Many properties of organisms show great robustness against mutations. Whether this robustness is an evolved property or intrinsic to genetic systems is by and large unknown. An evolutionary origin of robustness would require a rethinking of key concepts in the field of molecular evolution, such...

Resilience of an organism's physiological and developmental processes against mutations can have two principal causes, the first being overlapping gene functions. In this case, loss-of-function mutations in one gene will have little phenotypic effects if one or more other genes with similar...

Redundant gene functions are ubiquitous, and they are a potentially important source of evolutionary innovations on the biochemical level. It is therefore highly desirable to understand the mechanisms governing their evolution. Gene duplication is clearly a prominent mechanism generating...

The neutralist perspective on molecular evolution maintains that the vast majority of mutations effecting gene function are neutral or deleterious. Following a gene duplication where both genes are retained, it predicts that original and duplicate genes diverge at clock-like rates. This...

To delineate the astronomical number of possible interactions of all genes in a genome is a task for which conventional experimental techniques are ill suited. Sorely needed are rapid and inexpensive methods that identify candidates for interacting genes, candidates that can be further...

Systems involving many interacting variables are at the heart of the natural and social sciences. Causal language is pervasive in the analysis of such systems, especially when insight into their behavior is translated into policy decisions. This is exemplified by economics, but to an increasing...

For many organisms, and especially for the model organisms of molecular and cell biology, the primary locus of study is the laboratory, and not their natural habitat. Thus, a huge body of knowledge accumulated through a century of laboratory studies contrasts with the limited amount of...

Most duplicate genes are eliminated from a genome shortly after duplication, but those that remain are an important source of biochemical diversity. Much of their diversification arises via functional ÒspecializationÓ, loss of some functions of the duplicates remaining in the genome. I here...

Large scale gene perturbation experiments generate information about the number of genes whose activity is directly or indirectly affected by a gene perturbation. From this information, one can numerically estimate coarse structural network features such as the total number of direct regulatory...

We characterize the distributions of short cycles in a large metabolic network previously shown to have small world characteristics and a power law degree distribution. Compared with three networks of the same connectivity, the metabolic network has a particularly large number of triangles and a...