Again, you've imposed this notion of "preexisting inbuilt internal mechanisms" onto scientific work, even though it's just not there.
How else can these mechanisms be understood. The new genetic info that organisms gain from other organisms they cohabitate with from processes such as HGT stem from preexisting genetic info and not something that has been mutated and selected for. The epigenetic changes in the way genes are expressed becuase of the way a previous generation acted or lived is based on preexisting genetic material that is expressed differently. Recombination is based on changing preexisting genetic material as with genetic drift and flow which are using prexisting genetic material to make changes in living things.
As the Nature paper mentions
" Valuable insight into the causes of adaptation and the appearance of new traits comes from the field of evolutionary developmental biology (‘evo-devo’), organisms are constructed in development, not simply ‘programmed’ to develop by genes". It states that variation is not random because
"developmental processes generate certain forms more readily than others" (Laland, Uller, Feldman, Sterelny, Muller, Moczek, Jablonka, Odling-Smee, Wray, Hoekstra, Futuyma, Lenksi, Mackay, Schluter & Strassmann, 2014). This for me seems to be indicating that inbuilt developmental processes are at work rather than external adaptive mechanisms. The paper gives the example where one group of centipedes, each of the more than 1,000 species has an odd number of leg-bearing segments, because of the mechanisms of segment development.
Developmental bias — helps to explain how organisms adapt to their environments and diversify into many different species. For example cichlid fishes in Lake Malawi are more closely related to other cichlids in Lake Malawi than to those in Lake Tanganyika, but species in both lakes have strikingly similar body shapes
4. In each case, some fish have large fleshy lips, others protruding foreheads, and still others short, robust lower jaws. The standard evolutionary theory would explain this as convergent evolution: similar environmental conditions select for random genetic variation with equivalent results which requires extraordinary coincidence to explain the multiple parallel forms that evolved independently in each lake. A more succinct hypothesis is that developmental bias and natural selection work together
4,
5.
Rather than selection being free to traverse across any physical possibility, it is guided along specific routes opened up by the processes of development5,
6, (Laland, et al, 2014).
Another non-adaptive mechanism is plastisidy and an example is given how a leaf shape changes with soil water and chemistry. As the Nature paper states
"the key finding here is that plasticity not only allows organisms to cope in new environmental conditions but to generate traits that are well-suited to them". Another non-adaptive process is Niche construction where creatures change their enviroment to suit them rather than through adaptations changing creatures to suit enviroments. As the paper suggests this makes living things active directors in their own evolution thereby biasing evolution rather than always being subject to the forces of natural selection through adaptations (Laland, et al, 2014). There are other mechanisms such as from ecology and social science which affect especially more complex life such as humans which can also have an effect on changing life in different ways.
So all these mechanisms use pre-existing genetic info and are pre-determined in the sense that they are biased toward certain developmental pathways and outcomes rather than subjeect to adaptive forces which are based on adaptations and survival of the fittest. Life is subject to a range of influences which can alter their developmental trajectories or the expression of their genes without the need of natural selection. The point is Natural selection has been attributed with every change that happens and all change has been seen in adaptive terms which is not the case.
Does evolutionary theory need a rethink?
Ok. But you're aware that mechanisms other than selection have been known for quite some time now, right?
Yes but for many people they are not acknowledged and instead natural selection has been given the credit either through ignorance or purposely elevating natural selection becuase it is a simple way of making a case for Darwins theory of evolution. One particular famous promotor is Richard Dawkins who has given natural selection an all powerful creative ability to help promote his beliefs aboiut evolution for which Lynch states has come at the expense of these other non-adaptive mechanisms.
Evolutionary biology is treated unlike any science by both academics and the general public. For the average person, evolution is equivalent to natural selection, and because the concept of selection is easy to grasp, a reasonable understanding of comparative biology is often taken to be a license for evolutionary speculation. It has long been known that natural selection is just one of several mechanisms of evolutionary change, but the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise (6) in the popular literature. For example, Dawkins' (7⇓–9) agenda to spread the word on the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, a view that is in some ways profoundly misleading.
The frailty of adaptive hypotheses for the origins of organismal complexity