"the Behaviour of these Animals was so orderly and rational"
Gulliver with Horses
Public DomainGulliver with Horses

Gulliver begins to suspect the horses are intelligent and unable to conceive of intelligent horses, prefers the theory that they are human beings who have taken on the shape of horses through magical arts.

Swift describes the horses physically as simply horses. Science Fiction writers of modern day might try to describe the horse with an enlarged head to account for a larger brain and the intelligence the Houyhnhnms.

If Swift ignored the matter of the equine brain in postulating an intelligent horse, his comtemporaries would not have seen anything wrong.

Andreas_Vesalius
Public DomainAndreas_Vesalius

Andreas Vesalius

(1514 - 1564) the father of anatomy, had maintained that the brain was the seat of the intelligence,

 

 but this remained little more than a suggestion until the work of

Franz_Joseph_Gall
Public DomainFranz_Joseph_Gall
Franz Joseph Gall

(1758 - 1828) some seven decades after the publication of Gulliver's

Travels.