The Nucleus Paradox

Gameplay
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@Leinourdian has brought up an interesting thought about the nucleus which I want to bring up for discussion since the “nucleus paradox” has been a common issue of discussion for us here in Thrive.

He mentioned that we could change the nucleus a bit with three things…

  1. Make the nucleus less expensive energetically
  2. Have the nucleus have a more stringent unlock condition
  3. Have the nucleus provide a certain benefit to cells of larger sizes

To my knowledge, the nucleus evolved as a byproduct of endosymbiosis. In the exchange of genetic information between the primordial mitochondria and the host cell, it is believed that the membrane genome information of the mitochondria species got transferred to some host organisms accidentally. This could have resulted in the generation of a lipid membrane within the cell (lipids naturally form enclosed membranes). While this harmed undoubtedly harmed some host cells, the lipid membrane could have enclosed around the genetic information of certain hosts. This would have been an invaluable barrier against genetic parasites, allowing cells to maintain larger genomes with smaller chances of something going wrong.

I got the information above from a book which I forgot the name of at the current moment. I will edit this post when I remember the title and author.

Going back to the ideas, I think points 1 and 2 are pretty worthwhile, since the immense energy burden the organelle puts in a cell in Thrive currently makes it a very detrimental part to place in itself - hence making it a big balancing issue and hence making auto-evo treat it like it’s worth nothing. 3 is good too, but it needs careful thought.

I support the idea that we should attach an unlock condition to the nucleus based on reaching a certain size, as well as reducing the energy costs of the nucleus itself. Based on the information above, the nucleus wasn’t necessarily a costly organelle to develop; rather, it allowed the development of advanced biological process that are energy intensive. So placing down a nucleus shouldn’t necessarily be expensive, your organism should just have enough size to be able to host an internal structure like the nucleus in my opinion.

Looking at effects on gameplay, I think we can only benefit the player with these changes. One of the messier and less “accurate” components of Thrive is the fact that players have to prepare for the nucleus before placing it. While it presents a strategic consideration, I don’t think it’s really accurate to evolution as a whole, and as such, I don’t think we are encouraging realistic evolutionary strategies. I also think the detriments placed on auto-evo and AI by the nucleus are not worth whatever benefits we see currently.

Placing the constraints on the nucleus to be more unlock based can also make us control the pace of Thrive more. Depending on how quickly a player beelines energy production, they could easily get the nucleus within 10 generations. Having an unlock condition allows us to more clearly define a point in which the player should have access to the nucleus, therefore allowing us to accurately gauge and define the length of an average gameplay experience.

I will say though that having size as an unlock constraint could be a bit messy. Players could theoretically spam down larger parts until they reach the necessary size and then place the nucleus down. We could have the nucleus still take a good amount of energy to maintain of course, but not too much; that is the whole point of the unlock constraint after all, to lessen the energy burden of the nucleus. I guess rethinking the impact of size on osmoregulation would help, but that’s a whole conversation in itself.

Idea 3, as said before, requires more thought. I think we are due to consider things like non-linear osmoregulation scaling with size and surface area and volume, and I foresee the nucleus relating to that conversation. But for now, that will have to wait.

What do you guys think?

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Here are 3 solutions:

  1. The “Gamey” Approach
  • Introduce a arbitrary hardcoded size cap that unlocks adding nucleus
  • Nucleus should provide bonus MP, sufficient to incorporate one or two mitochondria (permnanently) once added, simulating its advantage against these “genetic parasites”
  • Upon placement in the editor, instantly award the bonus MP to the player, allowing them to immediately add mitochondria or some other organelle to aid in their survival in the next cycle
  • If an AI evolves a nucleus (roughly 1% chance rn), it should also gain instant access to this bonus MP on the “turn” it unlocks the nucleus. WHich woudl lead to a kind of life explosion. You could make it even more fun by splitting the species of the ai that unlocks them into several sub species right away, to then pressure the player to do the same.
  1. The Scientific Method
  • Investigate the evolutionary pressures that the theory suggests existed, then research the components used by these ‘genetic parasites’ and add them to the game, so the natural emergence of them (allegedly) leading to the nucleus innovation occurs and the playter has a reason to invest in the nucleus that actually helps them in game.
  1. The Unconventional Method
  • Implement endosymbiosis, add a small chance that consuming a bacterium results in a new organelle and nucleus unlocking; this would require balancing and maintaining player choice involvement somehow.

Either one of these could solve the issue while also improving the feel of the game.

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Okay, so I have a few thoughts in regards to this post. To start, I completely agree on the gameplay side of things the nucleus currently is poorly implemented. And I think that’s about all I’m qualified to say on the subject.

Theory wise, I have a few issues. When speaking on the forces and causes of the evolution of the nucleus, I agree with the conventional idea that the organelle evolved via a mitochondrial ”transfer” of the lipid bi-layer method. However, when it comes to the idea of parasitic DNA, I disagree.

Parasitic DNA, in reality and as referenced in the book, can be split into a couple different categories, but it’s worth referring to them solely as transposons for simplicity’s sake. As stated in your post, Transposons could have acted as an evolutionary force in the push for Nucleus evolution, however I don’t think that is the case. Transposons could have predated the split between prokaryotes and eukaryotes yes, however there is nowhere near enough substance behind the claim that they helped cause that split. And the fact that they exist today in most prokaryotes doesn’t help in the fact that we’ve only seen eukaryotic evolution once. The data and theory side of things widely support the evolution having occurred due to the benefits of having all genetic information localized in one region.

I feel that when looking for solutions to the Nucleus Paradox, love the name by the way, one should instead make use of the already planned endosymbiosis system then adding a whole nother genetic system. I’ll leave that to the gameplay team but I have a few ideas if y’all want I can send in the discord.

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For anyone not reading the Discord the book mentioned is “The Vital Question by Nick Lane”, which I was not acquainted with.

I think that from a speculative evolution point of view, the occurence of endosymbiosis is not critical to the evolution of a nucleus, as it has many advantages on its own, mainly for organisms with large genomes and large size. The real evolution of the nucleus is profoundly related with the endosymbiosis process but I don’t see why it should be in an alternative timeline/different planet. So I would maintain the nucleus separated from any endosymbiosis (mitochondria/chloroplasts).

I believe that autogenous origin of the nucleus is currently the most followed hypothesis (correct me if I’m wrong). If this is followed it would be pretty cool to have different stages of the nucleus evolution itself, as the formation of full Nuclear Pore Complexes, the formation of the Endoplasmatic reticulum, Golgi Complex, among others. Also for later stages of the game it will be very convinient to manage the Heterochromatin and Euchromatin. Also, has it been considered the possibility of a sort of multicellular organism of prokaryotic cells? As a more evolutionary sophisticated biofilm.

Some references, I believe that both papers are open-access:
Overview on Evolution of the Nucleus (Figure 3 has a quite interesting representation)
in contrast with the more recent Inside-out Hypothesis (Figure 1 is also very interesting)
also this wikipedia article about Planctomycetota, it might be useful to get ideas of plausible intermediate stages.

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Thank you theorists for some great notes.

That’s good to know about the origins of the nucleus. To be clear, I wasn’t proposing an entirely new system of “genetic parasites”; I was just providing what I heard previously about the origins of the nucleus. This information, however, definitely makes it easier to “gamify” the origins and benefits of the nucleus. Feel free to provide any ideas too, either on this thread or in Discord.

Currently, the only thing the nucleus is planned to relate to endosymbiosis is by increasing the number of times a player can unlock an advanced organelle. The endosymbiosis concept right now allows prokaryotes to perform endosymbiosis and unlock one specialized organelle of their choosing; but after that, the players will need a nucleus to unlock more advanced organelles. The nucleus will also allow for alternative unlock conditions for said organelles in the case that there are no suitable candidates for endosymbiosis.

This connection to endosymbiosis is meant to represent the benefits of more localized genetic information, and overall more specialized mechanisms surrounding the maintenance of genetic information.

Currently we aren’t planning to represent that much of a “tech tree” sort of upgrade strategy, where organelles have many iterative improvements. If we connect the nucleus to certain benefits for larger cells however, perhaps we can utilize this information to exaggerate one benefit in place of another. For example, if we decide that the nucleus will help manage osmoregulation costs and also help boost organelle processes, perhaps we can allow the player to choose whether or not they want to exaggerate one benefit in place of the other.

That is planned, but we still need to think through the balancing and benefits behind cellular colonies for eukaryotes in the first place, as well as the criteria for progressing from the Early Multicellular Stage to the Late Multicellular Stage. Then we will consider the balancing of benefits of colonial living for prokaryotic cells.

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So there’s the idea of making the nucleus energetically useful for big cells. The simplest way to try that out is to make it so the nucleus reduces osmoregulation costs by attaching a multiplier to them. @Buckly made this PR to test that.

Now, how powerful we want the nucleus to be is a design question. Do we want it to be energetically net positive for medium sized cells or just very big cells? And how do we avoid making it OP for giant cells?

Focusing on the former first, there’s a certain size a cell needs to reach before the nucleus becomes net positive. With the current system, this can be calculated with the formula

required hexes = 10 * multiplier / (1 – multiplier)

If the multiplier is:

  • 90%, then the cell needs 90 hexes before the nucleus to break even
  • 70%, then the cell needs 24 hexes
  • 50%, then the cell needs 10 hexes

Currently the PR has the multiplier at 90%. It makes getting the nucleus slightly nicer but is pretty far from making the nucleus net positive for normal cells.

As for the latter part, making giant cells OP, I can think of two options. We can either keep the cost reduction low enough that it’s not a problem, or we can implement some kind of scaling cost to size. The scaling cost could be osmoregulation or something else like slower processes. This ties itself well to the surface area to volume ratio that has been discussed here: Surface Area, Volume, and Ratios. I think I’ll make a more detailed post about my thoughts there later.

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Good thoughts here. I think we should first implement some sort of the non-linear relationship between osmoregulation and size discussed in the Surface Area thread, then consider the nucleus’ effect on that. That could lead to an interesting game of strategy where the player must contemplate at which size do they wish to put on the nucleus.

We could also add some sort of a cap on the beneficial effect the nucleus can have on osmoregulation. So that once a certain absolute value is reduced, no further bonus is applied, and osmoregulation scales as if you don’t have a nucleus going forward. Cells can only get so big after all, unless they basically have super-sized vacuoles.

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Have you also considered making it difficult to create a large sized cell without a nucleus? For example a typical human skin cell has 30 micrometers of diameter and a standard E.Coli 0.6 micrometers (mitochondria have a diameter around 0.8 micrometers; E.Coli and mitochondria have similar lengths, overall they can be considered to be about the same size). So the defined size of an Hexe defines the multiplier, but following the 90% multiplier, for example:

too many hexes = 11 * multiplier / (1 - multiplier)

so the number of hexes beyond the minimum to break even with a nucleus would be simply:

difference = multiplier / (1 - multiplier)

considering 90%

difference = 9

so there could be an osmoregulation penalty (or some other, e.g. max health, absorption rate) when a cell has over 100 hexes without a nucleus.

On the hand, if considering that, currently, the mitochondria is around 1.5 μm2 (equivalent to 2 hexes) and a human skin cell is aproximately 40 μm2, it would be 53 hexes. If considering this as the point where having a nucleus breaks even (which would be a very rough approximation) the multiplier would be 84%, thus the maximum number of hexes without a nucleus without suffering penalties would be 58.

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Maybe i should clarify, I think adding a nucleus should unlock more MP in general, eg 150 instead of 100

Thats what i mean by bonus. ANd i think it shoudl grant this bonus mp the second it is added (and every cycle after of course) so that the player could add the organelles to reduce their disadvantage next cycle and to aid in their survival. I think that is way more interesting than just reducing osmoreg cost or whatever. (This is how I also was thinking of different reproduction methods way back when i was aan active dev) eg, one thing we dont curently have in the microbe stage is differnet extent microbial reproduction methods like conjugation. (Conjugation is like mircobe sex, it lets microbes swap dna to help out their next daughter cells Bacterial conjugation - Wikipedia there are eukaryotes that also do something similar) but basically, that would also grant bonus mp in the editor for that cycle if you conjugate or wahtever. So having a nuceus would be like conjugating every cycle without needing to do anything.

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I’d like to once again remind that MP is a percentage, only discounts are allowed. So the nucleus could give a 50% discount on further MP cost once placed (similarly to how being multicellular gives a 50% discount to everything in the microbe editor). This isn’t a point against your idea, just saying that if the idea is accepted it should be worded the opposite way around i.e. as a discount rather than a bonus MP amount.

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One thing to consider about the nucleus is how powerful the organelles it unlocks make the cell.

I’m pretty hesitant to give the nucleus a significant osmoregulation bonus because a eukaryote can already become substantially efficient compared to a prokaryote. The 10% reduction to cost may not seem like much but it means just that much more ATP efficiency with the already capable parts you can unlock. Think of an osmoregulation bonus as making everything in the cell just a little more energy efficient.

Making the organelles less effective is not an easy solution to this either, as we want them to be more desirable and effective than their prokaryotic equivalents. Have we considered making the nucleus smaller in hex count? It’s 12 hexes right now but it could reasonably be compressed to 9.

Edit: I might actually just expand my nucleus branch to include all the things we want to try just so we can better get a feel for how it can play out. And experiment from there.

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I agree with being a bit prudent with the energy osmoregulation aspect of the nucleus since we don’t want to give the impression that it is inherently an energy-focused part, and for the balancing issues mentioned above. For energy, I think we would want to imply that the nucleus makes management of genetic information more efficient, which is a pretty important component of maintaining complex and large cells.

Hate to sound like a broken record, but again: I think the first matter to address with this concept is non-linear osmoregulation. We’re discussing two concepts at once here and running through hypotheticals around a lot of uncertainty, so we should take a step back and consider questions like: how big should the average prokaryote/eukaryote be? What size will we treat as “large”, therefore making such sizes less efficient? Atleast agreeing on that will give us an idea of how we should scale osmoregulation costs with mass.

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