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Before the genome project was completed scientists believed that there were some 100,000 genes in the human genome because there were 100,000 proteins produced in the human body. When it was found that there were only 35,000 or so genes, and that 95% of the genome did not code for proteins an answer to the mystery was looked for.

I realize I didnt do a good enough job clarifying my earlier point in regards to this. It has been known for some time that much of the human genome was "junk" (although the genome project gave us a much better estimate of how much of this there was in relation to the coding "non-junk"). There are quite a few studies if I remember correctly showing how enhancer elements can be found "intronnically" as well as in the conventional upstream portion of the start of transcription. For the most part these vast stretches of DNA which are non coding STILL dont advertise any obvious function. Currently researchers are investigating of those repeats are important for anything.

It had been thought that DNA only coded for 20 amino acids. Recently it has been found that 3 new amino acids occur and are coded by the stop codons.......This is more evidence of the interrelatedness of the entire genome to each other and also more evidence that the genome is not just a set of individual pieces randomly put together, but a very well organized system.

I am aware of the study you are referring to and I believe this is a very special case in very specific microorganisms. Recombinant DNA technology wouldn't work if this was ubiquitous. Your point about the complexity of the genome is appreciated though.

Yes there are vast stretches of non-coding DNA in the genome (which prior to the discovery of their purpose were called 'junk DNA' by evolutionists)

I am not sure how elucidating the function for junk DNA is the holy grail for intelligent design. It would merely imply nature is a bit more efficient than we had previously thought.

There are quite a few studies if I remember correctly showing how enhancer elements can be found "intronnically" as well as in the conventional upstream portion of the start of transcription. For the most part these vast stretches of DNA which are non coding STILL dont advertise any obvious function. Currently researchers are investigating of those repeats are important for anything.

We are in agreement on the above. Except that you must realize that we have just discovered how much of this non-coding DNA there is and even in such a short time we have found how some of it is used. Also, the search for the function will be harder than the search for genes. For genes we had proteins to help us find them. For the non-coding DNA we do not have such a clue - yet.

True, it is quite rare for these extra amino acids to be produced. Just pointing out one of the complexities of the genome.

I am not sure how elucidating the function for junk DNA is the holy grail for intelligent design. It would merely imply nature is a bit more efficient than we had previously thought.

Now that we know that the genes are controlled by DNA outside of the gene itself we have a strong hint that many of the questions we have been asking for a long time probably reside in the non-coding DNA. The questions are - why do cells develop differently even though they all (with 3 exceptions) have the same genes in them - the answer gene expression controlled by the non coding DNA. How does an organism develop from birth, where are the instructions for such development - most likely in the non coding DNA. Why do people age - we know that there is something that tells cells to stop replicating after a certain point - not found yet, but we know it is somewhere. What tells a cell to do a certain thing such as shed tears, make certain chemicals, replace itself, etc., etc., etc. - we don't know yet, but the only likely place is in the non-coding DNA. Quite a program if you ask me, not likely to have arisen or been modified at random.