Hi Jose,
Just looking at that paragraph, I don't see how most of the discoveries mentioned in that paragraph were made "through the understanding of evolutionary common ancestry" (abbreviated below as TUECA and ECA for the last part).
Ok, let's take a look.
Pseudogenes gradually accumulate mutations This is an observation that doesn't require TUECA, unless it really hasn't been observed, but just postulated from a TUECA perspective
Correct. That pseudogenes accumulate mutations by itself is not something that's directly derived from common ancestry. Rather, evolutionary theory (the part that covers the mechanisms by which evolution occurs) provides the understanding that non-functional sequences will accumulate mutations and not have any selective pressure to reverse or remove them.
However, larger-picture-wise and relevant to this paper, evolutionary common ancestry gives us the understanding that once an ancestral species acquires a disabling mutation that turns a gene into a non-functional pseudogene, all subsequent descendant species will inherit not only that pseudogene, but the original pattern of mutations that disabled it. Further, as descendant taxa evolve and diverge, each lineage will accumulate its own unique mutations in that pseudogene. That means the further apart (evolutionarily) the taxa are, the more divergent these mutations will become, and conversely the more closely related the taxa are, the more similar their patterns of mutations will be.
That's the framework under which this entire study was conducted. The above understanding--
entirely based on relative evolutionary relatedness--is what told the the geneticists which species to look at, what parts of their genome to look at, what to compare them to, and what the patterns they discovered indicates.
Analysis of the rhesus macaque major histocompatibility complex (MHC) extended class II region revealed two pseudogenes that were found to be homologous to the human HIV TAT-specific factor-1-like and zinc finger-like pseudogenes This is also an observation not requiring TUECA.
It absolutely is. Remember what I explained above, and then ask yourself, why choose the macaque's region to compare with humans? And when you do compare them, what are you looking for, and how do you make sense out of what you find?
Evolutionary common ancestry gives the answers to
all that, and the authors state just that in the sentences directly before and after the one you commented on...
Pseudogenes gradually accumulate mutations, and the number of mutations can give us an estimate of their age. Fascinatingly, the appearance of Alu elements in Old World primates coincided with the peak of processed pseudogene generation and subsequent radiation of primates ~40 million years ago (Ohshima et al. 2003; Zhang et al. 2003). Conservation of pseudogenes across different species has also been observed. Analysis of the rhesus macaque major histocompatibility complex (MHC) extended class II region revealed two pseudogenes that were found to be homologous to the human HIV TAT-specific factor-1-like and zinc finger-like pseudogenes, which was suggestive of evolutionary conservation (Sudbrak et al. 2003).
So not only does evolutionary common ancestry inform the study of pseudogenes and their relative status compared across species, their relative status compared across species informs us about the evolutionary history of those taxa.
the Makorin1-p1 pseudogene is conserved across Mus musculus and Mus pahari strains. "is conserved" makes this both an observation and an interpretation. The interpretation, as far as I can tell, assumes TUECA, but the observation doesn't require it, and if ECA is wrong, it makes the "discovery" of less worth than it might have been if unencumbered by the conclusion
It's what I described above. And they even describe how what I explained above played into the research and analyses...
This prompted a genome-wide survey for pseudogenes conserved between humans and mice in which human pseudogenes, along with their parent genes, were compared with the corresponding mouse orthologues and their pseudogenes (Svensson et al. 2006). Interestingly, many of the pseudogenes examined were found to have very few mutations within the regulatory regions they shared with their parent genes, which might suggest that these regulatory regions are of importance to the pseudogene and that the pseudogene may be functional.
many of the pseudogenes examined were found to have very few mutations within the regulatory regions they shared with their parent genes This also is an observation, not requiring TUECA.
Is there a reason you keep copying only the parts that basically say "this is what we found", but omit the parts that say "This is why we looked in the first place" and "This is what it means"?
the appearance of Alu elements in Old World primates coincided with the peak of processed pseudogene generation and subsequent radiation of primates ~40 million years ago
Other people may have a different take on which are "discoveries" mentioned in the paragraph, but I don't see how TUECA is necessary.
Then I suggest you not only re-read this paper, but follow up and read the linked papers it cites.
Regarding that last one, I'll admit I don't understand how this "discovery", which appears to be more an interpretation of data rather than a discovery, was made.
Again, the understanding of primate evolutionary history (humans included) led the researchers to figure out what species to look at, where in their genomes to look, what to look for, and how to interpret what they found.
Without any of that, how would this work be done? Why look at macaque DNA and compare it to humans? Why not pine trees? Or a virus? And why would you bother quantifying the differences between the two, unless you understood that they diverged from a common ancestor, and therefore inherited the original disabling mutations from that ancestor?
See what I mean? Evolutionary common ancestry is the
entire basis for this work.
I don't think anyone has analyzed the actual genes from 40 million-year-old creatures in order to determine 1. that Alu elements actually appeared then, or 2. processed pseudo-genes actually appeared then. I agree that this requires ECA
And that understanding is the basis for the comparative analyses between primate genomes.
but only to prove ECA, which is circular logic.
No, this paper is not at all about proving evolutionary common ancestry between primates. That was established a very long time ago. Rather this type of work takes that understanding and uses it to generate useful, productive results, as this paper demonstrates.
That's how science works. You build on the understanding established by those who came before you.
If I'm correct in my reading of the paragraph you cited, then it does support 6days' contention--that evolution didn't contribute to science in this particular example, and in fact, if the conclusions are wrong (hard to say yet), they might have actually had a deleterious effect on science.
Well, you're not correct. As explained above, evolutionary common ancestry is the entire basis for this work.
Basically, this type of research is referred to as "comparative genomics". And the field of comparative genomics is based on evolutionary common ancestry.
CLICK HERE for a good overview of how that works.