Reviews (1)

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

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)

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.

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.

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).

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.

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

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)

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.

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

EXCELLENT BEGINNING BOOK
I RECENTLY RETIRED AND DECIDED TO PLAY AROUND WITH GRAPHICS AND GAME PROGRAMMING, AND THIS BOOK IS JUST PLAIN EXCELLENT!!!!!. I WISH MORE AUTHORS COULD WRITE TECH SUBJECTS THIS WELL.

THANK YOU FLETCHER DUNN AND IAN PARBERRY!!!

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 .

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

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

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

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)

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.

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.

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.

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.

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

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)

"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]

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).

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.

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.

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

Book Description

Reviews (1)

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

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

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)

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.

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.

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."

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.

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

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)

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

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)

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!

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.

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.

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.

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

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)

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
Montreal

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!

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.

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

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)

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.

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