The Biology of Sex, Sexual Orientation, and Gender Identity

And why the homophobes are wrong

Jb Cabret
The Startup
8 min readJun 15, 2020

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Discrimination and abuse are not new to queer or nonbinary people and the homophobe’s argument is always “being gay is unnatural.” That is actually unscientific. This post summarizes what science has to say about the spectrum of sexual orientation and gender identities.

Photo by daniel james on Unsplash

Before we dive deeply into the topic, let us define some key terms first.

What is sex?

Sex refers to a set of biological characteristics in humans and animals and is primarily associated with chromosomes, gene expression, hormone levels and function, and reproductive or sexual anatomy (Canadian Institutes of Health Research, 2015). In humans, sex is classified into three types namely, male, female, and intersex.

What is intersex?

Intersex is a term used to describe individuals born with any of several variations in sex characteristics including chromosomes, gonads, sex hormones, or genitals that do not conform with the typical Male/Female bodies (Dreger, 2001; UN Commission on Human Rights, 2016).

What is sexual orientation?

Sexual orientation is an enduring pattern of romantic or sexual attraction to persons of the opposite sex or gender, the same sex or gender, or to both sexes or more than one gender (American Psychological Association, 2013). It is a complex trait that is shaped by multiple genes, biological, environmental, and sociocultural influences (Hamer, Rice, Risch, & Ebers, 1999).

The following are the common classifications of sexual orientation: heterosexual, homosexual, asexual, and bisexual.

What is gender identity?

Gender identity is the personal sense of one’s gender which may correlate with assigned sex at birth or can differ from it (Webb & Safer, 2019). One’s gender identity may or may not be similar to their sexual orientation.

The following are a few types of gender identities: male, female, transgender, fluid, nonbinary, gender-neutral, agender, genderqueer, and two-spirit. These examples of gender identities may or may not match one’s gender expression because of its variability or fluidity.

Shutterstock

The biology of sex

In the heteronormative world, sex is classified based on chromosomes and reproductive or sexual anatomy (Canadian Institutes of Health Research, 2015). If a person conforms to the characteristics known to a specific sex, they are assigned to that sex. However, the characteristics that serve as the bases for identifying a person’s sex are often the primary and secondary sex characteristics.

Primary sex characteristics include the development of internal and external sexual organs — the characters that are present at birth and are determined by the influence of chromosomes (e.g., penis, testes, vagina, ovaries)(Reid, 2018).

Secondary sex characteristics are the attributes that typically develop in adolescence such as facial hair, pubic hair, height, broad chest and hips, hormones, and even the anteroventral periventricular nucleus (AVPV) in the hypothalamus that determine sexual dimorphism in organisms.

Anteroventral periventricular nucleus (AVPV) in the hypothalamus of mouse brain. Photo by Evan Oto/Science Source

These sexual characteristics that appear in the entire human population can be statistically represented through a simple bimodal distribution graph.

Photo by Robert D. Martin, PhD on Psychology Today

Statistically, the curve will show that the biological characters do not appear in binary. Instead, the primary and secondary sexual characteristics show a bimodal pattern.

This curve also takes into consideration the people who are assigned female at birth although they have XY sex chromosomes.

Therefore, sex can be thought of as a spectrum where each part of the curve represents a varied set of primary and secondary sex characteristics. At two discrete points, the primary and secondary sex characteristics conform to the traditional definition of a male and female, while in the middle, the characteristics overlap creating the third sex, intersex (Griffiths, 2018).

Photo by Organisation Intersex International Australia, CC BY-SA 3.0

In the medical field, intersex is now termed as a Disorder of Sex Development (DSD) to move away from the taxonomies of hermaphroditism (Griffiths, 2018). Currently, DSD is defined as congenital conditions in which development of chromosomal, gonadal, or anatomical sex is atypical.

Publications that deal with DSD often include the widely known Turner and Klinefelter’s syndromes.

In humans, the X and Y chromosomes determine a person’s sex: most women are 46XX and most men are 46XY. However, new publications suggest that in a few births per thousand some individuals will be born with a single sex chromosome (45X or 45Y) (sex monosomies) and some with three or more sex chromosomes (47XXX, 47XYY or 47XXY, etc.) (sex polysomies).

Karyogram of human male. Photo by National Human Genome Research Institute

Moreover, there are males who are born 46XX and some females who are born 46XY due to the translocation of the sex-determining region Y (SRY) gene on the Y chromosome (World Health Organization, n.d.).

Cytogenetic Location of SRY gene: Yp11.2

The SRY gene

The SRY gene is an intron-less sex determining gene on the Y chromosome in placental mammals and marsupials (Wallis, Waters, & Graves, 2008) that is responsible for the initiation of male sex determination in humans. In humans, the gene is in the short arm of the Y chromosome at position 11.2 (Yp11.2).

The SRY gene produces a DNA-binding protein (gene-regulatory protein/transcription factor) that determines the sex of embryos in the sixth week of fetus formation (Berta, et al., 1990).

PBB Protein SRY image

Since the protein is a transcription factor, it binds to specific regions of DNA and helps inhibit the activity of genes that develop female anatomical structures and promote testis development (Mittwoch, 1988; Genetics Home Reference, 2015).

Cellular mechanism of SRY function. Photo by Kenichi Kashimada and Peter Koopman

Often, when a developing sperm cell undergoes crossover during its meiosis, the SRY gene stays on the Y chromosome. If it is transferred to the X chromosome, however, the resulting Y chromosome will not have an SRY gene and can no longer initiate testis development. Offspring which inherits this Y chromosome will have Swyer syndrome, characterized by an XY karyotype and a female phenotype. Offspring who inherit this X chromosome will have a condition called XX male syndrome, characterized by an XX karyotype, and a male phenotype (Margarit, et al., 2000).

Some examples of translocated SRY gene

Role of non-coding RNAs to sex development

Aside from coding genes, there are also non-coding RNAs that play a role in male sex determination.

A research conducted by Rastetter, Smith, and Wilhelm (2015) showed that different classes of non-coding RNAs (ncRNAs) are important in all developmental and physiological pathways of sex determination. This also means that gene expression is highly regulated at the molecular level.

Putative regulation of Sox9 expression by ncRNAs. Photo by Rastetter, Smith, and Wilhelm

The biology of sexual orientation and gender identity

In a report by Hamer, Rice, Risch, and Ebers (1999), a locus at the q28 region of the X chromosome was found to be involved in male sexual orientation in some, but not all, individuals.

The human X chromosome with Xq28 (green) located at the tip of the long arm of the chromosome.

The Xq28 hypothesis was formulated from a family pedigree analysis that revealed that gay men had more homosexual male relatives through maternal than through paternal lineages and that gay male siblings had significantly increased sharing of Xq28 DNA markers.

More recent studies have suggested that the differential heritage through the matriarchal lineage could also be the result of epigenetic modifications of the expression of genes located on several other chromosomes (Ngun, Ghahramani, Sanchez, Bocklandt, & Vilain, 2011; Bocklandt & Vilain, 2007).

Comparison of four studies of linkage between alleles on the X chromosome and male homosexuality.

Contrary to the report of Hamer, Rice, Risch, and Ebers, a recent genome-wide association study (GWAS) published by Ganna, et al. (2019), the largest study on homosexuality of the decade, reported that a single “gay gene” (Xq28) from the X chromosome is not responsible for homosexual traits.

Instead, five autosomal loci are much more related to same-sex sexual behavior indicating that it is polygenic.

A genome-wide association study (GWAS) of same-sex sexual behavior reveals five loci and high polygenicity.

Another study conducted by Rice, Friberg, and Gavrilets (2012) showed that homosexuality is affected by fetal androgen signaling and gene regulation or epigenetic changes.

The authors argued that sex-specific epigenetic modifications (epi-marks) cause reduced androgen sensitivity in XX fetuses and enhanced sensitivity in XY fetuses. This means that hormones affect the expression of phenotypes in the offspring leading to the common hormonal and neurological variations among homosexuals.

Fetal androgen signaling and gene regulation are also used to explain the brain development of transgender individuals.

In a 2014 study by Fernández, et al., the defeminization of female-to-male transgender men is caused by either insufficient estrogen production or poor (estrogen receptor β) receptor sensitivity during fetal development.

Insufficient feminization in transgender male

In a similar study published in 2000, it was found that the brain structure of transgender women is resemblant to that of cisgender women. The researchers studied the neuronal difference in the bed nucleus of the stria terminalis (BSTc) among cisgender men, cisgender women, and male-to-female transgender women and found that transgender women and cisgender women have a similar number of neurons in the BSTc.

The difference in the bed nucleus of the stria terminalus (BSTc) among cisgender man, cisgender woman, and transgender woman.

Although there is a rapidly growing literature that validates the underlying biology of transgender men and women, they still face the worst forms of discrimination compared to the other members of the LGBTQ+ community. Between 2007 and 2014, the Trans Murder Monitoring Project recorded 1,731 murders of transgender people globally (Human Rights Watch, 2016).

It’s 2020, yet the world is still far from fully protecting the rights of queer and transgender people. Most cisgender men and women, even the LGBTQ+ allies, lack the scientific information about being queer. The only way to improve this is by making all the information available to everyone, no matter how demanding this may sound to others.

Being queer is not a lifestyle. It’s biological.

There is not enough safe space to discuss sexuality and gender identity. We need more. And we need it now.

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Jb Cabret
The Startup

I'm a graduate student studying fungal systematics and plant pathology at the University of the Philippines Los Baños. Filipino / Non-binary