The Kerfuffle Over Whether Men and Women's Brains Are Different.

Nothing kicks up a firestorm in the Neuroscience blogosphere like talk of sex differences in brain architecture. Within days of PNAS's early December 2013 publication of what may be a landmark paper on the differing 'connectomes' (nerve fiber tracts connecting different brain areas) of 428 male and 521 female 8-22 year old humans, a storm of criticism of the work was bouncing around the internet, along with accusations of 'neurosexism'. (see, for example, here, here, here, and here.)
The critics make many points - 1. Men have bigger brains on average than women, possibly conflating results; 2. Maybe men and women move their heads differently while in the MRI machine; 3. The structural differences don't necessarily correlate with behavioral differences, and there are varying results on whether the structural results correlate with cognitive function tests. It is unfortunate that the authors of the study were spouting gender stereotypes...but...it seems to me that the objections are mainly nit-picking, the data are rather compelling on fundamental differences in sexual connectivity that arise from genetic/environmental/cultural factors during brain development. (There is no such thing as 'hard wiring'.):

The results establish that male brains are optimized for intrahemispheric and female brains for interhemispheric communication. The developmental trajectories of males and females separate at a young age, demonstrating wide differences during adolescence and adulthood...The brains of men exhibit a far smaller degree of interconnectedness, both within and across the hemispheres, than do those of women.

I decided to wait for the dust to settle a bit, and let the final publication appear, and sure enough in the same issue there is an essay commentary by Larry Cahill that argues essentially that the politically correct view in brain research has been to assume no significant difference between male and female brain, and to assume results obtained (mainly for male brains) apply also to female brains.  Mouse studies in particular have shown that this is not the case.

...we now know that sex influences—small to medium to large—are extremely widespread on brain function. The validity of the assumption that the sex of subjects cannot powerfully alter, negate, and even reverse findings (hence, conclusions) has been crushed under the weight of evidence proving that it can and regularly does and at every level of investigation down to genes, single neurons, and even ion channels...For neuroscientists cognizant of this striking development, the main challenge now is to better understand the dizzying plethora of sex influences being uncovered. Males and females appear to be two complex mosaics, similar in some respects, mildly to highly different in others

Here is Cahill's summary comment:

A comedian discussing men and women once described the male brain as a bunch of boxes that don’t touch one another and the female brain as a complex ball of interconnected wires. Amusing as the bit was, the analogies may be more apt than he could have known. The findings of Ingahalikar et al. do indeed point to a greater degree of modular function in the physical architecture of the male brain and of interconnectedness in physical architecture of the female brain. Given the size of the study, the consistency of the conclusions across various analytic approaches, and the seeming concordance of key findings with well-established literature addressing brain function, one cannot fairly accuse Ingalhalikar et al. of hyperbole when they claim that their findings “reveal fundamental sex differences in the architecture of the human brain.” Theirs is a landmark paper that should accelerate acceptance of the notion that, for those who want to understand how brains function, sex matters.

And here, finally, is the Ingalhalikar et al. abstract:

Sex differences in human behavior show adaptive complementarity: Males have better motor and spatial abilities, whereas females have superior memory and social cognition skills. Studies also show sex differences in human brains but do not explain this complementarity. In this work, we modeled the structural connectome using diffusion tensor imaging in a sample of 949 youths (aged 8–22 y, 428 males and 521 females) and discovered unique sex differences in brain connectivity during the course of development. Connection-wise statistical analysis, as well as analysis of regional and global network measures, presented a comprehensive description of network characteristics. In all supratentorial regions, males had greater within-hemispheric connectivity, as well as enhanced modularity and transitivity, whereas between-hemispheric connectivity and cross-module participation predominated in females. However, this effect was reversed in the cerebellar connections. Analysis of these changes developmentally demonstrated differences in trajectory between males and females mainly in adolescence and in adulthood. Overall, the results suggest that male brains are structured to facilitate connectivity between perception and coordinated action, whereas female brains are designed to facilitate communication between analytical and intuitive processing modes.