September 24, 2007 | David F. Coppedge

Upsets: Assumptions About Genes, Atmospheres Challenged

It’s not fun when a whole superstructure of scientific theories and models is found to rest on a shaky foundation.  That’s just what may be happening in two very different fields: genetics and planetary science:

  1. Lateral pass to the opposing team:  Building evolutionary trees by comparing genomes was supposed to be simple.  Sure, geneticists knew that some organisms could insert DNA into other organisms, but lateral gene transfer was supposed to be rare or limited to lower life-forms.  That assumption was called into question in Science on Sept. 21: a team of 20 researchers from 7 universities and genetics labs titled their paper, “Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes.”1
        Their findings from studying the Wolbachia genome may send shock waves through biology labs: “heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions.”  Their concluding paragraph calls for a complete reevaluation of basic assumptions about lateral gene transfer (LGT):

    Whole eukaryote genome sequencing projects routinely exclude bacterial sequences on the assumption that these represent contamination.  For example, the publicly available assembly of D. ananassae does not include any of the Wolbachia sequences described here.  Therefore, the argument that the lack of bacterial genes in these assembled genomes indicates that bacterial LGT does not occur is circular and invalid.  Recent bacterial LGT to eukaryotic genomes will continue to be difficult to detect if bacterial sequences are routinely excluded from assemblies without experimental verification.  And these LGT events will remain understudied despite their potential to provide novel gene functions and affect arthropod and nematode genome evolution.  Because W. pipientis is among the most abundant intracellular bacteria and its hosts are among the most abundant animal phyla, the view that prokaryote-to-eukaryote transfers are uncommon and unimportant needs to be reevaluated.

  2. Gasid indigestion in planets:  Another assumption under fire has to do with gas ratios emanating from planets.  For decades, scientists have assumed that ratios of inert gases tell us something about a planet’s history and interior.  Now, a paper in Nature by Watson, Thomas and Cherniak of Rensselaer Polytechnic Institute, found that argon-40 is not coming out as fast as thought.2  So?  Chris Ballentine explained in the same issue of Nature3 that this has far-reaching implications on models of planetary origins.
        “We thought we knew how much gas Earth gives up, and how it does it,” he began, “but a challenge has emerged to the prevailing model.”  The implications affect models of plate tectonics, the physics of the mantle, the movement of radioactive decay products, and the origin of the terrestrial planets.  It appears now that argon and helium can be recycled into the mantle rather than being released.  Physicists measuring gas ratios at oceanic ridges, therefore, can no longer assume what they took for granted: that the rate of helium-3 and argon-40 emission reveals something about the rate of convection in the mantle.  “So does the Earth hold its breath?,” Ballentine ended.  “Someone has got it wrong.  Let’s hope we don’t have to hold our own breath too long to find out who.”
        This problem was reported in the popular press by EurekAlert and PhysOrg.  The press release made the extent of the problem of this “Argon conclusion” clear in the first paragraph:

    Geochemists at Rensselaer Polytechnic Institute are challenging commonly held ideas about how gases are expelled from the Earth.  Their theory, which is described in the Sept. 20 issue of the journal Nature, could change the way scientists view the formation of Earth’s atmosphere and those of our distant neighbors, Mars and Venus.  Their data throw into doubt the timing and mechanism of atmospheric formation on terrestrial plants.

      Astrobiology Magazine also reported on this finding.  Watson remarked, “We can no longer assume that a partly melted region of the mantle will be stripped of all argon and, by extension, other noble gases.”  He added, “We may need to start reassessing our basic thinking on how the atmosphere and other large-scale systems were formed.”4

1Hotopp et al,“Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes,” Science 21 September 2007: Vol. 317. no. 5845, pp. 1753-1756, DOI: 10.1126/science.1142490.
2Watson, Thomas and Cherniak, “40Ar retention in the terrestrial planets,” Nature 449, 299-304 (20 September 2007) | doi:10.1038/nature06144.
3Chris J. Ballentine, “Geochemistry: Earth holds its breath,” Nature 449, 294-296 (20 September 2007) | doi:10.1038/449294a. 4Creation scientists may want to examine the implications of the Rensselaer study on radiometric dating methods.  An assumption underlying potassium-argon dating is that argon is not stored when lava is deposited.  If argon is not released readily, even at high temperatures, would this not make some deposits appear far older than expected?

Will the researchers at top levels notice these earthquakes in their underlying assumptions?  Will they explain them away?  What about the papers, books and press releases that now have to be rewritten?  We’ll leave it to specialists to explain the extent of the damage from these announcements, but here is an example of how science works.  Anything you thought you understood is always subject to challenge.
    We don’t accept the cynical description of a scientist as a blind drunk occasionally bumping his head into the lamp post of reality.  After all, we do successfully fly probes to the planets.  But beware the scientist who says “Now we know” this or that thing, especially when it comes to questions of unobserved history and unobservable domains.  The only thing about which you can say “Now we know” is that more such challenges lurk in the future.

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