Sleep Chemicals


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Source: Wikipedia Commons, AndrePeltier

Sleep is an essential part of normal body function. It is cued by the release of a neurotransmitter chemical called adenosine. Other neurotransmitters, serotonine and norepinephrine, keep parts of the brain active while we are awake.

Although scientists have not found brain cells that get tired and ‘need’ to sleep, there appears to be some brain cells that work harder while we are awake while others work harder when we are asleep. 

Unlike a baby who will sleep for up to 17 hours a day, an adult generally requires about 8 hours of sleep.

During sleep, you go through 5 or 6 sleep cycles. There are five stages to a sleep cycle:

  1. Light sleep
  2. Slower brain function with bursts of brain activity- adults spend 50% sleep time in this stage
  3. Extremely slow brain waves
  4. More extremely slow brainwaves
  5. Rapid Eye Movement (REM)- adults spend about 20% of sleep time in REM sleep.

Stages 3 and 4 combined make up ‘deep sleep’. It is hard to wake someone up from deep sleep and they will feel groggy and disoriented for several minutes after waking. Sound like anyone’s Monday morning?

We all know what happens when we spend too long without sleep. Lack of concentration, impaired memory and irritability are just some of the signs of fatigue.

Drowsiness, the last stage before sleep, is caused by the build up of adenosine in the brain. When a person has been awake for a long time, their cells release adenosine to signal a need for sleep.

Caffeine and other stimulants were shown in a 2005 study to interfere with adrenosine reaching the brain. This results in the brain being unaware that cells have been working for a prolonged time, delaying sleep.  

There is a good summary video explaining this 2005 study, courtesy of ScienCentral, available on youtube at


Lack of sleep

Did you know that you develop a ‘sleep debt’ when going without sleep for prolonged periods of time? Although people may get used to a sleep-deprived schedule, their judgement, reaction time and other brain functions remain impaired. Eventually the body demands repayment of the sleep-debt.

Sleep deprived people who are tested with a driving simulator or a hand-eye coordination test often perform as badly as people who are drunk.

In the years between 2006 and 2010 in New Zealand, there were 937 vehicle crashes involving 1244 serious injuries and deaths. Although not as large as the number of crashes alcohol was involved in, any number of crashes attributable to sleep is too large. It is so simple to pull the vehicle over and take a 20 minute power nap. Arriving safely at a destination is preferable to not arriving at all.


Health benefits of sleep

Experiments have shown that sleep is linked with both a healthy nervous system and immune system.

In the nervous system, sleep is thought to give brain cells the chance to exercise brain connections that might otherwise deteriorate due to lack of activity.

In the immune system, deep sleep has been linked to the release of growth hormones in children and young adults. Proteins crucial for cell repair are produced in greater quantities during sleep.  


The sleep-wake body clock

Our bodies are programmed to sleep at a certain time. Have you ever crossed a time line? Jet lag, severe fatigue, is the result of a confused body clock.

This ‘body clock’ controls the rhythm of waking and sleeping. It is cued by external light, and bright lights can apparently reset the clock. Some doctors are using ‘light therapy’, shining bright lights on people for several hours before they want to wake up, to help people adapt to new time zones.

Many people with total blindness have life-long sleeping problems because their brains cannot be cued for sleep by light.


In Western Society, people are burning both ends of the candle at once. When sleep is so crucial for good health, it is worth investing in at least 8 hours of sleep each night.



National Institure of Neurological Disorders and Stroke

South Western Medical Centre


Hip Material


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In January 2012, New Zealand media highlighted the health issues associated with metal-on-metal hip replacements. But what you might not be aware is of is the material chemistry behind the issue.

The metals involved in these hip replacements are cobalt and chromium, normally present in body tissue in tiny quantities (1.2 micrograms and 2 micrograms respectively). The friction from a metal-on-metal hip replacement joint causes metal fragments to wear away into body tissue.

Elevated levels of cobalt are recognised to cause brain tumours, heart irregularities and seizures. Elevated levels of chromium are linked to problems with the reproductive system. Click here for more about cobalt and chromium poisoning.

According an February article in the British Medical Journal, these metal ions can cause reactions that destroy muscle and bone, leaving some patients with long-term disability. The metals can leach into the bloodstream and spread to parts of the body such as the liver and kidneys, before being excreted naturally.

Britain’s The Telegraph reported on March 7th that a study presented to the British Hip Society conference claims these metal-on-metal hip replacements are responsible for causing cell damage that results in liver and bladder cancer. It also links the elevated level of cobalt and chromium to blood poisoning.    

In 2010 there was a wide scale recall of the metal-on-metal hip joints. According to New Zealand media (click here to see the online article), over 500 New Zealanders still have one of these artificial joints. These patients are being watched for any signs that their hip replacement is causing health problems.

It is clear metals that are going to be inserted in the human body should be chosen carefully to ensure safety. This choice of metals is a form of materials chemistry.

But materials chemistry is not only concerned with the nature of medical implants. Done well, it is useful in medicine for other reasons. 

Things like nanoparticles (particles so small they can be measured with 1 billionth of a metre) are being investigated for potential use in dental fillings. Leading researchers at the University of Otago are studying the antibiotic effects of silver nanoparticles in an effort to create a filling where there will be no associated bacterial activity. Click here to learn more about the research.

Materials chemistry is also involved in improving the delivery of pharmaceuticals to disease sites. One of these new drug delivery systems involves stents.

Stents are expandable wire mesh cylinders that are inserted into clogged arteries to keep them open and prevent heart attacks. The stents can be coated with drugs, to prevent to formation ons scar tissue around the insertion site, ensuring the artery remains open. It is a very clever way to get a drug exactly where it needs to work.

The hip replacement issues raised in January are an example of poor materials chemistry. If synthetic products are going to be inserted into the body, we need to understand what implications this will have for health and also how long-lasting the implants will be. There should be the equivalent of clinical trials for the implants before they are mass marketed.

The metal-on-metal hip joint replacements should have been investigated properly before they were mass-marketed. Careful screening of medical devices like these hip joints would prevent bad health effects on unsuspecting patients.



Notes from UCD chemistry papers

British Medical Journal, How safe are metal-on-metal hip implants? February 2012.

The Social Drug, Alcohol.


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Alcohol is a drug: the body behaves differently once alcohol has been consumed. Medicinal drugs have side effects enough that a prescription from the doctor is required to gain access to helpful drugs like inhalers.

So why is alcohol available in supermarkets? Does it not have as many harmful side-effects as helpful pharaceuticals?


Processing Ethanol

The alcohol consumed in such huge quantities in New Zealand, available from supermarkets, is ethanol. We use and abuse it carelessly. But what does it really do in the body?

Because alcohol is not a naturally produced substance in the body, it has to be processed to clear it out of the body systems. Chemistry is responsible for this process. Most of the ethanol consumed is oxidised first to acetaldehyde, then to acetic acid. This chemical reaction happens primarily in the liver.

Although acetic acid is harmless, acetaldehyde is toxic. Should a person drink lots of alcohol, lots of acetaldehyde will build up. The build up of this toxic compound can cause severe discomfort, nausea and vomiting. 

The alcohol not processed in the liver is excreted in sweat, urine or given off in breath. The alcohol content of exhaled air accurately reflects the alcohol content of the blood. This is the basis for breath-tests conducted by police.


Effect on the brain

Alcohol causes brain impairment in many ways.

Directly, it works as a depressant to decrease the activity of the nervous system. The effects of this are sometimes seen as increased activity, which seems counter-intuitive. In fact while the brain is normally functioning, it controls all body activity and will inhibit some of the possible activity. Alcohol decreases the brain’s control, allowing uncontrolled energy use.

As discussed in the Alzheimers and Memory post last week, brain cells communicate with each other via electrical and chemical signals using neurotransmitters. Alcohol has a direct impact on four neurotransmitters in the brain:

  • glutamate
  • gamma aminobutyric acid (GABA)
  • dopamine
  • serotonin

Glutamate is involved in learning and memory, while GABA is involved in motor control. Alcohol interferes with these neurotransmitters, preventing normal brain function. Dopamine and serotonin are normally involved in brain reward processes. Alcohol stimulates production of these neurotransmitters and uses them to cause the rewarding sensations associated with alcohol consumption.   

Brain function can also be altered indirectly by alcohol. Alcohol will affect the immune system and cause production of hormones that end up in the blood transmitted to the brain. It’s ability to alter behaviour can also result in violent behaviour causing head injury.


General health implications

Excess alcohol consumption has been found to cause:

  • Brain damage
  • Brain disorder called Wernicke-Korsakoff syndrome
  • Cancer of the oesophagus, liver, colon and other areas
  • Dementia and memory loss
  • Depression and suicide
  • Heart damage
  • High blood pressure
  • Inflammation of the pancreas
  • Nerve damage
  • Sleeping problems

For a more complete list of problems, click here.  To see an interesting page of alcohol-related facts, click here.


Drinking and driving: the lethal cocktail

New Zealand law does not allow drivers under 20 years old to drive after consuming any alcohol. Drivers older than 20 years have a blood alcohol limit of 400mcg breath or 80 mg blood, which (by my calculations) should equate to a BAC of 0.08%.

Because there are so many variables affecting the way the body processes alcohol, there is no easy way to quantify the amount of alcohol that can be drunk while maintaining enough brain control to safely -and legally- drive.

The safest rule: if you are going to drive, don’t drink.

Between 2006 and 2010 there were 2698 crashes involving alcohol. Many of these crashes involved impaired brain judgements in safe driving behaviour such as speed selection, overtaking and fatigue. There were 3565 serious injuries and deaths caused by these crashes.  

Accidents caused by drink driving. Statistics courtesy of the New Zealand Transport Association.

This chart (produced using the NZ Transport Agency Road Safety Reporting tool) shows the number of crashes involving either alcohol alone, alcohol and overtaking, alcohol and speed or alcohol and fatigue.

It is clear from the combination of these variables that alcohol impairs good judgement when driving.


Alcohol is a drug, even if a prescription is not necessary to access it. It changes the way the brain works and reduces behavioural control and judgement.

If you are going to drink, do it in moderation!

If you are going to drive, don’t drink.


Further resources:

White-tailed spiders: a rare reaction


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Linda’s story

On the 24th January 2012 during a normal workday, Linda Haussman felt what she described as a mosquito bite halfway down her shin. By Friday, what had been an itchy area now ‘looked a bit different’. In hindsight, Linda said that she should have gone to the doctor then.

Instead, she waited. Over the weekend this itchy area started to resemble a hole left by a scratched pimple.

By Sunday the sore area had grown to the size of her little fingernail, with a hole in the middle that ‘looked like a flesh-eating disease’.

Linda recalls walking her dog when all of a sudden her leg began stinging ‘like salt in an open wound’. It hurt so badly she wept.

Monday morning she was at the doctor. He told her it was likely an infected white-tailed spider bite and added that everyone reacts differently to the bites. The stinging pain she had experienced was due to raw nerves being exposed to air.

Because Linda’s bite was on the front of her shin, there was no fat behind it and the bite was right on her bone. This has meant a long and tedious healing process.

To begin with, Linda had to lie on a sofa with her leg elevated for 4-5 hours per day. She was at the doctor to get the dressing over the ‘open weeping hole’ changed twice a week. The hole smelt really bad due to infection. Nurses had to maintain a close watch on this infection, taking tissue samples that caused pain enough to take Linda’s breath away.

It was not until early April, over two months after the incident, that Linda could resume walking her dogs.

As of mid-April, Linda could keep each dressing on for 5 days before needing to change it. The hole in her leg was finally beginning to shrink. 

Linda was told that there are several factors that affect the severity of a white-tailed spider bite:

  • What the spider has last eaten (white-tailed spiders are said to be harmless themselves but in eating daddy long legs, they get poison on their teeth that can transfer to a bite)
  • Where you are bitten
  • Personal reaction (random)

Linda went at least three days too late to the doctor. Her advice?

“As soon as it looks like it’s not a normal bite, go to the doctor and get it checked out.”

Linda Haussman, spider-bite victim


When I first started writing this post, I intended to attack white-tails as a scourge in New Zealand. However, in looking through academic articles I could find little science to validate the white-tailed spider as the cause of flesh-eating wounds.

A 2004 article in the New Zealand Medical Journal discussed weakness in evidence identifying white-tailed spiders as the cause of these wounds and recognised debate as to whether white-tailed spider venom is toxic to humans. People generally do not see a spider biting them, which raises doubt about the complicity of white-tailed spiders in these wounds.

In a 2010 newspaper article in The Northern Advocate Ruud Kleinpaste, described as a ‘bugman’, says white-tailed spider bites are an urban myth. ‘Everyone with a puncture wound or bite says it’s a white-tail but in New Zealand we have dozens of other spiders that can give us a pretty nasty bite.’ He also said that white-tailed spiders are more likely to be eaten by daddy long legs than the other way around.

The Ministry of Health seems to share Kleinpaste’s opinion. In their Spiders in New Zealand pamphlet, they describe native katipo and redback spiders as potentially harmful. They are quick to assure the public that these spiders are rare and generally non-aggressive unless they feel threatened.

The dominant poison in both the katipo and redback spiders’ venom is a latrotoxin that interferes with the nervous system, prompting large-scale production of the neurotransmitter acetyl choline in the body. This neurotransmitter signals muscles to tighten, causing pain.

Other symptoms of these bites are sweating, shaking and nausea. Anyone bitten by such a spider is advised not to panic but to get urgent medical attention within three hours. Antivenom is available in all NZ hospitals.

White-tailed spiders get only a cursory mention in this pamphlet: ‘White-tailed spider bites are not considered poisonous to humans.’

The Ministry of Health’s website tells a slightly different story: ‘Most white-tailed spider bites are harmless, but just occasionally a severe reaction may result in a deep ulcer or wide area of skin necrosis (where the area of skin and flesh around the wound dies).’

Regardless of the identity of the culprit, there are bugs in New Zealand that can give a nasty bite with the potential to develop flesh-eating bacteria. Keep Linda’s advice in mind and get suspicious bites checked out by a doctor.



Interview with Linda Hauness, 12th April 2012

New Zealand Medical Association article (NZMJ 30 Jan 2004, Vol 117, No 1188) available at

2010 Newspaper article by Andre Hueber, available at

NZ Ministry of Health website and brochure available at

Alzheimers and Molecules of Memory


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Scientists have been trying to figure out how memory works for over a century. There is huge potential for such research to direct drug design for Alzheimers disease and other conditions involving memory loss.

There is no known cure for Alzheimers disease.


What is Alzheimers disease?

In Alzheimers, brain proteins form abnormal plaques and tangles, resulting in the death of brain cells and loss of memory. The protein changes are associated with a shortage of neurotransmitters, chemicals that convey messages between cells.

These neurotransmitters are very important and can be considered the ‘words’ of brain language.

The lack of neurotransmitter is addressed by drugs that treat symptoms of Alzheimers. One of these scarce neurotransmitters is acetylcholine. Several drugs focus on boosting existing levels of acetylcholine to address this chemical shortage.

Other drugs attempt to prevent further entrance of calcium into the brain. Excess calcium in brain cells damages them and causes a break-down in communication with other brain cells.

Memory Molecules

One of the challenges to understanding memory- and the brain in general- is that a mammal is estimated to have 1011 (100 billion) brain cells.

The regions of the brain
Source: Creative Commons, artlessstacey

In a human, each of these neural (brain) cells is estimated to connect to 1000 other cells, meaning there are 1014 (100 000 billion) interconnections. These cell connections are called synapses and are structures that transmit chemical signals between cells. This communication involves a chemical neurotransmitter and specific regions of different calcium concentrations.

Recent research

There has been much study done to begin unravelling the memory mystery.

“Memory is produced when two neural cells interact in a way that somehow strengthens future signalling through the synapse.”

Donald O. Hebb, Canadian psychologist, 1949


Short-term memory

Following on from Hebb’s research, in 2007 Professor Joe Z. Tsien reported that a protein complex known as the NMDA receptor is responsible for strengthening future interaction between two neural cells. His research involved genetically engineering mice with no NMDA receptor and mice with enhanced production of the NMDA receptor. The mice with more NMDA receptors ‘learned faster and retained memories longer than unaltered mice did.’ He concluded that activation and reactivation of this NMDA receptor links memory from the molecular to the network level.

In 2009 further research was reported by Kenneth S. Kosik, a neuroscientist at the University of California Santa Barbara. He explained the strengthening of the synapse (join between two neural cells) as being the result of protein production. Proteins build the connection between brain cells and make it stronger.

Kosik found that the production of new proteins can only occur when a ‘silencing complex’ is turned off. When synapses are activated, one of the proteins wrapped around the silencing complex gets degraded. This allows the cell to start making these proteins to strengthen the neural connections.

Kosik was able to observe some of the specific proteins involved in building memory connections between brain cells.


Long-term memory

The strength of neural synapse connections is important but short-lived. Synaptic long-term memories are encoded at a deeper molecular scale. The enzyme CAMKII (Calcium/calmodulin-dependent protein kinase II) has long been recognised as a major player in long-term memory production.

In 2012 a group of scientists from the Universities of Alberta and Arizona looked at long-term memory coding using molecular modelling. They showed a spatial connection between microtubules and the enzyme CAMKII. Microtubules are major parts of the structural cytoskeleton within brain cells.

This group, including physicists Travis Craddock and Jack Tuszynski and anesthesiologist Stuart Hameroff, have demonstrated a mechanism for encoding synaptic memory into microtubules. They believe that memory is written into the cytoskeleton of brain cells.



There is on-going research aimed at untangling the mystery of memory formation and retention. Science is not yet in a postition to try to prevent Alzheimers or memory loss, but greater understanding of how memory works will help design drugs to that do this.

It is worth noting that there are ethical implications to understanding the formation of memory in the brain. As soon as science understands something, it tends to replicate it.


Memory from Mind to Molecules, Larry R Squire and Eric R. Kandel, (2000) Scientific American Library, USA

NZ Alzheimers Society website:

How the Brain encodes memories, The Hindustan Times [New Delhi] 24 Dec 2009

Brain memory code cracked, Asian News International [New Delhi] 20 Mar 2012

The Memory, Scientific American July 2007

Life-saving science: F=ma


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One of the first times that I realised science could be useful rather than a slog, was (surprisingly enough) in physics.

Look familiar to anyone? As usual in physics, this formula looks singularly unhelpful. But in fact it relates force and time. If you troll through all the formulae behind acceleration, you learn that a force gets weaker when applied for longer.

The useful part? This idea is used in bike helmets, to stop your head from getting such a whack when you fall off your bike.

A bicycle helmet

The helmet has a ‘crumple zone’ made from expanded foam polystyrene, which has lots of tiny air bubbles in it that can be crushed. It takes time to crush these air pockets. The extra time this takes results in less force hitting your head. In other words, a bicycle helmet offers a layer of protection and helps to prevent head injury.

But we also have a ‘crumple zone’ in cars. Several, in fact. Usually there is one at the front and rear of the car, with a rigid cab in the middle. And there’s the airbags, which are a sort of ‘crumple zone’ too.

Crumple zones work by increasing the time it takes for a car and its occupants to come to a stop, causing a decreased force on the occupants. This is the same idea as a bike helmet, on a larger scale.

In a car, the airbag acts like a cushion and lessens the impact of a person hitting the cab. Again, this is related to increasing the time and so decreasing the force of collision.

A car crash test at the Insurance Institute for Highway Safety. Note the airbag has deployed and deflated. Source: Creative Commons, Brady Holt

But people don’t drive around with airbags inflated. The airbag must have some sort of trigger so that it inflates during an accident, before the occupants of the car are thrown around.

According to research from Washington University, for an airbag to be useful in preventing severe injury, it must deploy and inflate within 40 mili-seconds of a crash (0.004 seconds). It must also be able to tell the difference between a serious crash and a minor fender-bender.

This is where chemistry comes in.

Air bags are inflated not by compressed gas, but the products of a chemical reaction. Sodium azide, NaN3, is a chemical that releases nitrogen gas (N2) when it is ignited. A sensor causes ignition of sodium azide at the start of a severe crash, causing the airbag to quickly fill with nitrogen gas.

However, harmful sodium (Na) metal is also produced in this process. To prevent this from being an issue, additives such as silicon dioxide are used to react with this sodium metal and produce harmless by-products.

A test car crash, complete with model person. Note the air bag has deflated. Source: Creative Commons, Pava

The airbag only works to cushion impact if it has inflated and is deflating when the person hits it. The impact of hitting the airbag while it is inflating has been compared to hitting a stone.

Some fatalities have been caused by not wearing a seatbelt so that the person was too close to the airbag when it inflated. Many minor cuts and bruises have been caused by airbag impact.  Lots of research is being done by pyrotechnic companies to maximise the safety of airbags.

In the 21 years between 1987 when airbags were made compulsory and 2008, it has estimated that 25 782 lives have been saved by frontal airbags (US Department of Transportation).

Airbags have been shown to be effective not only in the number of lives saved but also in preventing a large number of life-threatening and debilitating injuries such as skull fractures and brain injuries.

Airbags and seatbelts together ensure the safety of car drivers and passengers. Use them both! Surely preventing a fractured skull is worth getting a bruise.


Bicycle Helmet Safety Institution:

Article: N Engl J. Med 1969; 320: 1361-7

US Department of Transportation brochure, available at

Washington University in St Louis website:

Allergies: the chemistry behind a runny nose


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The immune system is an intricately designed defense mechanism. It acts to neutralise infectious bacteria, viruses and generally protect the body from disease.

However, when the immune system is too sensitive, it can react to normally harmless substances in the environment. This is an allergic reaction.

The substances that cause an allergic reaction are called allergens. These can be biological (pollens, dust, bacteria), chemical (rubber, nickel, isocyanates in spray paint) or physical (heat, light, electromagnetic radiation).



So what’s going on in the body?

The body’s first response to an allergen is to release antibodies. These antibodies stimulate cells in the blood to release histamine.

Histamine affects lots of different body tissues. As we saw in the post Peptics Ulcers and Medical Treatment, there are histamine receptors in the stomach that release gastric acid. However, there are also histamine receptors in the skin, lungs, sinuses, and certain blood cells. This means that there are many possible responses to release of histamine:

  • Skin: a rash or itch.
  • Lungs: narrowing of airways. This can cause wheezing and difficulty breathing.
  • Sinuses: increased mucous production. This can cause a runny nose or productive cough.
  • Blood: widens blood vessels. This causes a rapid drop in blood pressure which can lead to shock.

Some of these reactions can be useful when fighting off a real infection and trying to get bacteria out of the body. For example, the widened blood vessels allow faster transport of white blood cells to attack a source of infection.

In addition to this, increased mucous production protects areas such as the lungs from bacterial invasion. Mucous is used to protect internal body tissue: in the lungs, it is a protective layer between bacteria-containing air and body tissue. Increased mucous production is intended to trap and expel bacteria from the body (when it is coughed out).


How serious are allergies?

The severity of an allergic reaction ranges from mild, such as hayfever, to severe. Anaphylaxis is an extreme all-body allergic reaction with symptoms such as difficulty breathing, itchiness, nausea and dizziness. It can have fatal consequences if not treated immediately by a professional.

If you come across someone who is in anaphylactic shock, the National US Library of Medicine advises following these steps: (

  1. Call 111 (in NZ)
  2. Calm and reassure the person
  3. If the allergic reaction is from a bee sting, carefully scrape the stinger off the skin with a credit card. DO NOT use tweezers: squeezing the stinger releases more venom.
  4.  If the person has emergency medicine on hand, help the person to take or inject it. Avoid oral medication such as pills if the person is having difficulty breathing.
  5. If there is no concern about suspected head/neck/back/leg injury, take these steps to prevent shock:
  • Have the person lie down
  • Raise the person’s feet 30cm or so off the ground
  • Cover them with a coat or blanket


Treating allergic reactions

Severe reactions: Adrenaline is the body’s natural histamine inhibitor, blocking the histamine receptors. An adrenaline dose is often carried by a person who has anaphylaxis. When given to a person in anaphylactic shock, the adrenaline should block the symptoms of an allergic reaction. This can be life-saving.

Mild reactions: Anti-histamines are often prescribed for people with mild allergies. These drugs also block histamine receptors, but particularly target the receptors in the skin and sinuses to prevent rashes and a runny nose. 


Doctors may use ‘allergy shots’ to prevent allergic reactions. The idea is to inject your body with very small doses of whatever it is you are allergic to. This should slowly change your body’s reaction to this allergen. The process is a slow one and may take up to 5 years.



The American Environmental Health Foundation website at

Article about anti-histamines: J Allergy Clin Immunol. 1997 Feb;99(2):S798-806. Available at

Thyroid and Iodine


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Where do thyroid hormones come from?

The thyroid gland has a crucial role in the body. A large butterfly-shaped gland that sits just below the windpipe, it uses iodine to produce several thyroid hormones. Two of these hormones are particularly important.

  • Triiodothyronine (known as T3)
  • Thyroxine (known as T4)


Why are thyroid hormones important?

Thyroid hormones control metabolism (the process of breaking down food into energy for cells).

T3 and T4 play roles in regulating body energy, growth and the body’s use of other hormones and vitamins. They also control production of serotonin, a ‘feel-good’ hormone. There needs to be a constant level of thyroid hormone maintained to ensure that the body functions properly.


Too much thyroid hormone in the body results in Hyperthyroidism. This is a condition that causes poor concentration, fatigue, goiter (visibly enlarged thyroid gland) and heat intolerance.

A woman with goiter, a swollen thyroid gland.
Source: Wikipedia Commons (Martin Finborud)

Hyperthyroidism is treated either with anti-thryroid medications or surgery or radioactive iodine to remove the thyroid. A patient then takes thyroid hormone replacement pills for the rest of his life.

For more information, refer to the US National Library of Medicine website at


Not enough thyroid hormone in the body results in Hypothyroidism. Depression, unintentional weight gain, sensitivity to cold and fatigue characterise this condition. Treatment involves minimal dosage of drugs used to produced more thyroid hormone and relieve symptoms.

Hypothyroidism is usually a life-long condition and pills have to be taken daily to maintain healthy thyroid levels.

For public health reasons, iodine is often put in salt. This ensures that the body has a ready source of iodine for production of these important thyroid hormones.

For more information, refer to the US National Library of Medicine website at


Nuclear accidents

Nuclear Power Plant in Cattenom, France.
Source: Creative Commons, Stefan Kuhn.

The thyroid gland is the only place in the body that absorbs iodine.

In the event of a nuclear accident, radioactive iodine may be released which, if absorbed into the body, will cause cancer and other disease.

Taking potassium iodide (KI) tablets at the beginning of a nuclear accident will saturate the thyroid gland. This prevents it from absorbing radioactive iodine from the environment.

The dosage and timing of taking KI tablets is very important and during a disaster, public health officials are careful to give detailed instructions for the public to follow.

Difficult Diagnoses: Appendicitis


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In the past, scientists have tended to agree that the appendix has no function in the body. It was regarded as a ‘vestigial organ’, something that has no function in the body. The appendix is thought to be left-over from evolution.

However, research shows that the appendix plays a role in the immune system.

The appendix is found in the abdomen, attached to the large intestine.
Source: Wikipedia Commons (Pearson Scott Foresman)

The appendix is associated with lymphatic tissue, which is closely associated with the immune system (J. Anatomy 126 (1978) 87-101). This observation was made over 30 years ago.

It has recently been proposed (Journal of Theoretical Biology 249 (2007) 826-831) that the appendix works as a storage house for ‘good’ bacteria that live in the gut. These ‘good’ bacteria help the digestive system to break down food.

Note: The gut or digestive system includes the small bowel (small intestine) and the large bowel (large intestine or colon).

A team of scientists under the leadership of William Parker, Ph.D., have observed that there are biofilms in the bowel that protect these helpful bacteria. They also observed that there are more biofilms in and around the appendix.

So, this team has suggested that the appendix stores helpful bacteria in biofilms to repopulate the gut when the contents of the bowels are cleaned out by diarrhea. The appendix can then release more helpful bacteria back into the gut to keep it healthy and working well.

Since there is no consensus on the normal function of the appendix, it is difficult for doctors to decide when it is a problem. However, appendicitis (swelling, inflammation and infection of the appendix) is a common health issue.

Interestingly, appendicitis is more common in males than females.


Appendicitis: My Story

When I was a young teenager, I had my appendix out. I had been sick with various complaints including stomach pains for over a year. Doctors could provide no diagnosis or cure for what was wrong with me.

In females, appendicitis is harder to diagnose as we have more complicated apparatus in the abdomen.

One night I was woken up with extreme stomach pain- so bad I couldn’t move or make a sound until it diminished. By the time I was seen in the ER, the pain had completely gone and I felt fine. However, the hospital admitted me for observation and I ended up going into surgery.

Even as I was going into the theatre, doctors were explaining that the surgery was exploratory and appendicitis may not be the cause of the pain.

As it turns out, I did have appendicitis. My swollen appendix had burst and this had caused peritonitis (inflamed abdominal tissue). I was sick for over a year afterwards and on extremely strong antibiotics for months to fix the infection.

Doctors told me that my appendix had been ‘grumbling’ for the last year and I was lucky it had been removed before any further damage was done.

It was not until after I had colonic irrigation (my colon was washed out and then healthy gut bacteria inserted, it’s gross I know) and went on a crazy-strict no sugar, no gluten, no dairy diet for nine months that my body began to recover from persistent illness.

Contrast this with my male cousin, who experienced bad stomach pain and within a week his appendix had been removed.

Reflection on the role of the appendix

In light of the proposed idea that the appendix is a storehouse of good gut bacteria, I find it interesting that it was after I had colonic irrigation that I began to recover my health again.

This would seem to support the idea that the appendix plays a key role in the immune system by maintaining levels of useful bacteria in the gut.

MRI scans: Why are they important?


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South Canterbury raises NZ$2.5 million for an MRI scanner

South Canterbury, a region half-way down the east coast of the South Island of New Zealand, has been working since June 2011 to raise NZ$2.7 million. Their goal: to buy an MRI machine for Timaru Hospital. According to the local paper, the appeal was only $250 000 off their goal as of the 27th March.

Currently, patients need to travel either 2 hours north to Christchurch or two and a half hours south to Dunedin to get an MRI scan done.

For a region of 55,318 people, fundraising just under $2.5 million within 10 months shows the value they place on having a local MRI scanner. 


An MRI scanner.
Source: Creative Commons (Tomas Vendis)

Magnetic Resonance Imaging. It’s a way to let doctors see inside your head, literally. Pictures that show the soft tissue of the body in slices, like the ones shown below, are produced.

MRI scans measure signals from Hydrogen atoms of water (H2O) in the body. Healthy and damaged tissue contain different amounts of water.

An MRI image shows the quantity of water present in different areas of body tissue using different shades of grey. This allows damaged tissue to be spotted. Injection of contrast agents (dyes) into the body is also used to get a clearer picture.


How does it work?

MRI technology exploits knowledge of atomic properties such as nuclear spin to create a recognisable picture of the brain.

The technology is based on the fact that damaged tissue and healthy tissue have different amounts of water in them. The hydrogen (H) atoms in this water are spinning in random directions around their individual magnetic fields.


If you apply a strong magnetic field to the body, all of the individual magnetic fields of the H atoms in water line up. The only difference between the spins is whether they are rotating clockwise or anticlockwise around the magnetic field.


This leaves a couple of H atoms out of every million that don’t cancel each other out (1 atom spinning clockwise cancels an atom spinning anticlockwise). This is still a considerable number of H atoms.

A radio frequency specific to Hydrogen is then applied to the body, which excites the H atoms with lots of energy for a short period of time. The atoms then emit this energy at a certain frequency.

While the radio frequency is applied, doctors can manipulate three gradient magnets within the machine to define the area that an image is produced from. This area or ‘slice’ pictured can be angled from any direction, a distinct advantage over other imaging techniques.

A computer watches all the frequencies emitted by the excited H atoms and maps them as an image. Where lots of H signals were seen, there was lots of water. The shade of grey on the MRI is proportional to the amount of water in that region.


Applications of MRI

A doctor can now look at the map of grey regions and detect if there are abnormalities.

Diffusion MRI technology is being used to map connectivity of different regions of the brain.

Because of the superiority of MRI technology in imaging soft tissue, MRI scans are being used to specifically locate tumours within the body in preparation for radiation therapy. The MRI scans will show the exact location, size, shape and orientation of the tumour. This allows for extremely precise radiation therapy to be applied to the cancer tissue.


A look at an MRI scanner from the technician's office. Source: Creative Commons (US Navy)

What’s it like for a patient?

Before going into an MRI machine, a patient is asked to remove all metal they are wearing. This includes zips, watches and credit cards. Anything magnetic inside the machine can be repelled by the magnetic fields and become a dangerous projectile.

Patients have to remain very still for between 20-90 minutes while the MRI machine makes a lot of noise. Any movement will blur the MRI image and a new scan will have to be made.

The noise inside the machine was described to me as continual hammering right beside your head. This is a result of rising electric current from the main magnetic field in the machine interacting with the three gradient magnets. Patients are generally given ear plugs. 

To avoid attacks of claustrophobia, there is a system of mirrors angled so that the patient see out of the machine.

Unlike other imaging technologies, MRI machines do not use ionizing radiation.

Once a patient emerges from the MRI machine the body and its chemistry reverts to normal. The dye may take a bit longer to pass through the system, but there are no known biological hazards that result from exposure to magnetic fields of the strength used in MRI machines.



University of Otago CHEM 205 lecture notes.

MRI patient interview