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== Biological research ==
The islands have become a major case study of [[island biogeography]] and [[Founder effect|founder populations]] in an ecosystem being built from the ground up in an environment virtually cleaned.<ref name="Wilson 1999">{{cite book | last=Wilson| first=Edward. O.| title=The Diversity of Life| year=1999| publisher=W.W. Norton & Company| location=New York| pages=425| url=https://books.google.com/books?id=FzPaB_6Pw4MC&pg=PA16|isbn=978-0-393-31940-8}}</ref>

The islands had been little studied or biologically surveyed before the 1883 catastrophe—only two pre-1883 biological collections are known: one of plant specimens and the other part of a shell collection. From descriptions and drawings made by {{HMS|Discovery|1774|6}}, the [[flora]] appears to have been representative of a typical Javan tropical [[climax forest]]. The pre-1883 [[fauna]] is virtually unknown but was probably typical of the smaller islands in the area.

=== Botanical studies ===
From a biological perspective, the ''Krakatau problem''<ref name="Backer">{{cite book|last=Backer|first=Cornell's Andries|title=The Problem of Krakatau, as Seen by a Botanist|publisher=author, at Weltevreden, Java|year=1929}}</ref> refers to the question of whether the islands were completely sterilized by the 1883 eruption or whether some indigenous life survived. When the first researchers reached the islands in May 1884, the only living thing they found was a spider in a crevice on the south side of Rakata. Life quickly recolonized the islands, however; Verbeek's visit in October 1884 found grass shoots already growing. The eastern side of the island has been extensively vegetated by trees and shrubs, presumably brought there as seeds washed up by ocean currents or carried in birds' droppings (or brought by natives and scientific investigators). However, the floral ecosystem on Rakata is considerably vulnerable to environmental factors, and has been damaged by recent eruptions at Anak Krakatau.

=== Handl's occupancy ===
In 1914, plans were to set aside Rakata as a nature preserve. In 1916, Johann Handl, a German "[[pumice]] collector", obtained a permit to mine pumice, against "strong community objections",<ref name="thornton" /> apparently to get away from World War I.{{sfn|Winchester|2003}} His lease of {{convert|8.7|km2}} (basically the eastern half of the island) was to be for 30 years. Handl took up residence on the south coast of Rakata, where he built a house and planted a garden along with "four European families and about 30 [[coolies]]". Handl found un-burned wood below the 1883 ash deposits while digging, and fresh water was found below {{convert|18|ft|m|order=flip}}. He and his entourage stayed there for four years, but left due to "violation of the terms of the lease."<ref name="thornton" /> It is his party that is believed to have inadvertently introduced the [[black rat]] to the island, which quickly proliferated.{{sfn|Winchester|2003}}