Networking Naturally

Khad Gadya, the 16th-century song concluding the Passover Seder, describes a succession of allegorical events leading from the purchase of a young goat to the striking down of the Angel of Death:

 

  Father bought a young

 

Cause-and-effect chains, spanning all aspects of life, have often baffled the human mind, which is naturally inclined to find the “order” behind things. The task becomes more mind-racking as the number of factors increases. The verse above mentions a dozen factors. Now, take our DNA. How do 30,000 genes in our DNA work together to form a large part of who we are? How does one neuron operate in the context of the whole nervous system?

 

Decades of pinpointed biological research have yielded profuse bits of information. Increasingly, scientists are feeling the need to meld the many fragments together to understand how we work as a whole. In an article published in Nature Genetics, Dr. Uri Alon, a physicist at the Weizmann Institute’s Molecular Cell Biology Department, proposed a mathematical technique to seek out the basic principles of biological systems. Using this technique, he has uncovered several motifs underlying genetic, neural and food networks.   

 

Alon surmised that patterns serving an important function in nature might recur more often than statistically forecasted. This guiding principle, he thought, might help one find the “wiring” underlying biological systems. Using an algorithm that he devised, Alon analyzed the scientific findings existing on networks in some well-researched organisms. He noticed that some patterns in the networks were inexplicably more repetitive than they would be in randomized networks. This handful of patterns was singled out as a potential bundle of design principles.

 

“For a physicist, looking inside the cell is like witnessing a succession of miracles,” says Alon. “The field of physics offered many ‘miracles’ in the past as well – lightning, for instance, evoked an image of Zeus casting a fiery spear. When this belief gave way to an understanding of electric charges, lightning became an ‘interesting phenomenon.’ The basic laws of biology, however, are still unknown, making biology seem ‘miraculous.’ Unearthing these laws is what makes this kind of research so exciting.”

 

Alon’s team has succeeded in uncovering “basic laws” in genetic systems, neural systems and food webs. “Surprisingly, we found two identical laws in genetic and neural systems,” says Alon. “Apparently both information-processing systems employ similar strategies.” Exposing the backbones of such networks can thus help scientists classify systems generically (just as butterflies and ants both belong to the same “class,” neural and genetic systems would also belong to a generic category). This would function as more than just an organizing principle: “One might be able to learn about the neural system by studying the genetic system, which is usually more accessible,” says Alon.

 

In each of seven ecosystems scrutinized, seven recurring patterns relating to food webs were found. One demonstrates that predators will not eat components in the diet of their prey – a lion will eat a gazelle, which eats grass, but it will not eat grass (see below). Humans, who are avid omnivores, are an exception to the rule.

 

Alon’s method detects such patterns – which he calls network motifs – on the basis of their frequency. Any patterns that are functionally important but not statistically significant will not be detected by this method.