The article did not clearly explain what cognitive science has to do with phonics, which AFAIT is a heuristic system for Western languages. So when I studied Chinese as a child, how did I learn to write Chinese, nonphonetically, without confusing horses and ponies? A heuristic is an optimization but not fundamental but the article clearly asserts that phonics is fundamental to language in that if you don't use phonics you get illiterate students... I think there's some conceptual conflation or some middle case being ignored by the author: A) Is [formal instruction in] phonics necessary? v.s. B) Is 3-Cue harmful? These are not proper opposites.
Here's a provocative claim made in a more sciencey article I just found:
"The linguist David Crystal (2003) estimates that the phonics can explain only about 50 percent of English spellings."
And further down:
"As the linguists Venezky (1967) and Carol Chomsky (1970) explained, English prioritizes the consistent spelling of morphemes over the consistent spellings of phonemes."
Before that ... who knows? I think English was mostly phonetic at the time, with modern inconsistencies being a more modern innovation. Sight-reading was almost unheard of, everyone read by sounding words out aloud (presumably subconsciously sight-reading as they got better at it). Presumably teachers used phonics of some kind since it never even occurred to anyone that people did anything other than read phonetically.
But, again, what were literacy rates like in 1890 or 1960?
In other words:
> For some people it doesn't matter what method you use
This is a theory cop-out. If people figured out how to read and write well without phonics, that's worth investigating too. And it's unlikely that they also succeeded just because they were geniuses or had some secret unknowable method.
Also, replying to someone asking a genuine question with totally different question is bad manners, and I'm going ask that not be done here.
The article makes the explicit point that significant percentages of children can learn to read despite being sabotaged by a bad learning system. (In part because some students figured out how to spell words out phonetically in their own.)
The formal phonics system might be recent, but the phonetic nature of our writing system is ancient.