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The video doesn't cover all of the details of the research since it is a high-level summary, but a more detailed description of the chromosome merger is in the section "Segmental duplications" in the original research paper here:
http://www.nature.com/nature/journal/v434/n7034/full/nature03466.html
The paper covers some methods how the merger could have have happened via genetic mutations and duplications, though some technical knowledge of genetics is assumed. More detailed theories concerning the exact temporal order and extent of the mutations and duplications are contained in the earlier research here:
http://www.genome.org/cgi/content/abstract/12/11/1651
http://www.sciencemag.org/cgi/content/abstract/215/4539/1525

Dr. Miller was an expert witness in the Kitzmiller v. Dover ID trial, so I think he knows the arguments on both sides of the ID debate fairly well. Dr. Miller's main point in that lecture segment was that that evolutionary theory predicted the merging of a chromosome, and later we seem to have found the location in human DNA where the merging occurred when compared to ape chromosomes. He is trying to counter the argument that it is not possible that humans and modern apes share a common ancestor because we have different numbers of chromosomes, or because evolution can not create new species, etc. So this segment of the lecture is more pro-evolution than completely anti-ID. Much of the rest of the lecture (if you locate the full version) is what I would call anti-ID, though. He generally disapproves of ID books such as "Of Pandas and People" and groups like Answers in Genesis that he believes are also trying to push ID as thinly veiled creationism and he does not agree with the "irreducible complexity" ID arguments. You can view the full lecture and decide for yourself if his arguments counter the specific version of ID you have in mind, or if you think some versions of ID are immune to his criticisms, but be aware he is specifically talking about ID as it is being argued in Pennsylvania and Ohio by those wanting to integrate ID into science classes, and he would likely have other arguments against other variants of ID.

There are certainly ID proponents that believe in common ancestry (Michael Behe is one of those), but also believe that, for example, a supernatural being guides evolution, instead of unguided genetic mutations and natural selection alone. But keep in mind that about half of Americans do not believe in human evolution of any kind, and instead think that that a supernatural being created humans basically as they exist today. In effect, there are hundreds of millions of people that reject common ancestry, so Dr. Miller certainly has some people that he could try to convince with his arguments, even if some ID proponents do not need to be convinced of this specific point. That said, many scientists would note that it is a little odd that a supernatural being would create a world where life comes into being, but do so using a method that ends up making it very uncertain whether or not any supernatural being is even necessary. The view that common ancestry and evolution are true but that a supernatural being guides evolution may also be largely indistinguishable from materialistic evolution, though some people like Behe claim statistical methods and science can prove that random genetic mutations are not sufficient to drive evolution (though he is in the scientific minority on this topic). I'm happy to let Dr. Behe and others continue their ID research, but I don't expect much real evidence to come out of it, myself. To each their own.

Ehlers A, Beck S, Forbes SA, Trowsdale J, Volz A, Younger R, Ziegler A: MHC-linked olfactory receptor loci exhibit polymorphism and contribute to extended HLA/OR-haplotypes.

Genome Res 2000, 10:1968-1978.
Abstract
Full Text

The research appears focused on the genetic variation, not the resulting changes (or lack of changes) to olfaction.

Agreed! However, I learned about it 8 years ago as an undergrad. For some more interesting current research, have you heard about the link between retro-transposons (the epitome of the selfish gene -- the human genome DNA content is roughly 10% of these guy and ~50% transposons in general. Contrast this to the 1.5% of the human genome that encodes for proteins.) and retro-viruses? In a nut shell, retro-transposons and retro-viruses are the same critter, but retro-transposons have lost their env gene that is required for extracellular travel. In any case, scientists last year were able to recreate an infectious form of a retro-transposon/non-functional retrovirus (HERV-K). Very cool (as slightly frightening stuff!) If interested, here is the abstract from their paper:

Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements

Marie Dewannieux1,3, Francis Harper2,4, Aurélien Richaud1,4, Claire Letzelter1, David Ribet1, Gérard Pierron2, and Thierry Heidmann1,5

Human Endogenous Retroviruses are expected to be the remnants of ancestral infections of primates by active retroviruses that have thereafter been transmitted in a Mendelian fashion. Here, we derived in silico the sequence of the putative ancestral "progenitor" element of one of the most recently amplified family--the HERV-K family--and constructed it. This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny. We also show that this element amplifies via an extracellular pathway involving reinfection, at variance with the non-LTR-retrotransposons (LINEs, SINEs) or LTR-retrotransposons, thus recapitulating ex vivo the molecular events responsible for its dissemination in the host genomes. We also show that in vitro recombinations among present-day human HERV-K (also known as ERVK) loci can similarly generate functional HERV-K elements, indicating that human cells still have the potential to produce infectious retroviruses.

The abstract with a link to the full pdf is available online. The pdf is available on campus from many universities. It is interesting that this is already in the news. This is not technically in print form yet, and was just posted to the journal's advance articles web site.

The abstract with a link to the full pdf is available online. The pdf is available on campus from many universities. It is interesting that this is already in the news. This is not technically in print form yet, and was just posted to the journal's advance articles web site.

But evolution THEORY is that somewhere along the line there were MAJOR DNA changes, there is no proof of this happening

No to both claims. Evolution could be in principle fully explained by a sequence of minor DNA changes. In practices there is evidence of major DNA changes in the past. See http://www.sidwell.edu/us/science/21bio/zfish/post er/gd.html , for example, or http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd= Retrieve&db=PubMed&list_uids=9729879&dopt=Abstract , or http://www.genome.org/cgi/content/abstract/8/6/577 (Just a couple of examples googled in 30'').

Yes, for-profits like IBM and United Devices are helping, but the Proteome Folding project is not theirs. Nor do you see an pharmaceutical companies here. The ISB in a non-profit academic center. The lead scientists are top-notch. This data is being published and shared. Check out the papers at http://genomebiology.com/2004/5/8/R52 and http://www.genome.org/cgi/content/abstract/14/11/2 221 for examples. They used the Halobacterium NRC-1 as a practice run and discovered the function of a number of its unknown genes.

(For example, they uncovered over a dozen Htrs--halobacterial transducer proteins--part of the machinery halobacteria uses to sense its environment. These things are amazing extremophiles. They show how life can survive just about anywhere. They're what make the salt ponds at the south end of San Francisco Bay turn purple. NRC-1 came from the Dead Sea.)

The latter, it turns out, is not remotely "junk", but contains important regulatory sequences which control gene activation/deactivation and the physical structure of the chromosomes.

actually, known regulatory sequences comprise only a small fraction of the junk....

a much bigger fraction is mobile DNA of various kinds (transposons, satellites, etc.) which may (or may not) be evolutionarily important.....

some more may be unannotated genes, e.g. small ORFs or noncoding RNAs... basically the content of intergenic DNA is still an open question...