Orphan genes do not often emerge from the divergence of predecessor genes. Instead, they must appear, ready for action, from previusly silent DNA, or be delivered by HGT. Three distinguished geneticists from Trinity College Dublin and the University of Pittsburgh reach this conclusion following a lengthy new analysis available online. — The persistent presence of orphans and TRGs [taxonomically restricted genes] in almost every genome studied to date despite the growing number of available sequence databases demands an explanation. Studies in the past 20 years have mainly pointed to two mechanisms: de novo gene emergence and sequence divergence of a pre-existing gene, either an ancestrally present or one acquired by horizontal transfer. ...[W]e conclude that the origin of most genes without similarity cannot be attributed to divergence beyond recognition. This implies a substantial role for other evolutionary mechanisms such as de novo emergence and horizontal gene transfer....
|20 Feb 2020
||What'sNEW about HGT |
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes by Nikolaos Vakirlis, Anne-Ruxandra Carvunis and Aoife McLysaght, eLife, 18 Feb 2020.
We have long advcated HGT for supplying all "new" genes. These may become activated promptly upon arrival, or remain dormant for long times. In either case, the genes may be designated de novo if an HGT source is not apparent. But if some orphan genes are simply there, ready for optimizing selection, without HGT, as supposed, we have a question: Where does the programming come from? And as for the few orphans that these geneticists think may have gradually, completely diverged from unrecognizable predecessors ...same question.
An attempt to answer our question comes from the same institutions. — Overall, our results support an experiential model for de novo gene birth whereby a fraction of incipient proto-genes can subsequently mature and, as adaptive changes engender novel selected effects, progressively become established in genomes in a species-specific manner (see illustration). However, ...while emerging sequences show no evidence of encoding a useful protein product in the present state of the organism, they have the potential to do so in the future.
De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences by Nikolaos Vakirlis et al., doi:10.1038/s41467-020-14500-z, Nature Communications, 07 Feb 2020.
We are standing by. Meanwhile, we are pleased that orphan genes are increasingly recognized for their ubiquity and importance. And we welcome the close scrutiny of gradual divergence. We think its power is oversold.
Genes from scratch - far more common and important than we thought, Trinity College Dublin (+PhysOrg.com), 17 Feb 2020, and
New and Maybe Important, Genome Web, 19 Feb 2020.
Viruses... is all about HGT.
04 Jan 2016 and
21 Aug 2016 are postings about de novo genes.
Three New Human Genes... cites McLysaght on de novo genes, with updates since 2009.
Astrobiology is as cool as it sounds. We've already found the hallmarks of life in many corners of our solar system.
...Finding Life Is Space's Final Frontier by Brad King, The Wall Street Journal, 07 Feb 2020.
The Coronavirus May Have Come From Space [local PDF] by N.C. Wickramasinghe and E.J. Steele, 06 Feb 2020.
Comment on the origin of the 2019 Novel Coronavirus [local PDF] by Edward J. Steele, N. Chandra Wickramasinghe, Jiangwen Qu, Robert Temple and Gensuke Tokoro, 03 Feb 2020.
Coronavirus latest: infections in China pass 20,000, Nature News, 04 Feb 2020, with updates.
Influenza from Space?, first posted Jan 2000, has related discussion and updates.
Phylogenetic investigations suggest ...the presence of [antioxident] enzymes in the last universal common ancestor, far predating the great oxygenation event (GOE) sometime between 2.3 and 2.7 billion years ago. These enzymes are found in all domains of life, even in obligate anaerobes.... The researchers noticing this puzzle suppose that the enzymes evolved long before GOE because reactive oxygen already came from strictly chemical sources. Or other chemistry mimicked oxygen. Or the enzymes also worked against sulfur. Whatever the reason, by darwinan logic there had to be one.
Sulfur Chemistry May Have Paved the Way for Evolution of Antioxidants by Anna Neubeck and Friedemann Freund, doi:10.1089/ast.2019.2156, Astrobiology, 27 Dec 2019.
Antioxident genes before oxygen are consistent with cosmic ancestry, in which genes always come first.
Metazoan Genes Older Than Metazoa? and Genes Older Than Earth? have many more examples.
The Big Bang is widely accepted as being the beginning ...but other theories ...are suggesting otherwise.
What if the Universe has no end? by Patchen Barss, BBCNews, 19 Jan 2020.
The End and the Big Bang and The Beginning have related discussion and updated links.
The growing number of these competing theories suggests that it might now be time to let go of the idea that the Big Bang marked the beginning of space and time.
..."I always regarded inflation as a very artificial theory," says Roger Penrose.
...With a period of insane expansion stretching out the Universe so rapidly that almost the entire thing ended up far beyond the region we can observe and interact with.
...One idea put forward by proponents of inflation is that theoretical particles made up something called an "inflation field"....
Paul Steinhardt, who was one of the original architects of inflationary theory, ultimately got fed up with the lack of predictiveness and untestability.
"We have to look for a better idea." ...In fact, it's possible that time has existed forever. — BBCNews|
The newest book from Chandra Wickramasinghe et al. begins with the assurance that panspermia is how we humans came to be here on Earth. Now it is time to explore the implications of this paradigm. These include new possible causes for extinctions, diseases, evolutionary innovations and the rise and fall of empires. In fact, the histories of science, philosophy and religion are all seen anew, with hopes that this awakening will make us more compassionate toward each other and more careful with our fragile planet. Overall, it is an impassioned plea for a fresh vision. Provocative, unorthodox and stimulating. We especially like the chosen title.
Our Cosmic Ancestry in the Stars: The Panspermia Revolution and the Origins of Humanity, by Chandra Wickramasinghe, Kamala Wickramasinghe and Gensuke Tokoro, Bear & Company, 14 May 2019.
Chandra Wickramasinghe has a background essay and updated links.
A Biological Solution to the Mystery of Methane on Mars by Dirk Schulze-Makuch, AirSpaceMag.com, 09 Jan 2020.
Methanogenic Archaea Can Produce Methane in Deliquescence-Driven Mars by Deborah Maus et al., Scientific Reports, 08 Jan 2020.
Life on Mars! has links about methane there.
Thanks, Theodore Rigley.
By 2020, in real or artificial life, sustainable evolutionary progress in a genetically closed system will not have been demonstrated. This was our online prediction of eighteen years ago. It has been upheld. This provides strong affirmation for cosmic ancestry.
Bet 44: our original posting at
Long Bets, now part of The Long Now Foundation.
09 May 2002: our local notice of the prediction.
The Evolution Prize, 2006, has elaboration for this issue.
...I only want to draw attention to an important test that the standard theory [of evolution] has not yet met.