Scientists have long wondered how much life can be stripped down and still remain alive. The answer seems to be that the true essence of life is not some handful of genes, but coexistence [or cooperation].
Nutrient-dependent/pheromone-controlled adaptive evolution [species-wide coexistence] Presented at Society for Behavioral Neuroendocrinology Annual Meeting 2013.
Background / Purpose: Model organisms exemplify nutrient-dependent / pheromone-controlled diversity in species from microbes to man.
Main conclusion: Nutrient-dependent / pheromone-controlled adaptive evolution refutes mutations theory.
All relationships that epigenetically effect any species begin with self vs. non-self recognition, which is a function of olfaction and of cellular regulation of immune system function. Conspecifics must recognize heterospecifics via their odors and pheromones to determine whether or not to eat other organisms or try to co-exist with them. Epigenetic effects of food odors and species-specific pheromones on genetically predisposed behaviors in unicellular and multicellular organisms enable cooperative coexistence via ecological, social, neurogenic, and socio-cognitive niche construction, which is required for adaptive evolution in species from microbes to man. A noteworthy author of science fiction has known this for more than a decade: See: When Genes Go Walkabout: Greg Bear (22 minute video).
Now, see the more technical representations of biological fact in: 1) Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells; 2) Patterns of population epigenomic diversity and 3) Global Epigenomic Reconfiguration During Mammalian Brain Development. Excerpt from 3: “…our genome-wide, base-resolution, cell-type specific DNA methylomes for brain cells through key stages of development are the first steps toward unraveling the genetic program and experience-dependent epigenetic modifications leading to a fully differentiated nervous system.”
Experience-dependent epigenetic modifications is the key phrase. Individuals interact! Finally, see: MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates, because species-specific experience-dependent interactions enable epigenetic modifications caused by pheromones. These modifications are not caused by random mutations. Nutrients are the most likely source of the microRNAs that drive the developmental remodeling of the brain, which is controlled by the metabolism of nutrients to species-specific pheromones.
None of the information contained in the published articles or presentations linked above is a matter of opinion, and the information on coexistence/cooperation does not incorporate random mutations theory. Yet, many people are content to express their opinions about mutations, which have never been scientifically substantiated, all the while the biological facts have become increasingly clear. For example, see my comments from: Science 7 September 2012: Vol. 337 no. 6099 pp. 1159-1161 DOI:10.1126/science.337.6099.1159 ENCODE Project Writes Eulogy for Junk DNA by Elizabeth Pennisi.
Excerpt: “This week, 30 research papers, including six in Nature and additional papers published online by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases.”
My comments (2)
James V. Kohl
Isn’t the concept that is extended the one that involves the epigenetic “tweaking” of immense gene networks in ‘superorganisms’ that ‘solve problems through the exchange and the selective cancellation and modification of signals [as indicated by Greg Bear]? For example, we’ve known that nutrient chemicals epigenetically effect intracellular signaling and stochastic gene expression and that pheromones do this also. Nutrient chemicals are required for individual survival and their metabolism to pheromones controls reproduction. If their epigenetic effects on stochastic gene expression was not responsible for de novo gene expression (e.g., for new odor receptors), we would have nothing but a theory of random mutations to explain species diversity that is obviously dependent on nutrition and species-specific pheromones for ecological, social, neurogenic, and socio-cognitive niche construction via adaptive evolution in species from microbes to man. Indeed, until now we have had only a theory to compare to the biological facts of evolved gene, cell, tissue, organ, organ system reciprocity, which is obviously due to the epigenetic “tweaking” of immense gene networks by nutrient chemicals and pheromones.
Submitted on Thu, 09/06/2012 – 22:31
Epigenetic tweaking also involves condensation and silencing (see Science reference 3 above). I would assume that environmental chemicals could affect both unfolding and condensation of chromosome regions.
Submitted on Mon, 09/10/2012 – 09:27
James V. Kohl
I should have posted the information on my recent published work. Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.
The concept of epigenetic tweaking that is extended more clearly includes the role of viruses and endocrine disruptors, which indicates an epigenetic “free-for-all” that helps to explain the similarities across species (due to shared molecular biology). But it also explains the diversity due to nutrient chemical metabolism to species-specific and individual organism-specific pheromone production.
Simply put, this means that we are what we eat (e.g. like all other organisms) and that our pheromones tell others what and who we are so that they can take or leave us — albeit at a level of unconscious affect, as in other animals.
Challenges to the facts (above) should be met with contempt, unless they include something more than just opinions or theories. The challenges must include biological facts or be dismissed as the simple musings of the uninformed. When science fiction novels incorporate biological facts that evolutionary theorists, philosophers, ethologists, behaviorists et al., have dismissed or ignored, how much worth can be attributed to their story-telling. How dare they tell stories about evolution that do not include biological facts?
The biological facts now tell us that one change in a base pair results in a single nutrient-dependent amino acid substitution that defines a human population, which arose in what is now central China during the past ~30,000 years (see for review Kohl, 2013). The correlates with climate change, with de novo genes for starch production in the leaves of sago palms, with modern human diet, and with the disappearance of the Neanderthals (or their replacement by the modern human population) suggest either a series of coincidences or the epigenetic cause and effect that is obvious in species from microbes to man (sans mutations theory).
Note also that the: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants (during the past 5-10,000 years). What some people might like us to label ‘mutations,’ are actually nutrient-dependent and pheromone-controlled epigenetically-effected advantageous alleles. In my model, more of these advantageous alleles arise due to our omnivourous diet and the metabolism of nutrients to human pheromones.
But see, for comparison, Jay Feierman’s opinion, as moderator of the ISHE’s human ethology group, that “Random mutations are the substrates upon which directional natural selection acts.” Ask him: “Is there a model for that?” He won’t answer that simple question when I ask it, and neither will anyone else who touts random mutations theory.
To people like Feierman, humans are little more than randomly mutated bacterium. Indeed, we are more like the peppered moth species that changed color due to naturally selected mutations, albeit by predation and only until pollution was reduced and the mutant moths changed their color again. No one commented on the fact that the color change occurred in the same pattern as would be expected if the increased lead and manganese on leaves that moth larva ate caused a difference in moth color and in production of female pheromones. Moth pheromones attract males from 2 kilometers upwind, which matched precisely the speed of the migration attributed to mutations and predation. The substitution of a critical amino acid is sufficient to create a new pheromone blend in my model of biological facts (i.e., in species from microbes to man).