I just do not understand this concept for whatever reason.

For instance, how is having a library only in your 'commerce/science cities' supposedly better than having one in all of your cities?

Why wouldn't you want to have a balance of commerce/shields in all cities?

If you focus only on commerce in certain cities, how can you produce the shields needed to build all the necessary buildings in that city for a 'commerce city'?

For instance, how is having a library only in your 'commerce/science cities' supposedly better than having one in all of your cities?
Because you've gotten the same benefit for much less cost. If you have libraries in your commerce cities, then you've already boosted most of your research - and the hammers that would have gone to build them everywhere else can be spent on other things. Like units.

Why wouldn't you want to have a balance of commerce/shields in all cities?
Because then you gain less benefit from each building, so that, again, you have to invest far more hammers to get the same benefits.

If you focus only on commerce in certain cities, how can you produce the shields needed to build all the necessary buildings in that city for a 'commerce city'?
Pop-rush, chop-rush, or cash-rush.

An illustration may make things more clear. Suppose I have two cities, one with 40 hammers and no commerce, and one with no hammers and 40 commerce. (I choose 40 to make the numbers come out nicely, but there's no specific relevance to them.) I can then build one forge, and one library (say I whip them) and get 10 hammers and 10 beakers (assuming 100% research).

Whereas if both cities had 20 hammers and 20 commerce, each building would only give a bonus of 5, instead of 10. So, I have to build twice as many buildings for the same effect.

An illustration may make things more clear. Suppose I have two cities, one with 40 hammers and no commerce, and one with no hammers and 40 commerce. (I choose 40 to make the numbers come out nicely, but there's no specific relevance to them.) I can then build one forge, and one library (say I whip them) and get 10 hammers and 10 beakers (assuming 100% research).

Whereas if both cities had 20 hammers and 20 commerce, each building would only give a bonus of 5, instead of 10. So, I have to build twice as many buildings for the same effect.

Alright, I guess that makes sense.

But since the numbers will never be that perfect and every city will be producing some amount of commerce, at what point (commerce-wise) do you decide to invest in a library or not?

Alright, I guess that makes sense.

But since the numbers will never be that perfect and every city will be producing some amount of commerce, at what point (commerce-wise) do you decide to invest in a library or not?

Here's a general rule: decide what the city will specialize in, and build improvements and buildings appropriate to that type.

If it's a Commerce-type city, then you'll be building cottages almost exclusively, and building libraries and Universities. You'll also be building banks in this type of city as well, since you need them to build Wall Street.

If it's a production-type city, then you'll be building mines and workshops (plus the farms to support them) and building forges and factories.

Generally, a Civilization needs only two production cities (one for units with Heroic Epic and West Point, one for Wonders with Ironworks) and a Great Person Farm (with National Epic)... all the rest of your cities should be commerce-type cities. This includes your Super-Science city (Oxford University) and your Wealth City (Wall Street plus your best shrine).

The key thing to remember is that each citizen consumes 2 food. Most production-heavy tiles do not produce enough food to support the citizen working them. That means you need other tiles producing excess food so citizens can work mines, quarries, and so on, while still allowing the city to grow. That almost always means farms instead of cottages.

For example, suppose you have a city with a mix of hills, grassland, and plains. You build a mine on one of the grassland hills. It produces 1 food and 3 hammers. To work the mine, you now need two farms on two grassland tiles; one to provide the extra food for the citizen working the mine, and another to provide a measly +1 food surplus for city growth. You can't put cottages on those tiles and still work the mine. Even if you were smart enough to include a food resource in the city's fat cross, you will, eventually, run into this food deficit your production tiles create.

Therefore, a city with high production potential (mostly tiles with hills and forests, and production resources like copper, iron, or stone) will have lower commerce production. And the opposite is also true.

Grassland on rivers and floodplains have an automatic +1 commerce bonus, and they produce enough food (1 extra for floodplains) to be worked. These are generally the best tiles for cottages; however, they provide no production. So a really good commerce city will usually have relatively lower production. This is not just a result of the tiles and how you choose to improve them, but a result of which tiles you have your limited population work.

(You could build cottages on plains and farm the grassland, and some players do. However, now you're trading what would have been a self-supporting commerce tile (grassland) for a 1 food deficit tile and one lousy hammer.)

So even if you choose a supposedly-balanced city site with a mix of the above tiles, by improving those tiles and assigning citizens to work them, you are, by those very acts, making that city specialize. By specializing your buildings to enhance the city's tile production, you are capitalizing on each city's strengths.

I think its best to specialize your home town (1st city) to commerce because the palace gives you +8 coins. It also makes sence to build a library there. But when? And I was thinking it is also worthwhile to produce Libraries in other towns just for the culture because a Library is better than an Oblisk, it has an added benefit of science. But, then doesnt your home city need to produce stuff initially too? So, the first town, usually has the best of everything, but beyond that specializing does make sence.

Specializing is all good, but there isn't anything wrong with building a few extra buildings in your specialized towns, when you dont need to make any more units.

:) Alright, thanks, I think I understand it alot better than I did.

It is not always possible to fully-specialize cities. Suppose you have some hills around a city, which would make it a good production city. But if at the same time it has more food than it is needed to work all the mines, you can just cottage the extra tiles, or farm them and run specialists.

In this case a "specialization" would mean that you build the usual stuff for a production city, like granary + barracks + forge, then units. You can even use the food surplus to whip a few units with Slavery.

But when you no longer need more units, you can switch it as well to build some city improvements, like libraries or banks.

There are things like Oxford or Wall Street: before you can build them, you need N Universities and Banks in your cities. Now if you build them in such "hybrid" cities, you can get your Oxford or Wall Street earlier, without waiting until your less-productive commerce cities complete theirs.

Strictly speaking, you should probably be using Workshops/Watermills instead of Cottages in that production city. But, sure, it isn't always necesarry to overdo the specialization.

Strictly speaking, you should probably be using Workshops/Watermills instead of Cottages in that production city.
Yes, that's true, but they come into play a little bit too late. In fact, they are pretty much useless before Biology-Electricity. After that, yes, I even replace sometimes quite a few cottages in my commerce cities to boost production.

But before, I'd rather build farms and use Slavery, if I really really need more production.

Strictly speaking, you should probably be using Workshops/Watermills instead of Cottages in that production city. But, sure, it isn't always necesarry to overdo the specialization.

Remember, you need enough food to support working every tile, and since you'll be running mines on your hills, you will probably need to farm up all those squares.

Remember, you need enough food to support working every tile, and since you'll be running mines on your hills, you will probably need to farm up all those squares.

My original comment was in response to the suggestion of using flatland for cots instead of farms once you had enough food to support hills.