@benkirk I’m not sure you’re thinking about the article I’m asking about. It’s the one by Venema I linked to in my OP. He is talking about nested hierarchies of mutations, even if you’re not. Perhaps you are talking about the same thing he is, but if so you’re using different terminology (“sequences” as opposed to “mutations”). That’s of course fine as far as it goes, but since I don’t know much about evolutionary genetics it would help me if you stuck to the terminology Venema used. He explained things well enough for me to feel like I understand the point he’s making.
I did read the other thread you and Chris mention, and if it helps with my question, the way in which it does needs some spelling out. See my first response to Chris to see why I don’t see why the other thread helps.
I think you’re getting hung up in the irrelevant parts of my car analogy. Let me try again. Here is the key part of the argument Venema makes (quoting):
“…in the data set from this study, twelve identical mutations were found to be shared between primates in a particular pattern…Three of these mutations are shared between humans and chimpanzees only; a further three are shared between humans, chimpanzees and gorillas; and a further six identical mutations are shared between humans, chimpanzees, gorillas and orangutans. This pattern is readily explained by the following: the common ancestral population of all four species has six mutations that occurred prior to the lineage leading to orangutans branched off; three more that occurred before the lineage leading to gorillas branched off; and another three that occurred before the lineages leading to humans and chimpanzees separated…Put another way, in this data set if we see a mutation shared between humans and gorillas, we see those exact mutations in chimpanzees without fail. Likewise, if we see a mutation shared between humans and orangutans, we see those exact mutations in gorillas and chimpanzees, again without fail. The shared mutations make a precise pattern that is exactly the pattern we expect if indeed these species share common ancestral populations that progressively divided into four lineages—a pattern known as a nested hierarchy.”
This is supposed to be an argument for common ancestry, I take it, because the best explanation for why these mutations would nest down the lineage tree in this way is that the lineage pattern they follow really does capture the historical lineage of humans, chimps, gorillas, etc.
My point is this: this nesting of mutations is evidence for common descent only if there are not other properties of the genomes of humans, chimps, etc. that follow the same nesting pattern and explain the nesting pattern visible in these mutations. And there must be other properties of the genomes that follow this same nesting pattern, otherwise there wouldn’t be grounds for positing the lineage pattern that Venema thinks gains additional support from this mutation nesting. In other words, there are reasons Venema and others think humans, chimps, etc. stand in this lineage, independent of nesting mutations. I assume the reasons Venema and others place these species in this lineal relationship is partly due to similarities in genome that also follow this nesting pattern. I mean, that’s how they got that pattern to begin with, right?
So the question just is: could any of these other shared genomic properties which also follow this nesting pattern explain the nesting pattern of mutations? And if so, how likely or unlikely would this be?
Without dealing with this issue, the sort of argument Venema is making here doesn’t work. I’m not saying his argument doesn’t work–maybe there are great reasons to think the sort of explanation I’m asking about can’t happen. I’m just asking for someone to explain why this sort of alternative explanation isn’t available.
(Also note: what I’m asking about is not “common design,” or whether these shared mutations could have randomly occurred in just the right pattern across these genomes of the species, or any other alternative explanation Venema addresses in his post).
Thanks again to all who are trying to help me out here! Any thoughts appreciated!