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It’s all essential. This paragraph from the Smithsonian describes the issue well

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Geneticists have come up with a variety of ways of calculating the percentages, which give different impressions about how similar chimpanzees and humans are. The 1.2% chimp-human distinction, for example, involves a measurement of only substitutions in the base building blocks of those genes that chimpanzees and humans share. A comparison of the entire genome, however, indicates that segments of DNA have also been deleted, duplicated over and over, or inserted from one part of the genome into another. When these differences are counted, there is an additional 4 to 5% distinction between the human and chimpanzee genomes.

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In other words the regions shared between the species are 98% or more on average.

But human have sequences chinos don’t have and vice versa. So the overall identity or similarity is 95% or so. The original press release from NIH in 2005 states 96%.

https://www.genome.gov/15515096/2005-release-new-genome-comparison-finds-chimps-humans-very-similar-at-dna-level/

This includes the extra/missing regions that ExDemMom criticized the author for including.

This author is saying that the 95-96% figure is higher, in his opinion, than it actually is and better characterization of the Chimp sequence would show this.

He could be correct, or not, but it would be difficult to determine and the Chimpanzee Sequencing and Analysis Consortium isn’t going to spend resources on a review.

The original 2005 article is here.

http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html

This author argues for a large margin of error and the probability of a lesser identity percent based on certain technical aspects described in the article, e.g.

“The observable insertions fall into two classes: (1) ‘completely covered’ insertions, occurring within continuous sequence in both species; and (2) ‘incompletely covered’ insertions, occurring within sequence containing one or more gaps in the chimpanzee, but revealed by a clear discrepancy between the species in sequence length. Different methods are needed for reliable identification of modest-sized insertions (1 base to 15kb) and large insertions (> 15kb), with the latter only being reliably identifiable in the human genome (see Supplementary Information ‘Genome evolution’).”

Which means not all the sequences are accounted for, and also that only 94% of the Chimp genome was sequenced:

“The draft genome assembly—generated from ~3.6-fold sequence redundancy of the autosomes and ~1.8-fold redundancy of both sex chromosomes—covers ~94% of the chimpanzee genome with >98% of the sequence in high-quality bases.”

Since this report I am not sure how many blanks have been filled in or what more analysis or publications have been done.

Oh, my, in your eagerness to post random trivia related to genetics and molecular biology, you have inadvertently posted an article that supports what I said several posts ago.

My previous post: "He left out a lot of very pertinent details--that is, he cherry-picked which facts to include and which to omit. That is not scientific. One of the very pertinent facts he "forgot" to mention is the difference between coding and non-coding DNA. If you compare regions of non-coding DNA between any two species or even sub-species, you will find far more divergence than if you compare the coding regions between the same two species. That is because there is little to no selective pressure to maintain the DNA sequences of non-coding regions. If the only purpose of that stretch of DNA is to fill space, it does not matter much what the sequence is. Thus, any mutations within that region have no effect on survival. On the other hand, the coding regions of DNA are far less tolerant of changes in bases. Some mutations within the coding region will have little effect: for instance, TAA, TGA, and TAG all mean "Stop" (as in, that is the end of the protein molecule). Thus, an A to G or G to A mutation in those sequences has little effect. But a change in that T to anything else would have an effect, because the stop would be lost, and the protein coded there would be unusually long--with potentially lethal result. So, if I were looking for the degree of genetic similarity between two organisms, I would look at the coding regions, and at the redundancy within the code."

Versus your quote from Smithsonian magazine (where you omitted a citation): "Geneticists have come up with a variety of ways of calculating the percentages, which give different impressions about how similar chimpanzees and humans are. The 1.2% chimp-human distinction, for example, involves a measurement of only substitutions in the base building blocks of those genes that chimpanzees and humans share. A comparison of the entire genome, however, indicates that segments of DNA have also been deleted, duplicated over and over, or inserted from one part of the genome into another. When these differences are counted, there is an additional 4 to 5% distinction between the human and chimpanzee genomes."

Of course, the major differences here are that I was not quoting any source while you were copy/pasting, and I understand and discuss the significance and implications of the information, and you have not offered any kind of explanation of how the information fails to support or even contradicts theory.

Far from invalidating any aspect of the theory of evolution, the fact that coding regions within two similar species are more similar than the non-coding regions is a direct consequence of evolutionary processes, and can be predicted by one who has a fundamental understanding of evolutionary theory.

The same can be said for the fact that intronless genes have been identified in eukaryotes. Most genes in bacteria have no introns--again, a consequence of evolutionary processes, not a "disproof" of the theory of evolution. (It is a consequence because bacteria are small and have high energy requirements; bacteria that do not shed useless DNA have a survival disadvantage compared to bacteria that do get rid of the junk. Eukaryotes do not have that energy disadvantage, so can continue to carry huge genomes, even when the bulk of the genome is non-coding.)

Oh, and I should point out here that I didn't bring up the term "junk DNA," you did--I only talked about coding and non-coding DNA.

Now, while you are on this spree of posting all kinds of molecular biology trivia, you have not provided any indication of understanding the biological implications of the trivia facts, or their relevance within the theoretical framework. The identification of a handful of intronless genes in eukaryotes does not change the fact that well over 99% of eukaryotic genes consist primarily of introns that are discarded during mRNA processing. I will also point out that the fact that histone genes have no poly(A) tail when virtually every other gene does is an interesting fact, but has no bearing on the validity of evolutionary theory.

Instead of throwing out an endless stream of trivia that does not address the theoretical framework of evolution at all (but is actually quite consistent with the theory, although you don't seem to grasp that fact), why don't you try to develop testable hypotheses that would be consistent with a theory of a one-time creation event that occurred ~6,000 years ago at a single geographic location? Surely, if such a singular event happened and all life on earth exists because of it, a whole slew of testable hypotheses can be generated and tested. Where are the researchers developing and testing those hypotheses? I have yet to see any--at most, there is a random (and exceedingly rare) scientist who discovers that being paid to "debunk" established scientific facts, methodology, and so forth is more lucrative than working in the field. But there is no genuine research going on in "creation science." Could it be because any testable hypothesis that could be generated is quickly rejected because the evidence does not support it?