Synesthesia is a condition where attributes associated with one sense (say colour with sight) can be experienced in another inappropriate sense (say colour with the perception of musical notes). There are many kinds, and rare ones are still being discovered. There is no longer any question that these are ‘real’ perceptions and not hoaxes. Synesthesia seems to have its roots at the sensory level and is a bottom-up rather than top-down phenomenon. There is evidence for heightened sensory activity levels and of additional connectivity between sensory modalities. A lack of normal ‘pruning’ is one of the possible causes.
It is no longer a question that the condition is inherited it is. But not the specific type of synesthesia. Rather the genetic tendency is for any one or more of 60 odd varieties. Brang and Ramachandran (see citation) discuss the possible reasons for this condition not to be eliminated during evolution. Perhaps it has no disadvantage; perhaps it is a side-effect of a useful gene(s); perhaps it is the extreme of a normal distribution that includes us all.
Another possible explanation is that synesthesia simply represents the tail end of a normal distribution of cross-modality interactions present in the general population. Partial evidence supporting this idea comes as sensory deprivation and deafferentation (i.e., loss of sensory input through the destruction of sensory nerve fibers) can lead to synesthetic-like experiences. For example, after early visual deprivation due to retinitis pigmentosa, touch stimuli can produce visual phosphenes, and after loss of tactile sensation from a thalamic lesion, sounds can elicit touch sensations . More remarkably, arm amputees experience touch in the phantom limb merely by watching another persons hand being touched. Long-standing evidence has also demonstrated that hallucinogenic drugs can cause synesthesia-like experiences, suggesting the neural mechanism is present in all or many individuals but is merely suppressed. However, no research has yet established the relationship between these acquired forms to the genetic variant and whether the same neural mechanism is responsible for both.
And perhaps, synesthesia is actually advantageous. What are some possible plus points?
Synesthesia may assist creativity and metaphor it is more frequent in creative people and is a little similar to metaphor.
It may assists memory there is some evidence from savants.
There is enhanced sensory processing such as finer discrimination of colours
These demonstrations of enhanced processing of sensory information suggest a provocative evolutionary hypothesis for synesthesia: synesthetic experiences may serve as cognitive and perceptual anchors to aid in the detection, processing, and retention of critical stimuli in the world; in terms of memory benefits, these links are akin to a method of loci association. In addition to facilitating processes in individual sensory modalities, synesthetes also show increased communication between the senses unrelated to their synesthetic experiences, suggesting that benefits from synesthesia generalize to other modalities as well, supporting their ability to process multisensory information. Furthermore, others have argued that synesthesia is the direct result of enhanced communication between the senses as a logical outgrowth of the cross-modality interactions present in all individuals.
The puzzle of how genetically, how physiologically, and why it is that synesthesia arises will be very illuminating to the questions of how qualia are bound to objects and why we have the vivid conscious experience that we have.
Brang, D., & Ramachandran, V. (2011). Survival of the Synesthesia Gene: Why Do People Hear Colors and Taste Words? PLoS Biology, 9 (11) DOI: 10.1371/journal.pbio.1001205