Similarity is based upon BLAST.
No, similarity is based upon the extent of sequence matches, and BLAST is but one way to assess this.
How was genome similarity assessed prior to the origin of BLAST? The initial version of BLAST came out in 1990. There were assessments of similarity before that (and after that) which did not use BLAST, such as DNA-DNA hybridization or direct sequence comparisons of however much sequence data you have. I did my first alignments and comparisons by eye using the XESEE sequence alignment and analysis program (DOS-based, all done by hand).
I have published 9 papers/chapters on this general subject, to include 5 that specifically looked at human/chimp phylogeny, and did not once use BLAST, and while the % similarity was not the focus of any of those papers, the % similarity does show up in the outputs of the programs I used to analyze the sequence data as a 'byproduct.'
So please stop misrepresenting the science.
What is done is that the genome is cut into bits. then any part found matching with any other part is considered similarity, regardless if they are not even on the same portion of the genome and may have completely different functions.
LOL!
Maybe that is how TOMKINS did it. There are rationales for doing that, but that is not required to assess similarity.
And while there will generally be 'similarity' via homology and the like on more than 1 chromosome, this will not matter if the 'pieces' used are large enough. A few years ago, after the original hyperbolic ENCODE papers came out, I searched an artificial chromosome of ~100 million bps in length for a particular group of known binding sites and got hundreds of thousands of hits. The nature of DNA all but guarantees that short bits of sequence will show up all over the place by chance alone.
Again, Tomkins had a reason for using the short bits he did, but do not assume that legitimate researchers do the same things for the same reasons.
Now when comparing human genomes this is never done, one simply compares the two as they are for relatedness. that they are required to cut up the genome of chimps and humans and match any portion to any portion shows the pseudo-scientific aspect of their results.
So, I guess you don’t know how any of this really works.
Here is a hint – again, I did DNA sequence comparisons WITHOUT using BLAST. None of the people I worked with at the time used BLAST for sequence comparisons (we used BLAST for other reasons, such as to search the databases for sequence data that we could incorporate into our matrices, but NOT for doing the actual analyses!).
I have done sequence analyses with humans and non-humans in the same analysis – and no BLAST was used, no ‘cutting’ things up.
And BLAST was not used to do 'similarity' assessments in the chimp genome paper.
But I do find your uninformed rhetoric interesting.
For example –
“…that they are required to cut up the genome of chimps and humans and match any portion to any portion…”
If this were the case, then how can it be that we can compare human chromosome 2 with chimp chromosomes 2a and b? Have you ever heard of chromosomal banding? You can compare entire chromosomes based on their staining characteristics – no cutting up or use of BLAST needed.
Also, keep in mind that BLAST is not just one program - there are several 'sub' or related programs with similar names (e.g., BLASTn, BLAT, BLASTZ) that perform different functions. The chimp genome paper, for example, used BLASTZ for aligning the human and chimp sequences - but these were not 'cut up' pieces ala Tomkins, these were entire sequences (entire chromosomes, for example).
So, you should read up on these sorts of things BEFORE making your usual over-the-top proclamations.
Don't even buy into their fakery...... You can't compare a sequence with another in a different place on the genome which may have completely different functions and then claim similarity.... FAKERY.........
See above.
Plus, if the sequences are quite similar over a long span, and the span includes coding sequence, then yeah, they probably do have similar functions.
