Indirect genetic effects (IGEs), associative effects and extended phenotypes


Beyond the Blueprint

In addition to serving as a set of instructions to build an individual, the genome can influence neighboring organisms and, potentially, entire ecosystems.

By Mark A. Genung, Jennifer A. Schweitzer, and Joseph K. Bailey | September 1, 2014

Excerpt: “…indirect genetic effects (IGEs), also called associative effects or extended phenotypes, are common and have profound implications for evolution. Beyond learning and behavior in social species, IGEs affect how organisms develop, how productive plants are, and whether individuals are attacked by predators, herbivores, and disease.”

My comment: Epigenetically-effected extended morphological and behavioral phenotypes link olfactory/pheromonal input from the conserved molecular mechanisms of nutrient-dependent changes to amino acid substitutions that differentiate the cell types of all cells in all ecologically-adapted species. Attempts to portray biologically-based cause and effect as if  “…indirect genetic effects (IGEs), also called associative effects or extended phenotypes, are common and have profound implications for evolution” would fail miserably if students learned how ecological variation leads to ecological adaptations in species from microbes to man. Instead of learning about ecology, UT Knoxville students are being taught to believe in the pseudoscientific nonsense of neo-Darwian evolutionary theory.

I have attempted to clarify the problem in a series of comments but, so far, no one else has responded to this article. Here are my comments:


Three published reviews link what was known about molecular epigenetics in 1996 to nutrient-dependent amino acid substitutions that differentiate cell types and to the pheromone-controlled physiology of reproduction in species from microbes to man via conserved molecular mechanisms of alternative splicings of pre-mRNA. Nutrient-dependent/pheromone-controlled adaptive evolution: a model. (2013) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. (2012) From fertilization to adult sexual behavior. (1996)

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Evolutionary models lack experimental evidence of evolutionary events that are required to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.

It is time to examine evidence that attests to the biologically-based cause of cell type differences in all cells of all tissues in all organs of all organisms and to stop claiming that the differences in morphological and behavioral phenotypes “evolved.”

Ecological variation leads to nutrient-dependent pheromone-controlled ecological adaptations manifested in biodiversity. There are too many model organisms that exemplify that fact. Evolutionary models must either include events associated with cell type differentiation or the models will only continue to add theories to theories all the while the evolutionary models dismiss experimental evidence of biologically-based cause and effect.


Re: “Evolutionary models must either include events associated with cell type differentiation…”

Two companion papers have done what evolutionary theorists have not done. See:

1) Altered proteostasis in aging and heat shock response in C. elegans revealed by analysis of the global and de novo synthesized proteome

2) Bio-orthogonal labeling as a tool to visualize and identify newly synthesized proteins in Caenorhabditis elegans

The de novo Creation of proteins via nutrient-dependent amino acid substitutions is antithetical to claims that mutations and natural selection somehow lead to the evolution of biodiversity. Indeed, claims that link auditory input to “…indirect genetic effects (IGEs), also called associative effects or extended phenotypes…” fail to link nutrient-dependent cell type differentiation to behavioral phenotypes.

We are left with examples of nutrient-dependent morphological phenotypes that appear to have somehow evolved  in the absence of pheromone-controlled behavior. So far as I know, there is no model for that.

I encourage comments from theorists who think there is experimental evidence of biologically-based cause and effect that supports their beliefs. Support for my model includes evidence from crickets that links ecological variation to biodiversity via cell type differentiation of mandibles and genitalia:

“Differentiation in the mandibles and male genitalia (figure 2) is quantified and used as a proxy for the presence of divergent selection 7. Studies on the functional morphology of insect mandibles have identified their ecological relevance 20, including in Orthoptera more generally, where their chewing ability appears to be under selection 21. Likewise, genitalia are a good proxy for sexual selection 13; genitalic characters not only show species-level divergence in Amphiacusta but have also been shown to mediate reproductive success in other taxa 13,14.” — Ecological selection as the cause and sexual differentiation as the consequence of species divergence?

In yeasts and nematodes, sexual differentiation of cell types is clearly nutrient-dependent and pheromone-controlled. It would be extremely unusual if the conserved molecular mechanisms of cell type differentiation that we detailed in our 1996 Hormones and Behavior review did not extend from what is known about yeasts, flies, and nematodes to what is known about primates.


The Erotic Endurance of Whale Hips

Excerpt: “Over the course of about ten million years, the ancestors of today’s whales moved into the water. They evolved seal-like bodies with stout limbs; later, their forelegs became flippers and their hind legs dwindled away. They lost their fur and their nostrils migrated from the tip of their head to above their eyes, where it became a blow hole. (I wrote about this transition in my book At the Water’s Edge.)”

These are the transitions attributed to evolution by theorists who typically seem to think in mutations and natural selection the leads to the evolution of biodiversity. However, science journalists who write about such transitions refuse to acknowlede what is known by serious scientists. See, for example:

A universal trend of amino acid gain and loss in protein evolution Excerpt: “We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.”

The universal trend argues against evolutionary events that Zimmer continues to report as if experimental evidence of biologically-based cause and effect supported his misrepresentations. Clearly, “Ecological variation is the raw material by which natural selection can drive evolutionary divergence 1–4.”

However, nutrient uptake does not typically result in mutations. That is why mutations cannot be linked to evolutionary events. Anyone who understands the difference between effects of perturbed protein folding in diseases and disorders can compare the effects to epigenetic effects on amino acid substitutions that stablize protein biosynthesis and the DNA of organized genomes in species from microbes to whales.


Re: “Ecological variation is the raw material by which natural selection can drive evolutionary divergence 1–4.”

DNA might have initially evolved for the purpose of storing phosphate, and the various genetic benefits evolved later,”

If ecological variation drives ecological adaptations manifested in morphological and behavioral phenotypes, biodiversity arises via the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to man.

It does not seem biologically plausible for DNA to evolve and for various genetic benefits to evolve after genes evolved. The problem is one of cell  type differentiation, which appears to be nutrient-dependent because the role of amino acid substitutions in cell type differentiation extends to self vs non-self recognition in species from yeasts to mammals.


Quote James V. Kohl

…the role of amino acid substitutions in cell type differentiation extends to self vs non-self recognition in species from yeasts to mammals.

Article excerpt: “To identify potential mates, female crickets listen with ears on their forelegs to the males’ songs, produced by the rubbing together of their forewings.”

Evidently, this pseudoscientific nonsense is being taught to biology students attending college at UT Knoxville. If so, I wonder if the students are being taught about the physiology of reproduction.

All invertebrates identify potential mates via the nutrients they ingest because the nutrients are metabolized to species-specific pheromones that vary with sex differences and all other cell type differences in species from yeasts to mammals. In our 1996 review, we wrote:

“Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).”

Are biology teachers at other universities still teaching pseudoscientific nonsense that defies accurate representations of biologically-based facts like this: “The diverse social behaviors that are enabled by the functional flexibility of the secrete-and-sense circuits (Fig. 5C) may explain the frequent occurrence of this class of circuits in nature.

What are your descendants being taught to believe by biology teachers who were taught to believe in neo-Darwinian theory? “ What Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. No, it wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.

It’s time that biological facts were taught as fact!

Quote James V. Kohl

…the role of amino acid substitutions in cell type differentiation extends to self vs non-self recognition in species from yeasts to mammals.


Why I am the only person commenting on the ridiculous assertions in this artcle? Do students at UT Knoxville know their professors are teaching evolutionary theory as if it could be linked by biologically-based cause and effect to ecology? Do their professors known the difference between theories and biological facts? Do the students discuss what they expect to be taught about biology and ecology by their professors?

For example: “…rearing larvae on an artificial diet containing different concentrations of the crude alkaloid extract decreased pupal viability and adult size in a concentration-dependent manner.

In crickets and flies, that fact can be epigenetically linked to nutrient-dependent differences in the morphology of male genitalia via the conserved molecular mechanisms of pheromone-controlled reproduction in species from microbes to man. That fact might help students understand the rather obvious nutrient-dependent link to ecological adaptations manifested in the genital morphology of all species that  reproduce via internal fertilization.

For examples, see: From Fertilization to Adult Sexual Behavior, which links what was known about the nutrient-dependent molecular epigenetics of alternative splicings of pre-mRNA to sex differences in cell types that are manifested in sex differences in morphology and behavior.

The nutrient-dependent pheromone-controlled sex differences in cell types exemplify how the epigenetic landscape is linked to the physical landscape of DNA by fixed amino acid substitutions in the organized genomes of all species. See for example, what’s known about flies. Rapid Divergent Evolution of Male Genitalia Among Populations of Drosophila buzzatii.

Are UT Knoxville students permitted to ask their professors why sexual selection for divergence in male genitalia appears to occur too quickly to be attributed to mutations, natural selection, and the evolution of biodiversity? If not, they may never learn why the theory of evolution is now being taught in Israeli middle-schools: “…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

If UT Knoxville students do not learn about the differences between what’s known about how ecological variation leads to ecological adaptations and how evolutionary theories misrepresent those facts, they may never learn how to compare what’s known about molecular epigenetics to the pseudoscientific nonsense represented in reports of studies based on population genetics. The problem for our descendants is that another generation of researchers will not be as productive as those taught to ignore ridiculous theories and focus on what they learn about ecology.

Conclusion: “Specifically, we show how miRNAs of the miR-106b-25 cluster, involved in the inhibition of several apoptotic pathways can be differentially expressed.

Nutrient dependent miRNAs that inhibit apoptosis may be important links from ecological variation to ecological adaptations. If so, biological facts could be compared to what UT Knoxville students are taught about how evolutionary theory links the sounds that male crickets make to nutrient-dependent pheromone-controlled ecological adaptations. Biological facts might then also limit what UT Knoxville students are willing to believe about evolutionary theories.  But perhaps all the UT Knoxville biology students are silently preparing to move to Israel to learn more about accurate representations of biologically-based cause and effect. If so, they will already be several years behind students who have been taught the difference between theories and biological facts from the time they start middle-school.

About James V. Kohl 1308 Articles
James Vaughn Kohl was the first to accurately conceptualize human pheromones, and began presenting his findings to the scientific community in 1992. He continues to present to, and publish for, diverse scientific and lay audiences, while constantly monitoring the scientific presses for new information that is relevant to the development of his initial and ongoing conceptualization of human pheromones. Recently, Kohl integrated scientific evidence that pinpoints the evolved neurophysiological mechanism that links olfactory/pheromonal input to genes in hormone-secreting cells of tissue in a specific area of the brain that is primarily involved in the sensory integration of olfactory and visual input, and in the development of human sexual preferences. His award-winning 2007 article/book chapter on multisensory integration: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences followed an award winning 2001 publication: Human pheromones: integrating neuroendocrinology and ethology, which was coauthored by disinguished researchers from Vienna. Rarely do researchers win awards in multiple disciplines, but Kohl’s 2001 award was for neuroscience, and his 2007 “Reiss Theory” award was for social science. Kohl has worked as a medical laboratory scientist since 1974, and he has devoted more than twenty-five years to researching the relationship between the sense of smell and the development of human sexual preferences. Unlike many researchers who work with non-human subjects, medical laboratory scientists use the latest technology from many scientific disciplines to perform a variety of specialized diagnostic medical testing on people. James V. Kohl is certified with: * American Society for Clinical Pathology * American Medical Technologists James V. Kohl is a member of: * Society for Neuroscience * Society for Behavioral Neuroendocrinology * Association for Chemoreception Sciences * Society for the Scientific Study of Sexuality * International Society for Human Ethology * American Society for Clinical Laboratory Science * Mensa, the international high IQ society