How Life Can Be The alternate world of artificial lives and intelligences - mauriceling/mauriceling.github.io GitHub Wiki
Biology can be thought as 2 different things - making use of what is available (this will be pursuits like finding new drugs from plants etc) and understanding what really makes it tick; what are the rules of this living chemistry we called life. This has significant impact. Is there a chemistry of genius? Is there a chemistry of Hannibal Lecter? These are massive questions that we do not know how to look for answers yet. However, there are a few things that can be done. We can test our knowledge of the rules of the game by creating prototypical organisms in the computer (digital organisms). For example, if we think evolution happens within the constraints of certain rules, can we simulate and test it with known data. It is almost like creating an ecosystem just to test one hypothesis. Like in Matrix trilogy, life as we know it today may well be a simulation in someone's computer after all...
I consider simulation to be an important tool to study about life. It allows us to merge mathematical modelling to life. How cells move? How wounds heal? How are genetic/protein gradients used? Protein gradients is a crucial concept in development biology. Different homeobox genes are activated by complex set of gradients. Cell cycle control proteins, like cyclins, are determined by protein gradients. Can we simulate these gradients from the protein level to the organism level? This will give us a simulatable cell/organism which can then enable us to examine hypotheses before even doing any wet-lab experiments.
Can we consolidate our current knowledge to re-construct a virtual representation of life? Maybe then, we can really construct life.
Hence, there are 2 aspects to this work. Firstly, I will need a simulator to conduct my computational experiments. In this aspect, I am developing Digital Organisms Simulation Environment or DOSE. Secondly, I will use DOSE to to run simulations to test biological hypotheses.