The secret cocoons are the ones with the white lights and there are 44 of them total in the game. For the most part they aren’t hidden very well either. Finding these unlocks concept art in the Extras in the Bonuses Materials menu.
The gene cocoons are the ones with the green lights and there are 74 cocoons to find, each containing 2 genes totalling 148. Finding these lets you up-grade your abilities. Most of these cocoons (secret and gene) are fairly easy to find, as they are mostly out in the open.
I suggest you max out your Alien-view ability since it allows you to see objects of interest in the environment like health kits, ammo, hidden enemies, and cocoons to make it easier. Also be as thorough as possible by exploring everywhere you can go in every level (1-8) with the Alien-view on.
There is a guide for the cocoons located here.