Genes Older Than Earth?
 What'sNEW since 2010
Many genes were "born" on Earth much earlier than expected by mainstream theory, according to an analysis from MIT. A new phylogenomic computer program enables its users to estimate the ages of individual genes without being confounded by horizontal gene transfer (HGT). Now it has been deployed to analyze 3,983 major gene families from the three domains of life. The results are surprising. Apparently 26.8% of extant gene families were "born" in a relatively brief period between 3.33 and 2.85 billion years ago, the "Archaean Expansion". Computational biologists Lawrence David and Eric Alm reported this result in 2010 (1).
The birth rate peaked sharply at the beginning of the period (as indicated in the figure by a red spike pointing right). The rate of gene loss also reached a maximum during this time, peaking at about 3.1 billion years ago (fat yellow arm pointing left). The analysis also measures HGT (green) and gene duplication (blue). Curious to know where genes come from, we focus on the births.
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"Rates of macroevolutionary events over time:
Average rates of gene birth (red), duplication (blue), HGT (green), and loss (yellow) per lineage (events per 10 Myr per lineage).... Events that increase gene count are plotted to the right, and gene loss events are shown to the left." © David & Alm, 2011 |
"...The inset shows metabolites or classes of metabolites ordered according to the number of gene families that use them that were born during the Archaean Expansion [top] compared with the number born before the expansion [bottom], plotted on a log2 scale...."
AE metabolites
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If life originated on Earth, one would expect the red graph of gene births to descend from a narrow beginning, broadening as life spreads over the planet, then becoming more-or-less constant as life continues to evolve. Instead, this graph begins as a broad front that soon widens dramatically. Then it narrows more dramatically and eventually dwindles to virtually nothing, well before the Cambrian Explosion of about 540 million years ago (lower dashed line in the main graph.)
Green illustrates HGT.
In this analysis, by 3 billion years ago, HGT has become the primary source of "new" genes, as it remains today. | | |
Two other points need making. First, the term "birth" implies a process that might include gestation — the gradual composition of new genes by darwinian mutation-and-selection. But not a bit of it. No such process is even claimed to be observed here. Gene "birth" refers only to the time when a given gene likely first became expressed and began to proliferate and diverge among (mostly prokaryotic) species. Since very many genes reside in viruses, or may otherwise lie silent and unexpressed for millions of years, all of the studied genes may have existed long before they were "born" in this analysis.
Second, the initial front would be even broader if David and Alm had not omitted the genes that are the most widely distributed of all. "Genes already present at the Last Universal Common Ancestor are not included in the analysis of birth rates because the time over which those genes formed is not known."
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Inset shows AE metabolites.
"...Genes that use molecular oxygen are more likely to appear in organisms that emerged after the Great Oxidation Event," at or soon after the upper dashed line at 2.5 Gya on the main graph. Yet many oxygen-using genes were born much earlier, during the Archaean Expansion.
This makes no darwinian sense. David and Alm wonder if the oxygen-related genes may have served another purpose originally. |
In cosmology, at least two groups now claim that the evidence (microwave background radiation) enables them to see beyond (before) the big bang (2). We suggest that an analogous phenomenon may be possible in biology. Here David and Alm show that many genes were available at the very beginning of life on Earth, and that many more genes apparently preceded the earthly advent of the features they encode. Other studies provide corroborating data. Could all of this be evidence for life older than Earth? We think so.
 11 Nov 2024: These observations suggest that the genetic programs responsible for embryonic development were already present before the emergence of animal life....
22 Jun 2023: ...a wholly separate eukaryotic phylogeny prior to the Last Eukaryotic Common Ancestor (LECA).
27 Aug 2022:
...animals arose only after the accumulation of genes....
18 Feb 2022: A Billion Years Before Sex, Ancient Cells Were Equipped for It.
14 Aug 2021: "Molecular time trees ...at odds with the record of fossil plants...."
07 Apr 2021: Genes underlying oxygenic photosynthesis look as old as life.
07 Mar 2021: Genes allowing oxygen metabolism were present among bacteria 3.1 billion years ago....
12 Feb 2021: ...the origin of tetrapods was something waiting to happen.
20 Jun 2020: Angiosperm genes look ∼70 million years too old.
21 May 2020 and 20 May 2020: research that ultimately points to ancient genes.
26 Jan 2020: Antioxident enzymes in the last universal common ancestor, far predating the great oxygenation event.
26 Sep 2019: Essential eukaryotic genes are very old and are shared with large viruses.
16 Aug 2019: There may be more genes in the collective human microbiome than stars in the observable universe, and at least half of these genes appear to be unique to each individual....
15 Aug 2019: Archaebacteria with ESPs have been cultured.
02 Aug 2019: ...ancestor of all multicellular animals ...already possessed an extremely complex genome.
27 May 2019: de novo gene birth
16 May 2019: The overall picture is still unclear. (Where do archaea belong?)
22 Aug 2018: LUCA before LHB?
29 Jul 2018: ...the one-celled ancestor of animals... was already well-equipped for multicellular life.
27 Jul 2018: Minerals may preserve free DNA for horizontal gene transfer (HGT) to facilitate evolution.
15 May 2018: ...many genes typically associated with metazoan functions actually pre-date animals themselves....
20 Feb 2018: Molecular clock analyses always come up with older dates than fossils....
27 Jul 2017: Geneticists in Scotland....
08 Mar 2017: New estimate predates earliest fossil evidence by 800 million years.
07 Mar 2017: ...the origin of viral replicative modules seems likely to hark all the way back to the precellular era.
26 Feb 2017: ...the common ancestor ...did encode many of the protein domains of all three super-kingdoms.
19 Feb 2017: Archeae contain many eukaryotic signature proteins (ESPs).
11 Jan 2017: ...they've been around for hundreds of millions of years.
17 Oct 2016: ...many genes involved in these regulatory processes have a premetazoan origin.
13 Jun 2016: Early complexity supports panspermia....
30 Apr 2016: ...The genetic basis for the evolutionary transition [to multicellularity] emerges much earlier than anticipated....
24 Apr 2016: ...The unicellular ancestor of Metazoa already had a complex gene repertoire involved in multicellular functions....
29 Oct 2015: ...The last unicellular ancestor of animals was already capable of elaborate specification of cell types.
16 Oct 2015: Algal ancestor of land plants was preadapted for symbiosis.
9 Oct 2015: [T]he signature advanced functional systems of the eukaryotic cells were already present in the last eukaryotic common ancestor....
7 May 2015: Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.
26 Sep 2014: 23,849 anthropoid-specific constrained (ASC) regions with "robust functional signatures"
12 Aug 2014: ...The set of known underground reactions has a significant potential both to increase fitness in existing environments and to exploit new nutrient sources.
2 Jan 2014: It appears that much of the genetic machinery necessary for a nervous system was present in the ancestor of all extant animals.
20 Dec 2013: Eugene V. Koonin's book, The Logic of Chance
28 May 2013: A large fraction of human PSs were already present in the last common ancestor of flies, mollusks, urchins, and mammals.
3 May 2013: The origin of...?
18 Apr 2013: Earth was seeded by panspermia. (Points to an article invoking Moore's Law to explain why life must be older than Earth.)
25 Jan 2013: Many of our genes have no obvious relatives or evolutionary history. So where did they come from?
31 Oct 2012: A simple route to animal vision?
16 Sept 2012: Very large viruses coexisted with or preceded the first primordial cells.
6 Sep 2012: A strikingly large repertoire ...appears to have been present ...consistent with the 'complexity early' view of eukaryotic evolution.
23 Jul 2012: Surprisingly, the genome of the Poriferan demosponge, Amphimedon queenslandica, contains an almost complete set of genes homologous to those found in mammalian synapses....
19 Mar 2012: ...Whether the course of Evolution can at all reasonably be represented as an unpacking of an original complex.... — William Bateson
15 Mar 2012: The origin of the exquisitely complex vertebrate brain is somewhat mysterious.
13 Mar 2012: The standard RNA World theory is disputed following a new phylogenetic analysis.
2 Nov 2011: Almost every month now we are seeing genes that were supposed to be exclusive to metazoans that are already present in their single-cell relatives.
7 Oct 2011: The protein was there to begin with.... — Gustavo Caetano-Anollés, University of Illinois.
12 Jul 2011: Genetic instructions for developing limbs and digits were present in primitive fish millions of years before their descendants first crawled on to land....
18 Jun 2011: ...The tool kit for more complex plant architectures was already in place long before angiosperms evolved.
26 May 2011: The common ancestor of life on Earth had more functional protein domains than the first cells!
13 May 2011: Many scientists now argue that viruses contain a genetic archive that's been circulating the planet for billions of years.
 Dr. Doron Golberg asks for clarification, 10 Feb 2011.
23 Jan 2011: Genes for using oxygen appeared... around 2.8 billion years ago, long before oxygen began accumulating....
References
1. Lawrence A. David and Eric J. Alm, "Rapid evolutionary innovation during an Archaean genetic expansion" [abstract], doi:10.1038/nature09649, p93-96 v469, Nature, 6 Jan 2011; and commentary, Scientists decipher 3 billion-year-old genomic fossils by Denise Brehm, MIT News Office, 21 Dec 2010.
2. ...The existence of an aeon preceding our Big Bang, 12 Dec 2010; and Rebuttal, What'sNEW, 14 Dec 2010; and
Other cosmologists claim to see beyond the big bang, What'sNEW, 20 Dec 2010.
Related CA Webpages
Metazoan Genes Older Than Metazoa? has related, earlier examples of corroborating evidence.
Viruses and Other Gene Transfer Mechanisms is relevant. The above graph illustrates for HGT (green) the pattern darwinism would predict for gene "birth" — descending from a narrow beginning and promptly broadening to become the primary source of "new" genes for the whole history of life.
How is it Possible? suggests that life might arrive with a wide range of capabilities, many of which are soon bypassed, consistent with the yellow "loss" category.
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