
In which the mun thinks about this FAR too much...
As anyone with a shred of realism will tell you, chemical increase of intelligence is still a far-fetched, science-fiction idea, right up there with X-genes and the development of psionic abilities from the absorption of drugs in uetero.
What follows is the wildest of speculations:
Standard Injections
From not-quite-exhaustive research regarding the action of neurotransmitters and neuropeptides, it can be extrapolated that manipulation of such chemicals can result in vastly accellerated synaptogenesis. Also, actual neurogenesis might not be unheard of. The cerebrum of the typical specimen of R. Norvegicus is notably smooth when compared to that of, for example, a primate, affording ample room for the increased formation of gyri and thus, increased neuroconnectivity.
What the injections would have to consist of, then, is not the neurotransmitters or peptides themselves, rather, chemicals that stimulate increased endogenous production of said chemicals, finely tailored so that an overproduction of, for example, Substance P, doesn't completely disregulate pain sensations, or that a sudden influx of adrenaline doesn't explode their hearts. I imagine a lot of test subjects died in monstrous ways before this final formula was devised.
The finished serum, apparently administered as a kind of chemotherapy over time, would nonetheless hold a lot in common with Clair's "Zombie Juice" neuroregenesis serum, with overstimulation of random cerebral areas a key side-effect. Once the test subjects were physically recovered, then the cognitive testing and conditioning would ensue, ensuring an at least partial crystallisation of the newly formed pathways.
The serum's apparently drastic effects on not only the neurotransmitters and peptides of the subjects' brains but apparently also a partial resequencing of their DNA (producing a viable mutation), and its documented effects on the cellular decay of said subjects (again, possibly a product of the genetic resequencing, eliminating or at the very least decreasing the potency of genetic factors responsible for cellular decay), cannot be beleived to be lacking in long-term side-effects, as well as a few unforseen comorbid (for lack of a better term) manifestations:
The Case of Brutus
While the species R. Norvegicus is not without its variations in morphology re: physical size, it is documented that the character referred to as Brutus was a rat of prodigious size, possibly rivalling that of R. Norvegicus' cousin, the African/Gambian Giant Pouched Rat, which can reach a weight of up to seven pounds. This can, in probability, be attributed to an increase in pituitary output, as the marked increase in neurogenesis/synaptogenesis, is not unlike that seen in a mammal's embryonic/infantile stage. Giantism isn't without its systemic shortcomings, most notably early death due to congestive heart failure.
The Case of Nicodemus
In which woolly science reaches dizzying heights of implausibility.
It can only be supposed that, unlike the other escapees, Nicodemus was not a part of the test group that held the majority of the characters, but rather of a different group, of which he is possibly the only survivor. This can most plausibly account for the marked difference betwen him and the others, as none of the others present even a hint of psionic abilities.
Most likely, in addition to the drug treatments the others had recieved, this group received an additional round of treatments, ones responsible for an apparent hyperactivity of cerebral regions either dormant in the original brain of R. Norvegicus or created during the drug-induced synaptogenesis/neurogenesis. It's a long-held theory that the potential for psionics lies in the unused portions of the brain, one which has never, to my knowledge, been concretely refuted. This can easily account for the documented instances of telekinesis, clairvoyance, possible low-grade telepathy, and possible precognition.
The ocular bioluminescence is, however, not easily explained, except as some exaggerated from of retinal reflectivity, after the fashion of a tapetum lucidum. One can only speculate how difficult it is to sleep when confronted with the problem of one's own bioluminescence, especially one attained so unnaturally.
The metabolic strain of such hyperstimulation can account for the character's apparent impossibly advanced age, and the genetic resequencing can theoretically account for his survival in such a state.