Evolutionary theory is not founded on Haeckel's observations or theories. Haeckel's work was discredited in the 19 th century, and has not been relevant to biology since the rediscovery of Mendel's laws of genetics. That the biogenetic law is false has been the consensus of biologists for over 100 years, and developmental biologists have been working constructively to provide alternative explanations, which have so far all been evolutionary in nature.

The similarities between vertebrate embryos are real. We must distinguish between observations of those similarities and hypotheses about their causes. The similarities are not in doubt; there are worthwhile studies of the degree and timing of the similarities, but none that question their overall existence. What Wells has described is one hypothesis about the cause, Haeckel's biogenetic law, which failed early and spectacularly. He has not addressed any modern hypotheses, nor has he provided a better alternative.

Evidence for common descent lies in the unity of form and process. We do not use Haeckel's outmoded, invalid mechanism to argue for evolution. Instead, we look at the marvelous convergence of disparate organisms on common principles: all animals use the same genes to define regions of their bodies, all vertebrates build their faces by unlikely rearrangements of odd pharyngeal protrusions, and even tailless mammals like us have to start with tailed embryos. The best explanation for these phenomena is that they are a consequence of a common heritage.

The article describes how hox genes are involved in "blueprinting" the way an organism develops. The remarkable similarity in how they work, in different species, is actually good evidence that they have a common ancestor.

You can find here an extract from a biology textbook which explains hox genes, how they control embryological development, and how they fit with evolution. This quote may be of particular interest here:

[quote]Hox genes evidently duplicated twice during the evolution of invertebrates into vertebrates, justas there were multiple duplications of the globin gene. Instead of one cluster of about 10 genes on 1 chromosome like the fruit fly, the mouse has 4 clusters of about 10 genes each, on 4 different chromo-somes. Hox genes in mice and humans are very similar in number and chromosomal arrangement. It isremarkable that only about 40 genes out of a total of about 100,000 control most of the development,architecture, and appearance of the body plan of complex mammalian species.