Gene creation (revisited)

(click to enlarge)
Abstract:
The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces, Drosophila, Plasmodium, Arabidopisis and human. From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease. Rather than an extremely rare occurrence, it is now evident that there is a relatively constant trickle of proto-genes released into the testing ground of natural selection. It is currently unknown whether de novo genes arise primarily through an ‘RNA-first’ or ‘ORF-first’ pathway. Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations.
Excerpt:
De novo genes are usually defined as protein-coding genes that have evolved from scratch from previously non-coding DNA.
Conclusion:
De novo genes are not only important for their functional and biological contribution to the lineages in which they originate; they are also very informative in terms of our growing understanding of the evolution the genome and of new gene functions. Evolution continues to tinker.
My comment: If you define de novo genes in the context of their evolution from scratch, you have no choice but to tout the pseudoscientific nonsense about neo-Darwinism that you were taught to believe in.
For contrast: The de novo creation of experience-dependent olfactory receptor genes links atoms to ecosystems via the conserved molecular mechanisms of nutrient-dependent RNA-mediated protein folding chemistry.
See also: Search Results for ‘de novo creation’
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0
The sum of our RNA-mediated parts
2 MIN READ
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microRNAs and memory: Why trust a theory?
2 MIN READ
0
Protein folding and Google page rank
2 MIN READ
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RNA-mediated development (2)
< 1 MIN READ
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Living the life that randomness created? (Sarcasm alert)
3 MIN READ
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microRNAs, glycosylation, and genomes
4 MIN READ
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Alternative splicings: epigenetics meets pharmacogenomics
4 MIN READ
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Epigenetic regulation of aging by glycine and GnRH
5 MIN READ
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Physicians who practice evolutionary medicine?
3 MIN READ
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Pattern recognition: biogeochemical structure and function
5 MIN READ
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Viruses and the human-like microbiome
3 MIN READ
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Informing the biologically uninformed
< 1 MIN READ
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Tweaking the story to fit the theory
5 MIN READ
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I forgot. How do mutations cause evolution?
4 MIN READ
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Batch effect vs epigenetic effects
3 MIN READ
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Gene expression, immortality, and cancer
6 MIN READ
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Bee-birthed epigenetics and primate cell types
5 MIN READ
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Vitamin B3 and DNA repair
4 MIN READ
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Bees and primates automagically evolve
3 MIN READ
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Ignoring systems complexity (it’s too complicated)
3 MIN READ
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Virus-driven cancer treatment and prevention
2 MIN READ
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The microbiome, pharmacogenetics, and privacy
< 1 MIN READ
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A special issue on nutritional epigenetics
5 MIN READ
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Retinoic acid + one receptor regulate the genome
3 MIN READ
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Epigenetics: microRNAs effect an integrative pathway
4 MIN READ
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Protein isoforms do not evolve
3 MIN READ
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From gut bacteria to breast milk and back
5 MIN READ
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Physics, chemistry, light, and life
2 MIN READ
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Epigenetics vs the fossil record
4 MIN READ
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An epigenetic mark links algae, worms, and flies
2 MIN READ
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Thermodynamics and protein folding landscapes
2 MIN READ
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RNA-mediated cell types and precision medicine
5 MIN READ
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DNA Methylation and organized genomes
7 MIN READ
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Misunderstanding cancer
7 MIN READ
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The Darwin Code by Greg Bear
13 MIN READ
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Mutisensory integration: watching the paradigm shift
12 MIN READ
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Origin of life and cancer (1,2,3)
2 MIN READ
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A genetic variant refutes neo-Darwinism
6 MIN READ
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The miRNA/mRNA balance: a suboptimal strategy?
2 MIN READ
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Nutrient-dependent microRNAs control cell types
6 MIN READ
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Life: conserved ion and amino acid transporters
3 MIN READ
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Deeply ingrained thoughts
< 1 MIN READ
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Graphic misrepresentations of ecological adaptation
2 MIN READ
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Too many targets for theories
3 MIN READ
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Creating nothing but a theory (3)
4 MIN READ
3
Creating nothing but a theory (2)
4 MIN READ
0
Creating nothing but a theory
4 MIN READ
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The quantum / classical RNA-mediated ‘tipping point’
3 MIN READ
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Epigenetic effects of soil bacteria on plants
< 1 MIN READ
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Epigenetic switch links MicroRNAs to RNA-protein interactions
4 MIN READ
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Quantum correlations/pseudoscience
3 MIN READ
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Correctly modeling life on this planet
3 MIN READ
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Correctly modeling biological energy
2 MIN READ
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Questions about life’s diversity
21 MIN READ
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UV-light mutations and gene loss (not gain)
5 MIN READ
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Virus-driven origin of life
2 MIN READ
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Luis P. Villarreal tells it like it is
3 MIN READ
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Walk towards the light
< 1 MIN READ
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Epigenetics Skeptism
5 MIN READ
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Is DNA-directed transcription RNA-mediated?
2 MIN READ
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RNA directed DNA methylation and cell types
4 MIN READ
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Implicating microRNAs in cancer
2 MIN READ
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Rejecting what is known about viral microRNAs and nutrient-dependent microRNAs
2 MIN READ
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Reverse phosphorylation
7 MIN READ
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RNA-mediated repurposing in microbes and adaptations in primate brains
2 MIN READ
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RNA-mediated “repurposing” is nutrient-dependent and pheromone-controlled
3 MIN READ
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RNA-mediated "repurposing" is nutrient-dependent and pheromone-controlled
3 MIN READ
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From 3-D to epigenetically-effected 4-D genome make-up
5 MIN READ
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Let there be anti-entropic light (1)
11 MIN READ
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An epigenetic trap (the prequel)
5 MIN READ
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Imagining that data historically supports evolutionary theory
7 MIN READ
0
Atheism: Arrogant, useless, and divisive ignorance
7 MIN READ
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The anti-entropic force of "Nature"
2 MIN READ
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Nutritional epigenetics, exercise, and immune system integrity
4 MIN READ
0
Military combat training to fight disease (2)
3 MIN READ
0
Military combat training to fight disease
3 MIN READ
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Theoretical physics and molecular biology
5 MIN READ
0
Atoms to ecosystems is not almost a molecular ecology
3 MIN READ
0
Epigenetic effects of viruses on cellular homeostasis (2)
2 MIN READ
0
RNA-mediated epigenetic modification via DNA-methylation
4 MIN READ
0
Quantum physics, quantum biology, and quantum consciousness
4 MIN READ
0
How fast can evolutionary theory be changed?
5 MIN READ
0
Biological energy and a microbiome model of a light-driven time machine
3 MIN READ
0
Quantum Superpositions: let there be light
4 MIN READ
0
Are viruses microRNAs? (2)
5 MIN READ
0
Sneaking up from behind
4 MIN READ
0
Quantum entanglement, mass, and biomass
4 MIN READ
0
Physicists: Desperate Acts
16 MIN READ
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Mute points: most are afraid to mention them
6 MIN READ
0
All of “like kind” (Part 2)
2 MIN READ
0
All of "like kind" in the (bigger) family
6 MIN READ
1
Environment epigenetically shapes the immune system
3 MIN READ
0
Beneficial microbes kill beneficial mutations
4 MIN READ
0
Constrained evolution is ecological adaptation
5 MIN READ
0
A single amino acid substitution differentiates cell types of E. coli
3 MIN READ
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Unconstrained evolutionary innovability
4 MIN READ
0
RNA-protein interactions reveal biophysical to ecological landscapes
2 MIN READ
0
Mutagenesis: Replacing facts with theories
5 MIN READ
0
ISHE's human ethology group
2 MIN READ
0
Understanding cell type differentiation
3 MIN READ
0
From Hydra to humans vs a Lakatosian research program
4 MIN READ
0
Unified nutritional and molecular mechanisms
9 MIN READ
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Removing natural selection; reshaping the horse; adjusting evolutionary theory
4 MIN READ
0
Models by evolutionary biologists are not models
2 MIN READ
0
The future of physics predicts no future for evolutionary theory
3 MIN READ
0
Model organisms: the birds and the bees
3 MIN READ
0
Chemical ecology and RNA-mediated control of DNA loops
< 1 MIN READ
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Atoms to ecosystems: Evolutionary theory vs the coelacanth
6 MIN READ
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Jumping back: Science or Pseudoscience? (2)
2 MIN READ
0
Jumping back: Science or Pseudoscience?
6 MIN READ
0
Single-cell level assay of protein biosynthesis and degradation
2 MIN READ
0
Glycine and GnRH: Am I being pedantic?
4 MIN READ
0
Extensive molecular evidence vs ridiculous theories
2 MIN READ
0
Dual genomes: exposing the evolution industry
5 MIN READ
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Epigenetic pharmacology and RNA-mediated transciptional landscapes
3 MIN READ
0
RNA-mediated events and "The Theory of Everything"
4 MIN READ
0
Eliminating correlations from evolutionary ecology
6 MIN READ
0
RNA-mediated species specificity
2 MIN READ
0
Are mutations beneficial?
4 MIN READ
0
The key to science: experimental evidence
5 MIN READ
0
Ecological adaptations reported as evolution in insects and mammals
4 MIN READ
0
Biologists puzzled by evolved RNAs and decaying DNA
6 MIN READ
0
More than a bag of chemicals?
2 MIN READ
0
Nothing new under the sun, except pseudoscientific nonsense
6 MIN READ
0
Making sense of quotes scattered across disciplines
2 MIN READ
0
Intelligent viruses and cancers?
10 MIN READ
0
Complex behaviors of cell types in cancer
6 MIN READ
0
De novo DNA methylation?
3 MIN READ
0
RNA eclipses the importance of DNA to cell type differentiation
4 MIN READ
0
We need pattern recognition, not a prologue
6 MIN READ
0
Pharmacogenomics
3 MIN READ
0
Sexual differentiation of cell types in plants
2 MIN READ
0
From deep time into real time: What evolutionary processes?
10 MIN READ
0
In theory, or supported by experimental evidence?
5 MIN READ
0
Are evolutionary theorists 'nob ends'?
5 MIN READ
2
ALPHA GENOMIX
7 MIN READ
2
No excuses: Creation and the meaning of organismal complexity
7 MIN READ
0
Nutrient-dependent gene duplication in plants (but not animals?)
4 MIN READ
0
Evolutionary theorists and evolutionary theists live under rocks
< 1 MIN READ
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Understanding physical forces of ecological variation and adaptation
< 1 MIN READ
0
Behavioral ecology: please continue to believe in our fantasies
3 MIN READ
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2014 and 2004 Nobel Prize in Medicine
3 MIN READ
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RNA-mediated genetic engineering (Part 3)
< 1 MIN READ
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RNA-mediated genetic engineering (Part 2)
3 MIN READ
0
RNA-mediated genetic engineering
2 MIN READ
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Genomic surveillance ends our world of RNA-mediated ecological adaptations
2 MIN READ
0
Metabolism, fixation, health or neurodegerative disorder
2 MIN READ
0
Physics, Chemistry, and Molecular biology (PCMb)
2 MIN READ
0
Physics denied; pseudoscientific nonsense accepted
2 MIN READ
0
Ecological variation and niche construction: 1, 2, 3
6 MIN READ
0
Epigenetically-effected metabolic shifts and ecological adaptations
3 MIN READ
0
Evolving DNA before RNA
4 MIN READ
0
Did our adapted mind evolve? (Revisited)
2 MIN READ
0
De novo gene Creation sans evolution of genes via mutations
4 MIN READ
0
Mathematical model: microRNA and epigenetic regulation
2 MIN READ
0
Seemingly futile cycles are not thermodynamically futile
3 MIN READ
0
New technique used in report of atomic-level ecological adaptations
3 MIN READ
0
Can epigenetic inheritance occur without concurrent changes in morphology AND behavior?
3 MIN READ
0
Memory of repression and memory of behavior
2 MIN READ
0
Quantum physics meets Evolutionary Psychology News
2 MIN READ
0
Watching and waiting for more retractions
2 MIN READ
0
Some neuroscientists think a mutation led to human language development
< 1 MIN READ
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Exploding genomes and chromosomal rearrangements via RNA-mediated events
2 MIN READ
0
Behavior: The first response is RNA-mediated not genetically-determined
3 MIN READ
0
A relatively young branch of science called epigenetics
4 MIN READ
0
Biophysically constrained beginnings of RNA and DNA
4 MIN READ
0
Baby talk: More misrepresentations of ecological adaptations
2 MIN READ
0
Comparing divergent model organisms
2 MIN READ
1
A microRNA-mediated mechanism that is epigenetically inherited
2 MIN READ
0
microRNAs differentiate neuronal cell types
3 MIN READ
0
microRNAs and species relationships
3 MIN READ
0
Drunks and Monkeys: Pseudoscientific nonsense
2 MIN READ
0
The quantum biology of consciousness
3 MIN READ
0
Behavior is receptor-mediated
10 MIN READ
0
Genes and Race: Human History?
2 MIN READ
0
Soft atheism: a case for Creation
< 1 MIN READ
0
Ecologically linked adapted ants and brains
2 MIN READ
0
MiRNAs methylation and ecological adaptation sans mutations
2 MIN READ
0
Not focused and self-aggrandizing
2 MIN READ
0
Cell-type differentiation
2 MIN READ
0
Darwinian theories vs Darwin's facts
2 MIN READ
0
The wrong picture of our evolution
4 MIN READ
0
96 fixed amino acid substitutions, not 96 genes
6 MIN READ
0
Don't tell the Creationists
2 MIN READ
0
Social experiences epigenetically effect gene networks
2 MIN READ
0
Seeds of life: astrobiological theory and mutations theory
3 MIN READ
0
Understanding the role of mutations and evolution
4 MIN READ
0
Alzheimer's, microRNAs, and olfaction
< 1 MIN READ
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Pheromones and cancer
4 MIN READ
0
Constraints on mutational drift
< 1 MIN READ
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Epigenetic effects underlie sexual preferences IV
< 1 MIN READ
0
Human Form by Karl Grammer
< 1 MIN READ
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Fatal attractions: a fear of pheromones
2 MIN READ
0
Disorders of development: altered microRNA / messenger RNA balance
< 1 MIN READ
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The Knowing Nose: Chemical Signals Communicate Human Emotions
< 1 MIN READ
0
A “new” form of natural selection?
2 MIN READ
0
Pheromonemotionally speaking
2 MIN READ
0
Copulins: Human pheromones effect physiology and affect social behavior
2 MIN READ
0
Human Pheromones: Diversity of signaling pathways and a common response
< 1 MIN READ
0
Human pheromones, social deprivation, and brain growth
< 1 MIN READ
0
Human pheromones and the visual appeal of other people (Part one)
2 MIN READ
0
Adam’s rib: Pheromones and the adaptive evolution of human sexuality
2 MIN READ
0
Human pheromones and your immune system
< 1 MIN READ
0
Human Pheromones: but No VNO; No Erox; No Human Pheromone Sciences
3 MIN READ
0
History of intelligence (550 words)
2 MIN READ
0
Explaining a good theory
< 1 MIN READ
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Effects of pheromones on menstrual synchrony and a gay man
2 MIN READ
0
Cookbook chemistry: food odors and hormones
< 1 MIN READ
0
Human pheromones and food odors
< 1 MIN READ
0
Misrepresentations of biologically based cause and effect:
3 MIN READ
0
An organizing principle for our sense of smell
< 1 MIN READ
0
Trust the science. Don’t trust the hype
2 MIN READ
0
The Sex Lives of Insects: Part III
3 MIN READ
0
The epigenetics of food choice and mate choice
< 1 MIN READ
0
Study results: Human pheromones affect women’s behavior
< 1 MIN READ
0
Human Pheromones and the Biology of Behavior
5 MIN READ
0
Honeybees, food odors, and perfume
< 1 MIN READ
0
Erox rises from the ashes
< 1 MIN READ
0
Human Pheromones Affect Women's Behavior
2 MIN READ
0
Creating a Myth
< 1 MIN READ
0
Dogs and humans: Then and now
< 1 MIN READ
0
Excellent new book about pheromones
< 1 MIN READ
0
Human Pheromones and The Philosophy of Science
2 MIN READ
0
Too many good-smelling males is not good
< 1 MIN READ
0
Exotic Pheromones and Concentrates
2 MIN READ
0
Dialogue on pheromones: Avery Gilbert / James V. Kohl
2 MIN READ
0
Study Results: Human pheromones increase flirtatious behavior and ratings of attraction
2 MIN READ
0
Results: increased flirtatious behavior and self-reported attraction
2 MIN READ
0
Conditioned sexual arousal to odor
2 MIN READ
0
Sold on the human VNO?
< 1 MIN READ
0
The Great Pheromone Myth (opinion/review)
19 MIN READ
0
Welcome to Pheromones.com
< 1 MIN READ
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An attempt to change the concept
< 1 MIN READ
0