There is a lot of confusion in this discussion (and in the original paper) about what "genes" are, and what "novelty" means. Human genes and shark genes (the D

There is a lot of confusion in this discussion (and in the original paper) about what "genes" are, and what "novelty" means. Human genes and shark genes (the DNA sequences) are not nearly identical, in fact, the DNA sequences that encode human and D. rerio (zebrafish, closer than a shark) hemoglobin share about 67% identity over about 2/3 of the mRNA coding length, which is which is quite statistically significant (expected 1 in 10^-30 by chance). But hemoglobin "genes" (the DNA) encode hemoglobin protein, and the human and D. rerio protein sequences share more than 50% identity over the entire length of the protein; a level of similarity expected by chance once in 10^45 searches (these low probabilities would be much much lower for an average length protein of 400 amino acid, globins are much shorter -- 145 aa -- so they have excess similarity or statistical significance). In the protein world, sequences with less than 30% identity often have very high statistical significance. As several writers mention, when the amount of similarity is so high that the odds of it occurring by chance are very low, the simplest explanation is that the similar sequences diverged from a common ancestor. Let me reassure you that computational biologists who do these kinds of analysis are very aware that evolution is not linear (hence the many methods for building evolutionary trees), and that similar mutations could (and do) occur in different branches of a tree. The argument being made here is that something new has appeared -- there are many new trees that emerged about 650 million years ago. (In the protein world, 650 million years is a relatively short time, so evolutionary relationships at that distance should be detected.) That said, it is very dangerous to talk about "novel genes" or "novel proteins" without being very clear about the nature of the novelty. Just as protein sequence comparison is more sensitive (has a longer evolutionary look-back time) than DNA sequence comparison, there are methods (not used in this paper) that can look back even farther, and we know that there are ancient evolutionary relationships that are difficult to recognize using sequence comparison, the approach used here. Moreover, many proteins are build from modules (called domains) that can be rearranged, so even though the module might be old, the particular arrangement might be newer. After a quick scan of the paper, it was unclear to me whether the authors are claiming that there are a large number of genuinely novel domains (unlikely), or simply arrangements (more likely), or perhaps simply duplications of existing genes (very likely, but not very novel).