He lived in Brazil for the rest of his life. He subsequently decided to study medicine. As a medical student, he began to question religion and in became an atheist , joining the Free Congregations and supporting free love.
Despite completing the course, he did not graduate because he refused to swear the graduation oath, which contained the phrase "so help me God and his sacred Gospel".
As a result, he emigrated to South Brazil in , with his brother August and their wives, to join Hermann Blumenau 's new colony in the State of Santa Catarina. The climate here is sub-tropical , and the vegetation typical of the Brazilian coast: it is not rain forest.
He negotiated a menu of botanical activities with the provincial government and spent the next nine years doing botanical research and advising farmers. A series of reports published in the Archivos of the National Museum record this work. At last this, the best period of his life, was brought to an end indirectly, by the overthrow of the liberal monarchy of Dom Pedro II in The new Brazilian Republic was riddled with corruption and nepotism, and eventually there was a civil war in One of the mistakes made by the Republic was to withdraw support from the regions, no doubt to make sure resources went to the new rulers and their families.
Travelling naturalists were to be based in Rio de Janeiro, and instructions were sent out to the regions. His wife and several of the daughters also pre-deceased him; these losses affected him more than all the practical difficulties of life in Brazil.
