Thankfully, since harnessing the power of restriction enzymes and other DNA analysis techniques we can have direct observable information that lends more support to evolution.
They want to dispute what the pattern in the fossil record really indicates, but I haven't yet heard one decent rebuttal to the line of evidence explained in SNG's post on endogenous retroviruses.
The specific Long Terminal Repeats and their location in genomes is best explained by linked genetic heritages. (i.e. descent with modification) And a pattern of simple to complex, analogous to the fossil record, can be directly inferred from that.