Goonhub
08-27-2014, 06:09 AM
AKA A Whole New World of Sickness and Health, AKA How to Make Pathology Not Be a Traitor-Only Job, aka A Proposal for the Unification of Genetics, Pathology and Botany Through the Element they Have in Common. Plus some additional medbay ideas.
So, here's a bunch of stuff I'd really like to see, even though I know it'd probably be too much work right now. A lot of this is probably already similar to what's in the current unimplemented pathology proposal. This is nothing more than a wishlist. It looks like a huge wall of text, doesn't it? It is. It's complex. But, I think it's worthwhile, or I wouldn't post it. I just want to see the best, funnest, most useful version of pathology we can get. Also, I wanted to get these ideas out of my head.
1. Basics
The center of this proposal is to take the genetics system currently only used for humans and monkeys and expand it. The genetics minigame as it currently exists will mostly continue to be used only by genetics, and mostly unchanged. However, a lot of interesting things could be done if infections and plants made use of the same system of genes as genetic mutations do. The idea is to construct the functions of the various diseases and plants out of genetic traits. So, in addition to having traits like heat resistance or telekinesis, there would also be traits for chemical production and symptoms. And just to get it out of the way, mutadone should have no effect on any of these native traits.
2. Changes to Genetics
2a. Just a few things here, which could probably be their own topic. Right now, the genetics minigame suffers from being too simple. All you have to do is know how to brute force it efficiently, combined with a simple strategy for properly using the gene sequence checker. So here's how I'd increase the complexity. Currently, DNA sequences are broken up into groups of four base pairs, each of which is individually checked by the sequence checker. Instead, change that to groups of three, like codons are supposed to be, and have the sequence checker only check if the whole codon is correct. An upgrade to the sequence checker could tell you how many individual base pairs are correct. Next, make the checker able to check twice (with an upgrade, three times) before needing to cool down for an extended period (with an option to trigger cooldown early). That would have the effect of making codons with only a single missing base pair super easy, but if two or three base pairs are missing then there'd be a lot more mastermind-style strategy involved in figuring out the correct combination. Combine that with an increase in the number of missing base pairs, and the game should be a lot more interesting.
2b. There's another function that I'd like to see added. Weak precision radiation emitters. These would be further down the tech tree than the current precision radiation emitters, near the bottom, and would only have the effect of damaging a gene sequence rather than rerolling it, and have a much shorter cooldown. This would move an already active gene to the "potential" section to be researched, minus a few base pairs. Of course, I know the reason why that particular restriction exists. If you damage a "human" or "monkey" trait in this way, the result should be instant gibbing if there isn't another species trait to take its place. But the computer should already have the "human" trait on file, so it can recognize it, and will refuse to zap that trait at all. As long as it's working properly and hasn't been compromised, natch. I'll explain how this will come in handy later (section 3d). Of course, repairing those genes would be super easy, since you'll already know the complete sequence. That's why it is very important that the completed sequences for traits that haven't been researched should always be invisible.
2c. Oh, and the whole "no researching already activated traits" thing is a little arbitrary, isn't it? Well, here's an in-universe explanation for why that would be. Every living thing has tens of thousands of genes to begin with. These form a baseline which exists in the computer in a simplified fashion, so it doesn't have to check billions of different chemical interactions. The potential mutations are just a few of them. Gene research works by approximating a partial gene's effect and predicting how the organism would be different from their baseline if it were stable. That means that already activated traits can't be analyzed in this way, because they're part of the baseline that the system is checking against. The analysis system is only capable of adding, not subtracting when it's simulating the result. But, when the gene is destroyed by those weak radiation emitters described above, what's really happening is the system is zapping genes left and right until something happens, then the changes in the organism that result can be used to determine what the effect of the gene was, so that's why they can be analyzed after being damaged.
2d. Moving on, independent of these other things, I'd like to see a memory bank added to genetics (maybe they get their own mainframe too?) that stores all of the unfinished potential mutations of every organism that gets put in a gene scanner connected to a GeneTek console, as well as the sequences of any genes that have been researched and solved, along with who has them. You can't modify the genes in those records, because it'd be pointless to do so without a living thing to demonstrate that the gene is stable and active. But, you can do a search on any unresearchable active genes to see if there are any possible matches in the records so you can find and activate them, and will automatically identify any unresearched activated gene if it can. This, too, will come in very handy later in this proposal (section 3f).
3. Pathology and Diseases
3a. Combined with what I previously described, I hope to have a pathology department that interacts heavily with genetics. You do that by having diseases be based on a collection of genetic traits. But pathology should probably have at least one GeneTek set of their own. They'll need it. Slightly different from humans and monkeys, the key trait for diseases should have a number of functions. First, it should identify the class of infection, which I'll go into more in a bit. Second, it should determine the species - cold, flu, etc. Third, it should determine the strain of the disease, with the possibility of multiple strains being generated at round start even if they don't appear. Once you've recovered from having a disease, your body will have antibodies for that strain, but you can still be infected by a different one. Also let there be a 1/100 chance that a disease will mutate and become a different strain every time it infects someone new, allowing it to reinfect people, while otherwise being unchanged.
3b. Infection classes have to do with what the infection's nature is. Class should determine what medicines may be effective, certain things about traits I discuss in section 6, and the number of traits that the infection may have when naturally generated, depending on the complexity. When naturally generated, depending on species an infection will have a base list of traits. Colds cause coughing and sneezing, for example, along with having a few other traits. But they will also have a chance to have additional traits up to the limit for their class. But on the other hand, the more complex the class, generally speaking the easier it is to treat. Prions make up the lowest class, with a hard limit of 2 traits, one of which is their class trait, and the other is for the type of tissue they attack (all real prion diseases attack brain tissue, but this doesn't necessarily need to be the case here). The next step up is viruses, then bacteria, then fungi, then parasites.
3c. Here's the part where pathology becomes useful beyond making and curing infections. The central part of pathology gameplay is, naturally, analyzing diseases. So, you'd take an infected blood sample, spin it in a centrifuge that automatically removes the blood after it cycles, leaving you with the disease reagent, then cultivate them in a separate machine. Cultivation requires an appropriate medium. Pathology should start off stocked with unlimited supplies of agar for bacteria and fungi, and cell media for viruses. Synthmeat or various synthorgans (and their natural counterparts) should also be usable, but not available from the start, and have various advantages, which I'll mention in the next section. Prions and parasites can only be cultivated with these materials. A "population" variable should also be a relevant factor in disease progression, which I'll go into more in section 5a.
3d. Once you have your cultivated disease population, you start testing it in the same machine. It should have numerous options. Temperature control, applying small amounts of basic anti-infection medication, radiation, electricity, other chemicals you load from a beaker, scans that give some basic physical information like the class and species (handheld health analyzers should detect symptoms only rather than diseases) or if the contagion itself is radioactive or if it glows or various other things, scans of the medium to detect if the contagion is attacking it (This is the advantage of using synthorgans, and synthmeat should cover various types not included in the other ones), scans to detect chemicals that may be appearing in the medium, exposure to water or air, and so on. Also, injecting unstable mutagen to generate new traits. As you carry out these tests, the population will go up or down in response (the reason you need to cultivate it first is mainly so you can notice the changes), and based on that the computer will detect various genetic traits. For example, if you dose the population with a drug that would normally kill it, and it doesn't, the machine will detect the "Drug Resistance" trait. This will primarily be useful for determining how to treat a particularly resistant strain, but if you find something interesting you can send the sample over to genetics where they'll use the weak precision radiation emitters (as described in 2b) to try to find the traits. Of course, on the genetics scanner they'll be unresearched, so you won't be able to tell them apart, and there will be a little guesswork involved as to which trait is which until you do. There's a lot of power in here though, which is the reason why the sequences for unresearched initially completed mutations need to be invisible, also as described at the end of section 2b.
3e. If a population is completely wiped out, it should turn into a "dead (whatever)" reagent which can be used as a vaccine against viruses only. For other classes, you'll have to use something I describe in the next section.
3f. Another thing for pathology to start with, a few generated disease strains to get players started, perhaps with one or more coming with a note saying "This has been spreading wildly on our stations. Study it and hope it doesn't show up on yours" which it invariably will after a while. Also, a separate machine to construct diseases. Once a trait has been researched, stabilized, and saved to the genetics memory bank (section 2d) it can then be added to a population in this way (With no limit on the number except for prions, which are limited to 2), and the database should start with a "DNA reverse transcriptase" trait on file so you can make retroviruses. Using retroviruses, you can give mutations to people. Every trait in the retrovirus will have a chance to be passed on with each biotick - it shouldn't be instantaneous. And the retrovirus is still a disease, so it'll make you a tiny bit sick while it's in you and will eventually be eliminated by the body. Basically, a worse version of injectors that are available much earlier in the round. This way, geneticists can do their thing, with pathologists taking over handing out the benefits of their work. That same machine should be able to remove traits as well, but again, only if they've been researched in genetics already. Traitors can also make very good use of this. Take a disease, strip it down, inject it in yourself, become immune to that strain, then load up the rest of your supply of that strain with tons of awful traits, and spread it on the station. A late-round option, but potentially an extremely effective one.
3g. Now, about initial infection vectors. Obviously, there's any uncooked meat or eggs. Any food that is put on the ground instead of a counter. It could be brought in my miners on their clothes, picked up from inside an asteroid. Small, hard to see fungal colonies that spread invisible spores could spawn in dark maintenance areas. Like space fungus now, except sneakier.
3h. One final note. Pathology is likely going to need to be a hell of a lot bigger than it currently is. And maybe have its own port-a-medbay to take in patients without dragging them through the whole station, infecting everyone on the way.
4. Botany
4a. I'm going to include some more pathology stuff in here, since for the most part playing as a botanist will remain unchanged. The underlying mechanics would be different in this proposal, but from the outside it should be identical. Just like with diseases, I would propose to have plants also use the genetic trait system. That means a trait for plant species, and traits for any chemicals they can produce, along with mutations that affect maturation rate, yield, etc. and potential traits for any plant mutations they may have and their associated effects. Again, for botanists nothing will change. They'll still plant, harvest, infuse, splice, and extract chemicals exactly as they have done. The main difference is that plants can be injected with new mutations once injectors are researched, and any traits the plants may have may be investigated by geneticists.
4b. Now, the problem with this should be immediately obvious. There are some incredibly potent chemicals available from hydroponics. Balancing that out is going to be tricky. Back in section 2a, I described changes I'd like to see in the genetics minigame. This is why. With the gene sequence checker, it doesn't really matter how many base pairs are missing. You can work through any gene in not too much time. Opening up incredibly powerful mutations like "Omnizine Production" is why I think it should be changed to a codon-based scan. Even still, the number of missing base pairs for something like that should be very high. But I also have two more ways to balance this out. The first is making unresearched complete sequences invisible, as I said in section 2b and 3d. Second, in order to produce chemicals in your body, just having the trait shouldn't be all it takes. It should also take a precursor trait, representing enzymes or metabolic pathways or what have you. Each of these precursors will enable your body to produce several different chemicals each, as long as you have the chemical trait too. Multiple precursors may be needed for chemicals that would be extremely obtuse for a human biology to produce (i.e. chlorine trifluoride, space lube, liquid dark matter) and of course if you don't have a plant or disease that starts out with the traits to produce those chemicals naturally, you'll have to stumble on them by luck. Furthermore, production rate and maximum cap should be determined by health (and how well fed you are?), just as it is with potency in plants.
And... that's pretty much all I have to say for hydroponics. Except for this: viewtopic.php?f=6&t=3309#p36797
5. Medbay Stuff and Disease Progression
5a. Now about disease population. I mentioned it as being relevant for testing diseases, but I think it should also be a factor in how they progress in your body. So the disease population is tracked within each sick person. At first the disease is asymptomatic, until it builds up to a certain population level (with the rate of growth increasing exponentially up to a ceiling). Each individual symptom should have its own threshold for when it starts to appear. For diseases that produce chemicals, the rate at which they do so should also be affected. But, from the first moment a disease appears in the body a timer starts to the time when the body will start producing antibodies, at which point the population will decline rapidly. This way, even if a person is reinfected the disease will be eliminated before it becomes symptomatic. Also, antibodies will develop if the disease is cured by medicine or any other way. The population should increase whenever you're near a source of it, instead of the disease only being caught a single time. Also, the body should deplete the population at a certain rate even before antibodies develop, so you won't catch a disease just from a single germ.
5b. Now, for treatments. I suggest a system with three tiers of drugs. The first tier should be basic drugs that will gradually cure non-resistant diseases. They should be readily available from the med dispensers, and not too difficult to produce, like spaceacillin, with one for each class of contagion except for prions (same for the next tier). Antifungals should be harder to acquire on every level than others. The second tier should be harder. One type may require a highly complex chem recipe, another a mutated plant, or only be available from space traders for not inconsequential amounts of money. This type will treat drug resistant strains (with any strain having a small chance to gain drug resistance whenever treated with a drug) but against very drug resistant strains, they'll only stall the disease at best. Tier three drugs should have nasty side effects, and only be findable in dangerous places, like derelicts and enemy stations, but will cure any disease of their class. The ambulance derelict seems a good place for one or two. Finally a good reason for people to fuck off into space for a while! Even prions should have a cure on this level, but it should be somewhere very hard to get. And maybe include Panacea too? Maybe make it creatable at the alchemical circle? But again, not easily.
5c. This is somewhat unrelated, but I'd also like to see an expanded set of organs, like the heart that was recently added. Mainly, this is to provide a greater variety of complex symptoms. And also, for those organs to be removable, transplantable, replacable with synthetic versions, and/or sellable. Grown synthetic organs can be affected by diseases, but cybernetic replacements will not, at the cost of some of them being not as good (There's surely plenty of ways for roboticists to help here, not just with cybernetic organs, but also with modules that enhance biological ones. But this is already bloated enough without adding another entire section to it). As far as procedure goes, since there are only so many areas you can target on the body, I think adopting a system I saw on the tgstation wiki might work. According to the guide, they use a drapes item on a patient to indicate which part of the body or organ they're targeting. Sounds simple enough. Organs should also be functional, and have health, which decays if they're not in a living person. There should also be contagion traits that damage them specifically, and they should have a small chance to take damage from strong blows to the body part they're in. This already exists with the brain being able to take damage from concussions or other sources. Basically, that, but applied to everything. Also, have drugs that can heal them (unless their health is below a certain level. They should also heal themselves over time, faster if they're close to full health.) and support their functions, like mannitol and oculine. Here are some of my suggestions.
Brain: Same as it is now.
Eyes: Damage affects vision. Eyes may be removed and replaced with artificial eyes. Using a screwdriver on thermal scanners, meson scanners, etc. to take them apart, then combining them with wire and artificial eyes should produce eyes that provide that type of sight without taking up the glasses inventory slot.
Heart: Damaged by sugar overdose and cholesterol. Very robust, causing problems only at low health so long as the lungs are providing air, but failure causes... well, heart failure, a condition that must be cured in order for the lungs to have any effect. Which brings us to...
Lungs: Damaged by very hot or cold air. Have a person take 8 suffocation damage per biotick, with the lungs healing 0.5*(Kpa of oxygen in air)*health of lungs (100%->0%) up to a limit of 20. This is to match up with the way things currently work, where you need 16 Kpa of O2 in the air to breathe properly. That also means that the lungs will have to be quite hardy, because you'll start slowly suffocating when they're at 80%.
Liver: Similar to the lungs, but for toxin damage. At full health, let it have a 20% chance to heal 1 point of toxin damage per biotick, with a decreasing chance until half health. Below half health, have a rising chance to inflict 1 toxin damage up to a 100% chance at 0 health.
Kidneys: Damaged by having a person's bloodstream container near the limit of its capacity. At about 80% health, this will start to affect the depletion rate of all chemicals, so they take longer to leave your system. Sounds beneficial? Well, in exchange, once your kidneys reach that level, suddenly a lot of chemicals that you couldn't overdose on, now suddenly you can, and the lower their health the lower all overdose thresholds become. Also, without these, you can't pee. This has no effect on boosts to depletion rate caused by charcoal or calomel.
Thymus: Also know as "the what?" It's a key organ in the immune system. So, as it loses health, it takes longer to develop antibodies.
5d. Just a few more random things having to do with health. First, fevers. They should happen automatically, with raised temperatures slowing diseases. Have pyretic drugs, which will take you to the safe limit for your body's temperature, or people can try the sauna for the same effect. Second, cryos. The cold should halt diseases in their tracks.
6. Symptoms and Interactions
So, I've talked about diseases and plants using the same genetic traits as are found in mutations, but these are very different things that behave differently in gameplay. Obviously, there has to be a difference in their effects. Also, for diseases, there's going to have to be a number of different ways that symptoms interact to create just the right blend. I'll be covering examples of both of those here, but there are tons of possibilities. Note that not all symptoms are things that should show up on a health scan. It'd get very crowded. For example, you can only have lung inflammation if you have a lower respiratory infection, so only the latter should show up. This will also preserve some of the surprises about what kind of disease you've got.
Current mutations
Heat resistance: (In diseases) Will no longer be slowed by fevers or similar defenses. Will not be killed by cooking. Bacteria and fungi will also grow faster the higher the temperature is.
Cold resistance: (In diseases) Will no longer be stopped by cryo tubes or other sources of cold.
Alcohol resistance: (In diseases) Where an infection may be living on a tile, in a splash of blood, etc. this trait will prevent it from being killed by common space cleaning chemicals.
Booster A1, B2, etc.: (In plants) Matches up with current plant mutations for high yield, fast maturation, etc. (In diseases) Increased rate of growth, with boosts equivalent to yield and maturation rate having a multiplicative effect.
Immolation: (In diseases) Causes symptom, hyperpyrexia. Very high body temperature, causes slow burn damage. Treat with salicylic acid.
Cryokinesis: (In diseases) Prevents fever. At higher levels of infection, may lead to hypothermia. Treat with pyretics.
X-ray vision: (In diseases) Very small amount of radiation generated. "Radioactive" trait does same thing, but also damages the disease.
Bad gas: (In diseases) Same effect as when a human has it.
Obesity: (In diseases) Slows disease growth, but makes it more resistant to drugs.
SMES human/organism: (In diseases) In tests, if you zap it, it will zap back. Causes symptom: Myoclonic jerk. Replaces effect of cough, causing you to spasm and randomly drop items.
Epilepsy: (In diseases) Makes germs more mobile, reducing effectiveness of immune system. (In plants-native:lasher) Causes plant to jerk about, attacking nearby people.
Cloak of Darkness: (In diseases) Disease will not manifest symptoms, allowing carrier to spread it far and wide. Delays antibody development.
New mutations:
Air resistance: (In diseases-native:cold, flu) Allows disease to be spread through the air, just by being close to someone. However, it will have to be very close, and for more than just a second or two unless another trait is combined with this. (In humans) Reduces the amount of chemicals taken in through smoke, for better or for worse.
Lung-attacking: (In diseases-native:cold, flu) Causes symptom, lower respiratory infection. Causes coughing, which will spread germs that have the Air resistance trait. Very mildly damages lung. Coughing reduces the suffocation damage healed by lungs each biotick. The lower lung health is, the more often you cough, sometimes up to multiple types per biotick. But it shouldn't make you drop things. That's too much. Also, this trait alone shouldn't inflict much damage on lungs. This trait is common cold-level.
Inflammation: (In diseases-native:flu) Causes muscle fatigue, lowering movement and stamina. Worsens some organ-attacking traits, not eyes. (In humans) Same.
Bacteriophage: (In diseases) The disease will attack bacterial diseases. (In humans) Large increase to pre-antibody immune strength against bacteria.
Red Queen trait: (In diseases) Allows disease to rapidly alter its chemical defenses, preventing the immune system from fighting it. (In humans) Greatly increases immune system strength, and counters same trait in diseases. (In plants) Increases chance of changing into mutant crop.
Water resistant: (In diseases) Allows disease to spread through contact with infected blood. Just being next to a blood stain when it appears is enough. Also, if a person explodes into gibs, the disease will be spread over a wide area in that moment. Combined with air resistance, infected blood will continue to infect a small area around it. (In humans) Reduces the amount of chemicals taken in through skin, for better or for worse.
Space resistant: (In diseases) Allows disease to exist in zero atmos conditions. May be transmitted in dust form onto a miner's clothes when working on an asteroid. In which case, they'll become infected if they take off their helmets. Also allows transmission from clothes to nearby people, but not person to person airborne transmission. (In humans) Reduces whatever effects exposure to low pressure areas causes. Allows holding breath longer in space?
Skin permeable: (In diseases) Allows transmission through skin contact. Punching someone, shaking them to wake them up, anything. (In humans) When touching someone, a small dose of any reagents present in blood will transfer over, with an alert in the chat box of some kind.
Drug resistance: (In diseases) Reduces effectiveness of all anti-disease medicines. Tier 1 medicines ineffective. (In humans) Reduces toxin damage from all sources by 1.
Drug resistance +: (In diseases) Reduces effectiveness of all anti-disease medicines. Tier 2 medicines greatly reduced in effectiveness. (In humans) Eliminates overdose thresholds.
Mercury enzyme: (In all) Rapidly depletes mercury in blood stream, replaces with mercury enzyme, which boosts stamina/growth rate.
Brain-attacking: (In diseases-native:space madness, necrotic degeneration, berserker, space kuru, etc.) Damages brain, enables various mental symptoms.
Auditory nerve alteration: (In diseases-native:space madness) Disrupts balance, making everything look upside-down. (In humans) Enhances hearing. Loud noises will show up with their coordinates of origin in the chat box.
Higher fuction suppression: (In diseases-native:necrotic degeneration) Random stun. At high levels of brain damage, body will start to be controlled by an NPC for short periods, then longer periods, then always. (In humans) Prevents you from using complex equipment, as if you were severely brain-damaged, but greatly increases all melee damage.
Spaceacillin production: (native:disease Space fungus) Produces spaceacillin. Requires penam group precursor.
Penam group precursor: (native:disease Space fungus) Enables production of spaceacillin, and other similar chemicals.
DNA reverse transcriptase: (In diseases) Chance to transfer each individual genetic trait from disease to host. Not a good thing generally. Many disease traits have the same effect in humans as in the diseases themselves. Diseases with these traits should be weighted to only rarely spawn with traits that would be beneficial to humans. If disease strain trait is transferred, disease population growth skyrockets, but if the disease is eliminated, that trait will be too. Traits transferred in this way cannot be eliminated with mutadone, only by the use of the geneticists' weak precision radiation emitters.
??? metabolic pathway: Replace the ??? with various bits of technobabble. Traits like this, of which there should be quite a few, should be a big part of pathology research. Each of them should generally boost a disease's virulence. But, these also represent weakpoints in the diseases, where each ??? corresponds to a separate chemical that poisons it. Not enough to kill it instantly, but enough to make resisted drugs effective again. Unlike other traits, these should be directly detectable by pathology lab scans, while being unable to be researched, at least not so you could find out the weakness. When it is, it opens a new minigame. Solve it, and you get the answer. The minigame I'd propose is simple, both in the generation and the solving, though it may take a bit of time. You're given a list of between 4-8 values, each of which may have 4 different states. You're given a number of inputs, maybe 4-6, representing various chemicals, which will increment all of the values by 0-3, randomly determined at the start. The goal is to get all of the values to 0, representing a completed metabolic cycle. Generating the puzzle is easy. Just flip all the inputs from positive to negative, and apply a sequence (invisibly to the player). The player will have to reverse that sequence to solve it, though this is not a logic puzzle confined to a single solution. Not super difficult, but not easy either. This is meant to be not a necessity, but an option, and one you have to work for.
So, here's a bunch of stuff I'd really like to see, even though I know it'd probably be too much work right now. A lot of this is probably already similar to what's in the current unimplemented pathology proposal. This is nothing more than a wishlist. It looks like a huge wall of text, doesn't it? It is. It's complex. But, I think it's worthwhile, or I wouldn't post it. I just want to see the best, funnest, most useful version of pathology we can get. Also, I wanted to get these ideas out of my head.
1. Basics
The center of this proposal is to take the genetics system currently only used for humans and monkeys and expand it. The genetics minigame as it currently exists will mostly continue to be used only by genetics, and mostly unchanged. However, a lot of interesting things could be done if infections and plants made use of the same system of genes as genetic mutations do. The idea is to construct the functions of the various diseases and plants out of genetic traits. So, in addition to having traits like heat resistance or telekinesis, there would also be traits for chemical production and symptoms. And just to get it out of the way, mutadone should have no effect on any of these native traits.
2. Changes to Genetics
2a. Just a few things here, which could probably be their own topic. Right now, the genetics minigame suffers from being too simple. All you have to do is know how to brute force it efficiently, combined with a simple strategy for properly using the gene sequence checker. So here's how I'd increase the complexity. Currently, DNA sequences are broken up into groups of four base pairs, each of which is individually checked by the sequence checker. Instead, change that to groups of three, like codons are supposed to be, and have the sequence checker only check if the whole codon is correct. An upgrade to the sequence checker could tell you how many individual base pairs are correct. Next, make the checker able to check twice (with an upgrade, three times) before needing to cool down for an extended period (with an option to trigger cooldown early). That would have the effect of making codons with only a single missing base pair super easy, but if two or three base pairs are missing then there'd be a lot more mastermind-style strategy involved in figuring out the correct combination. Combine that with an increase in the number of missing base pairs, and the game should be a lot more interesting.
2b. There's another function that I'd like to see added. Weak precision radiation emitters. These would be further down the tech tree than the current precision radiation emitters, near the bottom, and would only have the effect of damaging a gene sequence rather than rerolling it, and have a much shorter cooldown. This would move an already active gene to the "potential" section to be researched, minus a few base pairs. Of course, I know the reason why that particular restriction exists. If you damage a "human" or "monkey" trait in this way, the result should be instant gibbing if there isn't another species trait to take its place. But the computer should already have the "human" trait on file, so it can recognize it, and will refuse to zap that trait at all. As long as it's working properly and hasn't been compromised, natch. I'll explain how this will come in handy later (section 3d). Of course, repairing those genes would be super easy, since you'll already know the complete sequence. That's why it is very important that the completed sequences for traits that haven't been researched should always be invisible.
2c. Oh, and the whole "no researching already activated traits" thing is a little arbitrary, isn't it? Well, here's an in-universe explanation for why that would be. Every living thing has tens of thousands of genes to begin with. These form a baseline which exists in the computer in a simplified fashion, so it doesn't have to check billions of different chemical interactions. The potential mutations are just a few of them. Gene research works by approximating a partial gene's effect and predicting how the organism would be different from their baseline if it were stable. That means that already activated traits can't be analyzed in this way, because they're part of the baseline that the system is checking against. The analysis system is only capable of adding, not subtracting when it's simulating the result. But, when the gene is destroyed by those weak radiation emitters described above, what's really happening is the system is zapping genes left and right until something happens, then the changes in the organism that result can be used to determine what the effect of the gene was, so that's why they can be analyzed after being damaged.
2d. Moving on, independent of these other things, I'd like to see a memory bank added to genetics (maybe they get their own mainframe too?) that stores all of the unfinished potential mutations of every organism that gets put in a gene scanner connected to a GeneTek console, as well as the sequences of any genes that have been researched and solved, along with who has them. You can't modify the genes in those records, because it'd be pointless to do so without a living thing to demonstrate that the gene is stable and active. But, you can do a search on any unresearchable active genes to see if there are any possible matches in the records so you can find and activate them, and will automatically identify any unresearched activated gene if it can. This, too, will come in very handy later in this proposal (section 3f).
3. Pathology and Diseases
3a. Combined with what I previously described, I hope to have a pathology department that interacts heavily with genetics. You do that by having diseases be based on a collection of genetic traits. But pathology should probably have at least one GeneTek set of their own. They'll need it. Slightly different from humans and monkeys, the key trait for diseases should have a number of functions. First, it should identify the class of infection, which I'll go into more in a bit. Second, it should determine the species - cold, flu, etc. Third, it should determine the strain of the disease, with the possibility of multiple strains being generated at round start even if they don't appear. Once you've recovered from having a disease, your body will have antibodies for that strain, but you can still be infected by a different one. Also let there be a 1/100 chance that a disease will mutate and become a different strain every time it infects someone new, allowing it to reinfect people, while otherwise being unchanged.
3b. Infection classes have to do with what the infection's nature is. Class should determine what medicines may be effective, certain things about traits I discuss in section 6, and the number of traits that the infection may have when naturally generated, depending on the complexity. When naturally generated, depending on species an infection will have a base list of traits. Colds cause coughing and sneezing, for example, along with having a few other traits. But they will also have a chance to have additional traits up to the limit for their class. But on the other hand, the more complex the class, generally speaking the easier it is to treat. Prions make up the lowest class, with a hard limit of 2 traits, one of which is their class trait, and the other is for the type of tissue they attack (all real prion diseases attack brain tissue, but this doesn't necessarily need to be the case here). The next step up is viruses, then bacteria, then fungi, then parasites.
3c. Here's the part where pathology becomes useful beyond making and curing infections. The central part of pathology gameplay is, naturally, analyzing diseases. So, you'd take an infected blood sample, spin it in a centrifuge that automatically removes the blood after it cycles, leaving you with the disease reagent, then cultivate them in a separate machine. Cultivation requires an appropriate medium. Pathology should start off stocked with unlimited supplies of agar for bacteria and fungi, and cell media for viruses. Synthmeat or various synthorgans (and their natural counterparts) should also be usable, but not available from the start, and have various advantages, which I'll mention in the next section. Prions and parasites can only be cultivated with these materials. A "population" variable should also be a relevant factor in disease progression, which I'll go into more in section 5a.
3d. Once you have your cultivated disease population, you start testing it in the same machine. It should have numerous options. Temperature control, applying small amounts of basic anti-infection medication, radiation, electricity, other chemicals you load from a beaker, scans that give some basic physical information like the class and species (handheld health analyzers should detect symptoms only rather than diseases) or if the contagion itself is radioactive or if it glows or various other things, scans of the medium to detect if the contagion is attacking it (This is the advantage of using synthorgans, and synthmeat should cover various types not included in the other ones), scans to detect chemicals that may be appearing in the medium, exposure to water or air, and so on. Also, injecting unstable mutagen to generate new traits. As you carry out these tests, the population will go up or down in response (the reason you need to cultivate it first is mainly so you can notice the changes), and based on that the computer will detect various genetic traits. For example, if you dose the population with a drug that would normally kill it, and it doesn't, the machine will detect the "Drug Resistance" trait. This will primarily be useful for determining how to treat a particularly resistant strain, but if you find something interesting you can send the sample over to genetics where they'll use the weak precision radiation emitters (as described in 2b) to try to find the traits. Of course, on the genetics scanner they'll be unresearched, so you won't be able to tell them apart, and there will be a little guesswork involved as to which trait is which until you do. There's a lot of power in here though, which is the reason why the sequences for unresearched initially completed mutations need to be invisible, also as described at the end of section 2b.
3e. If a population is completely wiped out, it should turn into a "dead (whatever)" reagent which can be used as a vaccine against viruses only. For other classes, you'll have to use something I describe in the next section.
3f. Another thing for pathology to start with, a few generated disease strains to get players started, perhaps with one or more coming with a note saying "This has been spreading wildly on our stations. Study it and hope it doesn't show up on yours" which it invariably will after a while. Also, a separate machine to construct diseases. Once a trait has been researched, stabilized, and saved to the genetics memory bank (section 2d) it can then be added to a population in this way (With no limit on the number except for prions, which are limited to 2), and the database should start with a "DNA reverse transcriptase" trait on file so you can make retroviruses. Using retroviruses, you can give mutations to people. Every trait in the retrovirus will have a chance to be passed on with each biotick - it shouldn't be instantaneous. And the retrovirus is still a disease, so it'll make you a tiny bit sick while it's in you and will eventually be eliminated by the body. Basically, a worse version of injectors that are available much earlier in the round. This way, geneticists can do their thing, with pathologists taking over handing out the benefits of their work. That same machine should be able to remove traits as well, but again, only if they've been researched in genetics already. Traitors can also make very good use of this. Take a disease, strip it down, inject it in yourself, become immune to that strain, then load up the rest of your supply of that strain with tons of awful traits, and spread it on the station. A late-round option, but potentially an extremely effective one.
3g. Now, about initial infection vectors. Obviously, there's any uncooked meat or eggs. Any food that is put on the ground instead of a counter. It could be brought in my miners on their clothes, picked up from inside an asteroid. Small, hard to see fungal colonies that spread invisible spores could spawn in dark maintenance areas. Like space fungus now, except sneakier.
3h. One final note. Pathology is likely going to need to be a hell of a lot bigger than it currently is. And maybe have its own port-a-medbay to take in patients without dragging them through the whole station, infecting everyone on the way.
4. Botany
4a. I'm going to include some more pathology stuff in here, since for the most part playing as a botanist will remain unchanged. The underlying mechanics would be different in this proposal, but from the outside it should be identical. Just like with diseases, I would propose to have plants also use the genetic trait system. That means a trait for plant species, and traits for any chemicals they can produce, along with mutations that affect maturation rate, yield, etc. and potential traits for any plant mutations they may have and their associated effects. Again, for botanists nothing will change. They'll still plant, harvest, infuse, splice, and extract chemicals exactly as they have done. The main difference is that plants can be injected with new mutations once injectors are researched, and any traits the plants may have may be investigated by geneticists.
4b. Now, the problem with this should be immediately obvious. There are some incredibly potent chemicals available from hydroponics. Balancing that out is going to be tricky. Back in section 2a, I described changes I'd like to see in the genetics minigame. This is why. With the gene sequence checker, it doesn't really matter how many base pairs are missing. You can work through any gene in not too much time. Opening up incredibly powerful mutations like "Omnizine Production" is why I think it should be changed to a codon-based scan. Even still, the number of missing base pairs for something like that should be very high. But I also have two more ways to balance this out. The first is making unresearched complete sequences invisible, as I said in section 2b and 3d. Second, in order to produce chemicals in your body, just having the trait shouldn't be all it takes. It should also take a precursor trait, representing enzymes or metabolic pathways or what have you. Each of these precursors will enable your body to produce several different chemicals each, as long as you have the chemical trait too. Multiple precursors may be needed for chemicals that would be extremely obtuse for a human biology to produce (i.e. chlorine trifluoride, space lube, liquid dark matter) and of course if you don't have a plant or disease that starts out with the traits to produce those chemicals naturally, you'll have to stumble on them by luck. Furthermore, production rate and maximum cap should be determined by health (and how well fed you are?), just as it is with potency in plants.
And... that's pretty much all I have to say for hydroponics. Except for this: viewtopic.php?f=6&t=3309#p36797
5. Medbay Stuff and Disease Progression
5a. Now about disease population. I mentioned it as being relevant for testing diseases, but I think it should also be a factor in how they progress in your body. So the disease population is tracked within each sick person. At first the disease is asymptomatic, until it builds up to a certain population level (with the rate of growth increasing exponentially up to a ceiling). Each individual symptom should have its own threshold for when it starts to appear. For diseases that produce chemicals, the rate at which they do so should also be affected. But, from the first moment a disease appears in the body a timer starts to the time when the body will start producing antibodies, at which point the population will decline rapidly. This way, even if a person is reinfected the disease will be eliminated before it becomes symptomatic. Also, antibodies will develop if the disease is cured by medicine or any other way. The population should increase whenever you're near a source of it, instead of the disease only being caught a single time. Also, the body should deplete the population at a certain rate even before antibodies develop, so you won't catch a disease just from a single germ.
5b. Now, for treatments. I suggest a system with three tiers of drugs. The first tier should be basic drugs that will gradually cure non-resistant diseases. They should be readily available from the med dispensers, and not too difficult to produce, like spaceacillin, with one for each class of contagion except for prions (same for the next tier). Antifungals should be harder to acquire on every level than others. The second tier should be harder. One type may require a highly complex chem recipe, another a mutated plant, or only be available from space traders for not inconsequential amounts of money. This type will treat drug resistant strains (with any strain having a small chance to gain drug resistance whenever treated with a drug) but against very drug resistant strains, they'll only stall the disease at best. Tier three drugs should have nasty side effects, and only be findable in dangerous places, like derelicts and enemy stations, but will cure any disease of their class. The ambulance derelict seems a good place for one or two. Finally a good reason for people to fuck off into space for a while! Even prions should have a cure on this level, but it should be somewhere very hard to get. And maybe include Panacea too? Maybe make it creatable at the alchemical circle? But again, not easily.
5c. This is somewhat unrelated, but I'd also like to see an expanded set of organs, like the heart that was recently added. Mainly, this is to provide a greater variety of complex symptoms. And also, for those organs to be removable, transplantable, replacable with synthetic versions, and/or sellable. Grown synthetic organs can be affected by diseases, but cybernetic replacements will not, at the cost of some of them being not as good (There's surely plenty of ways for roboticists to help here, not just with cybernetic organs, but also with modules that enhance biological ones. But this is already bloated enough without adding another entire section to it). As far as procedure goes, since there are only so many areas you can target on the body, I think adopting a system I saw on the tgstation wiki might work. According to the guide, they use a drapes item on a patient to indicate which part of the body or organ they're targeting. Sounds simple enough. Organs should also be functional, and have health, which decays if they're not in a living person. There should also be contagion traits that damage them specifically, and they should have a small chance to take damage from strong blows to the body part they're in. This already exists with the brain being able to take damage from concussions or other sources. Basically, that, but applied to everything. Also, have drugs that can heal them (unless their health is below a certain level. They should also heal themselves over time, faster if they're close to full health.) and support their functions, like mannitol and oculine. Here are some of my suggestions.
Brain: Same as it is now.
Eyes: Damage affects vision. Eyes may be removed and replaced with artificial eyes. Using a screwdriver on thermal scanners, meson scanners, etc. to take them apart, then combining them with wire and artificial eyes should produce eyes that provide that type of sight without taking up the glasses inventory slot.
Heart: Damaged by sugar overdose and cholesterol. Very robust, causing problems only at low health so long as the lungs are providing air, but failure causes... well, heart failure, a condition that must be cured in order for the lungs to have any effect. Which brings us to...
Lungs: Damaged by very hot or cold air. Have a person take 8 suffocation damage per biotick, with the lungs healing 0.5*(Kpa of oxygen in air)*health of lungs (100%->0%) up to a limit of 20. This is to match up with the way things currently work, where you need 16 Kpa of O2 in the air to breathe properly. That also means that the lungs will have to be quite hardy, because you'll start slowly suffocating when they're at 80%.
Liver: Similar to the lungs, but for toxin damage. At full health, let it have a 20% chance to heal 1 point of toxin damage per biotick, with a decreasing chance until half health. Below half health, have a rising chance to inflict 1 toxin damage up to a 100% chance at 0 health.
Kidneys: Damaged by having a person's bloodstream container near the limit of its capacity. At about 80% health, this will start to affect the depletion rate of all chemicals, so they take longer to leave your system. Sounds beneficial? Well, in exchange, once your kidneys reach that level, suddenly a lot of chemicals that you couldn't overdose on, now suddenly you can, and the lower their health the lower all overdose thresholds become. Also, without these, you can't pee. This has no effect on boosts to depletion rate caused by charcoal or calomel.
Thymus: Also know as "the what?" It's a key organ in the immune system. So, as it loses health, it takes longer to develop antibodies.
5d. Just a few more random things having to do with health. First, fevers. They should happen automatically, with raised temperatures slowing diseases. Have pyretic drugs, which will take you to the safe limit for your body's temperature, or people can try the sauna for the same effect. Second, cryos. The cold should halt diseases in their tracks.
6. Symptoms and Interactions
So, I've talked about diseases and plants using the same genetic traits as are found in mutations, but these are very different things that behave differently in gameplay. Obviously, there has to be a difference in their effects. Also, for diseases, there's going to have to be a number of different ways that symptoms interact to create just the right blend. I'll be covering examples of both of those here, but there are tons of possibilities. Note that not all symptoms are things that should show up on a health scan. It'd get very crowded. For example, you can only have lung inflammation if you have a lower respiratory infection, so only the latter should show up. This will also preserve some of the surprises about what kind of disease you've got.
Current mutations
Heat resistance: (In diseases) Will no longer be slowed by fevers or similar defenses. Will not be killed by cooking. Bacteria and fungi will also grow faster the higher the temperature is.
Cold resistance: (In diseases) Will no longer be stopped by cryo tubes or other sources of cold.
Alcohol resistance: (In diseases) Where an infection may be living on a tile, in a splash of blood, etc. this trait will prevent it from being killed by common space cleaning chemicals.
Booster A1, B2, etc.: (In plants) Matches up with current plant mutations for high yield, fast maturation, etc. (In diseases) Increased rate of growth, with boosts equivalent to yield and maturation rate having a multiplicative effect.
Immolation: (In diseases) Causes symptom, hyperpyrexia. Very high body temperature, causes slow burn damage. Treat with salicylic acid.
Cryokinesis: (In diseases) Prevents fever. At higher levels of infection, may lead to hypothermia. Treat with pyretics.
X-ray vision: (In diseases) Very small amount of radiation generated. "Radioactive" trait does same thing, but also damages the disease.
Bad gas: (In diseases) Same effect as when a human has it.
Obesity: (In diseases) Slows disease growth, but makes it more resistant to drugs.
SMES human/organism: (In diseases) In tests, if you zap it, it will zap back. Causes symptom: Myoclonic jerk. Replaces effect of cough, causing you to spasm and randomly drop items.
Epilepsy: (In diseases) Makes germs more mobile, reducing effectiveness of immune system. (In plants-native:lasher) Causes plant to jerk about, attacking nearby people.
Cloak of Darkness: (In diseases) Disease will not manifest symptoms, allowing carrier to spread it far and wide. Delays antibody development.
New mutations:
Air resistance: (In diseases-native:cold, flu) Allows disease to be spread through the air, just by being close to someone. However, it will have to be very close, and for more than just a second or two unless another trait is combined with this. (In humans) Reduces the amount of chemicals taken in through smoke, for better or for worse.
Lung-attacking: (In diseases-native:cold, flu) Causes symptom, lower respiratory infection. Causes coughing, which will spread germs that have the Air resistance trait. Very mildly damages lung. Coughing reduces the suffocation damage healed by lungs each biotick. The lower lung health is, the more often you cough, sometimes up to multiple types per biotick. But it shouldn't make you drop things. That's too much. Also, this trait alone shouldn't inflict much damage on lungs. This trait is common cold-level.
Inflammation: (In diseases-native:flu) Causes muscle fatigue, lowering movement and stamina. Worsens some organ-attacking traits, not eyes. (In humans) Same.
Bacteriophage: (In diseases) The disease will attack bacterial diseases. (In humans) Large increase to pre-antibody immune strength against bacteria.
Red Queen trait: (In diseases) Allows disease to rapidly alter its chemical defenses, preventing the immune system from fighting it. (In humans) Greatly increases immune system strength, and counters same trait in diseases. (In plants) Increases chance of changing into mutant crop.
Water resistant: (In diseases) Allows disease to spread through contact with infected blood. Just being next to a blood stain when it appears is enough. Also, if a person explodes into gibs, the disease will be spread over a wide area in that moment. Combined with air resistance, infected blood will continue to infect a small area around it. (In humans) Reduces the amount of chemicals taken in through skin, for better or for worse.
Space resistant: (In diseases) Allows disease to exist in zero atmos conditions. May be transmitted in dust form onto a miner's clothes when working on an asteroid. In which case, they'll become infected if they take off their helmets. Also allows transmission from clothes to nearby people, but not person to person airborne transmission. (In humans) Reduces whatever effects exposure to low pressure areas causes. Allows holding breath longer in space?
Skin permeable: (In diseases) Allows transmission through skin contact. Punching someone, shaking them to wake them up, anything. (In humans) When touching someone, a small dose of any reagents present in blood will transfer over, with an alert in the chat box of some kind.
Drug resistance: (In diseases) Reduces effectiveness of all anti-disease medicines. Tier 1 medicines ineffective. (In humans) Reduces toxin damage from all sources by 1.
Drug resistance +: (In diseases) Reduces effectiveness of all anti-disease medicines. Tier 2 medicines greatly reduced in effectiveness. (In humans) Eliminates overdose thresholds.
Mercury enzyme: (In all) Rapidly depletes mercury in blood stream, replaces with mercury enzyme, which boosts stamina/growth rate.
Brain-attacking: (In diseases-native:space madness, necrotic degeneration, berserker, space kuru, etc.) Damages brain, enables various mental symptoms.
Auditory nerve alteration: (In diseases-native:space madness) Disrupts balance, making everything look upside-down. (In humans) Enhances hearing. Loud noises will show up with their coordinates of origin in the chat box.
Higher fuction suppression: (In diseases-native:necrotic degeneration) Random stun. At high levels of brain damage, body will start to be controlled by an NPC for short periods, then longer periods, then always. (In humans) Prevents you from using complex equipment, as if you were severely brain-damaged, but greatly increases all melee damage.
Spaceacillin production: (native:disease Space fungus) Produces spaceacillin. Requires penam group precursor.
Penam group precursor: (native:disease Space fungus) Enables production of spaceacillin, and other similar chemicals.
DNA reverse transcriptase: (In diseases) Chance to transfer each individual genetic trait from disease to host. Not a good thing generally. Many disease traits have the same effect in humans as in the diseases themselves. Diseases with these traits should be weighted to only rarely spawn with traits that would be beneficial to humans. If disease strain trait is transferred, disease population growth skyrockets, but if the disease is eliminated, that trait will be too. Traits transferred in this way cannot be eliminated with mutadone, only by the use of the geneticists' weak precision radiation emitters.
??? metabolic pathway: Replace the ??? with various bits of technobabble. Traits like this, of which there should be quite a few, should be a big part of pathology research. Each of them should generally boost a disease's virulence. But, these also represent weakpoints in the diseases, where each ??? corresponds to a separate chemical that poisons it. Not enough to kill it instantly, but enough to make resisted drugs effective again. Unlike other traits, these should be directly detectable by pathology lab scans, while being unable to be researched, at least not so you could find out the weakness. When it is, it opens a new minigame. Solve it, and you get the answer. The minigame I'd propose is simple, both in the generation and the solving, though it may take a bit of time. You're given a list of between 4-8 values, each of which may have 4 different states. You're given a number of inputs, maybe 4-6, representing various chemicals, which will increment all of the values by 0-3, randomly determined at the start. The goal is to get all of the values to 0, representing a completed metabolic cycle. Generating the puzzle is easy. Just flip all the inputs from positive to negative, and apply a sequence (invisibly to the player). The player will have to reverse that sequence to solve it, though this is not a logic puzzle confined to a single solution. Not super difficult, but not easy either. This is meant to be not a necessity, but an option, and one you have to work for.
