October 25, 1996: Metazoan Genes Older Than Metazoa? What'sNEW

Seven independent data sets suggest that invertebrates diverged from chordates about a billion years ago, about twice as long ago as the Cambrian. — Gregory A. Wray et al. (1)

Three scientists have analyzed the rates of divergence for seven metazoan genes with interesting results. Although the data are rather loose, all seem to indicate that these genes began to diverge from their respective common ancestor genes much longer ago than the Cambrian explosion. The three scientists conclude, "...the only reasonable interpretation is that the metazoan phyla began to diverge long before the Cambrian." This conclusion directly challenges the consensus of paleontology that dates the Cambrian explosion at 570 — or maybe only 530 — million years ago. But when the data are interpreted within the neo-Darwinian paradigm, this conclusion is not unreasonable.

The data look different from the perspective of Cosmic Ancestry. According to this paradigm, the genes for evolutionary advances were delivered to Earth in the same manner as life on Earth originally. Life originally came as bacterial spores delivered by comets. Genes for further evolution could come within bacterial spores or within viruses carried by comets. Such genes would reside within lower life forms as silent DNA until all the pieces were in place for the next evolutionary step. The pieces would include:

• evolutionary developments (mouths before teeth),
• genetic developments (all the genes necessary for lungs before lungs), and
• environmental developments (an oxygen atmosphere before oxygen metabolism).

However the dispute turns out, Cosmic Ancestry requires that genes precede the phenotypic expression of themselves, whereas neo-Darwinism requires the immediate expression of genes. So, if life evolves according to Cosmic Ancestry, we would not be surprised to find that genes are older than the resulting phenotypes. For additional evidence that genes for higher evolutionary developments reside as silent DNA in lower life forms, consider that five genes for histones are found in Methanococcus jannaschii (3), an archaebacterium. Archaebacteria are not known to use histones, but all eukaryotic cells do (4).

What'sNEW

Yuri I. Wolf et al., "The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages" [

abstract], doi:10.1073/pnas.0901808106, Proc. Natl. Acad. Sci. USA, online 7 Apr 2009.
Research links evolution of fins and limbs with that of gills, The Univesity of Chicago, 23 Mar 2009. "...The genetic circuitry that patterns paired appendages (arms, legs and fins) has a deep evolutionary origin that actually predates the origin of paired appendages themselves."
Jianli Wang, Alison P. Lee et al., "Large Number of Ultraconserved Elements Were Already Present in the Jawed Vertebrate Ancestor" [abstract], doi:10.1093/molbev/msn278, p 487-490 v 26, Molecular Biology and Evolution, 3 Mar 2009 (online 3 Dec 2008).
Matthew D. Herron et al., "Triassic origin and early radiation of multicellular volvocine algae" [abstract], doi:10.1073/pnas.0811205106 , p 3254-3258 v 106, Proc. Natl. Acad. Sci. USA, 3 Mar 2009. "...All of these changes were previously thought to have occurred in the last 50-75 million years.... Using a multigene data set with multiple fossil calibrations.... Our results show that Volvox diverged from unicellular ancestors at least 200 million years ago."
3 Mar 2009: For microbes, it appears that almost all of their major evolution took place before we have any record of them.....
27 Feb 2009: It is well documented that genes of viral origin are used by eukaryotes to ensure physiological functions....
A Much Earlier Start for Animals, by Phil Berardelli, ScienceNOW Daily News, 4 Feb 2009.
29 Jan 2009: The placula already had all the genes necessary to make all the building blocks [of a nervous system]....
28 Jan 2009: Lignin has been found in marine algae.
7 Jan 2009: Latent evolutionary potential was realized soon after environmental limitations were removed.
Snails and humans use same genes to tell right from left, EurekAlert!, 21 Dec 2008.
Seabed tracks suggest new origin of animal life, doi:10.1038/news.2008.1242, Nature.com, 21 Nov 2008.
Single-Celled Giant Upends Early Evolution, by Michael Reilly, Discovery News, 20 Nov 2008.
Discovery of giant roaming deep sea protist provides new perspective on animal evolution, PhysOrg.com, 20 Nov 2008. A possible account for the "wriggling tracks of worm-like creatures..." (Astrobiology Magazine, 12 Nov 2003) linked below.
Amandine Vanhoutteghem and Philippe Djian, "Ancient origin of the gene encoding involucrin, a precursor of the cross-linked envelope of epidermis and related epithelia" [abstract], doi:10.1073/pnas.0807643105, Proc. Natl. Acad. Sci. USA, online 22 Sep 2008.
20 Sep 2008: Woodstock of evolution?
22 Aug 2008: It is now completely clear that genomic complexity was present very early on....
21 Aug 2008: Sponges don't have nerve cells, yet they have genes for directing the formation of nerves.
10 Jul 2008: We don’t have a clue — Gerard Manning of the Salk Institute
Shengfeng Huang et al., "Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity" [abstract], doi:10.1101/gr.069674.107, p 1112-1126 v 18, Genome Research, online 18 Jun 2008. Extensive experimentation is still required to verify that these genes are functional and working together as a system.
4 Jul 2008: Multicelled animals use a three-part molecular toolkit....
21 Apr 2008: Placental genes have ancient origins.
11 Apr 2008: Earth's first animal... was probably significantly more complex than previously believed.
16 Feb 2008: More metazoan genes came before metazoa.
Joseph W Brown et al., "Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages" [abstract], doi:10.1186/1741-7007-6-6, BMC Biology, online 28 Jan 2008; and commentary: Avian origins: new analysis confirms ancient beginnings, University of Michigan, 5 Feb 2008. "...The strongest molecular evidence yet for an ancient origin of modern birds, suggesting that they arose more than 100 million years ago, not 60 million years ago, as fossils suggest."
15 Jan 2008: The latest morphological studies... have all shown significant gaps in the 'younger' fossil record compared to the much 'older' molecular dating....
15 Jan 2008: Did meteors cause the Great Ordovician Biodiversification Event?
19 Dec 2007: The ancestor of earthly life was molecularly complex.
Researchers Devise Way to Calculate Rates of Evolution, University of Florida Health Science Center or Newswise.com, 3 Oct 2007.
26 Aug 2007: The first analysis of the genome of the sea anemone shows it to be nearly as complex as the human genome.
Richard L. Cifelli and Cynthia L. Gordon, "Evolutionary biology: Re-crowning mammals" [text], 10.1038/447918a, p 918-920 v 447, Nature, 21 Jul 2007. The conflicting results of these palaeontological and molecular studies have profound implications for understanding the evolutionary history of mammals, and for understanding the pace and nature of evolution generally.
20 Jun 2007: Yawning gaps between molecular and palaeontological approaches to the dating of evolutionary landmarks....
24 May 2007: The genetic and developmental toolkit that builds limbs with fingers and toes was around long before the acquisition of limbs.
29 Mar 2007: I felt sick to my stomach.... — Jonathan Eisen
20 Mar 2007: All retroviruses are very old.... — John Coffin.
31 Dec 2006: Many genes once thought to be unique to humans have been in the tree of life for over a half billion years.
17 Nov 2006: The genes are the immortals — Richard Dawkins.
13 Nov 2006: The eyeless, earless [sea urchin] has genes that, in us, are involved in detecting sight and sound.
26 Sep 2006: ...Rhodopsin.... transduces the energy of light into a nerve signal to the brain. What it is doing in so many bacteria is not known....
Andrew B. Smith et al., "Testing the Molecular Clock: Molecular and Paleontological Estimates of Divergence Times in the Echinoidea (Echinodermata)" [abstract], 10.1093/molbev/msl039, p 1832-1851 v 23, Molecular Biology and Evolution, Oct (online 15 Jul) 2006.
Jessica A. Thomas et al., "There is no universal molecular clock for invertebrates, but rate variation does not scale with body size" [abstract], 10.1073/pnas.0510251103, Proc. Natl. Acad. Sci. USA, online 1 May 2006.
Preserved in crystal, by Elizabeth McCrocklin, EurekAlert!, 2 Feb 2006. "Scientists at the Weizmann Institute of Science recently discovered a new source of well-preserved ancient DNA in fossil bones."
8 Dec 2005: Simple sea anemones and coral have many genes thought to be exclusive to higher animals and some plants.
25 Nov 2005: A small marine worm has complex genes like humans'.
16 Sep 2005: ...All the genes for building those complex animals existed long before [the Cambrian] explosion — Lewis Wolpert
David Penny, "Relativity for molecular clocks," p 183-184 v 436, Nature, 14 Jul 2005.
Kevin J. Peterson and Nicholas J. Butterfield, "Origin of the Eumetazoa: Testing ecological predictions of molecular clocks against the Proterozoic fossil record" [abstract], doi:10.1073/pnas.0503660102, p 9547-9552 v 102, Proc. Natl. Acad. Sci. USA, 5 Jul (online 27 Jun) 2005.
Jaime E. Blair and S. Blair Hedges, "Molecular Clocks Do Not Support the Cambrian Explosion" [abstract], doi:10.1093/molbev/msi039, p 387-390 v 22, Molecular Biology and Evolution, Mar 2005 (online 10 Nov 2004). "Molecular clocks continue to support a long period of animal evolution before the Cambrian explosion of fossils."
3 Feb 2005: Complex early genes.
Arne Kusserow et al., "Unexpected complexity of the Wnt gene family in a sea anemone" [abstract], doi:10.1038/nature03158, p 156-160 v 433, Nature, 13 Jan 2005. "Thus at least eleven of twelve Wnt gene subfamilies must have already been present before the divergence of bilaterians and cnidarians."
Emmanuel J. P. Douzery et al., "The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?" [abstract], 10.1073/pnas.0403984101, Proc. Natl. Acad. Sci. USA, online 19 Oct 2004. "These relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be 100 million years more ancient than the Cambrian boundary."
Andrew Knoll, Life on a Young Planet: The First Three Billion Years of Evolution on Earth, ISBN: 0-691-12029-3, Princeton University Press, 2003. "Whatever their inconsistencies, all molecular clock estimates published to date indicate that animals began to diversify much earlier than fossils suggest" (p 202, Knoll's italics.)
2004, Aug 16: "Study Finds Anti-HIV Protein Evolved Millions Of Years Before The Emergence Of AIDS," a Reply from Jerry Chancellor.
S. Blair Hedges and Sudhir Kumar, "Precision of molecular time estimates" [abstract], p 242-247 v 20 n 5, Trends in Genetics, May 2004. "Molecular clocks have great potential but must be calibrated carefully."
Kevin J. Peterson et al., "Estimating metazoan divergence times with a molecular clock" [abstract], p 6536-6541 v 101, Proc. Natl. Acad. Sci. USA, 27 April 2004. "...We estimate that the last common ancestor of bilaterians arose somewhere between 573 and 656 Ma...."
Dan Graur and William Martin, "Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision" [abstract], p 80-86 v 20 n 2, Trends in Genetics, Feb 2004.
Worms in the Mist, by Leslie Mullen, Astrobiology Magazine, 12 Nov 2003. "The wriggling tracks of worm-like creatures can be found in ...rocks that formed long before multi-cellular mobile animals were supposed to have existed."
2003, July 20: More genes seem to precede the need for themselves.
Study Suggests Macroscopic Bilaterian Animals Did Not Appear Until 555 Million Years Ago, University of California, Riverside, 26 Sep 2002.
2002, July 14: Mouse vs Human
Francisco Rodrìguez-Trelles, Rosa Tarrìo, and Francisco J. Ayala, "A methodological bias toward overestimation of molecular evolutionary time scales" [abstract], p 8112-8115 v 99 n 12, Proc. Natl. Acad. Sci. USA, 11 June 2002. "...Molecular time estimates ...[are] constrained by a nonelastic boundary at the lower end, but not at the higher end of the distribution."
2001, December 21: A gene needed for multcellularity is present in a single-celled organism.
Sudhir Kumar and Sankar Subramanian, "Mutation rates in mammalian genomes" p 803-808 v 99 n 2 Proc. Natl. Acad. Sci. USA, 22 Jan 2002. "We find that mutation rate is approximately constant per year and largely similar among genes.... Our results suggest that the average mammalian genome mutation rate is 2.2 10^9 per base pair per year."
2001, August 12: Fungi much older than their oldest fossils?
Mark Pagel, "Inferring the historical patterns of biological evolution" p 877-884 v 401 Nature, 28 October 1999. A Review Article that considers the issue of estimating the ages of genes at length.
Richard A. Kerr, "Earliest Animals Growing Younger?" p 412 v 284 Science, 16 April 1999. "New radiometric dates nudge the pendulum back to about 620 million years for the fossil tracks."
Mike Foote and J. John Sepkoski Jr., "Absolute measures of the completeness of the fossil record" p 415-417 v 398 Nature, 1 April 1999. "We find that completeness is rather high for many animal groups."
Eugene E. Harris and Jody Hey, "X chromosome evidence for ancient human histories" [abstract], p 3320-3324 v 96 n 6 Proc. Natl. Acad. Sci. USA, 16 March 1999. Also see commentary by
Nicholas Wade, "Study Alters Time Line for the Splitting of Human Populations," The New York Times, 16 March, 1999. Molecular dating of a human gene indicates populations subdivided 200 thousand years ago, significantly earlier than the oldest human fossils. Thus, the problem persists at a much shorter timescale.
Evelyn Strauss, "Can Mitichondrial Clocks Keep Time?" p 1435-1438 v 283 Science, 5 March 1999: New data fuel fundamental challenges to the accuracy of molecular clocks, although researchers say they are tackling the problem.
1999, March 1: The problem is not missing fossils.
1999, January 20: Molecular clocks indicate species are more than three times as old as their oldest fossils.
1998, October 28: Another analysis ...finds genes to be much older than the fossil record would indicate.
1998, April 30: Another molecular analysis dates genes as older than the corresponding fossils.

References

1. Gregory A. Wray, Jeffrey S. Levinton and Leo H. Shapiro. "Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla" p 568-573 v 274, Science, 25 October 1996.
2. Francisco José Ayala, Andrey Rzhetsky and Francisco J. Ayala. "Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates" [abstract], p 606-611 v 95 n 2, Proc. Nat. Acad. Sci. USA, 20 January 1998.
3. Carol J. Bult et al. (39 others), "Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii" p 1058-1073 v 273, Science, 23 August 1996.
4. This evidence is discussed more fully in "Eukaryotic Genes in Bacteria?" on the Cosmic Ancestry webpage Can The Theory Be Tested?