I could have been writing your post a few years ago Dansta. We did all the tests (including the MRI) and they all came back annoyingly clear. My daughter also has low muscle tone (aka the ripped bean poll look), she is also A-typical autistic and used to fit... a lot. I'll walk you though our journey and you can see where it might help you, if at all.
The low muscle tone can effect a lot of areas other than just gross and fine motor, and has particularly affected her speech. My DD didn't crawl until 18 months, walk at 26 months, and talk more than two words until 28 months. The way I would describe it is that when she talks it is kind of plucking a loose guitar string, words and sounds that require more twang are a LOT harder to make, the muscles then have to be purposefully built up so to tighten the string. Games like trying to touch the tip of her nose with her tongue and putting a ball of gelatine (or peanut butter if they're no allergic) on the roof of her mouth and getting her to rub it off with their tongue helped. We will be getting a myomunchi next month which aligns the muscles to be in their best position, although it's most probably a therapy your DS would be a little young for yet. You can actually do a lot of things at home which are better then the occasional therapy session. Some fun games to help with motor skills are ripping long strips of paper down their length or pulling stickers off their backing and putting them on a piece of paper. Both help with fine motor skills. Also don't under estimate finger plays like the "Five little ducks went out one day" or thumbkin. Anything with steps, balls or trampolines are good for gross motor skills. The biggest thing we found helped was music as it requires less work from a different part of the brain and worked on the other side of her brain like jump starting a car. We did Kindermusik and it was amazingly beneficial. It's actually what got her walking and then running a week later.
We did integrated sound therapy and extra lesson through a psych when she was 5. While this mainly for her autism, it also helped balance and fine motor skills improve more dramatically then the health systems OTs and physios therapy as the vestibular system controls balance as well as hearing. Out of curiosity, was he posterior baby? Babies that are posterior generally have immature vestibular systems, and being possy is the first indication that it might be an area that needs work on.
We took her to see an osteopath. He put her on a pre GABA supplement. After four years of fitting and conventional medicine being clueless as to why, the fits stopped. We weren't sure it was the supplement until I forgot to give it to her one day. She got a mothball-like smell on her breath and then away she went. I've made sure never to forget to give it to her again. I later found research that the two main synapses that are involved in a febrile convulsion are the main ones that also produce GABA (Gamma-Aminobutyric acid) which is the amino acid that stops the brain from over-firing. A brain without GABA is like a car engine without oil, the gears (synapses) grind together and sparking (bad behaviour, sensory seeking/avoiding) until the engine catches on fire (fit).
We also give her on a no yeast, reduced gluten and cane sugar diet, as well as give probiotic and enzyme supplement every day to support her gut. Additionally, we bath her with epsom salts to help draw out any nasty chemicals/metals that linger in her system.
Over the years I've researched, I've come to believe that a lot of my daughter's issues have everything to do with absorption problems. This is why she needs the preGABA supplement as she can't create enough on her own, why she gets the smell on her breath, why she's a bean poll and also why she is autistic. I believe her CYP450 enzyme system has been damaged, partly from unneeded preservatives and additives in food, partly from cleaning chemicals I used to use in the home, partly from the toiletries I used to use that are full of sulfates and petroleum, partly from the medications I gave her like antibiotics, panadol and neurofen that sit in the liver for up to five years and inhibit the body from excreting toxic metals, and partly from the vaccinations that are, 1. Given before this enzyme system has even started to develop in a baby (it starts at two weeks and doesn't reach maximum until two years) and, 2. they're made on yeast that unbeknown to me she is intolerant to (whether she was intolerant to the yeast before or after the vaccinations I don't know). On top of this, I find out that yeast overgrowth inhibits white T cells from properly enveloping bacteria and virus's in the body and processing them, so those vaccinations were most probably for naught (even if they work to begin with which I'm not sold on) since she had had oral thrush indicating overgrowth at least three times by the time she was three months old and while I had treated the area of overflow from the overgrowth, I hadn't treated the root source - the gut. For years I had wondered why Vegemite would give her a red bum... its main ingredient yeast of course, duh!
Anyway, on to your little man... I noticed when you listed his breakfast that, 1. They are things that are very high in gluten and 2. That he eats a lot, meaning he either isn't getting enough out of what he is having or he is craving the peptide fix from the gluten. Either way, that's an absorption issue. Gluten feeds yeast, if baby boy has a yeast imbalance it will seriously effect how he absorbs food because the gut will create less digestive acids, the yeast will let off their own toxins, and it also rips little holes in the gut wall allowing heroin like peptides from the gluten into the bloodstream. It can be very easy to test. Remove all gluten, yeast and cane sugar from him for a couple of days (you can get gluten and yeast free bread from the supermarket so he can still have sandwiches and millet makes just as good porridge), if he seriously craves a piece of yeasty wheat bread and even melts down like a drug addict looking for their next fix if he doesn't get it, then you know you're on the right track. My daughter would try to get into the pantry and stuff her face with whole handfuls of raw sugar out of the container - insane.
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