­­What'sNEW in Cosmic Ancestry, beginning November 2020
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27 Nov 2020 What'sNEW about HGT
Green algae contain very many genes from large DNA viruses, we commented last week. Now we learn that DNA polymerase in the same type of virus may share significant homology with eukaryotic DNA polymerase. Under neo-darwinian philosophy, it's hard to say what this might mean. "...He hypothesized that the eukaryotic enzyme originated as a contribution from some ancient poxvirus." Huh? It existed among viruses before it originated? Nevermind. If existing genes aquired by transfer enable macroevolutionary progress, then eukaryotic DNA polymerase genes in viruses make good sense.

Did Viruses Create the Nucleus? The Answer May Be Near by Christie Wilcox, Quanta, 25 Nov 2020.
Viruses and Other Gene Transfer Mechanisms has background and updates since 1997.

19 Nov 2020 What'sNEW about HGT |
In cosmic ancestry, new genetic programs must be supplied by some means of horizontal gene transfer (HGT). Viruses are the most ubiquitous and efficient potential source of supply. Now a new report indicates that Nucleocytoplasmic large DNA viruses (NCLDVs) can contibute genes to eukaryotes in quantities previously unimagined.

Here we report the widespread endogenization of NCLDVs in diverse green algae; these giant EVEs [endogenous viral elements] reached sizes greater than 1 million base pairs and contained as many as around 10% of the total open reading frames in some genomes, substantially increasing the scale of known viral genes in eukaryotic genomes. ...Their endogenization represents an underappreciated conduit of new genetic material into eukaryotic lineages that can substantially impact genome composition.

Widespread endogenization of giant viruses shapes genomes of green algae by M. Moniruzzaman, A.R. Weinheimer, C.A. Martinez-Gutierrez et al., doi:10.1038/s41586-020-2924-2, Nature, 18 Nov 2020.
Giant Viruses Can Integrate into the Genomes of Their Hosts by Amanda Heidt, TheScientist, 19 Nov 2020.
Viruses and Other Gene Transfer Mechanisms has background and updates since 1997.

16 Nov 2020
NASA's Webb Telescope Will Investigate the Intertwined Origins of Dust and Life, Space Telescope Science Institute (+Newswise), 18 Nov 2020. Hoyle and Wickramasinghe's Analysis of Interstellar Dust has more.

16 Nov 2020
Controversy ...over whether phosphine really was discovered on Venus, Physics World, 06 Nov 2020.
Prospects for life on Venus fade–but aren't dead yet by Alexandra Witze, Nature, 17 Nov 2020.
Thanks Thanks, Martin Langford. 14 Sep 2020: Our notice and links about the phosphene.

an ancient and conserved, yet flexible, genomic regulatory syntax
06 Nov 2020
In cosmic ancestry, genomes would have operating systems that can recognize and deploy available programming, even for features previously unexpressed on Earth. New research shows how transfer factors and enhancers shared across the animal kingdom would be components of such systems.
Our results suggest the existence of an ancient and conserved, yet flexible, genomic regulatory syntax that has been repeatedly co-opted into cell type-specific gene regulatory networks across the animal kingdom. ...We posit that the expansion of TFs and enhancers may underlie the evolution of complex body plans.
Deep conservation of the enhancer regulatory code in animals by Emily S. Wong et al., doi:10.1126/science.aax8137, Science, 06 Nov 2020.
Robust Software Management in Genomes (under construction) has our elaboration.

02 Nov 2020
Our Galaxy may be teeming with rogue planets, gravitationally unbound to any star.
They are hard to see, but Polish astronomers report spotting one. Could they carry dormant life between stars?
A Terrestrial-mass Rogue Planet Candidate Detected in the Shortest-timescale Microlensing Event by P. Mróz, R. Poleski, A. Gould et al., Astrophysical Journal Letters, in press | arXiv, last rev., 20 Oct 2020.
An Earth-sized rogue planet discovered in the Milky Way, University of Warsaw (+Newswise), 29 Oct 2020.

02 Nov 2020
Ambitious new research about evolution caught my attention. A team from Spain and the Netherlands used comparative genomics to probe the evolution of eukaryotic cells:

Eukaryogenesis is one of the most enigmatic evolutionary transitions, during which simple prokaryotic cells gave rise to complex eukaryotic cells. While evolutionary intermediates are lacking, gene duplications provide information on the order of events by which eukaryotes originated. Here we use a phylogenomics approach to reconstruct successive steps during eukaryogenesis. ... Altogether, we infer that the host that engulfed the proto-mitochondrion had some eukaryote-like complexity, which drastically increased upon mitochondrial acquisition. This scenario bridges the signs of complexity observed in Asgard archaeal genomes to the proposed role of mitochondria in triggering eukaryogenesis.

from Julian Vosseberg, Jolien J. E. van Hooff et al., 2020 Besides the acquisition of genes via the endosymbiont, the proto-eukaryotic genome expanded through gene inventions, duplications and horizontal gene transfers during eukaryogenesis.

Invention is the phenomenon that I am most curious about. After studying the paper, I wrote to corresponding co-author Dr. Toni Gabaldón of the Comparative Genomics Group at Barcelona Supercomputing Centre, and the Institute for Research in Biomedicine, Barcelona. I asked, "...May I assume that no _process_ of invention was observed, only that the genes had no identifiable predecessors? They seem to 'have come from nowhere?'"

He replied, "Yes is as you say, we call 'invention' those gene families for which predecessors (homologs outside eukaryotes) cannot be identified. Part of these could be families that have diverged beyond recognition, and part of these could be newly originated families. How these families originate?, we do not  discuss this. My preferred hypothesis is that they originate de novo from non-coding pieces of the genome as it has been shown that this process can occur in some extant genomes...."

Timing the origin of eukaryotic cellular complexity with ancient duplications by Julian Vosseberg, Jolien J. E. van Hooff et al., Nature Ecology & Evolution, 26 Oct 2020. Thanks Thanks for sharing the full article, Dr. Gabaldón.
Three New Human Genes... has become our main page about de novo genes — genes that already existed, somewhere, as silent sequences, before activation. 19 Feb 2017: about eukaryotic genes in Asgard (archaea).
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