as for negative number in nature (as opposed to just in the brain), they don't really exsist. as was mentioned above, there are opposites; there are also really small amounts of things. but as far as we know, there isn't really negative "stuff". even if you have one anti-proton, you still have one of something, which is positive. IMO, negative numbers are a human invention.
when talking about the brain, chaos theory and attracting as detracting point are very usefull in the discussion of self-regulating systems. for instance, the presence of molecule x causes the amount of molecule y to go down. the lack of molecule y prevents the production of molecule x. there is therefore an attracting point for both molecules x and y, wherein a certain amount of each will most often be found in an uninterrupted system.
For a more concrete example, say you like philly cheesesteaks. you go and eat one. the next day, you have a second one. you do this for a month, and you realise you are really sick of cheese steaks. so you stop eating them all together. a few months go by, and you realise you miss the taste of cheesesteak, so you go have one. The amount of cheese steaks that you desire is being self regulated based on the amount of cheese steak you consume. the more you eat, the less you want, and vise versa.
so in this discussion, negative nembers equate to small amounts of, or a complete lack of a given molecule. positive numbers would equate to large or increasing amounts of a given molecule. these systems in the brain largley self-regulte based on simply chemistry, and behind that, simple physics. chemical bonds between like molecules and the breakdown of others will invite the desire to replace the supply. you don't need to know that you want more cheesesteaks, you just know you do because they provide both physical and psycological satisfaction.