700 million years of evolution?

Analysis of 5′ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals

It is our hope that each and every one of these regions will make interesting candidates for experimental analysis, helping to increase our understanding of regulation of gene expression, and particularly our understanding of regulatory elements in RNA.

My comment: In other words, they hope what has already been detailed in the context of how nutrient-dependent microRNAs link the epigenetic landscape to the physical landscape of DNA via RNA-mediated events will help others to understand what is known about biophysically constrained cell type differentiation in all living genera. Their hope can be placed into the context of two published works from 2013.
1) Human expression QTLs are enriched in signals of environmental adaptation

Environmental correlation is a way of detecting adaptation by testing whether the spatial distribution of the frequency of an allele could be explained by an environmental factor.

2) Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

My comment: Others have since established the validity of 2) the model, which links 1) environmental correlation to the detection of ecological adaptations. For example, ecological variation is consistently linked from nutrient-dependent microRNAs to the pheromone-controlled physiology of reproduction via feedback loops. The feedback loops were placed into the context of ecological adaptations across species in

All in the (bigger) family


…last week at a special symposium of the annual meeting of the Society for Integrative and Comparative Biology, researchers reported new parallels between these two very successful groups of animals and new insights about what it took for an ancient crustacean to give rise to insects.

My comment: (Submitted on Mon, 01/19/2015 – 11:51 and published to the “Science Magazine” site)

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400
Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.
Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.
Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.
Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

See also: Oldest DNA sequences may reveal secrets of ancient animal ancestors
This report on the findings from Analysis of 5′ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals places everything currently known to serious scientists about how nutrient-dependent microRNAs link ecological variation to ecological adaptation into the context of neo-Darwian evolutionary.
The report begins with this ridiculous claim:

700 million year-old DNA sequences from ancient animals have been unearthed by researchers at the Universities of Leicester and Warwick, shedding new light on our earliest animal ancestors and how they influenced modern species – including the sponge.

My comment: How did they determine that the DNA sequences are from 700 million year old animals? That is the first question every serious scientist I know would ask if they saw this report.
Here’s the answer (with my emphasis):

Among the CNEs that we identified were previously-studied regulatory elements, as well as many unidentified novel putative regulatory elements. As the majority of CNEs overlap 5’ UTRs, we calculated the likelihood of there being a conserved secondary structure in each CNE.

My comment: No serious scientist calculates the likelihood that a conserved secondary structure in any extant or extinct species could be linked to 700 million years of evolution.
I will have more to say on this later. I wanted to report it here, in case the “Science Magazine” site removes my comment as they did at least once before. The comment they removed was replaced with the author’s comment here: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

Here’s the comment that was removed:

The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.
The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.
If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).
If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.
Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

The fact that a single amino acid substitution in a virus can lead to changes across species that occur via amino acid substitutions in bacteria that re-evolved their flagellum in as few as four days is something that I have repeatedly addressed in blog posts here. I will continue to do so.
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