ROVING REPORTERS: Inside the Gauteng caves where rocks reveal the mysteries of Homo naledi

A Soweto-born geologist is investigating the rocks and sediments of the Rising Star caves for clues to how Homo naledi lived, buried their dead – and ultimately disappeared.

One wrong move could have sent Tebogo Makhubela plunging into a deep crevice inside South Africa’s Rising Star Cave system. Crawling through passages barely wide enough to squeeze through, the geologist was studying the cave’s sediments, searching for clues hidden in layers of ancient mud and rock. Those clues would help place him at the centre of an ongoing and contentious debate on human evolution.

The incident happened on the final day of an expedition in 2019. Makhubela, the only geologist in a team of five, was navigating a treacherous fracture when a boulder broke loose and came rumbling down the rock face, missing him by mere centimetres.

“It was rumbling, you know, rolling and beating both sides of the wall as it tumbled,” Makhubela recalls. Once the boulder passed, the near miss washed over the researchers.

“We had a very silent moment,” says Makhubela. “We all just became teary, appreciating that nothing (fatal) had happened.”

For the past decade Makhubela’s life has been intimately tied to the Rising Star Cave, where he studies the soft, flour-like sediments surrounding the fossilised remains of Homo naledi, an extinct species of archaic human discovered in 2013 in the Rising Star Cave system.

Despite Homo naledi having a brain “the size of a small orange”, Makhubela believes that Homo naledi deliberately buried its dead in the confines of the cave. His view is supported by research he co-authored with an international team, published in eLife in September 2025 (Evidence for deliberate burial of the dead by Homo naledi).  

The idea that a species existing 200,000 years before Homo sapiens engaged in burial practices has fiercely divided the scientific community. Makhubela says some global colleagues have dismissed the idea as “hogwash” and “impossible”.

Among the scientific challengers is University of Cape Town geologist Professor Robyn Pickering, whom Makhubela used to refer to as his “academic sister”. They both shared the PhD supervisor, geologist Professor Jan Kramers, although a decade apart.

Pickering has spent the past 24 years studying the geology and dating of cave systems across the Cradle of Humankind. Her co-authored research challenging the Rising Star burial claims concludes that the available sedimentological and geochemical evidence does not support deliberate burial. Makhubela remains convinced that it does.

Pickering stresses that the critique is strictly scientific: “This is not personal; our position is evidence-based,” she says. “The empirical geochemical data shows that the sediment around the fossils is not statistically different to the rest of the cave, and so cannot be used to support the deliberate burial hypothesis. How we tell the stories of human evolution is important – we need to be led by the data itself, not by presupposed interpretations.”

Extinction questions

Makhubela is now exploring a new mystery: What drove Homo naledi to extinction? Given evidence of rivers drying out and food availability shrinking during harsh winters, he is asking whether this extreme climate shift may have played a role in their disappearance.

“We can safely assume that they just never moved away from the Cradle and that they never adapted to the conditions,” Makhubela says. “So, they then became extinct.”

Makhubela is due to present this research at the Oppenheimer Generations Research Conference on Wednesday, 7 October. His presentation, titled “From cave to landscape: New insights into the depositional context, paleoenvironment, and behavioural significance of Homo naledi”, will explore the geological and environmental evidence surrounding the species.

Unlike other hominid species whose remains are scattered across the continent, Homo naledi has never been found outside South Africa’s Cradle of Humankind. For Makhubela, this suggests a tragic failure of adaptation. Reconstructing the ancient landscape of 300,000 to 200,000 years ago, his geological research shows that the region went through sweltering climates – much hotter than today – interspersed with periods of severe aridification. During these harsh, dry winters, rainfall was virtually nonexistent, springs flowed thin and the vegetation shifted, leaving Homo naledi highly vulnerable. Unable or unwilling to migrate, they met their end in the very landscape that had sustained them.

Makhubela’s own journey to tracing these ancient extinctions is itself a story of unexpected turns. Raised in Chiawelo, Soweto, by a single mother who sold food at the Johannesburg taxi rank after leaving a polygamous marriage, he became the first in his family to attend university.

Initially, his dreams lay in the courtroom. At high school, he became captivated by the American television series Boston Legal and resolved to study law. But his brother, a policeman, was strongly opposed to the legal profession. As a strong science and geography student, Makhubela pivoted towards engineering, a field in which corporate funding was abundant.

In January 2009, he stood in a slow-moving registration queue at the University of Johannesburg to sign up for electrical engineering, armed with three lucrative mining bursary offers. But as the queue crawled forward, he began to question his choice. He slipped away to the Faculty of Science to ask about geology – a field that had captured his imagination years earlier through repeated VHS viewings of the disaster movie Dante’s Peak.

After accidentally standing in a long queue meant for bridging-course students, an administrator noticed his stellar matric results, pulled him into her office and typed his registration details. When she asked what subject he wanted to pair with geology for his double major, he blurted out “mathematics” just to complete the process, later switching it to his passion of chemistry after his first semester.

His first real encounter with the underground had occurred years earlier, at the age of 17, when he was selected for a school trip to the Sterkfontein Caves – an opportunity earned because of his top-tier academic marks. “I just remember having so many questions,” he recalls of his first time underground. 

When he finished his honours degree, he turned down a lucrative job offer to work in a commercial gold mine. During a university field excursion to a platinum mine in Limpopo, he had raised his body in an 80cm-high working section and hit his helmeted head against the rocky roof with such force that it turned him off mining completely.

He chose to pursue master’s and PhD studies to stay in academia – only for his research to send him right back into the caves. “Ironically, my research sent me into the caves which are actually more chaotic spaces underground than mines.”

While Makhubela continues to defend the controversial burial hypothesis against global critics, his geological detective work has recently collided with an even more baffling genetic mystery.

He says recent protein analyses conducted on the teeth of the excavated Homo naledi fossils have revealed an astonishing pattern: every single individual analysed so far is female. There are no males represented across any of the different age groups in these chambers.

“Now, that’s a serious mystery,” Makhubela says.

It raises profound questions that the scientific team is still trying to untangle: Did Homo naledi bury their females separately from the males, or did they only practise burial for females? If so, where are the male remains?

For Makhubela, this ongoing detective story highlights a profound truth about our place on Earth. He quotes the phrase, “Heredity, nothing. Environment, everything” – a belief that upbringing and learning can completely shape a person, overriding their tribal or genetic background – and argues that we are not merely defined by our genetics, but deeply shaped and sustained by the geological environment we inhabit.

He wants modern audiences to realise that our connection to Earth is as physical today as it was for our ancient ancestors. The silica in our phone screens, the rare earth elements used in many technologies and the mineral resources that underpin modern agriculture and industry all ultimately connect us to the rocks beneath our feet.

“The Earth has always been part of our story,” Makhubela says, noting that as we face modern climate challenges such as sweltering summers and rising floods, we cannot afford to forget our geological roots. “We cannot escape that... hopefully, this will drive protection of the environment and the Earth.” DM

This article was produced by Roving Reporters in collaboration with Jive Media Africa, the science communication partner for Oppenheimer Generations Research and Conservation.

Dr Tebogo Makhubela’s presentation at the Oppenheimer Research Conference, taking place in Midrand from 7 to 9 October, will be live-streamed at this link: ORC 2026.