The finding last month that a group of fossils from a cave not far from Johannesburg belongs to a previously unknown human ancestor would appear to cement South Africa’s status as one of the world’s leading hotspots for research on human origins. But it also provoked a backlash from a few influential national figures who associate the finding with five decades of apartheid governance.

A paper in the journal eLife last month that pegged Homo naledi as a new member of our genus Homo prompted a leader on the South African political scene to engage in a muddled questioning of the theory of evolution and a denial that humans were in any way related to other primates. The comment provoked a flare-up that highlights the still-open wounds from the country’s apartheid’s past. Blacks during the apartheid era were often depicted, even in the universities, as less than human. (Scientific American is part of Nature Publishing Group.)

The spat began when trade unionist Zwelinzima Vavi tweeted: “No one will dig old monkey bones to back up a theory that I was once a baboon.”1 South African Council of Churches President Bishop Ziphozihle Siwa concurred: “To my brother Vavi, I would say that he is spot-on. It’s an insult to say that we come from baboons.”  The interdenominational council, which unites 36 churches today, played a major role in the anti-apartheid struggle when it was led by the likes of Archbishop Emeritus Desmond Tutu. Siwa’s words were echoed by African National Congress politician Mathole Motshekga who said “… it is offensive that the findings made are used to say that we are the descendants of baboons, because we are not.”

In responding to these remarks in press accounts, Lee Berger, lead researcher on the H. naledi study, explained that humans do not descend from baboons. Evolutionary biologist Richard Dawkins jumped in, tweeting back: “Whole point is we’re all African apes.” All living humans, regardless of race, are members of Homo sapiens, a species that originated in Africa and is ultimately descended from a common evolutionary ancestor shared with African apes.

The sentiment deriding H. naledi was by no means universal; most South Africans expressed great pride in the finds. Deputy President Cyril Ramaphosa, according to one local news report, said that H. naledi proves that “the Cradle of Humankind [the area where the fossils were found] is the umbilical cord of our humanity.”

The reaction by these South African public figures, and the social media storm, can be better understood in the context of apartheid’s persistent legacy. “A lot of Africans have some suspicions of scientific ideas, especially evolution,” says Zinhle Mncube, an associate lecturer in philosophy at the University of Johannesburg. “Craniology, phrenology, eugenics; they were all used to justify the idea of the African as subhuman.”

These pseudosciences of the 19th- and early 20th-century were a “foundational moment for the colonial project,” says historian Noor Nieftagodien, head of the History Workshop at the University of the Witwatersrand. “According to the social Darwinism of that era, the pinnacle of evolution was the blonde, blue-eyed man with the blonde, blue-eyed woman just beneath him and the colonial subject at the bottom of the heap.”

During the apartheid era, some prominent white churches also “mobilized to support the claim of black inferiority,” says Nieftagodien, an uneasy partnership that created a powerful and remarkably persistent ideology. To this day, the pejorative bobbejaan (baboon) is still used by some South Africans.

The white-man-at-the-top hierarchy left a deep impression in the minds of many Africans. Nowhere has the damage been as profound as in South Africa, colonized for more than three centuries and dominated by apartheid’s white minority government for 50 years.

Even today, two decades after apartheid rule, South Africans still receive reminders that the apartheid dogma of black’s racial inferiority was promulgated even in the universities. In 2013 a doctoral researcher in anthropology at Stellenbosch University found a human skull, glass eyes and hair color charts in a storage cupboard; these turned out to be tools developed by Eugen Fischer, the eugenicist who inspired Nazi theory, and were used to teach volkekunde (an apartheid form of cultural anthropology)—a stark demonstration of how the trappings of science were used purposefully to underpin and reinforce the idea of racial inferiority that linked black Africans with apes.

Bringing these effects out of the closet spurred the founding of a project called “Indexing the Human,” led by Steven Robins, a professor in the Department of Sociology and Social Anthropology at Stellenbosch. It aims to explore deeply-held assumptions by society and academia, emerging from the historical context of colonialism, about what it is to be human in South Africa and the Global South.

The experience of being treated as the relatives of apes and monkeys could explain why, as Mncube notes, this gut rejection to the link with H. Naledi tends to come from older rather than younger people. But young South Africans have not escaped the sting of these old wounds entirely. The current student protest movement that started with the slogan “Rhodes must fall” at the University of Cape Town seeks the decolonization and transformation of South Africa’s academic institutions. The statue of British imperialist Cecil John Rhodes at the university was seen as symbolic of the Western bias of academe—and was ultimately removed.

The response to H. naledi shows an unfamiliarity with the science that ultimately overthrew the racist pseudosciences, Nieftagodien says. Evolution is poorly taught, if at all, and little understood, Mncube adds—so people fail to see that the fossil finds support a common origin for all humankind and debunk the concept of races. “If scientists listen to what people actually know, they will understand the need for ongoing education projects that explain key concepts like evolution,” she notes.