Compartmentation is the term for the biological technique that allowed complex organisms with eukaryotic cells to develop from less complex prokaryotic cells. In the primordial period of life on earth, most organisms were simply bags of cytoplasm. They didn't really have a nucleus, or any complex organelles, simply taking care of all their functions in the soup swirling around inside their membrane. This is actually a pretty efficient way to live and reproduce, which is why there are still plenty of prokaryotes with us today like bacteria (with 'plenty' being defined as a whole fucking lot of them).

Through response to surroundings over time, however, something interesting happened. Larger prokaryotes began to absorb smaller prokaryotes, but instead of immediately digesting them, the smaller ones simply hung out inside the larger ones, continuing their more specialized activities. This happened enough, over thousands of years, that division began to incorporate the smaller prokaryotes as well, with both the larger and the smaller dividing at the same time to create twin compliments.* The smaller, surrounded prokaryotes became more specialized, more adapted specifically to aid their larger host prokaryote, and VOILA! You have compartmentation and a eukaryotic cell.

Compartmentation is an efficient method of allowing two unrelated, or even opposite reactions to occur within a cell without having them interfere with each other. It allows the cell to multitask. Each organelle or subsection of the cell isolates itself for a special metabolic pathway, and carries taking in raw materials and spitting out the needed compounds smoothly for another specialized section of the cell to handle. In your average cell there are hundreds of different metabolic pathways (series of reactions oriented toward a common goal) going on at one time, which would not be possible with compartmentation.

Another advantage of compartmentation is that it localizes everything one needs for a reaction in one spot. The reactants are concentrated and may catalyze each other, speeding up the reaction, wasting less energy, and all-around increasing efficiency. Nature adores efficiency. The more complex your organism, the more specialized and intricate compartmentation mechanisms you'll find. They can even be taken to the macro-level, with whole collections of cells compartmenting a specific collection of metabolic pathways in organs or tissues. The large-scale anatomy of the human body is really just a sort of metacompartmentation.

*: Ahh, but I hear some people objecting, especially devotees of creation science, where's the evidence?! There's plenty, actually. For example, mitochondria have their own genetic code entirely independent of the DNA in the nucleus of a cell. This happened for a reason. Mitochondria are suspected to have originally been their own cells, prokaryotes specialized in the break down of fatty acids for energy. An explination for the redundant DNA is difficult to make otherwise (unless one would like to invent a reason to fit one's own theory). Prokaryotes being absorbed for their special purposes in modern life include photosynthesizing bacteria which can develop into chlorophyl. It's not just a cockneyed idea, there's clear evidence of the process both today and in historic development. There are, of course, other conflicting scientifically valid explanations for the development of organelles, but this is the most widely accepted as far as I know.

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