CST Guide:

Foreword
The revolution in recombinant DNA that has swept through biomedical research over the past three
decades has been hailed as an unalloyed advance for almost every aspect of basic biological research.
The allure of nucleic acid technology, with its clear logic and mathematical precision, has proven irresistible
for the young researchers who have entered into this field during this period. But it has had its
downside as well: At the beginning of this era, aspiring research students studied basic biochemistry
as an essential part of their training. Now, it is viewed by many as an anachronism, a vestige of early
and mid-20th century experimentation that has been superseded by the far more powerful experimental
approaches involving manipulation and analysis of nucleic acids. Why study complex mixtures of
proteins when entire cellular genomes can be sequenced almost overnight
“use of procedures like these will
surely support the still-incipient
campaign of returning to protein
biochemistry...”
Dr. Robert A. Weinberg
The inconvenient truth is that nucleic acid analyses have reached their limits in terms of their ability
to shed light on the subcellular processes that underlie cell physiology and thus the phenotypes of cells
and organisms. We are still confronted with the complexities of signal transduction biochemistry that
underlie almost all biochemical processes. Progress in understanding protein function has lagged far
behind the molecular biology of nucleic acids, in no small part because studying proteins is so challenging.
Consider the complexity of a cell in which almost 20,000 distinct genes are being expressed, each
of which, on average, may specify five distinct protein species because of various alternative splicing
and post-translational modifications. And then consider the stupefying complexity of how these proteins
interact combinatorially to create biological function.
These notions help explain why many have fled protein biochemistry. As is now apparent, this flight
has left us with an underdeveloped sense of how the protein machinery actually operates to create
phenotype. As the pressure ramps up to convert basic biomedical discoveries into useful therapeutics,
our still-inadequate understanding of protein structure and function becomes increasingly apparent.
Thus, the failure of many ostensibly useful compounds to enter into the clinic can be traced directly to
our incomplete understanding of the wiring diagram of the cell and how it can be profitably perturbed.
The present manual represents one very powerful way to reverse this tide. Many of the techniques
and reagents described here—often involving monoclonal antibodies—can be wielded with the precision
that nucleic acid mechanics routinely employ. The use of procedures like these will surely support the
still-incipient campaign of returning to protein biochemistry so that we can indeed learn how things
really work inside cells. It will require another generation, but the time has come for us to return to the
old ways, to puzzle out, one protein at a time, how signals are really processed inside cells to create the
marvelously functioning apparatus—the eukaryotic cell.
Sincerely,
Dr. Robert A. Weinberg
Daniel K. Ludwig Professor
for Cancer Research at MIT
6
7