Natural Selection's Limitations

Basic Natural SelectionPro took some burden off me by accepting the validity and providing an example of the basic evolutionary process to an extent, which indeed demonstrates changes in traits. My assumption is that he's going to argue on the basis of what's considered an "additional" trait and an implied lack of observation of gain-of-function mutations. Additional traits can't be differentiated from preexisting traits based on the effect alone, however. A change in an animals colouration is not necessarily equivalent to a single gene change in the creatures genome unless evolution has played a part in optimising the process (more on this later), but often multiple gene's which all have to change in the right way. This common objection some have is one of the core points I'm going to be addressing.I'd like to use a more practical and explanatory example natural selection as my main example of this in play (1). The DNA of mice had changed in multiple places in order for the mice to adapt to a change in environment. The colour change of the rocks they populated caused mice to be seen easily by predators. When a darker mouse arose, it had an advantage and was able to reproduce more dark mice. Natural selection plays little direct role in the mutation, but the selection of the mutation itself - though natural selection can also be considered to have affected this mutation a long time ago.Mutations we observe aren't usually without limitation. Creatures very rarely mutate without a leg, or with extra toes, etc. which is also due to natural selection. More specifically, it's due to the way certain genes grow stronger through repeated generations. What I'll refer to as "base genes" may occur through many thousands of generations of particular genes, in which any creature without those genes would never survive - and possibly may never even be capable of being born - the importance of survival before birth as part of natural selection is often hugely underestimated (sperm also need to survive).TraitsTraits cover a huge amount of properties in living things. Anything about living creatures can be considered traits - the difference between small changes and a large ones can be trivial and subjective. Similar traits can form bigger ones which we recognise more clearly. With mice changing colour, the gene changes to do so could've happened in smaller increments, but once again this is an example of mutations becoming more fixed as a species becomes more advanced. In the simplest creatures, they're more likely to completely mutate into something unsuccessful because their "base genes" haven't had time to form. This can be observed in the E. Coli experiment (2) - many trials had to take place which could both end up resulting in dead populations and ones that evolved to survive testing conditions. Here we see function increases in the mutations, thanks to the simplicity of the bacteria. They haven't had the evolutionary progress to have established genes, used or unused, to cope with the citric acid, so the only way for a strain to survive is to acquire new genes and traits, which one did, and began using the acid as a carbon source (3). Dangers come and go, but most repeat themselves, so it's natural for most species' by now to already have an optimal genome size (too large, and they require more energy sources, which is bad) and many genes that aren't used, but could be to overcome a danger in future generations should that danger occur.The experiment shows a new trait forming by the processs of duplication and rearrangement. Information already existent was duplicated, then rearranged to create a more complex set, capable of being further mutated to evolve a new ability. There are other examples of new traits forming for survival and becoming a consistent part of the gene pool, some of which have caused insects to become immune to various pesticides (4). Immune systems of humans and mammals adapt during their lifetimes and the resulting changes can be passed down to offspring - not only the initial reproduction, but for even longer through other means such as breastfeeding, which help babies gain various immunities to colds and flus. This makes up for the long lifespan when compared to the smaller creatures which are capable of adapting much more quickly through generations by reproduction alone, otherwise humans and other mammals would be much weaker than small organisms when it comes to dieseases and wouldn't continue to survive.Traits can also include psychological and social behaviours, which can be gained as well as lost or changed, and are dependent on evolution of the brain. Another valued trait as Pro highlights are feathers, and theories are already being worked on precicely to explain these changes (5). It's obviously difficult to say anything for sure because of the unpredictability of mutations and the limited capability of studying undocumented past events, so it's more efficient to study evolution going on today. The difficulty there is that the species' today are now the result of millions of years of evolution and natural selection, and are less likely to need drastic changes in their genomes now. Mutation will always continue to happen, but natural selection becomes less effective in causing change when species become more effective at survival. Once they're at their most effective, a genetic mutation will more likey be bad than good and won't be kept around for long.Reapplication of Natural SelectionNatural selection solves some very underestimated problems and is more than just an explanation of evolution, but a theoretical process which can be applied to anything, and has. In fact, it is currently deemed an essential process for the progress of AI. So, the easiest way to prove natural selections effectiveness is to see an example of it in simulation.Polyworld is an open-source program intended to evolve artificial intelligence autonomously through natural selection (6). It uses a neural net which simulates how the brain works - there's no true answer to any input. For example, inserting 1 may output 0.3 for no reason (in Polyworld, the initial state of the neural net is based on a genome given to a creature on it's creation), and it has no way of knowing whether that is a correct result - it can also use sight as an input, but has no direct way of associating the input with anything. In it's earliest stage, an artificial lifeform is given a basic set of behaviours, and their use is determined by this neural net. The creatures usually require energy from food to continue surviving, and they can reproduce and pass their genome down, which affects the descendants neural net. The first creature may do nothing but go in circles or in a straight line, depending on the initial neural net. The second takes after it's parent and produce similar outputs as behaviours. Over time, the creatures grow and grow in complexity and begin actually exhibiting lifelike behaviours (7). They start using their vision input without being programmed to, they detect other creatures and food, and can eat either (8). This is all because of natural selection - it's not programmed or driven in any way, but simple logic dictates that surviving methods will continue surviving.This example alone directly addresses the main resolution, which questions natural selections effectiveness. Natural selection need not imply natural world evolution. Natural selection is merely a theory of logic based on how life works.(1) (2) http://sandwalk.blogspot.co.uk...(3) http://en.wikipedia.org...(4) http://en.wikipedia.org...(5) http://ngm.nationalgeographic.com...(6) http://en.wikipedia.org...(7) (8)