From Jeff Tomkins’ most recent paper that supposedly addresses the criticisms leveled at his work by myself and others:
“Another problem with the alleged cryptic centromere is its short length. The cryptic centromere site is extremely small compared to a real centromere — it is only 41,608 bases in length […] – a fraction of the size of human centromeres that range in length between 250,000 and 5,000,000 bases (Aldrup-Macdonald and Sullivan 2014). Thus, if this was in fact a relic centromere of an ancient chromosome fusion, its size should be greater than six times its current length at the minimum.”
No, the only problem here is Jeff Tomkins’ lack of familiarity with the literature and/or his complete unwillingness to research the topic.
In 2012, an excellent review paper discuss centromere inactivation in dicentric chromosomes (i.e. those chromosomes with two centromeres due to a fusion event). You can read the paper here: Dicentric chromosomes: unique models to study centromere function and inactivation.
Here are some pertinent quotes (emphasis is mine):
“[In budding yeast], the dicentrics could be stabilized if one of the centromeres underwent breakage and recombination that physically deleted one centromere.”
In fission yeast:
“Another ~10 % of the dicentrics remained fused, and the cells divided normally. These dicentrics were stabilized because one of the two centromeres had been physically deleted.”
But most importantly in humans:
“The remaining dicentric fusions underwent centromere inactivation between 4 days and 20 weeks after formation. […] Using semi-quantitative FISH, it was observed that the alpha satellite array of the inactive centromere became reduced in size after centromere inactivation. These results suggested that one mechanism of dicentric stabilization and centromere inactivation in humans involves partial deletion of the alpha satellite array.”
As you can see, centromere inactivation is a well studied phenomenon, and in humans in particular, has resulted in the inactivated centromere being partially deleted. This is precisely what we see in human chromosome 2.