I'm so glad others are thinking of this issue also. I've only ever taken one class in the Philosophy of Science, and ever since then the whole tech-tree approach to technology has seemed hollow (but in tech-tree's defense, it's easy to understand and gamify)
I think we could divide the population into two categories; the farmers and non-farmers. Of course the farmers need to be productive enough to feed the non-farmers. The non-farmers, even if they know nothing of the scientific method, will still do stuff that develops technology. (and of course the farmers would advance farming technology)
Now I would say for all eras, beakers should come from the portion of the population that doesn't need to produce food to feed itself. Of course this won't really fit in Civ, because it is common to have a large portion of your population doing things other then food production from the outset (ie you have a tile producing 2 food, then one population can do something completely non-food related). This is necessary for the Civ games because you need population to produce hammers to expand.
An alternative approach would be for a more organic spread of your civilization into adjacent regions. This expansion could essentially be limitless, but if you never focus on improving farming or literacy, you'll never have the excess population do non-food production tasks.
