Let's Make the Bacteria Explode Upon Clicking Self-Destruct ("APOPTOSIS") Button

     Good afternoon, and welcome to another blog installation of weekly update discussions.   In these articles, we at   Evolution Through the Ages  like to discuss the major advancements, both company and game features, that Sean and I have been working on during the previous week's timeframe.  

     Each Sunday morning, Sean and I get together to discuss tasks for the upcoming week. Additionally during these meetings, we sit down and tweak small components of the game in order to make a more biologically accurate or user-friendly gameplay interface. This week, Sean and I began by integrating a new biological feature into our game; the apoptosis feature.  

Apoptosis Update

     Apoptosis, or programmed-cellular death, is a mechanistic tool that cellular organisms are able to utilize.  Utilizing this feature, users are able to induce cellular "self-destruct"; where selected organisms will implode into themselves.  This will result in the death of the selected organism;  however, sometimes this may be for the greater good.  For instance, this could also be used to protect another species population from going extinct; if being overly hunted by a different competing organism in the surrounding environment. 

      The process by which apoptosis occurs has been depicted in the diagram to the right of this paragraph.  The process begins by the dying, or alter-self cells, condensing into smaller more confined areas.  The apoptotic cell will then begin to fragment around the edges of the cellular membrane (phospholipid bilayer). The ultimate goal of apoptosis is to remove dying or altered-self cells through the use of apoptotic bodies.  Apoptotic bodies are small  cellular-component-containing membrane bound bodies.  The purpose of these apoptotic bodies is to prevent the further interaction of potentially harmful cellular components with cells in the surrounding environment.  

     The image to the left is an in-game screenshot from "Cellular World" within the game   Evolution Through the Ages Within this image, you will see 16 individual "LUCA" (Last Universal Common Ancestor) cells in a singular cubic game environment.  A single LUCA is currently selected by the user in the image.  The user then utilized a multiple-creature selecting feature, discussed later in this article, to select all 16 individual LUCA cells in the environment.   The user then clicked on the red "Apoptosis" Button the Creature Menu to induce apoptosis of all 16 LUCA.

     The ending goal of the apoptosis process is the formation of the apoptotic bodies. These apoptotic bodies are depicted in the image to the right with the formation of the multiple red circles within the cubic environment.

Multiple Creature Selection Upgrade:

     With a little additional back-end coding, Sean and I have now also made it possible for users to select multiple organisms simultaneously within the game.   This feature will allow users to select a single organism, multiple of a single type of organism, all of a single type of organism within a cube environment, or multiple types of creatures at once;   depending upon what the user selects with this feature enabled. This feature can be enabled by the user holding down the keyboard buttons "CTRL" + "A" (on PC) or "Command" + "A" (Macbook).

     The multiple select feature can also be activated by left clicking on multiple organisms individually.   If you hold down the "CTRL" button and maneuver your cursor over multiple organisms, they will all become selected.   The organisms will become de-selected if the user clicks on the surrounding environment instead of an organism.

 Zone of Inhibition Feature Upgrade to Update

 Within the natural world, there are several known examples of organisms creating and releasing biological molecules that are harmful to other organisms in the surrounding environment.   There are several evolutionary reasons for an organism to utilize this technique for competition; many of which are discussed within the game  

Evolution Through the Ages .


    A Zone of Inhibition ("ZOI") is an approach that can be utilized to determine if a bacterial population is sensitive to a particular antimicrobial treatment/agent.   This is correlative to the medical field as this technique can be used in tandem with petri dish cultures to aid physicians in selecting a more effective antibiotic treatment in less time.   

                                                     This approach also allows physicians to determine the efficacy of an antibiotic treatment for an individual sampling size. When pertaining Petri dish cultures, a disk loaded with a specific antibiotic treatment is placed into the Petri dish containing bacterial nutrients known as "agar media".   The bacteria are allowed to grow on the dish for pre-selected period of time;   in this case 24 hours.

     The closer the bacteria can grow to the center of the antibiotic-loaded disk, the less effective the specific antibiotic treatment is in a particular case.  The further out the ZOI is from the antibiotic-loaded disk, the more effective the antibiotic is at inhibiting bacteria growth; through the process of inducing bacterial death. The creatures were merely being inhibited over time; by having a repeated pre-calculated singular damage value subtracted from an organism's health-bar. , now a more accurate version of a ZOI will be produced through a linear damage value which increases as creatures decreases in distance proximity toward a predatory/parasitic creature.

       As the organism being damaged draws closer to the predatory/parasite, the amount of damage value will increase consistently as distance separation decreases.   Additionally, this damage amount will be calculated based on a time scale.  This will more adequately represent the concept previously discussed pertaining: In short, a bacteria must have a certain level of resistance to withstand damage from the components produced within the central region of the antibiotic-loaded disk.   If an organism does not have the required level of resistance to withstand damage, then damage will ensue as the organism encroaches near the central region of the antibiotic treatment disk.


      With regards to microbial competition within "Cellular World" of the game, there are currently three major classes of organism types within the game world:  autotrophs ("photosynthetic organisms"), heterotrophs ("predators"), and parasites.   Within the heterotroph and parasite categories especially, we have incorporated damage calculation simulations within user gameplay.   These damage calculations are based on the distance proximity and time duration a creature is near a predatory or parasitic creature.

Modification to Cellular Organism Growth and Movement Rates

      While teaching the NGSS as a high school biology teacher, I noticed that I had inadvertently incorporated a misconception within our Evolution Through the Ages game simulator.  I made this discovery when I was teaching my students about bacterial colony formation on Petri dish cultures using another educational simulator by NetLogo. The NetLogo simulation  I used in class depicts how non-mobile (non-motile) organisms primarily stay in a central location and split into additional bacteria through the process of binary fission.   The bacteria continue to grow and divide in these central locations until they ultimately run out of nutrients or are killed by a predator.   This situation, and NetLogo simulation, pertain to the premise of bacteria growing within a cultured environment.   Therefore the principals of diffusion and mobility would be limited within their simulated environment.

     To incorporate the central bacterial colony concept within our game, we  began by slowing how rapidly the non-motile organisms will diffuse through the cellular world's environment.   Additionally, we added additional friction to the non-motile organisms; as a way to better represent the slow diffusion of the bacterium across the aquatic environment; instead of merely random motion. With these upgrades, our game now   better simulates how the bacteria are dependent upon their aquatic environment for movement.  The bacteria are then still growing and dividing within the game, however, they are now more confined to a central location with limited resources.   This update will cause a better simulation of limited environmental resources; ultimately leading to the promotion of microbial competition for limited resources.
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