The explanation is is very simple:
Random mutations created all sorts of tree characteristics. Most of the mutations were disadvantageous, and most of the mutant trees died. However, mutations to some ancient trees provided a simple defensive system and were not otherwise disadvantageous. All other things being equal, a smaller percentage of ancient trees that lacked the mutant simple defensive system survived than ancient trees that had the mutant simple defensive system. Over eons, that meant that what survived were trees with defensive systems. So today, we see only the trees with a defensive systems. Nothing "told" the trees to do this.
Organisms without the beneficial characteristics you seem to think are so extraordinary could not survived to the current era, so of course you don't see them. You see only organisms with well-adapted characteristics. "Instruction" from God is not required; only the brutal natural law that you adapt or perish.
Why is this so difficult for you to understand?
I do understand that and that does explain a large portion of evolution but I also believe some how our bodies can all be it very slowly manipulate DNA to suit our needs.
I found this on the net. It may explain my point better.
Current fossil evidence indicates that modern humans evolved from a species called Homo erectus. Homo erectus appeared about 2 million years ago. Looking at the skull of Homo erectus, we know that its brain size was on the order of 800 or 900 cubic centimeters (CCs).
Modern human brain size averages about 1,500 CCs or so. In other words, in about 2 million years, evolution roughly doubled the size of the Homo erectus brain to create the human brain that we have today. Our brains contain approximately 100 billion neurons today, so in 2 million years, evolution added 50 billion neurons to the Homo erectus brain (while at the same time redesigning the skull to accommodate all of those neurons and redesigning the female pelvis to let the larger skull through during birth, etc.).
Let's assume that Homo erectus was able to reproduce every 10 years. That means that, in 2 million years, there were 200,000 generations of Homo erectus possible. There are four possible explanations for where the 50 billion new neurons came from in 200,000 generations:
Every generation, 250,000 new neurons were added to the Homo erectus brain (250,000 * 200,000 = 50 billion).
Every 100,000 years, 2.5 billion new neurons were added to the Homo erectus brain (2,500,000,000 * 20 = 50 billion).
Perhaps 500,000 years ago, there was a spurt of 20 or so closely-spaced generations that added 2.5 billion neurons per generation.
One day, spontaneously, 50 billion new neurons were added to the Homo erectus brain to create the Homo sapiens brain.
None of these scenarios is particularly comfortable. We see no evidence that evolution is randomly adding 250,000 neurons to each child born today, so that explanation is hard to swallow. The thought of adding a large package of something like 2.5 billion neurons in one step is difficult to imagine, because there is no way to explain how the neurons would wire themselves in. What sort of point mutation would occur in a DNA molecule that would suddenly create billions of new neurons and wire them correctly?* The current theory of evolution does not predict how this could happen.