The above issues are not detrimental to evolution as such, nor do they necessarily lead to a conclusion that species were created as separate units by an external agency. For instance, the genomes of all organisms are clustered in a relatively small region of DNA sequence space forming a tree of related sequences that can all be inter-converted via a series of tiny incremental steps. So the sharp discontinuities between different organs and different types of organisms greatly diminish at the DNA level. What looks very different on the macro level, may not be so different on the DNA level:
...in DNA sequence space it is possible to move at least hypothetically from one adaptation (position) to another in DNA space via functionless or meaningless intermediate sequences. This is because a DNA sequence does not have to be functional to survive and be passed on through the generations. In fact, the greater part of all the DNA in nearly all the cells in higher organisms, although it is copied faithfully at each cell division, is never expressed... It is very easy to imagine how an evolving DNA sequence might be passed silently down through several generations before being expressed... [this] means that new sequences and hence new evolutionary innovations can be generated, at least hypothetically, via functionless intermediates. Thus, new organs and structures that cannot be reached via a series of functional morphological intermediates can still be reached by change in DNA sequence space. (Denton, 1998, p.278-279)
Some genetic changes, especially in higher organisms, have been largely a matter of the rearrangement of pre-existing genes rather than the emergence of new ones. Information specifying the future of evolutionary events may be stored in so-called junk DNA (non-protein-coding DNA). Many such sequences have been conserved over millions of years of evolution. This, however, does not explain the enormous increase of the DNA chain throughout evolution, and even if it is assumed that these dormant genes are the key, the questions remains why they are passed over to the next generations when they are not needed, and even more importantly, why they become active just when they are. To repeat, these objections do not invalidate the idea of evolution as an organising principle, only its reductionist interpretation. The above arguments are an attempt to show that mechanisms that Neo-Darwinists use to explain the evolutionary process are not sufficient, strongly indicating directed evolution:
The sudden emergence of an entirely new type of organism, or of a functionally perfect novel organ system, would be almost impossible to account for except within some kind of directed evolutionary or teleological framework. (ibid., p.296)
If this is the case, it is reasonable to consider what is the minimum that such a framework would require.