Similarities in organisms: designed or evolved?

Different organisms have similar properties, including appearance, and less obvious similarities, such as similarities between their DNA and proteins. The mainstream scientific explanation for such similarities is that the organisms are related by descent. Those who doubt that organisms which belong to different large taxonomic groupings, such as families -- humans and chimpanzees belong to the family Hominidae, but gibbons to the family Hylobatidae -- could have descended from a common ancestor argue that the similarities are there because the chemicals were designed to perform similar functions.

A recent post on the Panda's Thumb blog points out some weaknesses in the design explanation.

The post points out that marsupial organisms have biochemical similarities which seem to be based on common descent and relationship, rather than on their ecological niche. Thus, marsupial predators have molecules that resemble other marsupials far more than they resemble those of other predators.

The post also points out that non-functional, or "broken" genes show similarities which indicate common descent. Since they don't function, it's hard to believe that their resemblances are due to design to carry out a similar function.

Thanks for reading.