Welcome to the Genome: A User's Guide to Your Genetic past, Present, and Future

Overview

Praise for Welcome to the Genome

"In clear, engaging prose Welcome to the Genome provides the educated reader with a guide to understanding one of the most important moments in the history of biology. DeSalle and Yudell have provided a real service to all who want to participate in the great debate that is overtaking science and medicine today."
–David Rosner, Ph.D., Columbia University, New York, New York

"Welcome to the Genome is a fascinating and instructive journey through ...

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Overview

Praise for Welcome to the Genome

"In clear, engaging prose Welcome to the Genome provides the educated reader with a guide to understanding one of the most important moments in the history of biology. DeSalle and Yudell have provided a real service to all who want to participate in the great debate that is overtaking science and medicine today."
–David Rosner, Ph.D., Columbia University, New York, New York

"Welcome to the Genome is a fascinating and instructive journey through the science that increasingly tells us of our origins and offers the hope of improving our future. It is a terrific book for students of any age who want to learn more about the power and potential of DNA."
–Robert Bazell, NBC News, New York, New York

"This is a valuable and enjoyable read for anyone interested in the recently completed Human Genome Project and the ongoing genomic revolution."
–Eric Green, M.D., Ph.D., National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland

"DeSalle and Yudell have pulled off a remarkable feat: balancing a sophisticated and clear explanation of human molecular genetics while delving into a wide range of social and political issues. I know of no other book that has integrated these topics so seamlessly, and with such availability to a wide public."
–Troy Duster, Ph.D., New York University, New York, New York

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Editorial Reviews

From the Publisher
"...a welcome introduction to the broader aspects of how the genetic revolution will influence our lives." (American Journal of Medical Genetics, March 1, 2006)

"...the book fills a niche by providing a time-related commentary about the use of DNA and molecular genetics discoveries...a unique perspective seldom seen in other books about DNA." (Clinical Chemistry, February 2006)

"This is a great supplement to a textbook-based genetics unit, or it could be enrichment reading…Teachers who want a quick and easy update will appreciate it, too." (Journal of College Science Teaching, January/February 2006)

"...helpful introduction to one of the most compelling areas of modern biology." (The Quarterly Review of Biology, June 2005)

"...takes the reader on an adventure through the human genome...the implications will surely amaze and excite…" (The American Biology Teacher, May 2005)

"…a captivating story on genetics and genetics…an excellent resource…" (Annals of Biomedical Engineering, April 2005)

"Truly the 'user's guide' that it purports to be, this book provides in nine short, readable chapters a wealth of information..." (CHOICE, March 2005)

"…very well written so the concepts covered are accessible to all levels or readers." (E-STREAMS, March 2005)

"DeSalle and Yudell should be applauded for their ambition...a timely and readable book...[that] captures the excitement and potential peril of the Genome Revolution with aplomb." (Nature Genetics, February 2005)

"…engagingly written and illustrated in full-color...an essential guide for those who want to understand—and participate in—the accelerating promise of the genomic revolution." (Natural History, February 2005)

"…the first text we've seen to cover new discoveries in DNA research in a way that has the potential to capture a broad audience." (Electric Review, October/ November 2004)

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Product Details

  • ISBN-13: 9780471453314
  • Publisher: Wiley
  • Publication date: 9/17/2004
  • Edition number: 1
  • Pages: 240
  • Product dimensions: 7.80 (w) x 9.27 (h) x 0.71 (d)

Meet the Author

ROB DeSALLE received his B.A. in Biology from the University of Chicago and his Ph.D. in Biological Sciences from Washington University. His postdoctoral studies were completed at the University of California at Berkeley and he held an assistant professorship at Yale University. He currently is a curator in the Division of Invertebrates and the co-Director of the Molecular Laboratories at the American Museum of Natural History. His research utilizes high throughput DNA sequencing approaches to examine the systematics of insects, conservation biology problems, and bacterial genomics.

MICHAEL YUDELL re-ceived his B.A. from Tufts University and completed graduate work at both the Mailman School of Public Health at Columbia University and the Graduate Center at the City University of New York. He has held the position of researcher in the Molecular Laboratories at the American Museum of Natural History, where his work focused on genome policy and ethics, and the position of health policy analyst at the National Institute of Environmental Health Sciences. He is the editor, with Rob DeSalle, of The Genomic Revolution: Unveiling The Unity Of Life. Yudell is currently an Assistant Professor of Public Health at Drexel University.

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Read an Excerpt

Welcome to the Genome

A User's Guide to the Genetic Past, Present, and Future
By Rob DeSalle Michael Yudell

John Wiley & Sons

Copyright © 2005 Rob DeSalle and Michael Yudell
All right reserved.

ISBN: 0-471-45331-5


Chapter One

From Mendel to Molecules

Without any further ado, may we present to you the human genome!

This photo, also known as a karyotype, shows the 46 human chromosomes, the physical structures in the nuclei of your cells that carry almost the entire complement of your genetic material, also known as your genome. In almost all the cells in the human body there are 22 pairs of chromosomes and two sex-determining chromosomes. The double helices that make up your chromosomes are composed of deoxyribonucleic acid, also known as DNA, on which are found approximately 30,000 genes. These cells are called somatic cells, and they are found in almost all nonreproductive tissue.

Humans also have cells with 23 nonpaired chromosomes. In these cells each chromosome is made up of a single double helix of DNA that contains approximately 30,000 genes. These cells are called germ cells and are the sperm and egg cells produced for reproduction. These germ cells carry a single genome's worth of DNA or more than three billion base pairs worth of nucleic acids.

Chromosomes are somewhat like genetic scaffolding-they hold in place the long, linearly arranged sequences of thenucleotides or base pairs which make up our genetic code. There are four different nucleotides that make up this code-adenine, thymine, guanine, and cytosine. These four nucleotides are commonly abbreviated to as A, T, G, and C. Found along that scaffolding are our genes, which are made from DNA, the most basic building block of life. Through the Human Genome Project scientists are not simply learning the order of this DNA sequence, but are also beginning to locate and study the genes that lie on our chromosomes. But not all DNA contains genes. The long stretches of DNA between genes are known as intergenic or noncoding regions. And even within genes some DNA seems to be nonfunctional or "junk" DNA. These areas, called introns, are interspersed within the functional parts of a gene, known as exons. The term junk DNA may turn out to be a misnomer. Some scientists hypothesize that these noncoding regions of DNA may play a role in regulating gene function. Unlike the human genome and all other eukaryotic genomes, bacterial genomes do not have introns and have very short intergenic regions.

Let's begin our tour of the human genome with a very basic lesson in genetic terminology. For example, what exactly is genetics, and how is it different from genomics? Genetics is the study of the mechanisms of heredity. The distinction between genetics and genomics is one of scale. Geneticists may study single or multiple human traits. In genomics, an organism's entire collection of genes, or at least many of them, are examined to see how entire networks of genes influence various traits. A genome is the entire set of an organism's genetic material. The fundamental goal of the Human Genome Project was to sequence all of the DNA in the human genome. Sequencing a genome simply means deciphering the linear arrangement of the DNA that makes up the genome.

In animals, the vast majority of the genetic material is found in the cell's nucleus. The Human Genome Project has been primarily interested in the more than 3 billion base pairs of nuclear DNA.

A tiny amount of DNA is also found in the mitochondria, a cellular structure responsible for the production of energy within a cell. Whereas the human nuclear genome contains more than three billion base pairs of DNA and at least 30,000 genes, the human mitochondrial genome contains only 16,568 bases and 37 genes. Like bacteria, mitochondrial DNA, or mtDNA, has short intergenic regions and its genes do not contain introns. Another interesting characteristic of mtDNA is that it is always maternally inherited. This has made mtDNA very helpful to track female human evolutionary phenomena. These discoveries were made possible, in part, by sequencing mtDNA.

What about heredity? In the most basic sense we should think about heredity as the transmission of traits from one generation to the next. When we talk about heredity in this book we refer to the ways in which traits are passed between generations via genes. The term heredity is also sometimes used to describe the transmission of cultural traits. Such traits are shared through a variety of means including laws, parental guidance, and social institutions. Unlike genetics, however, there are no physical laws governing the nature of this type of transmission. Only genes can carry genetic information between generations.

What are genes? Genes are regions of DNA and are the basic units of inheritance in all living organisms. These words, genes and DNA, are too often used interchangeably. Both genes and DNA are components of heredity, but we identify genes by examining regions of DNA. In other words, DNA is the basic molecular ingredient of life whereas genes are discrete components of that molecular brew.

If you look at any family you'll see both shared and unique traits. Family members typically look alike, sharing many features such as eye color and nose shape, but they may also have very different body types and be susceptible to different diseases. This diversity is possible for two reasons. The first reason is that genes come in multiple forms. These alternative forms are known as alleles, and in sexual reproduction they are the staple of organismal diversity. According to the laws of genetics siblings can inherit different traits from the same biological parents because there is an assortment of alleles that can be randomly passed along. The second reason is that the environment can exert a significant influence on the expression of genes. For example, an individual may inherit a gene that makes him or her susceptible to lung cancer. Such susceptibility is typically revealed, however, only after years of genetic damage caused by cigarette smoking or other lung-related environmental impacts.

So how did science progress from thinking about the mechanisms of heredity to understanding that genes are the basic units of heredity, to deciphering and finally manipulating the DNA code that underlie all life on Earth? The results of the Human Genome Project were the fruits of over a century of struggle by scientists around the globe. Most historians of science would measure this progress beginning with Gregor Mendel's work on pea plants during the middle of the nineteenth century. Although premodern thinkers did have a basic grasp of the idea of heredity-that is, that identifiable traits could be passed down from generation to generation-it was not until Mendel that science began to understand the mechanisms underlying the transmission of these traits.

The journey from abstract notions of inheritance to the sequencing of the human genome abounds with stories of discoveries both great and small that led to where we are today. Science seldom progresses in a straight line. The genome was always there for us to find but took centuries to discover because knowledge and the technological application of that knowledge advance fitfully, revealing gradually more over time. Scientists have not always made the right choices. Even today, in the midst of the genomic revolution, we may be making assumptions about our genes that future generations look back on and ask, "How could they have thought that?" The trials and errors of science are part of what makes this process so interesting.

Several major building blocks of life had to be discovered to make possible our entry into the genomic world. First, scientists needed to determine what constitutes the hereditary material that passes from one generation to the next. Second, they needed to find out what constitutes the biochemical basis for the expression of this intergenerational legacy. This endeavor required the ability to take cells apart and analyze the chemical components from different parts of cells. Scientists then needed to determine the ways in which these chemicals, the building blocks of life, interacted, how they were structured, and how that structure influenced the hereditary process. Finally, technologies needed to be developed to use this information to improve human health, agriculture, and our understanding of our place in the history of life on Earth.

It took almost 150 years from the discovery of the hereditary principles to the sequencing of the human genome. The stories behind these discoveries explain how scientists came to understand the biological basis of heredity. What follows does not represent the comprehensive history of all the important genetic work of the last century or so. Yet without the discoveries we highlight, here the discovery of the genome would never have occurred or would have happened very differently.

IN THE ABBEY GARDEN

For close to two millennia few scientists approached Aristotle's understanding of genetics. Other theories of heredity were put forth during the centuries. Some, like the idea of the homunculus-the belief that every being was miniaturized and preformed in a reproductive cell-or the belief in panspermia-the idea that secretions from the entire body contribute to offspring-held sway for great lengths of time. But it was not until the Austrian monk Gregor Mendel bred peas in his abbey garden that anyone made practical sense of the rules of heredity.

Mendel was not just a monk tending peas. The child of peasant farmers, he was a classically trained scientist raised in the greatest traditions of the Enlightenment. Intellectually nurtured by his family and schooled in the best academies and universities of Central Europe, the German-speaking Mendel spent his life dividing his affection between God and science. In 1843, at the age of 21, Mendel entered the St. Thomas Monastery in Brünn in what is now the Czech Republic.

In the Church Mendel found a community of scientists-botanists, zoologists, and geologists among them-working diligently in their fields and making important contributions to the scientific literature. Perhaps the most important event in Mendel's early career occurred 10 years into his stay at St. Thomas. In 1851, at the behest of his abbot, Mendel was sent to Vienna University to study at the institute of Professor Christian Doppler, one of the pioneers of modern physics. For two years at Doppler's institute Mendel honed his scientific skills, taking courses in physics, chemistry, and mathematics, as well as entomology, botany, and plant physiology. The influence of physics was important to Mendel's later work on heredity. Physics taught Mendel that laws governed the natural world and that these laws could be uncovered through experimentation. But it was ultimately Mendel's exposure to ongoing debates in heredity that transformed him into the scientist we remember today.

Mendel and his predecessors understood that traits could be passed between generations. A child with his mother's eyes and his father's nose was easy evidence of that. Breeding experiments with domesticated animals also suggested that traits were passed to offspring. The prevailing theory during the nineteenth century, one to which even Charles Darwin mistakenly ascribed, was "blended inheritance." This theory held that the characteristics of parents blended in their offspring. Experimentation in this area failed because, as Mendel was able to eventually determine, heredity was not a lump sum but rather a series of individual traits.

In 1856 Mendel began to study the mechanisms of inheritance, working with varieties of garden peas from the genus Pisum. In the course of his experiments his garden flowered, as did his understanding of heredity. Mendel discovered several generalities from his experiments that remain the foundation of twentieth-century genetics. Any student of biology knows Mendel's work. Known as Mendel's laws, these basic tenets describe heredity in two simple mechanisms: the law of independent assortment and the law of segregation.

Mendel began an experiment with purebred peas. One breed had yellow seeds, the other green seeds. When purebred yellow-seeded peas were bred with each other, their offspring through the generations would have yellow seeds. Under the same circumstances, the green-seeded peas would always have green-seeded progeny. However, when he bred the purebred pea with yellow seeds to a purebred pea with green seeds, the offspring, or the first generation of this breeding cross, always had yellow seeds. The green seed trait seemed to be gone. Mendel called traits like the yellow seed trait dominating (now called dominant) because in first-generation crosses they would always appear. Traits like the green seed trait were called recessive-although they disappeared completely in the first generation, they reappeared in the second. Thus when Mendel took the yellow seeds from the first generation and either self-pollinated them or pollinated them with pollen from other yellow peas from the same first-generation breed, he discovered that some of these offspring, the second generation, again had the green seed trait. The plants, Mendel concluded, retained the ability to produce green seeds-of the second-generation seeds, 6022 were yellow and 2001 were green. Likewise, when he used six other traits, he found the same pattern in the second generation-traits that had disappeared in the first generation reappeared in the second. The chart below shows the relationship between dominant and recessive traits in second-generation pea plants in the seven traits Mendel experimented with.

Dominent Trait Receive Trait

Round seeds 5474 Wrinkled seeds 1850 Yellow seeds 6022 Green seeds 2001 Gray seed coats 705 White seed coats 224 Green pods 428 Yellow pods 152 Inflated pods 882 Constricted pods 299 Long stems 787 Short stems 277 Axial flowers 651 Terminal flowers 207

From these experimental data Mendel made several conclusions that are at the heart of his revolutionary contribution to hereditary theory. From the 3 to 1-dominant to recessive-ratio in the second generation, Mendel concluded that the traits he studied came in two different forms and that these forms existed in pairs in the plant. Mendel called these forms factors. Today we call them genes. During the process of making reproductive cells, Mendel deduced, these genes segregate from each other-that is, the two copies of a gene that you get from each parent segregates, and in the subsequent reproductive cells, only one half of the pair is passed on to offspring. At fertilization, a gene from each parent reconstitutes the pair. How else could Mendel explain how two yellow-seeded pea plants could produce offspring with green seeds? In this case the green seed trait was as much a part of the pea plant as the yellow seed trait despite sometimes being hidden.

Continues...


Excerpted from Welcome to the Genome by Rob DeSalle Michael Yudell Copyright © 2005 by Rob DeSalle and Michael Yudell. Excerpted by permission.
All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
Excerpts are provided by Dial-A-Book Inc. solely for the personal use of visitors to this web site.

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Table of Contents

Foreword.

Acknowledgments.

Introduction: Welcome to the Genome.

PART I: DISCOVERY.

1. From Mendel to Molecules.

2. The Building Blocks of Gene Sequencing.

3. Sequencing the Genome.

PART II: INFORMATION.

4. Keeping the Genome Safe.

5. 99.9%.

6. The Tree of Life.

PART III: ADVANCEMENT.

7. The World To Come: Medicine.

8. The World To Come: Agriculture.

CONCLUSION.

9. Caution: Welcoming the Genome.

Appendix 1, An Experiment: Seeing Your Own DNA.

Glossary.

Endnotes.

Photo Credits.

Index.

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