Tackling the Question "What Is Life?" with the Power of Computers

Akira Funahashi (Associate Professor, Department of Biosciences and Informatics)

The phrase "computers and life" might sound like an unlikely combination. Until I was a student in the Doctoral Programs, I had no connection to biology and was researching computer architecture. My research at the time was about maximizing the performance of massively parallel computers (supercomputers) by skillfully controlling the data flowing over their networks. In simple terms, this involved devising traffic control algorithms to prevent congestion, much like managing cars on highways and local roads. I was very fond of this research theme. This was because the idea of creating even faster computers by connecting multiple computers via a network was very novel at the time, and it was fascinating that the data flowing over the network sometimes exhibited complex and bizarre behavior, producing results completely different from what I had expected. I learned that a myopic approach is not enough to grasp the behavior of the entire network.

Meanwhile, the early 2000s marked a major turning point for biology. The analysis of the entire human genome sequence was completed, revealing all the components (proteins and genes) that make up the human body. With all the components identified, the next question in biology became understanding how they interact, and I thought that these interactions could be depicted as a network. Therefore, I moved from computer science to a then-fledgling research field called systems biology.

In systems biology, a network represents the interactions between molecules (proteins and genes). These interactions are biochemical reactions, and each reaction has a rate. If all biochemical reactions are known, an organism can be represented as a network. If we can assign the correct rate equations to all the biochemical reactions in the network, the networked organism can then be transformed into a system of simultaneous differential equations. We call this a mathematical model. An organism represented as a mathematical model can be simulated on a computer by performing numerical integration (Figure 1). By describing biological phenomena as mathematical models, we can elucidate the mechanisms and principles that govern them.

My laboratory's research is broadly divided into three areas: simulating biological phenomena using mathematical models, 3D reconstruction of the intracellular environment through image analysis (Figure 2), and techniques for manipulating cell fate. Computers are now indispensable for all of these research themes. This is natural, as simulation and image analysis are areas where computers excel, but recently, we have also been using computers in biological experiments to precisely control and automate them. High-precision experiments will become a crucial technology in the future from the perspective of quantifying experimental data.

More than a decade has passed since I entered the world of biology, drawn by the keyword "network." The world of biology is advancing at a surprisingly rapid pace, and it is a very exciting world where new technologies and findings emerge daily. Together with students interested in computers and biology, I hope to continue searching for the answer to "What is life?"