Transducing the Genome: Information, Anarchy, and Revolution in the Biomedical Sciences

Transducing the Genome: Information, Anarchy, and Revolution in the Biomedical Sciences

by Gary Zweiger


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"Captivating... hard to put down."­­Choice

"A bracing insider's account of why gene structure matters to science and commerce."­­American Scientist

How genomics is bringing biology into the Digital Age

In this important book, a scientist gives us an inside account of the historic paradigm shift under way in the life sciences as a result of the Human Genome Project and provides a philosophical framework in which to understand biology and medicine as information sciences. In a story told on many fascinating levels, Gary Zweiger introduces us to the visionaries who first understood genes as information carriers and chronicles how their early efforts led to the birth of the new science of genomics. He provides insights into the uneasy collaboration of private, government, and academic efforts, the role of the pharmaceutical companies, and the influence of venture capitalists on one of the most ambitious and potentially significant scientific undertakings in history. Most important, he explores the profound impact that the transducing of biological information into a digital format already has had on biological research and medicine, and the equally profound effect it is sure to have on our understanding of ourselves and all living creatures.

Product Details

ISBN-13: 9780071387613
Publisher: McGraw-Hill Companies, The
Publication date: 02/01/2002
Pages: 269
Product dimensions: 6.08(w) x 9.02(h) x 0.76(d)

About the Author

Gary Zweiger, PhD is a geneticist and Director of Business Development and Strategic Planning at Agilent Technologies, a leading producer of DNA microarrays (gene chips) and other biomedical tools. Prior to joining Agilent, he was Senior Strategic Advisor at Incyte Genomics, Inc., a founding company in the genomics industry. He has also worked as a consultant to venture capitalists, investment bankers, and other early backers of the emerging genomics industry, and has taught classes in human biology and biotechnology at several colleges. While at Incyte, Dr. Zweiger studied thousands of genes by using enormous biological databases and designed several powerful microarrays to help further his research into the molecular changes that accompany prostate, breast, colon, and pediatric cancers.

Read an Excerpt

2. Information and Life

All kinds of electromagnetic emissions, from visible starlight to stealthy cosmic rays, flow through the heavens. But one particular category of emissions, those emanating from a nonterrestrial source and having a bandwidth of less than 300 Hz, has never been detected. Known cosmic phenomena, such as the fusion infernos within stars, exploding stars, black holes, and the big bang do not appear to release energy of such limited spectra. It is for this very reason that a group of radiotelescopes have been programmed to scan the universe in search for such signals. The radiotelescopes are under direction of the renowned SETI program, which for those that do not know, is a code name for the Search for ExtraTerrestrial Intelligence. The SETI team, which is composed of a group of scientists of diverse expertise, speculates that intelligent life might produce such a narrow-banded signal and that searching for such a signal represents one of humankind's best hopes of finding evidence of distant life. Of course, confirmation of extraterrestrial life would require more than just finding a narrow bandwidth signal. The hope is that a narrow bandwidth signal will be a carrier signal within which coded messages could be found. By focusing on such a signal with very sensitive instruments, such coded information might be detected. Coded information, irrespective of content, is indicative of life. Coded information hurled through space in the form of electromagnetic waves, it is presumed, would be indicative of intelligent life.'

Although most biology textbooks neglect to mention it, information is as fundamental and unique to life as either metabolism orreproduction. Encoded messages occur in a myriad of forms and are transmitted between a myriad of different types of receivers and senders. Information is sent when a beaver slaps its tail on the water upon sensing a danger, when a plant releases a fragrant odor, when a bacterial protein signals a gene to turn on the production of catabolic enzymes, and when a nerve impulse causes a muscle to contract. In each case, whether between organisms or within an organism, a coded message is provided. Communications such as these are not just the foundation of life, they are its essence.

Human beings have distinguished themselves among other species on earth by continually developing and adopting new and improved ways of exchanging information. No other species comes close to matching our language, speech, and writing capabilities. Of course, human ingenuity and innovation have not stopped there. Modern information technology greatly facilitates the storage, processing, and conveyance of information. Weightless or nearly weightless electrons and electromagnetic waves travel at or near the speed of light (almost one billion feet per second). And, after only a few hundred years of development, these information conduits have enabled stunning advances, such as the Internet and other global communication networks and a machine that can outperform the best living chess player.

Welcome to the Information Age, where the movement of speedy electrons and electromagnetic waves has replaced much of our mechanical and mental work. Fewer and fewer people turn knobs on TV sets, rotate dials on telephones, write letters by hand, and/or tally bills on abacuses. We can (and, more often than not, want to) do it faster, better, and cheaper using devices that transduce our thoughts or desires into electronic signals. We telecommute and use e-mail, remote control devices, voice recognition software, and so forth. The resulting electric signals may be readily digitized, processed, stored, replicated countless times over, and transmitted over long distances before being converted into images, sounds, or other stimuli suitable for the human senses.

Information circuitry is not only external. The senses are portals to an internal information network. Ears, eyes, nose, skin, and mouth convert patterns of touch, sound, odor, taste, or light into patterns of nerve impulses. This information is passed along by waves of ions (charged atoms or molecules) moving across the outer membrane of neurons (nerve cells). These waves (action potentials) move at rates of up to 100 feet per second (68 mph). This may seem pitifully slow compared to today's electronic and electromagnetic speedways, but at the time that it developed, beginning about 500 million years ago, neuronal signaling was revolutionary. Neurons provide a much faster and more efficient channel of communication than either chemical diffusion or any sort of fluid pump. Neuronal signaling allowed quick and coordinated responses to environmental stimuli. It also led to the development of the brain, cognition, and consciousness.

The nervous system was derived from and superimposed upon yet another information network, a more ancient network, and the mother of all information networks. Living tissue is composed of millions of different proteins, nucleic acids, fats, and other chemical entities. These are the molecules of life and the subject of countless research studies. They can be understood in terms of their physical structures and their chemical properties. However, they can also be understood in terms of the information that they convey.

What kind of molecular messages are being sent within us? Who is the sender and receiver and what is being said? Genes are the most obvious conveyors of information within living beings. Gregor Mendel first characterized genes as units of hereditary information, agents responsible for determining particular traits and characteristics that are passed from parent to offspring. He referred to them as factors in an 1865 publication, but at that time and for many decades thereafter no one knew precisely how these units of hereditary information were stored or how they translated into traits and characteristics. In 1943 Erwin Schrodinger speculated that genes were "some kind of code-script," and this is indeed the case. We now know that genes are encoded by a series of molecules known as nucleotides, which are the components of deoxyribonucleic acid (DNA). Genes provide coded instructions for the production of millions of additional nucleic acids and proteins.

The word factor has a physical connotation, and thus from the very start genes have had dual personalities. Like a photon of light teetering between matter and energy, a gene teeters between matter and information. On one hand, a gene is not unlike the 100 or so chemical elements of nature. Each gene may be a distinct and rigidly defined composition of nitrogen, oxygen, hydrogen, carbon, and phosphorous; one that participates in a series of chemical reactions that results in the production of additional nucleic acids and proteins. But this is like saying that the United States Constitution is a particular construction of plant pulp and ink. Genes encoded in DNA convey information to additional nucleic acids, which relay the messages to proteins, which convey signals throughout the organism. A complete set of genes, the genome, carries instructions, or a blueprint, for the development and function of an entire organism.

As information it does not really matter how the gene is encoded, so long as the message can be received and decoded. There is redundancy in the genetic code; the same gene may be encoded by any one of a number of different nucleotide sequences. A gene may also be encoded in an entirely different medium. In a classic instructional film from the early 1970s, a DNA sequence is portrayed by dancers, each wearing one of four brightly colored costumes, representing four types of nucleotides. The dancers simulate the production of a protein through their choreographed movements. Nowadays, no matter whether the gene is encoded by a string of nucleotides, costumed dancers, words, or Os and 1s (binary code), in a laboratory it can be readily converted into biologically active proteins...

Table of Contents

Cancer, Computers, and a "List-Based" Biology.
Information and Life.
Behold the Gene.
Working with Genes One at a Time.
The Database.
Getting the Genes.
Prospecting for Genes with ESTs.
ESTs, the Gene Race, and Moore's Law.
The End Game.
Human Genome History.
Comparing Human Genomes.
A Paradigm in Peril.
The Ancient Internet - Information Flow in Cells.
Accessing the Information Output of the Genome.
The Genomics Industry.
The SNP Race.
From Information to Knowledge.
The Final Act.
Future Prospects.

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