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What causes autism? By this I don't mean what is to blame i.e. Vaccines, Gluten or Pharmaceuticals etc.. I mean what exactly is happening in the brain to cause the autistic behaviors such as little to no communication skills, regression of skills around age 3, hand flapping etc.. I see a lot of research looking for something to blame however I see little to no research on identifying the physical causes or links (maybe I'm not using the correct search terms).

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There's a significant body of anatomical research that is going on, both in neuropathology and neuroimaging, see ncbi.nlm.nih.gov/pubmed/21360830 for example. –  jonsca Jul 4 '13 at 20:38
    
Thank you both. Your answers are both awesome and both got a +1 from me. I wish I could mark both as the answer! –  Four_0h_Three Jul 8 '13 at 13:06
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Fragile X syndrome is a genetic disorder which is highly related to autism and is considered to be the most common single gene association with autism.

Establishing what actually happens in autistic people is difficult because it is hard to quantify someone as being autistic or not - it is common for some people to show some signs of autistic type behaviour and some people are more extreme than others - plus the symptoms are numerous:

Clinically, autism is defined by a “triad” of deficits comprising impaired social interaction, impaired communication, restricted interests, and repetitive behaviors.

Wikipedia splits the mechanisms in to two key groups, pathophysiology and neuropsychology. The pathophysiological aspects are perhaps better documented and some known correlates to autism are listed:

Our understanding of the mechanisms causing autistic behaviours does not go much beyond this. This paper is a review of the neuroanatomic associations with autism which could, at least in part, help you to identify the physical differences linked to autism.

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Here is a brand new article on autism the-scientist.com/?articles.view/articleNo/36379/title/… –  GriffinEvo Jul 14 '13 at 9:45
    
I just now read this article. That's very interesting and it fits into the pattern of Autism striking with the second child especially if they are conceived close together. –  Four_0h_Three Jan 31 at 20:30
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While still not entirely clear as to what causes autism, there is a growing body of research (as jonsca said), and a model is being developed.

A suggested explanation from "Causes of Autism Spectrum Disorders", that the disorder may begin in utero, with the interaction of genes and nutrients. However,

recent research suggests that Autism may result when a child with a genetic susceptibility and/ or abnormal Omega-3 fatty acid profile in cell membranes is exposed to one or more environmental insults (heavy metal exposure, virus or bacteria) resulting in malfunctioning cells (often in the gut and brain). This can happen “in utero” (during pregnancy) or after birth (post-partum). (from the first link).

Genes seem to certainly play a role, as in the article "Support for the homeobox transcription factor gene ENGRAILED 2 as an autism spectrum disorder susceptibility locus." (Benayed et al. 2005), the homeodomain transcription gene EN2 are associated with Autism, associated with about 40% of the people they tested.

Disorders in the serotonergic system have also been found to be a mechanism of autism, according to "Serotonin transporter genotype and neuroanatomy in autism spectrum disorders" (Raznahan et al. 2009).

I hope this goes part of the way in answering your question.

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