New species may have relatives in next villlage
There´s one HUGE problem with this "brain disease" theory. People with this disease are totally and utterly helpless for their entire lives. And the best specimen of Homo floresiensis is that of a 30-year old person. How likely it would have been that a person with microcephaly could have lived to an age which a healthy person at the same era often didn´t make? I think that the answer is very close to a zero. I don´t think for a second that they would have survived in any other society than the modern industrialized one, which can afford to save their lives and care for them.
And then it´s quite questionable to link 13 000 year old remains to modern people living at the same place, even if both are dwarf sized. At least without a DNA test. And I doubt that the modern persons are aflicted with microcephaly.
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