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The Energy Reboot Blog

by Moira Newiss


How You Make Energy, What Can Go Wrong & How To Fix It

Do you have brain fog, feel fatigued and completely mentally and emotionally exhausted? Are you unable to perform your normal daily routines, do your job effectively, perhaps even struggle to do the house work, look after your children or cook a meal? Do you feel worse after you have exercised or tried to push yourself to do something? Have you been diagnosed with Chronic Fatigue Syndrome or Long Covid? If you are answering yes to these questions then this blog is for you. I'm going to explain how your body makes your energy and what can go wrong with this process. Then of course we are going to look at how you can fix it!

Perhaps you may have wondered how you make your energy? I’m sure you know it has something to do with what you eat; you probably know a little bit about digestion but after that it is a bit of a mystery. Let’s look at what happens in a bit more detail. I believe it is important to have some understanding of the process as it will make you more likely to stick to the new healthy habits you need to get your energy back again. First I’m going to explain what happens when we are making plenty of energy.

How You Make Energy, What Can Go Wrong & How To Fix It

How You Make Your Energy

You eat your food; it passes down into your stomach where it starts to be broken down by acid and enzymes and then into your intestines where the nutrients are absorbed into your blood stream. Also entering the blood stream is the oxygen that you breathe in through your lungs. The nutrients and oxygen circulate to every single cell in your body and provide them with the building blocks to make your energy. This is where the magic begins, I like to call it magic as it is a really fascinatingly complicated process going on all of the time, inside all the millions of cells in our body, to make our energy. I find it really amazing but don't worry I am going to try and simplify it for you.

Inside our cells we have tiny little organelles called mitochondria, they are usually depicted like little cocktail sausages. It is inside these mitochondria that the oxygen and nutrients are used to make your energy which is why they are sometimes called your power houses or power plants. Some cells use more energy than others so cells in your heart, liver, muscles and brain, the organs that use a lot of energy, they have a lot of mitochondria, up to 5,000 of these little energy production powerplants per cell. That’s a lot of mitochondria!


Here is a Fun Fact for you if you are a Star Wars fan. The midi-chlorians that lived inside their hosts and which provided the Jedhi knights with their super human power, known as The Force, were loosely based on mitochondria. I don’t know about you but I want some of The Force, so keep reading…

Inside the mitochondria there are several steps in which our nutrients are used to make energy, these steps are collectively known as cellular respiration or cell bioenergetics. The process is dependent on how much oxygen is available and there are different routes for making energy if there is not sufficient oxygen for the normal process. If everything is good and well in your body then the nutrients enter the cell and glucose (sugar), from carbohydrates in your diet, is converted to a compound called pyruvate and then transported into the mitochondria. Fats are also transported into the mitochondria using a special carrier involving a substance called carnitine. At this point both the fats and sugars enter a process (called the TCA cycle or sometimes the Krebs Cycle) that converts them into two types of energy molecules known as NADH and FADH2.

Cellular Respiration

Your energy production reaches its final (and most important) phase by using a process called oxidative phosphorylation involving something called the electron transport chain. To keep it simple this is a chain reaction where electrons are taken off the NADH and FADH2 molecules and passed down a chain of complexes (called proton pumps) to create something called ATP or adenosine triphosphate. You can think of it a bit like a game of hot potato where the electrons are quickly passed from one pump to another until ATP is generated at the final stage. ATP is our ultimate energy molecule , it is what we use to fuel our body processes with energy. When our energy runs low it is generally because we are not making sufficient ATP.

Electron Transport Chain

Are you ready for another amazing statistic? Inside the mitochondria the electron transport chains are embedded in the inner membrane and each mitochondria can have up to 17,000 of these tiny assembly chains making our energy. In fact we make or recycle so much ATP each day that if we were to add it all up it would equal our body weight, I find that pretty astonishing!

I’m guessing you have probably gathered this is a complex process. I did use a few words you probably haven’t heard of before but tried to keep it simple. The overall idea is that your nutrients get into the cell, then into the mitochondria, high energy substances are produced that are then fed into an assembly line to make ATP, the ultimate fuel. That is all you really need to remember.

What we have covered so far is what is happening under normal circumstances when your body is balanced, healthy and functioning well. Next, we are going to have a look at what might be happening when our energy levels drop, we feel fatigued and we no longer are able to do the types of activities that we would expect to do easily.

What Can Go Wrong With Our Energy Production?

Mitochondria make our energy, but they have a very important second function too, cell defence. The mitochondria have a unique role in the body, they are like a command and control hub both sending and receiving lots of chemical messages all the time, thousands of times a second. They are constantly sensing and checking the environment around them to make sure everything is ok. If it is not, and they decide that what is happening is too much to cope with, they will opt to move into something called the Cell Danger Response. At the same time they will turn down energy production because they can’t do both effectively at the same time and they see cell defence as more important for survival. When chronic fatigue kicks in it is your bodies way of putting you into a kind of hibernation mode. It is a good defence against some kind of threat, but the problem is that we can get stuck in it and rather than being temporary it becomes ongoing.

I mentioned that the mitochondria are sensing their environment, by this I mean that they are reading the chemical messages that are being sent from cell to cell to check how safe the environment is for us. The kinds of messages that are being sent to the mitochondria include information about air pollution, medication, stress, food and drink, illness, infection, injury, your mood and mental health and how well you are sleeping. The mitochondria take all this information and make a decision about the total load of stress being placed on your body from all of these mental, emotional, physical and environmental stressors. You might not think of all these being things that trigger stress, but at a cellular level stress is simply anything that is not good for us that triggers a specific chemical cascade, your chemical stress response.

One of the problems with the way we live our lives as modern humans is that we are genetically adapted to be hunters and gatherers living on the plains of Africa, and yet here we are living in houses, sleeping too little, eating inflammatory food, not spending enough time outside in nature and exposing ourselves to chemicals, and all kinds of relationship, financial and work pressures. You probably get the idea why our mitochondria might not see things positively.

So our mitochondria can switch over into a defence mode and it is sometimes easy to think of this being a switch from a power plant to a battle ship. This defence mode is called the Cell Danger Response.

Ideally what should be going on in our bodies and in our mitochondria is a constant balancing process. The mitochondria are sending and receiving messages all the time and as I said they are a kind of command control centre, constantly receiving information and giving out orders and adjusting things all the time to try and keep your body in balance. This balance is called homeostasis and it helps your body maintain stable conditions while adapting to changes in your environment and is crucial for survival. But sometimes no matter how hard your body tries it can be overwhelmed or overloaded and the mitochondria reach a tipping point. They can no longer bring all your body systems back into balance and when that happens we lapse into ill health.

The Healing Cycle

In 2019 Robert Naviaux , a US doctor who has done a lot of research into mitochondria and chronic fatigue, proposed a new model for chronic disease called the healing cycle. I thought it might be helpful to explain this model to get an idea of what might be happening in chronic fatigue syndrome and how your can support your body to get well again. The model can be applied to other chronic diseases like diabetes, autism, cancer, heart disease and it is likely that it can be applied to long covid too.

In the model Naviaux describes how chronic disease takes hold when the cells in your body are not given sufficient time and support to fully recover from some kind of impact whether it be an injury, infection, stress or trauma. He explains how the cells end up caught up in a repeating loop of incomplete recovery, unable to fully heal and that almost every chronic illness we know of has this at its core.

The Healing Cycle

He points to the fact that doctors are very good at dealing with acute illness and there are great survival rates from things like heart attacks and strokes, but doctors struggle with chronic disease even though they spend most of their time on it. He suggests that this is because using the kind of methods that worked for acute illness don’t work well for chronic disease because it is a whole body disease, it is a body systems problem. Chronic diseases either block communication, by which he means that signalling between cells, or else it sends alarm cells between cells. The cells that cannot communicate normally and have lost their ability to send and receive signals properly become lost from the system. Over time more and more cells become disabled or have problems signalling and you end up with poor function which stops you being able to progress through the healing cycle.

In this image you can see the Health and Healing Cycles proposed by Naviaux. In his research papers he explains the different parts of the cycle: CDR1 (cell danger response), CDR2 and CDR3, and how the mitochondria change from an anti-inflammatory form to an inflammatory form and move into the Cell Danger Response. This changes the process by which the mitochondria make energy, they use less oxygen and reduce the energy supply to the body. At the same time communication between cells and the brain are reduced, particularly the signals sent using our vagus nerve from our tissues to our brain (I’ll come back to the vagus nerve). He suggests that the way back to health is by replacing damaged cells with new ones, teaching them their specialist roles and only then the mitochondria can shift back to being anti-inflammatory and go back to a normal process of making energy.

Tissue & Organ Performance

Here is another look at this same model where you can see the injury or insult happening to the body on the left of the graph and then the three stages of recovery taking you back to full recovery. Sometimes this process takes you beyond where you were previously, shown as hormesis. This is often explained by the saying that “something that doesn’t kill you makes you stronger” and that your body can adapt to cope better long term.

How You Make Energy, What Can Go Wrong & How To Fix It

Again another image from Naviaux’s paper. CDR1 the first stage involves the activation of your innate immune system, weeding out of unwanted things like infections (bacteria, viruses and fungi) and chemical toxins and containing any damage caused by them. The mitochondria send out an alarm signal to the cell and trigger the Cell Danger Response. The mitochondria change their function rapidly and within minutes change from the normal M2 form to M1, a pro-inflammatory form. This change results in less energy in the form of ATP being produced and effectively a shield is put up to try and protect them from damage. Less oxygen is used to make energy and the full energy process I described above grinds to a halt and different, less effective mechanisms come into play. So the mitochondria have move from being a power plant to a battleship ready for defence and fatigue kicks in.

At this point if there is no excess cell damage and loss then the cells can still complete the health cycle relatively quickly just through restorative sleep. You see this when someone recovers quicky from an infection having effectively slept it off. But if the mitochondria continues in the defence mode the cells begin to disconnect most lines of communication with neighbouring cells. Naviaux describes this as a kind of cell autism, which is beneficial and needed for healing, but comes at a cost as normal body organ processes are reduced and this can lead to a loss of function in the body which can last for weeks or months resulting an cause ongoing symptoms.

In CDR2 phase the body replaces cells. Every organ and tissue has an optimum number of specific types of cells needed for healthy function, so if cells are lost they must be replaced. Once the initial damage from the injury, infection, toxin or stress is resolved then stem cells are recruited to help replace lost cells. The mitochondria in these stems cells are known as M0, they are youthful and help to get energy production back on track using oxygen again, but they also use a lot for cell growth so energy is still depleted. Once these cells have completed their growth and established cell to cell signalling, they can move into CDR3.

In CDR3 the cells are finishing off differentiating for their specialist functions and the brain is able to re-establish communication with the cells in the organs and vice versa. This is a 2-way communication involving hormones and the nervous system, especially the vagus nerve. The mitochondria change from the M0 form back to their M2 anti-inflammatory normal state and any M1 also change back to M2 and go back to their normal energy production process. The cells also re-establish connection fully to the nervous system and communication is fully restored.

The Vagus Nerve Connection

I haven’t explained it yet, but the vagus nerve is very important in all this, it is the nerve that sends nervous signal communication between the tissues in your body to your central nervous system and brain. In fact 80% of all your nerve fibres are vagus nerve fibres sending signals from your tissues to your brain. The reason this is so important is because the default setting is the cell danger response to keep you safe. It is only by positive reinforcement and signalling non-danger, safety and security that the healing process can be completed. This is why brain inflammation can last a life time after physical injury, early life stress and psychological trauma and we need to work hard to keep it under control.

Vagus Nerve

Signalling Your Way Back To Health

You might have guessed by now, but we need to be sending our mitochondria the signals that all is well. So how can we do this? If you remember back to the mental, emotional, physical and environmental stressors I mentioned, what is needed is the antidote to these problems. In this blog I am going to focus on food and supporting the vagus nerve. Food is important because it provides the nutrients we need to make energy and help calm inflammation. Calming the vagus nerve is important so that it send the positive message to our brain (and from the brain to our cells) that all is well and we can come back our of the cell danger response.

For any dietary change to have effect you need to be patient and keep going with it, because research has shown it can take a minimum of 3 weeks and quite often at least 3 months to have lasting effects. This again comes back to the signalling systems in your body, bringing things back into balance takes a while as your cells need to get sufficient of the right signals to make the necessary changes. It also takes around 3 months for you to see changes in your brain through things like meditation or exercise too. So the message is not to get despondent if you don’t notice an overnight change, it can take a little while for your body to full respond.

How To Nourish Your Body for Energy

To fight fatigue you want a whole fresh food diet, we want it to be low in carbohydrates and higher in protein and fats. This is because fats are a cleaner fuel to burn in the body, they are more efficient and they cause less inflammation, which you don’t want. You need protein as it is a building block for most of our signalling molecules including our neurotransmitters in our brain and nervous system. Ideally you want to be eating a Paleoketogenic diet at least for 80% of the time. That means you want to be fuelling your body with fat and fibre (as well as protein) rather than sugar and starch. It will train your body to burn fat effectively.

You also want your diet to be rich in micronutrients, minerals like magnesium and iron, vitamins like vitamin C and the B vitamins. The paleo bit comes from our ancestry, as hunters and gatherers, we would have eaten seasonally with lots of diversity in our diet, there would have been times of plenty in late summer into autumn we would have had lots of berries, nuts, seeds, honey, pulses and root vegetables. The rest of the year we would likely (especially in the UK or similar latitudes) have survived on meat, eggs, fish full of protein and fat. These days we have an abundance of foods all year round so we need to actively move into period of ketogenesis (using fat as a fuel), hence the ketogenic bit. If we don’t do this we may put ourselves at risk of increasing inflammation and gut problems through over consumption of refined carbohydrates. This can lead to blood sugar problems, gut inflammation and even mood and hormone problems. Ideally, we should be in ketosis for most of the time and eating a bit more carbohydrate on occasions.

There is a lot more I can say about ketosis but I will save it for another blog. For now I just want to mention that you will know you are in ketosis by using something to measure your ketones levels such as urine test sticks of a breath analyser but you can also look for signs like a clean tongue and smooth clean teeth, improved mood, feeling calmer, improved gut symptoms such as bloating or reflux, improved sleep and increased energy.

Beware that before you try getting into ketosis it is important that you seek medical advice and professional support especially if you are on medication (such as for diabetes, high blood pressure or a mental health condition) as your medication may need to be adjusted.

I’m going to break it down more specifically for you.

1. Eat Plenty of Healthy Fat

You want to be eating plenty of healthy fats. You want to be burning fat as fuel as it burns cleaner and is less inflammatory for the body than carbohydrates. Plus you also need fats for your cells to work properly. Every single cell in your body has a membrane, and your mitochondria also have membranes that are important in making your energy. These membranes are mainly made from fats, so getting the right kind of fats into your diet is super important. Making sure your cell membranes are full of healthy fats allows them to function properly. Think of them a bit like an eggshell. If you opened up a box of eggs and they had no eggshell there would just be a blobby mess. Cells would be like this too without their membrane holding the cell contents inside. Our cell membranes have several functions in addition to a physical protection of the cell: they allow passage of molecules in and out of the cell including nutrients and toxins; and they have receptors that receive chemical messages like hormones and neurotransmitters. The membranes need to be fluid not static and the right structure requires a specific arrangement of fats.

Our bodies and our cells need a range of different types of fat and we get these from eating a wide range of food including: meat, fish, eggs, nuts, seeds, avocados, coconuts and from pressed oils such as olive oil, avocado oil and hempseed oil.

How You Make Energy, What Can Go Wrong & How To Fix It

2. Top Up Your Fibre

Fruit and vegetables are where you get your fibre from. In the main this should be leafy vegetables and seasonal berries as these are full of fibre and low in carbohydrates. When these plant foods pass through your gut you digest the sugar molecules in them, and the fibre gets left behind and passes into your colon at the end of your digestive system. In your colon lots of helpful bacteria ferment the fibre and make lots of very good anti-inflammatory molecules including some vitamins like vitamin K and short chain fatty acids which can also be used for energy.

The colour in the plant foods demonstrates that it is packed with phytonutrients too. These have a role to fight inflammation in the body and can help prevent damage to cells. There are thousands of different kinds, you might have heard of some of them like sulforaphane that is found in broccoli, cauliflower and cabbage or resveratrol found in blueberries, dark chocolate and pistachios.

The best foods that have fibre and phytonutrients but are still low in carbohydrates are things like kale, spinach, rocket, chard, broccoli, cauliflower, brussel sprouts, cabbage, lettuce, apples, pears, tomatoes, cucumber and berries like raspberries, strawberries, black and red currants, blueberries and gooseberries. Your plate should be full of colour with lots of little bits of these plant foods.

3. Get Your Micronutrients

The next most important thing is to make sure you are getting enough of the right micronutrients. In our modern lifestyle, along with intensive agriculture that depletes the soil, we can often be deficient in minerals. The foods we eat are often are refined and rich in calories but deficient in micronutrients, particularly minerals, and we don’t spend enough time in the sun to make sufficient vitamin D (through skin exposure).

Making sure you spend time outdoors in daylight and have a lot of variety in your diet helps to ensure you are getting micronutrients, but sometimes they can need a top up. In terms of making energy the key micronutrients that sometimes need to be supplemented include Vitamin D, potassium, iron, selenium, boron, iodine, manganese, copper, molybdenum, chromium and B vitamins including B12 and B3. There are good quality electrolyte and mineral complex supplements available, but you should seek professional help and advice to decide whether you need to supplement and it is a good idea to test for levels of deficiency before you start.

How You Make Energy, What Can Go Wrong & How To Fix It

4. Avoid Gluten & Dairy

These are two of the most common foods that people can be intolerant or sensitive to, and can potentially add to inflammation in your body. Gluten is found in flours such as wheat, spelt and barley, so in bread, cereals, cakes, biscuits, crackers and also beer and many sauces and processed foods. On a low carb diet you won’t be eating many if any of these anyway, but gluten is known to contribute to gut problems by opening the gap between the cells lining the gut and allowing more particles to cross into the blood stream, sometimes known as leaky gut. When substances like undigested food particles or bacteria or allergens like pollen cross into the blood stream they can cause your immune system to activate and an inflammatory response and your mitochondria will be sent messages flagging this problem.

With dairy many people are intolerant, meaning that they lack an enzyme needed to digest the lactose protein in foods like milk, yoghurt and cheese which can result in bloating, pain, indigestion and diarrhoea. Dairy can also cause allergies to another protein called casein, and is linked to things like migraines, sinus problems and IBS and fatigue. It is best avoided, especially if you have any of these symptoms, until you improve your gut health and resolve your fatigue. Butter (and ghee) is the exception because the proteins, lactose and casein have been largely removed leaving predominantly dairy fats. Instead you can use coconut milk and coconut yoghurt which are a good replacement.

Often when your gut health improves you will find you can tolerate these foods in small amounts.

5. Calming Your Nervous System

Finally, you might remember I mentioned the vagus nerve. Well there are things you can do to support your vagus nerve and keep it happy. This might include spending time in nature, listening to music that calms you, meditating, gentle yoga poses and deep breathing exercises. All of these can make a difference if done regularly.

Make sure that you also spend time outside in the sunshine to get your vitamin D (in the winter in the UK you will probably need to supplement). Being outside has more than one benefit and spending time outdoors in nature is very healing in general. It is calming, grounding and you get the benefits of chemicals produced by trees too (phytoncides) which we now know are really good for you. Just sitting under an oak tree or listening to the birds singing or walking bare foot on the beach … there are lots of ways to connect and be in nature.

How You Make Energy, What Can Go Wrong & How To Fix It

Delight & Not Deprivation

Eating in this way is not about deprivation, there are loads of really delicious, nourishing foods that you can enjoy. Your plate should be filled with foods that delight you and fill you up. Examples of breakfasts include smoked salmon with scrambled eggs and wilted broccoli or coconut milk, flaxseed and chia seed porridge with blueberries and strawberries. Lunch can be a mixed green salad with lettuce, watercress, rocket, spinach and some left over chicken or a boiled egg with olive oil and hummus. Dinner could be a meat stew with carrots, cabbage and sprouts or a BBQ of pork and apple burgers with kebabs made of red onion, peppers, tomatoes and mushrooms. My favourite low carb desserts including berries with coconut yoghurt or a decaf ground coffee with a couple of squares of 85% dark chocolate. Does this sound like you are depriving yourself?

What Can I Do If I Am Severely Fatigued?

Easy Meal Ideas

This might all sounds great but what if you are severely fatigued and struggling to cook? I do understand how difficult this can be, even working out exactly what to buy and eat when you have severe fatigue is very mentally draining. To help you I have designed a new ebook (click here to download) that tries to make feeding yourself easy. It provides you with a 5 day meal plan that requires no cooking and gets the right nutrients into your diet. It comes complete with a shopping list and 3 easy recipes, again none involve cooking. I hope it will be helpful for you, especially if you are still at an early stage on your journey back to health.

Download my free ebook here.

Disclaimer: Before changing your diet or lifestyle and taking any supplements always seek the advice of your doctor or another suitably qualified professional such as a nutritional therapist. The content of this blog is for informational purposes only and is not a substitute for professional medical advice. Always seek the advice of your doctor with regards to any questions you have about a medical condition.


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