The Current Status of Ewert's Dependency Graph of Life

[Rumraket (Mikkel R.)]

@colewd

I agree common descent predicts this. What it does not predict is the origin of thousands of unique genes.

Bill how would you get a nested hierarchy in gene presence-absence, if not by the origin of new genes and loss of old ones?

@colewd

In order to make this prediction you need a mathematical model of how this happens.

You don’t need a mathematical model of HOW gene gain or loss happens in order to explain a nested hierarchy in gene presence and absence. You just need to posulate THAT it happens. Of course we do KNOW that it happens as we’ve seen both gene gain and loss occur.

But regarding modeling gene gain, there was a thread on this recently.

Evidence favoring de novo gene evolution, and an actual population genetic model of de novo gene gain

First paper here gives evidence that non-coding DNA is generally speaking very close in sequence space to DNA encoding foldable protein secondary structural elements: Abstract The noncoding genome plays an important role in de novo gene birth and in the emergence of genetic novelty. Nevertheless, how noncoding sequences’ properties could promote the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic ORFs (Open Reading Frames) of S. cerevisiae with the aim of (i) exploring whether the large structural diversity observed in proteomes is already present in noncoding sequences, and (ii) estimating the potential of the noncoding genome to produce novel protein bricks that can either give rise to novel genes or be integrated into pre-existing proteins, thus participating in protei…

@colewd

Since this is not likely I would appeal to finding a different starting point than Luca for the hypothesis.

Nonsensical statement.