This reply needs to contain a number of links to qualify each of my claims. Unfortunately this site won't allow me to include more than two links because I am a new user. Please see this post which contains the same response and all the necessary links as well.
I would be very careful trusting any claims published by the young earther Jeffrey Tomkins. In my experience, each of his claims needs to be thoroughly researched because I have found him to be less than rigorous (sloppy) in at least one other paper he has published. He has faced similar accusations from others in the past.
I'm not saying dismiss everything he says: I'm saying take all of his claims with a grain of salt, expect there to be exaggerations, errors and misleading claims (he has a young earth creationist agenda)
If you are ever concerned about anything he writes, you will need to look at the evidence for yourself. I will attempt to answer your questions here.
In a 30 kb region surrounding the fusion site, there exists a paucity of intact telomere motifs (forward and reverse) and very few of them are in tandem or in frame.
This is true, but it isn't surprising (at least not to me). To quote popular science blogger, Carl Zimmer:
The ends of chromosomes are very vulnerable places. If they simply dangle loosely, DNA-cutting enzymes can nibble away at them, destroying the genes they encounter. The dangling end of one chromosome can also get attached to the dangling end of another, fusing chromosomes together. We are mostly protected from such changes thanks to special proteins called telomerases. They tack on little repeating bits of DNA, which form a loop–a telomere–so that chromosomes end as a hairpin curve, rather than dangling ends.
It is this loop that prevents chromosomes from undergoing the type of fusion that we see in the second chromosome. Now telomeres naturally shorten and become mutated with age. If we encountered two fused chromosomes (with the telomeres joined end to end) we should expect that this could only happen where the telomeres are short enough and mutated enough to allow this to happen. Only when they can no longer form that protective loop, can they become fused.
Experiments like this have shown that defective telomeres with few repeats are vulnerable to chromosome fusion.
Here is what the fusion site actually looks like - the highlighted repeating elements (TTAGGG and CCCTAA) are those that are still perfectly formed. If I relax my criteria a little and also highlight those repeating elements that have just one single mutation, this is what the fusion site looks like. To raise doubts that what we are looking at here are a series of repeats of "TTAGGG" joined to a series of repeats of "CCCTAA" is either asinine or dishonest.
Telomere motifs, both forward and reverse (TTAGGG and CCTAAA), populate both sides of the purported fusion site. Forward motifs should only be found on the left side of the fusion site and reverse motifs on the right side
(Note: it is CCCTAA not CCTAAA)
This is just pure nonsense, I am tempted even to call it a lie but I can't be sure. I have looked into this claim by searching through the 20,000 bases that surround the fusion site.
In those 20,000 bases there is exactly 1 instance of TTAGGG that occurs before the fusion site and 1 instance of CCCTAA that occurs before the fusion site (No more than we should expect to occur by chance alone in any sequence this long).
After the fusion site (and away from it), there is 1 more instance of CCCTAA and 3 more instances of TTAGGG (No more than we should expect to occur by chance alone in any sequence this long).
Don't take my word for it. Here are 20,023 bases that surround the fusion site.
The 798-base core fusion-site sequence is not unique to the purported fusion site, but found throughout the genome with 80% or greater identity internally on nearly every chromosome; indicating that it is some type of ubiquitous higher-order repeat.
This sounds like more rubbish (even a lie perhaps). Using BLAT to search for the actual sequence, there is no location in the human genome except for this place on chromosome 2 where we see a sequence of repeating TTAGGG joined to a sequence of repeating CCCTAA. If the authors claim to have found another site like this, why have they not linked to it?
We could also use BLAT to search for an idealised sequence of perfect repeats. Once again, the only hit that includes both the TTAGGG and the CCCTAA is in this exact location on chromosome 2.
We do unsurprisingly find sequences of repeating TTAGGG but what makes this fusion site unique is that those repeats are followed by repeating CCCTAA - that isn't found anywhere else in our genome of over 3 billion base pairs.
Think about that for a moment. A sequence with a signature as unique as this, found in the exact place where scientists expect to find it!
No evidence of synteny with chimp for the purported fusion site was found. The 798-base core fusion-site sequence does not align to its predicted orthologous telomeric regions in the chimp genome on chromsomes 2A and 2B.
First of all, this claim doesn't even make sense. The 798 bases he talks about are just the telomeric repeats. If they are telomeric repeats then they will be found on the telomeres of chromosomes 2A and 2B. Perhaps he made a mistake here and was talking about the wider region surrounding this fusion site?
It is true that there is a lack of synteny in the wider region surrounding this.
This became well understood with the sequencing of the gorilla genome. There was a paper published explaining how this happened in 2012. If you prefer, here is the layman's explanation with diagrams.
Queries against the chimp genome with the human alphoid sequences found at the purported cryptic centromere site on human 2qfus produced no homologous hits using two different algorithms (BLAT and BLASTN).
This isn't true either. Where does he get this nonsense from? I have downloaded the alphoid sequences from the defunct centromere on human chromosome 2 and used BLAT (against Chimpanzee Feb 2011) to find their homologs in the chimpanzee. Unsurprisingly they are exactly where we expect to find them on chimpanzee chromosome 2B - where there is a functional centromere.
Think about that for a moment. The very same sequences that form a functioning centromere on chimpanzee chromosome 2B are found exactly where we expect to find them at a defunct centromere on human chromosome 2.
I am busy constructing a detailed write-up on this. I will update this post to provide a link to that.
Alphoid sequences at the putative cryptic centromere site are diverse, form three separate sub-groups in alignment analyses, and do not cluster with known functional human centromeric alphoid elements."
I can't comment on the first claim but it seems irrelevant anyway. I can tell you that these alphoid sequences occur frequently at centromeres all over the human genome from X to 22. More importantly they are appear almost exclusively at centromeres. For example, alphoid 2 appears at centromeres on the following chromosomes: 21, 9 (twice), 11 (twice), 20 (twice), 7 (3x), 22 (5x), 16, 14, 15, 5.
It appears once at an unexpected location on chromosome 9 where there isn't a centromere, but that exact location is rich in other alphoid sequences suggesting that it too is a defunct centromere (or was perhaps duplicated from another centromere).
This will also be covered in that detailed write-up I mentioned.
edit (2 Oct 2015):
I promised to follow up on this post with a detailed write-up on the fossil centromere on chromosome 2. I've done that now (A year and a bit later) - you can find the information I've compiled on the centromere here