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When studying the human genome and its similarity to that of the chimp, scientists have recently concluded that 96% of our genome is similar. However, most people are unaware that this percent pertains to the regions of our DNA that result in proteins.

This is false. The 96% pertains to the entire genome, including both protein-coding regions and non-coding regions.,

The percentage of synonymous similarity for just the protein-coding regions is even higher, upwards of 99.7%. P> The percentage of similarity for non-coding regions is slightly lower than the overall 96%, but not by very much, since it comprises most of the genome. I don't have the numbers in front of me right now, but it'd be roughly 95% similar based on the above figures.

It seems logical that if a protein performs a certain function in one organism, then that same protein should perform the same function in a variety of organisms. This is evidence for a common designer as much as for a common ancestor.

If you're working ONLY from a single overall percentage of similarity, yes, you're right. But it's the specific *nature* of the many kinds of similarities and differences that clearly indicate evolutionary origins and not "common design". Common design produces very characteristic patterns of similarities and differences, and so does evolutionary common descent. Every conceivable method of examining the patterns of differences and similarities in the DNA between species matches the patterns that would be produced by evolutionary common descent, not the kind that would be produced by common design.

But most of the DNA sequence performs an unknown function and has been largely dismissed as “junk DNA.” However, increasing evidence supports the view that “junk” DNA performs an important role. For example, a recent report unexpectedly found specific sequence patterns in “junk” DNA which scientists have termed “pyknons.”1 It has been suggested that these pyknons may be important in determining when and where proteins are made. Within this “junk DNA” there may be large differences between man and chimp. The areas of greatest difference appear to involve regions which are structurally different (commonly called “rearrangements”) and areas of heterochromatin (tightly packed DNA).

While it has been long known that some kinds of non-coding DNA serve some kind of function in the genome, and new kinds are being discovered from time to time, the above paragraph vastly overstates the case. There are many kinds of independent lines of evidence which indicate that the majority of non-coding DNA is indeed non-functional, and not merely "all functional for which the function is not yet known".

Four of the more powerful lines of evidence are 1) the non-conservation of most non-coding DNA between lineages, 2) the existence of species (such as the fugu fish) in which almost all of these regions have been naturally eliminated with no detriment to the species, 3) experiments in which gigantic swatches of non-coding DNA have been snipped out from mice with no detriment to the test animals, and 4) a good understanding of how many of these sequences arise via "stutters" during cell replication and other kinds of errors during DNA copying and/or viral infections, etc. -- they clearly weren't "designed in" from the start. Large sections of our DNA is identifiable as the harmless remnants of such genetic malfunctions. For example, 42% of the human genome consists of retrotransposon copies.

Here are some other interesting differences between the human and chimp genomes which are often not reported:
*The amount of chimp DNA is 12% larger than what it is in humans.

This is "often not reported" because it is not true.

The fully sequenced human genome contains 3,107,677,273 basepairs. The fully sequenced chimpanzee genome contains 3,350,447,512 basepairs. This is 7.8% larger.

This is hardly surprising, however, nor significant, nor any kind of problem for evolution, nor does it invalidate the kinds of simimlarities and differences which are compared in order to trace evolutionary relationships.

It's not surprising because as I mentioned above, glitches in DNA replication (as well as transposons and other mechanisms) can easily add "stuttered" repetitions to the genome, increasing its size by "padding" it with numerous repetitions. Also as mentioned above, it's easy for large sections of DNA to get accidentally dropped, and when these are non-essential, non-functional sequences, the deletion gets passed on to future generations without incident. The amount of difference in overall genome size between humans and chimps is of the amount one would expect given six million years of evolutionary divergence.

*Several hundred million bases (individual components of the DNA) of the chimp genome are still unanalyzed.

You're being pretty vague here. What do you mean by "unanalyzed"? The chimp genome has been fully sequenced, if that's what you mean.

*In many areas of the DNA sequence, major “rearrangements” seem apparent. These account for perhaps 4–10% dissimilarity between chimps and humans.

Yes, but again this is no problem for evolutionary biology, and is indeed to be expected. I'm not sure what your point might be.

For what it's worth, there seems to be little if any indication that major rearrangements (wherein a section of DNA is successfully relocated to another chromosome or another location on the same chromosome) make any significant difference to how the DNA operates, any more than the location of subroutines in a program makes any difference.

*Chimps have 23 chromosomes and humans have only 22 (excluding sex chromosomes for both species)

True, and actually, this is a great example of how the specific details of similarities and differences between the genomes of various species indicates evolutionary origins, not "common design".

See this post of mine on the subject: http://www.freerepublic.com/focus/f-news/914961/posts?page=242#242

Short form: One chromosome in the human genome shows clear and unmistakable signs of having been formed by the end-to-end fusion of two smaller chromosomes in a common ancestor which had 24 chromosomes, and not via some original human(s) having been designed with 23 chromosomes from the start. For details, see the link.

Thus, the physical and mental differences between humans and chimps are most likely due to the differences in purpose and function of the so-called junk DNA.

Huh? Your "conclusion" does not follow from your earlier observations. You have yet to actually make a case for this assertion.

This understanding should leave us more mindful of the awesome complexity of the Creator and His creation of DNA.

Maybe so, but the DNA of countless species clearly indicates, in many different, independent and cross-confirming ways, that life on Earth has reached its present form via evolutionary common descent.