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Curiosity Guides: The Human Genome
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13 of 14 people found the following review helpful
on August 23, 2013
Format: Hardcover
In this small book, John Quackenbush seeks to explain what the Human Genome Project (HGP) is and the implications of its findings to science and medicine. Quackenbush may have been a late-comer to biology (having received his undergraduate and graduate degrees in physics), but since the early 1990s, he has conducted research in genomics under the auspices of prominent scientific institutions, including the Dana Farber Cancer Institute. The book is aimed at a general audience, and framed in non-technical language that will be easily understood by most interested readers. Following a brief introduction, the book begins with an overview of cells, genes, and protein synthesis. Chapter 2 considers the various species for which partial or complete genetic maps now exist. Chapter 3 explores the Human Genome Project itself, and what it has and has not revealed. Chapter 4 considers causes and treatments of the broad family of cancerous diseases. Chapter 5 considers other diseases with genetic components (i.e., diabetes, cystic fibrosis, and Huntington's disease).

Chapter 6 explores fascinating issues of what can be inferred from genetics about human prehistory, including our spread out of Africa throughout the globe. Quackenbush takes pains to rebut the potential misconception that "mitochondrial Eve" and her male counterpart were the only members of their species alive at their time. Unfortunately, he endorses a more common misconception, by asserting that mitochondrial Eve and Y- chromosome Adam "were our most recent female and male common ancestors" (p. 150). The quote is incorrect. These two person were only (by definition) our most recent common ancestors by strictly matrilineal and patrilineal lines. As work by Joseph Chang and others has shown, all living humans share a set of common ancestors of only a few thousand years ago (notwithstanding the much greater age of our matrilineal and patrilineal ancestors). (A highly readable account of this issue can be found in Richard Dawkins' "The Devil's Disciple".) Although "The Human Genome" states that "no DNA evidence suggests that humans and Neandertals interbred" (p. 151), compelling evidence of such interbreeding was published 10 months before this book was published. The final chapter ("A Brave New Genomic World") considers the future, touching on issues of stem cells, cloning, gene therapy, and ethical concerns.

Despite its general utility, The Human Genome contains many factual and conceptual errors. For example, to account for inheritance of maternal DNA, the text explains that "Male sperm cells do not contain mitochondria" (p. 147). On the contrary, sperm cells are packed with mitochondria, which provide all the energy that powers sperm locomotion. (What the author probably meant to say is that sperm mitochondria do not contribute DNA to the fertilized egg). As another example, the text states that "Mammals have been around for 510 million years" (p. 156). This is a mistake that an introductory student shouldn't have made. Mammals actually arose in the early Jurassic, about 190 million years ago. Perhaps the author was thinking of invertebrates, which date back over 500 million years.

To illustrate the pattern of Y chromosome inheritance, the text invokes the mutineers from the HMS Bounty who settled Pitcairn Island in 1790. We are told that the island was settled by 6 mutineers and 13 native women, and that 200 years later, only three of the original male surnames remain, due to "chance events that occur when men do not have sons" (p. 145). The example is misrepresented and misinterpreted. The early Pitcairn settlers actually included 15 men, 2/3 of whom were murdered in the first few years; only one was left by 1799. What's more, the original inhabitants of Pitcairn abandoned the island in the 1850s (see footnote *1). Descendants have come and gone since that time. Clearly present- day male surnames on the island do not simply reflect random patterns of mating.

The text attributes Charles Darwin's revelation about natural selection to his study of the Galapagos finches on the various islands (p. 24-25; p. 139). The account is misleading, since it was actually the island mockingbirds that led Darwin to question the stability of species. Further, Quackenbush credits Darwin with constructing a phylogenetic tree of the Galapagos finches (p. 139). On the contrary, no such phylogeny was constructed until the mid 20th century. In considering the genomics of evolution, Quackenbush mistakenly identifies "parsimony" as "the assumption that nature makes as few changes as possible as new species evolve from old ones" (p. 139). This an amateurish error that evidences significant conceptual confusion. Parsimony is a methodological principle, not an empirical statement about nature (much less, about evolution itself) (see footnote *2 below). In short, we do not assume that evolution is conservative -- rather, we adopt a method involving the fewest extra assumptions, as in all scientific enterprises. The difference is significant.

Such errors are troubling and would easily have been caught by a writer or reviewers with appropriate expertise. Given its errors, astute readers have good reason to wonder about the reliability of the overall work. Nevertheless, this book offers a reasonable account of the human genome and implications of the HGP in realms of science, medicine, and anthropology.

Footnotes

*1. The 1790 settlers of Pitcairn Island included 15 men (6 of whom were Polynesian), 12 women, and an infant. Through rivalries over women and ethnic conflict, 11 of the men (including all the Polynesians) had been murdered within four years (see T. Lummis' Life and Death in Eden). By five years later, only one man was left, and only some of the deceased men had left offspring. In 1856 the island was entirely abandoned. Only one family returned in 1859. Over the past 150 years, descendants of the original mutineers have come and gone from the island. Clearly the retention of male surnames among current residents of Pitcairn reflects historical events of multiple types.

*2. The principle of parsimony (sometimes known as Occam's Razor) is to make as few ad hoc assumptions as possible in making inferences and drawing conclusions. It is employed throughout the natural sciences and most human endeavors involving critical thinking. Whether a given pattern of evolutionary change has been conservative or not is an empirical question - and one that is only answerable through adoption of the methods of parsimonious analysis. In fact parsimony is what has allowed biologists to recognize innumerable cases where evolutionary change has been other than "conservative".
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10 of 11 people found the following review helpful
on February 19, 2011
Format: Hardcover
This book is awesome! I was pretty nervous about reading it, feeling worried that I would not be able to understand it or that it would be written "over my head." I was so wrong. This book is written for the "average" person who is simply curious about the human genome and is interested in learning more. It brought me back to high school biology, yet it was written even more clearly than back then. This book covers the history of the Human Genome Project, the science behind it, and even the ethical implications of the project. Dr. Quackenbush has a wonderful style of writing that is both objective and clear. He is able to discuss serious ethical issues without overwhelming the reader with his own views. This book is perfect for anyone who loves science and even the budding scientist.
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6 of 6 people found the following review helpful
on March 16, 2011
Format: HardcoverVerified Purchase
Oh no, not another book that is too sciencey for me to understand, I thought, when I first saw this little gem of a book. But when I picked it up I found myself drawn into a topic I know little about. Dr. Quackenbush's book makes mapping the human genome perfectly understandable. He writes of his early physics training: "I soon learned that biology was undergoing a revolution as profound as that which had occurred in physics in the late 1800s and early 1900s when... new methods of investigation set the stage for people like Niels Bohr, Erwin Schrodinger, and Albert Einstein to dramatically alter our understanding of the universe." So it is today. By combining biology, computer science, and information technology Dr. Q is able to map the human genome sequence--data that leads to "major advances in understanding, diagnosing, and treating disease." Dr. Quackenbush is a computational biologist at the Dana Farber Cancer Institute in Boston. The new technologies might actually lead to more effective treatments and managements of disease. The book is essential for both the lay person and the scientist. It also has its share of footnotes and citations, leading back to previous accretions of research. Bravo. A must have for anyone interested in understanding the evolution of cancer treatment.
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3 of 3 people found the following review helpful
on April 8, 2011
Format: HardcoverVerified Purchase
It's rare when a book is written about a branch of science and a specific research project that is so important as to be seminal to the future of the Human Race. Yet here, in clear and concise language, Dr. Quackenbush, as the title aptly describes, gives us the 'essential knowledge' to understand the kind of unbelievable changes the Human Genome Project will bring to us as a species.

We are bombarded with hyperbole, often about belief systems that have no basis whatsoever in science. When a book like this is written, it's hard to underestimate its importance. Ultimately the Genomic information that he describes has the power to cure thousands of diseases, and will bring revolutions in medicine, and all aspects of biology, including horticulture, crop production, and evolution itself.

Not only does Dr Quackenbush give us the basic history of the scientific discoveries that led to the continuing success of The Human Genome Project, he reviews the biological mechanics of heredity, growth, disease, and evolution of the human race.

In the Afterward, we get to appreciate the extraordinary set of intellectual and scholarly talents that Dr Quackenbush brings to this book. He is a man of superb intellect, impressive achievements and is a respected scientist in his field. His understanding of the recent medical and technological breakthroughs, and his ability to condense and synthesize them, is why this book is such a success. This is no small task, giving the complexity and the number of different fields that were directly involved in the HGP.

I look forward to reading Dr. Quackenbush's opinions on the future of our physical bodies, the effect of the digitalization and manipulation of DNA, and what he thinks we will look like 500 years from now, and even 5,000 years from now.
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2 of 2 people found the following review helpful
on March 25, 2011
Format: HardcoverVerified Purchase
Interested in genetics and the Human Genome Project? The Human Genome is a great introduction to the Human Genome Project (HGP) from someone that experienced it from the beginning. This book is quite approachable for people not versed in biology or genetics. I have a degree in biology, but I've been away from the field for over 15 years. I really enjoyed how Quackenbush applied the work and discoveries of the HGP to real-life issues that we are all dealing with everyday. In particular, he covers the genetic foundations of cancer, something that I have recently had to deal with in my family. The book is very succinct and does not stray too far from being what it is billed: a curiosity guide. I would highly recommend trying this book out first to build a foundation. Excellent stuff!
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4 of 5 people found the following review helpful
on April 19, 2011
Format: Hardcover
Dr. Quackenbush has put together a beautiful little informative book that clearly covers the results and history of a very complex subject. I am amazed on all that has been accomplished since I was in high school more than 50 years ago! In the trenches it may seem that progress is very slow at times [excluding Watson & Crick] but this book presents great hope and encouragement for not only researchers but for the practical applications of the knowledge of genomics in the future.
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1 of 1 people found the following review helpful
on October 4, 2011
Format: HardcoverVerified Purchase
Having known the author since attending college with him at CalTech, I can say unequivocally that he has done a fine job of mastering the field of Genomic Biology (Not a mean feat for a Physics major!) His book is a wonderful summary of the advances in understanding of Genomics and goes into reasonable detail on the Human Genome Project itself. It covers a variety of topics in just enough depth to make them interesting. I was even lucky enough to pick up a few details that will be helpful to me as a practicing Physician. My son, age 16, loved the book and was able to read and understand it without enormous difficulty. I will look forward to reading other books to come by Dr. Quackenbush!
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on November 10, 2013
Format: HardcoverVerified Purchase
I posted this review some months ago but it appears only as a comment to the review by danielx. I am re-posting it here simply to increase its visibility.

I am John Quackenbush, the author of The Human Genome: Book of Essential Knowledge. I typically don't respond to reviews, but I feel that this critical, unflattering, and somewhat misleading review warrants a reply.

First, as is true of all books, there are some errors that were missed as the book was prepared for publication. For example, as you point out, mammals did not arise 510 million years ago, but during the Late Triassic Period, approximately 210 million years ago. This was an unfortunate typographical error and I appreciate having it pointed out. Similarly, the review is correct in noting that sperm do contain mitochondria and, indeed, the text should have read, "Male sperm cells do not contain large numbers of mitochondria and these are destroyed within minutes of fertilization." And both of these will be corrected (as a few other minor errors I've found) should a second edition of this book be produced.

However, I must disagree with most of the other points raised here. While Rhode, Olsen, and Chang published a 2004 paper presenting mathematical models and computer simulations indicating humans shared a most recent common ancestor only a few thousand years ago, this idea is not widely accepted and not supported by experimental evidence. A little thought about the history of human migration and worldwide diversity underscores why such a recent common ancestor is so unlikely.

The example of sex-linked inheritance detailed in the book, describing the disappearance of surnames (inherited through the paternal line), is a well-established model. Indeed, the 48 inhabitants ([...]l) represent four main families: Christian, Young, Brown, and Warren. The first three are surnames belonging to descendants of Bounty crew members and the last belongs to descendants of an American who settled on the island not long after the original settlers.

Regarding Darwin and the Galapagos finches, they did play an important role in the development of Darwin's thoughts on evolution. Following the return of the Beagle to England, Darwin presented the finches, along with other mammal and bird species he collected, to the Geological Society of London on January 4, 1837. He gave the bird specimens to John Gould, a famous ornithologist, who, at the subsequent meeting of the Geological Society, reported that there were more finch species than Darwin had thought. In fact, birds Darwin had originally classified as blackbirds, "gross-beaks" and finches were in fact "a series of ground Finches which are so peculiar [as to form] an entirely new group, containing 12 species." This classification, together with information about the location of each species, helped Darwin establish his evolutionary theory.

As for parsimony, it can well be defined as "the assumption that nature makes as few changes as possible as new species evolve from old ones." This is not an empirical statement about the processes that operate in nature and it is never presented as one in the book. Rather, the highlighted sentence implies, it is a principle applied to the analysis of evolutionary data.

Finally, regarding my background. Although I did indeed study physics, I have worked in biology and genomics since 1992 when I received a Special Emphasis Research Career Award from the National Institutes of Health to work on the Human Genome Project. Since that time, I have published more than 220 peer-reviewed scientific papers in top journals and am recognized nationally and internationally for my work.

I am proud of this book and believe it presents a compelling history of the human genome project, a description of its importance, and a view of where it may lead us. As the cost of sequencing a genome is now only a few thousand dollars, genome sequencing is rapidly entering into the practice of medicine and has become an essential research tool. I believe the information in this book will be increasingly important not only to its readers, to all of us.
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1 of 1 people found the following review helpful
on November 17, 2013
Format: HardcoverVerified Purchase
Dr. Quackenbush makes the genome project understandable and makes me want to know more. His way of explaining things help me look at something I thought was way over my head to something that is right in front of my eyes. Bravo
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1 of 1 people found the following review helpful
on November 26, 2013
Format: HardcoverVerified Purchase
The Human Genome it is a good review of genetics and current technologies. It has the right level of detailfor a beginner.
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