Since the
genomes of hundreds of animals have been sequenced, it is impossible to grasp
even the basics of genetics and deny the fact that evolution happened over
millions of years, and to deny the fact that every species is genetically
related to each other in a tree of life. These are biological facts that are
impossible to reject. Don't get me wrong, evolution denial has never been in
the least bit credible, and always shameful and intellectually repressive, but
these days it's so abundantly and incontrovertibly clear that evolution by
natural selection is the correct explanation for the diversity of life on this
planet that the remaining attempts to persist in its denial are merely cases of
scraping the barrel and feeding a scientifically and theologically impoverished
minority.
The story of evolution over four billion years is this; all organisms can be traced back to a common ancestor, and so all of the diversity in life we see today is due to common descent with modification, through natural selection, genetic mutation, and genetic drift. We have a lot of evidence to back up this theory, including the fossil record, geologic evidence, and most comprehensively, genetic data. There are three mechanisms for evolution: natural selection, genetic mutation, and genetic drift.
Natural selection: Organisms who are better suited for their environment have a higher probability of surviving long enough to reproduce and pass on their genes. This is pretty much common sense.
Genetic mutation: Changes in genetic code occur naturally during reproduction, and at random. There are several types of genetic mutations, including the insertion of a base pair, the deletion of a base pair, and the switching of positions of two pre-existing base pairs. These mutations occur all the time.
Genetic drift: This is the relative frequency of how often an allele (a specific genetic trait) appears in a population, based on how many currently-existing organisms contain that trait. Over time, some alleles that are not well-suited for the environment may become less common and eventually disappear completely. This can reduce genetic variability.
The axioms of evolution claim that all life evolved slowly and gradually from the first life forms. Traits are inherited from one generation to the next with slight variations. This being true, we should be able to create a kind of family tree of organisms and their traits, just like we create a family tree for our human ancestors. If you hired a professional genealogist to study your genealogical tree, you'd find the branches form nested groups of families based on the name of the husbands. As new generations marry, the daughter lineages create branches with the names of their new husbands, and the sons simply create newer and more complicated branches with the same name. In my father's and mother's family tree, for example, even in just a few generations we have family members with over a dozen different surnames.
In biological evolution over 4 billion years, traits in organisms evolve in the same way. If you replace the new family line where the husband's name comes in with a new novel trait in an offspring, you find the same thing. That organism with a new trait creates a new branch where the descendants keep that trait and also accumulate new ones as they go along, much like how all the grand-daughters will take on new marital names and form their own branches. This is what is called in biology a "nested hierarchy".
The genome of every single organism contains the totality of genetic information within that organism – we each have a unique one (it’s mostly the same, but every individual has slight variations). A genome is like a book, consisting of chromosomes, which are like paragraphs. These paragraphs are made up of genes (sentences in this book analogy) and they act as instructions to make molecules. Each gene is like a sentence that defines its protein structure, and the letters in the sentence convey the building blocks of the DNA strand (a subset part of the gene). DNA is a molecule in the shape of a double helix, which is a long spiral staircase made up of nucleotides – and it is these that determine the genetic code of all living things.
As the genomes of so many animals and plants have been sequenced, we have a picture of evolution so clear that we know where every living thing appears on the tree of life. We know this because the information available to us from genome sequencing is computational – that is, from the sequences we can compute the relational distance of every species to each other, just as if we subjected books to a computational process and saw them undergo mutations, we would track the computational steps at every part of the journey and know which copies of books emerged from which other books and so forth. This is because genes are best thought of as passengers that use bodies as vehicles for propagation – just as in this analogy, letters and sentences would be using the book structure to get themselves passed on. The DNA code is a digital code that has no non-trivial difference from computer coding that can be mapped in precise accordance with the journey its constituent information units have taken. A gene is a sentence that conveys the structure of a protein, and just as would be the case if we subjected books to the same kind of evolutionary process and read every intermediary stage as the sentence structures changed bit-by-bit over time, the same computational process is analysable when it comes to code read in the cells of every living thing.
We can look at the rich diversity of species and map the phenotypic variation – variation due to underlying heritable genetic variation. We know from our genetic story that we are equally related to dogs as we are whales, and bats as we are hippos, and hedgehogs as we are deer, because the last common ancestor we have with, say, the dog, is the same as the last common ancestor shared with, say, the whale – even though regarding the appearance of an organism, characters and traits, the difference between a dog and a whale, or a bat and a hippo, is immense. Because we can read the code in the cells of every living thing, we also know that regarding the genetic distance on the phylogenetic tree, we are more closely related to mice, rats, rabbits and guinea pigs than any of the animals of the previous list (take most other animals and we’d know the genetic distance too). And genome sequencing shows us, beyond any doubt, that we are most closely related to other apes (chimpanzees, orangutans, gorillas, bonobos, etc) and all primates diverged from a common ancestor.
These studies show other conclusive evidence too. For example, inherited strands of past viruses (called endogenous retroviruses) show clear relatedness between species, and in a way that is exactly consistent with the tree of life. So too do the homologies – the common features and traits shared by organisms also matches both the genetic data of the family tree of all species, and the data that shows the trajectory of endogenous retroviruses.
The upshot of all this is, if you reject this as conclusive evidence for evolution, and remain unwilling to reject creationism and embrace these facts as instruments of God's creative genius, then you don’t understand how significant and decisive these data are, and how deep and wondrous the theology can get. There is simply no way of denying the fact of evolution and living with a clear conscience and a content mental state.
