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[expwnent]

I think I understand. I'm somewhere in between. Keep in mind that the game is representative, not literal. It doesn't represent a world with literal tiles, for example. Many of the mysterious game mechanics are actually part of the representation of the game, like the user interface. They aren't intended to be taken literally and a lot of the similar things are placeholders. When completed I support reducing the complexity of the miracles, but it's pointless to try to explain things like tiles with lore.

I support reducing the complexity of the deviations from reality, all else being equal. The notion of "one" deviation is artificial. The statement "Plants eat magic and zombies can fly on alternate Tuesdays" is one statement but it would be outside the spirit of minimizing complexity, which I think is a more accurate term for what we want.

There are magical things in game like zombies, artifacts, necromancers, and vampires, so I see no problem making magic a "normal" part of physics from the perspective of the inhabitants of DF. Since we're already supposing magic, we may as well suppose it in such a way that it explains other mysterious things in game. I'm mostly indifferent on chemosynthetic plants vs magic-eating plants, but I lean slightly toward chemosynthesis because it's neat to have fringe science stuff in the same world as magic (hard fantasy).

As for energy, why not make magic somewhat like sunlight? Just to be different let's say it's emitted by the core of the planet or by the magma itself. It doesn't break conservation of energy, but there's a lot of it in the same way that there's "a lot" of energy in the sun. With a slight tweak to photosynthesis I think we can manage something interesting. We want magic to be able to do magic-like things and also serve as a mundane source of ordinary old chemical energy. How about this: chemosynthetic plants absorb raw magic and produce "refined" magic / mana as a waste product. Mana interacts with consciousness in interesting ways so it's possible to have wizards who do things with it, but plants and magical animals and zombies can only sustain themselves with it. Necromancers infuse dead bodies with just enough mana that they obey a simple command until destroyed: mana can also cause a sort of consciousness under the right circumstances, just like magnetism and electricity can cause one another.

As for underground plants, maybe they're chemosynthetic, maybe they're xenosynthetic. If xenosynthetic then they should be the source of mana. Necromancers have magic gardens and zombies can sustain themselves for longer if they eat magical plants (or maybe if they just breathe the mana in the air if mana is a gaseous waste product). It is unlikely that an animal could sustain itself entirely on mana: animals require much more energy than plants do. Zombies cannot sustain themselves indefinitely unless maintained by a necromancer. Zombies are also horrible from an evolutionary perspective. Even ignoring the fact they don't reproduce they are incredibly stupid and don't bother doing things like running away from danger, which tends to get them killed. This is why you don't see many zombies out in the world except in necromancer towers, where they are maintained by a necromancer.

If plants are chemosynthetic then necromancers should have to build some sort of xeno-solar panels to harvest mana and implant it in themselves to do magic. I'm not sure about this.

Maybe with a certain minimum amount of mana a necromancer can build a magical raw magic converter in their own body to get their own supply without plants. Maybe with meditation the rate of consumption can be increased due to the interaction with consciousness.

[Tristan Alkai]

Okay, somewhat clearer statement of my position:
1. It is explicitly stated by Toady One that the current good/savage/evil surroundings are a place-holder, to be replaced at some point in favor of "lands with more variety." 
2. The game has a sphere system.  NW_Kohaku decided to invoke and extend this to achieve that variety, a decision I support.  This is where mana comes in.
(Edit)3. I also called in mana to explain undead, amethyst men, and other creatures that currently operate with no apparent source of food or energy.  Mana becomes their source of energy.
A. Support for undead and so on was an extension from something NW_Kohaku proposed: a magical source of energy to explain the cavern ecosystem. 
3. NW_Kohaku pointed out that cavern plants support a vibrant ecosystem of many active creatures, but can't be using light for the purpose.  They must be using mana instead.  I extended the mana explanation to certain creatures, like undead, that currently function without any apparent energy source.
A. There was also discussion of caverns being different by area like the surface is, and discussion of mana being different by season. (/edit)
4.

Just having it be nearly infinite like sunlight from some no-need-to-explain natural well is simpler, one-way only, only need the single mechanism for its conversion that evolved or whatever, no energy altruism is implied, etc.

This comes back to that goal of variety.  I assume that certain relevant behaviors of the current game will remain in place. 
A. Undead can spontaneously re-animate, but only in certain areas.
B. Creatures can achieve unnaturally large size, but only in certain areas.
C. Creatures can appear in approximately humanoid forms, but only in certain areas. 
> A single source of mana, especially with, as you describe, a single conversion process, will not explain these results.  This comes back to variety and the sphere system: I prefer to explain the differences by area in observed behavior by stating that the mana itself is different.  In other words, mana is always a particular sphere of mana, not just undifferentiated energy. 
5. Several kinds of mana require several respective sources.  I favored surface plants for this purpose.

I WAS working on a presentation about the ecology of magical plants, focusing on the magic-producing ones, and the various ways their ecological niche could affect the magic-consuming (xenosynthetic) ones.  Then GavJ derailed me.

Looks like I need to put this back on the front burner.  I NEVER invoked altruism.  It will also explain a few more of the behaviors I want to see.
6.

A mechanism of running out also permits a "the magic goes away" sequence of events, which I and others have mentioned before. 

Just divert or block the field. No need for it to run out.

If the field is getting diverted or blocked, then there must be something in place to KEEP it blocked.  Due to like reality unless noted, I consider "mundane" the default, and mana a deviation from that default, a reverse of the position you outline.  Your solution also implies that at some point the block will STOP and the magic will come back, which we do not observe.  The magic goes away, and STAYS away.  I prefer to explain this in terms of continuous local mana production, which creates a reserve that can be depleted and run out.
> This also permits two game scenarios I want:
A. A player embarks on an undead biome with the intention of wiping out all the undead.  With local sources and reserve of Death mana, the player can deliberately remove the sources to starve out the undead. 
B. A different player can create Death mana sources in a formerly undead-free area for the challenge and/or the laughs.
C. Both of these can be extended to other scenarios, such as the successors to Savage areas.
7. Undead are not the only magical creatures.  I invoke magic to explain giant animals and animal men as well.  All are primarily found in certain areas because they require certain kinds of mana, which is only found in those areas.  This directs and controls the variety.
A. However, all three CAN be found outside those areas, but usually nearby.  I invoke an internal storage of mana to explain this behavior.
B. This internal storage then extends back to plants, which permits the alchemy I want to see. 
(edit) In scenario A above, the Death mana source plants would have internal storage of mana. Killing one of them is likely to release that energy for a one-time, but significant, increase in the area's Death mana.  Challenge! (/edit)
8.

That respecting science article I linked to earlier explains what that means and why I care far more eloquently than I can.

By the way, this link doesn't really support the concept of "lots of physics violations, but not big ones, and that's totally fine." It in fact warns against ALL of the types of issues mentioned previously.

That's not how I interpreted it.  The entire site was written for a science fiction audience, and in many such series physics-breaking Faster-Than-Light travel is the order of the day (which was acknowledged on a different page of that site).  As I understood it, the advice was "You're almost certainly going to break SOMETHING.  Carefully decide WHAT to break, so you can avoid UN-intended consequences."  Consequences of NON-physics-breaking inventions like fusion power were also covered. 
A. I pointed out a wide variety of intended consequences of mana.  There is a world of difference between "lots of implications" and "lots of unintended implications that haven't been thought through."  The bad thing is consequences you haven't thought about; big physics violations are bad not for being big, but for being much more likely to present a problem you haven't thought about.
9.

I'm mostly indifferent on chemosynthetic plants vs magic-eating plants, but I lean slightly toward chemosynthesis because it's neat to have fringe science stuff in the same world as magic (hard fantasy).

This scenario comes across to me as "have your cake and eat it too."  If magic is demonstrably present, then I would rather not bother with "THIS part is plausible!" fringe science.  Just eat the cake and explain things with magic.
(edit) On that note, thanks for the help articulating why I didn't like the thermosynthesis and anaerobic ecosystem ideas GavJ was throwing around. (/edit)

[GavJ]

 
A. Undead can spontaneously re-animate, but only in certain areas.
B. Creatures can achieve unnaturally large size, but only in certain areas.
C. Creatures can appear in approximately humanoid forms, but only in certain areas. 
> A single source of mana, especially with, as you describe, a single conversion process, will not explain these results.

Why not? The sun is a single source of finite sunlight, yes?
There also exists no method by which to convert sugar back into sunlight, no?
Yet cacti or marigolds only grow in certain areas (full sun) and lavender and ferns only grow in others (shady spots).

Multiple sources are unnecessary to explain local differences -- they can simply have different amounts of mana. It is also unnecessary to explain spheres (spheres can just be different levels of sunny and shady spots of mana, and/or synergistic combinations of mana + other factors like how it interacts with lots of vegetation). And mana storage or transit is unnecessary either way -- with or without multiple types of mana.

I NEVER invoked altruism.

Implied it. Which organism is going around converting perfectly good chemical energy or whatever back into mana, and why is it doing that, what does it get out of the deal? That energy is going to go back into a communal pool, only some of which it might get back, when it could have kept it all for itself.

Just divert or block the field. No need for it to run out.

If the field is getting diverted or blocked, then there must be something in place to KEEP it blocked.  Due to like reality unless noted, I consider "mundane" the default, and mana a deviation from that default, a reverse of the position you outline.  Your solution also implies that at some point the block will STOP and the magic will come back, which we do not observe.  The magic goes away, and STAYS away.  I prefer to explain this in terms of continuous local mana production, which creates a reserve that can be depleted and run out.

No offense, but why does it matter what you arbitrarily "preferred" or "considered" previously? That's not a game design argument.  It's just as good at face value either way, yet mana on by default comes out significantly ahead, because it offers a significant benefit in simplicity by not requiring multiple conversion methods (even MORE conversions for multiple kinds of mana), not requiring as complex of an ecosystem, not requiring altruism or whatever elaborate explanation is needed for it not to be altruism...

It also offers a much simpler explanation of evolution, which I didn't mention before. If mana is vast in reserves and has been available since the dawn of time, etc., then of course organisms would evolve to use it if possible, over millions of years. IF, however, it is very finite in reserve, to the extent it can run out in a single fortress game, then there is pretty much ZERO chance that organisms would have evolved both a chemical reaction chain to harness it, and a separate chain to refill the reserves, all in what... 10 years? Evolution takes thousands and millions of years, during which time the reserves would have to not go empty in order to not have cut off the evolution process (if they run out even for a month or a year, all those organisms die and the development ends).

> This also permits two game scenarios I want:
A. A player embarks on an undead biome with the intention of wiping out all the undead.  With local sources and reserve of Death mana, the player can deliberately remove the sources to starve out the undead. 
B. A different player can create Death mana sources in a formerly undead-free area for the challenge and/or the laughs.

A) The player can just do something to block the mana access. Most likely something analogous to whatever nature is doing to shade certain areas from mana more than others.
B) The player can do the opposite, knock out the metaphysical cobwebs and let the mana flow in higher intensity which above some threshold starts turning things into zombies.

And/or as suggested above in this post, spheres can be some combination of mana + [other context]. In which case adjust the two scenarios above to = a combination of mana flow control and changing the context. Such as amount of vegetation combined with mana flow rate (high flow or raw mana + lots of normal vegetation makes nature mana in the area, etc.). So to alter mana, you might block or remove obstacles to mana flow, AND go cut down or plant more trees, etc.

7. Undead are not the only magical creatures.  I invoke magic to explain giant animals and animal men as well.  All are primarily found in certain areas because they require certain kinds of mana, which is only found in those areas.  This directs and controls the variety.

Birds use sugar to fly. Humans use sugar (disproportionately) to think. Elephants use sugar to grow really big. Lamps use kerosene to light a room. Airplanes use kerosene to fly through the air. We already know in real life that a single energy source can and will be used for hugely different purposes. Organisms in particular almost universally use the same basic energy and the same basic energy reactions.

Doing it the same way with mana is the simplest and most intuitive approach -- i.e., the animals are evolving (or being manipulated by necromancers) to use the same generic form of extra energy in different ways. The animals are primarily the difference in how it manifests, not the energy source. Although the amount of energy source does matter too, regionally, it's still not the main source of variety. After all, animal men and giant animals live in the same place. And eyeball grass and zombies live in the same place. Quite a lot of local diversity in the game already.

A. However, all three CAN be found outside those areas, but usually nearby.  I invoke an internal storage of mana to explain this behavior.

If you have a big brain and you stop eating for a couple of days while you make a weekend trip outside of your main feeding zone (on Earth), you don't just drop dead. Remember, I'm not suggesting that these animals not store their energy. I only said they don't need to store the MANA ITSELF. But the mana can still be used to drive the formation of mundane chemicals (like fat reserves or ATP or whatever else), which you can then store and use later to get through rough times. (or perhaps some creatures cannot, like maybe zombies, which might allow you to make them indeed drop dead instantly when you turn off the mana, just like you want. Again, diverse animals are the diversity, rather than the energy source)

the Death mana source plants would have internal storage of mana. Killing one of them is likely to release that energy for a one-time, but significant, increase in the area's Death mana.  Challenge!

This seems inconsistent with the fact that there are not big spikes of weird events when things just die normally in the game in their own areas. When I kill a giant jaguar just while out hunting or whatever, it's not like everything around it gets 30% bigger or something. It also seems inconsistent with other organisms being able to store and absorb mana from each other, because you setting off your spell would just be like, dinner, to all cave animals nearby, yes? It also presents a lot of logistical problems regarding the need to keep all of your specimens ALIVE up until the point that you need them. How do you keep a live tunnel tube in your alchemy lab when a tunnel tube is like 40x the size of your alchemy lab, etc.? Also come to think of it why do you need to study alchemy for 40 years to just look up a chart of mana and go kill something of that type for whatever you need? This seems like it has a lot of issues.

It seems more intuitive and more dwarven to me for alchemy to not be sspellcastery things (even in very high fantasy, dwarves are pretty much never wizards), but instead be the academic-flavor study of practical mana manipulation. Examples of things it does:
1) Splicing new organisms, sort of like GMOs, to maybe be faster or stronger with mana supplements by gaining organs or oganelles that convert it.
2) Necromancy is a sub branch of alchemy, and sort of an advanced, quicker, long range form of #1.
3) HERE is maybe where learned alchemists may be able to devise batteries for storing mana itself.
4) Making artificial converters. The equivalent of mana solar panels, instead of relying only on cave plants and natural conversion sources.
5) The art of using mana to help run machinery like pumps
etc.

This scenario comes across to me as "have your cake and eat it too."  If magic is demonstrably present, then I would rather not bother with "THIS part is plausible!" fringe science.  Just eat the cake and explain things with magic.

That's not what the phrase having your cake and eating it means...? I really don't know what you're saying here.
Limiting a necessary evil to... only the necessary amounts of it is perfectly logical.

It's "evil" because it promotes laziness, hand waving, and bad storytelling if you just use it to get out of puzzles that have other solutions.
It's necessary (perhaps) because if we TRULY can't explain certain critical plot points any other way, then the story won't get told at all.

You should only use it to exactly the point needed to be able to tell a coherent story and no more. Your "respecting science" page references this point in detail and the logic behind it several times.

[GavJ]

Oh also again, underground plants could merely be literally photosynthetic, from magma light, which doesn't burn them because of the way heat flow works in DF (existing miracle). Have mentioned this a couple times to no response. I think it's actually a pretty reasonable theory.

Mana is okay too, but not really with all the baggage. Although I don't agree on all his details, I think expwnent summed it up nicely by saying "Why not just treat mana like sunlight" but from a different source like the planet's core. Doing this would streamline most of the baggage away, if you just keep asking "would this make sense if we were talking about sunlight?" and what remains is largely automatically intuitive and simpler for people who are used to thinking about sunlight to simply reverse their direction on the same concepts.

[Tristan Alkai]

As promised, the post about the features and ecological niche of magic plants. 

NW_Kohaku and I share a habit of very long posts, and I am now copying another one: using spoiler tags to cut the length of absolutely huge ones to something more manageable (demonstrated very prominently here).  The ones in this post serve no other purpose. 

Part 1: Goals, Assumptions, and Definitions

Spoiler (click to show/hide)

1. I want to keep as much real science as feasible.  Natural selection, for example, is present and fully intact. 
2. There are mundane plants that use photosynthesis, the same process as in real life. 
3. Certain plants use a similar but distinct process, called “xenosynthesis,” which uses magic energy (“mana,” or "XE" in some of my older posts) instead of light.  This allows them to grow in areas where mana is present but light is not, including caves underground. 
4. Xenosynthetic (“xeno”) plants need a source of mana, and I nominate certain other “alchemical” (“alch”) plants for the purpose.  These live on the surface, and convert light energy into mana. 

Part 2: Magical Biochemistry

Spoiler (click to show/hide)

1. Both xeno and alch plants are viable living species.  The offspring of such plants retain the ability.  Otherwise, such plants could not spread in the ecosystem, and crops of either type could not exist. 
2. To permit the previous point, both abilities must have a genetic basis. 
3. To permit the previous point, both abilities must have a biochemical basis.  The plants (and animals) that interact with mana make and use specific molecules, unknown on Earth, that allow them to do so. 
4. In other words, the xeno and alch processes have an analogue of chlorophyll.  I assume that these analogues evolved from chlorophyll. 
5. For simplicity, I assume that xeno and alch plants replace the light reactions of photosynthesis, but the Calvin cycle is the same as in mundane plants.  Like chlorophyll, the xeno and alch analogues discharge their energy to ATP, which drives the Calvin cycle but can also be used directly for other metabolic purposes. 

Part 3: Mana Interactions

Spoiler (click to show/hide)

1. I want free-floating mana in the environment.  Xeno plants won’t work without it. 
2. To achieve this, I declare that the analogue of chlorophyll used by alch plants is able to release its energy (gained from absorbing light) either to the environment at large as mana or more directly into the mundane cellular machinery. 
3. According to my admittedly incomplete understanding of the physics underlying emission and absorption spectra, the ability to absorb and store energy from light implies the ability to emit it.  And, by extension, the ability to emit mana implies the ability to absorb it. 
4. Conclusion: Xeno and alch plants use the same molecule, which will be referred to as xeno-chlorophyll (“x-chl”). 
5. Summary: X-chl is able to convert between mana and light in both directions, with minimal (direct) interaction with other cellular processes.  It is also able to convert from either to biochemical energy, but (at least in practical terms) probably not vice versa.  I will assume that the plant can control this behavior, most likely by attaching other components to the molecule. 
6. As stated previously, mana is sphere-aligned.  X-chl comes in several different varieties, each interacting with a different sphere of mana.  All varieties interact with light, although not necessarily with the same preferred frequencies.  The divergent types of x-chl could have evolved directly from chlorophyll (independently of each other), or from other varieties of x-chl.
7. Another result is that both alch and xeno plants inherently have the ability to emit light.  Glowing cavern plants are cool, and glowing flowers could be useful for attracting pollinators. 

Part 4: Mana Storage and Its Consequences

Spoiler (click to show/hide)

1.

Fruit (and possibly other plant parts) can contain XE in portable form.  Intelligent creatures which require XE (such as necromancers) can carry appropriate types of fruit with them.  A player wishing to terraform his/her site can also import and use suitable plants.  This also has implications for alchemy.  It might also open certain exploits with prepared meals. 

I want at least some plants to be able to store mana internally for extended periods. 
2. To permit this, I declare that the high-energy state of x-chl is relatively stable.  For comparison, chlorophyll is also pushed to a high-energy state when it absorbs light, but quickly releases that energy into other cellular processes.  With x-chl, that release is much more difficult to trigger.  X-chl can therefore serve as both energy gatherer and energy storage. 
3. I want mana to be stored in locations other than the leaves, and long-term energy storage in x-chl is a way this could be selectively favored. 
4. To take maximum advantage of the storage ability of x-chl, “charged” and “depleted” molecules might be moved around in the sap, as a replacement or supplement to sugar. 
5. X-chl is (probably) a much larger molecule than glucose, or even sucrose or maltose.  This makes it somewhat more awkward to move around.  It is also likely (but, since this is magic we’re talking about, not guaranteed) to have lower energy density than sugar. 
6. A sufficiently high-magnification image of a leaf shows that a surprisingly large fraction of it is transparent, since chlorophyll is so concentrated in the chloroplasts.  With mobile x-chl, that would not be the case. 
7. Given the storage properties of x-chl compared to chlorophyll, it would probably take more molecules to absorb an equivalent amount of light (unless, of course, x-chl has multiple high-energy states; since this is magic we're talking about, it might).  Mundane chlorophyll still has a role within both plants and ecosystems.  Alch plants might still produce and use it.
8. The counterpoint is that storing the energy in sugar is an additional conversion step, so x-chl storage may be more efficient. 
9. Conclusion: X-chl will only be favored over chlorophyll under relatively specific circumstances.  Moving it around even more so.

Part 5: Basic Magical Ecology

Spoiler (click to show/hide)

1. Mundane plants are still observed, so alch plants can’t completely exclude them.  (Xeno plants generally grow in different areas, so they don’t count.) 
2. Certain areas have a lot of mana naturally present in the environment, and some mana is consumed in the caverns, both of which are a waste to the alch plant.  Natural selection still applies, so I need to describe situations where this behavior would be selectively favored.  Various such situations (“strategies”) are outlined below.
3. I am using the rule of thumb that the caverns have roughly as much primary production as the surface (say 10% at a minimum, probably closer to 50-75%, maybe higher). 
4. While the single "miracle" molecule x-chl would allow alch plants to switch to xeno and colonize the caverns (or switch back from xeno and colonize the surface), the two environments do involve somewhat different selective pressures. 
5. Caverns have near-constant temperature and humidity.  The surface has significant daily and yearly cycles for both.  Xeno plants, adapted to the gentler conditions underground, might find the surface overly hostile and fail to thrive.  Maximum efficiency of gathering mana may also lead to reduced efficiency when gathering light.
6. Certain plants in real life, particularly those living in temperate regions, produce seeds that need a freeze and thaw before they will sprout.  Caverns will not provide this, so such plants will grow poorly in the caverns. 

Part 6: Magical Animals

Spoiler (click to show/hide)

1. One of the central premises is that at least some animals are able to use mana. 
2. Such animals probably use x-chl to gather and store mana, but might use something different. 
3. As described previously, mana will allow animals to do certain things they wouldn’t be able to do without it.  Mana is usable as an energy source, but animals will seek it out for the other benefits as well. 
4. Since plants can store mana internally, this mana will affect herbivores (or other animals) that consume those plants. 
5. Since chlorophyll, on which x-chl is based, is primarily found in the leaves, x-chl is likely to be primarily found there as well, especially in the charged state that would be of interest to mana-using herbivores.  They are therefore likely to target the leaves.  This imposes specific selective pressures on the plants. 
6. Ideally, the plant would deflect herbivores from leaves to fruit.  This simplifies one of my other goals: a mana storage system with a relatively long shelf life. 

The format for describing the various alch plant strategies is as follows:
D. “Description” of the strategy. 
L. “Logic” behind the strategy, including, if possible, real-life precedents. 
B. “Biome,” or the environment likely to be favored by an alch plant using this strategy. 
P. “Plant,” or what an alch plant would be like as a consequence of this strategy. 
C. “Caverns,” or implications for xeno cavern plants living below an area dominated by alch plants of this type. 
M. “Miscellaneous” commentary. 

As a final note, very few of the strategies described below interfere with each other.

Cluster 1: Immobile xeno-chlorophyll
I assume that xeno-chlorophyll evolved from mundane chlorophyll.  Under most circumstances, chlorophyll does not move around the plant.  The main exception is deciduous trees removing it from their leaves in fall (which actually involves disassembling it and moving the pieces).  Occam’s Razor then leads to the assumption that xeno-chlorophyll will also, by default, not move around much. 

1. Modified CAM

Spoiler (click to show/hide)

D. Charge x-chl during the day, and use the stored energy to run the Calvin cycle at night. 
L. CAM is a strategy used by many real-life plants, especially ones that live in desert conditions.  At night, they open their leaves to air and gather CO2, which is converted to malic acid and stored.  During the day, they keep their leaves closed to control water use, and consume the stored malic acid in the Calvin cycle. 
B. This strategy is favored under the same conditions as CAM, namely arid ones.  It has similar ecological effects (hence the name). 
P. This strategy does not interfere in any way with CAM, and in fact helps compensate for some of its shortcomings.  Plants are likely to combine the two strategies.  They are also likely to have other adaptations common to desert plants, such as the thorns for which cacti are famous. 
C. Deciduous trees using this strategy will produce a large glut of mana during fall, when their leaves change color and drop off.  Other plants will, under normal circumstances, release little if any mana for the caverns.  Surface herbivores, however, will have access to abundant mana from their leaves, especially near sunset. 
M. This strategy produces a selective pressure favoring x-chl complexes that can store more energy (high energy density).  All of the strategies in the second cluster will benefit from this, as will mana-using animals. 

2. Xenosynthetic Roots

Spoiler (click to show/hide)

D. The plant produces mana in its leaves, and releases it to conduct xenosynthesis elsewhere in the plant.  The x-chl in the leaves is kept discharged as much as practical. 
L. This strategy is excellent under extreme water stress.  CAM and modified CAM reduce water use, but this strategy virtually eliminates it.  Under conditions of high sun and low water, the vastly improved water-efficiency may outweigh the wastefulness of broadcast power. 
B. Arid areas.  Other inhospitable areas like the tundra are more tentative possibilities.
> For best results, plants of this type would have mechanisms to discourage competition from other xeno plants, especially their own species.  Seeds would need extremely wide dispersal to avoid competing with the parent (synergy with Mana Fruit, below). 
> It may also be favored under sufficiently extreme pressure from herbivores, assuming mana-using ones are dominant.  They taste the leaves, get very little mana, and lose interest. 
P. The plant will still need to use the Calvin cycle to generate new tissue.  Given the conditions to which this strategy is best-suited, it will probably use CAM and/or “Modified CAM”. 
> Broadcast power also delivers energy much more rapidly than sap would.  A sufficiently large alch plant (say a 4-z or 6-z tree) may find that the convenience of broadcast power outweighs its inefficiency. 
C. Xeno cavern plants would have an abundant supply of mana throughout the growing season, potentially year-round. 
M. No other comments. 

3. Mana Nectary

Spoiler (click to show/hide)

D. The plant produces mana, and releases it to attract some kind of symbiotic animal that consumes that mana and helps the plant in other ways.  Examples include clearing out competing plants, delivering nitrogen and water from foraging elsewhere, and protecting the plant from other herbivores. 
L. Extrafloral nectaries do exist in real life, and this system serves the same ecological role, hence the name. 
B. This strategy is very useful in a fairly wide range of environments. 
P. This strategy, like “Xenosynthetic Roots,” has broadcast power as a basic feature.  They two strategies also have excellent synergy.  Either could have evolved from the other. 
C. Xeno cavern plants would again have an abundant supply of mana throughout the growing season, although not necessarily as abundant as a pure “Xenosynthetic Roots” alch plant.
M. I think this strategy is the best for alch plants.  In particular, it is the best one (possibly even the only viable one) in order to allow alch plants to really compete with mundane plants on their own turf, rather than merely grow where they can’t, or grow adequately where they grow poorly. 

Cluster 2: Mobile Xeno-chlorophyll
Now we’re getting to the more speculative stuff.  All of these strategies assume and exploit moving xeno-chlorophyll around the plant.  Given the "Immobile xeno-chlorophyll" strategies described above, this isn’t strictly necessary to support the cavern ecosystem, but it does offer possibilities for other goals I had.  See also: "Mana Storage and Its Consequence," above.

4. Mana Sap

Spoiler (click to show/hide)

D. Charge x-chl in the leaves, and carry that, rather than sugar, in the sap to distribute energy to the rest of the plant.  Of course, discharged x-chl must then be carried back to the leaves. 
L. Like “Xenosynthetic Roots,” this strategy vastly cuts water use.  Charging and discharging x-chl consumes virtually no water.  Carrying energy in the sap wastes less to the environment than broadcasting and collecting it. 
B. Like “Xenosynthetic Roots,” this strategy is most beneficial under conditions of extreme water stress. 
P. Since x-chl is assumed to be relatively difficult to transport (much more so than sugar), this strategy limits the size of the plant using it. 
C. The efficiency of this strategy is good for the alch plant doing it, but bad for the caverns. 
M. An interesting possibility, and it is a prerequisite of the other strategies outlined in this cluster.  It also shares another feature with “Xenosynthetic Roots”: reducing the amount of mana stored in the leaves, and thus the interest of mana-using herbivores in them.  It is, however, somewhat worse in this area.

5. Shaded Calvin Cycle

Spoiler (click to show/hide)

D. Charge x-chl in the leaves, then transport it to a more sheltered part of the plant.  Run the Calvin cycle there, not exposed to direct sunlight and the wind. 
L. Similar pressures and results to “Modified CAM.”  The plant reduces water use by gathering CO2 from areas where evaporation will be less significant.  “Modified CAM” separates things by time; this strategy separates them by location. 
B. Again, this strategy will be favored in areas where water is limited. 
P. I assume, by default, that plants that use “Mana Sap” will also use this strategy.  It may also offer some improvement supplementing “Modified CAM.” 
C. Again, plants of this type will not release much mana to the caverns. 
M. No other comments. 

6. Mana fruit

Spoiler (click to show/hide)

D. Move charged x-chl from the leaves, and store it in fruit. 
L. The ability of alch plants to move x-chl around was proposed specifically to permit this strategy.  I wanted a mana storage system with a long shelf life, and this was one of only two ways I could think of to get it. 
B. All of the factors that encourage real life plants to produce fruit apply.  Most obviously, the plant needs plenty of herbivores around to eat the fruit and disperse the seeds inside.  Fortunately, that is true almost anywhere. 
P. Again, x-chl is somewhat problematic to move around.  For best results, fruit needs to grow very close to the leaves. 
C. Excellent for mana-using herbivores.  Not so good for the caverns.  Orchards kept by sentients might allow more fruit to rot, which would release more mana.  X-chl might also be prompted to decay (release its mana) by brewing the fruit into alcohol.
M. To employ the “deflect herbivores from the leaves” feature, the fruit needs to be present through most of the growing season.  Certain real life plants (including the magnolia tree right outside my house) flower before they leaf out, so this is not as ridiculous as it might sound. 

7. Mana Tuber

Spoiler (click to show/hide)

D. Store the mana in a hard-to-access part of the plant, such as a tuber. 
L. Opposite in some ways to “Mana Fruit.”  This is a way for the plant to make things more difficult for mana-using herbivores.  It is also the second of only two ways I could figure out to arrange for plants to produce a mana storage system with a long shelf life.  It is somewhat better, since fruit tends to be consumed fairly quickly but tubers need, at a minimum, to remain viable through the winter.
B. Fundamentally, this strategy requires the plant to select charged x-chl over sugar for energy storage.  There are two scenarios likely to produce this result.  First, the same water stress issues mentioned under “Xenosynthetic Roots” and “Mana Sap.”  Second, the plant has a mana-storage molecule that is easier to produce (better input-to-output ratio) and store than sugar.  Ideally better energy density as well, but I don't consider this especially likely. 
P. Given the constraints on size mentioned under “Mana Sap,” the plants that benefit most from this strategy are herbaceous perennials.  As a crop, it would most likely be grown as an annual, since harvesting the tuber is likely to kill the plant. 
C. This strategy produces surplus mana for herbivores that manage to dig up the root, but not much for the caverns.  Mana would only get released into the region at large if the plant fell to pests or rot.  After harvesting by sentients, any processing that prompted fruit to release its mana would likely also work on the tuber.
M. No other comments. 

[TheDarkStar]

Because light is the ultimate source of energy in this ecosystem, I'd think that the energy efficiency of each process would need to be different. The plants that live on the surface would use light because photosynthesis is more efficient than xenosynthesis, but photosynthesis would also create mana as a byproduct (or maybe it is created as a byproduct from the plant's metabolism, similar to how RL plants release water and oxygen, which would mean that you can convert between mana and light), and that mana would somehow (radiation? a liquid? a gas? Maybe it is transferred like heat?) get down to the subterranean plants. Because there's always inefficiency, though, less mana energy would be produced than light energy taken in at the beginning (in RL, the factor for thing kind of thing is about 10, so you'd have roughly 10x as many surface plants as xeno ones and then 10x as many xeno plants as the things that eat them directly, etc).

[GavJ]

Biggest issue here aside from the more external complaints earlier: mana charging an x-chlorophyll molecule is not storage of mana. It's just an x-chlorophyll molecule in a higher energy state.

Things eating them would be eating slightly higher calorie mundane plant matter.

[Baffler]

PTW, for now.

[Tristan Alkai]

(M)ana charging an x-chlorophyll molecule is not storage of mana. It's just an x-chlorophyll molecule in a higher energy state.

Things eating them would be eating slightly higher calorie mundane plant matter.

Not quite. 

I glossed over this earlier, but the path in mundane plants from "high energy chlorophyll" to ATP involves a rather complicated series of enzymes and other molecules, which will be quickly ruined by any animal digestive system. 

As I have set it up, the path from "high energy xeno-chlorophyll" to ATP involves that same complicated series of bio-molecules.  Without them, only the light-release and mana-release decay paths are available. 

As stated there, high-energy xeno-chlorophyll can remain in the high-energy state for some time, and can probably survive longer in the digestive system than the much larger and more complicated extraction system.

I envision the mana-release as the default, with both light-release and biochemical release requiring supporting biochemical systems around the molecule (at least to occur at significant rates).  Storage of energy in xeno-chlorophyll therefore is storage of mana.

Having settled on the explanation that XE is (primarily) produced by certain plants, a new question emerges: How is outputting XE beneficial?  This seems like the plant is simply wasting energy it could use. 
(. . .)
2. The plant contains magical energy, and this has implications for herbivores.  Most can’t use the XE.  When mundane herbivores eat the magical plant, the XE is released into their bodies in an uncontrolled way, and causes an unpleasant and possibly dangerous syndrome.  The details obviously vary depending on sphere. 

Summary: I was explicit right from the start with an assumption that mana required special systems to handle it, and was harmful to life-forms that lacked those systems.

PTW, for now.

Um, I don't speak text message.  What does this mean?

The plants that live on the surface would use light because photosynthesis is more efficient than xenosynthesis, but photosynthesis would also create mana as a byproduct (or maybe it is created as a byproduct from the plant's metabolism, similar to how RL plants release water and oxygen, which would mean that you can convert between mana and light), and that mana would somehow (radiation? a liquid? a gas? Maybe it is transferred like heat?) get down to the subterranean plants. Because there's always inefficiency, though, less mana energy would be produced than light energy taken in at the beginning.

Okay then.  Next on the agenda: Properties of Mana.

[Redzephyr01]

Posting to watch.

[Baffler]

Posting to watch.

Aye. I'm somewhat able to speak at this level of detail, at least where animals are concerned, but I don't have time to write anything up (worth reading anyway) until this weekend.

[Tristan Alkai]

(Tristan Alkai cancels Write Presentation on the Properties of Mana: Interrupted by Schoolwork.) 

That left the project sitting in the back of my mind for a few days.  Those few days were enough distance from the issue for me to realize that I had been going about the debate wrong. 

My first post concerned HOW to implement xenosynthesis, because I (sub-consciously) took the question of WHY to be settled ("I like magic").  Later, I read the Improved Farming thread, linked to in the first post of this one, and consciously took the question of WHY to be settled.  Various comments from GavJ indicate that this opinion is not unanimous, but it took a while for me to realize what the problem really was. 

Most of WHY is covered there.  Xenosynthesis is one aspect of Improved Farming, as described by NW_Kohaku.  Discounting the sections describing the problem being tackled (3 sections in 2 posts) and elaboration of the basic goals and why those goals are important (5 more sections distributed between those same two posts and a third one) there are 20 sections describing the HOW of the solution.  Xenosynthesis is only one of those twenty.

Most of both WHY and HOW are covered by NW_Kohaku over the first 6 posts of the Improved Farming thread (sometimes via links to other posts farther in), in far more detail than I could ever manage.  I will only summarize the parts that are relevant to this issue in particular.

The goals:
1. Give the game more depth by presenting the player with conflicting goals.  These require the player to evaluate opportunity costs and prioritize which goals to pursue and which ones to sacrifice.  (NW_Kohaku, Improved Farming, original post, section "Choices".)
2. Assist Toady One in defining and implementing a stated goal of "lands with more variety."  (Me, this thread, reply #110.)
3. Provide a well-described physical mechanism for how cavern plants grow without sunlight.  (Requested by NW_Kohaku, Improved Farming thread, reply#236 (linked to in the same thread, reply #3). Also in this thread, original post.  Answered by me, this thread, primarily in reply #85 and reply #124.)
4. Explain why nearly all current cavern plants only grow in certain seasons, even though the temperature swings that define seasons on the surface do not occur underground.  (NW_Kohaku, this thread, reply #67.)
5. Explain why magical creatures (for example, the giant animals found in Savage areas) are different from their mundane counterparts.  Re-phrase: Explain how they got that way.  (Me, this thread, reply #85, section "Implications Part 3: Magically Altered Creatures".)
6. Make inorganic creatures an integrated part of the ecosystem.  (Me, same post, section "implications for how it should be implemented," item 3.)
7. Support increased numbers and diversity of magic-users. (Me, same post, section "Implications Part 2: Magical Creatures," items 3 and 4.)
8. Permit and support an alchemy system. (NW_Kohaku has started an entire thread on the subject.  Also by me, this thread, reply #110, section "Alchemy.")
9. Permit changes during play to surroundings, and give players the means to trigger those changes.  (Me, this thread, reply #121, section 6.) The main Improved Farming thread focuses instead on changing biome (NW_Kohaku, Improved Farming, reply #1, section "Forestry, Wild Soil, Soil Erosion, and Ecological Damage.")
10. Support a religion system, with real gods capable of answering prayers. (Me, this thread, reply #85, section "Implications for how it should be implemented," item 4; and section "gameplay implications," item 5.)
11. Minimize the impact of the various improvements on FPS and RAM use. 

I may edit this list later if I decide I missed something.

Yep, I missed something.  Was it somehow so obvious it got missed? 
Inserted as 3 and 4, with numbers after that shifted to match.

[Tristan Alkai]

With WHY explained, I need to explain HOW my system works toward those goals.  The one that I think needs the most elaboration right now is goal 1. 

1. Give the game more depth by presenting the player with conflicting goals.  These require the player to evaluate opportunity costs and prioritize which goals to pursue and which ones to sacrifice.  (NW_Kohaku, Improved Farming, original post, section "Choices".)

NW_Kohaku described how it applied to Improved Farming in general.  I need to describe how it applies to xenosynthesis in particular.

Again, i use spoiler tags to divide the the post into smaller, somewhat more manageable, sections.

Relevant Crop Types

Spoiler (click to show/hide)

As I have set it up, there are several different kinds of "crops" available for a player to grow. 
> I named six, with varying degrees of directness, in this thread, reply #124.
1. Mundane
2. Deciduous alch
3. Deciduous-dependent xeno
4. Broadcast alch
5. Broadcast-dependent xeno
6. Ingredient alch
> IndigoFenix, in this thread, reply #104 (and my response to it in reply #105) described another one. 
7. Portal-dependent xeno
> NW_Kohaku named another one, in the Improved Farming thread, reply #4, section "But what do I actually do as a Player?".
8. Fungus

These assemble into four clusters, each with strategic strengths and weaknesses. 

Cluster 0: Fungus

Spoiler (click to show/hide)

1. Fungi do not generate new organic matter.  At best, they can covert it from a form dwarves can't eat to one they can.
2. There are also mycorrhizae, which help plants gather nutrients and therefore grow better.
3. Fungi are a supplement to the other clusters, not a cluster in their own right.  They are, at least in principle, able to supplement any of the other four.

Features:
1. The post from NW_Kohaku that named fungi also named an important function for them: generate soil where there had not been any before.  The example presented was planting plump helmets on logs gathered from the surface.
2. After the visible mushrooms are harvested, the "roots" of the fungi will remain in the developing soil. If xeno plants were subsequently planted in the same field (which is all but guaranteed), that crop of plump helmets may be able to establish itself among them as a mycorrhiza. 
3. If successful, the plants would grow more vigorously, and the plump helmets would send up periodic volunteer mushrooms.
4. Dwarven farmers would be able to notice that certain fields grow more plants, and select plump helmets from those fields for planting in subsequently created fields, a selection pressure in favor of increased mycorrhizal ability and efficiency.

Cluster 1: Surface

Spoiler (click to show/hide)

1. Includes mundane and ingredient alch plants.  Neither generates any mana for the caverns. 
2. Human farming depends primarily on mundane plants, which are mostly grown for food and alcohol.  Some provide cloth or dye instead.
3. Ingredient alch plants are, of course, useful as ingredients in alchemical reactions.
3. Due to the circumstances under which mana energy storage is favored (described in reply #124, above), most ingredient alch plants probably won't be good for much else.

Features
1. Since neither plant variety grows underground, or supports plants that do, all the fields are on the surface.  This limits food security.
2. Again due to reasons covered in reply #124, most ingredient alch plants will be highly drought-tolerant.  They will favor desert and similar biomes.
3. On the other hand, they will, as a rule, be either highly flood-intolerant or easily out-competed by weeds when well-watered.

Trade-offs
1. "Cool stuff" (alchemical products) vs Easy embark
> Alchemical products will need to be quite powerful to make this a true trade-off rather than a style project.
2. Roof or Greenhouse (Security) vs. Rain-fed (Productivity and Maintenance)
> This trade-off also applies to Deciduous and Broadcast clusters, because they involve surface plants.

Cluster 2: Portal Xeno

Spoiler (click to show/hide)

1. Portal xeno plants, of course, use mana that enters the world through portals. 
2. The only such features currently in the game are the eerie glowing pits in the circus.

Features:
1. Productivity will generally be quite limited.
A. Most of the mana is probably blocked by the slade layer.  There's not much the player can do about that. 
B. Most of the rest is probably blocked by the cotton candy.  Removing this block is possible, but extremely risky.
C. Most of the rest is blocked by plants growing wild in the various cavern layers.  Reducing this block is possible.  While not nearly as deadly as the circus, the caverns aren't exactly safe either.
2. With only the one kind of mana, food variety is quite limited.  This opens the possibilities of dwarves growing tired of the food, and of malnutrition.
3. On the other hand, the portal is not (currently) susceptible to any attempt to disrupt or close it.
4. In addition, the fields themselves, being underground, can be made quite secure.

Trade-offs
1. Productivity vs. Security
2. Variety (supplied by other systems) vs. Security

Cluster 3: Deciduous

Spoiler (click to show/hide)

1. Includes deciduous alch plants and the deciduous-dependent xeno plants they support.
2. Deciduous alch plants release significant quantities of mana only during fall, when they drop leaves and go dormant.
3. Deciduous xeno plants thus have some similarity with surface desert plants: mana replaces water.  Mana is only available intermittently, but is predictable.  Xeno plants must either tolerate or avoid the long gaps of no mana.

Features:
1. Avoidance takes the form of an annual growth pattern.  The seed evolves to detect the "mana rain" as a signal to sprout, then the plant will grow quickly, flower, and produce seeds before the mana runs out.   Such plants would have very quick growth cycles, potentially two months or less.  That plant then dies, but the seeds remain for next year.
2. For dwarves to grow such plants, the optimal strategy is to plant the xeno seeds just before the alch plant is due for harvesting. 
3. This results in two distinct "harvest times" (some staggering of food production), but most food is produced in fall or early winter, and must then be stored until the next harvest.  It is potentially vulnerable to rot and vermin.
4. Mana "drought tolerance" would involve either a long dormant period or some form of mana storage.  I believe dormancy more likely. 
5. Most dormancy type plants would probably be biennial or worse.
6. Those that store mana would likely make valid alchemical ingredients, but harvesting that storage would kill the plant, and could easily interfere with seed production.

Trade-offs
1. (Relative to Surface) Productivity vs. Simplicity
2. (Relative to Portal) Productivity and Variety vs. Security

Cluster 4: Broadcast

Spoiler (click to show/hide)

1. Includes broadcast alch plants and the broadcast-dependent xeno plants they support.
2. Broadcast alch plans release significant quantities of mana throughout the growing season. 
3. The sheer quantity is also much greater.  The mana release of deciduous alch plants is essentially an accident, but the release of broadcast plants is an inherent aspect of how they grow.  Their steady output throughout the growing season almost certainly produces more mana per day than the deciduous mana rain, even at its peak.

Features
1. The broadcast occurs throughout the growing season, which is generally quite long. 
2. The broadcasting plant maintains itself using the broadcast, which requires sunlight but not water.
3. The plant needs water to generate new tissue, so it may have a dormancy period of sorts, but the broadcast is, as a rule, not subject to that constraint.  The "broadcast season" is likely to be much longer than the "proper" growing season.  Desert plants could easily keep it up year-round.  Alch plants growing in other hostile biomes like the tundra may or may not manage this.
4. Ignoring animals (plants only) and considering the conditions under which broadcast alch plants tend to compete best, most of the food production will probably occur underground (xeno plants).
5. Food production is relatively continuous, so storage and spoilage are less of an issue.  Pests attacking the growing crops might be more dangerous than otherwise, since there is no winter to make them freeze or starve.
6. Broadcast alch plants, more than any other variety, provide a niche for mana-using wildlife.  These are potentially better for food (giant animals, for example), but also potentially worse (undead and, barring mods, animal people).  They are universally much more powerful fighters either way, and thus more easily become a security concern.
7. If the player manages to capture and tame the magical animals, they become a substantial military benefit.

Trade-offs
1. (Magical animals) Risk vs. Reward
2. (Also) "Cool stuff" vs. Security and Easy embark
3. Security advantage, because broadcast alch plants are much easier to maintain than most others in a "greenhouse plus irrigation" environment.
4. (Relative to Deciduous) Harvest and store (vermin) vs. continuous production (pests)

[Tristan Alkai]

Okay, I am finally non-busy enough to give this thing proper attention. 

I would strongly prefer to actually win the debate with GavJ, not just chase him(?) off, so back to that, including some more articulate phrasings of previous segments of the argument. 

On Magma photosynthesis:

Since in DF, temperature doesn't move beyond 1 tile from a source, and since even then, it's only like 100 degrees F or something right next to magma, plants or bacteria could possibly grow immediately over the magma sea using magma light for photosynthesis (like on the ceiling of the magma sea), as a primary producer, and then the grass and stuff you see in the caverns just has "roots" (in quotes because they're for food nutrients more than water) that go down there and continuously gobble up the photosynthetic bacteria. This also relies on an EXISTING miracle of weird thermodynamics in the game that are unlikely to change.

DF is explicitly still in alpha testing.  When something in DF does not make sense, and is not blatantly magical (undead and mud men, for example), my default assumption is that it is a quirk or limit of the game's engine that will be corrected at some point.  "Existing miracle" is irrelevant. 

For magma not transferring heat properly, another explanation is Rule of Fun.  After all, magma forges would not be very useful if magma was hot enough to cook a dwarf alive from ten tiles away.  Plants nearby surviving to use the illumination would then be "collateral weirdness," which I have mentioned with distaste before. 

On "leaves" growing from above through the ceiling:  Rule of Fun does not protect this area (except through collateral weirdness), since dwarves are unlikely to be found there.  There is also the minor detail that the Manera, which (from its description in the raws) is supposed to crawl on the ceiling, currently can't manage it with the game's engine. 

On fringe science:

I'm mostly indifferent on chemosynthetic plants vs magic-eating plants, but I lean slightly toward chemosynthesis because it's neat to have fringe science stuff in the same world as magic (hard fantasy).

This scenario comes across to me as "have your cake and eat it too."  If magic is demonstrably present, then I would rather not bother with "THIS part is plausible!" fringe science.  Just eat the cake and explain things with magic.

That's not what the phrase having your cake and eating it means...? I really don't know what you're saying here.
Limiting a necessary evil to... only the necessary amounts of it is perfectly logical.

Magic and fringe science are both stepping outside established knowledge and physics.  As I understand them, the only difference is that magic admits its implausibility, making it more honest.  When presented with the choice, I prefer magic over fringe science for this reason.  Fringe science always comes across to me as "use magic but pretend we're not."  This is acceptable in some genres, but DF has blatant, unambiguous magic, so I don't see the benefit.  Using fringe science and admitted magic in the same setting comes across to me as hypocritical. 

That was what I meant earlier with "THIS part is plausible!" fringe science.  This part (fringe science) is "plausible" (have your cake ... too) but this other part (magic) is not (eat it).  Using magic and fringe science in the same setting is an attempt to be selective.  I see it as complicating things for no benefit. 

Note that none of this criticism of fringe science applies to real science. 

On mana vs mundane:

Just divert or block the field. No need for it to run out.

If the field is getting diverted or blocked, then there must be something in place to KEEP it blocked.  Due to like reality unless noted, I consider "mundane" the default, and mana a deviation from that default, a reverse of the position you outline.  Your solution also implies that at some point the block will STOP and the magic will come back, which we do not observe.  The magic goes away, and STAYS away.  I prefer to explain this in terms of continuous local mana production, which creates a reserve that can be depleted and run out.

No offense, but why does it matter what you arbitrarily "preferred" or "considered" previously? That's not a game design argument.  It's just as good at face value either way, yet mana on by default comes out significantly ahead, because it offers a significant benefit in simplicity by not requiring multiple conversion methods (even MORE conversions for multiple kinds of mana), not requiring as complex of an ecosystem...

What I arbitrarily considered was not the only thing I brought in.  I followed it up with the observation that, once "the magic goes away," it does not come back.  This is not some arbitrary preference of mine; it can be observed and verified within the game. 

Continuous local mana production during the Age of Myth that stops when the relevant plants and megabeasts get killed off prevents that return much more satisfactorily (i.e. much more permanently) than some sort of nebulous "mana shade."  It is also much easier and more intuitive for the player to figure out how to trigger and/or prevent, which IS a game design argument. 

On limited herd sizes:

Also overall amount of life is way less than on Earth.

I always took this as a limitation of the game engine, that would be corrected later.  I remember reading on the wiki that the game limits animal herd sizes at a fortress to about 50 per species (they don't get pregnant or lay eggs past that point), presumably for FPS and/or RAM reasons.  These are the ONLY logical reasons I can come up with for this behavior.

You mean, except the other logical reason I just gave...? More limited energy source = fewer organisms, fits perfectly.

The game as it stands now has a flat, arbitrary population cap.  My complaint is not that the cap is too low.  My complaint is that it is too "flat."  That is to say, that it does not adjust automatically to local circumstances.  If it were due to food issues, that should be reflected in the code, such as animals not being fertile for some time after being starving (and possibly "hungry" as well).  This would provide a dynamic cap that adjusts to current local circumstances.  A flat arbitrary cap is for either player sanity or keeping RAM and CPU use under control. 

Perhaps I phrased it badly earlier.  Food is an acceptable reason for the behavior itself (limited herd sizes), but hardware concerns were the only plausible reason I could come up with for the current implementation of the behavior. 

I will have that post on "Properties of Mana," and why I feel that each is important, in a few days. 

[MDFification]

Did you just say chemosynthesis violates the known laws of physics?

I don't think you have a very firm grasp on chemosynthesis m8. It's not fringe science- it's a real biological process that has been observed in both extinct and existant life forms. If you want, read up on it. It's practically the norm for ecosystems located in low-light environments.