Indels don't change the overall sequence, though
Sure they do, if by 'overall sequence' we mean the sequence within the genome. If you are talking about the 'overall sequence' of a gene which the indel is not occurring in then sure, they don't change it.
In terms of gauging evolutionary relatedness, frameshifts are largely misleading, because, even though there is a difference in location, the sequence is still the same.
Can you give some rationale for why small stretches of homologous sequence conservation are the best way of guaging 'evolutionary relatedness'.
If you think that only the protein coding sequence of traditional genes is important to evolution then you are well behind the curve.
Homology reaches farther than the 95% you give it by incorporating frameshifts.
This isn't just about frameshifts, you are still thinking at the gene level when we should be talking about the genome level.
If you want to say something overall about the genetic similarity of humans and chimps then why not look at the overall organisation of the genome. If you only restrict yourself to sequences from ORFs similar enough to align, as the research molbiogirl referenced did, then you are just front loading your search to give you higher similarity than might actually be the case in the genome as a whole.
So, skepticfaith's assertion--that we've now found that we're not so close to chimpanzees because the difference is 5%--is flawed.
In what way? molbiogirl said were were 1% different 'genetically', a vague term that could encompass any level of genetic organisation. Skeptic faith simply said he had heard a value for genetic divergence of 5-7%. In what way is his assertion any more flawed than molbiogirl's? They are both using the vague concept of genetic similarity but providing figures base on different specific genetic metrics.
Why should nucleotide divergence in alignable coding gene sequences be the holy grail of genetic divergence. We know that a large number of the mutations which appear to account for the differences between humans and chimps are not of this type.
Why is a single nucleotide substitution a better guage than a 2bp deletion for evolutionary distance? I can understand that indels can be more complex to dissect but discounting them for that reason is just one more way of biasing your analysis towards finding higher similarity.
Why restrict ourselves now that we have the tools for doing real full scale genome comparisons?
TTFN,
WK