NPC Auto-Evo Thread

Ohh ok.

Was the discovery of Species: ALRE of any use to the development of auto-evo?

AlexaiZ wrote:

Was the discovery of Species: ALRE of any use to the development of auto-evo?

The developer came around to chat for a while, but we agreed that since we're going for different goals, we both have to have different systems. He seemed fairly impressed with our workaround.

Hi evolutionists!

The engine is slowly taking shape, so I would like to take a moment and discuss the details of AutoEvo with you. I read through the Wiki article and some threads I found on the forum. The problem is, I still don't have a clear idea how this is supposed to work, much less how it's going to be implemented. I'll try and point out the major and minor problems I see with the specification. I will mainly refer to the relevant wiki articles, since those should be the final word anyway. If possible, I urge you to edit those articles to reflect the further discussion here.

Before I start, has anyone actually implemented AutoEvo as a prototype? Maybe in a scripting language or some simulation tool? If yes, great! If not, how do you know it will work? I don't want to be the party-pooper here, but the evolution is such a central part of Thrive and just "hoping" that it will work as described makes me a bit skeptical.

Anyway, here we go.

Niches
The Biomes page in the wiki talks about niches, but I had some problems with the article:

• Why introduce the term "slot" when it's replaced by "niche" shortly after? Two words for essentially the same thing should be avoided whereever possible. It makes the specification difficult to follow for newcomers.
  
• A niche is defined as a combination of creature size and food source. There's a nice list for the possible sizes, but the different food sources (or diets?) are vaguely implicated to be "herbivore", "detrivore" and so on.
  
• It would be helpful to have a short definition of the diets on the page itself. I had to google for the unusual terms like "autotroph" and "detrivore".
  
• A few more examples of niches would be good, especially to clarify the distinction between niches.
  

So much for the editorial stuff. Now about the concept of biomes and their niches:

• Is "food source" the same as "diet"? I feel like it's not (the first one being the available food, the latter being the required food), but it should be clarified in the article.
  
• Omnivores are a combination of herbivores and carnivores. Are there other such combinations? Like a decomposer that can also function as a carnivore if the need (or opportunity) arises?
  
• Is "midlarge carnivore" a completely different niche than "large carnivore"? If yes, do they still compete over a shared food source?
  
• What's the difference between detrivores and decomposers? The wikipedia article on detrivores suggests that it's the scale of the nutrient intake, but is that distinction important for us?
  
• Why do detrivores require a water environment?
  
• Are there niches for the microbe stage? If not, how does AutoEvo work then?
  

ETOs
Environmentally Transient Organisms get a passing note in the description of AutoEvo, but I promise you they need to be well fleshed-out before implementing the evolution. Introducing them after the fact will cause heaps of trouble if we don't plan around them.

• What does it mean for ETOs to be "in" a biome? Are they only ever in one biome at once? Does the population ever split up?
  
• Can omnivore ETOs fill the herbivore niche in one biome and the carnivore in another?
  
• What happens to dependent organisms when ETOs leave a biome? I.e., if an ETO is the only food source of a carnivore, does the carnivore die out if the ETO decides to leave?
  
• How do ETOs decide where to go next?
  

AutoEvo

• The "Retrospective" step is very nebulous. How am I, as a programmer, supposed to teach the computer to determine whether a species was affected by a mutation? What happens if there's no species affected by a mutation?
  
• What's a trophic level? Note: I already looked it up on Wikipedia, but stuff like this really needs a sentence or two. Don't assume we are all biologists.
  
• What's an "org"? I guess it's short for organism, but lingo like that makes a specification harder to read.
  

I would really appreciate if someone would address all these problems and questions. As I already said, it all sounds good on paper screen, but until someone shows me that it actually works in a program, I'll stay skeptical.

These are key problems, some of which I (and others) have thought over more since the page was written, but conclusions haven't really presented themselves. I thank you for bringing them to the forefront. I'll clarify the questions you have, and then discuss how we could make the system more manageable.

Spoiler:

We will most likely need to go through all of these problems one by one to iron out the concept once and for all. My most recent musings on biomes are as follows:

The old concept of a biome was a structured food web. This would be pre-programmed into the definition of a biome along with the physical factors that define the biome (sunlight, height, seasonality, etc.)
I now think that this might be too restrictive and rigid to work well, especially with very alien biomes that may appear. Programming wise, I don't know if it's easier to implement rigid structures with lots of little caveats for special cases, or to create a more fluid system. Here's the more fluid system I've been thinking about:

With the newer concept of compound management, we can have a really good understanding of how to define a creature's diet. All parts in the OE are made out of compounds ('bone' is made of bone, heart and limb muscle from 'muscle', exoskeletal parts from 'chitin'). All organisms have some digestive system. The parts in that system define what compounds they can eat. The basic diet of an organism simply consists of all compounds that its digestive system can process.
The basic diet is not what defines an organism's place in the environment, however, because an organism can't eat what it can't obtain. An organism has an actual diet that consists of all other organsms that it eats.
To determine the actual diets of organisms, we need to start out with plants. Plants have their own special, most likely flawed evolution rules as well as those of regular animals. The nice thing is that plants can live independently of animal life, so their presence in a biome can be generated fairly easily without animals there. Once the plants have been generated in a biome, animals can join in. Animals will eat the most convenient species that fulfill the needs of their basic diet. I'm trailing off here, so I'll continue on this later. Please, if you have any ideas, chime in.

~sciocont wrote:

Programming wise, I don't know if it's easier to implement rigid structures with lots of little caveats for special cases, or to create a more fluid system

This is really hard to answer in the general case. Usually, special cases are a bad thing. But there are degrees of special cases and ways to generalize so the special case practically disappears. The main question should be which model will yield the best results. If we make it too rigid, we may narrow down the possible eco systems too much. Too fluid, and it becomes chaotic, with whole biomes dying out because the system was unstable. Maybe the middle ground would be best, with a mostly fluid model and a few hard-coded constraints and safety mechanisms for stabilization.

Also, we should keep in mind that the quality of a model should be assessed from the player's point of view. Realism is good for a science project, but if the player can't perceive a difference between a simple and a complex model, we should go with the simple one.

As long as the specification is clear and complete (and I will interrogate you until it is), implementing it is mostly a question of time. Anyway, here are the inevitable follow-up questions / remarks.

Compounds

• So, organisms are characterized by what compounds they can consume and what compounds they produce, right?
  
• Will it be necessary to distinguish between "required" and "optional" diet? For example, do you want to have organisms that require at least 2 units of chitin and 3 units of "muscle or blood", or does a simple diet plan like "3 units of chitin, muscle or blood" suffice? Note that this also has consequences for gameplay. We could force the player to seek out specific food sources to fulfill their creature's needs.
  
• I guess we will need to distinguish between produced compounds that are released back into the environment ("What a pile of compounds!") and compounds that remain within the creatures body until it is harvested / killed (muscle / blood).
  
• Are there restrictions on what compounds can be converted into which products? From a biology standpoint it would be strange for a creature to only consume water and then excrete out chitin. If we want to forbid such a wonder, we'll need a graph of the possible conversions.
  

Biomes

• I read your post about Autotroph Evolution, where you mention maps for things like nutrients, precipitation, sunlight, etc. Do we need this kind of detail? It would be far easier to have the compounds be uniformly distributed throughout a biome.
  
• When and how will Compounds in a biome be consumed during each generation? If we just loop over the species in an arbitrary manner, it's "first come, first serve", penalizing the later species if there's not enough food for everyone. To aviod that, compounds need to be distributed proportionately to all species, but proportionately to what? And what about multivores ("look, Ma, I made a word!")? How would they decide which compounds to consume and how much of each?
  
• How will we "seed" biomes to create a starting point for the evolution?
  

• So, organisms are characterized by what compounds they can consume and what compounds they produce, right?
  

Yes, althrough what organisms they can kill to eat would also be important. We could calculate which organisms eat wich ones by the simulation (the one that comes out alive eats is able to feed on the other one)

• Will it be necessary to distinguish between "required" and "optional" diet? For example, do you want to have organisms that require at least 2 units of chitin and 3 units of "muscle or blood", or does a simple diet plan like "3 units of chitin, muscle or blood" suffice? Note that this also has consequences for gameplay. We could force the player to seek out specific food sources to fulfill their creature's needs.
  

Any diet would be enough, with a note: Depending on the mouth and digestive system, each compound will be used more or less. Chitin is probably quite hard to digest, so either it has a really low rate or the creature has an amazing stomach. The total nutrients ingested at the end of the calculations must be the same.

• Are there restrictions on what compounds can be converted into which products? From a biology standpoint it would be strange for a creature to only consume water and then excrete out chitin. If we want to forbid such a wonder, we'll need a graph of the possible conversions.
  

Water is a special case, and is factored outside of the rest of the compounds. However, for all other compounds, i dont see any reason why not to allow to go from any compound to any other compound.

• I read your post about Autotroph Evolution, where you mention maps for things like nutrients, precipitation, sunlight, etc. Do we need this kind of detail? It would be far easier to have the compounds be uniformly distributed throughout a biome.
  

I agree.


I hope this post made sense.

Daniferrito wrote:

Water is a special case, and is factored outside of the rest of the compounds.

Why? From an implementation standpoint, it would make perfect sense to treat everything an organism needs as a compound (resource may be an appropriate general term). That would include water and even light. Each turn, we can seed those compounds to simulate precipitation and sunshine. That way, we don't have to treat autotrophs as a special case, they just use those seeded compounds instead of anything generated by other organisms. This would also open up symbiotic relationships between luminescent organisms and those using photosynthesis in an emergent way.

Yes, but then we would need to define what compounds can convert into other compounds. Each organism would need specific amounts of each compounds (something like 2 lts of water and 1 Kg of effective biomatter, or 1 lt of water, 500g of nutrients from the floor and some light)

Ok, how about this:

• Define 3 resources: energy, water, and nutrients
  
• Digesting one unit of compound C gives E units of energy, W units of water and N units of nutrients
  
• Producing a compound C' takes E' units of energy, W' units of water and N' units of nutrients
  

So, "digesting" the compound sunlight through photosynthesis gives the resource energy and digesting the compound water gives the resource water. From these three resources, an organism can then produce the compounds it requires. A plant producing cellulose might need 2 units of water, 2 units of nutrients and 1 unit of energy.

Disclaimer: I'm not trying to change the plans you guys have for AutoEvo. I'm just trying to break your ideas down to clearly defined, simple data structures and procedures so that they can be implemented. So if I write about anything that has been discussed and decided on before, please tell me.

That would be it. The actual nembers of how much each unit of compound gives off depends on the compound itself and on the digestive system. Water would be extremelly easy to digest, and some other substances, like bones or woddy material would need very good digestive systems to be able to digest it and get usefull resources from it.

Autotroph distribution maps are important because the plants living in a space (living on a terrain tile) change the properties of that space (light, the number of nutrients available), and other features (water close by, a steep cliff) change the properties as well.

I don't quite understand this question:

Quote :

When and how will Compounds in a biome be consumed during each generation? If we just loop over the species in an arbitrary manner, it's "first come, first serve", penalizing the later species if there's not enough food for everyone. To aviod that, compounds need to be distributed proportionately to all species, but proportionately to what? And what about multivores ("look, Ma, I made a word!")? How would they decide which compounds to consume and how much of each?

Are you asking when the nutrient map would change?

There should be no restrictions on what compounds can be changed into other compounds, since all of the compounds we're working with are fairly nonspecific. So long as an animal gets enough food, it can keep growing and living. As for plants, they all use the same process to get food, so we don't have to worry about their digestion in the same way as animals.
The digestive system of an animal can evolve to digest a many different compounds with varying degrees of efficiency- efficiency meaning how much energy they put in per unit of compound for digestion of that compound.

To seed a biome, we just need to populate it with a few plants that can live in it according to its geophysical conditions.

In respect to diet, there are some general rules that underlay what eats what, and how much.
Animals will evolve into a dietary niche depending on two factors:
competition, or how many other animals are trying to eat the same thing- the animals try to minimize this
availability, or the total amount of other organisms that the animal can eat- this is to be maximized.

In a biome, a dynamic food web is created by linking every consumer species to every species it consumes. A grain-eating animal would be linked to all plants that produce grains. The rule for this is
[species] can digest [basic diet]
therefore, [species] can eat all orgs in [actual diet]

The complex part of this, the part that makes a niche, is the organism's niche diet. The niche diet consists of all organisms the species eats in practice. This means it's all of the organisms that the creature can find, catch, and properly prepare for eating. "properly prepare" is a bit difficult to explain, and may be difficult to implement. It means that if you're trying to eat a snail, you have to either break open it's shell, pull it out of the shell, or be able to digest it shell and all. Hopefully that example is descriptive enough to convey exactly what is meant by "properly prepare".

These three factors should be the basis for all mutations, except those that arise specifically from the geophysical properties of the biome (mutations to deal with the climate). This means that diet-specific mutations can either help the organism digest a food, or find, catch, or properly prepare food, or help the organism hide, evade capture, or protect itself from being prepared for food.

I would recommend putting the final and agreed upon concept from here on to the wiki, so people know what is the Current Concept. On the forums its hard to tell.

Also, although I usually don't partake in these discussions, this model seems very simple and intuitive. So basically, organisms' diets are based off of what compounds they can digest, and since all things are made from the same set of compounds, you only have to widen the number of compounds you can digest to widen the organisms you can eat?

Are you asking when the nutrient map would change?

He means who gets to eat first. Lets put an example:
There are 200Kg of plants avaible in a zone, and two possible creatures that could eat it, which are really similar in characteristics.
First creature eats 150Kg of plants. Second creature tries to eat, but as there are only 50Kg of plants left, it only gets to eat those. However, if we do that the other way around, the second creature would get 150Kg of plans, and the first creature the remaining 50Kg.

Actually, now that i see this as an example, i dont think this will be a problem. In the previous example, next time the creatures try to eat, there wont be any food left, and both will die of starvation anyway. For a ecosystem to work properly, only a small percentage of a food source should get eaten each time, so it can regrow for next time. However, this efectivelly means that there wont be any fight for resources in any case.

There should be no restrictions...

Except water. There is nothing else that you can get out of water, but you still need to consume it. A lot.

By properly prepare, i suppose you also mean killing the creature..

Edit: @Nick: Yes, that is what i understaund as well. However, there cannot be any kind of fight over a certain food, as if there is actually shortage of a certain food it will probably get delepted in a few cycles. The exception to this is evolutionary fight from the predator and the prey, as the prey tries to die less and the predator tries to kill more. A prey may become unavaible for the predator to eat so it gets forced to look for a diferent food source.

NickTheNick wrote:

I would recommend putting the final and agreed upon concept from here on to the wiki, so people know what is the Current Concept. On the forums its hard to tell.

Also, although I usually don't partake in these discussions, this model seems very simple and intuitive. So basically, organisms' diets are based off of what compounds they can digest, and since all things are made from the same set of compounds, you only have to widen the number of compounds you can digest to widen the organisms you can eat?

Yes. That basis is very simple. It's the interactions that it creates that are extremely complex.

Daniferrito wrote:

He means who gets to eat first. Lets put an example:
There are 200Kg of plants avaible in a zone, and two possible creatures that could eat it, which are really similar in characteristics.
First creature eats 150Kg of plants. Second creature tries to eat, but as there are only 50Kg of plants left, it only gets to eat those. However, if we do that the other way around, the second creature would get 150Kg of plans, and the first creature the remaining 50Kg.

Actually, now that i see this as an example, i dont think this will be a problem. In the previous example, next time the creatures try to eat, there wont be any food left, and both will die of starvation anyway. For a ecosystem to work properly, only a small percentage of a food source should get eaten each time, so it can regrow for next time. However, this efectivelly means that there wont be any fight for resources in any case.

This is the basics of competition. Each species wants the largest population possible, and can obtain more resources through broadening the number of other species it can eat. However, it can also try to crowd out another species from a resource, taking that resource for itself.
We need to keep in mind that not every single org gets eaten. In fact, most don't in any given generation. This is because organisms use the three strategies from my last post to avoid it.

~sciocont wrote:

This is the basics of competition. Each species wants the largest population possible, and can obtain more resources through broadening the number of other species it can eat. However, it can also try to crowd out another species from a resource, taking that resource for itself.
We need to keep in mind that not every single org gets eaten. In fact, most don't in any given generation. This is because organisms use the three strategies from my last post to avoid it.

Yes, to be stable it must. What i meant is that as there is always surviving prey, you never run out of food and the problem stated by Nimbal is not present.

So I realize that this thread has been untouched for 7 months, but I'm new around here and having just read the entirety of this thread as well as a few others and almost all of the wiki, I have some thoughts on the topics discussed here.


Firstly, in regards to number of evolutions per generation, some of what was discussed here is not reflected in the wiki page. Namely, the wiki still says that only one mutation can occur per generation cycle, whereas here the option of having probabilistic mutation selection was discussed (Each species is given a weighted chance to evolve based on it's population size and threat, allowing for multiple simultaneous mutations but trending towards very few per cycle 'on average'.) Was this established as the actual methodology for auto-evolution selection?


On that note, there were all sorts of ideas tossed around about threat, and calculating threat levels, and very nebulous ideas about what it was and how it could be measured but I saw nothing concrete come out of it. To that end, I have some ideas on the topic.

Instead of hardcoding a complex formula to determine how threatened a population is (and going through a lot of effort to find a formula that 'works'), why not teach the population manager how to determine if a population is threatened?

It would require quite a bit of work to set up I imagine, but if you generalized the process it would leave you with a very robust and versatile function that can accurately gauge how threatened every organism in a biome is, and feed that output into the mutation algorithm.

Explanation:

I also have another idea regarding how the auto-evo system chooses which evolution occurs at a given moment, but I'll save that for after this concept has been discussed.