Evolving Your Own Life: Introducing Biogenesis

Much of the software I've covered in the past has focused on engineering, chemistry or physics. However, a growing number of software packages are being written to applycomputational resources to problems in biology. So in this article, I want tolook at one particular package for biology named Biogenesis.

Biogenesis providesa platform where you can create entire ecosystems of lifeforms and seehow they interact and how the system as a whole evolves over time.

Youalways can get the latest version from the project's mainwebsite, butit also should be available in the package management systems for mostdistributions. For Debian-based distributions, install Biogenesiswith the following command:

sudo apt-get install biogenesis

If you do download it directly from the project website, you alsoneed to have a Java virtual machine installed in order to run it.

Tostart it, you either can find the appropriate entry in the menu ofyour desktop environment, or you simply can typebiogenesis ina terminal window. When it first starts, you willget an empty window within which to create your world.

Figure 1. When you first start Biogenesis, you get a blank canvas so youcan start creating your world.

The first step is to create a world. If you have a previousinstance that you want to continue with, click theGame→Open menu item and select the appropriate file. If you want to startfresh, click Game→New to get a new world with arandom selection of organisms.

Figure 2. When you launch a new world, you get a random selection oforganisms to start your ecosystem.

The world starts right away, with organisms moving and potentiallyinteracting immediately. However, you can pause the world by clickingon the icon that is second from the right in the toolbar. Alternatively, youalso can just press the p key to pause and resume the evolution of theworld.

At the bottom of the window, you'll find details about the worldas it currently exists. There is a display of the frames per second,along with the current time within the world. Next, there is a count ofthe current population of organisms. And finally, there is a display of thecurrent levels of oxygen and carbon dioxide. You can adjust the amount ofcarbon dioxide within the world either by clicking the relevant icon inthe toolbar or selecting the World menu item and then clicking eitherIncrease CO2 or Decrease CO2.

There also are several parametersthat govern how the world works and how your organisms will fare. If youselect World→Parameters, you'll see a new windowwhere you can play with those values.

Figure 3. The parameter configuration window allows you to set parameterson the physical characteristics of the world, along with parameters thatcontrol the evolution of your organisms.

The General tabsets the amount of time per frame and whether hardware accelerationis used for display purposes. The World tab lets you set the physicalcharacteristics of the world, such as the size and the initial oxygen andcarbon dioxide levels. The Organisms tab allows you to set the initialnumber of organisms and their initial energy levels. You also can settheir life span and mutation rate, among other items. The Metabolism tablets you set the parameters around photosynthetic metabolism. And, the Genestab allows you to set the probabilities and costs for the various genesthat can be used to define your organisms.

What about the organisms within your world though? If you clickon one of the organisms, it will be highlighted and the display willchange.

Figure 4. You can select individual organisms to find informationabout them, as well as apply different types of actions.

The icon toolbar at the top of the window willchange to provide actions that apply to organisms. At the bottom of thewindow is an information bar describing the selected organism. Itshows physical characteristics of the organism, such as age,energy and mass. It also describes its relationships toother organisms. It does this by displaying the number of its children andthe number of its victims, as well as which generation it is.

If youwant even more detail about an organism, click the Examinegenes button in the bottom bar. This pops up a new window called theGenetic Laboratory that allows you to look at and alter the genes making up this organism. You can add or delete genes,as well as change the parameters of existing genes.

Figure 5. The Genetic Laboratory allows you to play with the individualgenes that make up an organism.

Right-clicking on a particular organism displays a drop-down menuthat provides even more tools to work with. The first one allows you totrack the selected organism as the world evolves. The next two entriesallow you either to feed your organism extra food or weaken it.Normally, organisms need a certain amount of energy beforethey can reproduce. Selecting the fourth entry forces the selectedorganism to reproduce immediately, regardless of the energy level. Youalso can choose either to rejuvenate or outright kill the selectedorganism. If you want to increase the population of a particularorganism quickly, simply copy and paste a number of a given organism.

Once you have a particularly interesting organism, you likely will wantto be able to save it so you can work with it further. When youright-click an organism, one of the options is to export the organism toa file. This pops up a standard save dialog box where you can select thelocation and filename. The standard file ending for Biogenesis geneticcode files is .bgg. Once you start to have a collection of organismsyou want to work with, you can use them within a given world byright-clicking a blank location on the canvas and selecting the importoption. This allows you to pull those saved organisms back into a worldthat you are working with.

Once you have allowed your world to evolve for a while, you probablywill want to see how things are going. ClickingWorld→Statistics will pop up a new window where you can see what'shappening within your world.

Figure 6. The statistics window gives you a breakdown of what'shappening within the world you have created.

The top of the windowgives you the current statistics, including the time, the numberof organisms, how many are dead, and the oxygen and carbon dioxidelevels. It also provides a bar with the relative proportions ofthe genes.

Below this pane is a list of some remarkable organisms withinyour world. These are organisms that have had the most children, the mostvictims or those that are the most infected. This way, you can focus on organisms thatare good at the traits you're interested in.

On the right-hand sideof the window is a display of the world history to date. The topportion displays the history of the population, and the bottom portiondisplays the history of the atmosphere. As your world continues evolving,click the update button to get the latest statistics.

This software package could be a great teaching tool for learningabout genetics, the environment and how the two interact. Ifyou find a particularly interesting organism, be sureto share it with the community at the project website. It mightbe worth a look there for starting organisms too, allowing you to jump-start your explorations.