Hello, linguist here. It's a very interesting find, but I'd like to assure people this is in no way representative of either a writing system or spoken language. (Edit: No, the article does not claim it is. Redditors are. I'm sorry for the confusion). Both are fairly impossible to have occurred among Homo naledi.

The etchings are non-repetitive, drawn over each other, and seem to mimic natural shapes rather than geometric shapes. One wall appears to contain a depiction of a skeletal ribcage. We can only speculate as to what was going through the minds of our ancestors and cousins at the dawn of intelligence, but this is likely no more meaningful than a chimp playing with its poop. I'm intending accuracy, not glibness; there is nothing here.

Communication systems don't actually require enormous brains, and 'EQ' only gets you so far. Parrots and great apes are capable of learning many of our associative concepts. But they'll never learn syntax. Syntax, or word order, or more accurately the relationship between words, is an emergent property of the architecture of a human brain. It's inherited, and it's young. It's thought to date between 40K and 100K years in our evolution, probably between the last and second-to-last migration out of Africa. An inherited trait, it was only passed on sexually. It's the reason a parrot, for example, can have an impressive vocabulary and yet never learn pivots or theta roles that let it interpret complex human sentences. It can't acquire anaphors and recursiveness. In a sentence like Mary hit John, it can't tell you who was hit and who did the hitting, even if it understands who Mary and John are, and what hitting entails. We know this because modern humans in cases of abuse, who never acquired syntax before puberty, when that window of our development closes forever, can't make these determinations. We know at least this aspect of language has a biological basis that is species-centric and must be primed by one's environment.

Writing, which is not language but an imperfect means of encoding language, is much younger than the development of syntax in Homo sapiens sapiens. It has in fact only been independently invented 3-4 times in our species' history (China, Mesoamerica, and Egypt-Sumer depending on whether you accept those last two as distinct)—all of which in the last 6-7 thousand years, with 2000 of those years being proto-writing. That's 6000 years out of potentially 100,000 years of combinatorial spoken language, which Homo naledi would not have had.

Tl;dr: It's inconceivable that a species can independently create a writing system without having the spoken tools for the writing system to encode, and those tools never belonged to another Homo species than our own. This is the equivalent of very undetailed, very damaged cave art. I don't mean to downplay the discovery, but people are already jumping to conclusions and need to kick it back a notch and appreciate this for what it is.