One of the biggest surprises from DNA sequencing data is that many eukaryotic "orphan" genes have no detectable predecessors. Other de novo ones come from open or almost-open reading frames that apparently never underwent selection for their roles. They seem to need only to be switched on. A new survey of research about these genes includes a table counting the known or suspected ones in two dozen eukaryotic categories. In arthropods, for example, 65,000 orphan genes have been identified so far.

These genes have no ready explanation under mainstream darwinian theory, but suggestions are not lacking. Perhaps the selection process was so rapid and thorough that the orphan's homology with its ancestral gene is erased? Or selection for an outdated, unknown function also, luckily, prepares the de novo gene for its new role?

Such speculations lack plausibility, and demonstrations in quarantined biology or computer models do not succeed. Meanwhile, genes that "seem to have come from nowhere" are required in cosmic ancestry.

If prokaryotes all come from a common single ancestor, their lines of descent, logically, should branch like a tree. But with only today's genomes, of course it would be challenging to reconstruct the form this tree took billions of generations ago. Horizontal gene transfer (HGT), rampant among prokaryotes, makes it much more challenging. And when eukaryotic sexual reproduction appears, the difficulty is again compounded.

These quotations come in a brief essay about the deep biosphere, an environment of renewed interest. Biologists already knew that bacteria come in a wide variety, but now we glimpse a whole new world of them. If bacteria are so durable, resourceful and ubiquitous, perhaps they could persist in space and survive on other planets?

11 May 2019

What'sNEW about HGT |

We suppose that macroevolutionary advances must be ultimately supplied by the horizontal gene transfer (HGT) of lengthy new programming. The acquired enzyme analysed here, for example, is more than 200 amino acids (600 exonic nucleotides) long. After installation, we think accelerated point mutations allow new genes and their duplicates to become optimized for new situations. Optimization (microevolution by our definition) may be possible with only a few (1 - 10) amino acid substitutions in the right places, as Busch et al. report (see chart, right). In sum, this study affirms the scenario we advocate.

01 May 2019

What'sNEW about HGT |

Also of note to us, 60% of the Medusavirus genes, 279, are unfamiliar ones with unknown functions. So called "ORFan" genes are starting to look numberless, and they are especially abundant among large viruses. If ORFan genes are widely available from viruses, are they an inventory of potential de novo genes, the ones that "seem to have come from nowhere" in the evolution of eukaryotes?

A new study begins with the premise that protein domains are the basic units of meaning in genomes. The researchers, from the University of Alabama in Birmingham and the National Institutes of Health, compare them to words in a written language. They demonstrate that protein domains and words occur with mathematically similar patterns and frequencies, apparently following similar grammars. We welcome this insight, because it suggests a tool for the toolkit that we think life's evolution needs.

All life forms possess many multidomain proteins, but both the number of unique domains and the fraction of multidomain proteins increase with the organismal complexity (defined as the number of unique cell types in an organism): Eukaryotes have more multidomain proteins than prokaryotes, and animals have more multidomain proteins than unicellular eukaryotes. This trend of increased multidomain protein formation with increasing organismal complexity is known as domain accretion and apparently plays a major role in evolution, particularly in major evolutionary transitions such as the origin of multicellularity. Grammar of protein domain architectures by Lijia Yu et al., doi:10.1073/pnas.1814684116, PNAS, 26 Feb 2019.

08 Apr 2019

What'sNEW about HGT |

The authors focus on bacteria and yeast cells, but stress response-up-regulated mutation mechanisms have been discovered in plants, flies, and human cells. Edited by W. Ford Doolittle, the article concludes, regulated mutagenesis mechanisms greatly increase the probability that the useful mutations will occur at the right time, thus increasing an organism's ability to evolve and, possibly, in the right places. Assumptions about the constant, gradual, clock-like, and environmentally blind nature of mutation are ready for retirement..

The findings are consistent with our belief that genomes must have robust software management systems to keep them functional and adaptable. (And the necessary high-fidelity DNA repair might be difficult to evolve, the report mentions.) Robust software management would also manage horizontal gene transfer (HGT), which stress may also induce. We mention HGT in order to clarify its role in cosmic ancestry —

We agree, rearrangements within an existing genome can have profound effects, both positive and negative. For a positive one, suppose that a silent beneficial gene needs only to be turned on, or a key exon needs relocation. If this change is effected and inherited, a beneficial evolutionary step is enabled. But if the gene or exon is not available, stress alone cannot induce that evolutionary step. In other words, there is a near limit to the range of evolution within a quarantined genome. Suppose an evolutionary step requires a unique strand of, say, 200 or more properly sequenced nucleotides. If the strand is not already present, the evolutionary step will not occur. Of course, HGT could supply it. But without HGT, macroevolutionary progress would soon halt, we believe.

We scan the literature regularly for relevant evidence, and HGT is obseved frequently enough, in all domains. Also, we have proposed research programs in biology and in computer models to test the importance of HGT, with no serious takers. Meanwhile, we welcome these straightforward observations from Fitzgerald and Rosenberg.

These mechanisms reveal a picture of highly regulated mutagenesis, up-regulated temporally by stress responses and activated when cells/organisms are maladapted to their environments—when stressed—potentially accelerating adaptation. Mutation is also nonrandom in genomic space, with multiple simultaneous mutations falling in local clusters, which may allow concerted evolution—the multiple changes needed to adapt protein functions and protein machines encoded by linked genes. What is mutation? A chapter in the series: How microbes "jeopardize" the modern synthesis by Devon M. Fitzgerald and Susan M. Rosenberg, doi:10.1371/journal.pgen.1007995, PLoS Genet., 01 Apr 2019.