The idea of evolution answering all the questions of how life developed on this planet is a long way from a slam dunk. Although we can see examples of evolution (observable) and it can pass several tests for truth, it never seems to pass all tests.
We can observe that animals and plants are able to adapt to their changing environments. So variation is a given but does that mean we chalk it all up to evolution?
There are six mechanisms that produce variation in the gene system:
1. Built-in variation in the gene pool
2. Reproductive exchange
3. Independent assortment during meiosis
4. Crossing over during meiosis
5. Transposable elements
6. Recombination of chromosomes
These are all incredibly complex systems, and with them, animals have an incredible capacity for change. The question is no longer whether change can take place or not, but rather how much change and where the limits are.
BUILT IN VARIATION
Allele - A DNA coding that occupies a specific place on a chromosome. Alleles hold genetic information such as the colour of flower petals.
For most character traits present in organisms, more than one allele exists. Alleles can be active (patent) or inactive (latent). Active alleles will be expressed in the phenotype, or what the organism becomes. So basically think of the genetic code as being a string of lights. each light can individually be turned on and off and each represents a different biological characteristic. You may carry the allele for big feet, but you don't have big feet because that allele is switched off. Now your children will inherit your genes, it's possible for them that the allele for big feet is turned on. If it is your kid will have big feet. This is a simplification but you get the idea. The amount of variation that already exists in the gene pool is phenomenal. Often evolution is used to explain most changes as resulting from chance mutations, not variation due to pre-existing genetic data and this is not tenable. Why is there such a vast amount of pre-existing genes that are often not used? Where did they come from? Natural selection operates at the level of the phenotype and not the level of the genotype, this is a rule of evolution. If mutations occur in genes natural selection cannot act on them until they are expressed in an organism, in other words, natural selection cannot act on the big feet gene until someone is born with big feet.
Let us consider this by means of a simple analogy. If I have a book with detailed instructions on how to build several airplanes, how do I know which one flies best? I have to build the airplanes and test fly them, then I can select the one that flies best. In our example, the instruction book is like the genotype and the physically built airplane is the phenotype. Natural selection can only take place once at least two airplanes have been built and tested. There have to be at least two variants or else there is nothing to choose from. If you don't have two then one cannot be selected as "more fit" and one cannot be chosen "less fit". Selection cannot take place at the level of the book, as the words in the book only become meaningful once they have been translated into a physical airplane. So here are some questions this raises:
* Where did the book of plans come from (genotype)?
* If the book remained on the shelf and I never opened it, would I have any idea which plane flew better?
* How are the instructions translated into the physical airplane?
For myself, there are other questions that evolution has not answered either at all or inadequately.
How did sexual reproduction evolve? It provides no benefit in terms of survivability over mitosis, in fact, mitosis is much more efficient. Incredibly efficient. Evolution favours better systems and by its very definition reduces or eliminates inefficient ones. This could not have developed by the slow process of small changes at a time that is the heart of evolutionary change.
How did the life cycle of the order lepidoptera (moths and butterflies) develop? Consider what they do when they go through metamorphosis. The larva builds a cocoon or chrysalis and undergoes holometabolism or a "complete metamorphosis". The larva essentially liquefies in the pupal stage. There are a lot of theories but nobody really knows.
How did biochemical or cellular systems develop? Basically, the systems within cells that support the life of the cell. There are many components and processes within cells that are outright required to exist for there to be a possibility of life. Science is struggling to answer how any one of them came about not to mention the thousands that are required. At one time science called single-celled organisms simple. Now it is understood that single-cell organisms are anything but simple. The structures and processes that occur inside a cell are as complex as a modern city. https://www.youtube.com/watch?v=wJyUtbn0O5Y
Even prokaryotic cells which are thought to be simpler, are amazingly complex.
The palaeontological record reveals a far greater diversity of life in the past than in the present. The natural selection process operates by elimination, not addition. In order for the fitter to survive, there must have been a less fit that did not survive. Natural selection does not create features, adaptations, or even life, it merely selects for the feature that provides greater survival value. The features themselves must still come into existence by random chance processes. How can a process (natural selection) that eliminates species actually make more and a wide variety? It is NOT possible. All this requires a large amount of faith in the god of "chance," and in an occurrence whose improbability is enormous.
I have a lot more questions but not all are easily expressed in this forum.
Another one of my big problems that I will tell mention is not so much a problem with evolutionary theory itself but more with the community. When proponents of evolution respond to critics of the theory they tend to do several things that to me are off-putting. One, they mock and berate anybody that has the audacity to question the revered theory. Two, they have a tendency to pick the low-hanging fruit. In other words, they will usually respond to the easy questions, the questions that are not stated properly or are based on incomplete understanding. Especially popular are questions that are easy to mock. Science is based on asking questions. Often, it seems that for evolutionary theory questions are not acceptable. It's a great way to get ostracised in the scientific community in fact.