Antibiotic Resistance: The Real War on Drugs

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Are we at risk of a disaster movie becoming reality?

Almost all of us have required antibiotics at some point in our lives, but do we really understand what they do? How they work? More importantly, do you know that we could be much closer to losing their amazing protective power altogether? To explain why, let me ask you a question…

Do you remember a time before flat screen TVs? How amazing they were when they first arrived? How about mobile phones, or the internet?

Over time, we adjust and become used to new things. Imagine going back to a big, chunky TV now, or having to wait until you got home or to a phone box to ring someone. Time has a habit of making us forget how difficult things used to be, generating a complacency that can put that more comfortable way of life at risk. The same is true with medicine.

Antibiotics, in one form or another, have existed since the early 20th century. The most prominent early example is a man called Alexander Fleming’s apparent “accidental” discovery of a well-known antibiotic. The story goes that Fleming left out a small dish of Staphylococcus bacteria (often a cause of food poisoning) on his lab bench before leaving for the summer, where it was by chance contaminated by mould. When Fleming returned, he investigated further, and found that the mould was stopping the growth of the bacteria by breaking them down. The mould turned out to be Penicillium notatum, the byproduct of which Fleming branded the now famous ‘Penicillin’.

So let your flatmates//spouse/pets know that if you leave plates of unfinished food on the kitchen top for weeks to gather mould, you are actually attempting to discover a new and potentially lifesaving treatment. Do not be perturbed by the modern pharmaceuticals industry either. Sure, they have hundreds of millions of pounds to potentially pour into researching new antibiotic treatments, but there is not as much progress there as you’d expect. In fact, there have been almost no new antibiotics produced in the last 30 years. Why?

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“I’ll throw it away first thing tomorrow, I swear!” – The words of a genius biologist.

The worrying answer is that antibiotic use is seen as a big risk for healthcare professionals and policy makers. There is not much money to be made in something that hardly ever gets used. But why is antibiotic use so sparse?

Throughout modern medicine, antibiotics efficiency in dealing with bacterial infection has never been in question, but with extended use on such a large scale, a biological battle began to rage, unseen by most. A battle of resistance.

 

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A rare picture of the bacteria known as ‘flagstaph-ylococcus’

Antibiotics, from penicillin to the most recently discovered, were becoming non-functional, and the battle still rages on today.

How did this happen? Surely what killed bacteria 50 years ago should have exactly the same effect then as it does now?

For an explanation, we need to go to the frontlines of the war: the inside of your body. Like actual war, the technology has progressed, and the humble penicillin takes on new shapes, with a whole family of antibiotics to its name (with well-known examples including amoxicillin and ampicillin.)

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“Fight not to scale, as you’ll see soon”

Bacteria are the main cause of infection in broken skin, mainly because they’re already all over your skin before it breaks (don’t think about it too much). They have 2 layers of protection: an outer thick cell wall, made of proteins known as peptidoglycans, as well as a thin and wobbly inner cell membrane. The wall gives them a solid shape whilst also protecting from damage. It is a key part of their structure, without which the bacteria will die.

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There are other smaller bits of the cell wall, but peptidoglycans are the thing that gives it strength and structure.

The reason the penicillin family of antibiotics has been so successful in treating these sorts of infections is that it can block the production of this cell wall. So how does it do this?

Here is where the art of microbial war becomes interesting. Penicillin does not attack this very sturdy cell wall head-on, instead, it sneaks into the bacteria itself, behind enemy lines, where it finds an enzyme known as transpeptidase. These enzymes are the builders and repairers of the cell wall. Think of them as the ones who put the mortar between the bricks that are peptidoglycans.

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“It’s transpeptidase time” just doesn’t have the same ring to it.

Penicillin binds to these transpeptidases, blocking them from being able to maintain the walls strength as the bacteria grows. This results in a breakdown of the wall, and a rather embarrassed and weak bacteria.

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When you take penicillin, you’re sending waves and waves of these medical molecules to fight back the bacterial infection. After a few weeks, all that’s left are a few gutsy bacteria, they may be the most resilient, but even they cannot outlast the offensive power of penicillin much longer.

Unless…

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“Where are our reinforcements?” “Why hasn’t the general sent any?”

The general here, of course, is you. Every year thousands of people leave their antibiotic courses unfinished in the UK. Even though there are not enough bacteria for you to feel ill, they still exist inside you, and you’ve just given them the respite they need.

So why is this a problem? There are only a few bacteria left, and you don’t feel ill anymore! If it starts to get bad again you can just go back to the doctor for more medicine if you get ill, right? Unfortunately not. If the disease returned a month or so later, you may find the same treatment will not be as effective.

It turns out that the few remaining bacteria the first time had survived because they, out of all the other bacteria, were the only ones to possess a molecule called B-lactamase, which breaks down penicillin, keeping the transpeptidase builders safe.

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I did not want to show graphic molecule on molecule violence, so use your imagination to what happens to penicillin after this.

Not only that, but this time all of the bacteria, not just the strongest few, have this ability. How can this be?

The issue comes from the way bacteria multiply. They divide. If the penicillin course remains unfinished, all bacteria in the infection will then be children of the remaining penicillin-breaking bacteria. Bacteria that have already proved their resistance and resilience. Some bacteria can divide into two every half an hour, growing from just a single cell to over a million in only twelve hours.

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The bacteria don’t actually get smaller, its just the only way to fit them all in the picture.

This is obviously a problem on an individual level, but the resistance dilemma does not end there. Bacteria do not only transfer their ability when they divide, but can also transfer this ability to other nearby bacteria, even if they aren’t the same species. This is because they have a small circle of DNA encoding genes for this resistance. This little genetic instruction manual is passed between close-by bacteria, spreading the knowledge of how to prevent the damage caused by penicillin.

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Never has a book club been so terrifying.

The combination of dividing bacteria and this trading of information means that anywhere with a high number of people, antibiotics and infectious diseases is going to be on the front line of this resistance war. Hospitals now have to fight against strains of bacteria that are resistant not just to penicillin, but to many different drugs. MRSA, the super-bug, is short for Methicillin-Resistant Staphylococcus Aureus, and has been a threat to patients both hospital bound and visiting for years. It is the stronger and harder version of the bacteria you see fighting the penicillin above. Over 44,000 people die of sepsis a year in the UK (more than lung cancer), and many of these are due to antibiotic-resistant infections.

This is why there are so many guidelines in place to help combat this growing resistance. Antibiotics are only given when absolutely necessary, and only in bacterial infections. If you have a cold or cough, these may be viral infections. Viruses hide inside our own cells, reproducing there, so antibiotics will have no effect at all. It would be like treating a splinter with a bandage, you aren’t going to get anything out and it’ll most likely just make things worse.

In terms of what you can do, it is advised that you take all of the medication the doctor gives you, and especially for the length of time the medical professional states. This is to ensure you finish off the strongest of the bacteria and avoid creating even more resistant strains. Feel free to discuss why this is with your doctor, they’re normally more than happy to talk about it.

There is another problem, not just outside of hospitals, but outside of humans altogether. Livestock. The World Health Organisation (WHO) states that in some countries over 80% of antibiotic use is in animals. Many farms across the world including Europe and the US are still using antibiotics in animals even when they are not ill. This sort of preventative care would be devastating for humans, and yet this is occurring in food that ends up in our bodies anyway. Marks and Spencer’s took an important step to help combat this less than a week ago, stating they will begin to publish data on antibiotics used in their supply chain. This will hopefully encourage others to do the same, and allow consumers to see what is being put into their food.

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“I hear you work for big farmer”

These bacteria have no concerns jumping from livestock to humans and there were already cases last year of MRSA existing in livestock within Europe. We are using the same drugs on animals as we use ourselves, meaning we are sacrificing their potential medical use even quicker than necessary.

We’re putting all of our eggs in one basket, and we’re running out of eggs.

The second World health organisation (WHO) World Antibiotic Awareness week has just passed (14th-20th November). This annual event aims to help educate people, both public and professional, on the risks of antibiotic overuse. WHO are also advising farmers to only use antibiotics that are categorised as “least important to human health” in livestock.

In terms of what we as individuals can do, we can, on a personal level, ensure that we follow the doctor’s advice with how often we take our antibiotics, and advise everyone else that they do the same. We can spread the WHO’s message that current antibiotic use in animals is a ticking clock, and if it is not more carefully controlled we stand to lose a precious medical resource.

When they are turned to sparingly, and used appropriately, antibiotics can be an extremely effective tool against infections that would have previously been fatal. But without this control, we may risk living in what WHO describes as “the post-antibiotic era”. Like TV, phones and the internet, most of us have not experienced a world where antibiotics don’t exist, and one glance at history tells us that we don’t ever want to.

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If you want to read more about how genes affect humans as well as cells, read my previous blog: “Genetics: The Real Book of Life.

Genetics: The real book of life.

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Where there are humans, there are stories, whether it’s the ones we write down on a page, the ones we project on a screen, or the ones we live.

Although not well-known and often misunderstood, the story of genetics is, in many ways, the story of life itself. I hope to begin to scratch the surface of this immense body of biological literature over the next few blogs, and maybe explain how humans merely existing as we do now is an underdog tale worth telling.

The great author Sir Terry Pratchett, in one of his stories, created a vast library filled with nothing but individual autobiographies. Each book, dedicated to a single person, was continuously adding new words as it sat on its shelf, narrating the story of the individual as they went about their lives.

If you picked up one of these books, you would be able to read the events of a person’s past, see their present happening, and maybe predict something that could happen in their future. Clearly in the realm of fantasy, right?

Well, yes, in the sense of a physical book. However, there is another way to look at our own story, and it is hidden deep within our cells. Hidden there a genetic tale of a human being who grows to be a certain height, with a certain hair colour, who grows up with certain quirks and certain irks. A biological book describing why you’ve become both what and who you are. An origin story.

So what does this book look like? Where can you find it? And most importantly, can you read the bit from two days ago that says where you put your keys down? (Don’t worry, everyone does it.)

Part 1: The Book of Genes

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“That’s nice, but is it available on Kindle?”

Almost every book shares some basic characteristics, from Charles Darwin’s Origin of Species to that dodgy romance novel your Aunt wrote but you refuse to acknowledge exists. Books tend to be made up of letters, words and sentences, and are most often split into chapters, which leaves us with a hierarchy of structure that looks like this…

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As we all know, page numbers aren’t actually important, because they don’t really tell you how many words there are. If your book is font size 100 you’ll have two words and 50 pages.

Seems simple enough right? So a perfect starting point would be to find our genetic book, and see if we can apply this structure to it.

Finding where the genetic book is is relatively simple, as it exists in almost every single cell in your body. You could either think of it as a must-have bestseller, or one of those bibles you find in every hotel that most people don’t even realise exists.

The problem is, as you can see below, most cells kind of leave the book scattered around until they actually need it, equivalent to just having the pages strewn around your room. Cells like to make you think they are really organised but it’s chaos in there, trust me.

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“Oh yeah…Page 14…It’s definitely one of these…”

It’s fine though, we’ll just let the cell know we would like a gander and it’ll be cleaned up quicker than a student’s room when they need their deposit. We’ll check back on this cell in a minute, but for now, we can definitely say that this ‘mess’ is our genetic book, or the ‘Genome’. Our little bundle of information floating in the nucleus of our cells.

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Note: Your nucleus and genome do not look as much like blue cheese as this, it’s just my colour scheme.

Do not judge this book by its cover (or lack thereof) however, once the cell decides to organise itself we have something that looks both a lot easier to break down and perhaps rather familiar:

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My first ever activity at university was to make these out of pipe-cleaners, so don’t ever tell me you don’t learn important skills in art at primary school.

These fairly uniform bundles of stuff are chromosomes. Each 11-shape is actually two rod-shaped copies.  In humans, these pairs of bundles divide our genome into twenty-three bitesize chunks. This is why they are the perfect candidates for our book’s chapters.

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This is where we finally get to the term we are most familiar with: each chromosome contains upon it several genes.

A ‘gene’ means different things depending on who you ask. Most refer to genes as traits that are transferred from parent to offspring, which is why if you look like one of your parents it’s described as “having their genes” or that certain characteristics have been “passed down” (Hair colour, dimples and the ability to roll your tongue are well-known ones).

Gene’s biological structure is incredibly complex, but for now we only need to know two things:

  1. Each gene is a single unit of inheritable information
  2. These genes are passed down from parent to child

These are the units that “genetics” takes its name from, and the single units of information that have to make sense by themselves, with a clear beginning and end. This self-contained nature of similar units means these fulfil the role of “sentences” in our genetic book.

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“Genome” is actually a combination of the words ‘Gene’ and ‘Chromsome’, yet you never hear of books being called ‘Chaptences’ or ‘Senpters’.

So now we can see our genome as a book, and our genetic book as split into chapters of chromosomes, with each sentence of text equaling a gene. So what’s next? Well, the best way forward would be to read the words in one of these sentences…

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What sorcery is this??

Ah. Oops. This is my bad. I probably should’ve mentioned before now that your genetic book is not written in English. It’s actually written in a code, a genetic code.

 

The name's Bond, Peptide Bond

My genetics-based spy thriller script is still in its infancy. (The name’s Bond. Peptide Bond.)

The word ‘code’, even though it is the correct scientific term, may be unfair. The idea is not to hide meaning from us, in the same way everyone speaking a foreign language isn’t doing it so they can talk about you behind your back.

To read any further, we have to teach ourselves a new language, the language of DNA. You won’t find this language on an app (unlike Klingon, amazingly). It is difficult for many reasons, but one of the main ones is that this language doesn’t really have words in the same way we do, which tends to be a good starting point for learning.

So if we cannot start with words, where do we begin? Well, there is an even smaller denominator that must be looked at, and that is letters. There are 26 letters in our alphabet, and for reasons I’ll never understand I learned to recite them backwards as a child (although it may have been that deadly combination of having too much free time and someone telling me that I couldn’t do it.)

In the English language we can form words out of any of those 26 letters, with varying lengths of combinations with spaces in between. So how does the genetic alphabet compare?

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Ah, well that looks a bit easier, and it uses some of the same letters. I think anyone could say that one backwards.

The genetic language has some other rules, including that all your words have to be exactly three letters long, meaning words in this new alphabet would look as follows…

TAC-GGC-ACA-GGG-GCA-GCC.

So what effect does this have (beyond making spelling tests way easier)? Well, the main one is that it means it will take a lot more letters to get across even basic information, as many as eighty thousand per sentence (that would be a lot of commas).

These three letter ‘blocks’, known as ‘codons’ (literally ‘part of a code’), are formed by a string of molecules of DNA, and within its tiny alphabet lies all the information your body needs to function. It is normally presented in a “double helix” structure (or as I call it “two twisty things”) as seen here. The four different letters in the alphabet correspond to the four different types of ‘rung’ you can have on this twisting ladder, which are known as ‘bases’ (shown in four different colours below).

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Whilst often called a ‘Ladder’, I can’t imagine people would be happy receiving one from eBay. Imagine trying to clean the gutters…

As you would expect, with a limit of three letter words, and only four letters to work with, it is feasible to write out every word that could possibly exist in the genetic language (64). This is known as the ‘triplet code’ in typical exciting scientist vocabulary, but feel free to call it a ‘genetic dictionary’ if you’re feeling a bit adventurous. 

This leaves us with these triplets as the ‘words’ in our book, and the ‘bases’ as letters.

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To fit a full genetic ‘sentence’, this picture would have to be at least 2000 times bigger.

And with these examples, the diagram from book to genome is completed. I have hopefully begun to show how this information can be found within ourselves.

Yet I’m sure you feel it, that empty sensation of something being missing. You’re saying  “Yes, so now I know what’s IN the book, but what does it mean? What do I do with this book? What does my body do with this information?”

Well, this is where things get interesting. As I discussed before, this book is written in genetic code. This code took scientists years to decipher the language of, and it is also found within almost every cell in your body.

These two facts are not a coincidence, and point to the true purpose of this genetic book. To be read by our cells themselves.

Part 2: A best-celler.

So why do so many of our cells have a copy of this book? Is it the thrilling narrative? The cool settings? The character drama?

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Well, not quite, cells actually use the book an instruction manual on how to make everything they need.

“Hold on.” you may say now, “‘Instructions’? You told me this book would be an epic tale, a narrative of how my life has come to be what it is, and now you’re telling me this is more like reading an instruction manual?”

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“I feel cheated and lied to.”

I must admit, at a base level, these are a set of blueprints. Our book would have no room for narrative flair or dramatic irony upon first glance. But let’s be honest, for all most of us know, every instruction manual could be an undiscovered Shakespeare play. I mean someone has to write instructions, and jobs for writers are hard to come by these days. For all we know J.R.R Tolkien began his career writing the text of those little tags that tell you how to wash your clothes.

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This jumper is famously the only place to find Tolkien’s lost tale: The Lord of the Rinse

This isn’t any old instruction manual either, within it is contained the information required to make every single protein your body possibly needs.

Proteins are commonly referred to as the “building blocks” of the cell, and this is a fairly accurate comparison, almost all the important structures in the cell are made up of one or a combination of these building blocks. With our newly understood book, we should be able to follow our cell’s process from instructions to final product.

Here is our cell, he has just realised he needs a protein, let’s call it PROTEIN Z, because that sound interesting and mysterious.

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Note: Cells don’t actual have faces, I just find it makes them more relatable, the closest they have to a ‘brain’ is their nucleus.

So the first thing we have to do is find the correct gene, and thus sentence, in the book of life. We know this gene is on chromosome 5, so let’s flick to that section and see…

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As before, genes are incredibly long, and I can only draw so many twisting DNA spirals before my fingers starts to look like them.

So here we have a stretch of DNA on chromosome 5, we know that the sentence is in amongst these words and letters somewhere, but where?

Well, in a book a sentence isn’t hard to pick out, you just look for the capital letter and full stop, these indicate where each idea starts and finishes. Is there an equivalent in our gene?

As a matter of fact, there is, and they are appropriately referred to as ‘stop’ and ‘start’ codons. These are two specific words that tell our cell both where to start and where to finish reading, as you can see below.

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I got told off for run-on sentences at school. If only I could’ve told my English teacher we’re made up of thousands of them.

Once our cell knows it is reading the correct sentence, it produces a copy form the chromosome. This means that the original sentence does not get lost if it needs to use it again (back up your stuff people!) The original instructions are kept in the nucleus, a secure library that makes sure nothing damages the instructions (although this isn’t always possible, as we will explore in the next blog).

The small copied sentence is transported out of the nucleus to a protein production site in the cell…

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This site is known as the ‘Endoplasmic Reticulum’, but we can call it ‘ER’, coincidentally the sound I made after first trying to remember what it was called.

At this new site, the sentence is run through a little structure called a ‘ribosome’. This nifty little unit takes our instruction copy and then ‘translates’ the sentence. But how does it do this? Well, this is where having a genetic dictionary would come in handy for us humans.

Each ‘word’ in the code that we saw earlier, is an instruction for one “amino acid”, if proteins are the building blocks of the cell, then amino acids are the building blocks of the building blocks.

For instance, when a ribosome reads the letters A T and G, it translates this word as the amino acid Methionine: Our capital letter, oddly, is a word. No gene begins without this 3 letter combination, as it shows the ribosome where to begin.

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Each 3 letter base combination creates a building block with a specific name, but that isn’t too important at the moment.

After beginning with the “Met” amino acid, the ribosome has another 22 amino acids to choose from. These all have specific traits, but will be covered in another blog, all that is important now is that these are chained together in the order they are read.

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Once the ribosome reads a full stop in the sentence, of which there are three types (TAA, TAG, or TGA), it knows to stop reading, and lets the protein loose.

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Your cells had a 3D printer before it was cool, almost 4 billion years before! Talk about a trailblazer.

…and there we have it. Protein Z!

As I mentioned before, these proteins can be made up of up to 20,000 of these little amino acid building blocks, and it would take over 3 hours to read out the full name of it. This protein thankfully has a shorter name: ‘Titin’, and is part of what keeps your muscles springy. Another protein, MCR1, has a key role in producing red hair.

But then, if we all have DNA that is 99.9% identical, why does everyone not have red hair? Why do some people’s books have some sentences whilst others do not? What happens when our sentences have spelling errors, or we miss a full stop or capital letter? I mean, we’ve all done it…

These are questions that will be tackled in my next blog. The book of life 2: The ghost of genetics past. There, we’ll look at how our book came to be the way it is. After all, where do you think your story came from?

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Colourblindness: not just a black and white issue

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As a ten year old, I found myself waiting impatiently outside the nurse’s office. Like most of my time in school I was unsure of why I was there. No answers were provided as I was sat down, and I was instead shown a series of odd dot patterns similar to the one you see above. Some patterns contained numbers, some didn’t. I left the room even more confused than when I’d went in. The next day my parents got a note from the school explaining that I was red-green colourblind, and that’s when my life changed forever…

Except it didn’t really.

For people already aspiring towards certain careers, such as pilot, electrician or military work, this news could be devastating. However, due to a long list of reasons (including tremors, asthma, and a potent dislike of high stress situations) running around firing a gun or cutting potentially fatal electric wires never particularly appealed to me. I decided instead to pursue science, laboratories of course famous for being happy, stress-free environments that require no intense periods of perfect hand-eye coordination.

The only difference I really noticed, fairly instantly after my diagnosis, was the reaction of other people. Anyone else with a hue-viewing deficiency will be familiar with the classic ‘What colour is this object I’m holding?’ question, and equally familiar with the resulting shock from the asker as you correctly identify it (Most kids know Coke cans are red, even if they see red differently). I’m not just talking about when I was ten years old here either.

My personal favourite question was one asked of me as I had just begun learning to drive. I remember my friend’s frown clearly, “But Joe”, they had said, concern for fellow road users filling their voice, “Aren’t you colourblind? How will you know whether the traffic lights are red and green?”

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The same goes for the walking man on pedestrian crossings.

But I cannot blame people for being confused. Colourblindness, in my life at least, has seemed to occupy an odd sort of limbo between personality quirk and a genuinely limiting condition. Indeed, the UK does not classify colourblindness as a disability. However, as colourblindawareness.org states, it can be seen as more serious in other countries. In Japan the condition can get you excluded from many potential job roles, and some countries such as Romania and Turkey even ban people from driving due to their inability to see different coloured lights.

On the flipside, people with colourblindess have occasionally found themselves sought after. In World War Two it was thought men with colourblindness were more adept at seeing through camouflage, and researchers at both Cambridge and Newcastle universities recently discovered that red-green colorblind individuals have an ability to spot differences in shades of khaki indiscernible to the average person. It makes me worry I’ve actually been wearing nothing but differing shades of beige my whole life and no-one has had the heart to tell me.

So what causes this odd biological quirk? I believe the best way to explain would be to work our way forward from the very start, which would be colour itself.

Light is a wave, and whether you can perceive the light or not is defined by the frequency at which it waves. The visible light spectrum is found sandwiched between infra-red (Which powers your remote control) and ultraviolet (Which you probably don’t want to shine on your remote control) light.

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Waves not pictured: New, Mexican, Awkward

These different ‘wavelengths’ of light all enter through the retina of your eye, where they hit a layer of cells known as ‘photoreceptors’. There are two types of these photoreceptor cells, imaginatively referred to as ‘rods’ and ‘cones’

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Scientists’ imagination is often found lacking when it comes to naming things.

Rod cells, while interesting in their own right, are not colour processors, and thus our focus today will be on cones.

There are enough processes going on in each of the six to seven million cone cells in your eye to fill a year’s worth of blogs, but the key component in these cells is inarguably a protein known as ‘Opsin’. This protein has the handy function of changing shape when being hit by light, starting off a series of events which in essence causes the cone cell to send a signal to the brain saying ‘I can see light’.

What’s more interesting is that there are multiple types of opsins, and each one only changes shape when hit by a specific range of ‘wavelengths’. This makes the cone cells sensitive to different light shades depending on which opsin they have, and together the brain can use them to determine all colour in the environment.

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S,M,L =’Short’, ‘Medium’ and ‘Long’ opsins, corresponding to what range of wavelengths they change shape in. The height of the graph shows which colour they absorb the most.

You may now see where this is going, colourblind people such as me lack one of these opsins (The ‘Medium’ one in my case), and as a result cannot absorb a specific range of light wavelengths. As you can see, M and L overlap quite alot, meaning a deficiency in one of these opsins is not as serious as a deficiency in S. Thankfully S deficiency is alot rarer, as will soon be explained…

So what is the deeper mechanism here? What causes colourblind people to have lost the ability to perceive these different frequencies from birth? Well, as it so often does, it comes down to genes…

The instructions on how to build these three opsin proteins are found in three separate genes, for simplicity (a word that produces gasps from many geneticists) let us call them opsinL, opsinM and opsinS. Genes are long sections of DNA that in most cases contain the information on how to make a single protein, the rudimentary building block for all life. These genes are packed together into 23 pairs of chromosomes, which are in turn found within every cell of our bodies. These chromosomes contain all the instructions your body needs to function, with thousands of genes for thousands of proteins, but today we’re focusing on three.

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S is on the 7th pair, and M/L are both found on pair 23, which has two variations.

While most people will know very little about chromosomes 1 through 22, the 23rd pair are much more readily recognised. The ‘X’ and ‘Y’ chromosomes, the genetic definers of sex. The presence of both long and medium wave opsins here explains one key issue with colourblindness. Why it is so much more common in men.

When our genes are passed on, things can go wrong. The machinery makes mistakes in the instructions when trying to copy them, and that means they cannot be read. This means a specific protein cannot be produced. Thankfully, as the diagram above shows, almost all our genes come with a spare set of instructions, all that is, expect the X and Y in men. If a male inherits a damaged X, he has no insurance chromosome, and his body has to work with the damaged copy. S, due to being on a non-sex chromomsome, has an insurance copy in both men and women, explaining why a deficiency is much rarer.

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The leftmost female offspring is described as a ‘carrier’ as they have the ability to pass the disease on but non of the symptoms.

And so, depending upon whether you are missing the red (long wave) or green (medium wave) opsin gene, you never experience an entire part of the visual spectrum, and have to spend an inordinate amount of time trying to work out which type of Thai curry you’ve just made. Is there anyway back from this terrible fate?

Perhaps there is, extremely sophisticated gene therapy has potentially paved the way for cures at the gene level, fixing the mistakes in the instructions so your body can produce the correct opsin protein again. Although one of the main reasons it is easier is that you can push a needle containing the fixed DNA straight into your eye for direct treatment, which some may view as a sticking point, well I guess in a way needles are always sticking points, that’s how they work. However, at the minute it’s only being used to try and regenerate damaged rods and cones in fully blind individuals, this obviously bein the more medically pressing condition.

For colourblindness, a less gruesome solution seems to have unveiled itself in recent years, and it’s admittedly fairly stylish. The company ‘Enchroma’ have begun offering glasses that users claim increase the vividness of colour in the world around them. I haven’t had a chance to get my hands on some yet, partially in the fear that I won’t ever want to take them off, mostly because of the price tag. They claim to filter out wavelengths of light, simulating a greater distinction between colours that colourblind people have not experienced before.

So while colourblindness can be a hindrance to many, I can say I’m at least partially glad I have it, as it has opened up a whole new area of biology that may not otherwise have caught my eyes.

 

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Thanks for reading my second blog, Colourblindness is a more nuanced and interesting area than many think, and is actually a good entry point into learning a lot of things about genetics, evolution and inheritance. (Did you know that the M and L opsins were originally the same gene?) If you’re interested in learning more, let me know and I may expand on it in the future.

 

The shape of knowledge: squares, cones and needles

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So, are you a square, a cone, or a needle?

I suppose the correct response is: ‘What on earth are you talking about?’ and I guess you’d be right. It is up to me to elaborate on what I mean. But first I’ll have to explain how I came up with this question in the first place…

When you start university, the subjects, or rather sub-subjects you can specialise into are laid out before you in different ‘fields’. This is an appropriate word, considering how immense the number of choices seems. You are presented with more information and specialties than you can shake an overpriced textbook at, and it’s up to you to narrow it all down to one or two if you want to progress.

If you’d taken an overall measurement of knowledge at the start of mine and anyone else’s university education, it would probably look something like this…

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    An innocent square, unburdened by student loans, deadlines, and the thought that education must end and you have to start adulting.

I believe, in terms of knowledge breadth (how many things you know about) and knowledge depth (how much you know about said things) that most people start higher education fairly similar in both, while we may be more drawn to or naturally talented in certain areas of study, the inherent structure of A-levels or other post-school education tends to leave our knowledge bases about even across the board. But what happens after the beginning of university?

Starting a degree is the first time most people feel they are developing what I’m going to refer to as a “cone of knowledge”. A phenomenon by which you begin to specialise in one core topic, at the expense of knowledge about the surrounding ones, your square will begin to taper, and end up becoming a bit more…coney.

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Symptoms include being picky over the use of the word ‘significant’ and beginning sentences with “current consensus shows…”

For example, at the end of second year, a bright-eyed and bushy-tailed me uttered the words, “Oh, Genetics looks fun, I guess I’ll choose that”. Suddenly, a class of 350 trainee scientists was pulled in different disciplinary directions, with mine whittled down to just 16. Each discipline allowed students to evolve themselves in different ways. As a budding geneticist, I occasionally worried we’d picked the educational equivalent of an evolutionary dead end.

Thankfully, me and the rest of the genetics course fell into the ‘platypus’ category of oddity, instead of, for example, the ‘dodo’ variety. The knowledge and interest I gained on genes, DNA, evolution and inheritance is most likely going to make up or be involved in a large portion of the things I talk about in the future.

So after my bachelors, having finally found a subject I felt confident and settled in, with a few months lab experience under my belt, I made the logical decision and continued in this subject area switched to a completely different field. Neuroscience.

This wasn’t a completely random decision. Like genes, brains are something I’ve always been interested in. I seem to be unstoppable drawn towards things that are irreducibly complex or complicated, or at least that’s what I tell myself while trying to untangle the wires from beneath my desk.

I had hoped, going into it, there would be some overlap between the two subjects. I knew it was possible, as my undergraduate project had involved looking at gene expression in the developing brain. But I quickly found that just because neuroscience plays by the same scientific rules, it doesn’t mean it is in anyway the same game.

Genes, as some of you may know, are small individual units of heredity made up by DNA, that tend to code for a specific protein (except when they don’t, but that’s a caveat for another time). Each one can be described as a tiny little instruction manual for one building block of an entire organism, and like tiny little instruction manuals, the directions can be difficult to read. However, science has taken great leaps in the past decade and a half in learning to decipher it.

Brains, on the other hand, pose an entirely different problem. They raise the mind boggling question of whether it is possible to understand the very thing that powers understanding. It’s the sort of thing that leads to fellow neuroscientists narrowing their eyes at each other and saying things like ‘You better not be talking about philosophy’.

To compare to genes, trying to understand the brain’s instructions may be like opening the first page and reading “To understand this manual you must have first read the manual”. It could just be something we can never achieve, due to our lack of an outsiders point of view. In other words, it feels like the darned thing won’t sit still long enough for us to work it out.

To pull this back to the shapes I’ve been mentioning, my ‘cone of knowledge’ had definitely narrowed, and was becoming more of a pointed triangle by this point. It amazed me how quickly you can put on intellectual blinkers to other subject areas when you’re in a lab environment. Sometimes it’s simply necessary to get through the volume of information on your specific topic, and I think this is why you get the occasional ‘needle’ in a lab environment.

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Disclaimer: The look of horror and general scruffiness is my personal experience of a needly lifestyle, and is not indicative of the needle population at large.

A needle tends to be the one who would perfect their topic on mastermind or university challenge but shrugs on the general knowledge round in a pub quiz because they simply don’t have time for keeping up with daily events.

Don’t get me wrong, the overwhelming number of people I’ve met in science have somehow managed to hang on to their random facts and niche interests despite the sometimes frustratingly specific information they encounter. Everyone acts a bit square at times, and everyone can get a bit needley.

But science needs those needles, it needs those finely tuned points of specificity to pop the never-ending balloons of ignorance. And if you put enough of those sharp folks together, you get a figurative bed of nails, a carpet of points that together is strong enough to hold up the weight of human advancement.

I’ve now left the world of academic research, and I’ve noticed that the switch from ‘studying’ to ‘studied’ in regards to my relationship with genetics and neuroscience has unsettled me. It sounds too historic, too final. I can feel my knowledge on the subjects fading, and I think if I don’t do something about it it will become nothing but a passing interest, something for me to regurgitate a few facts about in polite conversation.

That’s the reason I set up this blog, to hopefully preserve a knowledge of science and research that I have always enjoyed and been interested in, while also presenting it in a form people can read and (in exceptional cases) enjoy.

So while I find myself trying to fix my cone, I salute to all those people who know exactly what their shape should be.

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This entry is a bit longer than I’ll be aiming for in future weeks (although I’m aware I’m now making it longer discussing it) and this blog post began as a 200-word section for the ‘About page’. So when I try to write an actual first blog post you can expect the novel out early 2017…