Evolution - common misunderstandings
Evolution - common misunderstandings
I would almost contend that if something fits in with common sense it almost certainly isn't science.

Lewis Wolpert
Misunderstandings @ New Scientist

We're comfortable with time, distance and probability scales of everyday life. Scales of gigayears (cosmic evolution) or nanoseconds (electronic transitions) are alien. Processes acting at extreme scales are beyond ordinary experience. Structures apparent at picometers (atomic nuclei) and light years (galaxies) have no counterparts in ordinary experience. Scientific training and fluency with exponents aid in navigating "extreme" scales.
Discussions of organismal variation center on mutation. They usually focus on point mutations because these are the simplest mutations. Changes in regulatory genes are often mentioned, but insertions and deletions are often ignored. Evolution proceeds via small changes, but these vary and some, for example, duplication of hox genes, can dramatically affect anatomy.
Harmful mutations-
Deleterious mutations outnumber advantageous mutations. Common sense dictates that this will prevent evolution. What's overlooked is purifying selection which eliminates these mutations. Purifying selection acts over generations. This is why evolution is slow and why it can't be reproduced at will in the laboratory.
Nucleotide sequence differences-
Do nucleotide sequence differences between homologous genes of similar organisms reflect differences in design or do they reflect common ancestry? Differences are either synonymous changes, i.e. those that don't affect protein sequence, or nonsynonymous changes, i.e. those that change protein sequence. If nucleotide sequence changes arise from design, they should be mostly nonsynomomous since only these change protein function. If sequences change by random mutation they should be mostly synonymous since these don't affect protein function and therefore aren't selected against. Patterns of sequence change conform to the latter hypothesis.
Humans are comfortable with deterministic events. Probabilistic events are less intuitive. Liquids and gases operate by probabilistic rules, but events are so numerous that probabilities can be averaged to make them appear deterministic. Rare events, such as being struck by lightning or winning lotteries, are less intuitive. Events occurring less than once in a hundred (or thousand) years are still less intuitive. Nonetheless, rare and probabilistic events play important roles in the universe.
Mating barriers between daughter generations lead to speciation. There are many speciation mechanisms; most are poorly understood. The barriers, particularly in early stages of evolution, are not absolute. Disruptive selection (selection against heterozygotes) can speed the process. Some types of speciation, for example chromosomal duplication in plants, are rapid and can be produced in the laboratory. Genome sequences will likely improve understanding of speciation in the near future.
Missing links-
The term "missing link" is an inappropriate relic of the medieval "chain of being" concept. Science is inherently incomplete. Missing information is what drives science.
Origin of life-
Precellular "life" is not understood. Since there are no precellular fossils, precellular "life" can't be analyzed. The best we can do is make and test guesses. Since the processes are unknown their probabilities can't be estimated. A few of the processes (e.g. origin of amino acids) can be reproduced. At this stage science can't rule out supernatural (nonscientific) events, however there's no evidence for them.
Evolution hasn't been proved-
Scientific theories are never proved. Scientific theories make predictions which are tested experimentally. Verification of many, independent predictions verifies a theory. Verifications of counterintuitive predictions are particularly convincing.