After reading the new analysis, our initial reaction is that the "cryptic gene" scenario, offered in 2008 as a possible explanation for the development, is the correct one — the "previously silent citrate transporter" being that gene. The recruited promoter, before getting its new assignent, was already active in a related role. The point mutations that enabled the first steps simply explored the genetic potential already present. The ones that refined the citrate metabolism exemplify optimization within a limited range. All of this would be consistent with both darwinism and cosmic ancestry. And none of it, in our opinion, demonstrates sustainable macroevolutionary progress in a quarantined system. We will stay tuned for additional news and informed comments.

FSFs are not equally distributed in the proteomes of Archaea (A), Bacteria (B), Eukarya (E), and viruses (V). In turn, FSFs exist that are uniquely present (groups A, B, E or V) or are shared by two (AB, AE, AV, BE, BV, EV), three (ABE, ABV, AEV, BEV) or all (ABEV).

Using new computer algorithms, the three compared related protein domains — fold families and fold super-families (FSFs) — among archea, bacteria, eukaryotes, and the large viruses. While many FSFs were unique to one or another category, the number shared between viruses and the others, especially unicellular parasites, was significant. The most parsimonious conclusion is that large viruses are at least as old as cells, and once contained even more genes than they do today. This would make viruses a fourth superkingdom of life.

These conclusions do not easily fit into standard darwinian theory, in which life on Earth began as a cell with a few genes and added more genes later. But the analysis readily suits and supports cosmic ancestry. Moreover, it suggests an even greater role for viruses than we formerly proposed.

If we accept that eukaryotes are chimeras built upon chimeras, we can expand the parameters within which to construct theories of eukaryotic origins.

These words come from a new paper by biochemist and microbiologist Michael Syvanen of UC Davis, an expert on horizontal gene transfer.

While the "complexity early" hypothesis is gaining support, it has no ready explanation under strict darwinian theory. By darwinian logic, life should start simple and only later become complex. Meanwhile, "complexity early" is a basic requirement in cosmic ancestry.

Tobias H Klöpper et al., "Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis" [

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The accompanying illustration of a synapse includes the major genes that enable synapses to function, with their products in the roughly appropriate locations, if applicable. All of the pink ones represent genes with close homologs in sponges. But sponges have no synapses.

...We were hoping to understand why the marine sponge, despite having almost all the genes necessary to build a neuronal synapse, does not have any neurons at all, comments one of the lead authors of the new report. She should be wondering how the genes got there. In the darwinian scheme, they are entirely out of order. Genes are supposed to be composed incrementally, under selection pressure. But in sponges, with no nervous systems, what selection pressure could compose the genes for nervous systems?

In cosmic ancestry, genes precede the features they encode. Finding them in species that cannot yet deploy them is anticipated.

In spite of the genome's small size, running the model requires a cluster of 128 computers, and the simulation of a single cell division takes nine to ten hours. Interestingly, cell division for living Mycoplasma genitalium takes about as long.

Comprehensive computer models of entire cells have the potential to advance our understanding of cellular function and, ultimately, to inform new approaches for the diagnosis and treatment of disease, comments James M. Anderson of the National Institutes of Health. We agree, but we notice no mention of possible contributions for evolution or origin-of-life research. Could those research programs be on the wrong track?

...The mosaic of these other key characteristics of viruses implies complex processes of multiple loss of ancestral genes (in particular, those for capsid proteins), gene exchange between distant viruses and transfer of viruses between distant hosts (such as fungi, plants, animals and protists, but possibly also between bacteria and fungi, even if only via endosymbiosis). A comprehensive history should integrate the histories of individual genes and can only adequately be conceptualized as a network of multiple evolutionary connections at the level of genes or even parts of genes encoding distinct protein domains. Gene exchange that can lead to the emergence of new groups of viruses is not limited to viruses with the same type of genome structure. ...Positive-strand RNA viruses might have pre-existed in archaeal ancestors of eukaryotes....If the archaeal host is confirmed, the impact of these findings on our understanding of RNA virus evolution will be dramatic.