Origin of Life: Exactly how and when did life on Earth originate? Which, if any, of the many hypotheses is correct?
Arthropod head problem: A long-standing zoological dispute concerning the segmental composition of the heads of the various arthropod groups, and how they are evolutionarily related to each other.
Biological aging: There are a number of hypotheses why senescence occurs including those that it is programmed by gene expression changes and that it is the accumulative damage of biological processes.
Extraterrestrial life: Might life which does not originate from planet Earth also have developed on other planets? Might this life be intelligent?
Cambrian explosion: What is the cause of the apparent rapid diversification of multicellular animal life around the beginning of the Cambrian, resulting in the emergence of almost all modern animal phyla?
Alkaloids: The function of these substances in living organisms which produce them is not known
Gall wasp: It is largely unknown how these insects induce gall formation in plants; chemical, mechanical, and viral triggers have been discussed.
Butterfly migration: How do the descendants of Monarch butterfly all over Canada and the US eventually, after migrating for several generations, manage to return to a few relatively small overwintering spots?
Homing (biology): A satisfactory explanation for the neurobiological mechanisms that allow Homing, has yet to be found.
Basking shark: Only the right ovary in this fish appears to function, the reason is unknown.
Hammerhead shark: The reason for their distinctive and unusual head structure is not known.
Blue Whale: There is not much data on the sexuality of the biggest animal ever.
Fairy circle (Africa): There is intense debate about the formation process of the circles. Research has shown that some can be explained by the activities of the sand termite, Psammotermes allocerus but there is no theory explaining all Fairy circles.
Loricifera: There are at least 100 species of this phylum that are yet to be described, but none of them is known to be present in the fossil record.
Adaptation: At present there is no theoretical model for how adaptation occurs that is close to being complete. Mathematical models of evolution (e.g. within population genetics) describe how the process of natural selection influences the frequency of already-existing gene variants based on their relative fitnesses. Only a small amount of theory treats the problem of modelling the generation of new variants through mutation, in terms of either fitness or phenotypic form.