human-evolution

Genomic surveillance ends our world of RNA-mediated ecological adaptations

Why is this woman smiling?

1) Identifying Recent Adaptations in Large-Scale Genomic Data

Senior author: Sabeti with co-author Rinn
Excerpt: “As natural selection can only act on mutations that drive phenotypic variation…”.

2) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak 

Senior author: Sabeti.
Excerpt: “Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.”

3) RNA and dynamic nuclear organization

First author Rinn.
Excerpt: “… it is becoming increasingly clear that lncRNAs are important at all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization.”

4) ‘Oming in on RNA–protein interactions

First author Rinn.
Excerpt: “…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6].”
My comment: Evolutionary theorists who think “…natural selection can only act on mutations that drive phenotypic variation…” may not realize that “…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities…” See our section on molecular epigenetics in From Fertilization to Adult Sexual Behavior “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation…” (e.g., of cell types in species from yeasts to man).
Serious scientists may realize, too late, that nutrient-dependent RNA-directed DNA methylation — and pre-mRNA-mediated events that lead to mRNA-mediated amino acid substitutions — differentiate all cell types in all individuals of all living species. For example, without thinking, the non-living Ebola viruses may ecologically adapt with as little as a single amino acid substitution, like the one that differentiates all cell types of humans from chimpanzees and gorillas.
See: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.” Dobzhansky (1973).
What evolutionary theorists continue to think about natural selection acting on mutations that lead to the evolution of biodiversity will not matter if the Ebola viruses destroy humanity. People may ask as our species dies out: “What were the evolutionists thinking? Did they not know that Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution?
Did the theorists never ask: How does epistasis arise from an evolutionary process that is conceived as proceeding through the incremental accumulation of mutations?
Does any serious scientist still think that the accumulation of mutations leads to increasing organismal complexity? How could that happen?
Biophysically-constrained receptor-mediated nutrient-dependent pheromone-controlled ecological adaptations link the physiology of reproduction to behavioral phenotypes and morphological phenotypes in all living species based on the molecular mechanisms conserved in viruses.
Is there another model for that? Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. See also: Origin of group identity: viruses, addiction and cooperation

achiral-glycine

Physics, Chemistry, and Molecular biology (PCMb)

Physics, Chemistry, and Molecular biology (PCMb) link ecological variation to ecological adaptations via a model of gene-cell-tissue-organ-organ system complexity that I first presented in 1992. After adding gene activation by pheromones, I co-authored a book that linked the pheromone-controlled physiology of reproduction across species from microbes to man: The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)
Since then, others have written books that claimed that pheromones evolved: Pheromones and Animal Behaviour (2003/2014) and one claimed that mammals don’t produce or respond to pheromones: The Great Pheromone Myth (2010).
Ignorance of biophysically-contrained biologically-based cause and effect continue to prevent scientific progress. Others have started to speak out against the pseudoscientific nonsense of evolutionary theorists and psychologists who have limited progress that could have been made by serious scientists from many disciplines. The theorists have continued to tout their pseudoscientific nonsense about mutations, natural selection and evolution, for more than 17 years after we detailed the facts about how epigenetically-effected RNA-mediated events link nutrient-uptake to the pheromone-controlled physiology of reproduction in species from microbes to man.

Many others must speak up each time they read or hear about the statistical nonsense of evolutionary theory as if it were supported by experimental evidence of biologically-based cause and effect. Tell the theorists to start making sense. Cite Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes and quote from it: “The rates of 4 types of elementary evolutionary events (hereinafter Genome Dynamics Events or GDE)…”
Help make others approach the psychology and the practice of medicine from the only perspective that makes sense: Physics, Chemistry, and Molecular biology (PCMb) — not the pseudoscientific nonsense of theorists. RNA-directed DNA methylation links RNA-mediated events to amino acid substitutions that differentiate the cell types of all individuals in all species.

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

neuronal-plasticity

Physics denied; pseudoscientific nonsense accepted

 

The events depicted are now portrayed in the context of Genome Dynamics Events, which are biophysically-constrained RNA-mediated events. RNA-mediated events lead to amino acid substitutions that differentiate the cell types of species. For example: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.” Dobzhansky (1973)
See also:

God, Darwin and My College Biology Class

Excerpt: “Since Darwin, however, we have come to understand that an entirely natural and undirected process, namely random variation plus natural selection, contains all that is needed to generate extraordinary levels of non-randomness.”
My comment: Only those taught to believe in pseudoscientific nonsense continue to claim, like many unenlightened theorists, that “…random variation plus natural selection…” leads to the evolution of biodiversity. They ignore the Laws of Physics and what is known about the biophysically constrained chemistry of cell type differentiation.
For contrast, serious scientists understand that
1) RNA-directed DNA methylation leads from ecological variation and
2) nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation to
3) RNA-mediated events such as
4) amino acid substitutions that
5) differentiate all cell types of
6) all individuals of
7) all species via
8) conserved molecular mechanisms of
9) nutrient-dependent
10) pheromone-controlled ecological adaptations.
The ecological adaptations link ecological variation to to nutrient-dependent ecological speciation, which is biophysically constrained, via the production of species-specific pheromones that epigenetically control the nutrient-dependent physiology of reproduction in species from microbes to man.
Pseudoscientists skip the steps that link creation from nutrient-uptake to controlled reproduction and claim that “…random variation plus natural selection, contains all that is needed to generate extraordinary levels of non-randomness.”
That’s where their ridiculous ideas about mutations, natural selection, and the evolution of biodiversity came from: IGNORANCE! Serious scientists continue to add experimental evidence of each successive step in the linear series of RNA-mediated events that refutes the pseudoscientific nonsense of evolutionary theorists each step of the way (e.g., from Let there be Light-induced amino acid substitutions in plants and animals to ecological speciation.)
Pseudoscientists skip the “Let there be light” part, and proceed with claims that species evolve via random variation plus natural selection. However, they have not described any biologically-based evolutionary event that links one species another. Instead, they look at morphological phenotypes and claim that morphological and behavioral phenotypes must have evolved outside the context of the Laws of Physics.
For consideration of physics, chemistry, and the molecular biology of ecological speciation see my 5.5. minute-long ISHE 2013 poster presentation video:
Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)

Click on the photo

IMG_2329-e1413855233208-958x718

Quantum physics meets Evolutionary Psychology News

Capturing the motion of a single molecule in real time as it oscillates from one quantum state to another

September 18, 2014


Excerpt: “It also moves researchers a step closer to viewing the molecular world in action — being able to see the making and breaking of bonds, which control biological processes such as enzymatic reactions and cellular dynamics.”

My comment: The making and breaking of bonds controls all biological processes. Luca Turin tried to do move researchers a step closer to viewing the molecular world in action and was hung out to dry by members of the Association for Chemoreception Sciences (AChemS). Chandler Burr wrote a book about Luca’s experiences. I sided with AChemS in a review of the book
The Emperor of Scent: A Story of Perfume, Obsession and the Last Mystery of the Senses. That was before they ignored details of RNA-mediated events and hung me out to dry as well.

Then I learned that Luca Turin was probably right about the “Molecular Vibration-Sensing Component in Human Olfaction”  I think that’s what Sinope Diogenes is trying to tell the Evolutionary Psychology News group and wonder why he is doing that.

Most evolutionary psychologists know nothing about molecular biology and they appear to believe that mutations and natural selection led to the evolution of biodiversity. Most have rejected all facts that show ecological variation leads to ecological adaptations via biophysically-constrained molecular mechanisms that ensure perturbed protein folding manifested in mutations does not lead to increasing organismal complexity. Simply put, the evolutionary psychologists I have encountered are less likely than serious scientists from AChemS to accept anything other than what they’ve been taught to believe in.
Most members of AChemS probably believe in the pseudoscientific nonsense of evolutionary theory, too. Few of their members could accept the fact that RNA-mediated events link insect to mammals via the epigenetic effects of olfactory/pheromonal input on hormone-organized and hormone-activated behaviors. In fact, no one publicly complained when Richard L. Doty, a sensory psychologist, proclaimed that mammalian pheromones don’t exist because of differences in the stereotypical behaviors of insects and mammals, which obviously are epigenetically-effected via conserved molecular mechanisms.
See: The Great Pheromone Myth ” In this provocative book, renowned olfaction expert Richard L. Doty rejects this idea and states bluntly that, in contrast to insects, mammals do not have pheromones.” But wait, see also: Humans Can Discriminate More than 1 Trillion Olfactory Stimuli. The disparity between the number of olfactory receptors and our detection abilities suggests two things.
1) Doty does not know that what humans and insects have in common, which links quantum physics via chemistry to the molecular biology of de novo Creation of odor receptors that detect food odor and pheromones in insects and in mammals.
2) Luca Turin’s ideas about links from biophysically-constrained ecological adaptations to nutrient-dependent pheromone-controlled hormone-organized and hormone-activated behaviors should be revisited whenever a generation of intelligent researchers learns enough about physics, chemistry, and conserved molecular mechanisms in species from microbes to man to look beyond the nose on their face, past the presentations at AChemS meetings, or up the nose of the sculpture in front of the Monell Chemical Senses Institute.

Physics

Some neuroscientists think a mutation led to human language development

Neuroscientists identify key role of language gene

Excerpt: “Neuroscientists have found that a gene mutation that arose more than half a million years ago may be key to humans’ unique ability to produce and understand speech.”
Excerpt: “…the gene that allowed us to speak may have something to do with a special kind of learning, The gene was first identified in a group of family members who had severe difficulties in speaking and understanding speech, and who were found to carry a mutated version of the Foxp2 gene.”
My comment:  See: RNA and dynamic nuclear organization. RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of amino acid substitutions and protein folding to increasing organismal complexity via molecular biology.
RNA-mediated events associated with nutrient-dependent amino acid substitutions can also be compared to unknown evolutionary events that might automagically arise in the context of an alternative theory about constraint-breaking mutations and natural selection without RNA-mediated events.
What theory suggests a mutation led to amino acid substitutions and a disorder of language development in one small group of humans, but also links a mutation to the increased organismal complexity of the human brain via the conserved molecular mechanisms of RNA-mediated amino acid substitutions that differentiate cell types in species from microbes to man?
Who believes in the pseudoscientific nonsense of mutations, natural selection, and the evolution of biodiversity, which can be compared to the biological fact that ecological, social, neurogenic and socio-cognitive niche construction are RNA-mediated events — not undescribed evolutionary events?

terrarium-eco-system

Behavior: The first response is RNA-mediated not genetically-determined

Diana Maria Petrosanu asked a question in an Evolutionary Psychology News discussion about Evolution’s Random Paths Lead to One Place. I’ve been very vocal in other discussions that tout ridiculous theories that have been repeatedly refuted by biological facts. My answer to her question might help others to understand the language of RNA-mediated events. That’s why I added details to my representation at Combating Evolution to Fight Disease.  Whether or not the addition to my comments is published or understood in its context, I hope that repeating the additional comment and adding to it here will be helpful to others who are interested in understanding how to combat evolution and fight disease, especially those who don’t know the difference between an RNA-mediated event and an evolutionary event.
First off, so far as I know, there is no such thing as an evolutionary event! Genetically-predisposed behavior is RNA-mediated. It is not genetically determined and behavior does not arise in the context of mutations and natural selection. That means evolutionary theory cannot explain the evolution of behavior. That explains why evolutionary theorists have not explained the evolution of behavior in terms that link an evolutionary event to morphological and to behavioral diversity manifested as differences in the behavior of individuals or of species with different morphologies. For example, there are sex differences in morphology and in behavior. Evolutionary theorists have not attempted to explain how an evolutionary event might lead to those differences.
Let’s see what happens if I take an RNA-mediated egg-to-chicken approach to the dilemma of “Which came first, the chicken or the egg?” In organisms with different cell types that enable sexual reproduction via internal fertilization, our 1996 review: From Fertilization to Adult Sexual Behavior helped limit attempts to end the dilemma by inventing more ridiculous theories, which are consistently framed in the context of undisclosed evolutionary events. Clearly, the RNA-mediated behavior of the unicellular egg comes first because RNA-mediated behavior occurs in all cells of unicellular and multicellular organisms. If DNA-determined behavior were exemplified in any organism, it could be linked to the behavior of the organism’s last universal common ancestor. Simply put, the behavior of a microbe could be linked to behaviors I have exhibited as a motorcycle enthusiast and to my brothers’ behaviors.
My comment (to Science Magazine): 9/17/14 update The following comment has not yet been published but it has become more pertinent given a recent report on the evolution of teeth in sticklebacks that I detailed HERE. Obviously, the starting point is behavior that leads to the ecological adaptation manifested in the teeth of P. pacificus. However, researchers still seem to want unknown evolutionary events to lead to changes in teeth in other species like fish. Until they describe the evolutionary event that led to changes in teeth in sticklebacks, it is prudent to think that ecological variation led to RNA-mediated events and amino acid substitutions that differentiated the cell types of nematodes and sticklebacks via the conserved molecular mechanisms of ecological adapations.

“An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).” http://www.sciencemag.org/content/332/6034/1161.short
This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans http://www.cell.com/cell/abstract/S0092-8674(14)00806-X
The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.
See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes http://linkinghub.elsevier.com/retrieve/pii/S0092867412015000
A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.
RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that include no mention of RNA-mediated events.