Thursday, May 23, 2013

DNA Computing: Is It Here Yet?

In 1994, Leonard Adleman, a computer scientist at University of Southern California, introduced the concept of DNA based computing in a paper in the journal Science. (1) He used DNA strands to solve the well-known traveling salesman problem (given a number of cities, what is the shortest route for a salesman to take without going to any city more than once?) The entire process took days and required a lot of human intervention. Since then logic gates, essential elements of any computer, have been created using DNA code with a variety of approaches. The circuits can solve simple mathematical problems, recognize patterns, play games and even detect disease states inside a cell.

All modern computers have three basic functions: storing, transmitting and performing logical operations. In 2012, Endy et al. made the headlines by announcing the development of the first two of those functions for DNA computers. (2) Now they announced the last component, that of computation.

In a paper published March 28, 2013 in Science (3) a team of Stanford University bioengineers led by Endy describe a biological transistor made from DNA and RNA which they named a “transcriptor.” This transcriptor uses proteins called integrases to digitally control the flow of RNA polymerase along a strand of DNA, analogous to the flow of electrons along a circuit in electronic transistors. Using these transcriptors, the team has created “logic gates” that can function inside a living cell.

Thursday, May 2, 2013

A Mathematical Model for Evolution

One of the fundamental criticisms of the theory of evolution has been that it lacks a mathematical basis. From its inception evolution has used qualitative concepts such as “random mutations” and “natural selection” to describe how genes can spontaneously mutate and cause the organism to be more adaptive to its environment, thus giving it an advantage in the number and “fitness” of its offspring. Now that may be changing.

A team of scientists from the Chinese Academy of Sciences and the State University of New York at Stony Brook, led by Professor Wang, has published a paper that examines evolutionary dynamics from a mathematical perspective. (1,2) The study uses mathematical formulas to describe a new theory of evolution in which two forces are at play: an underlying emergent 3-D “fitness” landscape and an evolutionary force called “curl flux” which causes individuals and species to move through the fitness landscape in a spiraling manner. The hypothesis envisions endless co-evolution between individuals within species or between two different species by movement through the fitness landscape via curl flux. The curl flux can be created by interactions between individuals of different species which can result in continuous and endless co-evolution, a version of the Red Queen Hypothesis.