# Pathology to Microbiology

## Pathology's Issues

**1. Pathogens were not fun to play around.**
Players on the receiving end of plagues did not enjoy their gameplay.
Effects that hindered player input (disorientation, brain damage, paranoia) served only as barriers to gameplay and provided no other substance. Players were forced to choose between isolation or suiting up to continue. Pathology discouraged player interaction.

**2. Pathogens decided rounds.**
Pathology had debilitating effects that caused rounds to effectively end.
There was little hope for anyone who got infected by a murdervirus without a vaccine supply. Suppressant curing was not reliable enough to justify the damage and time needed. As a result of mutation, deadly effects would manifest in rampant plagues without any effort from the pathologist who started it.

**3. Pathologists who could make pathogens decided rounds.**
Experienced pathologists had little trouble making deadly diseases.
Once the disease was made, pathologists could destroy their equipment to prevent players from creating the vaccine in-house.

**4. Making pathogens was confusing.**
Pathogen creation was complex. The process of discovering symptoms through DNA splicing forced pathologists to stay holed up in the lab. The lack of a wiki page did not help new players learn pathology.

**5. Admins lacked robust investigative tools to handle pathology complaints.**
As a result of malicious outbreaks during the 2020 testing week, admins were dealing with many ahelps. Admins did not have convenient logging or infection tracing tools and had to spend precious time investigating.

**6. The code used outdated UI techniques.**
The pathogen controller datum uses DM's integrated html procs to create UI. The pathogen creation UI does not use TGUI.

**7. The code structure was monsterously complex.**
Pathogens used dozens of vars to control its behavior and generation. Only a few of those vars were fundamental. Conditional if pyramids and massive switch cases were common in the symptoms datums. Hanging numbers and string returns were not simplified as defines.

*Do not get me started on the DNA code.*

**8. Documentation was seldom present.**
Marquesas and other developers left insufficient documentation to explain the structure and design behind the pathology code. New developers have to carefully pick through the code to grasp any sense of understanding.

**9. Development revolved around a single leader.**
Before Goonstation became open-source, Marquesas was the developer responsible for pathology. When Marquesas left, the code remained undeveloped and leaderless. The expectation seems to remain that a single leader must handle pathology.

**10. Pathology gained a poor reputation across the community.**
Pathology frustrated Goonstation. Members have mixed opinions about the system. Some have associated the entire premise of pathology to be defunct and incongruent. The notion of a rework brings bad memories.

## Design Principles

**1. Player interaction, first and foremost.**
Microbiologists must not be cooped up in their workspace. There should be plenty of strong incentives for pathologists to work with others and to voluntarily help other crew.

**2. Avoid overreliance on microbiologists to solve problems.**
Well-designed jobs and systems provide significant benefits to others and do not force requirements or restrictions onto others to self-justify its existence.

**3. Provide admins modern, intuitive, and thorough tools.**
Half of /pathology.dm is dedicated to html admin panel functions. Microbiology must include well-designed TGUI before any playtesting is permissible.

**4. Develop accessible code for players and future developers.**
Now that Goonstation is open-source, players interested in contibuting to the game have the opportunity to do so. The development cycle of microbiology should explore decentralization in lieu of having a designated developer.

## Core Mechanics

Microbiology revolves around a unique effects system that will have varying effects for **objects**, **turfs**, and **reagents**.
**Genetics already holds a monopoly on player mob upgrades.
Microbiology respects this monopoly and explores non-mob benefits.**

### Microbe Creation
Microbiologists can generate microbial cultures, extract effects, and design their own cultures. Creating microbes requires mixing certain reagents in the incubator to guarantee a desired effect in the generated culture. Effects are extracted by inserting cultures into the Path-o-Matic. New strains can be built through the microbiology console.

### Diverse Effects
**Effects primarily focus on improving station integrity, equipment, and resources.** On the /tg/ codebases, machines and tools are upgraded using a complex component system (RPEDs, lasers, matter bins, etc.). The science department oversees the research (and creation) of these parts. Outside of upgrading batteries using cerenkite and erebite, there is no equivalent upgrade system in Goonstation.

**What can microbiology provide?**
- **Yeasts or other microbial cocktails** to help the chef improve the **food quality/quantity** (imagine the chef hauling thousands of sourdough loaves to cargo)
- **Chemical-producing cultures** for the barman, scientists, and other medstaff (mass medchem production, space cleaner, silicate, salt, holy water, etc.)
- Medbay's **source of income** (selling and buying effects)
- **Investigative capabilities** (ability to get prints/leads from obscured glove fibers, postmortum autopsy)
- **Tool and Machine Upgrades** for mining (power tools), security (energy equipment), and engineering (self-recharging RCD, SMES)
- **Structural Regeneration** (utilizing silicate for windows)
- **Gas Production** to reduce the dependence on cargo and mining for gas replenishment.

## Transient Infection and Effect Probability [How Pathology Dies]

**I do not make the following statements to undermine or downplay the effectiveness of vaccination, nor am I seeking to arouse tension concerning IRL topics.
If this particular topic poses a problem, ping me on Discord and we will determine what should be done.**

Old Pathology forced players to actively suppress or vaccinate against any and all pathogens, because **untreated pathogen diseases did not naturally recede.**
**That is NOT how (most) infectious diseases work!**
It is true that certain infections (STIs, immunocompromising diseases, tuberculosis, leprosy, etc.) result in lifelong/life-ending illnesses, but for the large majority of microbial-based diseases, the human immune system is able to respond and eventually eliminate them.

**All infectious microbes now follow a duration-probability curve.**
Every microbe is given a duration limit that determines how long it may stay in an infected mob before being cured. The stage, advance speed, and spread mechanics are all simplified in one mathematical function:

P(t) = ceil(-a*t^2 + b*t)

where
P(t) is the effect probability at a given time
t is the number of lifeticks progressed
t_d is the total duration
a = 20/t_d^2
b = 20/t_d

a and b are balanced such that all values of t in any given t_d result in a maximum P of 5.

**Once a player meets the cure criterion for an infection, the duration is halved every onLife cycle:**

d = ceil(d/2) - 1

The resulting behavior is shown in the lower two figures: a cured player follows a new duration regimen that declines much faster than the natural life cycle.

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Figure 1: The probability effect curve without the ceiling function. This curve depicts an infection with a total duration of 240 life ticks.

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Figure 2: The probability effect curve with the ceiling function. The ceiling function serves to create the 'staging' divisions present in the disease systems.

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Figure 3: The continuous probability effect curve with stems depicting how a microbe recedes in a cured individual. The first stem indicates that the player met the cure requirement at the apex of the infection. Every onLife cycle, the infection proceeds from stem to stem to reach its final duration. The distance between stems is one half of the remaining duration minus one.

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Figure 4: The stepped probability effect curve with stems. The sudden drop in effect probability is qualitatively preserved after the ceiling is applied.

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**Strain-specific vaccines are replaced with simplified cures using the old suppressants code.**
Cures act permanently once the cure condition is met. As shown in the figures above, duration is depleted aggressively in a cured individual, representing the cure-assisted immune system fighting the microbes. This removes the waiting, ambiguity, and unfun RNG when fighting a microbial disease.

## Death, Decimation, and Antagonists

**Infectious spread is explicitly limited, and malignant aspects of pathogenic diseases will not be introduced unless the Goonstation community agrees to allow it.**
There is still controversy and bitterness caused by past deathviruses and abusive gameplay to expect anyone to be comfortable with a reintroducion of malevolent symptoms. Until public opinion changes, no intentionally harmful effects will be implemented.

**Traitor Microbiologists would share the same specialized options as other medsci personnel.**
There is no reason why microbiologists would need new unique traitor gear.

**Deadly plagues and aspects of old Pathology (if they even return) would be reserved exclusively for a Nuclear Bio-Operative class.**
The only context in which old pathology might make sense is with the nuclear operatives. Nukeop rounds are short and determined by the bomb instead of the shuttle. Expectations for survival are completely different compared to every other round type.
A nuclear bio-operative would be a powerful disperser class, forcing crew to withdraw, detour, or push through and deal with the consequences. Bio-operators would carry grenades of aerosolized designer germs and cures in case other ops get sick.

## Why This Effort Matters

**Pathology is thoroughly obsolete.** Aside from the UI, sprites, and lack of ownership, developments to genetics and the creation of a simplified disease system closes the small niche that pathogens provided. The disabling of Pathology over a year ago did not fundamentally diminish gameplay on Goonstation.

**The community agrees that this broken code must be addressed**, but we have different ideas on what should be done. I have been approached by some members who believe that the entire pathology code should simply be deleted. I have heard from others who wish for a 'rework', providing a spread of ideas and suggestions. Many are ambivalent or of no opinion.

**I believe that there exists a different space in Goonstation that microbiology can occupy, and I have briefly listed them in the Core Mechanics section. I appeal to the Goonstation community for help to see these ideas through.**