But the whole point of Lovecraftian horror is that science is scary, because it pushes boundaries that ought not to be pushed; and that human science is futile, because it cannot explain things in the depths of space and in other dimensions. The "magic" of Call of Cthulhu is applied science that human minds cannot understand (sufficiently advanced technology is indistinguishable from magic, indeed!) - dimensional travel uses bizarre mathematics, etc.
If you look at the various devices in the CoC 5/5.5 rulebook, they're all so incomprehensible and powerful as to appear magical to humans who come across them - that's the point.
The origins of humans in the Mythos are pretty muddled. I can't recall if there's any definite origin for them, but there's a relation - in some direction - with deep ones, for instance. The Elder Things were probably involved, yes.