What I eat these days

Breakfast:

I’ve got out of the habit of eating breakfast. I used to eat boiled or scrambled eggs, but recently I haven’t had much of an appetite. Instead of having a tea or coffee, I drink a tablespoon of double cream in hot water. I’ll drink this throughout the day if ever I feel peckish.

Lunch:

Eggs in their many glorious forms!

Sometimes I make a homemade quiche with a fat-heavy Elizabeth David recipe. The pastry has more butter in it than flour, and the filling is five egg yolks, one whole egg, and a pint of double cream. Mmm. I put bacon and cheese on my partner’s half. I leave my half plain and it tastes like a custard tart, or I sprinkle some mild cheddar on top as I can tolerate a bit.

Sometimes I make very fat pancakes – two eggs, a couple of fluid ounces of double cream, a slightly heaped tablespoon of flour and a pinch of bicarb, fried in an ounce of butter. You can eat them with savory extras, or add sugar. Pancakes like this are fragile and don’t flip. You need to slide them onto a plate and turn them over by hand.

Or I’ll have a couple of eggs plain – boiled, poached or scrambled – sometimes with a slice of bread slathered in butter, sometimes with sushi rice (egg fried rice), sometimes I’ll have a bowl of porridge or wheatgerm, or rarely a small portion of well buttered pasta. I’m trying to get used to the taste of goat’s milk.

Sometimes we’ll roast a fresh chicken and eat half the chicken for lunch and the other half for tea.

I oscillate with carbs at lunch time. Sometimes they make me want to snack during the afternoon or they make me feel fat or sick (anything with white flour in it can make me feel sick). If I’m dieting I’ll just have eggs and a creamy drink with a spoon of sugar and that tides me through. I’m lucky: I could eat eggs forever and not get bored of them.

Tea:

Tea usually consists of one portion of meat and one portion of carbs.

I usually eat a 4 ounce portion of beef mince. Though mince is supposed to decay faster, I actually tolerate it better than beef steaks. I’m convinced the farm shop where I buy it mince offcuts of meat that haven’t been hung. Alternately, lamb chops or chicken. We split down whole chickens. We freeze meat in meal sized portions, then defrost in hot water ten minutes before we cook. I fry in a tablespoon of beef tallow. About once a week I’ll get some white fish and shellfish in. Clams, mussels, oysters, and squid are all really nutritious.

If I haven’t had a bowl of porridge or wheatgerm earlier in the day, I might eat one after eating some meat, or have some rice, pasta, bread, or potatoes. I have problems with jacket potatoes – they give me glutamatey symptoms, but I seem to be okay with fried potatoes. I prefer wheatgerm and milk because it’s more nutritious than the other options, though it’s easy to get addicted. The size of this portion is quite small – one ounce of oats or one and a half ounces of wheatgerm with a cup of milk, two ounces of rice, a couple of slices of bread, one hand-sized potato.

I tend to go on and off wheat/oats/milk – two weeks on and two weeks off is my usual pattern. When I diet instead of having carbs I’ll have mince with a couple more eggs. Mince and eggs scramble together really nicely, I don’t know why people don’t eat it! I try to diet a little bit for a week or two then stop dieting for a week or two. I’m anxious not to upset my metabolism too much. The weight seems to stay off better if I take it really easy and stop pressurising myself. Since I started doing this I’ve lost my need to snack all the time and I’m not bothered nearly as much by bread, glutamate and salicylate-related weight gain. I’m the lightest I’ve been since the Christmas before last.

I am currently trying to get used to goat’s milk (yeuch). It does seem to be less addictive/analgesic than Jersey milk. I’ll probably do an isolated trial some time and use it to make rice puddings or just drink a cup plain as my teatime carb portion.

A one or two times a week I might have a portion of mixed beans and pulses instead of the regular carbs. I boil up and cook several different types in separate pans as they all have different cooking times, then split them down and freeze them in different portions. I cook them straight from frozen. For some reason they taste better and are easier to digest after being frozen and cooked again. They’re great for soaking up vast quantities of butter. I can’t eat them every day or I get aminey/glutamatey symptoms like tinnitus.

A one or two times a week I’ll cut up a ripe conference pear and either cook it and eat it with cream, or eat it raw with some big dollops of Häagen-Dazs vanilla ice cream instead of the regular carbs. I can’t eat this every day or I’ll have salicylate symptoms and wake up groggy.

Sometimes at the weekend if my partner is eating lettuce or cabbage I’ll have some with him. When it’s Brussels sprout season in the autumn and winter I might eat those a couple of times a week. One of the biggest psychological barriers I’ve had to get over is not eating fruit and vegetables every day. I feel better without them. Sometimes when I pass the kitchen cupboard I’ll dip my finger in my tub of powdered ascorbic acid and that’s my RDA.

That’s it. It probably sounds like I don’t get a lot of variety, but I actually really enjoy having the choice taken away from me. I never really liked strongly flavoured foods, and I used to be very indecisive and anxious about what to cook all the time. A lot of tribes people live on equally limited diets – just whatever meat they kill and the same local carbohydrate source every day, whether it be potatoes, yams, gourds or whatever.

It probably also sounds like I don’t eat much. I actually average 1,800 calories a day, appropriate for my height and weight, and much less when I’m dieting. I’m actually shocked when I hear the vast quantities other people eat. I could never even imagine eating half a kilo of meat or four or five servings of grains in a day.

A lot of my calories come from butter and cream. I actually feel really good since I started drinking so much cream. My teeth feel smooth and clean all the time in spite of eating carbs and sugar, even when I wake up in the morning. It must be the vitamin K.

I’m not worried about my nutrition at all. I’ve had people from WAPF patronise me about what I eat, but I’m not actually low on anything and I achieve the RDAs of several vitamins that many other people are really deficient in, like vitamins D, E, K, B6 and folate. When I see the way other WAPF members eat, I know in spite of all the talk that they’re not getting those RDAs! My diet is probably more nutritionally balanced and nutritionally dense than ninety five percent of the population, and none of it’s from vitamin supplements or fortified foods.

Eye contact in autistics

Brain tests at UW-Madison suggest that autistic children shy from eye contact because they perceive even the most familiar face as an uncomfortable threat. [...]

Tracking the correlation between eye movements and brain activity, the researchers found that in autistic subjects, the amygdala — an emotion center in the brain associated with negative feelings — lights up to an abnormal extent during a direct gaze upon a non-threatening face. Writing in the March 6 issue of the journal Nature Neuroscience, the scientists also report that because autistic children avert eye contact, the brain’s fusiform region, which is critical for face perception, is less active than it would be during a normally developing child’s stare. [...]

Notably, the UW-Madison study overturns the existing notion that autistic children struggle to process faces because of a malfunction in the fusiform area. Rather, in autistic children the fusiform “is fundamentally normal” and shows only stunted activity because over-aroused amygdalas make autistic children want to look away, says senior author Richard Davidson, a UW-Madison psychiatry and psychology professor who has earned international recognition for his work on the neural underpinnings of emotion.

“Imagine walking through the world and interpreting every face that looks at you as a threat, even the face of your own mother,” Davidson adds. Scientists have in the past speculated that the amygdala – which has been implicated in certain anxiety and mood disorders – plays a role in autism, but the study directly supports that idea for the first time. Eye contact triggers threat signals in autistic children’s brains

I’m totally freaked out by the picture of the man’s face on this page by the way.

It appears to be glutamate receptors in the amygdala that govern fear response, something that ties in with the suspicion of abnormal glutamate function in autism and asperger’s.

I have had a serious, socially disabling inability to make eye contact for most of my life. I only became self-conscious of this during my teens and it was something that really frustrated me and I tried very hard to correct it. Although all I wanted to do was stare at the floor when people talked to me, I would wrestle with myself to try to behave normally and make eye contact. What I felt when I made direct eye contact with people was fear, almost pain. The level of fear ranged from intimidation up to actual stabs of terror. Most often when I had to speak to strangers I would physically tremble.

People find it rude when you don’t look at them when they are talking to you, and I was told off many times for not making eye contact – people assumed that I wasn’t paying attention. The coping mechanism I developed was to repeatedly make eye contact very briefly before looking away again, and to try to appear to be concentrating on what was said to me when I looked away with a ‘concentration frown’ expression. Apparently I wasn’t very good at this expression because people often asked me “what’s wrong?” – misinterpreting what I was trying to express as worry or anxiety. This trait of mine was interpreted as shyness by my family. Asperger’s wasn’t even recognised until 1994.

I’ve chipped away at this fear over the years. It was only in my mid to late twenties that I began to make real headway. I still find it very difficult to look people in the eye for more than a couple of seconds, and often I can only do this by unfocused my eyes and looking through them, smiling and creasing up my eyes in the hopes that this disguises my unfocused gaze. The only people I can genuinely look in the eye for more than a couple of seconds are my partner and my sister.

The folate trials

For want of cash, medical resources and obscure genetic knowledge, I’ve been doing methylation experiments on myself for a couple of years now. I spent my house renovation time continuing that. The events described below are a dramatic portrayal not an actual diary, and are based on multiple, repeated experiments.

The quantities described below are all roughly EU RDA amounts – around 200mcg for folate (any more just doubles the symptoms).

Folic Acid

Day 1: This seems to have helped a lot with my brain fog.
Day 2: This stuff is pretty good. I feel on top of the world! Maybe I’m cured!
Day 3: Hmm, I feel pretty awful if I don’t take this stuff.
Day 4: What is with these rashes, insomnia and nightmares? Why do I have brain fog? I took my folic acid! Maybe I need a higher dose today… Yes, I feel a bit better for that.
Day 5: I am totally dependent on this stuff and it’s making me feel rotten. I have had brain fog all day in spite of taking folic acid. I can’t take a higher and higher dose every day to clear my brain fog!

Folinic Acid (5-formyltetrahydrofolate) – unfortunately this supplement also contains an RDA quantity of methylcobalamin, which obscures results somewhat

Day 1: This seems to have helped A LOT with my brain fog!
Day 2: Damn this stuff is amazing! I am going to use this all the time! I feel great! Wheeee!
Day 3: Why have I got the shakes and brain fog? Never mind, I’ll feel better when I’ve taken some folinic acid! Hmm, that didn’t work as well as I’d hoped.
Day 4: I feel like death warmed up. I am walking around like a zombie. I have to stop taking this stuff before it kills me.

Food Folate (5-methyltetrahydrofolate, 5-MTHF) from failsafe food (mixed beans/pulses)

Day 1: I am having minor issues with bean chemicals, but I feel pretty good and clear.
Day 2: More issues, but I feel pretty good and clear. This tinnitus is a pain.
Day 3: Issues are outweighing the good feeling; I may need to take a break soon. I seem to be gaining some weight. I have tinnitus and insomnia now.
Day 4: I still feel good/clear, but the symptoms are becoming a problem.
Day 5: I feel a bit foggy and my skin is not great, I really need a break.

Food Folate (5-methyltetrahydrofolate, 5-MTHF), Betaine and a bit of MeB12 from failsafe food (wheatgerm with milk)

Day 1: I am having minor bloating issues, but I feel pretty good and clear.
Day 2: More bloating issues, but I feel pretty good and clear. I want some more wheatgerm.
Day 3: I may need to take a break soon. I seem to be gaining some weight. I seem to be craving wheatgerm. Gosh it’s making me sleepy.
Day 4: I still feel good/clear, I seem to be gaining some weight. I feel pretty bloated. I can’t be bothered to do anything.
Day 5: I need to take a break before I get fat and lazy.

Food Folate (5-methyltetrahydrofolate, 5-MTHF), B12 and SAMe from NON failsafe food (liver)

Day 1: I am having some issues with chemicals, but I feel pretty good and clear.
Day 2: I seem to be feeling okay today. I am itching though and have some dermatitis.
Day 3: I seem to have a headache and be itchy and my skin looks awful. I don’t feel as clear today.
Day 4: I feel pretty foggy and awful today with the same symptoms as yesterday. Wish I could get rid of this horrendous back pain. This really can’t go on.

Low food folate failsafe diet

Day 1: I feel fine and I’m glad to be off the wheatgerm/beans.
Day 2: I feel much better but I have some wheatgerm cravings.
Day 3: I feel fine.
Day 4: I feel fine.
Day 5: I seem to be a little bit more sensitive than usual.
Day 6: I do seem to be a bit more sensitive than usual.
Day 7: I think I felt marginally better when I was eating wheatgerm.

Methylcobalamin (Methyl-B12, MeB12)

Day 1: This seems to have helped A LOT with my brain fog! Wish I could get to sleep though.
Day 2: Damn this stuff is amazing! I am going to use this all the time! I feel great! Wheeee! I can’t sleep but what the heck! My skin looks better! God I’m happy!
Day 3: Why have I got the shakes and brain fog? Never mind, I’ll feel better when I’ve taken some MeB12! Hmm, that didn’t work as well as I’d hoped. But my skin is still looking great and I feel really positive!
Day 4: I feel better again today. Hurrah. I really need this MeB12 though! Wish I could sort my sleep pattern out. I seem to have insomnia, yet I’m waking up early! I really need some more sleep! It seems to be making me twitchy too. I feel a bit aminey or glutamatey and I have tinnitus!
Day 5: I still feel pretty good but I really need this MeB12, I have shakes and brain fog without it! I have had some strange tingling sensations in my fingers and toes though. Also I still have that insomnia problem and I keep having hypnic jerks! Not sure I like all the weird dreams I’ve been having. Also, why do I keep getting this strange unpleasant trapped nerve sensation in my neck all the time? I hope I’m not wrecking my myelin with this stuff. But I feel really happy-high and I like the way I have stopped putting on weight when I eat bread!
Day 6: Oops I got overconfident with food chemicals because I thought I was cured. Guess strawberries and old meat were a really bad idea. I feel absolutely horrendous.
Day 7: I feel much better again today. Hurrah. I’m cured, I knew I was! I seem to have lost the ability to spell things though!
Day 7-21: Repeat above ad infinitum.
Day 22: Why have I come down with a cold? I never get colds anymore. Hang on, wait a minute, I came down with colds the last two times I supplemented with MeB12 for a while. Maybe I should stop taking it!

Betaine (Trimethylglycine, TMG)

Day 1: I feel pretty good! This stuff is giving me a bit of insomnia though!
Day 2: I still feel good! More insomnia and hypnic jerks though!
Day 3: I don’t feel as great as I do on MeB12.
Day 4: Yep, I’m fine. This stuff seems to contribute to hypnic jerking when I take it with MeB12.
[More experiments are needed to clarify this one as I rarely take it in isolation.]

S-adenosyl-L-methionine (SAMe) and Folapro (supplement form 5MTHF)

I haven’t tested these yet because I can’t afford the $$$ US shipping expenses.

Conclusions

For diagrams of what I’m describing visit this site.

I suspect as I do well on 5MTHF from food sources that I have a MTHFR polymorphism and can’t use synthetic folic/folinic acids in the same way as food source folate.

I do even better on MeB12, which makes sense as it is a form of B12 that has already been methylated by 5MTHF. Unfortunately the side effects from taking MeB12 aren’t very nice, and taking MeB12, whilst it seems to raise my reaction level, still does not protect me. The MeB12 also has some awful negative effects. It seems to make me manic and is probably raising my amine levels, yet also somehow allowing me to deactivate some of those amines – just not as well as I should be able to. Perhaps this is where an MAO-A or a COMT mutation comes in to play. MeB12 can interfere with melatonin levels, and I suspect this is why it gives me insomnia and makes me come down with infections, since melatonin is important for the immune system.

On top of this, it’s as though the other forms of folic acid are being used in other metabolic processes that are making me feel worse. What I don’t understand is why they make me feel ‘amined’, which seems contradictory *if* I have a MTHFR mutation – unless there is something I am missing. Folate also interacts with the glutamatergic system but I am not clear on what it does at what point in the folate cycle. Am I putting pressure on another polymorphism like MTR (methionine synthase) or MTTR (methionine synthase reductase)? Or am I putting pressure on my detox system in some way? PABA, a folic acid precursor is not failsafe and reactive in its own right. Perhaps regular folic acid is simply being degraded and becoming reactive in some way? Or am I using artificial folic acid to make purines? I must admit to feeling ‘gouty’ on rare occasions – aching toe joints and such, but never anything serious.

As you can see I have yet to make a big impact on my food chemical intolerances, and even if I did I wouldn’t be able to ‘cure’ myself, as my methylation enzymes will always be functioning at a slower rate. I have taken very high amounts of MeB12 (1000mcg) in the past and the result has been a very extreme version of the above portrayal. Sure, I felt great for a while but I had severe hypnic jerks and almost gave myself a seizure. I actually felt better when I stopped the supplements.

Update: I’ve now done a food folate trial with a 5-MTHF supplement (FolaPro). It does the same thing to me as folic acid and folinic acid, only it’s less ‘harsh’ than folic acid, and much less ‘harsh’ than folinic acid.

The grain trials

The problem with most grains is the same as with milk – ‘opioid-like’ proteins. In wheat, rye and barley, these exist in the gliadin fraction of gluten and are called gliadomorphins. Oats do not contain gluten. People on a gluten-free diet often complain of problems with oats and attribute this to the fact that oats can be contaminated with gluten from wheat processing in the factory. Despite the paranoia, the amount of cross-contamination that occurs is negligible, and gluten-free oats can be bought widely. People still tend to cling to the gluten myth because oats are a point of controversy for coeliacs, as some appear to tolerate them well, whilst others experience a return of their symptoms – such as upset stomach and weight loss.

Oats contain an gluten-related, opioid-like protein called avenin. To complicate matters, from what I can gather (which isn’t much), avenin, like gluten, also has lectin-like activity. How gluten-like the proteins are in different strains of oats seems to vary considerably, which might explain some of the contradictory results scientists return when studying coeliac disease. If you are intolerant of oats, it might be worth trying a few different brands and varieties (remembering to take breaks between reactions) to see if you tolerate some oats better than others.

While I’ve been house renovating, I’ve done a series of on-off grain trials over the last few months.

Ever since I was a child, I’ve known I have a problem with bread. I was always fed sandwiches for my school lunches, and I often felt sick trying to eat them. I know that bread makes my stomach feel funny when I eat it – sort of like it is plugging my stomach up. It bloats me immensely and makes my belly stick out within minutes of eating it. For some time now attributing other people’s big bellies to bread eating has been an in-joke between my partner and I. I also read a celeb gossip/fashion rag called Grazia that amuses me sometimes. I think one of the editors there must be a low-carber, familiar with the effects of bread on the belly. Frequently photographs of movie stars who are suffering a bit of bloat will be accompanied by the question, “Is she pregnant, or has she just eaten a bread roll?”

Wholegrain bread has the worst effect. A dense piece of wholegrain bread is like a depth charge. From there on it is downhill… very slowly. Bread constipates me completely. Eat bread: no poo for a few days. It doesn’t matter if it is high fibre bread or low fibre bread, both are equally bad. Fruit sometimes helps to remedy this situation but the results can be variable and often results in upset stomach. This is because the balance of fructose to glucose in fruit promotes diarrhoea (particularly in children, hence lots of babies with very nasty nappies).

It doesn’t matter if the bread is sourdough, homemade slow risen, or commercial bread, they all constipate. I’d say sourdough constipates and bloats a little bit less, but even when I didn’t know about amines, long ferments didn’t solve the problem. One thing I will say though is I tried eating a lot of homemade sourdough bread last summer, and if I stuck to only one slice a day, I actually managed to lose a measly half a pound a week on a strict calorie controlled, moderate (40-70g) carbohydrate diet that also included pears. This is the first and only time I have ever lost weight whilst eating wheat.

Slightly less constipating and bloating than bread is wheat per se – in the form of breakfast cereal, flour, or wheatgerm which I eat as a porridge with milk. These are still constipating and bloating, but I seem to have a better tolerance for them. When I was younger I had to avoid bread like the plague, but I could still handle pasta and some breakfast cereals – though I preferred Rice Krispies and Cornflakes and had to be very careful with Bran Flakes and Weetabix. Annoyingly, from what I can gather, baker’s yeast has both opioid-like and lectin-like activity of its own. I am pretty sure this effect is not a propionate effect, since I make my own bread or eat organic bread.

What happens with me is that if I go from eating no grains to eating grains, I tend to get an upset stomach for 1-2 days. Then I’ll switch from that to constipation. The weird thing about the constipation is that it doesn’t really back up my system. I think I have some very efficient starch-digesting bacteria in my gut that extract every last calorie out of what I eat. I can not go for a week and know I am not particularly backed up, it just melts away out of my colon and turns into fat instead.

As soon as I stop eating the grains I get an upset stomach again, then my bowels normalise. The only time I have normal movements is when I am failsafe, grain and milk free. Food chemicals tend to upset my stomach rather than constipate. Prior to the diet, the overall effect was a kind of mild IBS; constipated most days, diarrhoea sometimes.

Eggs have absolutely no ill effect on my digestion whatsoever. I’m half inclined to think that people who say eggs constipate them are probably comparing a Bran Flakes breakfast to an eggs breakfast. If someone can testify to having done a properly controlled experiment (Bran Flakes versus Bran Flakes plus eggs) I’ll believe them.

I had completely normal BMs for the honeymoon year I had when I started low-carbing. I attribute this to not eating grains or milk, and to the way I think my methylation cycle was behaving during this low-carb, calorie deficient period.

Something I noticed a long time ago is that methylcobalamin somehow counteracts the effects of bloat/weight gain from bread. Apparently people who are trying to detox from opiates use it. So I suspect it has some anti-opiate effect. This may be another reason why my reactions to bread and dairy lessened when I went on the failsafe diet. Having come close to normalising my methylation cycle, I had a higher tolerance of these opioid-like peptides.

My reactions to wheat are more or less the same as milk, except much less subtle:

• Cravings for more wheat, especially bread (must have it every day, any excuse to consume more)
• Increased snacking between meals especially in the few hours after eating wheat, especially bread
• Some drowsiness
• Loss of motivation
• Increased fatigue
• Increased social withdrawal
• Slight increased irritability
• Increased tendency to get headaches, especially sinus/neck/shoulder
• Bloating
• Constipates completely, sometimes upset stomach first
• Weight gain over a period of days (unlike milk which takes weeks)
• Inability to lose weight
• Slower brain

I get slightly different symptoms with oats:

• Irritability a couple of hours after eating, does not repeat if I eat every day
• Stimulant effect, some wakefulness and insomnia at night, does not repeat if I eat every day
• Cravings for more oats (must have them every day, any excuse to consume more)
• Increased satiety, feel full, don’t have to eat for hours
• Loss of motivation
• Increased fatigue
• Increased social withdrawal
• Increased tendency to get headaches, especially sinus/neck/shoulder
• Only slight bloating
• Upset stomach, followed by constipation
• Weight loss during the first 2-3 days, does not continue
• Further weight loss is inhibited

I suspect oats have a relatively small opioid effect, but also contain some sort of stimulant. Oats contain a polyphenol, avenanthramide that has bioactive, allegedly ‘heart healthy’ effects separate from the temporary cholesterol-lowering effects of oats. This polyphenol does not appear to be particularly reactive – it is large and clunky and does not have many O and OH groups sticking out from it, therefore should not be able to bind to as many sites.

Whereas these are my results from eating sushi rice:

• Slight increased irritability after eating, does not repeat after first day
• Stimulant effect, more wakefulness and insomnia at night, does not repeat if I eat every day
• Zero cravings for more (no desire to eat rice ever)
• Weight loss during the first 2-3 days, does not continue unless forced
• No inhibition of further weight loss

I suspect that rice contains some sort of stimulant. I know that on occasions in the past when I have eaten black rice or red rice, the stuff has kept me up all night and even made me throw up, like red wine does. I wonder whether this is related to rice tannins (tannins are polyphenols and also found in red wine). Theoretically white rice should have a very low tannin content, so it’s something I can’t really explain.

So why after all this, do I not give up grains and milk permanently?

Apart from the fact that there would be very little left in my diet if I did, wheatgerm has positive effects on me as well as negative ones. It’s the richest source of betaine (trimethylglycine, TMG) in the human diet, and if you want to achieve an appropriate dose, you need to eat about 1.5 oz of wheatgerm every day, enough to make a bowl of cereal. This will also provide you with about 160mcg of natural form folate. In addition, methylcobalamin is the most abundant form of B12 in milk, and milk is the only real source of methylcobalamin in the human diet.

I tolerate vitamin forms of folic acid, TMG and methylcobalamin very badly. A dose of TMG of half the quantity of that found in a serving of wheatgerm gives me insomnia. An RDA dose of methylcobalamin does the same, and sends me on a manic high. Most forms of folic acid also send me on a manic high. The high lasts for about a week before I crash and burn in an aminey hell or have some sort of rebound reaction of the worst kind. I spent a lot of time before I was on failsafe supplementing with methylcobalamin because it made me feel better in the short term – it has some very positive effects and has pretty much cleared up my dermatitis completely on a couple of occasions. It also has some very negative side effects in the longer term – nerve tingling, trapped nerve sensations, dependency (feel awful in morning until I have taken it), insomnia, hypnic jerks, and I can’t think of one occasion that I have taken it for more than a month without coming down with a nasty cold and crashing – this is why I advise against taking methylation supplements randomly without knowing your genetic makeup.

For some unknown reason milk and wheat don’t have this effect. Perhaps due to racemers in supplements, perhaps due to the forms of vitamins hiding in foods that you can’t get in supplements. 5-methyltetrahydrofolate (5MTHF) – the only version of folic acid people with MTHFR mutations can use, and they can’t recycle it once it has been used. 5MTHF is the predominant form of folate found in foods, but it is not found in regular supplements. The only 5MTHF supplement on the market is a patented version called Folapro, which is very difficult to source in Europe. Because liver and beans/pulses are too aminey for me, wheatgerm is the only real source of 5MTHF I have. Beans/pulses tend to make me feel better for a couple of days, then feel worse as the amines build up. Ideally I ought to rotate them.

In the periods of going off and on different grains and milk, I’ve realised that I actually seem to have a higher tolerance of food chemicals when I eat wheatgerm porridge, an effect I also associate with eggs, which are the only real source of choline in the human diet. I couldn’t eat wheatgerm every day though as I would be fat as a pig if I did.

The problem with the low oxalate diet

The yahoo group trying_low_oxalates is an experimental group promoting an experimental diet that is low in oxalates for a variety of symptoms, in particular for Autism spectrum children. The group has only been in existence since the August of 2005, and is only two years old.

I admire the trying_low_oxalates group in that the people there are focussed, systemised, and highly technical (one could definitely say ‘aspie’). The quality of the posting is much higher than the stuff on the WAPF groups and almost as high as the quality on the orthomolecular/Yasko/autism groups. Many of the people there have been through the wringer trying to cure themselves or their children and are highly familiar with orthomolecular medicine. On top of this their theories aren’t too wild and outlandish as so many aspie theories tend to be. I think that because the talk on the trying_low_oxalates group is so systemised and technical, it tends to attract aspies, rather like flies into a big sticky spider web. Whee, thinks the aspie, I like this; technical language, orthomolecular medicine, smart people like me, and lots of complicated theories!

However, being very aspie, they are also prone to demonstrating the cracked and warped logic that aspies are prone to. They don’t take account for all of their variables, and they pattern spot when there is no pattern. They don’t account for false negatives and false positives or retest what they think they have observed in the past. The difference between science and superstition is the ability to tell the difference between real patterns and false ones, and not to cling to the false ones. Apsies aren’t innately good at this, it has to be something we are trained into whether by ourselves, or by others.

On top of that, once aspies spot patterns, they will become attached to those patterns and believe whatever theory they want to believe regardless of how logical it is or how many flaws you point out. You can tell the average aspie ten times over that you must/must not do this or that to control your variables, and you will be talking to a brick wall. This is because in addition to becoming attached to underlying theories, aspies tend to have a lot of self-belief and a superiority complex and think that no one else could possibly have been through this before them and that they always know better about their bodies than anyone else.

Aspies also don’t like change. Someone, possibly Max Planck, once said “science advances, funeral by funeral.” As the entire scientific establishment seems to be run by mild aspies (‘geeks’) of various extremes, if there is something wrong with scientific progress in general, it is what is wrong with aspies. Aspies hate change. Aspies will build theory upon theory and castles in the sky to explain what does not fit in with their observations.

Back to the point. The major faults with arguments used on the low oxalate group are:

• Oxalates are in all of the same foods that are high in salicylates, amines and glutamates with a very few exceptions.
• Oxalate content of food varies wildly depending on how it is grown, so none of the charts are reliable and accurate and many contradict.
• Oxalates allegedly “cause” the same set of symptoms that people experience to salicylates, amines and glutamates, yet diets low in these chemicals are well documented to resolve those symptoms.

Based on this, it is impossible to regard a low oxalate diet for autism as scientific unless you first control your variables. It is therefore impossible to determine if you have an actual problem with oxalates unless you are first fully on the failsafe diet.

Not many people on the trying_low_oxalates group are on the failsafe diet. A fair proportion of the people there don’t even know what the failsafe diet is. As a result, there is virtually no controlled evidence to support the theory that people’s symptoms are caused by oxalates, since they are still eating salicylates, amines and glutamates. In addition to this, virtually every time I see people complain that they are having a reaction to a food, that food is typically a food that is very high in salicylates, amines or glutamates. Like chocolate or fruit, or a mysterious reaction to ‘protein’. But the people on the group do not see this and are attributing their reaction to oxalates.

How do people get to the trying_low_oxalates group?

People seem to arrive there having done GFCF and having seen only minor changes in themselves or their autistic/ADHD children. At least they have got this far: some people do GFCF and continue to blame every little problem with their health on tiny invisible bits of gluten or casein in their diet (“I/my child ate gluten-free, casein-free ice cream and have had a funny reaction, therefore it must still contain gluten or casein,”) is a cry I have heard several times over, and it’s one that can lead to hysterical levels of paranoia and amusing hidden gluten-hunts when people have reacted to GFCF processed foods – containing reactive ingredients that are usually obvious to an outsider, like tartrazine, artificial flavourings like vanillin, or sulphites that are routinely added to gluten-free flours.

Other people seem to arrive there having done the Feingold diet and also seen only small changes in themselves or their children. This is because the Feingold diet is outdated. The Feingold diet was an attempt in the seventies to cut out or reduce the salicylates and additives in salicylate-sensitive individuals’ diets. At the time not much was known about the salicylates in foods, and no connection had been made to the amines and glutamates in foods. The Feingold diet does not cut out all salicylates, some foods very high in salicylates remain, and it does not cut out amines or glutamates at all. Had Dr Feingold lived, I am sure he would have updated his diet, but unfortunately he died just as the Failsafe diet was being born. I don’t know why the Feingold organisation keep promoting Feingold and keeping quiet about failsafe, it’s embarrassing and rather shameful and probably the single most damaging thing to Feingold’s legacy. The Feingold diet regularly has the critique thrown at it that “this didn’t work for my kid/this only works for a small number of children/I did the diet and it didn’t work for me.” Whether the Feingold diet helps you or not largely depends on how you perform it. If for example you drink lots of Feingold-permitted pineapple juice (high in salicylates and amines), you are not going to see any improvement in your health and it may even worsen.

So some people arrive because GFCF has failed to work for them, and they go on the low oxalate diet, which involves cutting out most high-chemical fruit, vegetables, nuts, and chocolate. And they see a dramatic improvement! Sure, they aren’t perfect. Sometimes they have bad days as well as good days. These may well be days where they have eaten some chemicals, but not knowing it they assume these bad days are a sign that the oxalates are low enough in their blood stream that they are “dumping”, that is, the oxalates are decrystalising and leeching out of their muscles and into their bloodstream. “Dumping” oxalates is rather like candida “die-off”. It’s a great way to explain otherwise unexplainable symptoms in the context of retaining a firm grip on your pet theory.

Other people arrive to the group when the Feingold diet fails to work for them, deciding that they are “not” salicylate sensitive, because they are still eating salicylates, glutamates and amines and the Feingold diet has made no difference. Then they go on the low oxalate diet, which involves cutting out a more comprehensive range of high-chemical foods than Feingold. And they too see an improvement! Which is not surprising at all.

Others still have actually done failsafe. Now we are almost approaching true science. They arrive at the low oxalate diet having never reached baseline. When I see what they are eating or putting on their skin, most of the time I am not surprised they could not reach baseline and sometimes they will reveal mistakes when quizzed. In addition to this is the sad fact that some people are just so sensitive to chemicals and have so many disruptions in their methylation cycle that they will never properly normalise on failsafe. These are the people who really need to go out and spend a lot of money on Yasko’s protocol.

Another very important thing you need to do to reach baseline is sort out any underlying infections, whether fungal or bacterial. Food chemical sensitive people are prone to infections per se. It is well known in the medical literature that certain types of people – for example those with asthma and eczema – are prone to particular types of skin/stomach/ear/nose/throat infection. Food chemicals make these people more prone to infection, but removing food chemicals does not automatically clear up the infection.

Something amazing that I see people doing too, is blaming failsafe for health problems that suddenly appear when they go on the diet.

For example, they may have previously eaten a diet that is gluten free because they have spotted a problem with grains in the past. Though failsafe is quite clear that you should not reintroduce foods that you suspect are a problem, when people go on the diet, they will suddenly decide that they can now eat gluten grains or oats again (‘yippee…’). By doing this they are not controlling their variables. People who are food chemical sensitive seem to have problems, major or minor, with opioid-like peptides, and can also be more sensitive to the lectins in beans and grains and the solanine in potatoes. It is not surprising then, that these individuals suddenly become ill in different ways when they go on the failsafe diet. I have known people to go from a GF oat-free celiac-style diet to suddenly eating almost nothing but oat bran and taking all kinds of dodgy supplements in an impatient effort to ‘cure’ themselves of ‘vitamin deficiencies’ – then suffering all kinds of symptoms of ill health as a result and turning around and blaming the failsafe diet. See what I mean about cracked aspie logic?

Others still never notice a problem with grains before they go on the diet. They can have apparently normal digestion, but a multitude of other symptoms. When they go on the failsafe diet, their symptoms change. It is perfectly normal for symptoms to change when you go on the diet. Suddenly new and different symptoms emerge when you have infractions. Old symptoms disappear and don’t come back unless you commit a more extreme infraction. A person who may not have ever noticed a problem with grains in spite of their other symptoms, suddenly discovers they get an upset stomach when they eat grains once they are failsafe. In reality, the person has always had a problem with grains, but that problem was never noted, or expressed itself differently, for example with headaches, cravings or brain fog instead of stomach upset. It may even be that the grains are being eaten differently, for example the person has changed from using sourdough bread to regular bread to reduce amines, unfortunately resulting in an increase in lectins, hard to digest long-chain starches, and gluten opioid peptides. Either way the answer is not to blame the failsafe diet, it is to reduce these extraneous factors.

If you have been through all of this, controlled your variables properly, exhausted these options and you are still not at baseline, then you can start to clarify whether you have an issue with oxalates.

By this time you are probably about to complain that you have already incidentally cut out all oxalates from your diet, so how could you possibly prove your problem is oxalate related? Well, I never said life was easy, but it is possible to vary the quantity of oxalates you eat on the failsafe diet.

• If you have oxalate-based kidney stone symptoms, or start to pass little bits of grit in your urine, you probably have an oxalate problem.
• If you have an officially recognised oxalate-related problem, like gout, rheumatoid arthritis, or vulvodynia, you should see an improvement and if you do see an improvement you probably have an oxalate problem.
• Vitamin K MK4 dissolves oxalate crystals. Try yourself on small quantities over a few weeks and see what happens. Megadoses are likely to induce clotting, which may feel to you a lot like oxalate “dumping”, so it is important to be sensible and think about what you are doing and feeling. Other supplements like citrates and malates may also be helpful.
• If you have accounted for all of the variables mentioned above, and you are eating a low-salicylate, low-oxalate diet and have not improved over the timescale of a couple of months, you probably don’t have a problem with oxalates.
• If you have tried taking out and adding back in failsafe vegetables to your diet and this makes no difference to how you feel in general, try eating some of the very few high-oxalate, low-salicylate vegetables, versus some of the low-oxalate, low-salicylate vegetables. This should make an easily discernible difference to how you feel if oxalates are an issue. If it does not, you do not have an oxalate problem.

The problem with chelation therapy

Something that often happens when people realise they are food chemical sensitive and/or especially if they are on the autism spectrum, is they automatically think the problem must be connected to mercury poisoning, or another heavy metal poisoning. But rule #1 any scientist should abide by, is that correlation does not denote causality.

People don’t like to think that autism is genetic: there is a moral panic in our society regarding the health of and how we raise our children, and a second moral panic in our society regarding industrial chemicals and toxins and the harm they can do to our health. The persistent assertion in our shared popular culture is that both of these things are getting worse in our society. These two moral panics neatly bisect on the subject of autism, and the natural conclusion of anyone introduced to the subject is that, somehow, heavy metal poisoning must be causing both autism and food chemical sensitivities, because neither of these health problems could be ‘natural’, could they?

The next reaction is to go through all of the alternative health theories of autism: that autism is caused by ‘gut dysbiosis’, by ‘parasites’, by ‘the wrong type of carbohydrate’, by ‘gluten and casein’, by ‘heavy metal poisoning’, by ‘vaccinations’, or by ‘vitamin deficiencies’. A number of these problems do correlate with autism – but that doesn’t necessarily make them the cause, rather they are a feature of the same underlying condition.

People with autism thought to be low on glutathione, sulphate, and methyl donors. Sometimes they are and sometimes they aren’t. This means that they don’t detox a variety of chemicals and heavy metals from their body as well as other people. When autistic people are found to have high levels of heavy metals in their bodies (and not all are and non-autistics can have high levels of metals too), it is usually because they are not detoxing them as well as other people, not necessarily because they have been exposed to an abnormal level of a poison – be that thimerosal, MMR, amalgam fillings or any other chemicals or metals in the environment.

Heavy metal toxicity has a range of medically recognisable symptoms. If you have heavy metal toxicity and you are experiencing these symptoms, it doesn’t necessarily mean they are also causing your autism, or your food chemical sensitivities, or your fibromyalgia. It is more likely that you are experiencing all of these things due to the same underlying pathway in the body being compromised. Unfortunately these symptoms heavily overlap the symptoms food chemical sensitivity, so it is possible to become very confused and convinced that you have a problem with heavy metals when in fact you do not, or that heavy metals have caused your salicylate issue, when in fact they have not, they just coexist.

Sometimes when people suspect that they are heavy metal poisoned, they will panic and have their amalgam fillings removed. This is a very dangerous thing to do. Unless you have your amalgam fillings removed by a specialist who uses a dental dam and piped oxygen, you are liable to actually give yourself acute mercury poisoning by having the fillings removed! Amalgams release much more mercury when they are disturbed than they do when they are sat in your mouth. If, three months later, you then have a metal toxicity hair test done, you are liable to confirm your worst fears!

Next, if someone finds they have an unusually high level of heavy metals in their body, the first thing they usually do is arrange chelation therapy. Sometimes people are so convinced that heavy metals are the cause of their problems that they will do this even if their heavy metal levels are in the normal range or only very slightly raised. Any very slightly raised level is seen as confirmation of a problem that in reality may or may not actually exist.

The problem with this is that the chelation chemicals in themselves are reactive and cause unpleasant side effects:

DMSO therapy: DMSO (dimethylsulfoxide), a sulphur based compound, and the liquid version of MSM. Any individual who reacts to sulphur will usually react to DMSO. It’s known side effects include nasal congestion, shortness of breath or troubled breathing (asthma), skin rash, erythema, itchiness, scaly skin, skin thickening, hives, swelling of the face, blistering, skin pain, nausea, diarrhea, headache, garlic-like taste in mouth, garlic-like breath, garlic-like body odor, transient hemolysis, dizziness, sedation, kidney injury, light sensitivity, color vision disturbance, corneal opacities in animals and birth defects in animals.

DMSA therapy: DMSA (dimercaptosuccinic acid), is also sulphur based, containing two carboxylic acid groups and two thiols. Any individual who reacts to sulphur will usually react to DMSA. It’s side effects include diarrhea, loose stools, loss of appetite, nausea and vomiting, skin rashes, chills, fever, immune system impairment in developing foetuses, and unpleasant odour of urine, sweat and faeces.

DMPS therapy: DMPS (dimercaptopropane sulfonate) is also sulphur based. Any individual who reacts to sulphur will usually react to DMPS. It’s side effects include ‘allergic’ reactions, agitation, burning sensation of mouth, throat and eyes, chest constriction or feeling of tightness in the chest, cardiovascular reactions – dizziness, weakness, lowering of blood pressure, heart palpitations or tachycardia, nausea, vomiting, and tingling of the extremities.

Reactions usually vary in character based on dosage. At a low dosage, you might experience histamine degranulation causing rashes, or asthma, and at a high dose
you might experience vomiting and diarrhoea. All of the sulphur-based substances need to be detoxified in themselves through the sulfite oxidase (SUOX) enzyme. People who have an upregulated cystathionine beta synthase (CBS) enzyme are already putting an extra load on this pathway. These are two of the enzymes that has been flagged up by Yasko and others as having an association with autism, and of course an intolerance and reactivity towards sulphur and sulphites.

EDTA therapy: EDTA (ethylenediamine tetraacetic acid) is a chemical compound containing two amine groups and four carboxylate groups. It ‘looks’ suspiciously reactive. EDTA in itself needs detoxifying from the body. It is known to cause ‘allergic’ reactions, and reported side effects of EDTA include low blood sugar, skin irritation, diminished calcium levels, cramps and tics, headache, nausea and upset stomach, dangerously low blood pressure, kidney failure, organ damage, irregular heartbeat, seizures, and even death.

EDTA is the only chelation therapy that Dr Amy Yasko approves of, because all sulphur based chelators are known to be so problematic to the chemically sensitive. However Yasko does not seem totally clear on the importance of avoiding food chemicals. The side effects of EDTA seem just as ‘reactive’ as sulphur-based chelators, and EDTA superficially resembles gallates and amines in structure.

Sometimes so-called alternative therapists will diagnose mercury poisoning purely based on a DMPS or other challenge test, consisting of injecting a quantity of the chemical into the blood stream and watching for reactions. If the patient reacts to the drug, they are diagnosed as having been mercury poisoned.

The problem with this as you can see is that chelation drugs have some very powerful side effects. They are in and of themselves reactive and tend to affect those with food chemical problems. However, the lay person and any badly educated therapist or quack will attribute these reactions to “mercury being freed up and circulating around the body.” The ‘mercury’ whether it exists or not is blamed for the reaction caused by the chelation drugs, and the hypothesis of heavy metal poisoning is reinforced.

What I find disturbing about this situation is that people can become trapped in a spider’s web of the mind: they blame heavy metals for autism or food chemical sensitivities, they undergo chelation therapy and react to the chelators, and then blame the reactions on the removal of mercury, when in fact they are side effects and are inevitable in those who have food chemical sensitivities. Every time they undergo chelation therapy, they keep reacting, which reinforces in their mind the need to continue with the chelation therapy to ‘cure’ their problems with food chemicals. This can continue ad infinitum for year upon year, long after the heavy metals are actually gone – if they were even there in the first place.

This is why it is extremely important to test and retest your urine, blood and hair levels of heavy metals regularly, and to think about using alternative methods of detoxification.

There are less painful ways to detoxify your body of heavy metals. Most people can detoxify normal amounts of heavy metals naturally – the food chemical sensitive and those with liver/kidney problems are more of an exception. When someone who is food chemical sensitive goes on the failsafe diet, it helps to restore their normal detox systems. They often find that a wide range of chemicals and metals start to come out of their body naturally when they stop eating them on a continual basis. This process may take several weeks or months. Genetically appropriate methylation/sulphation supplements will also help to restore detox systems, as will alpha lipoic acid and selenium, sweating more, getting enough sunlight, and using a far infrared sauna.

Two genetic theories of autism

If you’ve had a chance to read and digest The Times article I posted yesterday, I’d like to elaborate.

I posted this article because it is a pretty good overview of where modern mainstream medicine is at the moment. Genes aren’t specifically named in the article, but the subtext of ‘many common polymorphisms’ seems to be there.

Autism is thought to be caused by polymorphisms and mutations in various different neurotransmitter receptor/signalling/transport genes – such as the dopamine receptor genes I mentioned. In addition scientists have been looking at alterations in glutamate signalling/function as well as serotonin signalling/function.

The article lays out the two main genetic theories of autism:

1. Autism is caused by a ‘cocktail’ of different single nucleotide polymorphisms that have different effects on the personality, and when a particular combination appears together, this produces an extreme result as in autism.
2. Autism is caused by ‘random new mutations’ that change the function of the brain, because many new mutations have been found in autistic children.

In my opinion, it is the first theory which produces the second effect.

In other words, the ‘cocktail’ of different genes are the naturally occurring, heritable polymorphisms. These polymorphisms are not new and have existed for millions of years. Similar polymorphisms occur in most other species and are not restricted to Homo Sapiens Sapiens.

There’s little substance and much belief among some members of WAPF at the moment that autism must be caused by DNA undermethylation – that autistics are Pottenger’s children because of the bad diet of their parents, and what you need to avoid autism is lots of folate during pregancy. In fact what is suggested by the science is that only a ten percent minority of autistics have ‘random new mutations’, and these may or may not be influenced by folate consumption.

It is unclear how much epigenetics has to do with autism. Just as poor DNA methylation and other  non-nutritional factors produce spontaneous mutations, methylation also has the effect of reprogramming or turning on and off existing ‘transposon’ genes – the small percentage of junk genetic code added to our DNA by viruses. There is no evidence that autism is an epigenetic condition or not an epigenetic condition, but there is plenty of existing evidence that it is a regular genetic cocktail effect based on normal genes. We seem to have a perfectly plausible and fully working understanding of autism spectrum without adding epigenetics into the mix. However, certain named and well understood forms of autism like Rett syndrome (missing X chromosome) and Fragile X have been connected to possible undermethylation of DNA in already risky genotypes.

People with polymorphisms in their methylation genes (like MTHFR variants) are known to have higher rates of neural tube defects and spontaneous genetic mutations than the rest of the population – a problem that is not always fixable with folate, particularly when an inefficient enzyme is already working to capacity. MTHFR polymorphisms in and of themselves reach high statistical significance within autistic populations, along with COMT and GST. MAO-A has been linked to autism severity, with sex-linked differences connected to the fact that MAO-A resides on the female X chromosome so boys only have one copy. Only MTHFR is directly related to DNA methylation. Further, there is a survival advantage in MTHFR variants, it’s a classic example of ‘the selfish gene’ at work – the more and faster you mutate, the quicker you can adapt to new environments, and the faster you will outpace other members of your species. The disproportionate number of new mutations found in the genes of autistic children could well be as a result of a crunched up methylation cycle in the parents that is perfectly natural. I prefer this theory to the over-simplistic parental-blame-apportioning theory from holier-than-thou WAPF members.

Epigenetics, transposons and Pottenger's cats

A Pregnant Mother’s Diet May Turn the Genes Around

With the help of some fat yellow mice, scientists have discovered exactly how a mother’s diet can permanently alter the functioning of genes in her offspring without changing the genes themselves.

The unusual strain of mouse carries a kind of trigger near the gene that determines not only the color of its coat but also its predisposition to obesity, diabetes and cancer. When pregnant mice were fed extra vitamins and supplements, the supplements interacted with the trigger in the fetal mice and shut down the gene. As a result, obese yellow mothers gave birth to standard brown baby mice that grew up lean and healthy.

Scientists have long known that what pregnant mothers eat — whether they are mice, fruit flies or humans — can profoundly affect the susceptibility of their offspring to disease. But until now they have not understood why, said Dr. Randy Jirtle, a professor of radiation oncology at Duke and senior investigator of the study, which was reported in the Aug. 1 issue of Molecular and Cellular Biology.

The research is a milestone in the relatively new science of epigenetics, the study of how environmental factors like diet, stress and maternal nutrition can change gene function without altering the DNA sequence in any way.

Such factors have been shown to play a role in cancer, stroke, diabetes, schizophrenia, manic depression and other diseases as well as in shaping behavioral traits in offspring.

Most geneticists are focusing on sequences of genes in trying to understand which gene goes with which illness or behavior, said Dr. Thomas Insel, director of the National Institute of Mental Health. ”But these epigenetic effects could turn out to be much more important. The field is revolutionary,” he said, ”and humbling.”

Epigenetics may indeed hold answers to many mysteries that classical genetic approaches have been unable to solve, said Dr. Arturas Petronis, an associate professor of psychiatry at the Center for Addiction and Mental Health at the University of Toronto.

For example, why does one identical twin develop schizophrenia and not the other? Why do certain disease genes seem to affect or ”penetrate” some people more than others? Why do complex diseases like autism turn up in more boys than girls?

For answers, epigeneticists are looking at biological mechanisms other than mutation that affect how genes function. One, called methylation, acts like a gas pedal or brake. It can turn gene expression up or down, on or off, depending on how much of it is around and what part of the genetic machinery it affects.

During methylation, a quartet of atoms called a methyl group attaches to a gene at a specific point and induces changes in the way the gene is expressed.

The process often inactivates genes not needed by a cell. The genes on one of the two X chromosomes in each female cell are silenced by methylation.

Methyl groups and other small molecules may sometimes attach to certain spots on chromosomes, helping to relax tightly coiled strands of DNA so that genes can be expressed.

Sometimes the coils are made tighter so that active genes are inactivated.

Methyl groups also inactivate remnants of past viral infections, called transposons. Forty percent of the human genome is made up of parasitic transposons.

Finally, methyl groups play a critical role in controlling genes involved in prenatal and postnatal development, including some 80 genes inherited from only one parent. Because these so-called imprinted genes must be methylated to function, they are vulnerable to diet and other environmental factors.

When a sperm and egg meet to form an embryo, each has a different pattern of methylated genes. The patterns are not passed on as genes are, but in a chemical battle of the sexes some of the egg and sperm patterns do seem to be inherited. In general, the egg seems to have the upper hand.

”We’re compounds, mosaics of epigenetic patterns and gene sequences,” said Dr. Arthur Beaudet, chairman of the molecular and human genetics department at Baylor College of Medicine in Houston. While DNA sequences are commonly compared to a text of written letters, he said, epigenetics is like the formatting in a word processing program.

Though the primary letters do not vary, the font can be large or small, Times Roman or Arial, italicized, bold, upper case, lower case, underlined or shadowed. They can be any color of the rainbow.

Methylation is nature’s way of allowing environmental factors to tweak gene expression without making permanent mutations, Dr. Jirtle said.

Fleeting exposure to anything that influences methylation patterns during development can change the animal or person for a lifetime. Methyl groups are entirely derived from the foods people eat. And the effect may be good or bad. Maternal diet during pregnancy is consequently very important, but in ways that are not yet fully understood.

For his experiment, Dr. Jirtle chose a mouse that happens to have a transposon right next to the gene that codes for coat color. The transposon induces the gene to overproduce a protein that turns the mice pure yellow or mottled yellow and brown. The protein also blocks a feeding control center in the brain. Yellow mice therefore overeat and tend to develop diabetes and cancer.

To see if extra methylation would affect the mice, the researchers fed the animals a rich supply of methyl groups in supplements of vitamin B12, folic acid, choline and betaine from sugar beets just before they got pregnant and through the time of weaning their pups. The methyl groups silenced the transposon, Dr. Jirtle said, which in turn affected the adjacent coat color gene. The babies, born a normal brownish color, had an inherited predisposition to obesity, diabetes and cancer negated by maternal diet.

Unfortunately the scientists do not know which nutrient or combination of nutrients silence the genes, but noted that it did not take much. The animals were fed only three times as much of the supplements as found in a normal diet.

”If you looked at the mouse as a black box, you could say that adding these methyl-rich supplements to our diets might reduce our risk of obesity and cancer,” Dr. Jirtle said. But, he added, there is strong reason for caution.

The positions of transposons in the human genome are completely different from the mouse pattern. Good maps of transposons in the human genome need to be made, he said. For that reason, it may be time to reassess the way the American diet is fortified with supplements, said Dr. Rob Waterland, a research fellow in Dr. Jirtle’s lab and an expert on nutrition and epigenetics.

More than a decade ago, for example, epidemiological studies showed that some women who ate diets low in folic acid ran a higher risk of having babies with abnormalities in the spinal cord and brain, called neural tube defects.

To reduce this risk, folic acid was added to grains eaten by all Americans, and the incidence of neural tube defects fell substantially. But while there is no evidence that extra folic acid is harmful to the millions of people who eat fortified grains regularly, Dr. Waterland said, there is also no evidence that it is innocuous.

The worry is that excess folic acid may play a role in disorders like obesity or autism, which are on the rise, he said. Researchers are just beginning to study the question.

Epidemiological evidence shows that undernutrition and overnutrition in critical stages of development can lead to health problems in second and third generations, Dr. Waterland said.

A Dutch famine near the end of World War II led to an increased incidence of schizophrenia in adults who had been food-deprived during the first trimester of their mothers’ pregnancy. Malnourishment among pregnant women in the South during the Civil War and the Depression has been proposed as an explanation for the high incidence of stroke among subsequent generations.

And the modern American diet, so full of fats and sugars, could be exerting epigenetic effects on future generations, positive or negative. Abnormal methylation patterns are a hallmark of most cancers, including colon, lung, prostate and breast cancer, said Dr. Peter Laird, an associate professor of biochemistry and molecular biology at the University of Southern California School of Medicine.

The anticancer properties attributed to many foods can be linked to nutrients, he said, as well as to the distinct methylation patterns of people who eat those foods. A number of drugs that inhibit methylation are now being tested as cancer treatments. Psychiatrists are also getting interested in the role of epigenetic factors in diseases like schizophrenia, Dr. Petronis said.

Methylation that occurs after birth may also shape such behavioral traits as fearfulness and confidence, said Dr. Michael Meaney, a professor of medicine and the director of the program for the study of behavior, genes and environment at McGill University in Montreal.

For reasons that are not well understood, methylation patterns are absent from very specific regions of the rat genome before birth. Twelve hours after rats are born, a new methylation pattern is formed. The mother rat then starts licking her pups. The first week is a critical period, Dr. Meaney said. Pups that are licked show decreased methylation patterns in an area of the brain that helps them handle stress. Faced with challenges later in life, they tend to be more confident and less fearful.

“We think licking affects a methylation enzyme that is ready and waiting for mother to start licking,” Dr. Meaney said. In perilous times, mothers may be able to set the stress reactivity of their offspring by licking less. When there are fewer dangers around, the mothers may lick more. A Pregnant Mother’s Diet May Turn the Genes Around

For more information on epigenetics, visit the Wikipedia definition of epigenetics, and to see similar articles on the subject visit this web page.

This subject has a possible relationship to autism. However, it isn’t quite the relationship that a typical Weston A. Price Foundation member thinks (“we just need to eat a really nutritious diet when we are pregnant and then our children will all grow up healthy!” which is very much a happy-sunshine-pretty-birds-and-flowers view of the world).

You can max-out the DNA methylation capacity of most mice with a few times the amount of nutrients found in the average mouse diet (I wonder what they were being fed incidentally?), and you can conceivably do the same thing with most humans – hence US guidelines to take about 600mcg of folic acid whilst pregnant. However, most is not all.

Some people are genetically predisposed to poor DNA methylation. These are people with naturally existing polymorphisms in methylation cycle. Several types of polymorphisms mean that some people do not process the folate from foods and folic acid from supplements in the same way as the average person. Their bodies find it hard to use folic acid to methylate vitamin B12. Polymorphisms exist throughout the methylation cycle, and in theory, the more you have, at the wrong combination of points, the harder it will be for you to methylate your DNA and the more vulnerable you will be to the expression of transposons. This isn’t all bad, because people with a lower turnover of DNA tend to live longer, however, you may be more prone to metabolic distortions such as some types of obesity, or certain inherited illnesses.

Some time after Pottenger did his cat experiments which produced epigenetic distortions that lasted through several generations, scientists discovered that cats are unable to synthesise taurine in their bodies. Taurine is a protein that is damaged by cooking food. Taurine is required for correct DNA methylation. It prevents DNA hypermethylation under some circumstances. In fact DNA hypermethylation can be just as harmful as DNA hypomethylation. By inactivating genes that ought to be activated, the body can become prone to cancer and other metabolic problems. It seems, like Goldilocks, the best state for DNA is not too hot, not too cold, but ‘just right’.

For more information about DNA methylation visit the DNA methylation page on Wikipedia.

Endogenous retroviral DNA consists of roughly 4-8% of the total human genome.

Autism genome project

This is an article I read today in The Times:

Parents and scientists are hoping that a new detailed analysis based on human genome will bring a big breakthrough within a year

It has become one of the most controversial and feared medical diagnoses of modern times. Autism was barely spoken of a generation ago but it has been forced into public consciousness by the row over the MMR vaccine and the growing realisation that it is much more common than doctors had imagined.

The suggestion that the developmental disorder can be triggered by the MMR vaccine has been shown to be scientifically unfounded, but it prompted thousands of parents to agonise over the cruel condition that seems to leave children walled off in a social and emotional world of their own, apparently beyond their love.

Their concerns have also been fed by reports of an autism epidemic. A disorder that was once rare has become alarmingly common, with as many as one in 100 children now thought to be affected in some way.

Even if much of this is explained by better diagnosis, the condition retains a brutal mystery. What is it that makes children who seem normal at birth regress suddenly a year or two into life? Now a change in science’s ability to decipher how genes influence health is promising to pin down what autism owes to inheritance.

Within the next year a new study is expected to identify many of the genes that underlie autism for the first time. At the same time, two new theories are challenging established thinking about autism genetics in ways that could ultimately transform diagnosis and treatment.

“The medics tell me we are at a tipping point,” said Dame Stephanie Shirley, the millionaire computer entrepreneur and philanthropist, who is the chairman of the research charity Autism Speaks and the mother of an autistic son.

That genetics are the chief cause of autism has been known for three decades. It was in 1977 that Professor Michael Rutter, of the Institute of Psychiatry at King’s College London, published a twin study that transformed the understanding of its origins.

Twin studies are one of the mainstays of genetics. Because identical twins share all of their genes while fraternal twins share only half, and both share broadly similar environments, comparisons can tease out the relative contributions of nature and nurture.

Professor Rutter found that if an identical twin was autistic, it was highly likely that the other twin was autistic too. Fraternal twins, however, were no more likely to share the diagnosis than ordinary siblings. This made it certain that genes played a large role and it is now thought that autism is among the most heritable of all psychiatric disorders. Genetics account for most of the variance and, although environmental factors matter too, they are less important.

The condition, however, has remained a genetic paradox. For all the certainty that genes are heavily involved, it has proved impossible to discover which ones are guilty. In the 30 years since Professor Rutter’s study, hundreds of genetic mutations that affect health have been found. Most are single-gene disorders, where inheriting a rogue gene invariably means developing a disease such as Hunting-ton’s, which affects the central nervous system. Most of the others have involved very high risks: women with abnormal variants of the BRCA1 gene, for example, have an 80 per cent risk of developing breast cancer.

Autism does not work like that: the search for genes with such large effects has failed. It might be influenced by dozens of genes, each of which raises the risk by amounts too small to have been detected. Or it could be the result of spontaneous mutations instead of more easily tracked defects that are passed from generation to generation. Science does not yet know.

The scientific success story of 2007 has been the coming of age of a new method of gene-hunting that can find the sort of genes with weak effects that are thought to influence autism. These genome-wide association studies compare the DNA of thousands of people who have a disease with healthy controls, using tools called “gene chips” to screen the entire human genome for hundreds of thousands of tiny genetic variations that differ between the two groups.

In recent months, the technique has revealed scores of genes that subtly influence common conditions such as diabetes, heart disease, breast cancer and multiple sclerosis, often raising the risk by as little as 10 per cent.

Autism is the next target. The Autism Genome Project (AGP), an international consortium that studies more than 1,000 families with at least two autistic members, is about to apply the tool to its database.

“We have been waiting ten years for the technology to do this,” said Antho-ny Monaco, of the University of Oxford, one of the project’s leaders. “We were never likely to understand until we were able to screen very large numbers. The probability has always been that autism is highly genetic, but highly heterogeneous – that lots of different genes are involved. We now have a great chance of picking them up.”

The AGP’s genome-wide association study is a classic example of win-win science. Even if it draws a blank, it will still shed new light on the genetic origins of the condition. No results would mean one of two things. It could be that the effects of the genes responsible are even tinier than suspected and bigger samples are needed. Or it could be that a radical new theory of autism genetics is correct.

Professor Michael Wigler, of Cold Spring Harbour Laboratory in New York state, believes that autism might be the result of single genes with big effects after all. These mutations, however, are not quite the same as the inherited ones that cause diseases such as Huntington’s.

According to his model, most cases of autism are caused by random, spontaneous mutations in the sperm or eggs of parents that are passed on to individual children. Most of these then develop the condition but some, particularly girls, do not. They are somehow resistant and, although they carry a potentially harmful mutation, they do not suffer its consequences.

This may explain why autism is an overwhelmingly male disorder, four times more common among boys than girls. It fits with data showing that the children of older parents are at higher risk: sporadic mutations of this sort increase with age. It also points towards an intriguing explanation for the existence of high-risk families with more than one autistic child. Professor Wigler’s research suggests that in these families, a mutation first occurred in one of the parents, usually the mother. While she was immune, probably because of her gender, her sons were not so lucky: half of them would be autistic, depending on whether they inherited the rogue gene.

“Sporadic autism is the more common form of the disease and even the inherited form might derive from a mutation that occurred in a parent or grandparent,” the professor said.

If mutations of this sort are responsible, they would not show up in the AGP: they are new and unique to individuals and families, so will not surface from large comparisons of DNA.

“That is one of the exciting things about our work,” Professor Monaco said. “If we find genes, it is interesting and if we don’t find genes, it is interesting too.”

What Professor Wigler’s theory does not account for is another aspect of new thinking about autism: that it may not be a single disorder.

For autism to be diagnosed, children must meet three criteria: they must show social impairment, communication difficulties and nonsocial problems such as repetitive and restricted behaviour. Yet there is an emerging consensus that these traits do not always go together and that there are people who meet the criteria for one or two characteristics but who do not receive any diagnosis. Autism, in short, may be the confluence of three separate developmental conditions. Only when they occur together is the result devastating.

Research by Angelica Ronald, Franc-esca Happé and Robert Plomin, of the Institute of Psychiatry, has suggested that each of these three problems is influenced by different sets of genes. The twin studies have shown that while each trait is highly heritable, they do not often overlap.

“The label autism is something that was applied to a set of behaviours that were first described in the 1940s,” said Dr Ronald, who is funded by Autism Speaks. “It’s not necessarily a label for a clear biological entity and in research it may be a misnomer to assume it’s one thing.”

This has important implications for gene-hunting. It could be that genes have not been found because scientists have been treating autism as a whole. If different genes affect the communication and social elements of the disorder, finding them might involve looking at people who are not autistic, but who have mild versions of one of the problems. “We need to tackle whether we should look at autism as a single phenomenon, or whether it would be better to look, for example, just at autistic social problems,” Dr Ronald said.

Such an approach would also be valuable by shedding immediate light on what any genes that are found actually do.

Dr Ronald added: “If we split up the symptoms, we can know that these genes are going to be involved in social problems and those ones in nonsocial problems. That is obviously going to be valuable when we look towards diagnosis and treatment.”

An understanding of which genes are involved in which parts of autism should help doctors to spot the condition earlier. It would also prepare parents for the way their child is likely to develop and it could help with the design of therapies.

Dame Stephanie is excited by the pace of change. “It is quite possible that in five to ten years, we will have a real understanding of this disorder,” she said. “That’s a timescale that means today’s children may be helped.” Hunting the gene that traps children in their own world

Sidebar:

Difficulties – and above-average intelligence

— Autism is a developmental disorder that first becomes apparent by the age of 3

— It is part of a group of disorders known as the autistic spectrum, which include Asperger’s syndrome, a milder form of the condition

— 1 in 150 children is given a diagnosis of autism

— Boys are four times more likely than girls to have autism

— Autism is defined by three main impairments:

Social interaction

This ranges from a lack of intuition of social stimuli to the inability to form attachments to carers

Communication

Autistic children show impairments such as delays in language development and a reduced ability to initiate and sustain conversations

Restricted, stereotyped repetitive behaviour

These include obsessively arranging objects or following very specific routines

— Other problems include phobias, sleeping and eating disturbances, tantrums and self-directed aggression

— Many autistic children show above average intelligence

— There are no current effective means to prevent, treat or cure autism

Sources: Autism Speaks, World Health Organisation, Institute of Psychiatry

Sidebar:

A better understanding of the genetics of autism would be of huge value to parents such as Julia Young, who struggled for years to establish the cause of her young son Alex’s behavioural problems.

While Alex, now 12, was apparently normal at birth, his development began to regress around the age of 14 months, soon after his sister, Jess, was born.

“The more the baby crawled and babbled, the less Alex spoke and the more he withdrew,” said Mrs Young, of Bognor Regis, West Sussex.

At Alex’s nursery school, the staff soon began to wonder whether he was deaf. “When you called his name he would not listen to you, he would just carry on doing what he was doing,” Mrs Young said. “If he was painting he would stay painting, and if you asked him to come out of the sandpit he would stay there.”

She took Alex to speech therapy, with no results, and nothing could be found wrong with his hearing. At his first school, his odd and inexplicable behaviour continued.

“He would not sit with the other children – he would sit with his back to the class, but still answering questions. He would not line up when told to, and he would just leave the classroom to go to the toilet without asking.

“His behaviour at home became more and more erratic. He would cross the road in front of cars. He would suddenly turn the hot water on and almost scalded himself. He had no sense of danger.”

At the age of 5, Alex was finally referred to a child psychiatrist. “We had been there for five minutes when he told us that Alex had high-functioning autism.”

Alex’s symptoms are at the less extreme end of the autistic spectrum, but he shows many of its classic signs. “He gets a word in his head and keeps repeating it, trying to get me or his sister to say it,” Mrs Young said.

“He gets obsessions that can last for a year. At one point he was obsessed with Thomas the Tank Engine, and wouldn’t do anything unless we could link it to trains.

“Now he is obsessed with his Play-Station, and with the band Muse. Every time we go in the car, he wants to hear Muse records, and he knows all the words.”

Family history suggests that genetics could be involved. Mrs Young herself has had attention deficit disorder diagnosed recently and her niece’s son has attention deficit hyperactivity disorder. Both often coexist with autism. Alex also has two uncles who have suffered from epilepsy.

Mrs Young said she would welcome genetic insights that help diagnosis, but also worries about where genetic screening could lead.

“It took an age to get Alex the help he needed,” she said. “The earlier you know, the better, and if this could help us identify autism as young as possible it would be wonderful.

“But I would not want a situation like Down’s syndrome, where you tell parents while the child’s in the womb and you have to make a decision.

“We also ask ourselves how much of Alex’s personality is Alex, and how much is the autism. Can we even separate the two?

“If you asked us could we have prevented it, we would have to think. Obviously in some ways it would be better for him, but he is happy in himself.” We ask ourselves, can we separate Alex and autism?

Not using cosmetics cures journalist of IBS

A lot of people don’t realise how important it is to stick to the failsafe rules about shampoos, soaps, cosmetics and makeup. A journalist recently went six weeks without washing or using any chemicals on her skin, and look what happened:

But by the end of the fourth week, something extraordinary happened. Nicky noticed that not only was she physically feeling better than she had done in a long time, her skin had begun to glow.

For years, she has experienced Irritable Bowel Syndrome (IBS), which bizarrely seemed to improve the longer she went without washing. Although there is no medical explanation for this, Nicky is convinced it is to do with a sudden break from the chemicals seeping into her body.

At the same time, a persistent cyst on her eye disappeared — Nicky believes because she stopped irritating it with mascara and eyeliner on a daily basis.

“I went to see Dr Val Curtis from the London School of Hygiene to seek her opinion,” says Nicky. “She told me that while I would eventually lose my teeth if I carried on not cleaning them indefinitely, not wearing make-up could well have helped my cyst.

“She said there was no known link between the use of beauty products and the prevalence of conditions such as IBS. But it is such a modern-day complaint and I believe it’s possible that it is somehow linked to the chemicals in all the products we use.

“Aside from that, the most extraordinary thing was that without a doubt — and despite not having washed my face for a month — my skin looked fresher and brighter than it had for a decade. Six weeks without a wash

The silly comment from the doctor suggesting she would lose her teeth if she doesn’t brush them is hilarious! Presumably that’s why no animals have teeth, and why everyone born before the invention of toothbrushes had no teeth!

Yes there is a medical explanation for this lady’s improvement in her IBS. But you don’t actually need to go without a wash to get the same effect!