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Digital Code of Life: How Bioinformatics is

Revolutionizing Science, Medicine, and Business

Article in Briefings in Bioinformatics · January 2004

DOI: 10.1093/bib/5.3.305

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 Book review
Digital Code of Life:
How Bioinformatics is
Revolutionizing Science,
Medicine, and Business
Glyn Moody
John Wiley & Sons; ISBN 0 471
32788 3; 400 pp; US$34.95 (hbk);
January 2004
Writing about an emerging field such as
bioinformatics is not easy. While
biologists today are still absorbing what it
means to use computational techniques
and genomic data for hypothesis-driven
biomedical research, the genomics ‘fad’ as
a viable business model has become past
history. How did bioinformatics arise
from obscurity of a biological sequence
analysis specialty 20 years ago? What
stories lay behind the recent publicised
race between the US government and a
biotech company to finish sequencing the
human genome? Who are the winners
and losers in commercialising genomics
data and software? Will proteomics,
metabolomics or systomics lead the next
revolution in human biology? In his new
book of nearly 400 pages, Glyn Moody,
also the author of Rebel Code that
described the open-source movement and
the Linux revolution, offers a similar
journalistic chronicle of bioinformatics in
the past two decades.
This book consists of 14 chapters.
Narrating as a third person, the author
unfolds episodic stories behind key past
bioinformatics moments in each chapter.
Chapter 1 reviews the significance of
Watson and Crick’s discovery of the
DNA double helix structure. Chapters
2–4 recount the creations of GenBank,
NCBI, the BLAST software, major
genome sequencing centres, and the
genomics company giant Celera. Chapters
5 and 6 examine the divided views
between the public Human Genome
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Project (HGP) and Celera over whole-
genome shotgun sequencing, genome
data access, scientific publication and
patent right issues in their ‘tied’ rivalry to
completely sequence the human genome.
Chapter 7 describes the ongoing genome
sequencing efforts of other organisms.
Chapter 8 describes the investigation of
human genome variations by the public
SNP Consortium and by a successful
Icelandic company – deCODE. Chapter
9 examines scientific opportunities and
bioethical dilemmas in genetic testing.
Chapters 10–12 each explores a post-
genome large-scale biology topic:
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transcriptomics, structural genomics and
proteomics. Chapter 13 raises the
scientific hopes of using systems biology
to integrate data from all sources and
study the effects of perturbations to the
whole cellular machinery. Chapter 14
concludes the book by summarising
promising genomics technologies for
treating human infectious diseases and
cancers.
The book presents readers with a
comprehensive and coherent picture of
the still ongoing bioinformatics
revolution. Its writing materials come
mostly from recent papers and editorials
published in Science and Nature magazines.
Remaining as much of an objective
observer as he did while writing Rebel
Code, the author does not attempt to
exude first-person opinions upon readers.
Instead, he carefully chooses speech
excerpts, quotes and synopses of research
articles to guide readers’ minds, in which
the writings of scientific fervours, business
misjudgments and witty criticisms often
interweave into vivid scenes of the
historical moments. This type of subtle
influence reaches its peak in Chapters
4–6, in which one reads in awe how
Craig Venter’s scientific ego and business
shrewdness played into the dramatic
305
Book review
competition between the HGP and
Celera. In the book’s second half,
however, there is a general lack of
storylines as good as those found in its first
half. In particular, a few chapter episodes
that describe post-genome biological
advances read like scientific literature
reviews – too drab for light readings in a
Sunday afternoon. After all, what attracts
a bioinformatician to this book may have
more to do with the book’s presentation
of rare information behind familiar
historical bioinformatics events than its
comprehensive coverage of research
topics.
The book abounds in behind-the-scene
bioinformatics stories. These stories were
primarily compiled from the author’s
interviews with luminary genome
scientists – Rodger Staden, Leroy Hood,
David Lipman, Douglas Brutlag, Eric
Lander, Pat Brown, among others –
between October 2002 and June 2003.
Take an example from Chapter 2,
‘BLAST from the past’. One reads from
an interview excerpt that Doug Brutlag
from Stanford University actually passed
on an invitation from the National
Library of Medicine to create the
National Center for Biotechnology
Information (NCBI). In a twist of fate,
David Lipman, whom he recommended
for the director of NCBI position, would
soon upset him by winning the contract
of hosting GenBank at NCBI instead of at
Brutlag’s bioinformatics start-up,
IntelliGenetics, which no longer exists
today. Elsewhere in the book, one can
also read about James Watson’s political
battles during his early leadership of the
HGP, or Walter Gilbert’s failure to
commercialise Genomics data as far back
as the late 1980s.
The book offers something for
everyone playing in the bioinformatics
field to ponder about. First, the scientific
breakthroughs presented in the book
almost unanimously came from major
genome centres and elite university
laboratories such as the European
Bioinformatics Institute, the MIT
Whitehead Institute, Stanford, Harvard
306 & HENRY STEWART PUBLICATIONS 1467-5463. B R I E F I N G S I N B I O I N F O R M A T I C S . VOL 5. NO 3. 305–307. SEPTEMBER 2004
and Washington University. These places
are flooded with multi-year, multi-
million dollar federal grant awards. In
other words, ‘size does matter’ in
genomics and post-genome biology. Is
there a role left for small laboratories and
underfunded projects?
Second, Craig Venter’s business motto
‘speed matters’ can be felt throughout the
past decade of genome research and
development. Take a few recent
examples. Jim Kent raced against Celera
scientists to finish the Golden Path human
genome assembly in mere three weeks,
resulting in the eventual tie of the public–
private human genome sequencing
competition. Myriad Genetics raced
against an UK cancer research group to
publish the paper about the BRCA2 gene
one day ahead of the competition,
therefore gaining the gene’s exclusive
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patent rights. Richard Young’s group at
the Whitehead Institute raced to publish a
significant piece of work on genome-
wide location analysis of regulatory
factors, submitting the paper to Science
three weeks later than a rival paper
submission to Nature by Pat Brown’s
group at Stanford; magically, Young won
the publication rivalry by two weeks
because Pat Brown’s paper at Nature took
a longer time to review. Can one still
afford to wait on the perfect opportunity
in post-genomics biological discovery?
Third, sustainable genomics businesses
seem to be those that break off the
genomics ‘fad’. Human Genome
Science’s success lays in its management’s
astute leverage of genomics database
subscriptions and the initial public
offering (IPO) money in the new drug
development buisness. PE Biosystems and
Affymetrix’s successes lay in their separate
inventions of large-scale sequencing and
gene expression monitoring platforms that
underpin Genomics and Transcriptomics
studies. deCODE Genetics’ success lay in
its solid biomarker discovery results and
strategic alliance with the big Pharma. In
contrast, DoubleTwist.com, although
backed by a prestigious venture capital
firm, could not survive by selling

expensive bioinformatics software.
Myriad Proteomics, although backed by
an initial investment valued at US$185m,
will perhaps never fulfil its executive’s
early audacious claims of mapping all
human protein interactions in three years.
Isn’t there any lesson to learn when the
new biotech investment picks up heat?
On the downside, the book may be a
result of its own ‘speedy’ race to become
published. Some sections of the book
need significant reorganisation and
redevelopment for readers to enjoy. The
introduction and unravelling of persons
and events also need to be planned
thoroughly in the context of the entire
scope of the book. For example, Eric
Lander as a key figure mentioned in half
of all the book chapters was only
perfunctorily introduced in Chapter 2
& HENRY STEWART PUBLICATIONS 1467-5463. B R I E F I N G S I N B I O I N F O R M A T I C S . VOL 5. NO 3. 305–307. SEPTEMBER 2004
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Book review
(page 72) and reintroduced many chapters
later several times. For another example,
the first half of the book contained an
interesting story of Leroy Hood being
selected by PE Biosystems as the first
candidate CEO of the Celera prior to
Craig Venter; strangely, his background
sketch did not appear until almost at the
end of the book in Chapter 13 (page 303).
As it is, the book will perhaps still remain
popular to casual scientific readers who
yearn to reflect on the recent Genomics
gold rush.
Jake Chen, Ph.D.
Assistant Professor of Informatics,
Indiana University School of Informatics,
Indianapolis, Indiana, USA
E-mail: jakechen@iupui.edu
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