Artistic License History / Serpent

• The whole premise of the novel, the claim that questioning Christopher Columbus' place in history was a heresy punished by fire by the Spanish Inquisition, is complete fantasy. The Inquisition did have their hands in civilian affairs, but keeping an official history of the discoveries was not among them, and the Spanish Empire in general was particularly bad at this job (as those very artistic licenses rather prove). Technically, there was no "heresy punished by fire" either, as any charge of heresy by itself could be escaped by publicly repenting; the Spanish Inquisition only burned heretics in the stake if they refused to plead guilty and repent despite overwhelming evidence or if they had committed a grave heresy more than once.
• In the novel, a Spanish historian claims that, because the Bible doesn't mention America, talking about the mere existence of a fourth continent was therefore heresy, which is why the Crown of Spain pretended that the New World was just part of the India or China. Even without going on the fact that the Crown of Spain was actually very quick to recognize the existence of a new continent, it should be noted that the Bible doesn't mention China either, as it simply doesn't go on about geography enough to clarify establish which lands is the Earth supposed to have. Anyway, this point in particular evidences a very Protestant-colored understanding of the Bible on Cussler's part; for the Catholic Church of the time, the Bible itself wasn't an ultimate authority on the topic of heresy (or any other), but rather the base of a doctrine that they administered and shaped to their judgement.
• Amerigo Vespucci didn't "scientifically demonstrate" that Columbus had discovered a new continent, only claimed so, and he did this in 1501, three years after Columbus himself had realized in the Orinoco river that he had found much more than a mere island (furthermore, it's now believed that Vespucci's 1501 booklet, where he made the claim, might have not been written by him to begin with). The name of America cannot even be attributed to Vespucci himself either, as it was actually the work of French and German cartographers who were impressed with Vespucci's supposed works and saw it fit to give that name to the New World. The same editors, by the way, later thought better and retired the name, but by then it had become popular in northern Europe and it stuck. In any case, the name America would take a long time for the Spaniards to acknowledge at all, as they usually referred to their overseas lands by the names of their viceroyalties (New Spain, Peru, New Granada, etc).
• It's also claimed that the Inquisition tried to eliminate Vespucci because his conclusions threatened Spain's sovereignty over America against other countries like Portugal. This fails to appreciate that, as Vespucci was a highly valued navigator for the Spanish crown, any conclusion of his about the New World's nature would have still placed it in Spanish hands. The claim is especially funny because Portugal of all nations had just struck an accord with Spain in the 1494 Treaty of Tordesillas, in which the two countries divided the world in two sections and agreed not to get in each other's domain (although both sides broke it a bit, Portugal by expanding Brazil more than initially agreed and Spain by taking the Philippines), so Portugal would have been the least of Spain's problems at the time.
• The novel also has Prof. Stefano Gallo claim, typically so, that the Spanish Empire was solely interested in "gold and slaves" during the Conquest of America. This succinct description would have fitted much more its Portuguese counterpart, a more commerce-oriented empire who had also the monopoly of the black slave market due to Africa falling on their side of the Treaty of the Tordesillas (and even so, the Portuguese were still interested in more things than solely gold and slaves). In the Spanish Empire, enslaving native people from the new territories was illegal, meaning that their official slave workforce, fed almost exclusively by the African market managed by the Portuguese, was never their priority; they were focused instead on turning natives into subjects and assimilating their indigenous political structures into productive provinces. They did adopt the native custom of turning war prisoners into slaves, but this was usually very limited in context and rules and wasn't that commonly done either.
• Contrary to what Professor Chi claims, there was no "genocide" of Mayan people by the Spanish Empire, and it would have been pretty difficult to achieve in any case. The Spanish Conquest of the Maya was very slow and gradual due to their highly decentralized society, their harsh terrain and climate, their lack of gold in plenty, and their remoteness from the main centers of development in México. Even whenever they made efforts to conquer it, the Spaniards generally adhered to their modus opperandi of teaming up with some local tribes, helping them conquer their nearest ancestral enemies, and Christianizing everybody to make them useful subjects and workers, so a gratuitous extermination was both difficult and self-defeating. In fact, given that those conficts were generally fought against small states every time, the conquest of the Maya didn't even feature the massive, bloody setpiece battles fought against the Mexica and Inca empires.
• Professor Chi also mentions Diego de Landa, a bloodthirsty Christian missionary who ordered the burning of most Maya codices, as an example of the Spanish Empire actively working to destroy Maya culture. He forgets to mention that De Landa was put in trial and sent back to Spain for his actions because their own superiors realized he was a complete loon. His destruction of the codices was lamented in the empire, as most higher-ups weren't usually opposed to conservate native artifacts or culture (which is, for instance, the reason why we have entire treatises on Nahuatl languages and why those very languages are still healthily spoken today in their native lands). In fact, two of the Mayan codices that still exist in real life were sent to Spain by Hernán Cortés himself as a tribute, and were conservaed and studied there.
• Speaking of Cortés, the book's character makes an unfavorable intellectual comparison to Napoleon because the latter included scientists in his expedition and Cortés didn't. The point is fallacious, as Napoleon's campaign toured through developed and familiar countries like Egypt and Syria, while Cortés was exploring fully uncharted territory three centuries earlier, in a time when scientific exploration was very primitive and the Indies were a veritable Death World – clearly not the kind of business for whose very first expedition you would summon non-combatant personal from the universities of Salamanca or Alcalá.
• Nina uses the Biblical name "Tharsis" to refer to Carthage. In real life, there are a lot of theories about what place did the Biblical authors mean by Tharsis, the main ones being Tartessos, Sardinia and the Phoenician coast itself, but Carthage is not among them. Tartessos has been traditionally considered the most likely option, with some authors having proposed that Tharsis was the native name of the Guadalquivir river, which the Romans got wrongly as Baetis because they mistook Tartessian script for Greek alphabet (the Tartessian T and R letters happen to resemble visually the Greek beta and delta, a confusion through which Tarsis became Badsis, later corrupted to Baitis).
• A possibly in-universe example happens when Gamay, while traveling with Chi, becomes shocked at the indigenous' knowledge of the jungle and wonders how did the Spaniards manage to conquer such resourceful people. This assumption is belivable, as there is no reason why Gamay, an average Jane not familiar with the Spanish Conquest of the Maya, should know anything beyond its Theme Park Version. In any case, the answer is very simple: as most Spanish conquests in America, the Iberians accomplished the submission of most Mayan tribes through the help of either other Mayan tribes or allied indigenous like the Tlaxcaltecs and Cholultecs.