Biology is the study of living things, such as animals, plants, and micro-organisms, and their vital processes.
All living things are composed of cells. A cell is the very smallest unit of living matter. For example, our brain is made up of billions of brain cells or neurons.
Human cells are like most animal cells. They contain a nucleus, cytoplasm, membrane, mitochondria, and ribosomes.
All cells are divided into two types: prokaryotic and eukaryotic cells. Prokaryotic cells are those that do not have a nucleus. They are much smaller and simpler than eukaryotic cells. Bacteria and archaea are both prokaryotes. Bacteria come in different shapes, such as spheres, rod shaped, and spirals, and sizes. Bacteria can be found in soil, lakes, rivers, oceans, acidic hot springs, and radioactive waste.
Eukaryotic cells have a true nucleus, which means the cell’s DNA is surrounded by a membrane. They are much larger and more complex than prokaryotic cells. Animals, plants, and fungi (yeast and mushrooms) are all eukaryotic organisms. Mitosis is the process by which the nucleus of a eukaryotic cell divides. The genetic material of eukaryotes is located in the nucleus and organized into chromosomes. A chromosome is made of DNA wrapped around proteins and contains all the genetic information for the organism.
DNA is an essential molecule for life. It contains all the genetic instructions that an organism needs in order to live, grow, develop, and reproduce.
We are going to explore a microbiology laboratory called Biogenesis. It simulates the processes involved in the evolution of unicellular organisms in nature. The organisms that will populate this world are formed by segments of different colors and lengths. These segments establish the organism’s properties and are a representation of its genetic code. Their descendants will inherit them with the exception of random mutations that can happen in each generation.
Organisms that obtain beneficial mutations will be the most successful ones, from an evolutionary point of view, and as a consequence, they will create a large number of descendants that will propagate their genes and mutations in the future. However, those organisms that suffer from less appropriate mutations will not take a long time to become extinct.
Installation and execution. First, it is necessary to have a Java Virtual Machine installed on the computer. Once the Java virtual machine is installed, download the latest version from its website and double click on the biogenesis.jar file in order to execute it. Alternatively, you can right-click on the file and select Open with Java Runtime, or run it from the command line: java -jar biogenesis.jar.
The main window is the place that represent the world, where organisms are born, live, reproduce, and die. Biogenesis is controlled from the menu and its main toolbar: New (Game, New) creates a new world; Start/pause (Game, Pause. It can also be activated by pressing the P key) allows you to make a pause at any moment and continue again at the same world’s snapshot where you left it off; Save (Game, Save. The shortcut is the S key) allows you to save the current world to a file; Game, Quit quits the program immediately and all unsaved changes are discarded.
World, Statistics opens the statistics windows, so you can obtain general information about the world: how much time the world has been active, population, atmosphere, remarkable organisms, etc. Increase CO2 (Actions, Increase CO2) / Decrease CO2 (Actions, Decrease CO2) adds / reduces 500 units of CO2 to the atmosphere. Actions, Kill all is self-explanatory. It kills all living organisms. This is a genocide button. World, Parameters… allows you to define different aspect of Biogenesis, such as its language, time per frame, width/height (world’s width and height in pixels), initial oxygen/carbon dioxide in the atmosphere, initial number (it refers to the number of organisms that are created in a new world), etc.
We can examine with more detail any of the organisms and interact with the world. Click over one of the organism, the selected organism’s state panel (Id -a number that uniquely identifies the organism-; age, energy, children, mass, reproduction, etc.) will appear, and the organism itself will be marked with a surrounding orange rectangle for reference. Observe that we can track a selected organism, feed or weaken it (ten energy points are added or subtracted from this being and an equivalent amount of CO2 is consumed from or freed to the atmosphere), rejuvenate/kill/revive it, copy its genetic code so it can be cloned later with the paste option, export an organism’s genetic code to a file, save an image in JPG format, etc.
You can create new beings with a new or modified genetic code, too: World, Genetic Laboratory.
The Game of Life is “a cellular automaton devised by John Horton Conway in 1970. It is a zero-player game, meaning that its evolution is determined by its initial state, requiring no further input. One interacts with the Game of Life by creating an initial configuration and observing how it evolves,” Consway’s Game of Life, Wikipedia entry.
Read our article Game of Life and Automatons to learn how to code it in Python.
Sheppard Software, Animals for Kids is a site with hundreds of educational games, information, quizzes, and more.
CELLS alive! provides information, activities, and animations about cell biology, microbiology, genetics, immunology, and more.
Switch Zoo lets you make animals, build habitats, play animal games, learn about animals, and much more.
Bugguide is a buzzing “community of naturalists who enjoy learning about and sharing our observations of insects, spiders, and other related creatures. We enjoy the opportunity to instill in others the fascination and appreciation that we share for the intricate lives of these oft-maligned creatures.”