All in the (bigger) family

Science 16 January 2015:
Vol. 347 no. 6219 pp. 220-221
DOI: 10.1126/science.347.6219.220

by Elizabeth Pennisi

Abstract: A decade of genetic data and other evidence has persuaded most researchers that insects and crustaceans, long considered widely separated branches of the arthropod family, actually belong together. The new arthropod tree puts hexapods—six-limbed creatures that include insects, springtails, and silverfish—as closer kin to crabs, lobster, shrimp, and crayfish than those “standard” crustaceans are to others such as seed shrimp. Traditionally, insect and crustacean scientists have taken different approaches, even when they have studied similar problems. Now they are exploring the consequences of the new family tree, and 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: Each time I begin to think I am catching up on the current literature, it takes a leap. That’s what happened with this report about the annual meeting of the “Society for Integrative and Comparative Biology.” Typically, reports are generated after works are peer reviewed published. Indeed, I might have seen the misrepresentations and reported on them individually. I might also have attended the meeting last week, but I was banned by a moderator of their FB group. That led me to decide they group might be too far behind the extant literature to waste any further efforts. I’m not happy to see I was right. The presentations on cell type differentiation at this meeting are clearly linked to those from the 2013 meeting, which I mentioned in the introduction to this review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, but the presentations are missing something important.

Excerpt: “Members of the Society for Integrative and Comparative Biology (SICB) recently organized and held an ecological epigenetics symposium (January, 2013). Clearly, a new generation is familiar with the concept of ecologically driven epigenetic effects, which can be caused by sensory input that effects hormones, which affect behavior.”

My comment: The 2015 SICB presenters are obviously even more informed. Some of them may also know about my model of RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species. It extends what was known about molecular epigenetics from our 1996 review to what is known about hormone-organized and hormone-activated in insects and to the life history transitions of the honeybee model organism. See Inching toward the 3D genome for more information and my comments on how understanding life history transitions is being explored in the context of the 4D genome.

My comment to the Science site:

Re: “…the nucleome structure changes as cells age, differentiate, and divide, and researchers want to understand how and why.”

Cell type differentiation is nutrient-dependent. RNA-directed DNA methylation links RNA-mediated amino acid substitutions to cell type differentiation via protein folding during life history transitions. Amino acid substitutions stabilize protein folding; mutations perturb it, during nutrient-dependent theromodynamic cycles of protein biosynthesis and degradation.

Life is physics and chemistry and communication

The metabolism of nutrients links metabolic networks to genetic networks via species-specific pheromones that control the physiology of reproduction. Simply put, pheromones link nutrient-dependent life via physics, chemistry, and the conserved molecular mechanisms of communication in species from microbes to man.

Until nutrient-dependent protein folding is linked via the conserved molecular mechanisms of amino acid substitutions and pheromone-controlled DNA stability in organized genomes, which links the epigenetic landscape to the physical landscape of DNA, researchers must take a piece-meal approach to integrating the requirements for life and successful life history transitions — despite the fact that life history transitions have been detailed in the context of the honeybee model organism. See: Honey bees as a model for understanding mechanisms of life history transitions

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Elizabeth Pennisi now reports the SICB presenters seem to have realized that perhaps the most divergent organisms on the Earth did not evolve their biodiversity. Something besides mutations appears to lead to biodiversity. In The ctenophore genome and the evolutionary origins of neural systems SICB dictator Billie Swalla and her co-authors claim that “Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” However, links from metabolic networks to genetic networks in a study of 10,000 patients appear to confirm that nutrient-dependent amino acid substitutions link their morphological and behavioral phenotypes. See also: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults.

The Val158Met substitution is one that links life history transitions in the context of the 4D genome where “… the nucleome structure changes as cells age, differentiate, and divide…” 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?

At the time of my 2013 review it already was clear that amino acid substitutions linked the nutrient-dependent cell type differentiation of all cell types in all individuals of all animal species via their pheromone-controlled physiology of reproduction. That means nothing evolved independently from anything in other animals. It means ecological variation leads to the biophysically constrained nutrient-dependent chemistry of RNA-mediated protein folding that links amino acid substitutions to all biodiversity in morphological and behavioral phenotypes of all species that have ecologically adapted. Many researchers still use the term “evolution” even though they know only ecological adaptation occurs. See for example: Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].

This year’s SICB presenters appear to collectively show that thermodynamic cycles of protein biosynthesis and degradation link the nutrient-dependent ‘conditions of life’ that Charles Darwin claimed must be considered before either natural selection or sexual selection were considered.  Simply put, you start with a species and examine what caused any changes between it and another species. You ask how did the species ecologically adapt?

You don’t dismiss what you don’t know about biodiversity with claims that mutations led to their evolution — unless you’re an evolutionary theorist who has not learned anything about biophysically constrained cause and effect. If you dismiss what’s been learned during the past decade, you might make claims about independent evolution. But sooner or later, as we can now see, someone’s going to show that there is no such thing as independent evolution of anything in any species. For example, see: Sequential actions of β-catenin and Bmp pattern the oral nerve net in Nematostella vectensis.

Excerpt: “The fact that these markers are expressed during the neural development in ctenophores is questioning, whether the nervous system of ctenophores had really a different evolutionary origin from the cnidarian-bilaterian clade as recently proposed66.”

Their citation #66 is to The ctenophore genome and the evolutionary origins of neural systems co-authored by SICB dictator Billie Swalla. This exemplifies the fact that the May 21, 2014 to Dec 23, 2014 marriage of their findings didn’t work. The findings must be separated until the divorce is final. Even if Swalla does not issue a retraction, her results are now meaningless. Collaboration works best among serious scientists when they do not exclude facts published in the context of models that refute their theories.

Unfortunately, the SICB presenters still seem to be individually examining respiration, vision, metabolic rates, respiratory proteins, microRNAs, and the heat shock proteins. The microRNAs and heat shock proteins can be linked from nutrient stress and social stress to hormones that affect behavior in insects, standard crustaceans, and mammals via conserved molecular mechanisms. All other aspects of ecological adaptations such as respiration, vision, metabolic rates, respiratory proteins etc., must first be examined in the context of Darwin’s ‘conditions of life.’ For example, they can be placed into the context of Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.

See the video representation of this unpublished work: Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)  It was an invited review on nutritional epigenetics, but reviewers refused to review the manuscript.

In extension of my model from atoms to ecosystems, achiral glycine is the nutrient-dependent amino acid substitution that stabilizes the DNA in the organized genomes of all vertebrates. Now that other members of SICB have presented on issues of importance to links between metabolic networks and genetic networks, which I have already detailed, perhaps Billie Swalla and others will let me comment on the SICB’s FB page.

That won’t change anything except the slow learning curve of some scientists who chose to ignore contributions by other scientists — or block them in their entirety.

SICB thrives as it nurtures new disciplines

Prof. Billie Swalla, the current President of the Society for Integrative and Comparative Biology (SICB), describes the fluidity and welcoming culture of the society that’s been around for more than a century in this Science article.

This is the same person I described above as the SICB dictator. She removed me from the SICB FB page because I accurately represented the biologically-based cause and effect linked from ecological variation to ecological adaptations in species from microbes to man via conserved molecular mechanisms — not via mutations in ctenophore neural systems, and possibly mutations in muscle specification that evolved independently from those in other animals.

With SICB leadership that makes claims like that, scientific progress clearly will be delayed by at least two more years. SICB is excluding nearly all of what is currently known about the biophysically constrained chemistry of nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation in species from microbes to man.