Information Management in Living Organisms

Nature has an article by Paul Nurse (Life, Logic and Information), where he discusses some ideas on studying living organisms as information management systems.

Paul Nurse suggests that analyzing the information flow in living organisms would help to understand certain behaviors, which are not completely clear nowadays.

From a computer systems researcher standpoint, the interesting aspect of Paul Nurse's idea is that it goes on the opposite direction of previous studies: instead of drawing inspiration from nature to build information management systems (e.g. ant inspired algorithms), the author proposes to use information science tools to study the nature.

A piece from the article:

Systems analyses of living organisms have used a variety of biochemical and genetic interaction traps with the emphasis on identifying the components and describing how these interact with each other. These approaches are essential but need to be supplemented by more investigation into how living systems gather, process, store and use information, as was emphasized at the birth of molecular biology.

This sounds exciting, as a better understanding of living systems could feedback into the bio-inspired approach of designing distributed computational systems.

A couple of years ago, I briefly explored the design of a distributed storage system based on the behavior of the Messor Barbarus ants (for more details on the M. Barbarus ants see Anderson, C., J.J. Boomsma, and J.J. Bartholdi, III. 2002. Task partitioning in insect societies: bucket brigades. Insectes sociaux 49(2): 171-180).

The rationale behind it is quite simple: every time an unloaded larger ant encounters a loaded smaller ant, the load is passed from the smaller to the larger ant. This naturally spread the work among the workers according to their capacity (strength and speed).

Bringing it back to the context of distributed storage systems, the idea is to enable a self-organizing load balance scheme by making larger nodes to request more load from lower capacity nodes. The goal is to improve throughput and data availability.

Obviously, a comprehensive performance evaluation is necessary to claim that this strategy would lead to an globally efficient system.

HPDC'08 - Part II

Gilles Fedak delivered an invited talk at the UPGRADE-CN workshop (part of the HPDC'08). He presented the BitDew - a programmable environment that targets data management in Desktop Grids [1].

The rationale behind BitDew is that applications can define routines for data manipulation. These routines are expressed via predefined metadata, which are used by the infrastructure mechanisms to perform data management tasks, such as replication.

In a Technical Report, Gilles and colleagues present use cases and performance evaluation of mechanisms that provide data management functionality in BitDew.

In particular, I found the approach of leveraging metadata interesting. The predefined set of metadata allows the application layer to communicate requirements to the infrastructure regarding the desired level of fault tolerance and transfer protocols, for example.

In fact, this intersects with one of our projects at the NetSys Lab, where we investigate the use of custom metadata as a cross-layer communication method for storage systems [2].

As we use the file system interface to separate between the application and the storage layers, the two approaches (BitDew and our Custom Metadata approach) seem complementary. The metadata passed by the applications via BitDew could propagate to the file system, where it would interact with the Extended Attributes interface (which is exploited by our solution).

More coding fun to come...

[1] Fedak et al. "BitDew: A Programmable Environment for Large-Scale Data Management and Distribution". Technical Report, 6427, INRIA.

[2] Elizeu Santos-Neto, Samer Al-Kiswany, Nazareno Andrade, Sathish Gopalakrishnan and Matei Ripeanu. "Enabling Cross-Layer Optimizations in Storage Systems with Custom Metadata". In HPDC'08 - HotTopics. Boston, MA, USA. September, 2008.