepts used in compiler construction can be generalized to the probabilistic case and then applied to computational biology. The PROSITE database is given as an example of the application of regular grammars to sequence matching. This chapter is fascinating reading, and there are some straightforward exercises illustrating the main points.

The last chapter covers RNA structure analysis, which introduces the concept of a pseudoknot. These are not to be confused with the usual knot constructions that can be applied to the topology of DNA, but instead result from the existence of non-nested base pairs in RNA sequences. The authors discuss many other techniques used in RNA sequence analysis and take care to point out which ones are more practical from a computational point of view. Surprisingly, genetic algorithms and algorithms based on Monte Carlo sampling are not discussed in the book, but the authors do give references for the interested reader.

The best attribute of this book is that the authors take a pragmatic point of view of how mathematics can be applied to problems in computational biology. They are not dogmatic about any particular approach, but instead fit the algorithm to the problem at hand.

5-0 out of 5 stars Brief and clear
I keep coming back to this book for its readable, applicable summaries of basic algorithms.

One chapter covers the basics of dynamic programming for string matching: a staple of bioinformatics computing. The authors come back to it a number of times as they introduce new variations on the string-matching theme. They give about the clearest description of the Needleman-Wunsch and basic variants (including Smith-Waterman) of any book I know.

The bulk of the book is devoted to Hidden Markov Models (HMMs), as one might have guessed in a book with Eddy as co-author. It covers the basics of model construction, motif finding, and various uses for decoding. Again, it covers all the basics so clearly you'll want to start coding as soon as you read it.

The later sections of the book cover phylogeny and tree building, along with the relationships to multiple alignment. Good, solid, clear writing prepares the reader for texts that may be more specialized, but possibly less transparent.

The next-to-last chapter, on RNA folding, is weaker than the ones before, in my opinion. It ties to the other chapters reasonably well in terms of algorithms, but I don't think it does justice to the thermodynamic models of RNA folding. If there is any weakness in this chapter, though, it does not detract from the strengths elsewhere.

The final chapter, the "background on probability", is the one that I think needs the most support. If you don't already understand its topics, I doubt that this will help very much. (If you do understand them, you won 't need the help.) There's nothing inherently tricky about probability, but individual distributions carry many assumptions, and I did not see those spelled out well.

This shouldn't be the only book in your bioinformatics library. If you really want algorithms, though, it's a good book to have in the collection and one you'll keep coming back to.

3-0 out of 5 stars Good bargain, but...
not suffciently precise for being an academic textbook. The definitions are sometimes incomplete, correctness proofs are missing, some exercises are incorrect. On the positive side, it does cover important topics, and brings good examples to illustrate main concepts and algorithms (which partially compemsates for the lack of precisenss).

5-0 out of 5 stars Simply Excellent!
This book explained topics I was interested in above my personal expectations. All the mathematics and probabilistic models were explained in detail with a practical approach. I was even able to refine some of those models for specific needs without much previous experience nor knowledge. I highly recommend this book, it is one of the best I ever read.

5-0 out of 5 stars Don't let the title mislead you.
Don't let the title fool you. This book is a great if you'd like to understand the algorithms used in any type of sequence analysis, for example speech recognition, speech synthesis, and natural language understanding.

I used this book for a bioinformatics class. The instructor's notes were basically a rehash of the textbook. This didn't bother me as there really is no way to improve on what's already in the text. Explanations of the different ways to use HMMs made it easy to write the genefinder we did for our final programming project.

I've also written natural language processing software (for text and speech) and I've found this book to be a great reference for probabilistic language modeling algorithms. The material is similar to that found in Jurafsky and Martin, or Manning and Schutz, but the presentation in DEKM provides more insight into how the algorithms work. This should come as no surprise, as the human genome project is perhaps the most successful artificial intelligence project ever undertaken and the authors were instrumental in creating the software used by the HGP.

The book by Gusfield is also great for sequence analysis, but there the emphasis is on deterministic modeling, which has it's place if one can't make a probabilistic sequence model.

Mining databases of text, image, and sound sequences is becoming more important as more data is available on the web. Books like DEKM are valuable algorithm resources for extracting knowledge all sorts of sequence data. ... Read more

63. 3D Math Primer for Graphics and Game Development
by Fletcher Dunn, Ian Parberry
list price: $49.95
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Asin: 1556229119
Catlog: Book (2002-06-15)
Publisher: Wordware Publishing
Sales Rank: 12069
Average Customer Review: 4.44 out of 5 stars
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Book Description

3D Math Primer for Graphics and Game Development covers fundamental 3D math concepts that are especially useful for computer game developers and programmers. The authors discuss the mathematical theory in detail and then provide the geometric interpretation necessary to make 3D math intuitive. Working C++ classes illustrate how to put the techniques into practice, and exercises at the end of each chapter help reinforce the concepts.

This book:

* Explains basic concepts such as vectors, coordinate spaces, matrices, transformations, Euler angles, homogenous coordinates, geometric primitives, intersection tests, and triangle meshes.

* Discusses orientation in 3D, including thorough coverage of quaternions and a comparison of the advantages and disadvantages of different representation techniques.

* Describes working C++ classes for mathematical and geometric entities and several different matrix classes, each tailored to specific geometric tasks.

* Includes complete derivations for all the primitive transformation matrices. ... Read more

Reviews (18)

5-0 out of 5 stars Very good book to get started with
The authors state early on that this book is intended as the first book an aspiring game programmer should read, and I would agree that for the most part it lives up to that goal. Many 3D game programming books include math primers covering a chapter or two, but really, 3D math is a huge topic deserving an entire volume. This book provides a great service, then, in that it thoroughly covers most of the basic topics that graphics programmers need to know, in a tutorial style that should be accessible to all beginners. Hopefully, we'll start to see more game programming books that focus on their core material and defer coverage of 3D math to books like this one rather than trying to pack unavoidably incomplete coverage into a few dozen pages.

So, what exactly does it cover? It starts off with a couple of chapters on coordinate systems, and then spends three chapters on vectors, followed by another three chapters on matrices and transformations. It then covers orientation, comparing matrix, Euler angle, and quaternion representations (including one of most clear explanations of quaternions that I've encountered), before diving into several chapters covering geometric primitives, including detailed coverage of working with triangle meshes.

The book closes with a chapter applying 3D math to graphics in areas such as lighting, fog, coordinates spaces, LOD, culling and clipping, and so on, and another chapter on visibility determination, touching on things like quad- and octrees, BSP trees, PVS, and portal techniques. The explanations in these chapters are much less complete, taking more of an overview approach. Others have criticized the book for this, but I feel that an overview is appropriate, since it then sets the stage for these topics to be covered in detail in other game programming books.

I'd definitely recommend this book to anyone just getting started with game and graphics programming.

5-0 out of 5 stars Best bet for getting a solid understanding of 3D math
Our goal in writing this book was not to cover as many topics as possible, like some other books, but rather to hit the most important concepts thoroughly. If you are a beginner, or have some "holes" in your understanding of matrices, Euler angles, left-handed vs. right-handed coordinate spaces, or key graphics concepts like zoom or the lighting equation, this book is for you.

A feature of this book over other books is the extent to which we have tried to develop the reader's geometric intuition, rather than just presenting numbers and equations. We show what the geometric interpretation of each mathematical operation is, why you would ever use that operation, and, in many cases, how the equation was derived in the first place. We do not gloss over "minor details" such as row vectors versus column vectors, or left- versus right-handed coordinate spaces. These "minor details" make all the difference in the world when you are trying to use an equation out of a book.

For the more advanced reader, we offer some of the clearest and complete discussions of some more advanced topics such as quaternions and barycentric coordinates. The book can be used as a reference for many important vector and matrix operations and identities. It also has a toolkit of many important equations for geometric primitives and intersection tests.

Our focus is on theory, so the book is not a big code dump like many books. The code we have provided consists primarily of "utility" classes for vectors, quaternions, and matrices. I think you will find that our code is simpler to read and understand than most code you will find elsewhere. We also offer some unique and thoughtful advice on good class design, specifically targetted to classes for doing 3D math and getting it right the first time, without twiddling minus signs or swapping numbers experimentally until it looks right



5-0 out of 5 stars the best book on math now
this book assume your beginner in that filed .
authors covers alot of topics in math and its application in a clear style with pictures,examples and finally code !.
i recommend this book for beginners in game programming .

Ahmed Saleh , Computer Graphics Programmer .

5-0 out of 5 stars Deceptively good book
I need to create a 3d math library for a project I was working on and wanted to take a look at some book on the subject. This one looked like one of the 14 year old 'how to make a video game' type books and I wasn't expecting much, however I was pleasantly suprised by the depth of the 3d mathematics in the book.
As an example i was unclear about how to calculate the inverse matrix correctly for an n-dimension matrix and the book goes over calculating adjucts and determinats, and inverses for a n-dimensional matrix both supplying the general math and some C code. The code i didn't find helpful, simply because I coding in the python c api and not straight c, however it could be helpful to someone writing in C.
I would recommend this book to anyone looking to brush up on quaternions, eulers, matrices, and vectors as this book is simple and to the point. I think the author did a great job balancing the complexty of the math with simplicity in the book's text. The book goes over what is really the essentials of any 3d math library. ... Read more

64. Introduction to Population Genetics
by Richard Halliburton
list price: $102.00
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Asin: 0130163805
Catlog: Book (2003-09-23)
Publisher: Prentice Hall
Sales Rank: 371873
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Book Description

Making the theory of population genetics relevant to readers, this book explains the related mathematics with a logical organization.It presents the quantitative aspects of population genetics, and employs examples of human genetics, medical evolution, human evolution, and endangered species.For an introduction to, and understanding of, population genetics. ... Read more

65. Earth : An Intimate History
by Richard Fortey
list price: $30.00
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Asin: 0375406263
Catlog: Book (2004-11-02)
Publisher: Knopf
Sales Rank: 1470
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Book Description

From the acclaimed author of Life and Trilobite!, a fascinating geological exploration of the earth's distant history as revealed by its natural wonders.

The face of the earth, crisscrossed by chains of mountains like the scars of old wounds, has changed and changed again over billions of years, and the testament of the remote past is all around us. In this book Richard Fortey teaches us how to read its character, laying out the dominions of the world before us. He shows how human culture and natural history-even the shape of cities-are rooted in this deep geological past.

In search of this past, Fortey takes us through the Alps, into Icelandic hot springs, down to the ocean floor, over the barren rocks of Newfoundland, into the lush ecosystems of Hawai'i, across the salt flats of Oman, and along the San Andreas Fault. On the slopes of Vesuvius, he tracks the history of the region down through the centuries?to volcanic eruptions seen by fifteenth-century Italians, the Romans, and, from striking geological evidence, even Neolithic man. As story adds to story, the recent past connects with forgotten ages long ago, then much longer ago, as he describes the movement of plates and the development of ancient continents and seas. Nothing in this book is at rest. The surface of the earth dilates and collapses; seas and mountains rise and fall; continents move.

Fortey again proves himself the ideal guide, with his superb descriptions of natural beauty, his gripping narratives, and his crystal-clear, always fascinating scientific explanations.
Here is a book to change the way we see the world.
... Read more

66. What Evolution Is
by Ernst Mayr
list price: $16.00
our price: $10.88
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Asin: 0465044263
Catlog: Book (2002-10)
Publisher: Basic Books
Sales Rank: 23918
Average Customer Review: 4.11 out of 5 stars
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Book Description

Mayr provides as convincing a testament to Darwin's genius as you are likely to find." --New York Times Book Review.

At once a spirited defense of Darwinian explanations of biology and an elegant primer on evolution for the general reader, What Evolution Is poses the questions at the heart of evolutionary theory and considers how our improved understanding of evolution has affected the viewpoints and values of modern man.

Science Masters Series ... Read more

Reviews (38)

4-0 out of 5 stars Modern evolutionary science clarified
Ernst Mayr is a commanding figure in the field of evolutionary biology. Having published an awesome average of nine scientific papers a year since 1925, he has produced (at age 97) a comprehensive book on evolution for the general public. I think "What Evolution Is" will best suit readers who already have some familiarity with biology as well as with science in general.

The author does not take the reader's acceptance of evolution for granted. On the contrary, he pays considerable attention to opposing views and carefully builds a case using the mass of evidence which has accumulated in the 140 years since Darwin's speculative missile burst on a comfortably religious 19th-century world. That world was almost universally assumed to be inhabited by specially-created humans presiding over a vast array of plants and animals provided solely to sustain, entertain and amuse them.

Mayr ably describes and explains the chain of factual evidence and logical inference which has established (with extremely high probability) that in actuality all living things evolved over billions of years through a partly random, partly directed, wholly automatic process which tended to suppress harmful changes and reinforce beneficial ones. The inevitable conclusion is that humans were not supernaturally created as finished products, but rather were simply fortunate enough to emerge from a very lengthy parallel development contest as hands-down winners in the intellectual capacity category. Implicit in Mayr's section on human ethics is the idea that along with markedly superior intelligence should come a self-imposed sense of moral responsibility.

As an active participant in the development of evolutionary science, Mayr doesn't hesitate to state clearly and defend vigorously his positions on controversial issues. He freely acknowledges (as did Darwin) that evolutionary rates can and do vary considerably, but he views the Eldredge-Gould punctuated equilibrium concept as no more than a minor modification of the classical picture. On another contentious question, Mayr holds firmly that natural selection should be viewed as acting on the whole animal (the phenotype) rather than on individual genes or subsets of genes.

The last chapter contains Mayr's views on the current frontiers of evolutionary biology. As major unsolved problems he cites a) finding the true extent of biodiversity; b) solving the mystery of static species ("living fossils") which hardly change over hundreds of millions of years; and c) explaining the relatively rapid (200-300 million years) proliferation of new structural types in the early Cambrian. The second of two appendices is a sort of rap session in which the author gives pithy responses to twenty-four FAQs about evolution. These serve as a quick-reference guide to many of the points Mayr has tried to drive home in the main text.

"What Evolution Is" includes a generous complement of good quality illustrations and charts. Mayr makes liberal use of technical terms, but is careful to compensate by providing a fairly comprehensive glossary. I recommend this book to anyone ready to step up a notch from the normal run of popular books on evolution.

4-0 out of 5 stars Good primer for the serious lay student
In the foreword, Jared Diamond says the book excels in filling a mid-level gap for educated lay people between biology texts and introductory material. He is right on the money. I was introduced to evolution in high school and college biology courses but further confused by television shows that are all over the map and all claiming to support evolution. I am a Christian Creationist but I do not hesitate to recommend this book for those interested in seeing a coherent account of evolution told by a true expert in the field. Mayr did not change my mind about macroevolution, but he did help me clear up a lot of my thinking about the current state of both evolutionary and creation science. I view the book as a very informative explanation, even a defense, of contemporary evolutionary thought. Mayr's gradualism is presented as the contemporary extension of Darwin's first revolution 150 years ago and of the evolutionary synthesis of the 1940's that brought molecular biology into the evolutionary fold. Other views of evolution and creation through the past 200 years are contrasted to Mayr's well-developed vision of how life gradually evolves. He generally builds a positive case for his position rather than directly attacking others.

Since Amazon has the technology to show the table of contents I will only summarize the contents of the book in an alternative way that Mayr himself hints at throughout the book. Chapters 1-4 are largely observations from the living world that suggest some sort of evolutionary process is at work. Chapter 5 devotes a lot of pages to modern theories of genetics and inheritance. Chapters 5-7 describe processes occurring within populations of living organisms. Throughout the book, Mayr stresses that diversity among populations, rather than unity of types, is the prevailing lesson of evolutionary biology. Chapters 5-9 form a major unit that describes the various mechanisms of microevolution including speciation. Chapters 10-12 get into higher-level macroevolution and use humans as a case study of mosaic evolution in a social species. I found these final chapters the least convincing and poorly backed by evidence (though it is well written and interesting to read). Mayr often admits the fossil record, especially for humans, is sketchy proof for evolution. To his credit he builds much of his case around observable biology rather than sketchy paleontology. Marvin Lubenow's "Bones of Contention" is an interesting and detailed analysis of the hominid fossils for those open to a very different (creationist) perspective.

Though I find much to disagree with in the philosophical assumptions and in some leaps of naturalistic faith used in the book, I think it serves its intended audience very well. The book could be better if it had more footnotes for further reading, especially to fossil statements and other phenomena such as rafting reptiles, teeth in baleen whale embryos etc. The bibliography is very extensive and Mayr does provide a list of anti-creationist books so the info can probably be located in those. If you are not well versed in biology and genetics you will probably want a dictionary handy, but this is exactly the sort of book I wanted as a deep introduction. Mayr is an honest, balanced and gifted writer for his position.

5-0 out of 5 stars Outstanding complete compresion of the evolution concept
If you are a Biologist or are a curious naturalist this is a book for you. Mayr makes an outstanding abstract of evolution, he clearly defines it with mastery. I would just like to add that this is my favorite subject and have read a good amount of books on evolution and this is clearly one of the best (don't be mislead by the size nor the price). Of course there are huge treatises on evolution (like The Structure of Evolution, of Stephen Jay Gould), but such a Bible is, for most of the cases, unpractical and unnecessary. Mayr clears evolutions' place in Biology putting it at its' very center. Great book, great style.

3-0 out of 5 stars What Evolution Was
Although it might be a good introduction for beginners, the views presented by Mayr have a feeling of 80s and 90s. Mayr does little to include the cutting edge research in evolutionary biology and his vision for the future of evolutionary biology is at best short-sighted.

4-0 out of 5 stars In depth look at evolution
This book covers almost every aspect of evolution. A good book for understanding darwinism and evolution. This book is written for people of various backgrounds. Moreover, the charts and text boxes are used in a manner that add substance to the book. The second appendix is awesome. Twenty tough questions about evolution are asked, including questions such as: is darwinism a dogma and is evolution a scientific fact. The answers though are less than convincing and tend to sidestep the questions.

Mayr has some of the best material on speciation that I have read. In this book, Mayr covers issues such as human evolution, macroevoution, natural selection, variational evolution, mutations, etc. He goes in depth but not so much so that laymen cannot follow.

Overall, the author has written a good book. Problems revolve around Mayr's refusal to adapt his writings and beliefs to current facts. In other words, Mayr still argues that the fossil record is the best evidence for evolution. A fossil record showing stasis best illustrates evolution??? Is not this the ultimate display of blind faith. Horse evolution is the most complete picture of evolution?!? WOW!

Maybe Mayr has grown hardheaded in his age and needs to keep update with current findings. Further, Mayr says embryology supports darwinism. Haven't we got past this yet? Problems like this show how old myths die hard and prove that perception is actually more important than reality.

Buy the book if you want a great reference for what evolution is, just remember when reading that dogma dies hard. ... Read more

67. The Journey of Man : A Genetic Odyssey
list price: $13.95
our price: $10.46
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Asin: 0812971469
Catlog: Book (2004-02-17)
Publisher: Random House Trade Paperbacks
Sales Rank: 10379
Average Customer Review: 4.3 out of 5 stars
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Book Description

Around 60,000 years ago, a man--identical to us in all important respects--lived in Africa. Every person alive today is descended from him. How did this real-life Adam wind up father of us all? What happened to the descendants of other men who lived at the same time? And why, if modern humans share a single prehistoric ancestor, do we come in so many sizes, shapes, and races?

Showing how the secrets about our ancestors are hidden in our genetic code, Spencer Wells reveals how developments in the cutting-edge science of population genetics have made it possible to create a family tree for the whole of humanity. We now know not only where our ancestors lived but who they fought, loved, and influenced.

Informed by this new science, The Journey of Man is replete with astonishing information. Wells tells us that we can trace our origins back to a single Adam and Eve, but that Eve came first by some 80,000 years. We hear how the male Y-chromosome has been used to trace the spread of humanity from Africa into Eurasia, why differing racial types emerged when mountain ranges split population groups, and that the San Bushmen of the Kalahari have some of the oldest genetic markers in the world. We learn, finally with absolute certainty, that Neanderthals are not our ancestors and that the entire genetic diversity of Native Americans can be accounted for by just ten individuals.

It is an enthralling, epic tour through the history and development of early humankind--as well as an accessible look at the analysis of human genetics that is giving us definitive answers to questions we have asked for centuries, questions now more compelling than ever. ... Read more

Reviews (23)

5-0 out of 5 stars "Y" is the answer - not the question
A few years ago a furor arose over the announcement that a calculation of mitochondrial DNA mutation rate formulated an "African Eve". Since then other genetic ancestral studies have been undertaken. Most notable of these was the determination that Neanderthal was not a direct ancestor of modern humans. Spencer Wells provides an enthralling overview of the research tracking changes in the Y [male] chromosome. The studies verify again that our origins are African. Somewhere, around 60 000 years ago, lived one man, a flesh and blood individual, from whom we've all descended. His progeny, in an amazingly short span, scattered around the globe. The scattering isn't news, but the verification of the paths and chronology is lucid and vividly outlined in this book.

The key to the tracking, as Wells makes abundantly clear, are various polymorphisms [changes] in the Y chromosome. These mutations are reflected in today's populations and the rate of their diversity indicates the approximate age of the various regional groups. These changes, nearly all prefixed "M" [male?] are used as ingredients in recipes Wells offers as illustrative metaphor. It's a clever ploy, so long as you remember ingredients may only be added, never removed nor replaced. That's how genetics works, he reminds us. He portrays the build-up of recipe ingredients with maps and diagrams. The diagrams are almost redundant as the clarity of his prose enables you to envision them.

Following the paths of migration, Wells shows how some archaeological finds offer support for the patterns he sees. Fossils are rare, elusive and sometimes misunderstood. Genetics, buried deep in our cells, are unequivocal in providing their evidence. Dating methods are briefly described and their shortcomings mercilessly paraded. Wells doesn't give the paleoanthropologists much voice. His story needs telling and the reader may go elsewhere for countering information. Yet he acknowledges the importance of confirming information from various digs around the world.

Wells firmly addresses a great anomaly - if modern humans arose from the evolutionary bouillabaisse about 60 millennia ago, how did the Aborigines arrive in Australia at nearly the same time? His answer is that the track followed shore routes, not inland ones. Hunter-gatherer groups, subject to the whims of climate, food resources and population pressure took the softest trail. Africa to Australia during ice ages was a gentle, if lengthy, stroll.

Nit-picking department: Wells' opening gun is turned on the racial "expert" Carleton Coon, who asserted the human races each followed a separate evolutionary path. Coon has been refuted in so many ways by so many researchers, Wells' effort seems superfluous. There are more competent scientists adhering to the "Multiregional" thesis. Some of these researchers might have been given a small voice in an annotated bibliography. While Wells offers a reading list for each chapter, a full bibliography would be an enhancement. Many of his references are remote. That doesn't tarnish the value of this book. [stephen a. haines - Ottawa, Canada]

5-0 out of 5 stars Death Blow for the Multiregionalists
After reading this book, I don't know how anyone can seriously entertain the theory of multiregionalism anymore. The genetic evidence is conclusive and proves that we have all descended from a band of anatomically modern humans somewhere in Africa 50,000 years ago.

Wells has written a cogent and persuasive book that looks at every phase and aspect of the human odyssey from these African origins to modern times. If I have any criticism, however, it's that the book tends to slow down a bit after the settlement of the Americas is discussed. The chapters on the spread of agriculture and the evolution of language were less coherent than the others and seemed to digress from the central thesis. Still, I highly recommend the book to anyone interested in the recent origins of modern man. It shows that only 2000 generations ago, we were all one family living in one place. The racial differences we all note today are thus very recent and very superficial. This is all the more important to understand now that the world is heading toward genetic convergence rather than genetic divergence. In another couple thousand years, we will probably all look like Tiger Woods (one of the multi-racial examples Wells cites in his book).

2-0 out of 5 stars Impressively little content.
One doesn't learn a lot about evolutionary genetics from this book. When the author talks about how statisticians arrive at a result he does a really poor job of explaining the calculation for a layman. He presents almost nothing at all, just stating results. The book contains a lengthy list of results from many different fields. Most people want to know a lot more about how the various quantities are deduced, even a newspaper article goes more in depth. Science via inductive logic is a little sketchy, but you get the impression that the author doesn't understand that what he studied in grad school is inductive. One receives the impression that the author doesn't question much of anything at all.

This is a book about everything he learned as a post-doc, all the people that he met, and all of their theories. But, I don't think that many people will take anything away from The Journey of Man - it lacks the substance that readers of layman's science books desire.

5-0 out of 5 stars Why I love this book!
I am Indian (with roots in the Indian subcontinent) and I like the way Spencer Wells touches upon our "aryan" Y-chromosome that (as he explains) we share with the eastern europeans. Take that Hitler. And yes I too feel this book beats Seven Daughter of Eve (by Bryan Sykes)by far.

1-0 out of 5 stars No photos in the paparback edition!!!
The paperback edition does not include any photographs. They are essential and included in the hardcover edition in a great number!!! ... Read more

68. Our Family Tree: An Evolution Story
by Lisa Westberg Peters
list price: $17.00
our price: $11.56
(price subject to change: see help)
Asin: 0152017720
Catlog: Book (2003-04-01)
Publisher: Harcourt Children's Books
Sales Rank: 117871
Average Customer Review: 4 out of 5 stars
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Book Description

All of us are part of an old, old family. The roots of our family tree reach back millions of years to the beginning of life on earth. Open this family album and embark on an amazing journey. You'll meet some of our oldest relatives--from both the land and the sea--and discover what we inherited from each of them along the many steps of our wondrous past.
Complete with an illustrated timeline and glossary, here is the story of human evolution as it's never been told before.
... Read more

Reviews (1)

4-0 out of 5 stars A planet where men descended from apes?
It takes guts to write a picture book. Putting your work out there to speak for you. The criticism of hundreds of thousands of adults just waiting to tear you apart. It takes even more guts to write a non-fiction picture book. Now you have to deal with parents passing over your story for, oh I dunno, "Mr. Peabody's Apples" because they're afraid that they themselves will be bored. Pompous adults like that. And finally, it takes a kind of bravery most humans would be lucky to possess to write a non-fiction picture book that sports the word, "evolution", on its cover. So please take a moment to mentally applaud the gutsy efforts of one Ms. Lisa Westberg Peters and one Ms. Lauren Stringer for their moxie laden little number, "Our Family Tree: An Evolution Story".

A delicate rendering of Lascaux acrylics on watercolor paper, the story is one of the oldest ones on earth. Peters begins, "All of us are part of an old, old family. The roots of our family tree reach way back to the beginning of life on earth. We've changed a lot since then". Slowly we learn about DNA and the birth of cells in the seas. We hear about oxygen filling the planet and how the seas rose and fell, changing the landscape. About how animals crawled up onto the land and how after an asteroid our particular branch of the family tree survived. Finally, the monkeys evolved, and we evolved out of the monkeys. The book ends with further details for the inquisitive child about each step of the family tree. A helpful timeline follows these facts at the end.

For those human beings that dislike the notion of evolution and prefer a more creation-laden viewpoint, this is not the book for you. It's pretty darn clear in the text that life began 3,800 to 3,600 million years ago. End of story. You will not find a religious note in this book. It's scientifically written and happy to remain that way. Not that the facts presented are full-proof. I may be wrong, but I don't believe the asteroid theory has ever matter-of-factly killed off the dinosaurs as it does here. Also (as more professional reviewers have pointed out) the timeline really does make it look as if it was just a hop, skip, and a jump from single celled organisms to wormlike vertebrates.

On the whole, however, this is a good informative text. Children reading it should be a little older, in order to fully grasp exactly what is being said. For them, however, this book serves as an excellent resource. The pictures are lovely and the facts are mostly on the ball. A lovely addition to any children's evolution library. ... Read more

69. The Phylogenetic Handbook : A Practical Approach to DNA and Protein Phylogeny
list price: $75.00
our price: $65.25
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Asin: 052180390X
Catlog: Book (2003-09-01)
Publisher: Cambridge University Press
Sales Rank: 104286
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Book Description

The Phylogenetic Handbook is a broad introduction to the theory and practice of nucleotide and amino acid phylogenetic analysis. As an unique feature of this book, each chapter contains an extensive practical section, in which step-by-step exercises on real data sets introduce the most widely used phylogeny software including CLUSTAL, PHYLIP, PAUP*, DAMBE, TREE-PUZZLE, TREECON, SplitsTree, TreeView, SimPlot, MEGA2, PAML and BOOTSCANNING. The book provides a strong background in basic topics: the use of sequence databases, alignment algorithms, tree-building methods, estimation of genetic distances, and testing models of evolution. ... Read more

by Michael J. Behe
list price: $15.00
our price: $10.20
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Asin: 0684834936
Catlog: Book (1998-03-20)
Publisher: Free Press
Sales Rank: 2203
Average Customer Review: 3.45 out of 5 stars
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Book Description

Virtually all serious scientists accept the truth of Darwin's theory of evolution. While the fight for its acceptance has been a long and difficult one, after a century of struggle among the cognoscenti the battle is over. Biologists are now confident that their remaining questions, such as how life on Earth began, or how the Cambrian explosion could have produced so many new species in such a short time, will be found to have Darwinian answers. They, like most of the rest of us, accept Darwin's theory to be true.

But should we? What would happen if we found something that radically challenged the now-accepted wisdom? In Darwin's Black Box, Michael Behe argues that evidence of evolution's limits has been right under our noses -- but it is so small that we have only recently been able to see it. The field of biochemistry, begun when Watson and Crick discovered the double-helical shape of DNA, has unlocked the secrets of the cell. There, biochemists have unexpectedly discovered a world of Lilliputian complexity. As Belie engagingly demonstrates, using the examples of vision, bloodclotting, cellular transport, and more, the biochemical world comprises an arsenal of chemical machines, made up of finely calibrated, interdependent parts. For Darwinian evolution to be true, there must have been a series of mutations, each of which produced its own working machine, that led to the complexity we can now see. The more complex and interdependent each machine's parts are shown to be, the harder it is to envision Darwin's gradualistic paths, Behe surveys the professional science literature and shows that it is completely silent on the subject, stymied by the elegance of the foundation of life. Could it be that there is some greater force at work?

Michael Behe is not a creationist. He believes in the scientific method, and he does not look to religious dogma for answers to these questions. But he argues persuasively that biochemical machines must have been designed -- either by God, or by some other higher intelligence. For decades science has been frustrated, trying to reconcile the astonishing discoveries of modern biochemistry to a nineteenth-century theory that cannot accommodate them. With the publication of Darwin's Black Box, it is time for scientists to allow themselves to consider exciting new possibilities, and for the rest of us to watch closely. ... Read more

Reviews (425)

5-0 out of 5 stars The Deathknell of Evolution as We Know It
Michael Behe's revelation of the profound flaw inherent in modern day evolutionary theory is nothing short of genius. He clearly illustrates his point in a manner so simple (as you can see by some of these reviews) he has left even the coolest evolutionary theorists babbling. This book has gained much attention and it is no wonder! With crippling reasoning, Behe exposes an area completely unknown to Darwin at the time he formed his theories - the microbiological level of life (Darwin used magnifying glasses!). Using examples of highly complex systems existing on this level, Behe clearly shows that such systems could not have developed in accordance with the theory of modern evolution - by gradual change over time. Evolutionary theory is based upon the principle of progressive change to form a more complex organism. Behe takes this principle to task by illustrating systems existing on the microbiological level (sometimes no bigger than a conglomeration of several cells) composed of multiple parts and functioning in highly specified ways. There is no possible way for such systems to have evolved, one, two, three, or even ten parts at a time, because without all elements functioning together, they are completely useless, or worse yet, harmful! Evolutionists cannot explain how such highly complex systems could have evolved. Such intricate and complex systems would have had to appear all at once in time. This is nothing short of a miracle - which diehard evolutionists, sadly, cannot accept. The logic in Behe's reasoning is airtight. To understand the beginning of the end of modern day evolutionary theory -- this book is a must read.

5-0 out of 5 stars Darwinian Evolution is a Theory
As a molecular biochemist, physician and christian I found Dr. Behe's book accurate, well-written and fair. He neither preaches to those who are unbelievers, nor forces a concept of God onto the reader. Instead, he attempts to explain where and why Darwinian Evolution fails. I've gradually come to this same conclusion prior to reading his book. (As for the issue of the number of proteins in flagella, as discussed in one review, if you were to calculate even 20 proteins mutating simultaneously, using only a very short protein chain--as the likelihood is a function of protein chain length, the probability would be well over 10^50 power, in other words: impossible. I'd refer you to various Chuck Missler audio tapes for more details.)

A couple of areas where Dr. Behe did not elaborate, and perhaps would have calmed some irrate reviewers of this and his other book if he had, is the topic of micro-evolution. A perfect example of this phenomena is antibiotic resistance in bacteria. Creationism is not incompatible with this concept (and BTW, as one reviewer incorrectly stated, Scripture does not say the world is flat, nor to drink poison; a more careful reading would be in order).

Similarly, Dr. Behe did not discuss another concept of molecular evolution that also supports intelligent design: amino acid conservation. That is, the small differences between animal species with respect to amino acid substitution in hemoglobin is not necessarily an argument for microevolution, but an argument for a designer. A designer will tend to re-use parts rather than create whole new systems (eg, modular programming).

Aside from these minor topics that would further strengthen his book, Dr. Behe offers the lay reader an excellent discussion of why intelligent design is a compelling topic and needs to be placed along side of Darwinian evolution in the classroom. His discussion is definitely not a re-hash of the arguments put forth in the Scopes Monkey Trial (as in the movie "Inherit the Wind"). His logic is not poor, as one review suggested, and Dr. Behe encourages the reader to look for topics in other books. The problem is not that these books cannot be found, again as one reviewer suggested, but that the level of discussion is those books is meager at best and usually does not fully address the stated topic. In any event, you should read his book and decide for yourself.

1-0 out of 5 stars Scientific Knowledge Shouldn't Be Decided By Popular Vote
I can appreciate that Michael Behe's supporters might fail to grasp the effectiveness of some of the more technical refutations of this book that have been presented. But I'd expect others - like those of cell biologist Kenneth R. Miller, for instance - to be readily understandable by anyone capable of following Behe's own rather difficult arguments.

Miller has won several awards for outstanding teaching, and is co-author of well-received high school and college textbooks. He can communicate. He's also a conscientious Roman Catholic, acutely aware of the conflicts that can arise when sincere religious convictions confront the sometimes disturbing and often counter-intuitive findings of modern science.

A little sampler from Miller's writings may hopefully stir the more conscientious among Behe's sympathizers to look into what Miller and other interested scientists have to say about the book and about the intelligent design argument in general.

In March 2002, Miller and physicist Lawrence Krauss took part in a debate before the Ohio Board of Education. Their opponents were Stephen Meyer and Jonathan Wells, senior fellows (as is Behe) at the Discovery Institute. The Institute, ID's home base, is a 'think tank' advocating what it calls "the renewal of science and culture". Its primary funding comes from wealthy conservative Christians, notably Christian Reconstructionists Roberta and Howard Ahmanson.

Miller wrote a blow-by-blow account after the debate (the full text is on his website), in which he recalls Krauss' insight that "the two-on-two format of this presentation wouldn't render a fair picture of the sentiment in the scientific community. A more reasonable arrangement .. would have one member of the Discovery Institute on one side, and ten thousand scientists on the other .. two of the Discovery Institute's nine senior fellows were the ID speakers who were there; if they had not been there, the only place to find more advocates for ID would be back at the Discovery Institute. If Krauss or I had not been there, however, we could have been replaced by scores of scientists from just about any college or university anywhere in the state of Ohio."

In another article, "Answering the Biochemical Argument From Design" (also on his website), Miller gives Behe credit for recognizing that "the mere existence of structures and pathways that have not yet been given step-by-step Darwinian explanation does not make much of a case against evolution. Critics of evolution have laid down such challenges before, only to see them backfire when new scientific work provided exactly the evidence they had demanded. Behe himself once made a similar claim when he challenged evolutionists to produce transitional fossils linking the first fossil whales with their supposed land-based ancestors. Ironically, not one, not two, but three transitional species between whales and land-dwelling Eocene mammals had been discovered by the end of 1994 when his challenge was published."

Darwin's theory states that "evolution produces complex organs though a series of fully-functional intermediate stages. If each of the intermediate stages can be favored by natural selection, then so can the whole pathway." Behe argues that due to the "irreducible complexity" of biochemical systems like those described in his book, there can be no fully-functional intermediate stages; all parts must be present for any function at all. Miller asks, "Is there something different about biochemistry, a reason why Darwin's answer would not apply to the molecular systems that Behe cites?

"In a word, no.

"In 1998, Siegfried Musser and Sunney Chan described the evolutionary development of the cytochrome c oxidase protein pump, a complex, multipart molecular machine that plays a key role in energy transformation by the cell. In human cells, the pump consists of six proteins, each of which is necessary for the pump to function properly. It would seem to be a perfect example of irreducible complexity. Take one part away from the pump, and it no longer works. And yet, these authors were able to produce, in impressive detail, "an evolutionary tree constructed using the notion that respiratory complexity and efficiency progressively increased throughout the evolutionary process".

"In 1996, Enrique Meléndez-Hevia and his colleagues published, in the Journal of Molecular Evolution, a paper entitled "The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution" .. this paper does exactly what Behe says cannot be done, even in principle - it presents a feasible proposal for its evolution from simpler biochemical systems .. what all of this means, of course, is that two principal claims of the intelligent design movement are disproved, namely that it is impossible to present a Darwinian explanation for the evolution of a complex biochemical system, and that no such papers appear in the scientific literature. It is possible, and such papers do exist."

Miller shows in detail that even systems Behe proposes as "irreducibly complex" are not so. "Nature presents many examples of fully-functional cilia that are missing key parts .. this leaves us with two points to consider: First, a wide variety of motile systems exist that are missing parts of this supposedly irreducibly complex structure; and second, biologists have known for years that each of the major components of the cilium, including proteins tubulin, dynein, and actin have distinct functions elsewhere in the cell that are unrelated to ciliary motion .. what this means, of course, is that a selectable function exists for each of the major parts of the cilium, and therefore that the argument [for irreducible complexity] is wrong."

Miller demonstrates similar difficulties with Behe's claim regarding the bacterial flagellum. He concludes, "At least four key elements of the eubacterial flagellum have other selectable functions in the cell that are unrelated to motility .. by demonstrating the existence of such functions, even in just a handful of components, we have invalidated the argument".

Miller's verdict: "Prof. Behe argues that anti-religious bias is the reason the scientific community resists the explanation of design for his observations:
I would suggest that the actual reason is much simpler. The scientific community has not embraced the explanation of design because it is quite clear, on the basis of the evidence, that it is wrong."

5-0 out of 5 stars Excellent Resource
The book that basically started it all, where whispers in the scientific community against neo-Darwinism became public discourse. Whether you're an IDist or a Darwinist, this is a good book to have on the shelf just as a reference point.

A lot of people on both sides just talk pass each other, and project their image of the "other" side the way they wish to see it. When Darwinists think of Intelligent Design, they think of 7-Day Creationists who want to burn scientists at the stake. When 7-Day Creationists think of evolution, they think of that athiest Joseph Stalin shoving Christians into Gulags (and Daniel Dennet apparently thinks religious people should be in cages, so maybe that assumption isn't very far off).

Behe's book is not about the Bible, or Christianity, or Creationism, or even anti-evolution. It is anti-aimless natural selection. Behe sets up many examples w/in biology and biochemistry that show how the human cell and its processes are dependent on complex plans that could not have developed gradually. Blood coagulation requires "knowledge" of the end result in order for the process to begin. The immune system requires separate parts to evolve at the same time to meet a common goal w/in the system. There are "blueprints" w/in life that mutation and natural selection cannot explain, especially w/in the timeframe of earth's development. Does this disprove evolution? No. Does it prove the existence of God? No, not necessarily, although you'd have to provide a funky explanation involving (gasp! oh no!) metaphysics. The Power of "Life" as the Grand Unified Theory of Physics, or something. So this book does prove the need for a new explanation that is going to have to account for the borderline miraculous development of life, since life is so "irreducibly complex". Francis Crick, probably seeing the writing on the wall because of his analysis of DNA, jumped on the panspermia bandwagon early on. I always wondered why he did so, because in High School and College I was never told of the weaknesses w/in Darwinism, and here comes Crick w/ this funky idea of panspermia. Why, I thought? Crick's obviously a genius, wasn't he aware that natural selection is flawless and infallible? Now I know why. Of course, panspermia has its own problems, as it just pushes the problems of chaotic life ex nihilo back a couple of galaxies and epochs.

Behe also shows how many of the arguments against Intelligent Design are Strawmen fallacies, such as "Well, God wouldn't have done it that way!" Well, why not? That's not an observation of nature, but a metaphysical argument, and one that comes from Sartrian "bad faith". Behe takes from the bottom up, and shows how the observation of cells and cellular mechanisms leads to planning and design. The identity and characteristics of the Designer--is he perfectly Good or does he have a mean side, is he Deistic or Theistic, would he make the universe perfect from a human perspective or would he make the universe glaring w/ imperfections--is for another book and another time. Like a good Belisarius (the Byzantine commmander who ushered in the strategy of defensive warfare), Behe merely stakes out a sound corner w/in science that orthodox scientific opinion cannot explain (irreducible complexity), and he sits there, secure.

3-0 out of 5 stars Good Argument, So-So Writing
Behe presents a solid challenge to a Darwinian view of how life started on Earth (though he leaves the question of how it could begin elsewhere unchallenged). Unfortunately to do this, he relies on several esoteric biochemical processes (though i think that is the only sort of biochemical processes available to a neophyte like myself). The first half of the book reads as several iterations of the same argument, though delivered with increasing amounts of sarcasm. The second half of the book, in which he delivers his answer to the questions raised earlier, seems rushed. So if you tire of the seemingly endless stream of enzymes and proteins, skip to the second part -- it's much easier reading for the layperson.

Though to say that this book disproves or even dismisses evolution and natural selection as viable scientific theories is disingenuous at best, and dishonest at worst. Behe even says that beyond a limited set of structures that appear to be evidence of intelligent design, there are many structures that are not clearly designed (and most likely aren't, he admits). To explain these structures and organisms, he gives a variety of options, ending with what is clearly natural selection, though he declines to name it as such. Finally, while criticising evolutionary proponents for attacking a straw man (the watchmaker for darwinists, Richard Dawkins for intelligent design-ists), this is exactly what he does -- since Darwin's followers haven't demonstrated a valid argument/scenario for the basic structures of the cell, then entire theory is invalid (including portions that have been experimentally shown true on an organism level).

Finally, Behe doesn't give any sort of explanation or theory for how some basic structures of the cell are evidence of design, but others are not. He implies that those not showing evidence of design could have evolved, but does not explain why some more complicated structures could be designed before other more basic structures evolved.

Enjoy this book and the questions it opens, but it is far from the final word on the origins and progression of life on Earth (just as Dawkins' books aren't, either). ... Read more

71. Fundamentals of Queueing Theory (Wiley Series in Probability and Statistics)
by DonaldGross, Carl M.Harris
list price: $110.00
our price: $110.00
(price subject to change: see help)
Asin: 0471170836
Catlog: Book (1998-02-06)
Publisher: Wiley-Interscience
Sales Rank: 353192
Average Customer Review: 5 out of 5 stars
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Book Description

This look at queueing theory stresses the fundamentals of the analytic modeling of queues. It features Excel and Quattro software that allows greater flexibility in the understanding of the nature, sensitivities and responses of waiting- line systems to parameter and environmental changes.

"...this is one of the best books available for use as a textbook for a course and for an applied reference book. Its excellent organizational structure allows quick reference to specific models and its clear presentation coupled with the use of the QTS software solidifies the understanding of the concepts being presented. I highly recommend this book to educators and applied researchers."--IEE Transactions on Operations Engineering ... Read more

Reviews (1)

5-0 out of 5 stars The Classic Queueing Theory Text
Fundamentals of Queueing Theory (third edition) by D. Gross and C. Harris is THE classic queueing text book. It is up-to-date, thorough, rigorous, intuitive, and even fun to read (for the mathematically inclined). This book can be read at different levels, none of them easy. It is intended for an audience of graduate students in operations research, industrial engineering, management science, or mathematics. There are other excellent queueing books out there, but this has to be the overall best seller! Highly recommended. ... Read more

72. How Humans Evolved, Third Edition
by Robert Boyd, Joan B. Silk
list price: $86.30
our price: $86.30
(price subject to change: see help)
Asin: 0393978540
Catlog: Book (2002-11)
Publisher: W. W. Norton & Company
Sales Rank: 183921
Average Customer Review: 5 out of 5 stars
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Book Description

How Humans Evolved uses the broad perspective of behavioral ecology, drawing on Robert Boyd's expertise in evolutionary theory and Joan Silk's specialty in primate behavior in a uniquely integrative text. For the Third Edition, the authors have revisited many chapters in depth, added new supplemental readings, and incorporated the latest archaeological findings, including coverage of the fossil cranium Sahelanthropus tchadensis, whose dating was announced in the summer of 2002. ... Read more

Reviews (6)

5-0 out of 5 stars Superior text for the Upper Crust Undergraduate
There's plenty of textbooks on the subject of physical anthropology, of varying quality. This, however, is by far the most theory-oriented, detailed, and clear. Compared to a text like Jurmain's (2004) this book truly caters to an intelligent undergraduate who's capable of understanding what Australopithecus boisei means. I assign it to my students with the understanding that students rise to the expectations we as instructors hold for them. I found Jurmain's text to be belittlingly simplistic. Thanks Boyd and Silk!

5-0 out of 5 stars Great textbook
I was assigned this book for my physical anthropology class. Overall, it's very easy to understand. THe authors explain difficult concepts well for the most part, and they usually include diagrams or pictures to reinforce the point. Granted the chapters on genetics weren't the easiest things on earth to understand, but I had a firm biology background from high school so it was not an issue. The authors also do a good job of making the concepts very interesting and alive, a difficult task for a college textbook.

Overall, it's a great book and very informative.

5-0 out of 5 stars Great textbook
I never thought that I would enjoy biological anthropology, let alone understand it well, but this text has made the class easy and even fun (seriously, I'm not joking). The book is layed out simply with outlines at the beginning of each chapter and clear subheadings within the chapters to help get across the main points. The points are all connected together nicely to leave the reader with a complete picture of human evolution.

5-0 out of 5 stars Good Overview of Evolutionary Theory
This book was the required text for an anthropology course I took recently. The book explained things well and actually made complex biological concepts simple to understand, even for a undergraduate. It provides a very detailed and easy to understand overview of human evolution and the biology of human culture. I would recommend this book.

5-0 out of 5 stars The best textbook!
This was a clear and fascinating textbook on human evolution. It became "the homework I did to procrastinate from my real work." The professor in my course wasn't the greatest, and this book really helped to bring everything together. It will make you examine humans, where we've been, and where we're going in a completely new fashion. ... Read more

73. Data Analysis Tools for DNA Microarrays
by Sorin Draghici
list price: $79.95
our price: $65.56
(price subject to change: see help)
Asin: 1584883154
Catlog: Book (2003-06-04)
Publisher: Chapman & Hall/CRC
Sales Rank: 387756
Average Customer Review: 4.75 out of 5 stars
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Book Description

Technology today allows the collection of biological information at an unprecedented level of detail and in increasingly vast quantities. To reap real knowledge from the mountains of data produced, however, requires interdisciplinary skills-a background not only in biology but also in computer science and the tools and techniques of data analysis.To help meet the challenges of DNA research, Data Analysis Tools for DNA Microarrays builds the foundation in the statistics and data analysis tools needed by biologists and provides the overview of microarrays needed by computer scientists. It first presents the basics of microarray technology and more importantly, the specific problems the technology poses from the data analysis perspective. It then introduces the fundamentals of statistics and the details of the techniques most commonly used to analyze microarray data. The final chapter focuses on commercial applications with sections exploring various software packages from BioDiscovery, Insightful, SAS, and Spotfire. The book is richly illustrated with more than 230 figures in full color and comes with a CD-ROM containingfull-feature trial versions of software for image analysis (ImaGene, BioDiscovery Inc.) and data analysis (GeneSight, BioDiscovery Inc. and S-Plus Array Analyzer, Insightful Inc.).Written in simple language and illustrated in full color, Data Analysis Tools for DNA Microarrays lowers the communication barrier between life scientists and analytical scientists. It prepares those charged with analyzing microarray data to make informed choices about the techniques to use in a given situation and contribute to further advances in the field. ... Read more

Reviews (4)

5-0 out of 5 stars Far from superficial...
When entering the minefields of microarray data analysis, one has to understand and keep up with state-of-the-art technologies and interdisciplinary literatures. A background in molecular biology is clearly not enough to evaluate the pro and cons of the various statistical methods for selecting truly modulated candidate genes in a given experimental biological system. Choosing between the available analysis software's is not an easy task either. Draghici presents a complete visit of the microarray underworld by initiating the reader to all the facettes of this domain. From the fundamentals of slide production and target hybridization to image processing, statistical analysis, experimental design, data management and biological interpretation, all aspects treated herein are described with pertinent details. Draghici slowly, but successfully, tames the reticent molecular biologist to the arid world of statistics and even entertains the reader with anecdotes and humoristic citations.
Clearly written, with appropriate mathematical examples for each topic, this book even includes exercises at the end of some chapters, for the zealous student sleeping in all of us. It constitutes a very good didactic tool and the included CD's allow a good peek in some of the available image/data analysis software's on the market.
As a core facility manager and eternal student, I strongly recommend Draghici's book to life scientists and students who are struggling with statistical analysis and data mining techniques.

Brigitte Malette, Ph. D.
Project Leader, Microarray Platform
Centre for Structural and Functional Genomics
Concordia University

4-0 out of 5 stars Detailed and understandable
Draghici managed to write a manual on applying microarray (data) with a great feeling for explanation of hard issues. The book is relatively easy to read, very complete and covers most, if not all, analysis techniques that are currently around for microarrays.

Highly recommendable!

5-0 out of 5 stars Good Overview of Microarray Technology
I have had the book for about a month now and I consult it quite frequently. Great coverage of Microarray Data Anlysis. It manages to be thourough without being dry or using excessive jargon. It's very readable and useful for both novices and experienced readers.

It's main strength lies in the use of excellent examples that show the main pitfalls encountered in analyzing microarray data. It has great coverage of statistics and their potential misuse and misunderstanding when they are applied to gene expression data sets. The experimental design section is especially helpful for researchers that are designing a project.

The graphics are excellent and the book is printed on good quality paper.

The book includes two CD's with demo versions of several commercial software packages.

Overall a great buy.

5-0 out of 5 stars Data Analysis Tools for DNA Microarrays
A much needed book for the biologist interested in using DNA/protein microarrays. Examples are specific for microarrays. The material starts from ground zero and begins
with image analysis. All major methods for analysis are discussed.
Well worth the cost, quality graphics, includes software (have not used as yet).
A must read before discussing experimetnal design with your stats person. ... Read more

74. Introduction to Computational Biology: Maps, Sequences and Genomes
by Michael S. Waterman
list price: $69.95
our price: $69.95
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Asin: 0412993910
Catlog: Book (1995-06-01)
Publisher: Chapman & Hall/CRC
Sales Rank: 332221
Average Customer Review: 4.5 out of 5 stars
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Book Description

Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences.Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology. ... Read more

Reviews (2)

5-0 out of 5 stars A modern classic
The first name people learn in bioinformatics is the Smith-Waterman algorithm. Some people never learn anything else. This is by that Waterman. Although written in 1995, it still has some of the best discussion I've seen on the topics it addresses.

The first few chapters deal with the "digest problem," reconstructing a DNA or protein sequence from the fragment sizes of enzyme digests. The technique is not used as much now as it was then, but it's always good to know the background of modern techniques.

The digest problem doesn't stand alone, though. It introduces concepts - islands, anchors, etc. - that still matter. The problems in reconstructing molecules from digests yield the same kinds of intermediate results and the same ambiguities that arise in modern sequencing. As Waterman advances the discussion, shotgun sequencing appears as a logical extension, at least mathematically, of digest assembly.

Sequence assembly involve end matching, perhaps in the presence of sequencing errors. That introduces the topic for which Waterman's name is famous, approximate string matching. The next few chapter progress through dynamic programming and multiple alignments. The logical connections between the techniques shown are so tight that chapter boundaries are almost artificial. It was a real pleasure to see the computational and practical relationships laid out.

The final topics, RNA structure and phylogenetic trees, lack the continuity that characterized the first dozen chapters. The RNA structure may be the weakest chapter in the book, but still a very competent introduction.

Throughout, Waterman emphasizes mathematical rigor without insisting on uninformative theorems. Every topic is presented in rich detail, with special attention to scoring and background models. Perhaps there are newer discussions of some topics. I don't know of any clearer discussions, though. Best, I think, is how Waterman prepares the reader to ask all the right questions in any future discussion: what are the elements of the computation, how can elements be recombined, how good is a result, and how does the result stand out from the statistical background.

The final chapter is what a bibliography should be. It doesn't just list authors, titles, and dates of publication. It actually discusses the contribution that each source made to this book. Rather than leave the reader to wander aimlessly among obscure titles, Waterman shows which sources are most informative on which topics. I wish more authors took the time for such commentary.

This is a book worth having. It covers topics that I haven't seen elsewhere, and shows how many different topics relate to each other. It is rigorous without giving distracting detail. Most of all, it keeps the biology in sight of all calculations. Some authors seem to forget that anything exists but the arithmetic; Waterman puts the math clearly in the service of its subject. I enjoyed it immensely, and look forward to applying its content in my own research.

4-0 out of 5 stars Packed full of good information
This book gives a good survey of the different techniques employed by computational biologists. After a brief review of molecular biology in Chapter 1, the author treats the mathematical modeling of restriction maps in Chapter 2 using graph theory. His presentation is somewhat hurried, but he does give references and gives the reader three exercises at the end of the chapter. Multiple maps are treated in Chapter 3, wherein the author first makes use of probability theory, via the Kingman subadditive ergodic theorem. The proof is omitted but the author does a good job of explaining its use in studying the double digest problem (DDP). The best part of this chapter is the author's explanation of the difficulties of using Kingman's results for solving the DDP, and goes on to discuss multiple solutions of the DDP. Graph theory is again used in the discussion. This sets up the discussion in Chapter 4, which outlines algorithms for the DDP. The author gives a very compact introduction to P- and NP-complete problems in the theory of computation, then proves that DDP is NP-complete. The author does a good job of discussing subsequent approximate methods used for the DDP, such as simulated annealing. Markov chains are introduced in the book here for the first time, but due to the shortness of the presentation, the reader should do outside reading as a back-up. The author does a great job of explaining the difficulties if measurement error is introduced in the DDP at the end of the chapter. Cloning is discussed in Chapter 5, with tools from probability theory used to deal with partial digest libraries. The chapter is really short though, and the working the problems at the end of the chapter is essential for the understanding the results of this chapter. The author switches gears in the next chapter, wherein physical maps are discussed. The discussion is fairly detailed and interesting. Sequencing is discussed in the next two chapters, and the treatment is very good. Hashing is introduced here, and psedocode is given throughout. The very important method of dynamic programming is outlined in Chapter 9, which is beautifully written, and again pseudocode abounds throughout. Genetic mapping is left out though, but the this, the longest chapter of the book, is a detailed introduction to this area. The results in this chapter are used to study multiple sequence alignment in Chapter 10, wherein hidden Markov models are introduced for the first time. The discussion of these models is very curt, but there are other books and notes available if the reader needs further guidance. The best chapter of the book follows, which discusses probability and statistics for sequence alignment. The theory of large deviations is brought in, and the author does an excellent job of discussing this important, and powerful theory. The reader's level of mathematical sophistication is assumed to be a lot greater than the rest of the book in this chapter. Knowledge of measure theory and martingales are assumed here. The author uses the very powerful tool of relative entropy, so indispensable in other applications of probability. The problem set at the end of the chapter is challenging but working them through is definitely worth the time involved. The next chapter also uses some heavy guns from probability theory to study sequence patterns. The author returns to matter of a more empirical nature in Chapter 13, which deals with RNA secondary structures. The reader with a background in simple combinatorial theory should find the reading straightforward and informative. Continuous-time Markov chains are introduced in the next chapter to study trees and sequences. The treatment here is rather hurried, so again the reader should work the exercises at the end of the chapter. The book ends with a discussion of the literature and references. All in all a very nice book, worth the price, and worth spending time reading. The only minus might be the total omission of actual source code, but that really was not the intent of the book. Readers with a strong mathematical background will like the book, as well as anyone interested in going into the area of computational biology. ... Read more

75. The Cartoon Guide to Genetics
by Larry Gonick, Mark Wheelis
list price: $16.95
our price: $11.53
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Asin: 0062730991
Catlog: Book (1991-07-01)
Publisher: Perennial
Sales Rank: 15778
Average Customer Review: 4.54 out of 5 stars
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Having trouble deciphering your genetic code? Do dominant genes make you feel recessive? Let reigning nonfiction cartoonist Larry Gonick and microbiologist Mark Wheelis ease your way through Mendelian genetics, molecular biology, and the basics of genetic engineering. Gonick's drawings range from a moderately detailed look at ribosomes in action to loony pictures of dancing scientists, talking peas, and opinionated fruit flies. Matthew Meselson, co-discoverer of the "one gene-one protein" principle, says, "it puts textbooks to shame"--and he's right. --Mary Ellen Curtin ... Read more

Reviews (26)

4-0 out of 5 stars Demystifies DNA
I'm no science genius and college zoology left me still in the dark regarding DNA. I bought this book because one reviewer said that his colleague was using it for a genetics course and I knew a student who needed some help with genetics. I read the book myself, and then spoke with the student. This book would be great for someone in Introductory Biology but for someone in a genetics course it's simply not advanced enough. But the book did help me understand DNA for the first time. It also showed me that a good instructor can make the whole field understandable and interesting unlike my college zoology professor who only made it intimidating and boring. Now if the genetics instructor I'm thinking of would read this maybe she'd figure out how not to bore her class to sleep.

Seriously I loved the historical approach to the field, the cartoons and the jokes were great. This book took the intimidation factor out of biology to a degree. Now I can at least talk intelligently about the subject. High school students could learn a lot from this, and struggling college freshmen might not struggle quite so badly in introductory biology with this at their side.

5-0 out of 5 stars Historical tour through genetics in a comic book
The cartoon guide to genetics is like a comic book through the history of genetics starting with ancient times and going through modern genetic engineering. The chronological arrangement of information is informative and interesting. In the age of the sequenced human genome it is often hard to think of what science was like without information that is now taken for granted. The scientists that paved the way for modern genetics -Mendel, Beadle, Griffith, Chargaff and many more and their landmark experiments are all given a moment in the spotlight. Even some incorrect theories are introduced including the reasoning behind them at the time. The section on Mendel's famous pea plant experiments is especially well done. There are several pages of Punnett squares (though the author doesn't really use that word) and drawings of what causes the different ratios. This concept is often hard for students to understand, but it is explained well and simply here.

This book does not assume that the reader has any scientific background and everything is explained from the basics. It also does not get into real detail about anything, but that kind of detail isn't necessary for a broad understanding of genetics. Most of the comics aren't really that funny, but even so they bring levity to an often difficult topic. I happen to enjoy the picture of the human-strawberry hybrid. This is a great book for visual learners who like to see everything; the diagrams in this book make complicated systems simpler without leaving out too much. This is a good background resource for anyone who wants to understand the hot topic of genetics. Granted a lot has happened since this book was published, but the foundation is still the same.

4-0 out of 5 stars An excellent intro to an important field
Genetics, as you've probably heard, is a field of study that's likely going to play a very big part in society's near future. It's also a tough branch of science to grasp. What's the difference between DNA, a gene, a chromosome and a genome? How much of a role does genetics play in your health - is DNA destiny?

This book is a solid introduction to understanding genetics: the basics of the science, the history of humanity's knowledge of it, how it relates to other fields (ie evolution) - all explained well, in both word and the highly helpful illustrations. As always, Gonick tosses in some humor with his cartoons, but don't be fooled into thinking this is kid stuff. He delves into serious science. (And I noted with great amusement that one reviewer who hated the book was a big fan of the "for dummies" series. Irony much?)

I liked this book a lot - not quite as good as The Cartoon Guide to Physics, and bear in mind that current advances in genetics may well render parts of the book outdated soon... but it's still well worth reading.

4-0 out of 5 stars Introduction to Genetics
I use this book to introduce 8th graders to Genetics as it is entertaining, gives them good basic information and keeps them amused (and therefore reading!). Because we are working with basic genetics and because I am able to bring them to the present once they understand the basic concepts this book works very well as a text. I also find that it works well with a variety of ability groups. For the poor reader it is very visually stimulating and the writers are pretty funny. It also reads well in spurts or chunks. For the more advanced reader or student it is good because they can read through it quickly and get all the basic information that I need them to have for this class. I highly recommend the book for any middle school teachers that want to introduce a fairly abstract topic to a group of students who are predominantly still concrete learners. If you are looking for a book to inform you on new discoveries in the field this is not your book, but if you need a book to introduce genetic concepts to young people (or older non-readers), this is an excellent choice.

3-0 out of 5 stars Fun, but not doesn't cover more than the basics
I purchased this book to review the basics of genetics, mostly to be able to sound more knowledgeable than my pre-med significant other. I was very dissapointed to find that the book covered fundamentally the same material I remembered seeing as a freshman in high school 15 years ago. Not only has it not been updated to reflect the explosion in genetics, it basically covers the same fundametals one has gotten in a basic high school course. If you didn't understand it then, this book will help, otherwise it will just give you an interesting hour or two. I love Larry Gonick's other works (especially the History of the Universe series), but this one just doesn't measure up. ... Read more

76. What Makes Biology Unique? : Considerations on the Autonomy of a Scientific Discipline
by Ernst Mayr
list price: $30.00
our price: $24.00
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Asin: 0521841143
Catlog: Book (2004-08-09)
Publisher: Cambridge University Press
Sales Rank: 25476
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Book Description

This collection of revised and new essays argues that biology is an autonomous science rather than a branch of the physical sciences.Ernst Mayr, widely considered the most eminent evolutionary biologist of the 20th century, offers insights on the history of evolutionary thought, critiques the conditions of philosophy to the science of biology, and comments on several of the major developments in evolutionary theory. Notably, Mayr explains that Darwin's theory of evolution is actually five separate theories, each with its own history, trajectory and impact. Ernst Mayr, commonly referred to as the "Darwin of the 20th century" and listed as one of the top 100 scientists of all-time, is Professor Emeritus at Harvard University. What Makes Biology Unique is the 25th book he has written during his long and prolific career. His recent books include This is Biology: The Science of the Living World (Belknap Press, 1997) and What Evolution Is (Basic Books, 2002). ... Read more

77. Beginning Perl for Bioinformatics
by James Tisdall
list price: $39.95
our price: $26.37
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Asin: 0596000804
Catlog: Book (2001-10-15)
Publisher: O'Reilly
Sales Rank: 20851
Average Customer Review: 4.44 out of 5 stars
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Biology, it seems, is a good showcase for the talents of Perl. Newcomers to Perl who understand biological information will find James Tisdall's Beginning Perl for Bioinformatics to be an excellent compendium of examples. Teachers of Perl will likewise find the text to be filled with fresh programming illustrations of growing scientific importance. Seasoned Perlmongers who want to learn biology, however, should search elsewhere, as Tisdall's emphasis is on Perl's logic rather than Mother Nature's.

Departing from O'Reilly's earlier monograph Developing Bioinformatic Computer Skills, Tisdall's text is organized aggressively along didactic lines. Nearly all of the 13 chapters begin with twin bullet lists of Perl programming tools and the bioinformatic methods that require them. Likewise, the chapters end with exercises. String concatenation is illustrated with gene splicing, and regular expressions are taught with gene transcription and motif searching.

Tisdall emphasizes sequence examples throughout, leading up to an introduction to a Perl interface for the NIH GenBank biological database and the widely used BLAST sequence alignment tool. After a brief discussion of three-dimensional protein structure, he returns to sequence extraction and secondary structure prediction.

Tisdall's goal is to boost the beginning programmer into a domain of self-learning. He imparts essential etiquette for the success of programming newbies: use the wealth or resources available, from user documentation to Web site surveys to FAQs to How-To's to news groups and finally to direct personal appeals for help from a senior colleague. A well-plugged-in bioinformatics Perl student will soon discover Bioperl, an open-source effort to bring research-grade bioinformatic tools to the Perl community. Bioperl is described briefly at the end of Tisdall's book and will reportedly be a forthcoming title of its own in the O'Reilly bioinformatics series.

Although he introduces bioinformatics as an academic discipline, Tisdall treats it as a trade throughout his book. He indicates that open questions and computational hard problems exist, but does not describe what they are or how they are being tackled. Ultimately, Tisdall presents bioinformatics as another arrow in a bench scientist's quiver, very much like HPLC, 2D-PAGE, and the various spectroscopies.

As odd as a "bioinformatics-as-tool" book may be to its research proponents, the reduction of bioinformatics to trade status both deflates and vindicates the years of research, as Tisdall's work attests. --Peter Leopold ... Read more

Reviews (16)

4-0 out of 5 stars Decent intro to the subject
As the banner above the title of James Tisdall's Beginning Perl for Bioinformatics indicates, this book is 'an introduction to Perl for biologists.' What the banner doesn't mention is that it's also an introduction to biology and bioinformatics for Perl programmers, and it's also an introduction to both Perl *and* biology for people that have never really been exposed to either field. The author has clearly thought a lot about making one book to please these different audiences, and he has pulled it off nicely, in a way that manages to explain basic topics to people learning about each field for the first time while not coming off as condescending or slow-paced to those that might already have some exposure to it.

Superficially, this book isn't all that different from a lot of introductory Perl books: the Perl material starts out with an overview of the language, followed by a crash course on installing Perl, writing programs, and running them. From there, it goes on to introduce all the various language constructs, from variables to statements to subroutines, that any programmer is going to have to get comfortable with. Pretty run of the mill so far. Tisdall starts with two interesting assumptions, though: [1] that the reader may have never written a computer program before, and so needs to learn how to engineer a robust application that will do its job efficiently and well, and [2] that the reader wants to know how to write programs that can solve a series of biological problems, specifically in genetics and proteomics.

As such, there is at least as much material about the problems that a biologist faces and the places she can go to get the data she needs as there is about the issues that a Perl programmer needs to be aware of. The author introduces the reader to the basics of DNA chemistry, the cellular processes that convert DNA to RNA and then proteins, and a little bit about how and why this is important to the biologist and what sorts of information would help a biologist's research. The main sources of public genetic data are noted, and the often confusing -- and huge -- datafiles that can be obtained from these sources are examined in detail.

With the code he presents for solving these problems, Tisdall makes a point of not falling into the indecipherable-Perl trap: this is a useful language, well-suited to the essentially text-analysis problems that bioinformatics means, and he doesn't want to encourage the kind of dense, obscure, idiomatic coding style that has given Perl an undeservedly bad reputation. Some of Perl's more esoteric constructs are useful, and they show up when they're needed, but they're left out when they would only serve to confuse the reader. This is a good decision.

Rather, the focus is on teaching readers how to solve biological problems with a carefully developed library of code that happens to leverage some of Perl's most useful properties. The result is pretty much a biologist's edition of Christiansen & Torkington's Perl Cookbook or Dave Cross' Data Munging With Perl. The author presents a series of issues that a working bioinformaticist might have to deal with daily -- parsing over BLAST, GenBank, and PDB files, finding relevant motifs in that parsed data, and preparing reports about all of it. If a bioinformaticist's job is to be able to report on interesting patterns from these various sources, then following the programming techniques that Tisdall explains in clear, easy-to-follow prose would be an excellent way to go about doing it.

And when I say "programming techniques," note that I'm not specifically mentioning Perl. The code in this book is clear and organized, and all programs are carefully decomposed into logical subroutines that are then packaged up into a library file that each later sample program gets to draw from. Each new program typically contains a main section of a dozen lines of code or less, followed by no more than two or three new subroutines, along with calls to routines written earlier and called from the that is built up as the book progresses. Each sample is typically preceded by a description of what it's trying to accomplish and followed by a detaild description of how it was done, as well as suggestions of other ways that might have worked or not worked.

This modular approach is fantastic -- too many Perl books seem to focus so heavily on the mechanics of getting short scripts to work that they lose sight of how to build up a suite of useful methods and, from those methods, to develop ever-more-sophisticated applications. It isn't quite object-oriented programming, but that's clearly where Tisdall is headed with these samples, and given a few more chapters he probably would have started formally wrapping some of this code into OO packages.

If I have a complaint with the book, in fact, it's that Tisdall doesn't go any further: everything is good, but it ends too soon. Seemingly important topics such as OO programming, XML, graphics (charts & GUIs), CGI, and DBI are mentioned only in passing, under "further topics" in the last chapter. I also have a feeling that some of the biology was shorted, and the book barely touches upon the statistical analysis that probably is a critical aspect of the advanced bioinformaticist's toolbox. I can understand wanting to keep the length of a beginner's book relatively short, and this was probably the right decision, but it would have been nice to see some of the earlier sample problems revisited in these new contexts by, for example, formally making an OO library, showing a sample program that provided a web interface to some of the methods already written, or presenting code that presented results as XML or exchanged them with a database.

But these are minor quibbles, and if the reader is comfortable with the material up to this point, she shouldn't have a hard time figuring out how to go a step further and do these things alone. It's a solid book, and one that should be able to get people learning Perl, genetics, or both up to speed and working on real world problems quickly.

5-0 out of 5 stars No need to have any previous programming knowledge
I had zero programming experience when I started reading this book. It allowed me, step by step, to get familiar with the language and start writing programs related to the field I am interested in.
It is fun and very helpful. You don't feel the frustration of being lost in the middle of unreadable code. The comments and explanations to the programs are great. It allows you to start learning the simple things first and then, as you get familiar with the language, go into more detail.
You can chose, as the author suggests, to go sometimes to the Perl documentation and read about the operators or functions introduced in the different programs; but what is great about the book is that you are given examples and exercises to use them. This is really the way to learn.

3-0 out of 5 stars OK tutorial. Poor reference.
I have used this book in a beginning Perl programming course for biology majors. While it is good if you sift through it from start to the end, I often found it impossible to find things when I needed to go back to remind myself of something. The index does not help, and there is no concise language reference anywhere.

Also, I do not like the fact that it uses "quick and dirty" Perl (no "use strict" pragma). While it might be less confusing to skip it at the very beginning, very soon students start to waste too much precious class time trying to locate bugs that would make the program not compile with "use strict" in the first place (e.g. mistyped variable names).

4-0 out of 5 stars Good intro for biologists;poor intro for computer scientists
"Bioinformatics" is the new sexy term for what used to be called simply "computational biology". Simply put, it involves pretty much any application of computation techniques to biological problems. The reason for the new nomenclature and the greatly increased interest in the topic is, like much in modern biology, a more-or-less direct consequence of the many genome sequencing projects of the last decade.

The consensus in the field seems to be that it's more productive (and certainly easier) to teach biologists how to program, rather than try to get programmers up to speed on the intracities of molecular biology. For similar reasons, Perl is a popular language to learn: it's easy to get off the ground and be productive with it, without requiring a heavy computer science background. (This, of course, has downsides as well...)

Never one to miss out on a trend, I'm going to be teaching a course on Bioperl and advanced Perl programming, starting next fall, which means I'm doing a lot of reading in this topic area, trying to develop lectures and find good background reading material. One of the first books I grabbed was _Beginning Perl for Bioinformatics_, which has been sitting on my "to read" shelf since O'Reilly sent me a review copy in December of 2001. It's a typical O'Reilly "animal" book (the cover bears three tadpoles), which does a decent job of introducing the basic features of the Perl language, and it should enable a dedicated student to get to the point where she can produce small useful programs. However, I'm not completely happy about the book's organization, and I think the occasional "if you're not a biologist, here's some background" interjections could have been cut without hurting anything.

The initial chapters in the book cover "meta" information, such as theoretical limits to computation, installing (or finding) the Perl interpreter on your computer, picking a text editor, and locating on-line documentation. Some general programming theory stuff is covered as well -- the code-run-debug cycle, top-down versus bottom-up design, the use of pseudocode. There's also some biology background, but it's very introductory level stuff -- DNA has four bases, proteins are made of 20 amino acids, and so on.

In chapter four, the book begins to get into actual Perl, with some coverage of string manipulation. Examples deal with simulating the transcription of DNA into RNA. Chapters five and six continue to flesh out the language, covering loops, basic file I/O, and subroutines. Chapter seven introduces the rand() function, in the context of simulating mutations in DNA. Subsequent chapters introduce the hash data type (using a RNA->protein translation simulation), regular expressions (as a way to store the recognition patterns of restriction endonucleases), and parsing database flat files and BLAST program output.

I'm clearly out of the target audience of the book, as I already have a strong working knowledge of Perl. Perhaps that's why I found the order that concepts were presented in to be a bit strange -- for example, hashes, which are a fundamental data type, aren't introduced until halfway through the book, and regular expressions (one of the key features of Perl) first appear even later. As I said above, I also found the biological background sections to be more distracting than anything, but I've also got a strong biology background, so perhaps I'm off base here too. That said, I think a person with a CS background would be better served with a copy of _Learning Perl_ and an introductory molecular biology text than with this particular book.

One of the things I did enjoy about the book were the frequent coding examples, all of which presented realistic computational biology sorts of problems and then demonstrated how to solve them. I'm sure that when I get around to writing lectures, I'll be leafing through this book looking for problems I can use in class.

Overall, recommended for biologists without programming experience who would like to get started using Perl for simple programming. Not recommended for people with computer science backgrounds looking to get into bioinformatics.

5-0 out of 5 stars Great introduction
This is the first book that I read about Perl and also the first one that I read about Bioinformatics. I think it has an enough level of details so that readers who have little or no Bioinformatics background can easily understand the basics, and readers who wants to focus more on Perl usage in Bioinformatics can also get quick and useful examples such as interpreting BLAST output, and regular expressions. ... Read more

78. Finding Darwin's God: A Scientist's Search for Common Ground Between God and Evolution
by Kenneth R. Miller
list price: $14.00
our price: $10.50
(price subject to change: see help)
Asin: 0060930497
Catlog: Book (2000-09-15)
Publisher: Perennial
Sales Rank: 10478
Average Customer Review: 3.86 out of 5 stars
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Book Description

Question: Who made us?
Answer #1: God made us.
Answer #2: Evolution made us.

Which is it? What is the true answer to the age-old question of where we came from? Is it even possible to know for sure?

In Finding Darwin's God, Kenneth R. Miller offers a surprising resolution to the evolutionism vs. creationism debate.A distinguished professor of biology at Brown University, Miller argues that the genuine world of science is far more interesting than either the scientific mainstream or its creationist critics have assumed. He begins by systematically demolishing the claims of evolution's most vocal critics, showing that Darwin's great insights continue to be valid, even in the rarefied worlds of biochemistry and molecular biology. As he puts it, evolution "is the real thing, and so are we."

Does this mean that evolution invalidates all worldviews that depend upon the spiritual? Does it demand logical agnosticism as the price of scientific consistency? And does it rigorously exclude belief in God?

His answer, in each and every case, is a resounding No. Not, as he argues, because evolution is wrong. Far from it. The reason, as Miller shows, is that evolution is right.

In this lively, fast-paced book, Miller offers a thoughtful, cutting-edge analysis of the key issues that seem to divide science and religion. As his narrative shows, the difficulties that evolution presents for Western religions are more apparent than real. Properly understood, evolution adds depth and meaning not only to a strictly scientific view of the world, but also to a spiritual one. Miller's resolution of the issues that seem to divide God from evolution will serve as a guide to anyone interested in the classic questions of ultimate meaning and human origins.

... Read more

Reviews (65)

2-0 out of 5 stars Great start; disappointing end
As many of the reviewers below have eloquently noted, the majority of Miller's book is devoted to debunking the poor science of creationists and fundamentalists who attack evolution. Miller offers an excellent presentation of the basics of evolution and refutes the arguments of several recent detractors. The story is highly readable and builds towards the inevitable conclusion that religion must conform to the truths that evolution and science in general have discovered. Along the way, Miller demonstrates the futility of stuffing God into the gaps of scientific knowledge; doing so only leads to a new crisis each time science explains what was previously thought to be the domain of God.

Having presented a compelling case for a universe that evolved according to knowable rules, Miller then attempts to show how a personal God can be consistent with our apparently Godless universe. Where does this God go? You guessed it! Into the gaps of science! In this case, it's the

indeterminacy of quantum mechanics that provides the space for Miller's God.

After such a clear explanation of the science that compels us to reject fundamentalist cosmologies, it's surprising to see Miller fall into the silly quantum mechanics mysticism of such books as "The Tao of Physics" and "The Dancing Wu Li Masters." Many aspects of quantum theory are recent and presently evolving; perhaps some yet-to-be-articulated model will explain simply what today appears indeterminate. If so, yet another gap will be filled, displacing God in exactly the way Miller decries in the first part of the book!

But even if the indeterminism of quantum mechanics remains forever a feature of the theory, there's still no reason to insert God into it. Again, after so carefully explaining the _reasons_ to reject religious dogma and creationist pseudoscience, it's jarring to see Miller assert his religious speculations with absolutely no rational justifications whatsoever. His explanation of God-in-the-quantum-indeterminacy-gap offers no hints to the nature of this God; for that, the reader apparently must turn to one of the dogmatic religions Miller has previously defenestrated.

Ultimately, Finding Darwin's God reads like the ruminations of a smart guy who is trapped by his intellect: unable to justify dogma, he accepts the material world. But unwilling to let go of the seduction of religion, he relaxes his intellectual rigor to create a little space for a God he can't otherwise find.

5-0 out of 5 stars Lucid, balanced guide to the challenges of science for faith
This book is a "must read" for anyone interested in a thoughtful analysis both of the most popular approaches for defending a belief in creation and also for those that oppose a belief in creation in light of the findings of modern science. Kenneth Miller is a professor of biology at Brown University and a committed Christian (although the book stresses the shared convictions of the major Western religions, rather than adopting a sectarian approach).

Miller considers first the arguments of young-earth creationists (Whitcome and Morris, Duane Gish, et al.) and answers these with an avalanche of scientific evidence. He then examines in two chapters the claims of old-earth creationists, especially Philip Johnson (who stresses a lack of transitional forms in the fossil record) and Michael Behe (who identifies what he considers are "irreducably complex" biochemical machines in the cell). In his careful analysis of these views, Miller helps the reader appreciate how both approaches are, in effect, misguided attempts to defend creation with a "God of the gaps." Each offers examples which, the authors hope, defy explanation by modern science. This (temporary) inability of modern science is then taken as evidence in support of the work of the Creator at that point. Miller shows the consistent failure of this mode of argumentation in the past and cites evidence published since the appearance of Johnson's and Behe's writings, which, unfortunately for them, fills in their hoped-for gaps.

One of the greatest dangers of a God of the gaps argument, Miller notes, is that each time science succeeds in filling one of these alleged gaps its success is misconstrued by atheistic scientists as proof that God must not exist. Miller turns his attention in the second half of his book to a refutation of the equally deficient views against creation that have been advanced by atheistic scientists.

In the end Miller affirms the wisdom of resting one's faith in a God who is the God of the stuff in between the gaps - whose handiwork is best seen in facts and qualities of the universe which are well known to science, rather than in those which are as yet undiscovered. Although he strongly affirms evolution, natural law, and chance, he sees these as means which God used for accoplishing His creative intention and safeguarding the genuine freedom and independence of His Creation. Miller affirms that the existence of the universe is not self-explanatory. Although he recognizes that the convictions of faith cannot be proven absolutely, he considers faith in the Creator to be reasonable and supported by such evidences as the anthropic principle. He also favors the possibility that God may utilize quantum indeterminacy and chaos as subtle means for interacting with His creation.

5-0 out of 5 stars Terrific book
This is a tremendous book that will help any seeker reconcile both evolution and the existence of evil with a caring and loving God. This may help you believe in a Theist God but for me it falls short of the Christian God because it doesn't show the role and purpose of Jesus. Nevertheless, a great book for any theist or those considering theism.

3-0 out of 5 stars Best of Type
I have been intrigued by the on-going debate regarding evolution. As a result, over the last year I have read a range of books on the issue starting with Darwin's Origin of Species, and, including works by Pennock, Dawkins, Johnson, Behe, Dembski and others. Of recent works defending the theory of evolution Finding Darwin's God is the best that I have come across for a popular audience.

In the early portion of the book Miller provides a good and succinct case for evolution (something I find Dawkins incapable of). The author then addresses several of the different challenges to evolution (Young Earth Creationists (YEC), Johnson and Behe). He is most successful against the YEC, but his responses to the others challengers, if not decisive, are well articulated.

A point that is particularly well done is the discussion with respect to why evolution is such an emotionally charged issue. I agree with Miller that one of the causes of this is the extreme extrapolations atheists such as Dawkins, Gould et al make from what at the end of the day is a limited scientific theory (albeit an interesting one). For those unfamiliar with this aspect of the discussion, many "popularizers" of evolution attempt to use the theory to argue for materialism/determinism and eliminate the possibility of the supernatural.

In the second part of the book Miller goes on to argue that evolution and belief in God are not incompatible. In doing so, he touches on a range of scientific and theological issues including: deism, quantum theory, cosmology and apologetics. This part of the book was not as well done. I support Miller's general contentions but, believe that he tried to accomplish too much and got out of his intellectual depth. Although it had some good points the second half was repetitive and a bit disjointed. I will just offer a few comments on some of these latter arguments before closing.

First, Miller reads too much into quantum theory. Neither God's ability to act in the word nor free will are contingent on quantum indeterminacy. Readers seeking an introduction to free will can refer to sections in intro level philosophy books such as Pojam's Introduction to Philosophy (an excellent collection of essays on various philosophical questions). Additionally, similar to other scientific fields much work is on-going in quantum theory and many of the current limitations in this area could prove to be methodological.

Second, Miller's handling of cosmology and its theological ramifications are weak. Readers seeking a better understanding of this issue can seek one of Bill Craig's many excellent works in this area.

Third, it is not surprising that the author as a scientist approaches the issue from a classic modernist standpoint (i.e. science is the only source of truth). Much fascinating discussion has taken place around this issue and, some significant challenges have been raised by postmodern thinkers. For an introduction to postmodern philosophical work Stanley Grenz's A Primer on Postmodernism is simply outstanding.

Finally, the author gives to much credence to the threat evolution poses to religion. In contemporary apologetics the argument from design plays a limited role and, when used it revolves around the fundamental relationships in the universe not evolution (Miller touched on this issue). All but the most literal of Christians (YEC types) do not see evolution and a Christian worldview as incompatible.

In conclusion, good book, well worth the money. For those exploring the evolution argument I recommend it along with Behe's Darwins's Black Box and a work by Philip Johnson such as The Wedge of Truth (to get a fell for both sides).

2-0 out of 5 stars Contains many major mistakes
Although this book has much good material, it contains many major mistakes. For example,research by ophthalmologists has clearly shown why the human retina must be of the "inverted" design. Miller claims that this design is suboptimal because the photoreceptors are on the inside curvature of the retina, forcing the incoming light to travel through the front of the retina to reach the photoreceptors The photoreceptors (rods and cones) MUST face AWAY from the front of the eye in order to be in contact with the pigment epithelium on the choroid, which supply it with blood. The verted design claimed by Miller to be best would not place the photoreceptors in contact with their source of nutrition (the choroid). This is a serious problem because rods and cones need an enormous amount of energy for repair and they completely replace themselves at a very high rate (about every 7 days or so), due to phototoxicity, and other damage. Miller's design simply would not allow the rods and cones to function because of their extremely high rate of metabolism. Furthermore, placing the neural components of the retina in front of the photoreceptors does not produce any kind of optical handicap, since the neural elements are separated by less than a wavelength of light, so very little or no scattering or diffraction occurs, and the light travels through this area as if it was near-perfect transparency. ... Read more

79. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition
list price: $79.95
our price: $79.95
(price subject to change: see help)
Asin: 0471478784
Catlog: Book (2004-10-15)
Publisher: Wiley-Interscience
Sales Rank: 70570
Average Customer Review: 3.62 out of 5 stars
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Book Description

Reviews of the Second Edition

"In this book, Andy Baxevanis and Francis Ouellette . . . have undertaken the difficult task of organizing the knowledge in this field in a logical progression and presenting it in a digestible form. And they have done an excellent job. This fine text will make a major impact on biological research and, in turn, on progress in biomedicine. We are all in their debt."
--Eric Lander, from the Foreword to the Second Edition

"The editors and the chapter authors of this book are to be applauded for providing biologists with lucid and comprehensive descriptions of essential topics in bioinformatics. This book is easy to read, highly informative, and certainly timely. It is most highly recommended for students and for established investigators alike, for anyone who needs to know how to access and use the information derived in and from genomic sequencing projects."
--Trends in Genetics

"It is an excellent general bioinformatics text and reference, perhaps even the best currently available . . . Congratulations to the authors, editors, and publisher for producing a weighty, authoritative, readable, and attractive book."
--Briefings in Bioinformatics

"This book, written by the top scientists in the field of bioinformatics, is the perfect choice for every molecular biology laboratory."
--The Quarterly Review of Biology

This fully revised version of a world-renowned bestseller provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. Using relevant biological examples, the book provides background on and strategies for using many of the most powerful and commonly used computational approaches for biological discovery. This Third Edition reinforces key concepts that have stood the test of time while making the reader aware of new and important developments in this fast-moving field. With a new full-color and enlarged page design, Bioinformatics, Third Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists.

This new edition features:

  • New chapters on genomic databases, predictive methods using RNA sequences, sequence polymorphisms, protein structure prediction, intermolecular interactions, and proteomic approaches for protein identification
  • Detailed worked examples illustrating the strategic use of the concepts presented in each chapter, along with a collection of expanded,more rigorous problem sets suitable for classroom use
  • Special topic boxes and appendices highlighting experimental strategies and advanced concepts
  • Annotated reference lists, comprehensive lists of relevant Web resources, and an extensive glossary of commonly used terms in bioinformatics, genomics, and proteomics
Bioinformatics, Third Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, clinical research, proteomics, and computational biology. ... Read more

Reviews (13)

5-0 out of 5 stars Great book, easy to follow, expert authors
Five stars, a great place for people like me (trained as a biochemist) to start in a field that I know is going to be more and more important as to how I do my work in the future. I've been able to use basic things like BLAST more effectively, and finally understand that there are other ways to look at sequence besides BLAST and how to apply those tools to my own sequences. I really like the Entrez chapter, since Entrez does so much more than I ever realized it could do! I haven't ventured into the advanced territory yet (like microarrays), but at least I understand what I'm hearing in seminars now and what all those red and green spots actually represent.

I read the review by "a reader in Cambridge, MA", and don't understand what their beef is with this title. The authors have tried (and have succeeded) in pointing the readers to the best PUBLIC DOMAIN software out there, augmenting documentation that's generally lacking. Have you ever tried finding good docs on the NCBI Web site? Well, these two editors got them for you. UNIX-centric? I can't speak for the first edition, but check out the second edition and see that there's tons of Netscape screen dumps demonstrating the tools and making things as easy as possible for the reader. I originally bought this because of the reviews published in Science and Cell and a slew of other journals, all favorable, so the "reader in Cambridge" seems out of step with all of the published journal reviews of the book. Everyone's entitled to their opinion, but I just wanted to point this out for a sense of balance here, especially since my own experience was so different.

3-0 out of 5 stars Somewhat more than an out-of-date catalog of tools
The book is a collection of chapters by different authors addressing software tools for various problems: database search, multiple sequence alignment, gene prediction, protein structure prediction, etc. A big flaw is that all of the authors assume a different level of prior background and have rather different emphases.

I'd have to agree with the other reviewer that Chapters 1 & 17, which constitute 10% of the book, are wasted paper. No one in 2001 (when the book was published), let alone 2004, needs Chapter 1's lengthy explanation of what e-mail and web browsers are. And the perl program at the anticlimax of Chapter 17 was ... anticlimactic.

The book is to a great extent a catalog of available software tools. With the exception of the chapters on multiple alignment and phylogeny, the emphasis is on not on how the tools work but how to operate them -- to the of saying "at this URL there is a web page where you can either paste in your sequence or upload a file". The idea of invoking a program through a Unix command line is more than once presented as a truly daunting prospect. The authors generally do a good job of emphasizing that the programs are the beginning of analysis and not the end; the results must always be viewed somewhat skeptically with an expert eye.

If you're coming at the book as a biologist, you will probably find it to be a useful catalog of software, though undoubtedly dated by now. If you're coming at it from the informatics side, you're going to need some background... a book like Dwyer's, Setubal and Meidanis's, or Mount's will get you up to speed on the algorithm aspects of the field with simplified versions of many of the big problems. Then you can look at this book to find good pointers to the ways the real-world versions have been addressed.

The book was published three years ago and, being to a large extent an index of the work of others, is necessarily no longer up to date in a fast-moving field. It needs a revision and, in the meantime, it would make more sense to snag a used copy than to pay full price for a new book.

4-0 out of 5 stars A survey tor tool users
Like any survey, it seems to touch the major features only. And, as others have pointed out, the tools change but the book doesn't.

I think this is a good, brief introduction to the wide variety of bioinformatic tools and databases on the internet. It describes the major features of each, and the kinds of results that each tool is good for. After that, the serious user will go to the sources of each tool or database, to learn more about the specifics as of the moment. No book can hope to keep up with the weekly enhancements at the major repositories.

I emphasize that this is for tools users, not tool makers. It addresses the working scientists who already know their subjects and their needs. This skips over the algorithms in favor of higher level descriptions, and skips over many of the biological reasons for the tools described. Better-informed tool users get better answers from the tools, true. At some point, though, the biologists want to skip the theory, skip the introduction to subjects in which they're experts, and get on with their science. I don't think this book was ever meant for people - and I'm one - who want full details of the algorithms.

I agree, the book treats its many subjects in a shallow way. I think that is by intent, since the book's real goal is breadth and its target is a reader who knows the basic science. It's a bit off the center of my interests, but I've found it helpful.

4-0 out of 5 stars Bioinformatic for the beginner...
I guess that everybody interrested by this kind of book knows already a little about bioinformatic and wants to improve his bioinformatician skill. So forget about this book:
This is really a well-documented introduction to all the methods currently used by every biologist or biology student, such as Blast, Clustal, multiple alignement or use of web-interface for submiting sequence.
So get it if you need a clear introduction to the field, but if you already know a little bit about bioinfo, immediately choose a more detailed book.

2-0 out of 5 stars Poorly organized overpriced book
Although the book is presented as an introduction to the topic, its organization assumes that the reader has already been working in the area. Two of the chapters (1 and 17) are a waste of space. The first chapter presents a (useless) introduction to internet, while chapter 17 attempts (and fails to do so) to explain Perl in the context of bioinformatics. For the same money you can find far better books in the market. The good thing is that I only borrowed the book :) ... Read more

80. Games of Strategy
by Avinash K. Dixit, Susan Skeath
list price: $93.75
our price: $87.75
(price subject to change: see help)
Asin: 0393974219
Catlog: Book (1999-06-01)
Publisher: W.W. Norton & Company
Sales Rank: 217713
Average Customer Review: 4 out of 5 stars
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Book Description

All introductory textbooks begin by attempting to convince the student readers that the subject is of great importance in the world, and therefore merits their attention. The physical sciences and engineering claim to be the basis of modern technology and therefore of modern life; the social sciences discuss big issues of governance, for example, democracy and taxation; the humanities claim that they revive your soul after it has been deadened by exposure to the physical and social sciences and to engineering. Where does the subject "games of strategy," often also called game theory, fit into this picture, and why should you study it? Dixit and Skeath's Games of Strategy offers a practical motivation much more individual and closer to your personal concerns than most other subjects. You play games of strategy all the time: with your parents, siblings, friends, enemies, even with your professors. You have probably acquired a lot of instinctive expertise, and we hope you will recognize in what follows some of the lessons you have already learned. This book's authors will build on this experience, systematize it, and develop it to the point where you will be able to improve your strategic skills and use them more methodically. Opportunities for such uses will appear throughout the rest of your life; you will go on playing such games with your employers, employees, spouses, children, and even strangers. Not that the subject lacks wider importance. Similar games are played in business, politics, diplomacy, wars--in fact, whenever people interact to strike mutually agreeable deals or to resolve conflicts. Being able to recognize such games will enrich your understanding of the world around you, and will make you a better participant in all its affairs. ... Read more

Reviews (6)

5-0 out of 5 stars Excellent Starter
I'm learning game theory on my own and found this book an excellent starter. The book provides a wide range of topics, building from what strategy means in game theory, to the sequential and simultanous play of games, to more specialized areas and applications of the theory.

Although it keeps the mathematics rather minimal, you'll need to do your own workings to better understand the text. To get more from this book, you'll need to be involved in the examples the book provides... breezing through may not help you understand the theory better.

While I do read other books on game theory, I find myself going back to Games of Strategy to review the basics and the examples. The example on the tennis game has provided me some starting ideas on the issues I've to face in some research areas I'm working on.

3-0 out of 5 stars From a student perspective
I used this book as a student in an undergraduate Game Theory course and have mixed feelings about it.

Positives: the book is written in a simple style with relatively good examples that promote conceptual understanding.

Negatives: the book is very poorly laid out. Some chapters don't seem to follow any logical progression, so the reader must frequently jump from one section to another. Additionally, the book doesn't utilize some fairly standard terms, and the index doesn't facilitate the book's use as a reference manual.

The reason I wrote this review was because I came online to try to find a better Game Theory textbook -- I ran into problem studying from this one.

4-0 out of 5 stars Good and interesting introduction to game theory
I really enjoyed this book. There were some areas where it was kind of confusing, but I found that overall it kept me interested. Their approach is good especially for those who want to learn about the topic and its applications but don't have much background in math or economics. Game theory is a really interesting field, and this text provides a good introduction for those who want to learn about it without getting bogged down in the math. The book does its best job I think in tying the principles to the real world.

5-0 out of 5 stars Excellent Textbook
I used this book when teaching an undergraduate course in game theory at Smith College. The course had a one semester calculus prerequisite and no econ prerequisites. The book is fantastic. It makes material very accessiable to students. It provides very interesting examples.

3-0 out of 5 stars Why won't anyone just call it the Battle of the Sexes?
I used this book for the second half of a principles of micro. course, to supplement the shoddy, one-chapter-on-the-Prisoners'-Dilemma treatment found in most principles textbooks. Everything said here should be interepreted according to this. From this instructor, the book gets points for being the best one available for teaching low-level undergraduates, but it could have been a LOT better. For example:

The notation and terminology are in many cases non-standard, and tend to change from chapter to chapter. The BoS is the Battle of Cultures (though this is not the first book to mess with this game). Chicken is a Game of Assurances, except in Ch. 10. SPE are (quasi-)formally described in Ch. 6, but they are actually introduced in Ch.4, where they are called Rollback Equilibria. Many times, I would have to tell students, "this is what your book calls a..."

The authors use confusing and convoluted examples to motivate concepts. For example, it takes a confusing, two-page story about advertizing in a political race to motivate study of sequential-move games. A simple entry-deterrence story gets the point across.

Also on this point, sequential-move games appear before simultaneous-move ones. I reversed this, in part ot be able to show that the set of SPE is merely a subset of the set of NE (again, using the entry-deterrence story). In fact, there's no real attempt to relate many of (seemingly unrelated) concepts to one another, as equilibrium refinements, each of which conforms to some intuitive concept of the "right" way of playing a given game.

The disucssion of the special case of two-person, zero-sum games, introducing pre-Nash notation and solution concepts is merely confusing for the uninitiated. I see no reason that anyone not yet in graduate school should have to know the min-max theorem.

In some ways, the books seems to suffer from over- and under-reach at the same time. The subject of infinitely repeated games gets two pages on TFT and Grim strategies in a repeated Prisoners' Dilema. There's no real discussion of rationalizability, or Bayesian games; many important concepts are smooshed into a couple of chapters, like they're being swept under the rug. There IS, however, a chapter on evolutionary games, and a (math-free) chapter on auctions.

Again, these are points that, I think, led to undue confusion, and required undue effort to counteract. However, I don't mean to be unduly harsh. I'm not suggesting that the authors should merely have mimeographed Fudenberg & Tirole, and whited-out the math. This is a useful book, ahead (as far as I know) of other treatments appropriate for students at this level. But it could have been much better. ... Read more

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