The Neo-Darwinian synthesis has stood as the mainstream view of evolution for some fifty years. It is the result of integrating Charles Darwin’s theory of evolution with insights from the field of genetics launched by the research of Gregor Mendel. Darwin asserted that the fossil record of plant and animal life records a history of descent from a common ancestor with the successive evolution of more complex forms being guided by natural selection operating on heritable variability; genetics offers a means for generating the heritable variability through random mutations and random genetic crossover. Today, the Neo-Darwinian synthesis stands in need of a major upgrade to incorporate newly gained insights into the sources of greater complexity and of heritable variability. Included in these new insights are symbiogenesis, genetic transfer between organisms, non-random variation, Inherent Directive Nature, and Prototypes.
Symbiogenesis is evolutionary change initiated by a long-term symbiosis of dissimilar organisms. Margulis and Sagan (2002) claim that the standard model of Neo-Darwinism greatly overemphasizes random mutation as the source of hereditable variation. Rather, they maintain, the major source of transmitted variation is acquired genomes—entire sets of genes fully functional in whole organisms (usually microorganisms or small organisms) that are acquired and incorporated by other organisms. This long-term biological fusion of organisms, beginning as symbiosis, is held to be one of the important mechanism by which new species can be formed.
For example, lichens are a composite comprising a fungus and a photosynthetic partner (usually either green algae or cyanobacteria, but in some cases yellow-green algae, brown algae, or both green algae and cyanobacteria) whose metabolisms are so well harmonized and intertwined that they together act as a unit distinct from either of the component parts. Lichens are considered to be a prime example of symbiogenesis in which fungi have acquired cyanobacterial or algal genomes.
Another example is the photosynthetic animals or plant-animal hybrids in the form of slugs (shell-less mollusks) that have green algae in their tissues (such as Elysia viridis). These slugs are always green, never need to eat throughout their adult life, and are "permanently and discontinuously different from their gray, algae-eating ancestors" (Margulis and Sagan 2002). This is held to be another example of a symbiosis that lead to symbiogenesis.
Yet another example is cattle, which are able to digest cellulose in grass because of microbial symbionts in their rumen. Cattle cannot survive without such an association. Other examples of evolution resulting through merger of dissimilar organisms include associations of modern (scleractinian) coral and dinomastigotes (such as Gymnodinium microadriaticum, a marine protozoan with two flagella) and the formation of new species and genera of flowering plants when the leaves of these plants integrated a bacterial genome.
The formation of eukaryotes is postulated to have occurred through a symbiotic relationship between two kinds of prokaryotes, a theory called endosymbiosis. According to this theory, mitochondria, chloroplasts, flagella, and even the cell nucleus would have arisen from prokaryote bacteria that gave up their independence for the protective and nutritive environment within a host organism.
Margulis and Sagan (2002) state that the formation of new species by inheritance of acquired microbes is best documented in protists. They conclude that "details abound that support the concept that all visible organisms, plants, animals, and fungi evolved by "body fusion."
The conventional paradigm of the theory of descent with modification presumes that the history of life maps as the "tree of life," a tree beginning with the trunk as one universal common ancestor and then progressively branching, with modern species at the twig ends. However, that clean and simple pattern is being called into question due to discoveries being made by sequencing genomes of specific organisms. Instead of being simple at its base, the tree of life is looking considerably more complex. At the level of single cells, before the emergence of multicellular organisms, the genomic signs point not to a single line of development, but rather to a bush or a network as diverse microbes at times exchange their genetic material, especially through the process of lateral gene transfer.
Other complicating factors are proposed based on the relatively sudden appearance of phyla during the Cambrian explosion and on evidence that animals may have originated more than once and in different places at different times (Whittington 1985; Gordon 1999; Woese 1998; Wells 2000).
The current paradigm of the theory of natural selection is that the process has a major stochastic (random) element, with heritable variation arising through chance, and then being acted upon by the largely non-random force of natural selection made manifest as various species compete for limited resources. An alternative view is that the introduced variation is non-random.
In particular, various theistic perspectives see directed variation, from a Supreme Being, as the creative force of evolution. Natural selection, rather than being the creative force of evolution, may be variously viewed as a force for advancement of the new variation or may be considered largely inconsequential. Some role may also be accorded differential selection, such as mass extinctions. This view sees the evolutionary process as progressive, non-materialistic, and purposeful.
Neither of these contrasted worldviews—random variation and the purposeless, non-progressive role of natural selection, or purposeful, progressive variation—are conclusively proved or unproved by scientific methodology, and both are theoretically possible.
For a theological point of view, there is the concept that everything in creation has an inner aspect or mind. This mind can be considered the impulse behind self-generated order, complexity, and the evolutionary process. Thus, there is an inner force in nature that directs nature toward greater complexity and eventually consciousness.