The more fundamental question to ask is: Is evolutionary theory even complete? There is no possible way that an incomplete theory can be factual within any framework of science. Being incomplete doesn't necessarily mean it's wrong, but it cannot be both factual, and yet incomplete.
Charles Darwin devoted an entire chapter of “The Origin of Species” to instinct. He correctly states that instincts are as important as structure, meaning that useful anatomical features become useless unless they are used by the life form. Instincts, although barely defined, are understood by most people: they are the behaviors in life forms which use the features of anatomy for a specific function, and they are passed down to the next generation with such accuracy and fidelity, that the offspring don’t even have to learn the behavior, it’s just “there.” A perfect example is the nest building instinct in weaver birds.
What makes evolutionary theory incomplete is that there is not even an explanation as to how these instincts might work. The conundrum is that we are told to believe that DNA is the only way in which to pass on heritable information, which is well understood in its ability to code for proteins. Proteins and amino acids have a discreet code in DNA, so where and how are instincts encoded into DNA?
Remember that hard evolutionary theory has given itself DNA as the only mechanism for inheritance. It is not enough to merely say that instincts must be in DNA. It is also not enough to claim that tinkering with genetic code alters some instincts, therefore genes control instinct. Considering the millions of physical cells and systems that must be present in order for a life-form to properly function, it is not surprising that tinkering with DNA might appear to be causing a change in instinct, but this is an argument from ignorance. Just because you can destroy a complex machine, does not mean you know how it works.
The subject of instincts and genetics puts the whole theory of evolution into unknown territory, a place where we lack knowledge of the brain, which is key in instincts, and an absence of a science of consciousness. This one subject alone is perfect support of the fact that evolutionary theory is at best incomplete, and an incomplete theory defended as if it was factual, is most definitely bad science.
What is the origin of instinct?
The discovery of DNA should have brought the "instinct problem" to light, but it did not. And this is the tell-tale proof that skepticism of evolutionary theory is dead, and the religion of it thrives instead. DNA showed us it is the actual structure that holds heritable information, DNA is the actual substance that evolves. So anything about a creature that can evolve must be in the DNA. So what about instincts? Where are instincts in DNA?
What should have happened after the discovery of DNA, is a massive effort to unravel the method by which congenital knowledge (instinct) is encoded in DNA. This is absolutely demanded by logic. Darwin wrote a whole chapter on instincts, and laid down the logical claim that they must have evolved, in the same way that a creature's physical structures did.
This required reconciliation between DNA and instincts is not possible with our current philosophies about life, which I will show shortly, and no-one to my knowledge is even trying. If you were to look in any book that explains or supports evolutionary theory, you will probably not find the word "instinct" in the index! If you do find it, it will not say a word about the problem about reconciling instincts with DNA.
So why is there a complete black-out on the subject of genetic instincts? Because Darwinian evolutionary theory cannot afford to tackle something which reveals its own failure. I realize "failure" is a strong word, but trying to bend the facts around, to make DNA capable of encoding instincts and allowing them to evolove the same way a bird beak does - is not scientific. So instead of dealing with this issue, evolutionary theory avoids it all together.
Here is the problem: If instincts really are encoded in DNA, there are two reasonable ways it could happen: The DNA would contain a complete blueprint for the assembly of a creatures brain, down to the last neuronal connection, and thus creates instinct by way of pre-configuring the brain. An analogy to this would be building a computer's memory with data already in the circuits. This scenario is most likely ruled out from the start because the amount of digital information required to construct a complete brain to that exactness would exceed the amount of DNA available in the average genome.
The second possibility is that within the genome of a creature, is a gene devoted to an instinct (such as nest building). The creature's brain would then have the ability to read this gene as a program instruction. This section of DNA would be compact enough to fit in the genome, written in a format that allows for slight errors, or has "room to evolve," but is still specific enough to direct the critical, and life sustaining behaviors of an animal. This also would mean that the brain has the ability to extract information from DNA and turn it into behavior, which seamlessly integrates with the creature's intelligence.
In my opinion, trying to fit the phenomenon of instincts onto a one-dimensional string of data (DNA) is not supportable by evidence. Trying to do so opens up a Pandora's box of even bigger questions, like: "What if instincts are not in DNA?" or "what if the brain is not a computer, but a reciever?" And so on. If there were an answer to the instinct question by evolutionary theory, we would have had it by now. I suspect that to get an answer, evolutionary theory must be put aside. This is a question left behind for more than fifty years, and I say it is no accident - Evolution has no answer, and better for the theory that nobody knows about it