Epigenetic algorithm accurately predicts male sexual orientation

October 8, 2015, American Society of Human Genetics

An algorithm using epigenetic information from just nine regions of the human genome can predict the sexual orientation of males with up to 70 percent accuracy, according to research presented at the American Society of Human Genetics (ASHG) 2015 Annual Meeting in Baltimore.

"To our knowledge, this is the first example of a predictive model for sexual orientation based on molecular markers," said Tuck C. Ngun, PhD, first author on the study and a at the David Geffen School of Medicine of the University of California, Los Angeles.

Beyond the genetic information contained in DNA, the researchers examined patterns of DNA methylation - a molecular modification to DNA that affects when and how strongly a gene is expressed - across the genome in pairs of identical male twins. While have exactly the same genetic sequence, environmental factors lead to differences in how their DNA is methylated. Thus, by studying twins, the researchers could control for genetic differences and tease out the effect of methylation. In all, the study involved 37 pairs of twins in which one twin was homosexual and the other was heterosexual, and 10 pairs in which both twins were homosexual.

"A challenge was that because we studied twins, their DNA methylation patterns were highly correlated," Dr. Ngun explained. Even after some initial analysis, the researchers were left with over 400,000 data points to sort through. "The high correlation and large data set made it difficult to identify differences between , determine which ones were relevant to sexual orientation, and determine which of those could be used predictively," he added.

To sort through this data set, Dr. Ngun and his colleagues devised a machine learning algorithm called FuzzyForest. They found that methylation patterns in nine small regions, scattered across the genome, could be used to predict study participants' sexual orientation with 70 percent accuracy.

"Previous studies had identified broader regions of chromosomes that were involved in sexual orientation, but we were able to define these areas down to the base pair level with our approach," Dr. Ngun said. He noted that it will take additional research to explain how DNA methylation in those regions may be related to . The researchers are currently testing the algorithm's accuracy in a more general population of men.

"Sexual attraction is such a fundamental part of life, but it's not something we know a lot about at the genetic and molecular level. I hope that this research helps us understand ourselves better and why we are the way we are," Dr. Ngun said.

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JVK
1 / 5 (4) Oct 08, 2015
http://www.hawaii...ion.html
From Fertilization to Adult Sexual Behavior

Excerpt: Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called "chromo domain" proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes... Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans ... That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
JVK
1 / 5 (4) Oct 08, 2015
Excerpt 2) 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).

It was only a matter of time until others reported on our accurate representation of biologically-based cause and effect. Why did it take them nearly 20 years?

Does anyone else not yet know that olfaction links the immune system to nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions that differentiate all cell types in all tissues of all organs and all organ systems in the context of the biophysically constrained chemistry of protein folding?

See also: Feedback Loops Link Odor and Pheromone Signaling with Reproduction http://dx.doi.org...5.09.027
showArticle Info
JVK
1 / 5 (4) Oct 08, 2015
Our colleagues from the Society for the Scientific Study of Sexuality and my colleagues from the Association for Chemoreception Sciences largely ignored the overwhelming support for our model of epigenetically effected RNA-mediated cell type differentiation in the context of RNA-directed DNA methylation.

However, this year's Nobel Prizes in Physics, Chemistry, and Physiology and/or Medicine collectively link the anti-entropic epigenetic effects of the sun's biological energy to the nutrient-dependent biophysically constrained RNA-mediated amino acid substitutions that differentiate all cell types in all living genera via DNA repair mechanisms, which are required to link sexual differentiation in yeasts to sexual differentiation of cell types in humans via protection from virus-driven entropic elasticity that would otherwise lead to genomic entropy -- the source of all virus-driven pathology in the context of mutations that perturb protein folding.
JVK
1 / 5 (4) Oct 08, 2015
See also: The Mind's Eyes: Human Pheromones, Neuroscience, and Male Sexual Preferences
http://www.sexarc...kohl.htm

The biggest issue seems to always have been the human-pheromone deniers. Although they could not link their gene-centric perspectives to biologically-based cause and effect, they did not want to learn about molecular epigenetics or anything else that linked physics and chemistry to biologically-based cause and effect.

Clearly most people will be amazed by the systems complexity but not amused that they were taught to believe in pseudoscientific theories because others were taught to believe in them and to not ask questions about where ridiculous theories come from. They come from theorists who never became serious scientists because the science of biologically-based cause and effect was too difficult for them to understand.
Vietvet
5 / 5 (2) Oct 08, 2015

However, this year's Nobel Prizes in Physics, Chemistry, and Physiology and/or Medicine collectively link the anti-entropic epigenetic effects of the sun's biological energy to the nutrient-dependent biophysically constrained RNA-mediated amino acid substitutions that differentiate all cell types in all living genera via DNA repair mechanisms, which are required to link sexual blah, blah, blah.

Another example of JVK's delusional thinking.
JVK
1 / 5 (4) Oct 08, 2015
See also: http://medicalxpr...ret.html

All that my antagonists have ever done is claim that I am delusional or ignore the published works across 20 years that clearly link biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry from microbes to man via the conserved molecular mechanisms we detailed in our 1996 review of sex differences in behavior.

No one has denied this: "...similar proteins perform functions in humans [which] suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes."

Anyone who denies that fact now will be immediately recognized as someone who is horribly biologically underinformed.
JVK
1 / 5 (3) Oct 09, 2015
The immediate response from one sex researcher includes these claims.

1) Much more research is needed before a more definite answer can be given on the role of epigenetcs in sexual orientation.

2) Seven sites were identified that are involved involved, which suggests there still may be grades of homosexuality-heterosexuality.

3) Epigenetics is environmental, and the study does not show what influence change the sites.

Food odors and pheromones cause the changes in all vertebrates via epigenetic effects on gonadotropin releasing hormone (GnRH)

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors http://www.socioa...ew/17338

See also: Human pheromones: integrating neuroendocrinology and ethology http://www.nel.ed...view.htm

Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...24693353
JVK
1 / 5 (3) Oct 09, 2015
Other researchers who consider pretending that not enough is known to separate the nonsense of their theories from facts about how sexual preferences develop should see:

Gay, Straight, and the Reason Why: The Science of Sexual Orientation by Simon LeVay.
(p. 210) "This model is attractive in that it solves the "binding problem" of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics. If all these characteristics come to be attractive because they were experienced in association with a male- or female-specific pheromone, then they will naturally go together even in the absence of complex genetically coded instructions." [cont]
JVK
1 / 5 (3) Oct 09, 2015
[cont]
Gay, Straight, and the Reason Why: The Science of Sexual Orientation by Simon LeVay.
(p. 210 - 211) "Still, even in fruit flies, other sensory input besides pheromones -- acoustic, tactile, and visual stimuli -- play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don't know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another."

I reiterate. See: See also: Feedback Loops Link Odor and Pheromone Signaling with Reproduction
http://dx.doi.org...5.09.027

Also, the sequencing of the octopus genome extended what is known from microbes to humans via what is known about microRNAs, adhesion proteins, and RNA-mediated cell type differentiation in all cell types of all individuals of all living genera.
JVK
1 / 5 (3) Oct 09, 2015
Jay R. Feierman has posted a link to this article to the International Society for Human Ethology's yahoo group. It will be interesting to see if any ISHE experts respond or any experts from other groups.

See also: Q&A: Karl Grammer http://www.nature...11a.html

Excerpt: "We believed that what applies to the scorpion fly also applies to humans. And that is how the whole thing took off."

How could the conserved molecular mechanisms of RNA-mediated nutrient-dependent protein folding biochemistry not link scorpion flies to humans? Who do these people think they are fooling with their claims about the relative salience of other sensory input to the development of sexual preferences?

See also: VIRUS EVOLUTION ( AMAZING DOCUMENTARY) https://www.youtu...04x6MvMY

Oxytocin expert, Larry Young, links viruses from prairie vole monogamy to the evolution of human heterosexual love. What about non-heterosexuals?
JVK
1 / 5 (2) Oct 09, 2015
http://www.thegua...accuracy

Excerpt: "Without validation of the result in an independent data set, it is not really possible to know whether there is any substance in this claim."

What data set was independently validated and used to support the ridiculous claims of theorists about the development of sexual orientiation during the life history transitions of species from yeasts to vertebrates?

Has anyone who is not a biologically uninformed theorist ever called this much attention to their own ignorance? How can anyone not recognize the pattern across species that links the life history transitions of the honeybee model organism to humans?

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults http://link.sprin...4-0895-5
JVK
1 / 5 (2) Oct 09, 2015
http://www.ncbi.n...15925525
Honey bees as a model for understanding mechanisms of life history transitions

http://www.ncbi.n...24693353 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Excerpt: "The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012)."

http://www.thegua...accuracy "Previous studies had identified broader regions of chromosomes that were involved in sexual orientation, but we were able to define these areas down to the base pair level with our approach."

The end to the nonsense comes with examination of chromosomal rearrangements.
JVK
1 / 5 (2) Oct 09, 2015
No one who has continued to tout their pseudoscientific nonsense based on theories about sexual orientation wants to stop touting it based on experimental evidence of biologically-based cause and effect.

See for example: "Dr Qazi Rahman, of King's College London and author of Born Gay: The Psychobiology of Sex Orientation, said: "This new study is not about a purely genetic link per se. What this suggests is that factors such as other important genes, or environmental factors, such as exposure to prenatal androgens, might affect brain development differently in twins who become straight or gay." http://www.thegua...accuracy

Where does Dr Qazi Rahman think that androgens come from? How can anyone at his level of examination not link epigenetic effects of food odors and social odors on GnRH to downstream effects on other hormones that affect behavior?
JVK
1 / 5 (2) Oct 09, 2015
I just realized that perhaps Rahman and others never learned the difference between "effect" and "affect."

Could that be the problem that has plagued sex researchers throughout the history of the theories they invented to attempt to explain sexual orientation outside the context of what is known to serious scientists?

See for example:
Correction for McEwen, Brain on stress: How the social environment gets under the skin
http://www.pnas.o....2.short

The authors note that on page 17184, right column, first paragraph, line 4, "effect" should instead appear as "affect."

My comment: Epigenetic effects on hormones are readily linked to affects on behavior in all invertebrates and vertebrates. The white-throated sparrow may be the best model of links between the epigenetic landscape and the physical landscape of DNA that include nutrient-dependent chromosomal rearrangements. http://www.pnas.o...abstract
JVK
1 / 5 (2) Oct 09, 2015
http://www.ashg.o...er.shtml
See also: PgmNr 445/T: Masculinizing gene expression and DNA methylation in XX neural stem cells and their differentiated progeny by a single exposure of testosterone: An in vitro approach of understanding hormonal organization.

Abstract excerpt: "...neonatal androgen exposure is capable of altering DNA methylation patterns in sexually dimorphic regions of the rodent brain. The methylation differences may be an early molecular explanation as to how gonadal hormones permanently alter the developing brain, through the process known as hormonal organization.

From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

Excerpt: …the nature/nurture debate is much more than simply a scientific argument. It is a clash of cultures, of ideologies and of politics.-- Robert Pool (1994)

Many sex researchers are like many politicians.
JVK
1 / 5 (2) Oct 09, 2015
Many sex researchers are not serious scientists. For an example of what serious scientists know about epigenetically-effected RNA-mediated cell type differentiation, see: Epigenetic regulation of ageing: linking environmental inputs to genomic stability http://dx.doi.org.../nrm4048

Conclusion: Reference epigenomes have transformed our understanding of transcription and have highlighted key differences in chromatin states between tissues in young individuals. To better understand the integrative changes that occur during ageing, epigenome maps throughout lifespan would be particularly helpful. Such an ageing roadmap should help to develop better strategies for delaying or reversing aspects of ageing and age-related diseases.

Extant reference genomes link the nutrient-dependent pheromone-controlled RNA-mediated physiology of reproduction in species from microbes to humans via similarities and differences in their metabolic and genetic networks.
JVK
1 / 5 (2) Oct 09, 2015
For an interesting perspective on what happens during a paradigm shift of this magnitude -- one that links the epigenetic landscape to the physical landscape of DNA via the physiology of reproduction in all living genera, see this brief video.

It helps to explain why nothing happens until long after the paradigm shift has occurred. As we have seen by the lack of comments by theorists or sexologists here, they will continue to tout pseudoscientific nonsense for up to one more generation of what might otherwise have started to become serious scientists two decades ago.

http://www.ted.co...tic_apes
JVK
1 / 5 (2) Oct 09, 2015
See also: The RNA World as a Model System to Study the Origin of Life http://www.cell.c...900681-8

Excerpt: "...a simple peptide synthetase ribozyme might evolve into an increasingly large and complex system of molecular alignment, leading to the modern ribosome. Indeed, the ribosome can be thought of as essentially an entropy 'trap' for carefully aligned substrates [199]..."

Has any other sex researcher put this entropy 'trap' into the context of an accurate representation of biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry? Protein folding links nutrient-dependent RNA-mediated amino acid substitutions to cell type differentiation in all cell types of all individuals of all living genera via the physiology of reproduction. Has anyone else mentioned that substitution of achiral glycine in the GnRH decapeptide links food odors and pheromones to biodiversity via chromosomal rearrangements?
JVK
1 / 5 (2) Oct 10, 2015
See also: The Hidden Effects of Epigenetic Discoveries
https://www.labro...d-oct28?
New discoveries uncover that exposure to current environmental, dietary, behavioral, and medical conditions can significantly affect the future development and health of an individual and their offspring. Which correspondingly means, that the development and health of an individual is influenced by past experiences of that individual's parents.

Research shows, that enriching environments offer opportunities for improved sensory, motor, cognitive, and social stimulation. This improved stimulation has a multitude of positive effects, from increasing learning and memory, to reducing the possibility of acquiring depression or many brain disorders including Huntington's diseases, Alzheimer's and stroke. In this webinar we will talk about how current investigation in Epigenetics can affect patient treatment and impacts research in general.
JVK
1 / 5 (2) Oct 10, 2015
Re: "...a simple peptide synthetase ribozyme might evolve into an increasingly large and complex system of molecular alignment, leading to the modern ribosome.

Andrew Jones suggested something similar in his thesis.

http://www.scribd...s#scribd

"The evolution of a successful RNA polymerase ribozyme is a lofty goal. ...its discovery would ... represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered."

This is the kind of pseudoscientific nonsense that's expected from a biologically uninformed science idiot, not from those who offer: "The RNA World as a Model System to Study the Origin of Life"
JVK
1 / 5 (2) Oct 10, 2015
In the context of their published work: the RNA world is theoretical.
http://dx.doi.org...5.06.016

In Criticisms of the nutrient-dependent pheromone-controlled evolutionary model http://www.ncbi.n...4049134/ Jones claimed:

"Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research."

Let's compare my model, which integrates two anti-entropic traps and links the 1) sun's biological energy to RNA-mediated nutrient-dependent cell type differentiation via de novo gene creation and 2) the epigenetically effected physiology of reproduction to cell type differentiation in all living genera.

Whose model is sloppy? The one that starts with experience-dependent biophysically constrained de novo gene creation, or the one that starts with a model system?

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