Sex, Gender, Genome and Hormones: Part I

Steve Vigdor, February 13, 2022

I. introduction

There is probably no area of science relevant to public policy that is subject to a greater diversity of misconceptions and denial than the biology of sex and gender. The misconceptions run across many parts of the political spectrum. Social conservatives believe that a person’s sex is determined by their genitals at birth, and that gender identity and sexual orientation are personal choices subject to change. Liberal trans activists and many young people insist that gender is a social construct, rather than biologically determined, and they are supported in this by a number of social scientists. These groups have identified such a proliferation of gender types as to render the term “transgender” practically meaningless. Many feminists insist that male and female brains are identical. Transgender female athletes claim that their athletic abilities are the same as those of birth females. But the biological sciences provide evidence that each of the above perceptions is incorrect.

Figure I.1. The four aspects of sex, sexuality, and gender in humans.

The science and the social controversies center on the four distinct, but related, categories represented in Fig. I.1. Biological sex is determined by the reproductive organs, ovary capable of producing eggs in females and testis producing sperm in males. Gender identity resides in the brain, but in ways also determined by genetics and epigenetics – the impacts of environment on gene expression, here, the influence of hormone exposure on brain development in the womb, just after birth, and through puberty. Because the reproductive organs and the brain are developed in different stages of pregnancy, with distinct influences, it is entirely possible for gender identity to differ from biological sex. Sexual orientation, though represented by the heart in Fig. I.1, appears also to be determined during brain development. Gender expression – how one presents oneself in appearance and behavior to the outside world or in private – is an individual choice with influences from gender identity and sexual orientation.

As suggested in Fig. I.1, sex and gender identity are not absolutely binary. For example, in rare cases an individual’s genitals at birth do not match their reproductive organs, leading to an incorrect designation of sex on birth certificates. The deviations from male and female in both sex and gender identity are interesting subjects of active ongoing scientific research. But scientifically they represent a considerably smaller percentage of individuals than suggested by recent upsurges in teenagers declaring themselves as “non-binary” or presenting themselves at clinics to treat gender dysphoria – the psychological distress that results from an incongruence between one’s sex assigned at birth and one’s gender identity.

The misconceptions about sex and gender fuel passionate public controversies. The gay rights movement has made considerable progress during the present century, culminating in the approval of same-sex marriages in the U.S. and other countries. But the rapidly growing incidence of individuals who self-identify as “transgender,” though they may be only at very early or intermediate stages of actually transitioning, has led to vigorous public debates about transgender rights, sparked by policy controversies concerning bathroom use, prison assignments, and sports participation. In addition, there are vigorous ongoing debates regarding the proper treatment of children with gender dysphoria. While I will discuss these controversies and the science relevant to them in Part II of this post, I focus first on what current research tells us about sex and gender in the age of DNA sequencing and functional MRI brain scans.

While these issues are far from my personal specialization, I have tried to learn about the state of research on sex and gender topics. Among a number of good sources for lay audiences are the book The End of Gender by Debra Soh, the article Neurobiology of Gender Identity and Sexual Orientation by C.E. Roselli, a series of articles on The Conversation by Jenny Graves (here, here, here and here), and the review article Untangling the Gordian Knot of Human Sexualityby Marianne J. Legato. The latter article appears in a new research journal called Gender and the Genome (see Fig. I.2), which Legato launched in 2017 to cover a burgeoning field. Beyond these, I have consulted a significant number of research articles dealing with specific topics described in this post.

Figure I.2. The cover of the new research journal Gender and the Genome.

Part I of this post deals with: the science of genetic origins of male-female differences and of various intersex conditions; differences between male and female brains; and current research into the biological origins of gender dysphoria. In Part II, I deal with: research into the biological origins of homosexuality; the stages of gender transitioning, especially for children; public controversies over transgender rights; and a brief summary of both parts of the post.

II. the Genetic origins of sex: male-female differences

The human genome consists of 23 pairs of chromosomes. The number of base pairs and of protein-coding genes on each of these is shown in Fig. II.1. An individual’s biological sex is determined by the X and Y chromosomes: females have two X chromosomes, while males have a single X and a single Y. When chromosomes from the two parents are combined in a fertilized egg, the mother can only contribute an X, while the father contributes either an X for a daughter or a Y for a son.

Figure II.1. The number of base pairs (divided by 100,000 in the blue bars) and of protein-coding genes (orange bars) on each human chromosome.

As seen in Fig. II.1, the Y chromosome is a pipsqueak, containing only 45 protein-coding genes, far fewer than for any other chromosome. Why is it so short? David Page and his research team at the Whitehead Institute of MIT have tracked the Y chromosome back over hundreds of millions of years by analyzing the sex chromosomes in a variety of mammals populating evolutionary branches that separated in sequential stages from the one leading finally to human evolution. 200 million to 300 million years ago, the Y chromosome appears to have shared some 600 genes with the X. But it shrunk in stages to its present length, which appears to have been stable over the past 25 million years.

Siddhartha Mukherjee speculates that the shrinkage has occurred because the Y is “the most vulnerable spot in the human genome.” The vulnerability arises because it is the one chromosome which is never paired with a duplicate. When breaks or other errors occur occasionally during DNA replication, most chromosomes can use a homology-directed repair mechanism to repair the error by copying the matching section from its paired chromosome. (This feature facilitates the design of gene drives to introduce engineered DNA changes throughout a population, as we have reviewed elsewhere on this site.) This repair mechanism is unavailable to the Y. According to Mukherjee, “The Y is thus pockmarked with the potshots and scars of history…As a consequence of this constant genetic bombardment, the human Y chromosome began to jettison information millions of years ago. Genes that were truly valuable for survival were likely shuffled to other parts of the genome where they could be stored securely; genes with limited value were made obsolete, retired, or replaced; only the most essential genes were retained.

In fact, only 10 of the 45 genes on the human Y chromosome do not have a counterpart on the X. In addition, there are three Y genes that have similar copies on the X but have mutated to acquire male-specific properties, such as sperm production. In addition to these 13 male-specific genes, there are 150 X genes that may contribute to some male-female differences, such as susceptibility to certain diseases. What distinguishes those 150 X genes from all the other X genes is that those 150 escape a process known as X chromosome inactivation, which acts in females to silence the expression of most genes on one of the two X chromosomes. These particular 150 genes can then be expressed twice in females but only once in males. According to Jenny Graves, there are thus a total 163 X or Y genes that “are either male-specific, or are active in different doses in men and women.”

The most critical Y gene in sex determination, labeled SRY, is the one that determines that an embryo with XY chromosomes will, under ordinary circumstances, develop as a boy. In male embryos the presence of SRY “kick-starts a cascade of dozens of genes that are either turned on in male embryos or turned off in female embryos during testis or ovary development. Most of these [kick-started] genes are not on sex chromosomes. But they are turned on to different extents – or at different times or in different tissues – in males and females.”

One of the critical genes activated by SRY in the embryo is SOX9, found on human chromosome 9. SOX9 codes a protein that regulates the activity of other genes, particularly those that influence skeletal development and testis rather than ovary development, including the gene that produces the AMH hormone. In the male embryo AMH causes the deterioration of the so-called Müllerian ducts, which would otherwise develop into the female reproductive tract: fallopian tubes, uterus, the uterine cervix, and the upper end of the vagina. The critical role of SOX9 expression is illustrated in Fig. II.2. A competing set of genes, triggered by DAX1 on the X chromosome, lead to ovary development in XX embryos.

Figure II.2. The expression (via SRY activation, left) or suppression (right) of the SOX9 gene is critical to the formation of reproductive organs and sex determination in the embryo. Proteins and estrogen receptors critical in maintaining SOX9 suppression in females are indicated.

While the AMH hormone suppresses the formation of the female reproductive tract, other hormones – testosterone and its derivative dihydrotestosterone (DHT)– trigger the development of the male reproductive system in the embryo. The secretion of these male sex hormones, called androgens, begins after formation of the testes at about 7 weeks of embryo development in the womb. As explained by C.E. Roselli, “The female reproductive tract in the embryo develops in the absence of androgens and later matures under the influence of hormones produced by the ovary, in particular oestradiol.” The exposure to testosterone in utero and just past birth leads to systematic differences in the development of the body, the brain, and behavior of males and females. Jenny Graves: “Androgens turn on hundreds (maybe thousands) of genes that determine male genitalia, male growth, hair, voice and elements of behaviour.” Debra Soh point out that “In a 2016 study in Nature’s Scientific Reports, researchers at the University of California, Los Angeles found that testosterone exposure alters the programming of neural stem cells responsible for brain growth, leading to differences between the sexes before the brain has finished developing in utero.”

We will survey in section IV some of the differences between male and female brains, which begin in the womb under the influence of testosterone exposure. Roselli: “The times when testosterone triggers brain sexual differentiation in different species correspond to periods when testosterone is most elevated in males compared to females…in humans, the elevation in testosterone occurs between months 2 and 6 of pregnancy and then again from 1 to 3 months postnatally…In humans, the genitals differentiate in the first trimester of pregnancy, whereas brain differentiation is considered to start in the second trimester. Usually, the processes are coordinated and the sex of the genitals and brain correspond. However, it is hypothetically possible that, in rare cases, these events could be influenced independently of each other and result in people who identify with a gender different from their physical sex.”

Biologically, sex is determined by the presence of the testis to produce sperm or the ovary to produce eggs for sexual reproduction. This aspect of an individual is permanent and unchanging. It is usually matched by a baby’s genitals, though we will explore some intersex conditions in section III where this is not the case. During the Trump administration the Department of Health and Human Services proposed in a 2018 draft memo “to establish a legal definition of whether someone is male or female based solely and immutably on the genitals they are born with.” Like many attempts by federal agencies under Trump, this attempt is at striking odds with the known science. Individuals whose gender identity differs from their biological sex may decide eventually to undergo gender reassignment surgery. This procedure used to be colloquially called a “sex change operation,” but it does not alter biological sex, even though it may change genitalia.

III. intersex conditions

The processes described in the preceding section refer to the normal development of male and female embryos. Roughly 1% of humans are affected by some form of biological intersex condition, where chromosomal, genetic or hormonal anomalies lead to anatomical and physiological development at odds with the reproductive cells (eggs or sperm) their embryos develop.  As explained by Marianne Legato in Untangling the Gordian Knot of Human Sexuality, some of these conditions arise from errors in sex chromosome pairing, e.g., XO (Turner syndrome, single X but no Y) or XXY (Kleinfelter syndrome). In the former case, the child has female internal and external structures, but impaired ovarian development, leading to limited development at puberty and infertility. In the latter case, the child has male internal and external structures, but low testosterone, some female physiological characteristics, and infertility.

Very rarely (about once per 20000 or 30000 males) there are males with two X chromosomes, but a small piece of DNA from the Y chromosome, including the SRY gene, is accidentally transferred to the X chromosome during meiosis (here, the formation of sperm cells from the father). This condition leads to a male with small testes, low testosterone, and infertility.

Some conditions aborting the development of testes arise from mutations or deletions in the genes that contribute to normal male development. According to Legatomutations in SRY produce 10% of sex reversal, while deletion of the SOX9 gene produces male to female reversal in humans. Conversely, duplication or over-expression of SOX9 can cause female-to-male sex reversal.”

Other intersex conditions arise from anomalies in hormone secretion in utero. For example, chromosomal (XX) female embryos with congenital adrenal hyperplasia (CAH) are exposed to too much testosterone in the womb and are born with male or ambiguous genitalia and often masculine physical and neurological attributes, despite having ovaries that produce eggs. On the other hand, Dessens et al. have found that “The large majority (94.8%) of the [CAH] patients raised female (N=250) later developed a gender identity as girls and women and did not feel gender dysphoric.” Some girls with androgen insensitivity have XY chromosomes and male internal organs, but their body can’t respond to testosterone, and thus they appear feminine.

Debra Soh describes another anomaly especially prevalent among some boys (guevedoces) in a remote location in the Dominican Republic. These boys have XY chromosomes and testes, but they appear feminine until puberty, because they suffer from a deficiency of the enzyme 5-alpha-reductase, which “normally converts testosterone into dihydrotestosterone (DHT), which masculinizes the body in the womb and leads to the development of male genitalia. For boys with 5-alpha reductase deficiency, the lack of DHT disrupts this growth. It is only when testosterone is produced by the body at puberty that virilization occurs, leading to the growth of a penis and scrotum, a deepening of the voice, an increase in muscle mass, and hence, the change from female to male.” The greater prevalence of this condition in a remote location in the Dominican Republic suggests that the condition is heritable, and therefore genetic in origin.

The chart in Fig. III.1 summarizes the types of intersex condition, their effects at birth and at puberty, and possible treatments. The chart is too dense to read easily at the size we can reproduce it, so interested readers are referred for more details to the 2017 Scientific American article in which the chart appeared.

Figure III.1. A chart summarizing the variety of intersex conditions and their effects at birth and at puberty. The chart is reproduced from a Scientific American article.

Intersex conditions often lead to an incorrect assignment of sex on birth certificates, which is normally chosen according to the appearance of genitals. In several U.S. states parents now have the legal option to designate sex on birth certificates as “X” rather than “male” or “female” to accommodate the occurrence of intersex newborns. It also makes sense that individuals who learn of their intersex condition later in life be given the right to legally change the sex assigned at birth if it disagrees with the sex they identify with. Some intersex individuals may later identify as transgender, but they account for a small fraction of transgender individuals. Most (but not all, as we will see later) people who transition do it as the ultimate treatment for gender dysphoria, and gender identity and gender dysphoria arise mostly in the brain, rather than in the anatomy and physiology, as is characteristic of intersex conditions.

IV. differences between male and female brains

As described in section II, the masculinization of the human brain begins during the surge of testosterone experienced in the womb in the second trimester of pregnancy. Male brain development is also influenced by estrogen because an enzyme, aromatase, converts the testosterone that surges around the time of birth of a boy into oestradiol, an estrogen. The areas of the brain that are affected by these hormone surges, and that therefore differ on average between males and females, are called sexually dimorphic. The differences show up in both grey matter, where the brain’s processing is done, and white matter, which provides the communications between different parts of the brain and between the brain and the body. The white matter is so-called because it contains many nerve fibers or neurons that are sheathed in the white fatty insulating protein called myelin.

For example, neuroimaging studies on many men and women have exposed differences in the size and interconnectivity of various brain sections between men and women. Debra Soh points out that “Research investigating white matter connections (or connective tissue) in the brain has also demonstrated differences, showing that men had a greater number of white matter connections running from the front to the back of the brain, while women had a greater number of connections running between the two hemispheres.” This difference is illustrated in Fig. IV.1.

Figure IV.1. An illustration of the differences in white matter connecting various parts of the human brain between typical men and typical women. Basic impacts of these differences are described in the figure.

Structural and processing differences between typical male and female brains are summarized in Figs. IV.2 and IV.3. Soh speculates about the likely evolutionary origin of these biological differences in brain structure and function: “Women, who are tasked with the role of bearing children, evolved to be more sociable, empathic, and people-focused, while men, as hunter-gatherers, were rewarded for strong visuospatial skills and the ability to build and use tools.”

Figure IV.2. An indication of the major structural differences between typical male and female brains.
Figure IV.3. Some of the processing differences caused by differences in grey and white matter between typical male and female brains.

The average differences induced by hormone exposure in physiology, neurology, and brain structure and functioning give rise to the average differences that are normally, culturally associated with masculinity and femininity. However, biological variations in genes and hormone exposure among individuals also give rise to wide variations in physiology, neurology and brain function among members of a given sex. Thus, there are more masculine women (still women because they produce eggs) and more feminine men (who still produce sperm). We believe that those deviations from the average are also determined biologically and can affect gender identity, as we will explore in the next section. In severe cases, they may lead to gender dysphoria. Even when an individual still identifies as a gender conforming to their biological sex, they may exhibit gender-nonconforming behavior: styles of dress or hair, tomboy or “sissy” characteristics, predilections for sports, arts or professions atypical of their gender. Soh says: “from a scientific perspective, women who are gender-atypical, like myself, were likely exposed to higher levels of testosterone in utero. This can occur due to a variety of factors, including normal variation, young maternal age, maternal weight gain, genetic conditions, and hormonal treatment during pregnancy.”

V. the origins of gender dysphoria

Gender dysphoria:

The diagnosis of gender dysphoria in children and adults is guided by the Diagnostic and Statistical Manual of Mental Disorders (DSM-5): “To receive a diagnosis, a person must express a strong and persistent cross-gender identification for more than six months, a persistent discomfort with his or her sex or sense of inappropriateness in the gender role of that sex, and the experience must cause clinically significant distress or impairment in social, occupational, or other important areas of functioning.” Treatment for gender dysphoria is informed by “clinical guidelines contained within the Standards of Care for the Health of Transsexual, Transgender, and Gender Nonconforming People, produced by the World Professional Association for Transgender Health and drawing on the best available science and expert professional consensus.“

We will describe some of the stages in that recommended treatment in section VII. But the final stage may involve undergoing gender reassignment surgery. Such transgender individuals are not exceedingly rare: about 1 in 200 birth males transition to female and about 1 in 400 birth females transition to male. It is from DNA sequencing on such transitioning individuals that we are beginning to learn some of the possible genetic causes of gender dysphoria. A genetic origin is suggested by the observation that identical twins are significantly more likely to both experience gender dysphoria than fraternal twins or siblings. For example, a large Australian study compared genomes for 380 transgender women (who had, or planned, gender reassignment surgery) and 344 control group men. The study focused on alleles (i.e., gene variants) among 12 specific hormone-signalling genes (not necessarily on the X or Y chromosomes), and it found that certain alleles on four of these genes were overrepresented among the transgender women. It was then proposed that these alleles may alter hormone secretion in utero and thereby influence the embryonic brain development.

Another recent study at Yale University sequenced all the protein-coding genes in the DNA of 13 transgender males and 17 transgender females, and compared them to a control group of 88 non-transgender individuals. Among many genetic variants identified (see Fig. V.1), “21 variants in 19 genes were found to have associations with previously described estrogen receptor activated pathways of sexually dimorphic brain developmentOur findings suggest a new avenue for investigation of genes involved in estrogen signaling pathways related to sexually dimorphic brain development and their relationship to gender dysphoria.” While this type of research is just beginning, it already suggests a strong association of gender dysphoria with genetic variants that hinder sex hormone (both testosterone and estrogen) secretion during fetal and infant brain development.

Figure V.1. Flow chart indicating how researchers filtered over 120,000 gene variants found in the genome of transgender individuals down to 21 variants on 19 specific genes that affect hormone pathways relevant to sexually dimorphic brain development.

Brain imaging on adult transgender men and transgender women who were not currently taking hormone supplements (which might, in principle, have affected results) reveal that the transgender adults, in comparison with non-transgender control participants, “have typical [for their birth sex] gray matter volumes (or cell bodies), but differences in white matter (connective tissue)…Transgender women demonstrated a white matter trend in between women and men… suggesting that their white matter tracts were only partially masculinized during development. A similar trend was seen in transgender men [showing] a brain connectivity pattern closer to people who shared their gender identity (that is, men) than those who shared their birth sex (that is, women).”

The Cultural Gender Spectrum:

Although research in this field is at an early stage, it seems already to be rejected by many progressives and some social scientists who insist that gender identity is not biologically determined, but is rather a “social construct.” They maintain that a significant fraction of humans are non-binary, falling well outside the “male” and “female” boxes in a gender “plane” (Fig. V.2). The Gender Wiki page presents nearly a thousand distinct non-binary “genders,” including “genderfluid” (changes with time, place or mood) and such exotica as “duoquinquagintigender” (feeling as though one has an unlimited number of genders) and “schrodingergender” (male and female at the same time, just as Schrödinger’s cat was both dead and alive until pinned down by measurement). (They may want to eliminate the last one in the light of the recent revelation that Erwin Schrödinger, while a Nobel prize-winning physicist and a father of quantum physics, was probably also a pedophile.)

Figure V.2. One example of several attempts to produce a two-dimensional representation of the gender spectrum, according to many progressives. We have no idea what the numbers along the axes represent.

The growing number of individuals who now self-identify with one of this rainbow of social “genders,” but are not considering actually transitioning, are presumably feeling various levels of gender-nonconforming feelings and behavior, or general confusion about their gender, which may change with mood or environment. The genetic and hormonal variations in brain development do lead to a wide spectrum in gender nonconformity short of gender dysphoria. But the origin of these feelings is biological. Debra Soh puts it this way: “Whether a trait is determined ‘masculine’ or ‘feminine’ is culturally defined, but whether a person gravitates toward traits that are considered masculine or feminine is driven by biology…For someone who is gender-nonconforming…the extent to which they will feel comfortable expressing their gender nonconformity (through, say, the way they dress or carry themselves) will be influenced by social factors, like parental upbringing and cultural messaging. Societal influence, however, cannot override biology.”

Gender-nonconforming people deserve to be referred to by their preferred pronouns and to be treated with respect. But the new cultural acceptability, even celebration, of non-binary gender labels and trans activism is also leading to potentially dangerous confusion among teenagers. This can be seen in the recent surge in rapid onset gender dysphoria (ROGD), illustrated in Fig. V.3. According to Debra Soh, this phenomenon, “seen primarily in teenage [post-puberty] girls and college-age young women, is characterized by a sudden desire to transition to male, often out of the blue, without any previous history of gender dysphoria.” According to the Centers for Disease Control, about 2% of high school students now self-identify as “transgender.”

Figure V.3. The number of young people per year referred to a transgender service in the United Kingdom. There is very rapid recent growth in adolescents, predominantly female adolescents, who are self-identifying as “transgender.”

A 2018 study of 256 ROGD girls by Lisa Littman of Brown University has drawn the furious ire of trans activists who accused Littman of transphobia and convinced the journal PLOS One to conduct a highly unusual post-publication review of the paper (they subsequently published a revised version). Littman’s online survey of the girls’ parents revealed that many of the girls had come out as gay or bisexual, or had mental health disorders such as autism or borderline personality disorder. Nearly 40% of the surveyed girls had several friends who had recently also self-identified as transgender. Littman concluded that none of the 256 girls met the DSM-5 diagnostic criteria for gender dysphoria in childhood. The phenomenon then appears to be a form of social contagion. Some of the ROGD girls appear to have been sexually abused or threatened, and think they would feel safer and more widely accepted as males.

Debra Soh says: “There are any number of reasons why a young woman may feel uncomfortable or dislike being female; they don’t necessarily mean that transitioning is the right solution for her. With ROGD, a girl’s proclamations of gender dysphoria usually have nothing to do with gender.” Or at least not with gender as understood scientifically, as opposed to in current popular culture. As indicated in Fig. V.4, based on case histories, the act of transitioning does not solve the underlying problem unless it truly results from clinical gender dysphoria, caused by a brain more characteristic of the sex opposite to one’s reproductive organs.

Figure V.4. Some of the psychological reasons a young person may self-identify with gender dysphoria. For most of these reasons (in blue ellipses), actually undergoing transitioning is likely to make the underlying problem worse in the long run.

Continued in Part II