31 Mar 2017

What'sNEW about HGT |

In the legend for the figure here they write, "...The three Cyanobacteria classes likely acquired aerobic respiration independently after the rise of oxygen (atmospheric oxygen is represented by the red shading). Squares and triangles indicate acquisitions of complex III, whereas circles and diamonds indicate acquisitions of complex IV. ...Square brackets denote operon fusions, and a red 'X' indicates putative loss of ETCs." The report continues, "If true, we expect that other phyla will exhibit the same pattern for aerobic respiration as the Cyanobacteria—a lack of aerobic respiration in their last common ancestor, with a later acquisition involving lateral gene transfer."

The term "origin" appears in the article and title, but it seems to mean "first deployment." Certainly, coordination and testing must follow the acquisition of genes and other genetic components to complete the installation of programs for aerobic respiration, photosynthesis, or any comparable evolutionary innovation. But the "origin" of any complex functional genetic program remains unobserved and unexplained. Meanwhile, evidence for horizontal gene transfer (HGT) grows daily. We think the underlying assumptions about evolution need to be reconsidered.

These distinguished cosmologists have witnessed the bias with which the story of modern cosmology is usually told. For one example: until 1998, the big bang theory confidently held that the expansion of the universe is decelerating. Then the very opposite, acceleration, was discovered. The shock was quickly swallowed with no mention of an interesting fact: acceleration was a basic prediction of the leading alternative, the steady-state theory.

Although the original steady-state theory of Gold, Bondi and Hoyle is now abandoned, a newer "quasi-steady-state" cosmology (QSSC), which Fred Hoyle also helped to develop, is well-explained and supported in the book. Along the way we learn about the contributions of astronomers seldom noticed elsewhere, like Viktor Ambartsumian and Hans Arp.

Narlikar and Burbidge confess that no theory today satisfactorily explains all the data, and since 2008, this situation has not improved. Meanwhile, dogmatic support for the big bang inhibits scientific imagination and hinders progress. The dogma also requires life to somehow originate, which, to us, looks forbiddingly improbable.

07 Mar 2017

What'sNEW about HGT |

To make sense of this apparent absurdity within a strictly darwinian paradigm, Krupovic and Koonin ultimately imagine unexplained, unobserved "origins." But we endorse their fully-grounded observations: These findings reveal a stronger connection between the virosphere and cellular life forms than previously suspected. ...this view is compatible with the scenario of multiple recruitment events occurring throughout the course of evolution of life.

Now more ESPs are seen among a newly-designated clade of archae named Asgard. They include a subunit of eukaryotic DNA polymerase, a eukaryotic ribosomal protein, key components of the eukaryotic cytoskeleton, and membrane trafficking proteins. The schematic representation of a eukaryotic cell (right) highlights ESPs that have been identified in Asgard archaea, with colored tables indicating their distribution among those species.

The overall picture indicates that the archaeal ancestor of eukaryotes already contained many key components underlying the emergence of cellular complexity that is characteristic of eukaryotes, this research team says in summary. As darwinists, they suppose that an archaeal ancestor must have had some use for the ESPs after all. But in cosmic ancestry, genes always come first. If they weren't often found in species preceding the need for them, we would be surprised.

17 Feb 2017

What'sNEW about HGT |

The researchers are specifically interested in the phylogeny and ultimate origin of the mimiviruses. Were their [viral?] ancestors even more complex, or less complex? Despite many theories, the origin and evolution of mimiviruses remains a breathtaking mystery. It is not yet possible to exclude any specific scenario of giant viruses' evolution.

In that case, we hope evolutionary theorist will consider the scenario we advocate. In cosmic ancestry, viruses are the main vector for the horizontal transfer (HGT) of cellular genes into species that can use them. We are not surprised if mimiviruses contain genes for tRNAs, protein synthesis, translation factors and more.

We take this synopsis from a comprehensive new study by geographers at the University of Exeter, UK, who modeled the processes in the biosphere that produce and consume oxygen. Its history, including the long stasis, is puzzling. With isotope data, they make a plausible case that mineral, tectonic, biological, climatic, weathering and sedimentary processes with feedback loops can explain it. The study also supports our belief that slow Gaian processes can make a planet habitable, and then more advanced life can develop and flourish without delay.

The mechanism we describe provides a potential explanation for the overall stepwise evolution of atmospheric oxygen on Earth. Recycling of sedimentary organic carbon and its kinetically limited oxidation could have sustained low Proterozoic atmospheric oxygen levels.... The rise of oxygen to present levels simply required an increase in organic carbon burial rate, which may have begun in the Neoproterozoic Era, but in our model was not completed until the mid-Palaeozoic Era with the colonization of the land by plants and fungi, liberating nutrient phosphorus from rocks and producing high C/P material for burial.

The new method, pioneered in Joe Thornton's lab, apparently opens a new way to study adaptation. In our understanding, adaptation on the scale examined here would be categorized as microevolution. Macroevolution, by contrast, requires wholly new genetic programs that have not been shown to come from adaptive mutations of one or a few nucleotides. Therefore, the same method cannot be simply extended for studying macroevolution. Nevertheless, we are intrigued. ...because of technical and conceptual advances, it should now be possible to experimentally assess the causal predictions of many previously untested or weakly tested hypotheses of historical molecular adaptation....

In a new, wide-ranging essay, Eugene V. Koonin of the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, considers the fitness landscapes of prokaryotes (large populations) versus eukaryotes (small populations). The latter allow for greater inventiveness, he concludes. To cope with this inescapable burden [introns], eukaryotes have evolved a global solution, the highly efficient splicing machinery. ...The nucleus itself may have evolved as a damage-control device that prevents the exit of unprocessed transcript to the cytoplasm. (How are these not more "Just-So" stories?)

Koonin is well aware of horizontal gene transfer (HGT) and de novo genes. Also, mobile genetic elements (MGE) ...genes have been recruited for essential functions at key stages of eukaryotic evolution. But where the programming for these functions comes from is not a concern to him. If he wants a theory of evolution with testable predictions, may we suggest testing them with quarantined experiments in biology or computer models?

11 Jan 2017

What'sNEW about HGT |

New research provides another example of genetic systems older than standard darwinism expects them to be. The report also confirms that the studied retroviruses can be transferred across diverse species and become permanently installed into their genomes. Genetic programs that look too old, and horizontal gene transfer (HGT) by viruses are phenomena that surprise darwinism and support cosmic ancestry.