Science academies generate 4 culture per turn on marathon, and Military academies 3 per turn, so it's well worth creating both a science and military academy in each of your 3 culture cities if you are going for a culture victory, as the culture multipliers from cathedrals, certain wonders, Free Speech, etc all go to make the base 7 culture well worth the investment. Two academies generating a base of 7 culture is more than double the culture of most national wonders and even more than certain world wonders.
Even if you are not going for a culture victory, the additional culture they generate can help in the early / middle period. Example: you may have an important border city with a key resource that can't hold it's borders, because it's to culturally weak, but you are not in a position to go to war.
Aside from the culture benefit, you have to think carefully about creating academies in the early / classic period if you plan on having an early war as your economy will probably crash. If it does crash your economy may result in 0% science, in which case you are far better off settling an early scientist, because of the 6 beakers it gives you, (more with Representation). So, if you are in the early / classic period, have a scientist to use, and are about to go to war, fiddle about with the science slider and your crystal ball and try and work out if you are better off with an academy or settling him/her.
The first scientist in the early / classic period may be better spent on that first Golden age, if you are wonder building. If you follow the top of the tech tree, and chop libraries + run 2 scientists specialists in your cities, then there is a strong chance you will get an early Great Scientist at circa Aesthetics, which has 3 wonders to attached to it.
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The combined power of the Great Library + the scientist specialists will generate so many great person science points that you are guaranteed more and more Great Scientist. This can be a good thing if you want more of them, but it will get in the way of your producing different types of Great People from other cities. With the Great Library under your belt at that stage of the game, and some interesting wonders just up ahead, you may want to think about easing up on the scientists a bit, so as to give another city a chance of producing a Great Engineer. As you are running Representation, you have the Pyramids, so providing that it's not in the same city as the Great Library, then you do have the capacity to pop a Great Engineer just when you need one. If the Pyramids is in another city, then in your shoes I would ease up on the scientists and go for a Great Engineer and pick up one of those wonders before you hit the the long dry spell when there are no wonders to buld.
Regards -Mr P