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All of "like kind" in the (bigger) family (2)

See first: All of “like kind” in the (bigger) family

Excerpt:

Researchers who want to understand why the changes occur should be among the first to examine how fixation of the amino acid substitutions occurs in the DNA of organized genomes. For example, fixation of amino acid substitutions appears to occurs via the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to man.

Instead SICB dictator Billie Swalla and her co-authors made a ridiculous claim. How could their data support the null hypothesis of evolution in ctenophores, when they seem to claim evolution somehow occurred outside the context of the biophysically constrained chemistry of protein folding?

See also: First living example of giant ancient mollusc found in the wild

The giant shipworm is the world’s longest bivalve and the only known extant species of its genus. Unlike other shipworm species that typically burrow into and eat driftwood, the giant shipworm inhabits organic rich, noxious mud and doesn’t seem to feed much at all. Instead it relies on symbiotic bacteria in its gills.

“Bacterial symbionts have been cropping up in various bivalve families,” says John Taylor at London’s Natural History Museum, who was not a member of the expedition. “It’s only since the early 1980s that we recognised that bivalves have bacterial symbionts at all.” Finding them in the family that K. polythalamia belong to as well expands this relationship.

The bacteria break down the mud’s hydrogen sulfide, which give the shipworm’s habitat a distinct rotten egg smell, and produce organic carbon, feeding their host. The shipworm is so reliant on the bacteria that many of its internal digestive organs have shrank from lack of use.

Experimental evidence of biologically-based cause and effect link bacterial symbionts from survival of virus-driven messenger RNA degradation to all biodiversity via the physiology of pheromone-controlled reproduction.
4/22/17 Billie J. Swalla April 22 at 10:25am

It’s Earth Day today, and I am joining the Seattle March for Science. This is to remind our leaders that science is an important way of understanding the world and should be funded and used to make good decisions about the future. I am marching for a better world for everyone, through informed decisions and policies that protect the Earth for future generations. I march for my family, my granddaughters, students and researchers around the globe. I march for the ocean and the mountains, and the prairies. I march for humanity and love for all the people on Planet Earth!

Billie J. Swalla, and others like her, marched in an attempt to support ridiculous theories about evolution that have been replaced with facts about energy-dependent biophysically constrained RNA-mediated cell type differentiation in all living genera.
See who else is living in the dark ages compared to what is known to serious scientists about energy-dependent protein folding chemistry and supercoiled DNA.
The ctenophore genome and the evolutionary origins of neural systems

…we were unable to experimentally detect microRNAs…

Absence of experimental evidence is not evidence of absence, and no experimental evidence links anything except microRNAs from ecological variation to ecological adaptation in all living genera. The failure to detect microRNAs is no excuse for continuing to tout ridiculous theories about evolution.
See for comparison: The phylogenetic utility and functional constraint of microRNA flanking sequences

Conclusion
Both miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes. Such alignments exhibit strong conservation across populations, which can add utility for inference of relationship above the species level, but limits the use of miRNA sequences for biogeographic inference. Despite historic issues regarding their use for phylogenetic inference [8], miRNAs can be employed as both qualitative [9] and quantitative markers, with the latter demonstrated clearly here. Our investigation demonstrates the utility of miRNA sequences as classical phylogenetic markers, and shows this usage is robust to different algorithms of phylogenetic analysis and the analysis of fast-evolving lineages. Such a method provides novel characters for assessing phylogenetic relationships that will be of use in a range of contexts for resolving branches across the tree of life.

Re: biogeographic inference
See also: Virus-mediated archaeal hecatomb in the deep seafloor

…viral infections can be one of the main drivers of chemoautotrophic production in deep-sea sediments…

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

No biogeographic inference was made in the context of global biogeochemical cycles. Bacterial symbionts in shipworms were linked from their nutrient energy-dependent survival in ocean sediments, which clearly shows that all extant species are survivors of virus-driven messenger RNA degradation. Survival is biophysically constrained via the physiology of pheromone-controlled reproduction, which can readily be linked to all biodiversity on Earth in organisms that must find food to reproduce.

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