Long-standing arguments against the theory of natural selection arise from the appearance of incipient structures and complex traits in organisms despite the apparently stochastic nature of mutations. Many complex adaptations observed in nature today are thought to have originated from less complex adaptations with simpler functions. We therefore think that these characters were “pre-adapted”. To move from a simple to a complex structure, there must have been a transition phase, where both structures operate simultaneously or where the new function is assumed without interfering with the old function. These structures are characterized as incipient or incomplete, and given what we know to be true about natural selection and evolutionary theory, it becomes difficult to reconcile the idea that natural selection continued to favor these structures despite the lack of selective value. Incipient structures are thought to be neither large nor elaborate enough to serve an adaptive function and so it also becomes difficult to understand how larger complex characters arise. A discussion of morphological and developmental genetics explains that these structures serve useful functions from their simple origins, therefore being selectively favored while evolving to become large enough to accumulate new, more complex functions. Modification of pre-existing genes and regulatory circuits during early development has been widely studied in metazoans, Hox genes, and the development of complex structures such as eyes, limbs, and appendages. Phenotypic variation is therefore generated via modification of existing genes, regulatory processes and developmental processes and this variation is achieved in the middle of the article......7.Gould, SJ and Vrba, ES 1982. Exaptation- a missing term in the science of form. Paleobiology, 8(1): 4-15. Kirschner, M. and Gerhart, J. 1998. Scalability. National Academy of Science, 95 (1): 8429-8427. Liubicich, DM, et al. 2009. Knockdown of Parhyale Ultrabithorax recapitulates evolutionary changes in crustacean appendage morphology. PNAS 106 (33): 13892-13896Oster G. and Alberch, P. 1982. Evolution and bifurcation of development programs. Society for the Study of Evolution, 36 (3): 444-459. Shubin, NH and Marshall, CR 2000. Fossils, genes and the origin of novelty. Paleobiology, 26(4): 324-340. Shubin, NH, Tabin, C. and Caroll, S. 2009. Deep homology and the origins of evolutionary novelty. Nature, 457: 818-823. West-Eberhard, MJ 1998. Evolution in the light of developmental and cellular biology, and vice versa. PNAS, 95: 8417-8419.