E novo genes are “sufficiently small”, and that they only need
E novo genes are “sufficiently small”, and that they only need “minimal functionality” to “get started” [192]; and that with so much transcriptional noise, and minimal requirements, occasionally some pieces of neutrally-evolving junk fortuitously acquire use in the organism. But how can we be sure that the de novo genes are small enough, that the amount of transcriptional noise is large enough, and that opportunities for functionality, even minimal, are common enough? Say that a LurbinectedinMedChemExpress Lurbinectedin person has left Jerusalem by foot, and that we believe that he performs a random walk, stepping in entirely random directions forever after; and say that we all agree that he would never reach Paris in this manner, because it is too far for a random walk. Now say we observe him in Istanbul. Would we say that it makes sense that he got there, because Istanbul is closer to Jerusalem than Paris is? Or should we perhaps reexamine our assumptions about the person? This example shows that there is a severe problem of lack of quantification of the amount of chance that we call upon, not to mention such facts as that the Poldi de novo gene arose already with an alternative splicing pattern [11]. The reason that we say that de novo genes must be “small enough” is not because we know that this “explanation” works, but because we have not had any other explanation up to now. In fact, de novo genes are small because they are new genes, and there is a trend whereby the length of a gene increases with age. This trend would be expected from the present theory, which upholds a mechanistic, gradual origin of de novo genes. Last but not least, according to the present theory, the fact of transcriptional promiscuity is indeed eminently relevant to the situation, but in a mechanistic way, as will be discussed later in this paper. f To clarify, like Jacob, I do not think that a protein can be constructed without natural selection. But if protein parts are brought from elsewhere, in a long-term evolutionary process enacted by the writing phenotype, which itself gets continuous feedback from natural selection, then it is possible that we will see here things that are contradictory to traditional notions. g Note that the word “selfish” in “selfish elements” comes from an analogy to human behavior, where in fact it is a key principle of economics that actions in the actors’ self-interest contribute to the economy as PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/25962748 a whole.Abbreviations cSNP: Coincident SNP; ENCODE: The Encyclopedia of DNA Elements consortium; FoSTeS: Fork stalling and template switching; LCRs: Low copy repeats; MMBIR: Microhomology-mediated break-induced replication; NAHR: Non-allelic homologous recombination; NHEJ: Non-homologous end-joining; ns/rm: The natural selection and random mutation process; RBMs: Recombination-based mechanisms; RS: Replication slippage; SDs: Segmental duplications; SNP: Single nucleotide polymorphism; SRS: Serialereplication slippage; TEs: Transposable elements; TP: Transcriptional promiscuity. Competing interests The author declares that he has no competing interests. Authors’ information AL graduated from Princeton University, Ph.D. in Ecology and Evolutionary Biology, and is now an Assistant Professor in the Department of Biological Sciences at Virginia Tech. He has done work in theoretical population genetics, the evolution of sex and recombination, and work at the interface of biology and theoretical computer science. He conceived this project while being a Postdoctoral Research Fellow.
