A Roadmap for the Microbial Stage - What Does Thrive Need?

Looking through concepts, I sometimes get overwhelmed because it’s hard to keep track of what exact purpose said concept serves in the grand scheme of the game. It is difficult to zoom out and see how each mechanic to be planned will result in a coherent phase of life’s evolutionary history. The GDD helps a bit with this, but I find it to be too patchy a lot of times, covering some details but neglecting others. And besides, the GDD seems to describe Thrive as it currently plays more than it does explain where each concept fits.

As such, I wanted to have a thought experiment focusing on what exactly Thrive needs as a baseline from each of its components - where the agent/toxin system, endosymbiosis, environmental tolerances, etc. - fit in so to understand how each individual part of Thrive will work with other components to create a whole. In other words, instead of defining how each part of Thrive will work, I will be focusing on how these factors should interact to create an engaging and realistic game experience.

I will focus primarily on the prokaryotic part of the Microbe Stage for now. If I feel like this has been a productive thought experiment, I will consider the Eukaryotic part of the Microbe Stage later. Keep in mind that this isn’t meant to be a definitive concept on how every system of Thrive should work out – rather, it is an analysis of where certain mechanics should and will have a heavy role. For example, I will discuss the agent/toxin system here, but I won’t be focusing on how it should work in the game; that would best be discussed in another topic. I will instead be highlighting where the concept should fit in within the microbial stage, and as such, what purpose it will fill in the grand scheme of things.

BACKGROUND INFORMATION

I will be using the book “Evolution on Planet Earth: The Impact of the Physical Environment” edited by Rothschild and Adrian M. Lister, as a source of information. I heavily recommend it to all, as it does a great job of depicting how microbes on planet Earth developed in our earliest moments, covering scarcely discussed aspects of our history.

Life likely evolved early on Earth (4.2 – 3.8 billion years ago) on a planet very different from our own. The creation of the Moon through a planetary collision, as well as continuous collisions from rocky material, likely meant that the very early ocean was incredibly warm. Life was likely largely thermophilic, having formed near alkaline vents and living in a heated ocean. However, the oceans cooled off rather quickly – otherwise, a lot of the water on Earth would have evaporated and runoff from our primitive atmosphere – allowing different forms of metabolism to form by around 3.7 bya.

Once temperatures cooled off, it is generally believed that sulphuric-metabolism evolved first and then anoxygenic photosynthesis followed, but we aren’t 100% sure. Regardless, anoxygenic photosynthesis evolved rather early in life, around 3.6ish bya, and much of the carbon cycle was rather well-developed by then. Rubisco, the iconic photosynthesis enzyme crucial for oxygenic photosynthesis, probably evolved in response to life’s inherent adversity to oxygen; perhaps rubisco served as a method for cells to get rid of oxygen rapidly, or perhaps rubisco was evolved in response to toxin warfare amongst bacteria from another cell which utilized oxygen-based poison. Rubisco allowed microbes to colonize shallower and less chemically-populated areas – before then, microbial communities were probably limited to specialists evolved to survive around various chemolithotrophic processes, such as sulphur or iron. The arrival of cyanobacteria and their oxygenic photosynthesis likely meant the rapid proliferation of cyanobacteria and a huge shift in ecological dynamics as they oxygenated local areas, although it would be a long while before enough oxygen is created to render the entire atmosphere aerobic. So pretty soon after life first evolved, photosynthesis, the carbon cycle, and the sulphur cycle could have been in place.

Another important biogeochemical process to bring up is the Nitrogen cycle, which evolved in multiple steps in response to the available amount of Nitrogen on Earth. Nitrogen is Earth’s most abundant gas and is endlessly important for life in the creation of proteins, but life cannot easily utilize atmospheric Nitrogen (N2); most lifeforms depend on breaking more accessible forms of Nitrogen, such as ammonia, nitrate, and nitrite, to meet their needs. There was a decent supply of accessible nitrogen in the ecosystems of natural Earth from lightning strikes, impacts, and other forms of chemical processes in those forms, with cells preferring ammonia due to how easy it is to breakdown – once this ammonia dwindled as life spread however, innovation needed to happen. Ammonification developed, which essentially is what decomposers do – break down organic (dead) material to create ammonia, and so did the reduction of nitrate and nitrite. The next step of the nitrogen cycle to evolve was likely denitrification, which essentially is utilizing nitrite and nitrate to generate ATP with Nitrogen (N2) as a waste product (not as efficiently as aerobic respiration). Although one form of bacteria is able to denitrify aerobically, the enzyme responsible for denitrification is incredibly sensitive to oxygen, meaning the process can be thought of as strictly anaerobic. Finally, nitrogen fixation, which is the ability of organisms to directly use N2 to create ammonia, evolved. Nitrogen fixation is also heavily sensitive to oxygen, but cyanobacteria, and another bacteria symbiotically attached to plants, have evolved the capability to perform fixation in aerobic environments. The final stage of the nitrogen cycle to evolve is nitrification, which essentially is autotropism based on nitrogen; being aerobic, it likely showed up after the arrival of oxygenic photosynthesis.

Aerobic respiration also evolved rather quickly after the arrival of cyanobacteria; in fact, oxygenic photosynthesis and aerobic processes appear to have emerged in almost the same geological instant. Again, the oxygenation of the entire atmosphere would be a while away from the emergence of oxygenic photosynthesis – atmospheric oxygen concentration was around 3% until the Cambrian Explosion, when it jumped to around 13% before rising through fluctuations to modern levels. However, localized oxygen contents, such as near the cyanobacteria dominated ocean surface layers, were high enough to support a healthy population of aerobes. Obligate anaerobes, such as red sulphur bacteria, were relegated to the open and lower levels of the oceans. The oxygenation of the entire ocean likely occurred around 600 million years ago.

PROGRESSION OF THRIVE IN THE MICROBAL STAGE

Looking at nature’s example, I think the chronological challenges a player should face can be summed up in 6 steps…

The Opening Act: Establishing a Foothold – At this point, life is rather low energy and inefficient, but much metabolic diversity is present. Based on which compounds are available on your planet and environmental conditions, make the best use of whatever anaerobic metabolic pathways you have to establish a decent population size, while competing with other prokaryotes through reproduction rates, auto-evo resource acquisition, and agent warfare as you stake out a place on a young planet.

  • Life is very simple and low energy, so much of the gameplay is based on seeing what resources are most abundant and competing with other species through Auto-Evo to get a sizable population. The first few turns of a Civilization game comes to mind; you can’t do much yet, but can set yourself up rather well for the stages to come as you see what environment surrounds you and take advantage of early leads.
  • Because there isn’t much to do, this part of the Microbe Stage shouldn’t take too long, and the player’s gameplay at this point should be rather short and straight to it. Explore the patches around you, and once you find a source of energy you want, start adapting.
  • The two biggest obstacles in the way of the player are adapting to the environment and toxins from other cells. I think this part of the stage should serve as an introduction to the toxicology and immunology aspect of the game, and toxins should generally be the major weapon utilized by species.

Handling the Arrival of Oxygen – The first and, eventually, most consequential major environmental shift on the planet, the decision a player makes in this moment will dictate a good chunk of the Microbe Stage. Although oxygen remains largely exclusive to the surface patches, it unmistakably begins spreading.

  • Oxygen represents a hurdle to be overcome which has immense benefits on the other side, as many metabolic strategies are supercharged once they become aerobic. Also, the metabolosome will become useful.
  • Players will make the choice between being anaerobic or aerobic. Realistically, unless a specific lifestyle choice or challenge is sought out by the player, most players will eventually gravitate towards aerobic activity, which is fine. The goal is to become a complex multicellular organism, which requires a bunch of ATP. But this will add some flavor to the story of life on your planet. Did life largely remain anaerobic and relegated to the abyss on the planet before rapidly proliferating in oxygenic environments, or did life rapidly shift to utilizing oxygen?
  • There should be metabolic pathways which are obligatorily anaerobic (can only be done in anaerobic environments), metabolic pathways which can be upgraded to be aerobic, and fully-aerobic processes, like the metabolosome. The first ensures some consequences to your choices, the second allows a player an option to gradually transition to an aerobic environment, and the last represents the next “stage” of evolution.

Supercharging your Metabolism with Oxygen – With oxygen now fully present, upgrade your metabolic pathways to take advantage of aerobic respiration. Develop a proficient metabolosome, which sets you steaming towards a path of complexity.

  • Upgrading parts will become important at this point, with certain metabolic pathways having aerobic options that generally provide more ATP. I think metabolosomes should be heavily encouraged here and should generally be the best option since it makes things as smooth as possible; oxygenic respiration has been demonstrated to by far be the most efficient form of energy generation.
  • A challenge to becoming aerobic could be fluctuating oxygen levels at first and a limited amount of patches your species can live in, being dependent on cyanobacteria (if anything goes wrong in these patches, you’re limited in mobility). So utilizing oxygen can represent a more high-risk and unstable option at first than utilizing anaerobic pathways, but with high rewards allowing more complex function.

Endosymbiosis and Acquiring the Nucleus – Acquire your first proper organelle either through endosymbiosis or upgrades, which will provide your cell a figurative leap in the face of its competition.

  • Endosymbiosis represents a more difficult to pull off yet more rewarding and less expensive leap when compared to traditional organelle upgrades. You can just upgrade a metabolosome a lot of times to reach the capacity of becoming a mitochondria, but a player who knows what they want can just go through the process of endosymbiosis for a cheaper and more immediately beneficial process.
  • Endosymbiosis in reality probably only occurred twice, the first event creating the mitochondria and the second event creating the chloroplast. I think players will be incentivized to act in this way because mitochondria and chloroplasts are the most versatile and universally useful organelles, so players might prefer acquiring them first in order to support whatever other complex cell functions they have an eye for.

Acquiring and Finetuning Your Organelles – With new capabilities bestowed by the nucleus, being able to fully adapt your parts into incredibly efficient organelles, alongside the other unique adaptations eukaryotes are able to manage, having the nucleus represents the peak of the Microbe stage.

  • This ties into the benefits of being a eukaryote, which is a rather complex and multi-faceted conversation. Regardless, this should represent the endgame of the Microbe Stage, where you battle other unique organisms to establish a place in the food web.

The scope of this particular topic – prokaryotic gameplay – is limited to parts 1, 2, 3, and sections of 4 from the above breakdown. And from it, I think we can extract certain things about how prokaryotic gameplay should be structured. I have attached some broad suggestions outlining ways these conditions can be achieved. Of course, many of these suggestions have already been discussed and are already planned; again, this just presents a better format to think about where these concepts fit into the grand scheme of the cellular stage.

The Challenge of Unstable and Rapidly-Shifting Environmental Conditions

Especially near the beginning of the game, with temperature fluctuations, impact events, and variations on the availability of energy sources/resources, bacteria inhabited an unstable world and incredibly volatile environments. Players will have to pay attention to reports on patch conditions and rapidly shift their strategy in light of it until the environment stabilizes.

I think the two things at the beginning of the game which players will have to pay attention to is the availability of compounds and temperature in the wake of intense events, such as eruptions and impacts. Players will constantly have to keep in mind the temperature of the oceans, which starts heated due to the youth and bombardment of the planet and naturally starts cooling, but may unexpectedly increase due to random impacts. As such, they will have to be mindful of their environmental tolerances.

Along the above line of thought, I think the amount of iron, sulphur, available nitrogen, and light conditions should also fluctuate pretty dramatically near the game, as the biogeochemical cycles which offer stability today have yet to be established. Players will have to be quick on their feet as they deal with uncertainty – they might not be able to rely on a specific compound due to these fluctuations, so a player is incentivized to remain simple so that they can rapidly shift metabolic strategies. This adds some replayability to the Microbe Stage, as certain compounds will be more or less available across different playthroughs. In one save, iron might be most immediately available with very little available nitrogen or hydrogen sulfide, or hydrogen sulfide might be the most prevalent compound. In another save, perhaps the atmosphere remains hazy, so the amount of light reaching the patches isn’t as stable, delaying the arrival of photosynthesis. You get the picture – a certain level of variability in compounds can spice up gameplay.

Eventually, this variation will stabilize as biogeochemical processes emerge; Nitrogen, sulphur, and iron stabilize into their predictable patterns, and with less major impacts, temperature doesn’t fluctuate as extremely. This is when players can start organizing themselves around specific metabolic pathways instead of having to worry about being flexible and simple, increasing the complexity of life and establishing specific niches. Life becomes less a scramble and more an organized competition between species. The production of oxygen from oxygenic photosynthesis will introduce another dynamic which will be more definitive and permanent than previous fluctuations as life begins to become organized into aerobic and anaerobic distinctions, but will generally be the last “major” dramatic environmental shift a player will encounter.

So, as a summary – environmental tolerances and variability in how available resources are will be important aspects of diversifying the beginning of the microbial stage, with certain worlds/saves likely having different dominant metabolic resources in the early game. Players will have to make sure they are on top of their environmental tolerances to ensure their species has a good auto-evo number and spread, allowing them to rapidly pivot their strategy if they face a dire circumstance. As the world stabilizes, environmental tolerances and conditions will become the more familiar definers of habitable range we know them to be today.

The Need for a Pre & Post-Oxygenic World

Oxygen is an essential chapter in the evolution of life’s history, and thus, in Thrive, due to how simultaneously deadly and efficient oxygen-based respiration is. A transition of sorts from anaerobic to aerobic will likely characterize the majority of Thrive Microbe playthroughs on the route to later stages, which implies the existence of a pre-aerobic and post-aerobic game stage. This distinction is largely lacking in game because, one, oxygen isn’t toxic to unadapted organisms yet, and two, selections of aerobic and anaerobic processes aren’t clearly defined or exclusory. I think microbes are especially limited anaerobically – specifically, besides thylakoids, the only strictly anaerobic metabolic options are chemosynthesizing bacteria (hydrogen sulfide).

To properly implement a pre- and post-oxygenic world, we need three components – we need a few metabolic pathways which can only be performed in anaerobic conditions, we need a few metabolic pathways which can be either anaerobic or aerobic through upgrades, and we need strictly aerobic pathways. We obviously need the distinction between aerobes and anaerobes to be pretty clear so that players can’t just ignore oxygen, but we also need an in-between so that players are able to pull off a switch with some effort if they wish to. It would be annoying if a player was stuck as an anaerobe if they wanted to become aerobic – their organism would die in the presence of oxygen with their existing structure. So having certain metabolic pathways which can transition between the two conditions allows those players to pivot their morphology instead of having to completely switch from aerobic to anaerobic, which will be a rather difficult task to pull off.

The good news is that I think the game already has enough compounds in place to warrant sufficient diversity in anaerobic methods of respiration and energy-generation. First, various aerobic processes in the game already have anaerobic counterparts which are less productive, such as Iron-based metabolism. But second, I also would like to bring up the biogeochemical cycles on Earth which microbes play an essential part in. Specifically, I am focusing on Nitrogen and Sulfur (Hydrogen-Sulfide). There are various phases of the Nitrogen and Sulfur Cycle where microbes play a key part – and furthermore, parts of those phases are oftentimes facilitated by anaerobic organisms. In fact, certain organisms essentially respire Sulfur or Nitrogen (sulfate and nitrate/ite to be more exact), using it like we use oxygen to burn food into energy. Considering both Sulfur (hydrogen sulfide) and Nitrogen are already implemented, I think we have what we need to create an anerobic world, and in fact, create very basic and rudimentary forms of both the Sulfur and Nitrogen cycle.

Of course, we don’t need every single step of the Nitrogen or Sulphur cycle incorporated into the game – I think that would be unnecessary work, as I would hope that the later stages run on the assumption of stable biogeochemical processes (unless otherwise toggled by the player). In fact, I honestly think that we just need to add denitrification as a sort of precursor to metabolosomes and we’d be fine with nitrogen respiration and chemosynthesis, along with other forms of simplified respiration such as anaerobic iron respiration and such, to have a solid game. Adding other strategies, such as thermoplasts, sulfate respiration, radiotrophism, and more would be bonuses.

Also, as a general note: we can pace the arrival of oxygen by pacing the arrival of oxygenic photosynthesis. Anoxygenic photosynthesis, as performed by purple photosynthetic bacteria, is pretty similar to modern photosynthesis, except it doesn’t utilize water to split compounds, and thus, doesn’t create oxygen. Such processes can eventually evolve into oxygenic photosynthesis, thus resulting in the production of free oxygen in the atmosphere.

So, as a summary – we have what we need in the game to create a pre- and post- oxygenic world in the presence of sulfur and nitrogen in the game, it’s just about creating balanced parts and choosing which aspects of each biogeochemical cycle to represent in gameplay. Aerobic respiration will represent a challenge due to the inherent toxicity of oxygen, the initially limited number of habitats with sufficient oxygen in them, and the fact that as oxygen first arrives, its concentration will fluctuate. However, since oxygen represents an incredibly efficient and powerful respiration method, it makes sense that eventually, a player will want to adapt metabolosomes/mitochondria. Until then, anaerobic respiration will represent a low-energy, yet stable and widely-present option.

Toxins and Uptakes – Conflict in a Prokaryotic World

As previously mentioned, because prokaryotes are otherwise limited in how they compete with other microbial species, agent warfare and speed of nutrient uptake are essential weapons in the prokaryotic world. Here is a useful article for this purpose, which I will highlight important components from: Bacterial competition: surviving and thriving in the microbial jungle - PMC

There are generally two types of bacterial competition: scramble competition and contest competition. Scramble competition can basically be thought of as taking up as much as whatever limited resource you can before other cells take it up, almost like a crowd scrambling for paper bills dropped on the floor. Contest competition is a lot more direct and antagonistic, where cells essentially fight off other cells for a specific resource – think of the crowd-money example, except this time, people fight and steal money from each other as well. Thrive already simulates a simplified process of both forms of competition. Scramble competition shows up in auto-evo, where the organisms which are best able to process whatever resource they need wins. Contest competition currently is minimized in auto-evo calculations, but is represented in game, where different cells stab, poison, and eat each other.

It is important to note that these in-game interactions are a lot more predatory than they probably are in the real-world – in other words, whereas prokaryotes contest other prokaryotes to beat them off a nutrient, Thrive prokaryotes contest other prokaryotes in hopes of eating them. Predation is really a strategy perfected by eukaryotes. I don’t think this is a bad thing, as although predation among prokaryotes isn’t too realistic, the early parts of the microbe stage might be rather uneventful. And besides – as many people note – predation isn’t that effective of a strategy regardless. We previously amounted that as largely being the fault of a lack of balance and incomplete auto-evo – but perhaps it actually is a result of the nature of prokaryotic life.

Instead of completely locking out predation for prokaryotes if we want to make it as realistic as possible, perhaps we should just have it be rather unrewarding for prokaryotes and more rewarding for eukaryotes, instead focus the crux of contest competition between prokaryotes as being expressed through agent warfare. Players should be incentivized to interact with the agent system, and agent warfare should really matter in the prokaryotic part of the microbe stage much more than it does for the future stages of the game. Perhaps toxins and agents should have more intense impact on auto-evo numbers for prokaryotic/smaller organisms, therefore inherently making it so eukaryotes are generally less effected by agents.

Since predation is unrewarding for prokaryotes however, the question then is what incentive or bonus the player should receive when in engaging with the agent system. Of course, the “defense” side of agent warfare is pretty obvious, where players want to make sure they have some immunology built up so their auto-evo numbers don’t take a hit and so that they don’t get creamed in-game. But how should the player be rewarded for utilizing agents against other prokaryotes? Perhaps the game can somehow emphasize which cells you directly compete against for resources, and editing your toxins to be targeted towards those cells will provide you with auto-evo benefits which will clearly be highlighted in gameplay? Part of this can be solved by just making predation via toxin much more desirable – having the toxin particle move faster or effect more area or whatever – hence having it be useful for small microbes.

One small note I’d like to bring up is that toxin warfare becomes a tiny-bit less emphatic for eukaryotes because of their increased ability to develop resistance that doesn’t just involve them dying out and hopefully having the right mutation in place, like with bacteria. They naturally have a greater ability to cope with accumulated toxins – however, bacteria represent a crucial factor in our modern understanding of illnesses and infection, so we can’t just completely neglect their role. But that is a discussion to save for the eukaryotic aspect of this discussion.

Regardless, the big takeaway is that the toxin/agent system should be a very important tool for prokaryotes to utilize in modifying their auto-evo numbers, and concepts should account for the ability of agents to dramatically effect the rate at which important resources are taken up by competing bacteria. Instead of focusing on how to make general predation more useful for prokaryotes, perhaps we should instead focus on making agent warfare a more potent weapon for prokaryotes to use, and make traditional phagocytosis and predation more rewarding for eukaryotes. As such, the agent/toxin concept can be seen as the main weapon of choice for prokaryotes.

Endosymbiosis as a Worldbreaker

I created another post with a lot of relevant information for this topic here: How Early Cellular Life Evolved

We oftentimes think of the nucleus as being the organelle which provides eukaryotes such an edge over prokaryotes in terms of complexity, but perhaps that credit should instead be lent to mitochondria. The big struggle prokaryotes face when becoming larger/more complex is the fact that they are so limited in energy generation. Eukaryotes produce sooooo much more energy than a prokaryote because the mitochondria is basically the energy production of a cell without any of the maintenance costs; eukaryotes literarily have multiple copies of a whole cell’s worth of energy generation within themselves without any added costs, thus allowing intense generation of ATP.

As such, the endosymbiont event – or more specifically, the development of the mitochondria – should be seen as a definitive moment in the microbial stage, a leap in bound in the capacity and capabilities of cells. The first stop on the road to becoming multicellular.

I think this is one of the more potentially fleshed out “rough” concepts we have, so here is a discussion post related to endosymbiosis here: Endosymbiosis Concept - Feedback Based on Developer Forums Thread "Endosymbiosis Theory" - #22 by Deus

TAKEAWAY POINTS

Once again, this shouldn’t in anyway necessarily represent a complete list of what features should be included in the prokaryotic part of the microbial stage. It only represents what I think should characterize each aspect of the prokaryotic aspect of the unicellular stage – the beginning of the game. Here, we have a rough picture of what a player will generally experience in the game as a bacterium in the primordial origins of your planet…

The beginning of the microbe stage will be characterized by quick, extreme, and dramatic shifts in the environment, with impact events still frequent as the young solar system forms and with unestablished biogeochemical cycles. A heated ocean and fluctuating availability of various important compounds, such as nitrogen, iron, sulfur, and sunlight, means that life will initially be thermophilic and simple. The first struggle a player will face is maintaining the ability to be as flexible as possible, and yet, adequately taking advantage of whatever resources are available before competitors arrive; a balance between making sure to not be too specialized around a specific energy path, but also not letting go of opportunities to assert yourself as a dominant species in auto-evo, thus allowing you more flexibility in how you customize your cell in the near future, and affording you more of a safety net for experimentation. Similar to the beginning of a game of Civilization, while you don’t really have a lot of functions and game mechanics to interact with yet, how well you perform can have a strong impact on how well you keep up with your competition, and your first choices can strongly influence the near future.

A player is presented with many choices to make already. When they first spawn in, they’ll make choices based on what compounds they see are available. In a save where iron appears to be abundant, you’ll be drawn to putting on iron-based parts; in a save where sulphur is abundant, you’ll be placing sulphur-based parts. But will the player choose to begin adapting themselves around this energy path early on, or will they wait? Specializing in the early game will give you the reward of a huge auto-evo boost, but comes with the cost of the risk of having your resource eventually fluctuate downwards, and thus, the risk of extinction. Waiting comes with the risk of forgoing a potentially definitive energy resource, meaning if it turns out that resource remains highly prevalent, you’d be a latecomer – you’d have to compete with other more specialized cells when you break into competition for that resource. But, it allows you to be a lot more flexible in the future, so that, incase the resource doesn’t last for long, you won’t take much of a cut and will be able to transition away from it.

Then, as compounds appear to stabilize around their consistent levels, a battle of specialization will become more prevalent. Instead of you scrambling to even have a foot in the door of whatever fleeting compound there is, you will now have to compete against other cells who are seeking the same resource you are seeking. With agents and toxins now affordable, the first arms race breaks out as you stay on top of your immunology while constantly sharpening your own weaponry to fight against cells which share your niche. Other more complex behaviors, such as flagella-based motility and pilus, also start appearing – the emphasis has shifted away from just establishing a foothold and towards making as much space at the table as you can.

At some point, oxygenic photosynthesis will evolve, and another decision will have to be made. Should you immediately break into the surface patches and build up oxygen tolerance, living in cyanobacteria dominated waters, or will you avoid oxygen for now, preferring the less-energetic yet more expansive and diverse lower patches?

I think the above presents a rough outline of how the prokaryotic stage should look, and where each concept might have a place.

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