I'm of the opinion that most synthetic/unnatural drugs end up destabilizing the equilibrium under which neural feedback pathways work.
Woah, woah, woah. You are barking up the wrong tree here my friend. There is no such thing as "unnatural". That's a complete fallacy. You're claiming that two chemicals that are identical, one derived from an organism, and the other synthesised in a lab, yet functionally equivalent, will have different effects when consumed in identical situations?
Not exactly. I'm claiming that synthetic molecules that would not exist from organically (perhaps co-)evolved processes (i.e. not in a lab from fallible humans playing God) tend to not be meant for our bodies which evolved in for the most part untampered nature for the majority of our timeline. As an example, synthetic Vitamin C (D-ascorbate) is not the full Vitamin C complex (L configuration of ascorbate):
"Ascorbate may also act as an antioxidant against oxidative stress. However, the fact that the enantiomer D-ascorbate (not found in nature) has identical antioxidant activity to L-ascorbate, yet far less vitamin activity,[3] underscores the fact that most of the function of L-ascorbate as a vitamin relies not on its antioxidant properties, but upon enzymic reactions that are stereospecific.
[3]Aboul-Enein HY, Al-Duraibi IA, Stefan RI, Radoi C, Avramescu A (1999). "Analysis of L- and D-ascorbic acid in fruits and fruit drinks by HPLC". Seminars in Food Analysis 4 (1): 31–37.
So, my supposition is that things like MDMA and amphetamines are typically bad for you because 1) the chemical reaction from breaking these molecules down is not something our bodies evolved to break down and 2) the bioactivity from these reactions taking place in our bodies disturb the sensitive equilibrium they were meant to operate at.
Oh ok. I misunderstood what you were getting at. I see what you're trying to say but it's just one of those things that people can only speculate on for now. Personally, I think our bodies have evolved to be quite adept at breaking down a wide variety of molecules. But it's not something we're going to really know the answer to for a long time. It's going to take a lot science to begin to answer those type of questions.
It is the Golden Age of Neuroscience. The field is learning new things every day.
http://www.ncbi.nlm.nih.gov/pubmed/15228154
Human pharmacology of MDMA: pharmacokinetics, metabolism, and disposition.
MDMA metabolism is rather complex and includes 2 main metabolic pathways: (1) O-demethylenation followed by catechol-O-methyltransferase (COMT)-catalyzed methylation and/or glucuronide/sulfate conjugation; and (2) N-dealkylation, deamination, and oxidation to the corresponding benzoic acid derivatives conjugated with glycine. The fact that the polymorphic enzyme CYP2D6 partially regulates the O-demethylenation pathway prompted some expectations that subjects displaying the poor metabolizer phenotype may be at higher risk of acute toxicity episodes. In this metabolic pathway a mechanism-based inhibition of the enzyme operates because the formation of an enzyme-metabolite complex that renders all subjects, independently of genotype, phenotypically poor metabolizers after the administration of 2 consecutive doses. Therefore, the impact of CYP2D6 pharmacogenetics on acute toxicity is limited. One of the interesting features of MDMA metabolism is its potential involvement in the development of mid- to long-term neurotoxic effects as a result of progressive neurodegeneration of the serotonergic neurotransmission system.