Here's a interesting bit from PNAS a couple weeks ago:
One of the mysteries of creation is the origin of natural evil. We know that some of it came directly from the Curse (e.g., weeds), some probably from degradation of an initially perfect condition, and some from what I've called redesign - the needed re-configuring of creation and ecology to accommodate animal death. In the latest Answers magazine, Joe Francis distinguishes three possible origins of natural evil: modification, uncontrolled growth, and displacement - the movement of creatures or substances out of their intended environment, which can cause pathology. It would be nice if examples of natural evil followed one model of origin or another, but sometimes, it gets complicated.
The Plasmodium genus is one such complicated case. Plasmodium parasites need to get inside eukaryotic cells in order to complete their life cycles. If they would just do their business quietly, it would probably be no big deal, but when an animal or human becomes infected, they can develop malaria. Human malaria can be caused by four different malaria parasites, the most virulent of which is P. falciparum. A recent paper published in PNAS reveals that P. falciparum is a recent invader from a group of much older chimp parasites called P. reichenowi. That makes P. falciparum an example of displacement. Sort of. Joe describes displacement as "Microbes ... originally designed to perform beneficial functions in restricted places, but after the Fall they spead to other places and began to cause disease." Perhaps the chimp host was just a stepping stone to humans in a chain of displacement from some as yet unknown original, benign environment?
The highly complex life cycle, however, implies a group of diverse parasites designed to live inside eukaryotic cells. I do not know why God would make such creatures, but I do know that intracellular symbionts are not uncommon in creation. This could be an example of one that went wrong (by modification) and then diversified to infect many different species. Or it could be one of those re-designs.
Whatever it is, the answer is far from simple.
Francis. 2009. Good designs gone bad. Answers 4(3):32-35.
Rich et al. 2009. The origin of malignant malaria. PNAS DOI 10.1073/pnas.0907740106