Demystifying gender identity and homosexuality

This post is a collection of questions arising from my curiosity about intersex individuals, transgenders and homosexuality. Some of the answers found are listed along with references. Sometimes the content is simply a summary or a quote from my interactions with people, who may or may not be actively working in these fields. Although not meant to be an article written in the tone of peer-reviewed scientific journals, the scientific spirit of questioning and answering in an objective manner is maintained, and this post strictly does not attempt to discuss social/legal/political/personal issues related to these topics. Some of the references are semi-informal instead of being papers published in scientific journals. Discussions to improve the content and/or answer the unanswered questions are strongly encouraged in the comments section below, but the scientific spirit is to be maintained and due references will be appreciated. Feel free to contact me if you want the conversation to be personal instead of public, or you are not able to comment.

This post is dynamic, i.e. it will be updated from time-to-time as better answers or references are found, or more questions are raised from my interactions with people. Last updated: 17th April 2018.

Disclaimer: I cannot stress enough that this post is not meant to discuss any social*/legal/political/personal issues pertaining to these topics, but is purely meant to satisfy scientific curiosity.

*You can hover over to The f-word for that.

Question 1:

If the pairing of one sex chromosome from each parent determines the gender of the offspring in humans, how come there are people who have traits from both genders? Specifically, the pairing can either be X/Y or X/X (egg from mother always has X but sperm from father can have either X or Y). Then, the sex determination is a yes/no question (Is the baby female/male?), and there doesn’t seem to be a way out to have a mixture of traits.


The inter-sex characteristics are sometimes acquired during birth, because individuals are born with 47 chromosomes rather than 46, due to the presence of both the sex chromosomes (from the father, both X & Y) in the winning sperm, see an informal reference. In a normal childbirth, both the reproductive organs, the penis and the vagina, grow simultaneously till roughly the 35th week inside the mother’s womb, after which the symmetry is broken by the sex chromosome pair (XX/XY) in the DNA. There are signatures of these growths in both the adult male (the scrotum on the testis is stitched in the middle, it started out as the vagina) and the adult female (the clitoris above the vagina). For inter-sex individuals, both keep growing.

Gender, however, is not determined at birth in all cases (Q: What is the rough ratio?). In fact, the age at which an individual appreciates inter-sexuality can vary between 4 to 23. The likely reasons are:

  • Hormonal imbalances caused by one of the other 22 pairs of genes (called “autosomes” as opposed to “sex chromosomes”), at any age from infancy to full development of organs, which is around 21 years for an average human.
  • During the development of a baby inside the mother’s womb, wrong hormones may be secreted by the mother which affects the development of the brain of the child. The question is still open whether such changes can give rise to intersexuality in the baby, but indications from recent studies are in the direction that there are subtle differences in the male and female brains, and these pre-natal (before birth) growth differences caused by the mother’s hormones are enough to cause inter-sexuality. For example, even if the off-spring develops male sex organs and has regular hormonal discharges during its growth outside the womb, the subtle differences in the brain can lead the person to feel like a female trapped inside a male body.

This is a good time to point out that “transgenders” are individuals different from “inter-sex” individuals. As my friend points out: Inter-sexuality “is a physical condition that does not necessarily involve the brain. Transgender people, on the other hand, do not show any ambiguity in physicality, secondary sex characteristics, genital development etc. It is something only concerned with the brain.

Here is a link explaining the terminology.

As this article asserts, “Those persons who identify as transgender (the “T” in many queer community acronyms) are those who identify with a gender that differs from their assigned sex (Figure 1). This juxtaposes cisgender, or those who identify with their assigned gender. Though the typical assigned sexes are “male” and “female,” often designated at birth, being transgender does not limit gender identity to these two categories, as many who identify as transgender do not feel they are exclusively masculine or feminine. Importantly, transgender identity is independent of sexual orientation. The subset of transgender individuals who choose to undergo sexual reassignment surgery are often denoted as transsexual.

“An incomplete and incomprehensive representation of gender identity and sexual orientation. Transgender individuals are those who identify with a gender that differs from their assigned sex. This is a facet of identity that is completely distinct from sexual orientation. These graphs do not represent the full spectrum of either facet, as they are multidimensional. For instance, there may be genders that some identify with that are neither “male” nor “female. Furthermore, there are no “lines” that divide these identities, and they may be considered malleable and overlapping.” Copyrights: Katherine J. Wu and Brad Wierbowski (

The same article also makes two fine points:

  1. Transgender women tend to have brain structures that resemble cisgender women, rather than cisgender men.” … “, suggesting that the general brain structure of these women is in keeping with their gender identity.” See this paper for more details.
  2. Brain development is heavily influenced by the prenatal environment – what hormones the fetus is exposed to in its mother’s uterus. Some scientists believe that female-to-male transgender men, for instance, may have been exposed to inadequate levels of estrogen during development (Figure 3). This phenomenon could have two causes: 1) not enough estrogen in the fetus’s immediate environment, or 2) enough estrogen in the environment, but poor sensitivity in the fetus. Think of it like a cell phone tower controlling remote calls – the tower may not be producing enough signal (scenario 1), or the receiving phone may be unable to process the message (scenario 2). In either case, the call doesn’t make it through.”

Below I list some more references giving more evidence to these ideas, along with notable quotes from the same:

  • (“FtM” means Female to Male) Our results show that the white matter microstructure pattern in untreated FtM transsexuals is closer to the pattern of subjects who share their gender identity (males) than those who share their biological sex (females). Our results provide evidence for an inherent difference in the brain structure of FtM transsexuals.”
  • “Gender-dependent differentiation of the brain has been detected at every level of organization — morphological, neurochemical, and functional — and has been shown to be primarily controlled by sex differences in gonadal steroid hormone levels during perinatal development.”
  • Transsexual differences caught on brain scan.”
  • Brain scans show trans people feeling at odds with their body: “There was also less activity in an area called the supramarginal gyrus. This has been implicated in the ability to attribute a sense of “this belongs to me” to our body parts. For example, stimulating an area close to the supramarginal gyrus can elicit out-of-body experiences. The reduced activity in this area seen in the trans volunteers when the breast is touched suggests that the brain may not treat the breast as strongly belonging to the “self”, says Case.” This is the published paper.

Question 2:

How is it possible that all different organisms have different numbers (or pairs) of chromosomes, there being so many species?
It is counter-intuitive to think that the space of the number of chromosomes has a one-to-one to mapping with the space of the number of species: if Orangutan, Homo erectus and Homo sapiens were so similar, and the change along the evolutionary track was a continuous rather than a discrete one, then it is hard to believe that the number of chromosomes is different for each of these species. If that was the case, one could tell the difference between the different species by counting the number of chromosomes (assuming that is possible via palaeontology).


The number of pairs itself does not necessarily separate the species. There are details related to the types of chromosomes and their functionalities that make different species different. For example, Guppy (Poecilia reticulata) is a type of fish that share the same number of chromosomes as humans (46). Hence, only counting number of pairs of chromosomes is not enough. Mutations at the level of the DNA (which make up the chromosomes) and its structure can distinguish between different species, and the change is indeed continuous.

Question 3:

What makes some individuals homosexual? We know that there is a tendency of animals to fall in love or stay committed, which are basically driven by the urge to reproduce and keep the offspring safe. What, if any, such ulterior motive drives people to be attracted to people of the same sex?

Partial answer:

Quoting a friend from email conversation: “There is nothing wrong with having a range of sexualities. Just like humans have heights ranging from 4 feet to 7 feet, the sexual tendencies of a man can range from violent attraction to beautiful women, to gentle liking for women and tolerating men, to liking towards men, to sexually getting attracted to men.” Summary: The scale of sexual attraction of individuals towards others of the same gender to very heavily for those of the opposite gender, is a continuous one.

Rephrasing my question:

What exactly sets the continuity, if so, on this scale? The answer could be the pH level of a certain substance in some component of the DNA/RNA/whatever or the amount by which a certain hormone is secreted (very uneducated guesses!). If that is indeed so, then is it dependent on the levels of this determining factor at a certain age (if not then the sexual orientation of a certain individual can change over time) or is it determined during birth/puberty/certain-age once and for all? On the other hand, it could be something discrete: for example, the number of certain protein molecules in the DNA: if the number lies within a range, people are “straight”, whereas if not, they are homosexuals.

Satisfactory answers have not been found.

Question 4:

Is homosexuality limited only to humans? If so, why? Is it then an evolutionary trend? If that is the case, the question of homosexuals surviving, in the long run, seems to be nil by natural selection.

Answer attempts/opinions:

  • No, homosexuality is common across species. For example, see the Wikipedia article containing further references. In fact, that homosexuality is not uncommon in the animal world and hence not “unnatural”, was cited as one of the reasons for making it legal in certain nations/states across the world.
  • Summarizing a conversation with a student of Biology: Current research is not being able to answer much simpler questions like — What exactly causes sexuality in zebra-fishes? (The reason zebra-fishes are interesting is that they are in certain ways similar to humans, and Biologists hope to answer the questions of human nature through the study of zebra-fishes.) No study until now has been able to identify any sex chromosome in them, but they certainly have sexual reproduction. If only the autosomes define the gender, then at what stage does the sex get determined? Currently, the male/female ratio in a zebra fish community seems to strongly respond to parameters like temperature, food, etc. However, patterns, if any, seem to be eluding scientists.
  • Quoting a friend from email conversation: “Evolution may be moving in a totally different direction! Instead of an individual fighting for the survival of its genes, the fight could be the survival of the society as a whole. Instead of having a man fighting to death to protect his genes making a deal with a woman to take care of their off-springs, we may be moving towards a collective responsibility. Let there be two societies. Society A kills all homosexuals, every individual fights to protect his/her genes. Society B, instead, develops a collective trend. Instead of every individual fighting for his/her survival, every individual fights for the collective survival. Suppose homosexuals are endowed with empathy and tendency to take care of children, invalids and old, they will be valuable members of this society. There could be a situation where society B survives and that society rewards/encourages homosexuality to the extent of having a good balance in the society for its survival as a whole. In such a case, homosexuality will survive for a long time.” Summary: Whatever be the reason behind homosexuality, the trait can survive by the survival of that community which encourages this trait over that which doesn’t. Thus, even though individuals who are homosexuals do not reproduce and pass on their genes, the trait survives.

Satisfactory answers have not been found.

This post is dynamic. It will be updated as answers (to the unanswered questions) and/or references (to statements already made) are found, or more questions are raised. Last updated: 17th April 2018.

4 thoughts on “Demystifying gender identity and homosexuality

  1. This is really profound, and a clever way of addressing the LGBT issues, Debdutta. I’d never thought about the aforementioned in a biological manner and after reading this, it all makes (near) perfect sense. I already had a fair idea of how these things work but now having understood them wonderfully in layman’s terms, I’d say your article makes for an interesting read. Of course, you already know I am bisexual (halfway to homo?) so it really delights me that this sexuality is not being looked down upon (especially in a country like ours), and heterosexuals, like yourself, are actually trying to comprehend it better! On a side note, I doubt that homosexuality is a ‘trait’ that can be passed on, it’s very much a psychological thing than it is a biological one; but that’s just my gut feeling.

    Liked by 1 person

    1. May-hek! Thanks for the appreciation. 🙂

      Just clarifying, I am in no way trying to address LGBT issues, that’s not the point at all. This is coming from curiosity, which I have seen in many around me, specially while growing up, but mostly addressed in a hush-hush tone and satiated by misinformation. If anything, I am trying to address ignorance and/or misconceptions, to bring out the science behind it.

      Also, about homosexuality being a trait: Of course it is a trait, if you look at it from the point of view of evolution. Individuals are devised by genes, they function on hormones: there is a cause of homosexuality. The fact that homosexual individuals are found across generations, is equivalent to saying that this is a trait that is passing on (even if each homosexual individual is due to some mutation, that kind of mutation is itself a trait).


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