Chemistry. Proteins and amino acids. In human body, as far as I know, all the proteins we use are made outta L-amino acids, meanwhile there are also D-amino acids and those last mentioned are mainly toxic for us.
When I was reading <PERSON> answer, it reminded me about a case with one frog/toad that has poison on her skin all over the body. I don't remember the species name of it but that's not the thing. When this frog was discovered scientists tried to make a lab sample of its poison. The poison was in fact a protein, so they've made a sample using necessary for this protein amino acids, but when it came to testing... It was harmless.
Several years later, it was discovered that the reason for this was in two amino acids that were of D-type, meanwhile scientists were working with L-types. So, as soon as they've changed the L-types to D-amino acids, poison started working as it was supposed to.
The main point of mentioning proteins and amino acids is to show how the structure of something's chemical formula might affect its characteristics. Now for the answers:
1) Where is this "miasma" coming from: let's suggest that plants or some minerals (or a combo) do produce some sort of gas (further NPG – nature produced gas), which is spreading pretty fast and that they produce it in large amounts due to the current atmosphere balance of elements and gases.
2) Why there was no “miasma” before: it was but in a much lower amount. When humans and others arrived their activities have changed the balance of elements and agents in the atmosphere as well as other factors like temperature and more or less – climate. 1022
This ended up in plants/minerals/combo being able to produce ways more NPG and allowed NPG to stay longer in the atmosphere without wearing off as it used to be before. Also check № 4).
3) Why not all the living things are affected: for wildlife forms (birds, animals, insects and apparently orcs and others too) - they do either eat the plants, or the fruits of those plants, or do lick/add to the food while cooking the minerals (like some wild pigs to get salt and some other minerals) which makes them Immune due to feeding chains. Alternatively, they eat/harm themselves with the crystals to store them/their parts in the blood/bodies, which provides constant resistance while the crystals are in.
4) How do crystals work: Those crystals are natural antidotes, due to producing agents/substances (further CPS - crystal produced substance) that are binding the NPG particles. The short-area effect is due to that CPS is wearing off in a changed atmosphere/climate unlike NPG, which is now able to be more stable. Also that is onother reason why there was no “miasma” before – original atmosphere’s balance of gases and temperature allowed CPS bind with all the NPG produced, but now crystals produce less CPS and it is not so stable.
5) Alternatively, in case the wildlife/orcs & Co do not eat/harm themselves with crystals, but do add NPG-producers to their meals – crystals might be affecting them negatively (same way as “miasma” affects humans & Co) but only when crystals are close enough. This might also be a reason for faction conflict.
P.S.: I have only a slight knowledge of biochemistry (attended couple of lectures and seminars). Also some (or many) grammar/spelling mistakes might acquire. I’m really sorry for this, I was using MS Word to check it. Feel free to correct me where I was wrong. Thank You. 1022