The Biology of Gender

Part 1: Beyond The First Glance

A Multi-Layered Reality

A baby takes its first breath and the room waits for a single announcement: boy or girl!
For centuries that quick glance at external genitals was treated as the whole truth of a person’s sex. But it turns out that human biology is far more intricate than what can be seen in that first moment. Many parts of our body determine the sex of a child, including chromosomes, hormones, internal anatomy, and the body’s own response to those signals. History is full of stories that remained invisible to the delivery room eye yet shaped a person’s life in profound ways.

It turns out that biology tells a more complex story. Scientists describe several markers that determine the baby’s biological sex:

Chromosomes (XX, XY, and variations such as XXY, X0, mosaic patterns, etc.)

Gonads (ovaries, testes, or mixed/atypical tissue)

Internal reproductive structures (uterus, cervix, vas deferens, etc.)

External genitalia (clitoris, penis, labia, scrotum, and variations)

Hormonal profiles (relative levels of estrogen, testosterone, androgen sensitivity, etc.)

When all these markers don’t align in the typical “all male” or “all female” pattern, the umbrella term intersex applies. Doctors and geneticists often describe dozens of variations of this that occur and call it “differences of sex development” (DSDs): Chromosomal variations such as Klinefelter syndrome (XXY), Turner syndrome (X0), Triple X (XXX), XYY, variations in hormone production or sensitivity such as Androgen Insensitivity Syndrome (complete or partial), 5-alpha-reductase deficiency, Congenital Adrenal Hyperplasia, Gonadal differences like ovotesticular DSD (both ovarian and testicular tissue). And so many more. See all a glossary of all the different combinations here.

A Hidden Spectrum

Some aspects of sex are visible at birth, while others (such as chromosomal or hormonal differences) may remain hidden. Biological sex traits exist along spectrums and medical professionals now emphasize that “male” and “female” are categories that describe common patterns, not absolute boxes that fit everyone.

While biological sex might be what the doctor assigns to the child, gender identity, on the other hand, is what the person feels as a whole. So, if the baby has male genitalia, but all other markers are female, that child might grow up to feel more female, than male. They would identify as female, even though the doctor marked them as male. Gender is a person’s deeply felt sense of being male, female, both, or neither, which may or may not align with the sex assigned at birth. While sex and gender often overlap, they are not the same thing.

Part 2: The History of Gender Research

Tracing the Steps

Between 1869 and 1910 European doctors and writers such as Karl Westphal, Karl-Maria Kertbeny, and Magnus Hirschfeld documented people whose inner sense of gender differed from their assigned sex, coining terms like sexual inversion and laying groundwork for early gender-affirming care.
Already in the 1920s and 30s, hormone therapy was explored and Hirschfeld’s Institute for Sexual Science in Berlin became a center for research and treatment until it was destroyed by the Nazi regime.
From the 1940s through the 1960s researchers including Alfred Kinsey, Harry Benjamin, and David Cauldwell popularized the terms transsexual and later transgender, framing gender identity as an innate human variation. By the 1980s the American Psychiatric Association formally recognized gender-related diagnoses. But much harm was done along the way.

Monsters & Doctors

The Catholic church had a big influence on western world when it came to sexual activity and sexual organs. Any babies born with ambiguous genitalia were hidden and deemed a judgment from God. Documents show that when genitals were not fully male or female at birth, the babies were called “monsters sent by God for warning”. All the abnormalities were punishments from God.

In the Byzantine Empire, doctors performed surgeries on intersex babies as early as the 2nd century. In Victorian times, people thought to be intersex, were just labeled “male” or “female” and expected to act in accordance with their assigned gender (Inntersex History of North America, “Hermaphrodites and the Medical Invention of Sex” by Alice Domurat Dreger).

Before 1950, babies that were born with neither 100% male nor 100% female, were at the doctors mercy. Without discussing the defect with the parents, they would often choose a gender and correct the defect on the spot. Doctors were taught to make the genital decision based on the length of the penis. If the penis was longer than an inch, it was a boy. If the penis was less than an inch, it was a girl. And then parents were instructed to raise the child as the gender role assigned during surgery. Most of the time the doctors told parents after the surgery.

A Horrific Experiment

There is a tragic story of a doctor (Dr.John Money ) who performed an experiment on a boy who was deformed during circumcision. To “fix” the mistake, the doctor removed his testicles and constructed rudimentary female genitals on him, telling his parents to raise him like a female (an experiment he had been wanting to make).

Bruce Reimer was his name. The parents changed his name to Brenda and raised the child as a girl, never being told he had been born male. “Brenda” never displayed female behaviors, always felt like a boy and experienced severe gender dysphoria (a condition in which someone experiences distress as a result of their assigned gender). Bullied in school for masculine traits and experiencing distress, “Brenda” tried to commit suicide several times. At the age of fifteen, Reimer’s father told Bruce the truth about his birth and the subsequent procedures, but was not allowed to be a boy until 21.

Bruce chose the new name “David” and eventually got a penis implant and married a woman. Life had taken it’s toll already though, and took his own life on May 4, 2004, at the age of 38.

Between 1950-2000, babies born with ambiguous genitalia were treated according to Dr Money’s assumption that gender was not inborn but created with the environment before age three. The stories are many.

Dr. Money was finally exposed for fraud in 1997, but is tragically still influential and followed today. His terminology is still used: “gender identity”. His core theory is rejected by most modern researchers, but many non affirming people still follow that belief.

Part 3: Our Response

Understanding Science

Science does not create. It explains.

Science does not create this reality. It reveals it.

Just because something is newly explained doesn’t mean it’s newly invented. For generations, transgender people have shared their experiences, often at great personal cost, and now scientific research is beginning to catch up, offering insight into what they’ve always known to be true. Studies in neurology, genetics, and endocrinology are showing that gender identity involves more than what’s visible on the outside—it’s shaped by complex factors in the brain, biology, and early development. These discoveries validate the persons lived experience. Science is not uncovering a problem—it’s uncovering truths that can lead to greater compassion, understanding, and care.

Gender diverse people (intersex, third gender, transgender…) have existed across cultures and centuries, long before modern research tools existed. What science is doing now is catching up—putting language and understanding to what so many have felt all along. It’s not inventing something new; it’s revealing what has always been there, often hidden or misunderstood. Scientific studies in neurology, genetics, and development are showing us that gender identity isn’t just about anatomy—it’s also wired into the brain, shaped by hormones, and formed in the womb.

Understanding Terminology

Intersex
A natural variation in physical sex traits. Intersex people are born with chromosomes, hormones, gonads, or genitalia that do not fit typical male or female definitions. These traits can include a mix of male and female anatomy, or patterns that are neither.

Transgender
A person whose sense of being male, female, both, or neither, differs from the sex assigned to them at birth. Awareness of this difference can appear in early childhood or later in life.

Nonbinary
An umbrella term for people whose gender identity is not exclusively male or female. A nonbinary person might identify as both, as somewhere in between, or as outside those categories entirely. Physical sex traits vary widely.

Understanding God

These differences aren’t flaws or mistakes. They are part of the rich diversity within God’s design (Psalm 139:13–14). The more we learn about biology, the more we see that human sex and gender are not simply black and white, but exist along a spectrum. Recognizing this doesn’t erase male and female. It helps us see the full picture. It invites us to respond not with fear or judgment, but with compassion, curiosity, and humility. God’s creation is far more diverse than we often imagine, and the science that helps us understand it is not a threat to faith. It offers a deeper glimpse into the wonder of being human.

Scottish theologian John Swinton writes that human differences are not flaws in creation but part of its goodness. He invites the church to rethink what “perfect” means in God’s eyes. When we see someone who was made different or has a disability only as something to correct or overcome, we imply that people who live with differences are less complete, less holy, or less welcome.

When sexual attraction or gender differences are treated as defects to be repaired rather than a difference to be understood, we fail to see the diversity of God’s image reflected in humanity. Scripture tells us that creation was good, not uniform. God’s creative work includes a wide range of bodies, minds, and identities, all capable of love, faithfulness, and beauty.

Just as society can “disable” someone through inaccessibility or exclusion, the church can spiritually disable LGBTQ people through rejection and silence. In both cases, the harm does not come from how someone was created, but from how others respond to that creation.

The more we come to know about biology, the more we understand people. The more we come to know about God, the more clearly we begin to see that his design was never about sameness or conformity. It was about relationship, interdependence, and the beauty of difference. The better we understand who God is, the better we understand that all of us, in our varied forms and experiences, were created good.

Understanding People

Hearing their side of the story is the beginning of understanding.

Emily Quinn was 10 years old when she realized she wouldn’t be able to have children. She born with a typically female outward appearance (she has a vulva and was raised as a girl), but inside she did not have uterus. Instead, she had testes. Emily is a woman, but her biological sex doesn’t fully fit into a female category.

Rajgir Mistri, a 46-year-old man, was undergoing hernia surgery, when the doctors discovered female reproductive organs in his body, a uterus and ovaries. He had always felt like a woman, but didn’t know why. His body had female hormones being produced.

Chen Li, a 33 year old man, experienced blood in his urine for a couple of years. He was finally diagnosed with possible appendicitis, but during the surgery, they discovered he had female internal organs and he had had a period for two years.

Steve Crecelius, a Denver photographer, said he’d felt a little different all his life. As early as 6 years old, he felt like a girl, loved wearing dresses and trying on his mom’s makeup. One day, in 2012, he ended up at the ER for Kidney Stones. To his shock, the doctor found something in his ultrasound results. He had internal female sex organs. Sometimes, people are born with abnormal visible genital differences. Sometimes, people are visibly one gender, but don’t know why they feel a different gender inside.

Articles

Is sex still binary?
Studies finds that Transgender People’s Brains Are Wired Like Those of Gender They Identify With
Transgender brains are more like their desired gender from an early age
Biological Science Rejects the Sex Binary
Parents used to be encouraged to keep these “abnormalities” a secret from the child
Doctors instructed parents to conceal intersex diagnosis from their children
There are at least 40 known variations that fall into intersex classifications.
What Studies Say About Transgender, Gender Dysphoria, and Gender Affirming Care (video)
Dr. Anthony Youn, M.D. F.A.C.S
Science Proves There are More than Two Human Sexes (video)
The biology of gender, from DNA to the brain with (Ted Talk by Trans woman Karissa Sanbonmatsu)
The way we think about biological sex is wrong (Ted Talk by Intersex woman Emily Quinn)

An interesting side note is to take a look at the animal kingdom:

PIGS: intersex abnormalities have been found in pigs.

BEARS: a percentage of female bears have genitalia that resemble those of male bears.

MOLES: all female moles have ovotestes (gonads that are a mix between ovaries and testes).

CRAYFISH: 1-8% of crayfish are intersex (having female chromosomes with male sexual structures

CATTLE: Cows have a common intersex conditions called Freemartinism.

PACIFIC SPADENOSE SHARK: This shark has internal male and female reproductive tracts, as well as a pair of “ovotestes”.

LIONESS MMAMORIRI: This lioness has a genetic mutation where she has female parts but looks and sounds like a male lion.

BANANA SLUGS: have both male and female sex organs.

Articles

I am not a mistake

In the absence of information, we tend to fill in the blanks with fear or negativity. So, let’s fill in the blanks and take little biology journey.

“For it was you who formed my inward parts;
you knit me together in my mother’s womb.
I praise you, for I am fearfully and wonderfully made.
Wonderful are your works;
that I know very well.” Psalm 139:13-14

These differences aren’t flaws or mistakes—they’re part of the rich diversity of how God created us. The more we learn, the more we realize that human sex and gender are not just black and white—they exist along a spectrum.

Understanding this doesn’t erase male and female—it helps us see the full picture. It invites us to respond not with fear or judgment, but with compassion, curiosity, and humility.

God’s creation is more diverse than we often imagine, and the science that helps us understand it is not a threat to faith—it’s a deeper look at the wonder of being human.

Artwork by nakedpastor.com, used with permission.

Next Page: Not a new phenomenon