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The University of St. Mark's at Lima enjoys the reputation of being the oldest in America; it has the distinction of having first begun its course by royal decree. The university in Santo Domingo in the West Indies was the first to be established by a papal Bull. Other similar institutions soon arose all over Spanish America, flourishing during the colonial period, under the joint auspices of Church and State. Then, when the Revolution came, they passed from the direct control of the former to that of the latter, with the exception of the University of Havana, which remained in possession of a religious order until late in the nineteenth century. It was in 1538 that a Bull of Paul III established the pontifical University of St. Thomas in Santo Domingo, at the request of the Dominicans. However, the institution was not definitively established, until Philip II gave it legal existence in 1558, seven years after the foundation of St. Mark's in Peru. The University of Santo Domingo had faculties of theology, jurisprudence, philosophy, and medicine, and lasted throughout the colonial period. The University of Lima was founded by decree of Charles V in 1551 in the monastery of the Holy Rosary, remaining under the direction of the Dominicans until 1571, when, being confirmed by Pope Pius V, it passed into the hands of seculars. The Dominicans still continued, however, to occupy posts of honour. For centuries the university exercised an influence that spread over all the colonies of Spain in South America, and many eminent men went out from its lecture-rooms. The renowned Pedro Peralta and the French savant, Godin, were among its professors in the eighteenth century, while such men as the poets Oña, Castellanos, and Olmedo, and the first American bibliographer, Leon Pinelo, were among its students. The faculties of the university included theology, jurisprudence, philosophy, medicine, and, for a time, the language of the Incas.

The next in importance of the Peruvian universities was that of Cuzco, founded, in 1598, as the University of San Antonio Abad. In the seventeenth century the University of Guamanga in Peru was established with the same faculties as that of Cuzco. In the meantime, university studies had been inaugurated at Quito with the establishment, in 1586, of the University of San Fulgencio, under the Augustinian fathers, by a Bull of Sixtus V. A second University of Quito, the one which gained the greatest prominence in the colonial period, was that of St. Gregory the Great, founded by the Jesuits in 1620. The early seventeenth century was a period of considerable literary activity and educational work in Spanich America, and several universities were founded. In 1627 the Dominicans succeeded in establishing their royal and pontifical University of Santo Tomas, at Santa Fe de Bogotá, while the Jesuits continued their old College of San Luis, founded in 1592, as the Xavierian University. The University of Santo Tomas obtained renown through such eminent jurists as Luis Brochero, and such linguists as the Dominican, Bernardo de Lugo. The celebrated historian of New Granada, Fernández de Piedrahita, Bishop of Panama, was a doctor of this university.

The Jesuits arrived in Chile in 1593 and at once inaugurated higher studies with chairs of philosophy and theology. However, the honour of founding the first university in Santiago belongs to the Dominicans. It was established in the Monastery of the Holy Rosary, under the title of Santo Tomas in 1619, by a Bull of Paul V, that permitted its existence for ten years. In 1684 its privileges were renewed by Innocent XI for a period to last until Santiago should possess a public university. The faculties included logic, history, mental philosophy, physics, mathematics, canon law, and theology. In the meantime, as early as 1621, the Jesuits had obtained from Pope Gregory XV the Bull "In eminenti" which granted the privilege of conferring degrees for ten years. This privilege was renewed by Urban VIII for another ten year s, and finally granted without limitation in 1634. There were thus two pontifical universities in Santiago. Finally, in the first half of the eighteenth century, Santiago beheld the foundation of its Royal University of San Felipe by a decree of Philip IV in 1738, with chairs of theology, canon and civil law, mathematics, cosmography, anatomy, medicine, and Indian language. About the time that the Jesuit and Dominican universities were established at Santiago, Characas, in Upper Peru, now Bolivia, beheld a university arise in that of St. Francis Xavier, founded in 1623. This became one of the most famous in the New World. Towards the end of the eighteenth century, however, the spirit of this university had grown to be quite anti-clerical. Yet it produced a number of distinguished men, such as Mariano Moreno, Bernardo Monteagudo, José Ignacio Gorriti, and José Mariano Serrano. In 1622 the Jesuit college at Córdoba del Tucuman, founded a few years earlier in what is now the Argentine Republic, was raise d to the rank of a university by a Bull of Gregory XV and a decree of Philip III. After the expulsion of the Jesuits, it passed for a brief period to the Franciscans, until towards the end of the eighteenth century it was taken over by seculars. Two universities were established in the eighteenth century, the one in Venezuela, the other in Cuba. In 1722 the old seminary of Santa Rosa, founded at Caracas by Don Diego de Baños y Sotomayor, was raised to the rank of a royal and pontifical university by a decree of Philip V and a Bull of Innocent XIII, the faculties of civil law and medicine being added to those that already existed. The year before the granting of the faculties to the University of Venezuela, the Dominicans of Havana had obtained from the same pope the privilege of establishing a university, which owing to some misunderstanding with the bishop, did not finally begin in the Dominican monastery until 1728. The title of Royal and Pontifical University was accorded to it in 1734.

Such was the condition of university education in the West Indies and South America up to the Revolution. Most of the old universities continued, but no longer under the direct control of the Church, passing generally, in course of time, to the Department of Public Instruction. St. Mark's at Lima still exists, and preserves its autonomy, with the old title of pontifical, and with a faculty of theology, though it is said that in its secular departments, its religious influence has passed away. The University of Cuzco occupies today a portion of the former Jesuit college. That of San Cristobal at Guamanga became extinct in 1878. The University of St. Augustine at Arequipa still exists, and Trujillo, where a college was founded in 1621, enjoys today the benefits of a university. The University of Sucre (Characas) is still regarded as the best in Bolivia, where the Universities, also, of La Paz, Santa Cruz, and Cochabamba exist. The Bolivian universities have faculties of theology, subject to ecclesiastical control.

Colombia has today a national university at Bogotá, consisting of faculties in separate colleges. There are also universities at Cauca, Antioquia, Nariño, and Cartagena. At Quito higher education is imparted in the Central University of Ecuador, priests, among them Jesuits, being permitted to hold chairs. Venezuela has actually two universities, the Central University and that of Los Andes. The old Jesuit University of Córdoba is today one of the three national universities of Argentina. At Santiago de Chile, the convictorium of St. Francis Xavier has become the Instituto Nacional, that serves as a preparatory school for the National University which is the historical sequel of San Felipe. The University of Havana remained in charge of the Dominicans until 1842, when it was secularized. It still exists, with faculties of letters and science, law, and medicine. At present there are two Catholic universities in South America, the one of Santiago de Chile, founded by Archbishop Casanova in 1888, and the other at Buenos Aires. The former has faculties of law, mathematics, agriculture and industry, and engineering. The Catholic University of Buenos Aires, still in the formative period, has faculties of law and social science. The tendency of South American universities today is rather practical than theoretical and classical, much stress being laid upon such studies as engineering and others of a practical nature.