Now onto something a bit meatier than usual. The subject is the Human Brain, and Intersex.
Does Brain Intersex Exist
1. Anomalies during foetal development sometimes happen. This can give rise to all sorts of somatic variations.
2. These anomalies can be due to genetic, environmental, or a combination, of causes. Very often they happen for no apparent reason. Sometimes we can strongly correlate them with environmental factors e.g. ingestion of thalidomide during early pregnancy. Often the correlation is weak.
3. Observation of low-technology societies suggests that some degree of somatic variation is good for the society - the person who is colour-blind can sometimes see animals in vegetation when others can't. Abnormalities that may not be good for the individual can be good for the group.
4. Some harmful Genetic variation is also useful - Tays-Sachs gene provides protection against Typhoid IIRC, Sickle-cell Anaemia gene provides protection against the Malarial parasite. 2 copies, you die, 0 copies, you probably die of disease, 1 copy, you're fine. Evolution will sometimes positively select for a small amount of variation in somatic norms.
5. There's a mountain of evidence that boys and girls think differently. There's evidence from dynamic MRI that they use different parts of the brain. There's evidence from autopsy that their brains are different morphologically.
6. Intersex conditions exist, some genetic, some environmental, some ideopathic (ie we have no idea what causes them). These result in sexually dimorphic parts of the body being abnormal, feminised in a masculine body, masculinised in a feminine body, or just plain mixed.
7. (Emphasis Added) The Brain is a Sexually Dimorphic Organ If people with male brains in female bodies, or the reverse, didn't exist, we would have to ask, why not? Why should the brain, alone of all organs, be somehow 'protected' against being Intersexed, in a way no other sexually differentiated part of the body is?
8. My studies have indicated that far more of our behaviour is "hard wired" than is commonly believed, in particular, gestures, mannerisms, and "body language". There is a societal component, but girls everywhere, from Tierra Del Fuego to Newfoundland, toss their hair, and twiddle with their ear-rings or hair when looking at someone they're interested in. Pupils dilate in both sexes when an "object of sexual interest" is seen.
My chain of logic is inductive, and as follows:
1. We know (P=1.0) intersex conditions occur in all sexually dimorphic organs except the brain 
2. We know (P>0.9999) that the brain is sexually dimorphic ,,,
Hypothesis : Intersex conditions happen in the brain too. (Or why is it a special case?)
Test of Hypothesis:
1. Figure out what the consequences of an Intersexed brain would look like.
2. Look for observations in the Real World that match those consequences, for which there's no other good (ie with reasonable evidence rather than mere supposition) explanation.
If we find them, then the Hypothesis is proven (P>~0.9).
Corollary : The consequences that have been observed are the consequence of an Intersexed brain (P=~0.9).
Consequences of an Intersexed Brain
So, what would be expect from a hypothetical person, such as a female-pattern brain in a male pattern body?
First, the same "gender dysphoria" shown by both natal females and natal males who have hormonal abnormalities, natural or therapeutically induced. For example, many men prefer to die a horrible death rather than partially feminise from hormonal treatment and a bilateral orchidectomy as a treatment for unresectable prostate cancer. The suicide rate in women with hirsutism is very high.
Such cases of clinical depression occur even when there are no visible somatic effects : it is not societal pressure, it is either psychological, biochemical, or both.
Treatment of such a hypothetical person with Hormone Replacement Therapy would be likely to reduce symptoms of depression from having the wrong hormonal mix for the brain's neuro-chemistry.
Second, the Identification of the hypothetical person as someone of the opposite somatic sex. This would be due to them thinking differently from their peers: a female-brained "boy" would think like a girl, a male-brained "girl" would think like a boy. It would be likely that neither group would accept the hypothetical person as a societal member, they would be ostracised and isolated from an early age. "Loners".
This would probably lead to an almost obsessive need to "blend", to become "one of the herd", "part of the crowd", after treatment to make the body and brain congruent. Societal sanction, which would tend to threaten anyone too far outside societal norms with violence, would only increase this tendency.
Objectively, such an obsession with "Stealth" may seem pathological: but given the years of misery, and the very real danger to employment, life and limb, such an obsession may in fact be neccesary for survival, as well as being a quite undrestandable coping mechanism for past psychic stress.
Third, some degree of body dysmorphia, where the instinctive and hard-wired gestures and mannerisms are eiether impossible to implement due to the wrong body shape, or societally discouraged. For example, a female-brained male-bodied person may not be physically able to cross their legs in the "natural" way, due to being musclebound, having the wrong-shaped pelvis, less supple cartilage, and having external genitalia that the brain's body-map insists shouldn't be there.
Adoption of a different societal role (thereby "allowing" certain gestures and mannerisms), and HRT to somatically change things like cartilage suppleness, and fat and muscle distribution, would allow the hypothetical indiidual to act more on instinct, and with less discomfort due to constantly having to censor natural impulses that are hard-wired.
Body dysmorphia, and discomfort with physical appearance, could also lead to a greater than normal pre-occupation with personal appearance post-treatment. Again, societal sanction against anyone looking too "different" would reinforce the perceived and sometimes real need for "heroic measures" such as plastic surgery as part of the therapy. Psychologically, most would require genital correction, both for personal and practical reasons so they could have a "normal relationship".
Fourth, some degree of sexual preference skewing. One estimate is that approximately 10% of males are exclusively Homosexual, and another 10% behaviourally bisexual. The rate for females appears to be 5% exclusively homosexual, and 30% behaviourally bisexual. The mechanism for determining sexual preference is not well-understood, but it's reasonable to assume that it is well-correlated with both brain morphology and hormone levels.
We could expect about 65% of female-brained male-bodied individuals to be apparently "homosexual", 30% to be "bisexual", and 5% to be "heterosexual", ignoring the effect of both societal pressure to conform, and masculinising hormones. Taking those into account, it would be reasonable to expect 40% to appear homosexual, 20% bisexual, and 40% heterosexual, with the proportions reverting to 65/30/5 after hormone and other therapy. Similar arguments for male-brained female-bodied individuals apply, but the vast majority of these would appear Lesbian before therapy, perhaps 25% being attracted to Men beforehand.
Fifth we would expect these symptoms to not be amenable to change except by extensive brain-washing techniques, and then only partially or temporarily. They would also tend to vary with the individual : "male-brained" or "female-brained" is a simplification, in fact, there's a spectrum with two distinct maxima, the traditional bimodal distribution.
We would expect many of the bisexual or seemingly heterosexual female-brained male-bodied individuals to marry and have children, due to the normal female maternal urge. This would contrast with relatively few male-brained female-bodied individuals.
This could lead to a distinct differentiation : those female-brained male-bodied individuals with an unshakeable heterosexual or very mildly bisexual orientation (40-50%) would tend to request treatment early. Those at least partly bisexual or lesbian would seek treatment later, if at all, and mostly only after having had children. This could be reasonably expected to peak at Andropause, when the decreased support of male hormones reaches a critical threshold, so many such people seeking treatment would do so between 45 and 55. Many ( ~50%) such people would find their sexual orientation changing after treatment.
Sixth Some degree of brain anomaly found during autopsies or high-definition dynamic MRI scans. People with the symptoms reported above would, in general, have gross brain structures corresponding to those of the gender oppsite to their body. As the Hypothalamus appears to be associated strongly with sexual identity, that would be a good initial place to look for any differentials.
Seventh Because of the abnormality of brain development, a greater than normal incidence of other minor brain developmental abnormalities could reasonably be expected, such as Asperger's Syndrome or Autism, Ambidexterity, and/or Dyslexia. Hyposmia or Anosmia may be correlated too, as in Kallman's Syndrome.
Speculatively, there may be some Evolutionary advantage to offset the disadvantages of decreased fertility for the individual. Homosexuality appears to be correlated with a 1 SD increase in IQ. Brain Intersex may have a similar correlation with high IQ or other talents.
Summary That is what we could reasonably find should there exist the expected "Brain/Body Gender Mismatch".
There may be other expectations I haven't included, but this seems a reasonable list to begin with. I may easily have included unwarranted suppositions, or missed out important psychological considerations that an expert in the field would consider crucial. Nonetheless, the list would seem plausible as a first approximation.
If we can find a population of individuals with all or most of these symptoms clustered together, the individual symptoms in isolation otherwise being rare, then the case for Brain Intersex existing is very strong: and its corollary, that this population is Brain Intersexed, is also strong.
Does Such a Population Exist?
Any Psychologist or Psychiatrist with knowledge of Gender issues will immediately recognise that the description matches perfectly with one population - those suffering from "Gender Indentity Disorder" with "Gender Dysphoria", namely, Transsexuals.
Trnassexuals, being individuals, do vary: but a surprising number of features are common, so much so that they themselves are astounded that so many others have similar life stories and personality quirks.
The only thing not predicted would be the phenomenon of "CrossDressing", which some 80% of somatically male and 20% of somatically female transsexuals indulge in, ostensibly as a coping mechanism to relieve distress. Apart from that, it's word-pefect. From the otherwise unexplained "primary" (early-transition and "homosexual") and "secondary" (later-transition, and "heterosexual" but with 50% of them changing sexual preference) sub-groups, through to the anomalies in the BSTc layer under the hypothalamus reported in autopsies of transsexuals with or without treatment. Even the consistent reports of intensification of the sense of smell when male-bodied transsexuals start hormone therapy, and the existence of such Yahoo groups as "transsexual-PDD", specifically for the comparatively large number of transsexuals who have Asperger's or similar conditions, "FFS", "trans-surgery", and even individual surgeons' support fora for transsexuals "obsessing" about surgery.
The counter-hypothesis, that Brain Intersex does not exist, but that a population which coincidentally has exactly the expected characteristics of someone Brain-Intersexed (but from another unknown cause) does, and at the same rate as other Intersex conditions (1 in ~1000 to ~10000), defies credulity.
I've made many assertions without adducing the evidence (such as the proportions of Hetero/Bi/Homo-sexuals in a given male/female population), and to make this a reasonable scientific paper, I'd have to add an awful lot of cross-references and studies. It's not in anywhere near a final form, and will have to be revised before I could consider submitting it to a peer-reviewed journal. Nonetheless, despite being open to challenge on the details, I'm very confident my methodology is sound, and only slightly less confident in the conclusion. Add the cross-references, supporting evidence, arguments pro-and-con on each point, and I think a Jury would convict. Or at least fund additional research to confirm or otherwise.
Good enough for a blog entry, anyway.