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I think the question is if Mother Nature can genetically mod things over time.. should we do it too.. only on a quicker timescale?

The fact is, that humans have been genetically modifying foods since we first started developing agriculture. It is the nature of living things to change genetically over time; every offspring contains new mutations not seen in either parent. In humans, there are about 120 new mutations per person. Depending on the selective pressures, those new mutations can persist in following generations, disappear, or even become more prevalent if they confer a survival advantage.

Through the practice of selective breeding, humans attempt to give a survival advantage to certain mutations. By hybridization, humans attempt to create new organisms containing favorable traits of its parents, while avoiding the noxious traits. In the early 20th century, humans found that they could radiate seeds--which breaks up the DNA and forces the tiny embryos inside the seeds to try to repair the DNA, which they can never repair to its original form because of the way radiation damages DNA--and come up with completely new variations of plants.

The thing about all of these older methods of genetic engineering is that they are random and unpredictable. The practitioner must assess a large number of offspring to determine which ones have desirable traits and lack noxious traits. Old-method genetic engineering methods have resulted in many modified organisms that are unfit for human consumption, usually due to high levels of natural toxins (which all plants produce). This article about an attempt to breed (i.e. genetically modify) potatoes to come up with superior potato chips talks about that issue and discusses some of the many issues that arise with old methods of genetically engineering foods.

Our new methods are targeted in a way that is not possible with older methods. This all but eliminates random effects while maximizing the desired effects. Instead of randomly mixing up a plant's entire genome--or randomly mixing up tens of thousands of genes by making hybrids--we can insert, remove, or modify a single gene in a plant (or animal) whose qualities we already know. Since modern genetic engineering methods are far less random, they are orders of magnitude less likely to result in plants that produce high levels of toxins.

A comparison of old versus new genetic engineering methods can be visualized by an analogy to sculpting methods. Old methods would be comparable to trying to repair a flaw in a marble statue when your only tool is a hammer. Maybe you can repair the flaw, but the most likely result is that the statue will look worse after you finish your "repair" than it did before. New methods would be comparable to having a set of chisels, hammers, sandpaper, crack filler, etc., to fix the statue. In that case, your statue will most likely look better after the repair than before.

One other thing about the tools of modern genetic engineering: every single one of them comes from nature. The majority of them are enzymes made by bacteria, and a few are enzymes produced by plants and animals. These enzymes are extremely specific: an enzyme that recognizes a certain sequence in DNA will not act on DNA at any other point than where that sequence occurs. For example, an enzyme called EcoR1 cuts DNA at the sequence GAATTC. With those natural tools at my disposal, I can precisely edit any gene to achieve any end result I want. If I want to change a single letter (nucleotide, base-pair) in a gene, I can. I did many genetic engineering experiments while earning my PhD.