Networks - Bioinformatics Computing - page 86

People seldom improve when they have no other model but themselves to copy after.
— Oliver Goldsmith
Comparing a data network to a living organism, the hardware provides the skeleton or basic
infrastructure upon which the nervous system is built. Similarly, a few hundred meters of cable
running through the walls of a laboratory is necessary but insufficient to constitute a network.
Rather, the data pulsing through cables or other media in a coordinated fashion define a network.
This coordination is provided by electronics that connect workstations and shared computer
peripherals with the networks that amplify, route, filter, block, and translate data. Every competent
bioinformatics researcher should have a basic understanding of the limits, capabilities, and benefits of
specific network hardware, if only to be able to converse intelligently with hardware vendors or to
direct the management of an information services provider.
According to Chaos Theory, the ability to adapt and the capacity for spontaneous self-organization
are the two main characteristics of complex systems—systems that have many independent variables
interacting with each other in many ways and that have the ability to balance order and chaos. In
this regard, computer networks qualify as complex systems, always at the edge of failure, but still
working. In some sense, it's difficult to define success and failure for these systems, in part because
of the so-called law of unintended consequences that stipulates these systems can provide results so
beneficial, so out of proportion to the intended "success" that they overshadow the significance of the
intended goal. Consider that gunpowder was intended as an elixir to prolong life, or that the adhesive
on 3M Post-It Notes ® was intended to be a superglue, Edison's phonograph was intended to be a
telephone message recorder, and Jacquard's punch card was intended to automate the loom, not to
give the computer its instructions or determine presidential elections. Such is the case with the
Internet, one of the greatest enabling technologies in bioinformatics, allowing researchers in
laboratories anywhere on the globe to access data maintained by the National Center for Biological
Information (NCBI), the National Institutes of Health (NIH), and other government agencies.
The Internet was never intended to serve as the portal to the code of life, but was a natural
successor to the cold war projects in the 1950s and early 1960s. During this time, the military
establishment enjoyed the nearly unanimous respect and support of politicians and the public.
Universities with the top science and engineering faculties received nearly unlimited funding, and the
labors of the nation's top scientists filtered directly into industry. Military demand and government
grants funded the development of huge projects that helped establish the U.S. as a Mecca for
technological developments in computing and communications networks.
The modern Internet was the unintended outcome of two early complex systems: the ARPANET
(Advanced Research Project Agency Network) and the SAGE system (semiautomatic ground
environment), developed for the military in the early 1950s and 1960s, respectively. SAGE was the
national air defense system comprised of an elaborate, ad hoc network of incompatible command and
control computers, early warning radar systems, weather centers, air traffic control centers, ships,
planes, and weapons systems. The communications network component of the SAGE system was
comprehensive and extended beyond the border of the U.S. and included ships and aircraft. It was
primarily a military system, with a civil defense link as its only tie with civilian communications
system.
Government-sponsored R&D increasingly required reliable communications between industry,
academia, and the military. Out of this need, and spurred by the fear of disruption of the civilian
communications grid through eventual nuclear attack, a group of scientists designed a highly
redundant communications system, starting with a single node at UCLA in September of 1969. By
1977, the ARPANET stretched across the U.S. and extended from Hawaii to Europe. The ARPANET
quickly grew and became more complex, with an increasing number of nodes and redundant cross-
links that provided alternate communications paths in the event that any particular node or link
failed.
Although the ARPANET's infrastructure was an interdependent network of nodes and
interconnections, the data available from the network was indistinguishable from data available from
any standalone computer. The infrastructure of the system provided redundant data communications,