Phenotypic traits may look the same but the genetic changes may be different and variable:

http://www.the-scientist.com/?articles.view/articleNo/47314/title/Many-Evolutionary-Pat...

"Many more genetic changes can result in the same phenotype than previously suspected, according to a study of birds spanning 56 divergent species. Analyzing the structure and function of their hemoglobin proteins, Jay Storz of the University of Nebraska, Christopher Witt of the University of New Mexico, and their colleagues uncovered a wide breadth of mutations that all resulted in higher hemoglobin affinities for oxygen among birds living at high altitudes.

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"Storz, Witt, and their colleagues sought to understand whether there are many different ways genes can evolve to the same hemoglobin function. The researchers collected 56 bird  species from the Andes and Rocky Mountains and sequenced the three genes that make up the hemoglobin subunits. Considering the species as 28 related pairs—one species that lives at high altitudes and one lowland species, the team found that, as expected, the high-altitude bird of each pair had a higher affinity for oxygen, but of the 28 high-altitude species, only four had the same amino acid changes.

"Because few amino acid changes were thought to affect the hemoglobin protein’s oxygen affinity, researchers had assumed that the evolution of the underlying genes was predictable. But the authors of the new study unexpectedly found that many of these amino acid changes were not in the active site of the protein that interacts with oxygen. 

"'We were addressing whether genetic evolution is predictable and we found that evolutionary changes may be highly predictable at the at the level of biochemical phenotype, but that there can be far less predictability at the underlying genetic level,” Storz explained.

"He and his colleagues then tested whether the observed hemoglobin mutations were affected by the sequences already present within the hemoglobin genes. They introduced the most common mutation (found in hummingbirds and a flowerpiercer species) into a plasmid encoding the ancestral hummingbird hemoglobin genes, then expressed and purified the protein and found that it had a higher affinity for oxygen. The same mutation introduced into a more ancestral avian hemoglobin gene did not increase the protein’s affinity for oxygen, however.

“'An important implication of our work is that, for any given gene, the substitutions accumulated through evolutionary history determine the set of mutations acceptable or beneficial in the future,” said Storz. “The evolutionary mutation options available to one species may not be available to another.”

“'The different paths that evolution takes depend on a lineage’s evolutionary history, with molecular changes in the distant past opening or closing doors for particular changes in the future,” agrees McGlothlin."

Comment: What is missing from our knowledge of genetics is how a code change translates to actual phenotype. The gene is identified as cause, we see the effect, but none of the process inbetween. It is a huge black box. This indicates that the code has several pathways to a successful result, which makes it easier for evolution to progress to better adaptations. This is an equivalent finding that fits dhw's thought about organism's ability to invent. I think God made the code with this variability which lead to comparable but not exactly the same results of adaptation. It is the same concept as individual variability allowing for adaptation and survival in the bacteria/ antibiotic challenge study previously discussed. Less rigid constraints in the mechanisms. With similar effective results, this is how I view my concept of guidelines may work.

Glowing enzymes that are the same are found in different unrelated organisms:

http://www.the-scientist.com/?articles.view/articleNo/49850/title/The-Unlikely-Relation...

"Although the long-tentacled brittle star (Amphiura filiformis) differs from the stout sea pansy (Renilla) in both appearance and phylogeny, researchers have now demonstrated that they share a similar luciferase—an enzyme that catalyzes the light-producing reaction that results in the invertebrates’ bioluminescence.

"When an international group of researchers searched the brittle star’s genome and transcriptome for known luciferase sequences, they detected sequences in the echinoderm that were homologous to those of the luciferase of the sea pansy—a cnidarian. The sequences were so similar, in fact, that antibodies specific to the sea pansy luciferase could also detect the brittle star luciferase.  

"Conventional dogma states that every taxonomic group has its own distinct luciferase, explains lead author Jérôme Delroisse of the University of Mons; but previous work has found similar homologies in distantly related species. How such different species acquired similar luciferases remains unclear, however.

"The sea pansy’s luciferase has known homology to a nonbioluminescent bacterial enzyme, and the authors uncovered similar proteins in other nonluminous organisms. The data suggest that both brittle star and sea pansy luciferases evolved “from a common ancestral protein originally not involved in light emission,” says Delroisse, and that the gene for this protein horizontally transferred from bacteria to a common ancestor. It’s becoming clearer that “not all independently evolved bioluminescent enzymes have to be structurally different,” says Miriam Sharpe of the University of Otago who was not involved in the study."

Comment: The study's tortured explanation is an attempt to stick with standard Darwinism. There are bioluminescent bacteria that have symbiotic relationships with other organisms. Invoking horizontal transfer is an attempt to get around the issue of the size and complexity of enzymes and the improbability of chance discovery of the same molecule by chance mutation. Convergence is a theory that suggests there is an overall underlying plan for evolution, championed by Simon Conway Morris. Makes as much sense as the author's suggestion or perhaps more sense.