Yes, organisms have indeed evolved over time – most former species are now extinct, many species remain much as they are in the fossil record, and new species continue to evolve. Before the discoveries of science, it was intellectually excusable to believe that a God planted all those bones, but to believe so nowadays is a sign of ignorance.
Historically, scientists observing biological evolution first sought to explain observed morphological (body shape) changes over time – the phenotypic evidence of changes in body structure found in the fossil record.
Microfossils dating from more than 3 billion years ago demonstrate that bacteria were the first life-forms on the planet. Bacteria and Archaea, both prokaryotic, ruled until the advent of nucleated cells with membranous organelles, such as those of which we are constructed (eukaryotic cells). The earliest known fossilized evidence of early life forms are found in stromatolites – large reef structures created by communities of Cyanobacteria. Mistakenly called ‘blue-green algae’, the Cyanobacteria are bacteria that evolved relatively late. They are believed to have “invented” oxygenic photosynthesis over 1 billion years ago. As oxygen levels rose, organisms were forced into endosymbiotic unions as – to them – toxic levels of oxygen threatened their continued existence. (Anaerobic bacteria, which are killed by oxygen, persist to this day in environments with very low levels of oxygen.) These serial endosymbiotic transfer events paved the way for evolution of eukaryotic cells, which in turn enabled multicellular assemblages.
Since the advent of modern molecular genetics, biological evolution has come to be understood as a change in genotype – a genetic variation resulting from mutation and alteration in the intergenerational frequency of alleles in populations. That is, an alteration in the frequency of alternative forms of genes between generations. By this definition, the human species is demonstrably still evolving.
The term 'microevolution' refers to small-scale evolutionary events that involve changes in allele frequencies from one generation to the next, and that results in slight changes in affected organisms. The term 'macroevolution' refers to that accumulation of microevolutionary events that is associated with the origin, diversification, extinction, and interactions of organisms. Macroevolution, being cumulative, involves large scale evolutionary change such as the evolution of new species, genera, and families (or even higher taxa). Some creationists favour the ridiculous, fallacious straw man argument that microevolution occurs, but that macroevolution could not have occurred by the same mechanisms, or is impossible.
Biologist Ersnt Mayr suggested that a biological species be defined by its inability to produce fertile offspring when mated with another species. Mules are an example of such a mating – between a horse and a donkey. Mules do rarely produce offspring, but the gene-based, phylogenetic classification of species remains more useful than taxonomies based on physical characteristics. Molecular geneticists are able to compare the genomes, the total complement of nucleic acids, of different species and to estimate the evolutionary distance between species. This is time since the compared species last shared a common ancestor.
Speciation depends upon genetic mutation and alteration of allele frequencies, yet morphologic changes may reflect alterations in the regulation of genetic expression without a major alteration in genotype – body type may appear very different without considerable change in genes.
If this seems unlikely, just consider the considerable differences that selective breeding has wrought in size and configuration within one canine species. Mechanics might prevent the union of a Chihuahua with a Great Dane, but such a union could produce fertile offspring.
Similarly, the paramount importance of gene regulation almost certainly explains much of the morphological difference between humans and chimps – two species who share more than 98% of their DNA. Just a comparatively few regulatory genes are responsible for the developmental changes that render us distinct from our closest relative.
Along the same lines of modification of genetic expression, epigenetic mechanisms, such as alternative splicing or alternative promoters, enable a single gene to give rise to multiple versions of a protein. Thus, through epigenetic mechanisms, the biological complexity confered by genes is greatly expanded. Proteins are much, much more variable in structure, and hence in biochemical activity, than are nucleic acids such as DNA and RNA. Formed from amino acids, proteins regulate cellular metabolism (as enzymes), regulate genetic expression (cofactors), and regulate communication between cells (ion channels, pumps, receptors). Structural proteins form the cytoskeleton that supports cells, and specialized transport proteins move materials and organelles within cells and effect muscular contraction.
There are two basic types of mechanism involved in biological evolution. First are the genetic causes of alteration of genes within the genotype of individuals. Most genetypic alterations are not the result of point mutations, which may, or may not result in abnormal proteins through alteration of a single nucleobase in the genetic code. Creationists create fallacious straw man arguments by focussing their arguments on point mutations, conveniently ignoring the other, more important mechanisms of genetic change, such as duplications.
Single nucleotide polymorphisms, as point mutations are correctly termed, as well as alteration of longer segments of DNA may be neutral, beneficial, or deleterious. Clearly, neutral or beneficial alterations, whatever their genetic mechanism, will persist while deleterious alterations will ultimately be eliminated if they render the organism less capable of reproductive success. Gene duplications, while guaranteeing a functional copy of a gene also provide duplicate copies of the gene that may be altered without destroying the organism's viability, thus providing opportunity for the accumulation and transmission of a variety of mutations.
This brings us to the second type of mechanism operating in biological evolution, the statistical population mechanisms that determine the fate of an altered gene. These are the mechanisms that increase or decrease frequency of an allele – an alternate gene at a particular chromosomal position –within a population. Natural selection, the Darwinian explanation for biological evolution, remains one of the mechanisms acknowledged by biologists, yet not the only recognized mechanism. Genetic drift, gene flow, and horizontal gene transfer in prokaryotes have also been demonstrated to have operated in bringing about evolutionary change. Creationists typically focus their fallacious straw man attacks on "Darwinian" evolution, avoiding dealing with the much stronger "Modern Synthesis of Evolution", which combines understanding of population genetics and molecular genetics.
"Darwin made it possible to be an intellectually fulfilled atheist." ~ Richard Dawkins, The Blind Watchmaker.
"No intervening spirit watches lovingly over the affairs of nature (though Newton's clock-winding god might have set up the machinery at the beginning of time and then let it run). No vital forces propel evolutionary change. And whatever we think of God, his existence is not manifest in the products of nature." ~ Stephen Jay Gould