Humans are apes. And as a matter of fact we've found more than a few organisms linking humans to other apes.
But, leaving that aside, why should it call it into question? Humans aren't special; we're just another species. There's no reason that a human/chimp common ancestor should be considered more important evidence for the ToE than the hippo/whale common ancestor.
There existed a common ancestor of all humans and chimps/bonobos who had two children, one of whom was the common ancestor of all living humans but no chimps/bonobos, and the other of whom was the common ancestor of all living chimps/bonobos but no humans.
PC@t3 is the most recent common ancestor of C and H@t5 in your diagram.
But to save you drawing more, and more, convoluted diagrams I'll point out that it is inevitably possible to draw a diagram that includes no common ancestor because you have control of the time window you choose to represent. The solution then for finding the common ancestor is to draw further backwards in time.
Might I suggest that rather than drawing further diagrams you address the logical argument that Dr. A presented a few posts back? It looks watertight to me.
Dr A's drawing is not based on evidence. It is purely speculative. There is no DNA evidence of those species that lived 2.5 million yrs ago when they split. Today's DNA between them are not identical or even close.
2.5 million? Huh? The human/chimp split was much earlier than that. As for no evidence, you're just being silly. There is a tremendous amount of evidence that chimps and humans are more closely related to each other than they are to any other species.
There are no fossils of gorilla and only a few of orangutan. The fossils of chimps look very much like they do today.
Genetics claim that a fresh water dolphin is not related to the salt water dolphin so do you really expect me to believe we are related to chimps based on a silly diagram?
Actually it says that fresh water dolphins are more closely related to each other than they are to salt water dolphins. Even that's a simplification since the Amazon River Dolphin is more closely related to the salt water La Plata Dolphin than it is to other river dolphins.
What is it about this you find implausible?
And, finally, no-one expects you to believe based on a diagram. The diagram Dr. A kindly provided for you is a summary of our knowledge on the subject not the evidence for it.
his is roughly my argument, yes. Our 'final ancestor' though is not likely to be a single individual, but a group of individuals, which may be representative of one or the other of PH or PC or B; in fact, it is likely that the 'final ancestors' (or common ancestral genetic pool) contained all three types of individuals. And if we decide to settle on just the last contributing one of these, it is not going to be properly representative of the common ancestral pool. Unless we just want to call our common ancestor the last beast that contributed anything at all to each species—even if its children contributed more to one than to another (that is, more variation than was previously present in that population—not the same child, but different children who contributed solely to one species each)—, we have to accept that there is not likely to be a single form to the common ancestor, but that the common ancestral pool consisted of a large variety of beasts. The other option is to go way back to before the beginning of the speciation event, but then the question we must ask ourselves is whether or not such a population represents the most recent common ancestor. It would clearly be less recent than any of the others, but also clearly more ancestral.
No-one is arguing for a single, unique common ancestor. Nor a single common ancestor to whom all genes can be traced.
No. What we're arguing for (now Dr. A convinced me) is that there exists at least one individual who is a common ancestor of both humans and chimps and who has children of whom at least one is ancestor of humans and not chimps, and at least one is ancestor of chimps and not humans.
Nothing about this suggests that aren't many, many more individuals involved in the population genetics of chimps and humans or that this individual is the only such individual.
I have absolutely no clue what common ancestry means. I do not understand when the Time Tree says a different date for mitochondria that is not the same as the nuclear date. How can they evolve separately when they are part of the same organism?
It's a pity that website does not show the margins of error on its estimates. The separation of nuclear and mitochondrial DNA need not be exactly the same in time, but is unlikely to be as different as suggested by the figures you gave.
The primary reason for the difference is that these are estimates, they are not - and cannot be - exact dates.
Many of the dates I listed were before dinosaurs went extinct and I cannot imagine anything resembling today's critters could live along with them.
All of the major groups of mammals separated before the distinction of the dinosaurs, this does not mean that they shared features that would allow you or I to easily recognise them as the ancestors of modern groups. At the time, the largest mammals were perhaps the size of a small dog and, apparently, largely nocturnal.
The Time Tree gives a split date for eukaryotes and bacteria of a nucleotide date of 2622.0 mya. Can someone please explain this to me?
What do you need explained?
What formula is used for the molecular clock model?
You look at a gene or bit of genome in a bunch of organisms (in this particular case it is almost certainly rRNA). Then you work out the rate of divergence between the particular bits of genome you are looking at by plotting the degree of divergence against the time the organisms split based on other evidence. By taking the gradient of this line you can then use it to estimate the time at which other organisms diverged by looking at the level of divergence they have.
You can test the internal validity of your estimate by testing multiple organisms that should have the same divergence time and seeing if your estimates are similar. You can also check that your original plot follows a roughly straight line.
Is carbon dating of bones used in the model?
It won't be for molecular clocks on that scale, but other radiodating methods will have been. It is possible that the calibration of the clock(s) used may have involved using shorter period data derived in part from radiocarbon dating.