Because sponges contain a variety of chemicals that affect living organisms (bioactive compounds), they have become the subject of research to find drugs to treat human diseases. Haplosclerida sponges have been especially fruitful for bioactive compounds. The upwards of 30 compounds called 3-APs found in haplosclerids have properties such as keeping bacteria from growing and stopping cells from dividing. Not only might they be valuable for human medicines, but they also help the sponge stay healthy. A greasy coating of 3-AP compounds on the surface of a haplosclerid sponge is like a repellant for bacteria and other organisms that could contaminate it. The trick for our using these compounds is how to get large enough amounts without hurting wild populations of sponges. Scientists are working to synthesize (make copies of) compounds like the 3-APs rather than take them directly from sponges.

Sponges have an internal skeleton, but it is not made of bone like ours. Their skeletons are made of stiff, mineral rods called spicules, or a matrix of strong but flexible protein called spongin, or both. Spicules may be loosely scattered in the body tissue of a sponge, gathered into little bundles, or arranged in symmetrical patterns to form a structured skeleton. You can judge a sponge by its spicules. They come in many shapes, from as simple as toothpick-straight to complex, branching stars. The end of each spicule is specialized too; it may be pointed, flat, shovel-like, or even look like a mushroom cap. By using microscopes to look at spicules (which are tiny), scientists are often able to identify the type of sponge they came from. Given that the spicules are often all that remain of a dead sponge, this is quite handy.

Because sponges cannot move quickly, they need ways to defend against predators other than fleeing. Some sponges have sharp skeleton parts (spicules) that protrude from their bodies and are also shed to make a spiny carpet around them. Chemical defenses are critical for sponges, too. Their bodies contain a range of chemicals that can make them bad-tasting or even poisonous to predators. Some of the chemicals are produced by microscopic organisms (such as bacteria and fungi) that colonize them. Both the sponge and the microbe get something out of such mutualism, with the sponge providing a home and nutrients for the microbe and the microbe working with the sponge to make defensive chemicals. Humans may benefit from this relationship as well, because many chemicals isolated from sponges have anti-cancer and anti-bacterial properties. Scientists are isolating specific chemicals from sponges to create life-saving drugs such as the anti-cancer Ara-C.