gender dysphoria
What is Transgender?

What is Transgender?

Transgender Explained

Transgender, scientifically known as gender dysphoria, is the condition in which a person’s sexual anatomy differs from what certain brain structures determine their gender identity to be.

Feelings of being trans, or other than what one’s anatomy appears to represent, may begin at a very early age (before school age or as a toddler) or anytime later, such as at the time of puberty or as an adult.

While it might be assumed that one’s sexual anatomy aligns with one’s genetic sex as determined by the individual’s sex chromosomes, that isn’t necessarily the case. For now, suffice it to say that XX and XY are not the only two configurations for sex chromosomes in humans; additionally, there are XXY, XYY, XXXY, XO and others. (The book Not a Choice: What you weren’t taught about the biology of sex and gender, author PJ Paulson, provides further information regarding sex chromosomes in humans.)

As of April 2023, neuroscientists have found three particular brain structures—of numerous sexually-differentiating brain structures that develop and function differently between men and women—to be associated with gender identity:

  • Central nucleus of the bed nucleus of the stria terminalis (BSTc)
  • Interstitial nucleus of the anterior hypothalamus, subdivision 3 (INAH-3)
  • Infundibulum nucleus

Scientifically speaking, transsexual is the term used for an individual who has undergone the hormonal and surgical treatments to bring their anatomy in line with their gender identity-determining brain structures.

Note: I have been told that ‘transsexual’ has become a pejorative term. However, it is the scientific term used in neuroscience and in professional publications. Since this publication is about the science, and specifically about the biology of gender identity, we follow the usage of the scientific community as technically correct; it is in no way intended in a pejorative manner.

How do an individual’s brain and anatomy diverge in sexually-differentiating development?

First, be aware that internal sex organs and external genitalia develop in the first half of fetal development, and certain sexually differentiating brain structures develop in the second half of fetal development. These sexually differentiated brain structures include both those associated with gender identity, and others associated with sexual orientation. These areas develop at different times and independently of one another, with the exception of the INAH-3, which has been found to affect both gender identity and sexual orientation. These timing differences – across development of internal sex organs, external genitalia, brain structures determining gender identity, and brain structures associated with sexual orientation – allow for variation in the degree to which each area of development is influenced by male hormones, drugs administered to the pregnant mother, environmental chemicals, and other factors.

There is no flip of the coin that results in strictly and completely binary male-or-female development in the fetus. Sexually differentiating anatomy and brain structures develop independently on a continuum, or spectrum. This results in a potential mosaic of female-to-male development to differing degrees in each area.

This website explains how this occurs. For the moment, let’s explore how binary sexual development could occur. However, that’s not how it does work.

How Binary Sexual Development Could Work – But Doesn’t

You’re probably aware that computers work based on bits that are set or not set. These translate to ones and zeros—1s (on, or set) and 0s (off, or not set).

Having spent many years as a software engineer, I’ll run through a possible implementation of how sexual development could work if it were binary.

First, we need to understand conditions that we can’t change under this scenario. That is, there are at least four components that make up an individual’s sexual aspects:

  • Genetics, specifically sex chromosomes
  • Internal sex organs
  • External genitalia
  • Sexually-differentiated brain structures

Each of these develops in the fetus at a different time, and they develop independently of one another. That is, a subsequent stage of development is not dependent on the status of a previous stage of development. Independent phases of development create a set of assumptions and restrictions that we need to accommodate in our binary model.

In software, if multiple processes must align with a particular pre-condition, the setting or status of that pre-condition would be checked as the first step of each process. Each individual process would then proceed in a specified manner according to that pre-condition. Let’s define development as either ‘A’ patterning or ‘B’ patterning.

If development of each stage is binary, then patterning for each stage is either fully A or fully B.

In our example, the Y chromosome is our defining factor for initiating each of four processes:

  1. development of internal sex organs
  2. development of external genitalia
  3. development of brain structures that define gender identity
  4. development of brain structures that define sexual orientation

That is, if a fetus has a Y chromosome, and development is binary, then when internal sex organs begin development, presence of the Y chromosome (the Y bit is set) causes internal sex organs to all develop entirely as ‘B’, or male. If there is no Y chromosome (the Y bit is not set), then internal sex organs all develop entirely as ‘A’, or female. The decision factor—the Y chromosome—is a binary one: it is either present or it is absent. The subsequent choice for development—either ‘A’ patterning or ‘B’ patterning—also is binary: there are only those two choices, and one or the other must be selected. Whichever type of patterning is set in motion will occur in its entirety for that particular process.

Similarly, when external genitalia are to begin developing, check for the presence of a Y chromosome. If present, develop entirely as ‘B’, or male; if not present then develop entirely as ‘A’, or female.

Internal and external sexual anatomy develop during the first half of pregnancy. Sexually-differentiating brain structures develop during the second half of pregnancy.

Again, check the status of the Y chromosome for each process. If the Y chromosome is present (set) then all the sexually-differentiating brain structures, including those that set gender identity and those that set sexual orientation, would develop entirely with ‘B’, or male, patterning. If there is no Y chromosome, then all would develop entirely with ‘A’, or female, patterning.

If this were the way sexual development worked, then it would be possible simply to check for a Y chromosome as the first step in each phase of fetal development. If present, the individual is a genetic male and would have developed with male internal sex organs, genitalia, and brain structures with attendant male functioning. If there is no Y chromosome, then all aspects of sexual development—internal, external, and brain—would proceed entirely as female.

That’s how a binary system functions. That’s the scenario for binary sexual development. And THAT IS NOT HOW HUMAN SEXUAL DEVELOPMENT ACTUALLY WORKS!

How Sexual Development Actually Works – Short Version

The rest of this website explains at a high level how it does work. In short, human sexual development is largely based on the endocrine system, which is in turn affected by various genes. Each stage of sexual development in the fetus does not check for presence of a Y chromosome as we did in our binary model.

Instead, male sexual development is initiated at about six weeks into embryonic development, when the SRY gene on the Y chromosome kickstarts male development in concert with other genes on other chromosomes and initiates production of male hormones in the fetus. Each phase of sexually-differentiating organs, anatomy, and brain structures develops based on presence or absence of male hormones, and the amount, or strength, of androgens.

Further, each phase of development is not a binary system triggered by an on-off switch. It’s not akin to a light switch that’s either on or off. Think, instead, of a dimmer switch. The switch is off to begin with. No sexual differentiation has been noted during the first six weeks of embryonic development. After six weeks, absent male hormones, development proceeds as female. Kickstarted by the SRY gene on the Y chromosome, at six weeks into development in the embryo, androgens/male hormones begin to push the lever on, with brightness, or degree of male development, determined by the level of male hormones. However, that dimmer switch can slide back and forth throughout fetal development, based on several factors.

The level of androgens detected by the fetus can be affected by endocrine disruptors, such as those found in plastics or environmental toxins. Other factors are the state of other genes in the fetus that affect sexual development, certain genetic conditions, drugs (prescription or otherwise) administered to the mother during pregnancy, maternal stress, and others. These all can slide that dimmer switch back and forth throughout development of the fetus, and may turn off androgens or their effects altogether.

Human sexual development is not a binary light switch. It’s a continuum or spectrum, like a dimmer switch, with various influences throughout pregnancy that can affect the degree to which the dimmer is on or off.

Not only does overall sexual development occur on such a sliding scale, or continuum, but each aspect and each sexually-differentiating structure may also develop on a sliding scale, or continuum.

The result is a mosaic of varying degrees of sexual differentiation in the internal sex organs, genitalia, and several structures within the brain, including those that determine gender identity and others that determine sexual orientation. Due to variations in androgens and other factors previously mentioned, all of these bits can fit together to define an individual’s “sex” with varying degrees of congruity or incongruity.

The brain structures thus far found to be associated with gender identity are:

  • central nucleus of the bed nucleus of the stria terminalis (BSTc)
  • interstitial nucleus of the anterior hypothalamus, 3rd subdivision (INAH-3)
  • infundibulum nucleus

Gender dysphoria occurs when the aforementioned structures (and potentially others yet to be determined) within the brain tell a person that their gender is mismatched with their sexual anatomy.

To understand the complexity of fetal sexual development and defining an individual’s sex, there’s an article for that here. It’s also one of the other blog articles (The Complexity of Defining Someone’s Sex or Gender) on this website.

For more thorough explanations of sex chromosome configurations, factors driving or influencing fetal sexual development, the biology of gender identity and sexual orientation, and associated topics, read Not a Choice: What you weren’t taught about the biology of sex and gender by PJ Paulson, which can be found as Kindle eBook, hardcover, and paperback (black and white interior) on The paperback with color interior printing is available on the Barnes and Noble website.

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