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Thank you for your post!

Can you expand on what those considerable assumptions are?

As an example, every now and then Vade posts skeletons which have been constructed partially from fossils and partially from assumptions. The scientists usually color the fabricated bones so the observer can tell the difference.

Likewise, I suggest there will be a lot of the classic tree which cannot be spoken to directly by genetic research for lack of genetic material in fossils. As with Vade's skeletons, those parts (if shown) would be fabricated. Since most of the tree represents extinct life over time, the part which is reinforced by genetic information on extant species correlates to the leaves, or "lawn" to me or "onion" to others.

My daughter's research over the years involves knocking out genes to discover function. Considering the vast number of extant species, and the state-of-the-art I do not see how you can go any further without considerable assumptions.

And what if we presume to find out how the Great Designer fit it all together, how would the assumptions differ?

My "lawn" remark does not speak at all to Intelligent Design. It speaks only to what information can be discovered by genetic research.

And it is based on my understanding that genetic information cannot be derived from fossils. If that is not true, then please tell me so - because it would be very interesting to see a genetic comparison of Lucy to any modern female!

My question to you was what are those assumptions. You've proceeded to give examples of where assumptions were used, but you've given no indications of what the assumptions are.

Let's use your example of the skulls. One assumption might be that the major bones making up the skull are maintained. If a parietal bone shows up in two pieces, it is reasonable to glue those two pieces together rather than assume that for that fossil extra parietal bones are involved. You see, the assumption is based on what we know.

Your daughter also uses considerable assumptions when she looks for lack of function by knocking out genes.

Where I'm trying to lead you is that the assumptions for phylogeny do not start with the idea that everything must point to a universal common ancester. The assumption is that organisms beget other organisms. DNA is inherited in this process. Your lawn analogy doesn't use this information. Why not?

There is a promising tool in osteocalcin, a protein that is preserved in fossils for millions of years. There was a recent thread on FR about it.