• Astronomers hold that the Sun formed from a cloud of gas which originated from the explosions of earlier generations of stars. Some of the gas condensed at the centre to form the Sun, while other material aggregated into planets – solid planets close to the Sun and gaseous planets further out, along with chunks of rock which we know as asteroids. Problems with this ‘nebular hypothesis’: (a) simulations indicate that the proto-planets would have spiralled inwards and been gobbled up by the Sun within 100,000 years, (b) asteroids on investigation are not primitive objects but consist of fragments from much larger bodies, and (c) present-day rates of radioactive decay are insufficient to account for the melting that occurred in those bodies. Accordingly, ‘the origin of the Solar System represents one of the oldest unsolved problems in science’ – see The old world destroyed for details.
• There is no satisfactory explanation for the existence of large amounts of water on the primeval Earth. During the formation of the Solar System, Earth is believed to have been red-hot and therefore could not have hosted liquid water, yet the very oldest mineral evidence shows that continents and liquid water were already present. Discussed in Water everywhere.
• Astronomical theory dictates that the early Sun must have been 25–30% cooler than its present temperature. However, the oceans of the then Earth were not, as expected, frozen solid but hotter than they are today. This is known as ‘the early faint Sun paradox’. Hot Precambrian oceans are evidence of faster rates of seafloor spreading and higher rates of radioactivity in the mantle, with implications for all radioactivity-based clocks.
• Fossils are the remains of dead organisms, and in studying them we can easily forget that there is more to life than just what we see. The most distinctive property of animal life is consciousness, a state which we know first-hand because we ourselves are both conscious and self-conscious. If this property could be reduced to solely physical causes, human thought would have no rational quality, and Darwinism itself, being determined by physics rather than the metaphysical assessment of evidence, would have no rationality. Unlike computers, animals (including human beings) are informed by a spirit. Death occurs when the body ceases to have any sense of subjectivity and the spirit leaves the body. With its most fundamental premise that life consists only of atoms, evolutionism fails at the first hurdle.
• As measured by radioactivity-based clocks, three quarters of the fossil record consists only of microscopic organisms, after which both diversity and complexity increase abruptly, not little by little. The sudden appearance of mutually unrelated, complex organisms is known as ‘The Cambrian Explosion’ and was well known already in Darwin’s time.
• The explosive appearance of nearly all the distinctive body plans of marine animals in the Cambrian period is not a unique phenomenon. The appearance of terrestrial animal kinds is similarly explosive. Examples include the sudden appearance of insect orders in the Carboniferous and mammal orders around the beginning of the Cenozoic.
• All the major plant groups (‘divisions’) also appear out of nowhere – mosses, ferns, horsetails, cycads, ginkgos, conifers, gnetophytes, monocots and so on. There is no gradual evolutionary progression leading up to these forms.
• Evolutionary trees are frequently contradicted by the phenomenon known as ‘convergence’, i.e. the appearance of the same feature in independent lineages. It is called convergence because, although blind and undirected, Evolution appears to ‘converge’ from different directions upon the same or a very similar idea, e.g. the independent evolution of gliding among eight different groups of mammals (From reptile to mammal), the independent evolution of the spider form in trigonotarbids and harvestmen, or the independent evolution of the scorpion form in eurypterids and pseudoscorpions (The first land animals).
• The all-determining timescale depends on the assumption that the speed of light has always been what it is now (the prime assumption, whether we are considering stellar distances or radioisotope decay). In geology this can be tested against the direct evidence of what is being dated. It fails such tests. The processes recorded in geological strata indicate rates of activity more than 20,000 times faster than those extraneously imputed by radioisotope dating (see How old is the Earth?).

There are also fundamental problems of a biological nature, not dealt with here. Evolution in the genome discusses, in a simple way, some of the genetic mechanisms underlying evolutionary change.