January 12, 2011

I simply remember my favourite things…

I have been banned from reading at work. This arises from an email I sent to my supervisor about a week ago, in which I asked him to help me try and understand a concept in a paper that I was trying to read. “No, no, no, Alice! No more reading! You’re working too hard and getting bogged down! Just concentrate on your lab-work and enjoy your research”. Oh, I have a cushy job. (Sometimes – for ‘twas only yesterday I was complaining about it).  Anyway, since indeed I was doing one hell of a lot of reading, I now find myself at a bit of a loose end this morning whilst I’m waiting for my experiment to quietly simmer away for the next hour or so. Rather than sit around on Facebook all day, I thought I’d tell you about my five favourite, most marvellous and exquisitely beautiful examples of biology that I have ever come across.  Indeed, one of the reasons I am writing this is because I am acutely aware that, now that I have graduated and no longer have to study anything except diabetes, I am rather likely to forget most of the detail that I learned through my degree. This idea saddens me very much, so I make it my aim to continue reminding myself of those topics that I don’t deal with any more.

Anyway, the five topics that I’m going to talk about are these:

·        Kinesin-mediated movement

·        Insulin signalling pathway

·        Nervous transmission

·        Gills of bony fish

·        Suckling reflex

If you’ve heard of one or two of them I’ll be impressed – I don’t think I knew any of them before A Level. Anyway, I hope you enjoy it, and I hope there is somebody else out there who can appreciate these little natural wonders, and hope that they will bring a smile to your face as they will always do for me.


The first on my list (in no order of preference!) is kinesin movement. In order to explain what this is, I need to go into a little bit of detail about cell biology.

Very generally, a cell is comprised a nucleus and various other smaller structures, all suspended in a jell-like fluid called cytosol, and all wrapped in a cell membrane. However, cells are not just shapeless, jelly-like blobs that flop around all over the place; they have a very highly organised structure which is constantly changing and reforming according to the cell’s needs. Cells need to be able to co-ordinate what goes on within them. They need to have mechanisms in place for transporting things from one place to another, making sure things get to – and stay in – the right places, disposing of waste products and a whole multitude of other things. They’re exceptionally complex – indeed, in many universities, cell biology is a degree subject by itself.

To keep things ordered and structured, cells have a phenomenal network of long protein filaments, collectively known as the cytoskeleton. This is literally a scaffolding network within the cell, and its job is to maintain the cell’s structural integrity. Think of this like the iron girders in a skyscraper. If you would strip away everything about the building to leave just the girders, you would see that they form a complex network all over the building which literally prevents it from collapsing under its own weight. This is exactly the function of the cytoskeleton; to prevent the cell from collapsing in on itself.

Structural integrity, is not, however, the only function of the cytoskeleton. It is also involved in movement of bulky items from one part of the cell to another, and this is where kinesin comes in. You’ve probably guessed that kinesin is a protein – everything awesome in biology is a protein! Kinesin has a complicated structure; it starts off with a round, head region which becomes a thin linker region. The linker joins the head to a thin stalk which ends once more in a rounded tail. The complete kinesin molecule comprises two such subunits with the stalks wrapped around each other, rather like a lollipop with feet.

Going back to my skyscraper, if I wanted to haul a piano from the ground floor right up onto the roof, one of the ways I could do it would be to get a giant, piano-sized rucksack and climb my way, bit by bit, along the girders right up to the roof. In the cell, this is the job of kinesin (although it’s more likely to be transporting new bits of cell machinery, not pianos). Kinesin moves along the cytoskeleton bit by bit.

Now, where the beautiful bit comes in is the way in which this movement is brought about. It’s so amazing; I’m grinning just thinking about it. Remember I said that the kinesin is made of two identical intertwined subunits? This means that there are two heads and two tails. The substance to be transported is tethered to the tails, while the heads are the interesting bits that do the moving.

Initially, one of the heads binds to a site on one of the cytoskeletal filaments. This causes some structural changes to occur within this head, which leads to the other head being forcibly thrown forward where it can then bind to another binding site, further along the filament. Once again, changes occur in this head, and the first head is then thrown forward again. See? By this mechanism, the kinesin molecule quite literally ‘walks’ along the filament, repeatedly putting one head in front of the other until it reaches its destination. So beautiful!!

Now, if I were going to lug that blasted piano all the way up to the roof of my skyscraper, I’m going to need a hell of a lot of energy! Surprisingly enough, the kinesin molecule also requires a lot of energy in order to carry out this job if it’s got a big fat chunky bit of machinery stuck to the end of it.

In biology, energy is stored in the form of a molecule called ATP; adenosine triphosphate. This is simply a chemical molecule called adenosine with a chain of three phosphate groups attached to it. When the cell requires energy, it just nips off one of the phosphate groups from the ATP molecule. The resulting molecule is ADP – adenosine <span>DI</span>phosphate. The reason this works is because when the bond between two phosphate groups is broken, it releases a lot of energy, and this is used to power whatever is going on in the cell.

So how is ATP actually involved? Well, in the resting state, the kinesin heads are tightly bound to ADP. When the head encounters the binding site on the cytoskeletal filament, this is quickly exchanged for ATP. Now, when ATP binds the head, some magical things happen which cause changes in the way the heads behave. ATP is converted to ADP, and energy is released. The linker region that I spoke about earlier tightly zips up along the side of the bound head, and it is this action which throws the second head forward. The second head now binds to the next binding site. Meanwhile, the first head is now bound to ADP, and releases from the filament. Now, we’re back to the same position we started in, except for being one notch further along the filament. The whole process starts again, and continues over and over again until eventually, the transportee (is that a word?!) reaches its destination. It’s so awesome!!

Kinesin movement is extremely detailed, and I know it’s probably a bit difficult to picture just from this explanation…take a look at this video (it’s got some cool sound effects)



Wow, that took me longer than I thought it would do. I thought I’d only need a few paragraphs. Anyway, I’m finished on that topic now – the second beautiful mechanism on my list is the insulin signalling pathway. Since I am doing a PhD in this topic, I do get pretty fired up on this once I get started, so stop me if I get too over-excited.  Right, where to start.

Insulin; most people have heard of it, but few could accurately describe what it does. “regulates blood sugar, innit?!” well flatly, yes, but it’s not quite as simple as that. And besides, what does that MEAN?  Insulin is a hormone which is secreted into the bloodstream from the pancreas following food intake. Its job is to cause cells to take up glucose from the blood, thus lowering the amount of free sugar floating around in the blood.

I’ve just come off my lunch break, and, befitting our jobs as obesity and diabetes researchers, we’ve just eaten a shamefully large amount of Quality Street. Oh, I wish I had some willpower, but chocolate seems to evaporate it all! Anyway, as we are MORE than aware, chocolate contains a lot of sugar. The increase in the concentration of glucose in my blood as I digest that sugar is detected by my pancreas, which will progressively release insulin. As this insulin starts to do its job, more sugar is taken up into my cells, and before long the concentration of sugar in my blood will be pretty similar to what it was when my stomach was rumbling before lunch. It’s absolutely astounding, really. It doesn’t matter how much chocolate you eat, or how little you eat, or how big a meal you’ve just had, or how old, young, big or small you are: if I simultaneously tested the sugar of everybody reading this post and compared it to mine, I bet you there would be hardly ANY variation between them; all of us would have blood sugar levels (glycaemia, as it’s known in the trade) within very close values of each other. That’s awesome in itself! I find it absolutely astounding that blood sugar levels can be fixed to within such narrow limits, all down to the action of ONE HORMONE! Absolutely fascinating! Such a beautiful, simple, ingenious mechanism for regulating something to within tiny ranges despite anything you might throw at it.

So now that you know what insulin does, how does it DO it? This is where the insulin signalling pathway comes in. When insulin is released, it circulates in the bloodstream. Now, one of the main sites of insulin activity is the liver (but almost all cells can respond to it). So insulin happily circles round in the blood until it reaches the liver. Here, it binds to RECEPTORS on the surface of liver cells.  As is insulin, these receptors are proteins, so it goes without saying that they have some amazing properties. The receptors are the proteins responsible for translating a signal from the OUTSIDE of the cell to the INSIDE, where the effects of the original signal are felt.

When there’s no insulin around, these receptors are on their own just floating around in the cell membrane and not really doing very much. However, all of this changes when insulin comes along. Insulin binds to its receptor, and the receptor then aggregates with another receptor in the membrane to form a molecule made of two subunits – it’s called a DIMER. This aggregation causes a striking shape-shift in the part of the receptor on the inside of the cell, and it then becomes an active enzyme. (An enzyme, if you’re not sure, is another type of protein which hastens (or permits) a chemical reaction in a cell). This is the first crucial stage in the insulin signalling pathway. The change in shape of the receptor also causes lots of smaller molecules, called IRS-1, inside the cell to bind to the receptor on the inside. From the IRS-1 molecules, the signal is further conveyed through a great long cascade of proteins. It’s like a chain reaction; IRS-1 allows activation of other proteins and enzymes, which in turn activate further proteins and enzymes, which activate further proteins and enzymes. This cascade eventually culminates in the movement of glucose transporter proteins onto the cell membrane. These glucose transporters (GLUT4, they’re called) are incorporated into the membrane, and their job is to facilitate glucose entry into the cell from outside.  Ah! So now we know how insulin does its work.

So, to summarise the insulin signalling pathway;

Insulin binds to its receptors on the cell surface, and these dimerise and change shape. This activates a long cascade of events within the cell, eventually causing glucose transporters to appear on the membrane. Thus, the cell’s capability to take in glucose is increased. And so I come to the end of my second explanation. I’m impressed I’ve kept it to a few hundred words!


Ah! The nervous system! After an awful, utterly traumatizing and wholly disastrous final year project in neuroscience, I never again thought I’d live to see the day when nerves actually became interesting again. Funny really, since the final year neuroscience course was unquestionably my favourite final year module. The bits of neuroscience that I enjoy are the nitty gritty details of how nerves actually WORK; I’m not interested in any of the psychological or behavioural shit, or what happens when they don’t work properly – I think they’re pretty fascinating just as they are. So, how does a nerve work?

A nerve is a bundle of neurones – the individual cells that make up the nervous system.  Nerves are the main way by which the brain communicates with the rest of the body. Communication about the state of the body is sent back and forth via electrical impulses along NERVES. The patterns, frequency and timing of these electrical impulses can co-ordinate the responses of the body.

I’ll give you an example. In a short while, I am going to have to make the short journey out of my warm, comfortable office out into the fresh air to go to the Café to buy some coffee. It’s freezing outside, and, because I was a little late this morning, I forgot to bring my coat with me. I can tell it’s gunna be an unpleasant experience! When I go outside, the temperature-sensing nerves in my skin will be triggered to fire impulses by the change in temperature. My brain will interpret these impulses and will send out further nervous impulses to various muscles in my body to make them shiver in the attempt to make myself warmer again. (And, indeed, the very thought that I am already dreading it tells me that there is nervous transmission going on between the different areas of my brain, telling me that I should associate cold with unpleasantness. (Although that’s not quite so simple – the guy who figures out how that works will win the Nobel Prize!)).

So okay, you get why nerves are important – I won’t bore you any longer. But what is really really reallllllly awesome about them is how the electrical impulse is actually brought about. Normally, if you gave an electric shock to a cell, it would kill it, so how are nerves different?

Neurones are loosely comprised a cell body, one or more long extensions known as axons, and lots of branches called dendrites. A neurone is stimulated by a change in its VOLTAGE, and essentially this voltage change initiates a wave of electrical activity in the neurone, and this shoots down the axon at high speed. So now let’s go into a bit more detail.

As I mentioned earlier, cells are surrounded by a membrane, and it is the membrane that encloses all the cell contents and controls what enters and leaves the cell. This latter function is exceptionally important for all cells, but particularly so in neurones. A neuronal membrane is encrusted with these proteins known as ion pumps. These do exactly what they say on the tin: they pump chemical ions across the membrane.

What’s an ion? Argh, it’s difficult to explain without getting into A level chemistry territory (and let’s face it, nobody wants to go there). The omniscient Wikipedia – my most trusty resource – defines an ion as:

“An atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge”.

Basically, atoms consist of positive protons, negative electrons, and neutral neutrons. Usually an atom has exactly the same number of electrons as it does protons, so there is no overall electrical charge on the atom. However, there are many circumstances under which this is not the case, and an atom can gain or lose electrons, thus giving it either a positive or negative charge.

So, why is this important? Well the membrane-bound ion pumps that I was talking about specifically deal with two ions: Sodium (Na+) and potassium (K+). In a resting state, the ion pumps actively pump Na+ outside of the cell, and actively pump K+ into the cell. However, for every one K+ ion pumped inside, three Na+ ions are pumped outside. So, we have a situation in which there is way more Na+ outside the cell than there is inside the cell, and slightly more K+ inside the cell than there is outside. Because of this imbalance, the overall charge on the membrane is NEGATIVE – there are more positively charged ions on the outside than on the inside, so the inside of the cell is MORE NEGATIVE than the outside. In this state, a cell is all set up to fire an electrical impulse when stimulated.

Okay – I expect I’ve confused you! Picture in your mind two big rooms separated only by a locked door. One of the rooms is absolutely packed full to the rafters of great big fat people called Nathan, and the other has a few skinny little Kevins floating around. Because the Nathan room is packed, it’s all hot and sweaty in there and everybody is uncomfortable. On the other hand, the Kevin room is cool, calm and definitely the place to be. So what do you think will happen if the security guard comes along and unlocks the door? There’s going to be a mass exodus of Nathans into the Kevin room!

When the neurone is stimulated, “gates” in the membrane open which allow Na+ to freely enter the cell. Remember, it’s negatively charged in there, thus the positive Na+ ions are attracted inside. This causes a change in the cell’s voltage which causes sequential opening of more and more gates all the way along the axon, and the electrical impulse zips along the axon.

Okay, so once all the Nathans have descended onto the Kevins, the security guard thinks it might be a good idea to open another door back into the first room to ameliorate some of the crowding. The problem is that the door he’s just opened is only big enough for the skinny Kevins to fit through. So, while all the Kevins can leave again, the Nathans have to stay put.

When these K+ gates open in the membrane, the efflux of K+ once again restores the membrane to its original voltage – negatively charged. Slowly but surely, the pumps once again restore the membrane to its resting state in which the Na+ is on the outside and the K+ is on the inside, and the whole system is poised to respond as it was before.

I’d love to be able to explain the physics of this, but frankly, I’ve spent the last ten minutes or so trying to construct a paragraph that accurately explains it without getting the facts wrong, but I simply don’t understand it well enough (I SUCK at physics!). Forgive me. You’ll just have to do with the biology instead which, as I know you’ll agree, is way more interesting anyway.

For those of you, like me who find animations much more helpful when trying to imagine something, this video explains the nerve impulse very well. Take a look:


So once the electrical impulse has reached the end of the axon, what happens next? The axon of one cell typically makes contact with another neurone. When the impulse reaches the end of the axon, it reaches what is known as a SYNAPSE; a point where the axon of one cell comes into very close proximity with the cell body of another (they never touch, but come very, very close). When the electrical impulse reaches the synapse, a neurotransmitter substance is released by a complicated – but ingenious – mechanism. This neurotransmitter then binds to its RECEPTORS on the second cell. This receptor binding causes another chain of events that causes the electrical impulse to be propagated in the SECOND cell, and so it continues.

So there you have it. That’s how nerves communicate with each other, and I’ve reached the end of explaining my third biology miracle.


My fourth is a little less complicated; you’ll be pleased to know. It is so wonderfully simple and seemingly insignificant that you may wonder why I’m even mentioning it here amongst the great wonders of the biological world. But nonetheless, this made me laugh out loud when I discovered it – it’s so, SO simple, yet makes such unbelievable, perfect sense.

As we all know, fish have gills which enable them to access oxygen that is dissolved in water. Gills are actually quite fascinating; they are beautiful, elaborate structures which are honed to perfection to carry out their job in a way more fantastically efficiently than any man-made machine.

The concentration of oxygen dissolved in water is decidedly lower than that in the air we breathe, yet by virtue of their gills, fish are still able to extract colossal amounts of oxygen from water in order to meet their demands. Humans wouldn’t stand a chance under water – our lungs are just not set up to be able to absorb oxygen at such low concentrations.

Gills consist of very thin filaments of tissue, all stacked on top of each other like stacks of paper. Each filament consists of comb-like structures known as lamellae, and are intertwined with an extensive capillary network. Together, the massive surface area and blood supply mean that the gill structure is optimised for maximum gaseous exchange. The whole gill structure can be found on either side of the head, covered by a scaly flap of skin known as the operculum.

I used to keep a goldfish in a little tank whilst I was at school, and I remember learning about this mechanism and then staring for ages at the movement of my goldfish’s gills, and marvelling at their simplicity. You must have seen fish open their mouths repeatedly, as if they were gulping down water? Well, when the fish opens its mouth, the operculum and the buccal cavity (the floor of the mouth) move outwards and downwards. This creates a negative pressure in the mouth, which draws in water. The fish then closes its mouth and the operculum, and the water pressure increases, forcing the water back over the gills. Then the exciting bits happen.

The simple concept behind gaseous exchange is this: a substance will always move from an area of its high concentration to an area of its low concentration. Simple, really. So simple that without this seemingly insignificant physicochemical phenomenon, there would be no life on earth. The difference in concentration between one area and another is called the diffusion gradient: the steeper the gradient, the more diffusion will happen. Got it?  Anyway, water is passed over the gills from front to back. As water passes through the gill, more and more oxygen is absorbed from it, and so the concentration of oxygen in the water steadily decreases from left to right. Yes? Concurrently, it could be expected that the concentration of oxygen in the blood INCREASES from left to right. Right? Wrong.

Think about this for a second. If blood were to enter the gill system on the left hand side, same as the water, then what would happen? Initially, large amounts of oxygen would happily diffuse into the low-concentration blood. But quickly, as the amount of oxygen in the water was depleted and the amount in the blood was increased, there would soon reach a point where the concentrations in both water and blood were equal, and no further oxygen exchange would be able to happen. What a waste! There is still quite a lot of dissolved oxygen in the water, but the fish can’t access it because there’s no more diffusion gradient!

Of course, inefficiency isn’t in the vocabulary of Mother Nature; of course she’s come up with a way to elegantly circumvent this little problem. Suppose the blood entered the gill system from the right, not the left. As before, the water that comes in has a high concentration, so it will easily diffuse into the blood. But instead of reaching this equilibrium point somewhere in the middle, this counter-current mechanism allows oxygen to keep diffusing out of the water into the blood right the way along the length of the gill. Think about it: although water on the right hand side of the gill has a lower concentration before, the blood that is on the right hand side has only just entered the gill: its concentration of oxygen is also exceptionally low! In fact, the concentration of oxygen in the blood is still considerably lower than that of the water, despite the latter having been already depleted of much of its oxygen. So, gaseous exchange will still occur. Thus the diffusion gradient is maintained all the way along the gill surface, and the fish is able to extract the maximum amount of available oxygen from the water. So simple, so ingenious! I love it!


I know I said that there was no order of preference for my writing these five mechanisms, but I have left my favourite until last. For some, intangible reason, I can’t put my finger on exactly why I find this so overwhelmingly beautiful, but I do. I remember very clearly learning about this in a second year lecture. I remember the lecturer, where I was sitting, and who I was sitting with. I also remember being more than a little bit embarrassed at being so emotionally affected by hearing the description for the first time. Okay, I’m a loser – get over it!

Have you ever stopped to think about how a newborn baby instinctively knows how to suckle and swallow milk from its mother? A tiny little baby that can’t do anything for itself, can’t control its breathing, can’t control its bladder, and can’t look after itself. A little baby is absolutely dependent on its parents for survival, yet instinctively, the moment it is born it knows exactly what a breast is for, and how to extract milk from it. I find that so breathtaking I can’t even describe. This behaviour is caused by the rooting and suckling reflexes.

A reflex is an action that is performed involuntarily or automatically. Other examples of reflexes include closing your eyes when you sneeze or encounter bright light, and that weird kick thing you do if the doctor uses the hammer just below your knee.

The rooting reflex is the term used to describe the phenomenon by which a newborn baby will turn its head to the side when something strokes its cheek or mouth – such as the mother’s breast. The baby will search for the object by turning its head in movements of increasing size until the object is found. Furthermore, what is even more beautiful is that there is refinement of this reflex if the baby is continually exposed to the stimulus. Once a child has been breastfeeding for a few weeks, it will move directly to the nipple without needing to display these rooting movements – it has learned where the nipple is, and doesn’t need to keep searching.

The suckling reflex follows the rooting reflex. Once the baby has found the mother’s nipple, the suckling reflex is activated when anything touches the baby’s lips, and stimulates the baby to grasp the nipple between its gums and start sucking. The tounge is used to also draw milk out of the breast.

These reflexes are the same in all newborn babies, so for me, this begs the obvious question of HOW does it do that? What’s causing it? It’s frustrating, I can’t seem to find the answer in any of the literature – it MUST be there somewhere, but I can’t find it. I have a few ideas, but I don’t know for certain. I can, however, find some information on how the baby’s suckling stimulates the mother’s breast to let out milk. The two maternal reflexes involved in suckling are the milk production and milk ejection reflexes, respectively controlled by two hormones called prolactin and oxytocin. You may have heard of oxytocin; the media like to call it the “love hormone”, because it is thought to be responsible for partner bonding, feelings of love, trust and sexual pleasure. It is also the hormone that they give to pregnant women to induce labour if the baby is overdue. Anyway, its role in breastfeeding is thus. When a baby suckles, it stimulates nerve endings in the nipple, and these fire impulses to the pituitary gland (in the brain). This is the body’s factory for various hormones – eight, in fact (one of my second year exam questions was to list them!). Anyway, two of these eight are prolactin and oxytocin, and these are subsequently released into the bloodstream, where they reach the breast tissue.

In exactly the same way as insulin has its receptors on liver cells, prolactin and oxytocin have their receptors on breast tissue cells. Binding of these hormones to their receptors triggers a great long cascade of events inside the cells (using very similar mechanisms to the insulin signalling pathway), which eventually culminate in production and ejection of milk. So amazing! The very action of a baby suckling can cause such profound changes in the way the mother’s breasts behave that she can feed her baby on demand, at any time, whenever necessary.

(Interestingly, as a side note here – you know I mentioned that the insulin signalling pathway and prolactin/oxytocin signalling pathways are very similar? Well actually all signals act in similar ways. The specifics do vary, but essentially it is the same molecules involved in all kinds of diverse and unrelated signalling processes in the body. What’s MORE intriguing is that these molecules are found across ALL OF EVOLUTION! Often it is exactly the same molecules that are found in frogs, snails, worms, humans, elephants, monkeys and mice – don’t you think that’s pretty awesome? One universal, flawless language that unites almost all life forms on earth).

So there you have it; my five favourite bits of biology. I admit, there are many, many others that I can instantly think of that are just as amazing, but for me, these certainly stand out above the others. Right, daydream over for the day, I’ve now got to go and develop my Western Blot!

August 03, 2010


June 18th, 2010

It has been a long, long time since I last had a day off without worrying about work. Since I last sat out in the sun with a glass of wine and enjoyed the company of some of my good friends, and since I could fully relax knowing that, for the first time in three years, I actually have nothing to do. It’s a strange feeling, let me tell you. After our final lecture today, some of my good friends and I went to sit on the grass to enjoy the sun. After trooping round campus for a good while, trying to find a spot of grass minus the duck poo (!), we finally settled by the lake and enjoyed what may well have been our last afternoon together. By everyone else’s accounts, it has been a glorious day; blazing sunshine, baking hot, and not a cloud in the sky.

Hrumph. I don’t like summer very much. Hayfever, exams (usually), uncomfortable, hot, sticky, sleepless nights...no, summer is not my favourite time of year. Every year I TRY and like summer – I always think, ooh, it’s summer, it’s gunna be good this year. It never is.

One of my major problems with summertime is this: my skin is so fair that ten minutes in the midday sun is enough to turn me BRIGHT RED, and make me curse the sun even more than I already do. I can hear you all saying, “well if you’d only wear suncream, you wouldn’t get burnt”. Well, I have given up on suncream – it doesn’t seem to work for me unless it’s AT LEAST factor 50, and that’s both difficult to find and very expensive. I usually just cover my shoulders and wear tights throughout summer instead.
Today was no different, although there must have been about 15 minutes this afternoon where I was so hot that I simply had to remove the cardigan covering my shoulders. I’m paying dearly for this moment of foolishness, and am bitterly wishing that I’d paid attention to the voice of reason in my head that told me that it was a bad idea at the time.

They say that sunburn is really bad for you; that it’s a cause of cancer, and that even getting burned once has lasting damage, blah blah blah. Well, I don’t like scaremongers in general – in fact, I am one of their biggest critics – but it is true that sunburn is exceedingly bad for you. Let me tell you why.

Every cell in your body contains DNA. Most people know that DNA contains the “genetic information” for an individual, but what does this actually mean? Virtually every function that your body carries out is carried out or controlled at some level by proteins. I honestly can’t think of ANYTHING in the human body... (now you’ve got me thinking)... no, really, can’t think of anything that doesn’t involve proteins at some level.

Haemoglobin: the molecule that makes blood red and carries oxygen round your body – that’s a protein. All the digestive enzymes – they’re proteins. Insulin: the hormone that keeps your blood sugar constant – that’s a protein. The light-sensing units in your eyes – they’re proteins. Neurotransmitters, muscles, hair, fingernails... need I go on? I think you get the picture. But back to my point, DNA is a code which contains all of the information needed to MAKE these proteins.

DNA is a quite complicated molecule, but essentially it’s got a backbone made of a type of sugar and a chemical group known as a phosphate group. Attached to this backbone are BASES, and this is where the information is encoded. There are four bases: A, T, C and G, and it is the sequence of these bases which is the code.

Now, many of you will know that proteins are long strings of individual units called amino acids. Simply, how the genetic code works is that the machinery that makes proteins “reads” along the DNA molecule, and puts the right amino acid into the protein that’s being made, according to what is encoded in the DNA.

Let me explain this a bit further.
I’ve got a DNA molecule, and its sequence of bases is GATAGTAAGCCATCACGT. Now, the protein factory reads this in groups of threes: GAT-AGT-AAG-CCA-TCA-CGT. Each of those groups of threes codes for one amino acid. So, that sequence in the DNA will translate into a protein that might be something like this: Ala-Gly-Leu-His-Tyr-Trp. I have no idea what it actually is – I’d have to look it up – but do you get the idea? Then, it is the chemical properties of the amino acids themselves that makes all the different proteins do different things.

Now, what I have just described to you is the central dogma of molecular biology. It is the most fundamental, absolutely basic, elementary function of all life on earth; the ability to translate DNA code into protein.

So how does all this relate to my roasted shoulders? Why did I bother telling you all that stuff?
Well, in light of what I just said about how essential proteins are, and how all proteins are made from DNA code... imagine how catastrophic it might be if that DNA got damaged.

Think of this as like me building a Lego model using an instruction manual. If someone rips out a page, or scrambles up all my pages, or scribbles in them, or adds in a page that shouldn’t be there, then I’m going to get confused and I’m just not going to be able to make the model the way it should be. This is the same with DNA and protein: if DNA is damaged in some way, then the protein that’s made from it just won’t be what it should be, and it might not work properly.

So many human diseases are caused by exactly that; damage to DNA causing non-functional proteins to be made. Skin cancer is the one that everyone knows about with regard to sunburn, so let me concentrate on that.

Sunlight contains ultraviolet radiation, which is just a very high frequency type of electromagnetic wave. Now, because it is high frequency, it has a lot of energy – far more than those poor atoms in the DNA in your skin cells, so when UV rays hit them, it actually makes the atoms behave in a different way. Now, this becomes a massive problem when two T bases or C bases are adjacent to each other in the DNA sequence (TT or CC). This high energy from UV light causes them to physically fuse together, to create a weird molecule that is never usually found in DNA. Now, the machinery that reads the DNA simply can’t read this molecule – it just doesn’t recognise it.

Going back to my Lego analogy, if someone stuck a page into my instruction manual that was written in Chinese, I would be completely stumped. I just wouldn’t understand what I was supposed to do. So what could I do? I could throw my hands up and say, “I give up”, or I could take a wild guess at something and just add in a piece to my model at random. This is what the cell does; often, the DNA damage is so severe that the cell will just give up, or it will add in an amino acid at random (a mis-read, rather than a non-read). Either way, the protein gets screwed up.

...But what if that protein was really important in controlling cell division? What if that protein was absolutely essential in making sure that cells don’t divide when they shouldn’t do? What if the cell absolutely couldn’t do without it...? Cancer is just that; when the proteins that control cell division get screwed up because of underlying DNA damage.

Imagine that I am sitting in a little booth by the side of a busy junction, manually controlling the traffic lights. My job is to change the lights at the right time to make sure that the junction keeps working properly and that there are no accidents. Imagine then, if some very mean person comes into my booth and ties me up. I wouldn’t be able to perform my duties properly, and the state of traffic at the junction would disintegrate into pandemonium. Imagine what chaos could be caused, and how catastrophic may be the consequences. Well, it is the same in the cell. If cells just divide uncontrollably, then you get a lump – a tumour – and this can have disastrous effects on neighbouring cells, and can completely disrupt the way that that tissue works. This is why cancer is so devastating – because these cancerous cells just keep dividing and dividing and dividing out of control until they physically disrupt surrounding tissues. Bad stuff.

So let me bring all this together. All the while I was so foolishly sitting out in the sun all exposed earlier on, those ultraviolet rays from the sun were beating down on my unsuspecting shoulders and causing the bases of the DNA in my skin cells to become damaged. The machinery that reads my DNA and translates it into proteins simply can’t read this – “it may as well be written in Chinese!”, and subsequently can’t make the proteins the way they should be made. If I were unlucky enough to have this damage happen in the parts of DNA that encode cell division genes, then maybe the control of cell division might be lost and I’d end up with skin cancer. Make sense?

That’s a pretty scary thought, huh? I thought so. But like I said earlier, I hate scaremongering, so let me ALSO tell you that a skin cancer will not develop just from one bout of sunburn. Why? Because, as all you faithful readers of my previous notes might be beginning to appreciate, cells are BLOODY COMPLICATED!! There is never such a thing as *ONE* protein that controls cell division – there are several. There are some back-up mechanisms, and many levels of control. Cancers develop following inactivation of all of these mechanisms through lots of cumulative DNA mutations. Ever wondered why cancers are generally a disease of old age? It simply takes time for these mutations to accumulate.
Nonetheless, one bout of sunburn may indeed have contributed one to these mutations – I might have lost one of my nine oncological lives! So it’s best to stay covered up in the sun if you’re fair skinned – even 15 minutes is enough! I’m going to go to bed now, and rub moisturiser into my sore and sorry-looking shoulders. Hrumphh. Summertime.

Just as a heads up, Cannon Park Tesco’s sells factor 50 suncream ;-)

The most beautiful of all the biological systems

May 25th, 2010

Week three in the neuroscience house. Well, lab. I just thought I’d tell you a bit about the project I’m doing, because quite a few people have been asking me what I’ve been up to. Truth is, I’ve not really known myself until fairly recently – it’s been a pretty sharp learning curve and I’ve not really had a chance to sit back and take things in. Sick of feeling like an absolute chimpanzee, having to be told everything, and not understanding why certain things are done the way they are, and what the whole damned point is anyway, I’ve not really been enjoying my project. However, after having a chat with one of the guys in the same lab, who explained step by nit-picking step with me, I finally feel a bit more comfortable.

Essentially, I’m looking at the actual events that take place that underlie learning and memory in the brain. As you know, the ability to learn and remember things declines quite markedly in old age, and this has been linked with a palpable change in cells of the brain – I’m looking at which molecules bring about this change. I guess you’re feeling a little bit lost; let me start at the beginning.

Brains are beautiful. Their complexity, magnificence and mystery have fascinated scientists for decades, and despite countless years and lifetimes of research, their secret workings still remain almost entirely elusive. Even at its most basic level, the brain is exquisitely complex. There are gross anatomical areas; each of which loosely controls a different function, or set of functions, and then within these areas there are smaller, but still discrete areas, which have their own circuits and interactions with other areas, and indeed, other parts of the brain. Smaller than these circuits, the very fundamental unit of the brain is the brain cell; the neurone, and it is the phenomenal complexity and precision with which these cells communicate with each other that permits us every movement, every action, every emotion; everything that makes us who and what we are.

Neurones are beautiful in their own right. Fascinatingly complex, beautifully simple, each has its own properties and role to play. The first time I saw a neurone – stained bright green – under a microscope, it literally took my breath away; I have never seen something so serene and beautiful.

So, how do they work? Neurones are loosely comprised a cell body, one or more long extensions known as axons, and lots of branches, called dendrites (I will add a picture if I can work out how...). A neurone is stimulated by a change in its VOLTAGE. This is a really beautiful mechanism, which I won’t explain here, but essentially this voltage change initiates a wave of electrical activity in the neurone, and this shoots down the axon at high speed. The axon of one cell typically makes contact with another neurone, and thus the cells can communicate with each other. When the impulse reaches the end of the axon, it reaches what is known as a SYNAPSE; a point where the axon of one cell comes into very close proximity with the cell body of another (they never touch, but come very very close). When the electrical impulse reaches the synapse, a neurotransmitter substance is released. This neurotransmitter then binds to its RECEPTORS on the second cell. This receptor binding causes another chain of events that causes the electrical impulse to be propagated in the SECOND cell.

So, to summarise:
It’s like a relay race. The first runner hears the stimulus, the gunshot, and he starts running as fast as he can. When he reaches the second runner, he passes over the baton, and the second then starts running as fast as he can. A cell is stimulated and fires an electrical impulse. The action potential shoots along the axon, and reaches a synapse with another cell. Neurotransmitter is released, and binds its receptors in the second cell. This triggers an impulse in the next cell, and so on, and so on.

This athletic analogy is very limited. Brains are complicated, man! Very complicated. I know how annoying it is when people do this, but I have to say that I have somewhat oversimplified this model. There are literally tens of different neurotransmitters which do different things, lots of different types of neurone with different dynamics, different transmission speeds, different strengths, different stimulus thresholds needed to fire.... They’re REALLY complicated. So you can imagine that the trillions of interactions of different neurones and networks of neurones with each other can (somehow) create enough computing power to carry out complex functions. We just have no idea how it does it!

One of the most mind-boggling functions of the brain is that, in the same way as a computer can, a brain can interpret integrate and interpret information, but it can also store information in the form of learning and memory. We still don’t really know how memory works at its most complex levels - why is it that I can remember what I did on my 6th birthday, but can’t remember where I put my keys when I got in? Why can I remember what I had for breakfast yesterday, but can’t remember what I had for dinner? Indeed, memory is a curious and compelling area of research, and at the moment our understanding is still sorely limited.

The current, most plausible paradigm for learning and memory concerns the STRENGTH of, and NUMBER of synapses in the brain (remember, synapses are the connections between neurones). By changing these two parameters, you can change the way that neurones behave, and by changing the way neurones behave on a long-term basis, you change the way the whole system behaves, and this is thought to underlie learning and memory.

Remember I said that a neurotransmitter binds to its receptors on the post-synaptic cell? Well, these receptors have everything to do with learning and memory – at least according to our current understanding. Loosely speaking, the more receptors that are at the synapse, the stronger and more sensitive that synapse is. Conversely, taking them away makes the synapse weaker.

If I’ve got a neurone, and I’m stimulating it with an electrical impulse, it will keep firing impulses until I stop stimulating it. If then, in the same cell, I suddenly start to stimulate it with a really high voltage, but without changing the frequency, the cell will recognise that the stimulus it is receiving must be quite important, and will change its activity accordingly. The cell puts PHYSICALLY MORE neurotransmitter receptors on the cell surface. This way, there are more receptors to respond to the stimulus, so the synapse becomes STRONGER. This is known as long term potentiation (LTP); a mechanism by which cells become more acutely wired to respond to a stimulus in future.

If you’re feeling a bit confused, think of this like the boy who cried wolf. If the boy were to run out of the woods and cry wolf once every two months, he might always get a response from the shepherd, who would put his sheep away. Yes? Say then, that suddenly two months later the whole of the local primary school run out of the woods and cry wolf – the shepherd is gunna think, “Ohh Man, this must be really important!”, and he will put away his sheep in double quick time. If this whole primary school were to continuously come out of the woods every 2 months and cry wolf, then very quickly, the shepherd might put in place some measures to make it easier for him to put the sheep away. He might build a closer pen, or he might buy some more sheepdogs. This is what the cell does with its receptors! It is a LONG-TERM, PALPABLE CHANGE IN CELL BEHAVIOUR.

Okay, now I’ve got another neurone, and I’m stimulating it again with an electrical impulse, and duly it is firing its action potentials. But then, I massively up the frequency, but not the amplitude of the impulse. The cell will call time out, and will take in some of receptors so that in future, it responds LESS STRONGLY to the same stimulus. This is long term depression (LTD).

Going back to my cute little analogy; if the boy who cried wolf suddenly started running out of the woods every day, instead of every two months, the shepherd would very quickly get fed up with it (On yer bike!!) and will stop responding to it, or will respond in a half-arsed manner. Now, this is also a long term, palpable change in behaviour, because now that the shepherd has been somewhat cheesed off, it’s going to take much more of a stimulus to get him to react in future. It might need all of the local primary school to cry wolf before he even reacts at all.

Okay, so now you’re at the cutting edge of what we understand about learning and memory. I’m not joking; we really don’t know much! My project is involved with looking at one aspect of LTD; dendritic spine shape.

Dendritic spines are these cute little structures also found on neurones which are the exact places where the cell RECEIVES a synapse from another cell – that’s where all the receptors are. Usually, they’re little mushroom-shaped knobs, but they vary, and THAT’S what I’m looking at.

Quite a marked change in shape and number of these spines can be seen in models of memory loss, so we’re interested in how that happens. It’s very complicated, but basically, the receptors are anchored to a scaffolding protein called actin, which keeps things nice and structured. Movement of this scaffolding protein is what allows the receptors to be added or removed from the cell surface, but it also causes CHANGES IN SPINE SHAPE. Now, specifically (you’re forgiven for being a bit lost at this point – it’s getting a bit hardcore) I’m looking at a protein called COFILIN, that is involved in the regulation of the way that actin moves.

I want to determine the PRECISE role that coflilin plays in the regulation of spine shape. How do I do that?! Well, I’m effectively messing around with cofilin in various different ways to see what the effects will be. Hopefully, HOPEFULLY, when I subsequently look at the neurones under the microscope, I will be able to see distinct changes in the shape of the spines, which will give me some idea about the role that cofilin plays. Well, that’s the plan, anyway – science is notorious for not working the way it should do! My task for the next few days is to analyse my results that I got last week: I’m counting dendritic spines until I’m blue in the face. Or green in the face, as it is, because they’re stained with Green-flourescent protein. I have a vague idea what I SHOULD see, but whether I will or not is another matter. Wish me luck!


May 21st, 2010

Have just been tidying up “My Documents”, and found this that I wrote a few weeks ago but had forgotten about. Have fun (btw, I won't be offended if you can't be bothered to read all of this) :-P

If any of you have seen any of my recent Facebook updates, you should have some idea about how much I hate revision. I’ve got eight productive days of revision left before the exams start, so you must be wondering why on earth I’m wasting my time writing a Facebook note. Well, you see all day I have been trying to entice my brain to take in the most boring facts possible, but I think it has shut up shop for the night. “Get lost, no room at the inn!” The cause of this mental barrier? Are you ready?

...brace yourselves...

... it’s the Vaccination and Gene Therapy module.

I do a fair bit of complaining about this module, as some of you will know, and again, as all you poor buggers who’ve also got to take the exam on this evil subject will understand, my complaining is not entirely unjustified. It consists of 12 lectures just listing the different classifications and statistics of literally tens of vaccines. No biology involved – just statistic after statistic after statistic.

Indeed before the year had even started I went to speak to the head of department to beg him to let me drop the module – he refused. So anyway, I find myself trying all sorts of tactics to try and learn some of this shit, and after having tried:

• Writing out facts over and over and over again
• Writing in pretty colours
• Reading out-loud
• Highlighting
• Mind-mapping on rolls of wall paper

I’ve had enough. I can’t take it anymore. So I Googled, “how to learn something really boring”, and clicked on a link at random. One of the suggestions was “to write an article or blog”. AHA! I rather enjoy writing those, and I hadn’t thought of that before. Maybe I can make a very boring subject into something more interesting by telling other people. So yes, the purpose of this blog is as a last-ditch attempt at a revision aid – and to tell you something about vaccination. The topic is rather large, so I’m just going to talk about vaccinations for meningitis, because it’s quite a nice, round topic.

Meningitis is nasty. Really nasty. It causes the deaths of literally thousands of people each year, and leaves many of its victims brain damaged or severely disabled. Not surprising really that there have been various attempts to control it via vaccination attempts.

There are two types of meningitis; viral and bacterial. Viral meningitis is the most common type, and tends to be less severe than bacterial (although we’re talking about meningitis here – none of it is particularly desirable) and usually patients make a full recovery.

There are three main types of Bacterial meningitis caused by three different bacteria:

• Streptococcus pneumoniae (known in the trade as pneumococcus)
• Haemophilus influenzae
• Neisseria Meningitidis (meningococcus)

I’ll talk about each one in turn.

Pneumococcus is the most common cause of meningitis, causing 25% of meningitis deaths in the UK. It’s a nasty little beast that’s responsible for quite a few infections, including Otitis media (earache), influenza, septicaemia, sinusitis, peritonitis and arthritis. Usually, however, it lives perfectly harmoniously in your nasopharynx; part of the nasal cavity behind the nose. For all you singers out there, your “head voice” is generated by resonance of air in this cavity.
By the time you reach your first birthday, everyone, yes EVERYONE carries Pneumococcus in their nasopharynx, but usually it lives there causing no trouble. Invasive disease is caused only occasionally, and the reasons why it might suddenly become activated are complicated, and in many cases aren’t completely clear.
Like a lot of diseases, the risk of Pneumoccoccal meningitis massively increases if your immune system isn’t working properly. The main cause of immunosuppression that springs to mind is HIV infection. HIV destroys a major group of cells in the immune system, laying your body open to lots of diseases that usually would not cause a problem, including Pneumococcus. There are an estimated 27 million people worldwide who are living with HIV, and HIV infection increases your chances of catching Pneumococcus forty-fold. Pretty sobering fact, eh?

If you catch an infection from Pneumococcus, you’ll know about it. About 30% of Pneumococcal infections require hospitalisation, and about 25% of those patients who develop meningitis will die - a rate which can increase to 75% in very young children. That’s a hell of a lot – by comparison, tetanus has a 10% fatality rate, and MRSA has a fatality rate of 11.2%. Of those that don’t die, mental retardation, deafness, epilepsy, blindness and behavioural problems are common.

Meningococcus is just as nasty as pneumococcus, causing really really severe meningitis. It’s carried in the nasopharynx by around 20% of the population, but can increase to as much as 70% during outbreaks. Imagine that! 70% carrying such a dangerous pathogen with them everywhere they go. Meningococcal Infections are characterised by a very sudden onset of all the typical symptoms of meningitis, (headache, photophobia, stiff neck, etc – all the symptoms on the posters stuck up all over the halls of residence), and if infections are left untreated, they cause 100% mortality within days. That’s more deadly than Ebola, leprosy, malaria and cholera.

There are 13 types (serogroups) of meningococcus, and six have the potential to cause infection in humans. They have different global distributions, with Serogroup A being found primarily in Africa, and Serogroup B distributed globally. Serogroup B causes around 80% of the Meningococcus cases in Europe. However, outside of Europe, Serogroup A is responsible for virtually all human cases.
Partly due to the severity of these diseases, their widespread nature, and the massive HIV pandemic, the development of pneumococcal and meningococcal vaccines was seen to be somewhat of an emergency. There are currently two types of vaccine available each against Pneumococcus and meningococcus. For Pneumococcus; a 23-valent polysaccharide vaccine, and a 7-valent conjugate vaccine. For Meningococcus, similarly a polysaccharide vaccine and a conjugate vaccine.

Valent? Conjugate? What on earth am I talking about?!! Polyvalent just means that the vaccine contains multiple strains of Pneumococcus. Let me explain. Viruses and bacteria evolve very quickly – much faster than plants and animals, and if you were to round up all of the Pneumococccus bacteria from all over the world and look at their DNA, you would find that there were some differences where they have mutated and become slightly different from each other. Some of them would have become sufficiently different so that the immune system would actually recognise them as two different viruses – these would be said to be two different strains.
One of the pneumococcal vaccines contains 23 different strains, and the other contains seven different strains. There are around 90 different strains of Pneumococcus, but to include ALL of them in a vaccine would be impossible. Instead, the strains that are the most common culprits for disease were picked. Make sense? As for conjugate, I’ll explain that later.

Polysaccharides are long strings of sugar molecules all bonded together. Starch is a polysaccharide, for example, which is made from a long string of glucose molecules. Many bacteria have a coat of polysaccharides on their surfaces which carry out lots of different functions for the bacterium. Unfortunately for them, the immune system is able to detect these polysaccharides and recognise them as pathogens that shouldn’t be there, so mounts a great big offensive response against them.

The 23-valent, polysaccharide Pneumococcal vaccine is pretty good at inducing immunity. About 70% of adults will develop immunity after vaccination. HOWEVER, it does have some pretty major disadvantages.
As I said earlier, the majority of infections and deaths occur in children under two years of age, and sadly, the vaccine is not very effective in this age group. There are two reasons for this. A baby’s immune system is still immature at the time of birth, and simply cannot respond to the injected vaccine in the same way as an adult could. However, a baby is not completely unprotected. Before birth, some of the antibodies in the mother’s blood are able to cross the placenta into the baby’s blood to give the child some protection until its own immune system is ready. Antibodies are also found in breast milk, so by breast-feeding a child, a mother is using her own immune system to protect her baby. But, unfortunately for vaccine scientists, these maternal antibodies interfere with the vaccine. They inactivate the vaccine before the child can respond to it, so giving a vaccine to a baby is, in a lot of cases, completely pointless.

Also, rather crucially for a vaccine, the current 23-valent vaccine does NOT provide any immunological memory. What that means is that the vaccine will initially produce an effective response, but this quickly wanes (after around 5-10 years) and a booster vaccine dose is needed. This is fine if you’re trying to vaccinate only a small group of people, but trying to administer repeated doses to an entire country is just expensive, time consuming and impractical.

The 23-valent vaccine also won’t give you any protection against any bacterial strains that are not contained within the vaccine, not only is this terribly annoying, this is more than the trivial problem that it might seem. There is no such thing as a bacterial vacuum – if you remove one type of bacterium from an environment then another one will very quickly take its place. But what if the bacterium that moves into its place is WAY more dangerous than the first one? What if it is untreatable with antibiotics? This strain will spread like wildfire throughout the vaccinated population because you’ve removed all of its competition. In cases such as these, vaccination may cause more harm than good...

Despite these quite severe shortcomings, any safe, moderately effective vaccine is better than nothing, so the 23-valent, polysaccharide-conjugated vaccine has been recommended for healthy elderly people in institutions, and high-risk adults (such as those with underlying health conditions, such as diabetes).

A more modern vaccine, the 7-valent conjugated vaccine was developed to try and overcome some of the shortcomings of the original polysaccharide vaccine. We already know what 7-valent means, but what about conjugate? A conjugate is, biologically speaking, a “hybrid” molecule.
Some of the surface antigens (the bits of the Pneumococcus which elicit the immune response) are not particularly effective if they’re given on their own, so they’re chemically attached to a much more potent molecule – in the case of Pneumococcus, the protein that’s used as the conjugate is actually a toxin from a totally different bacterium – the Diphtheria toxin (Dtx), responsible for the eponymous disease. So the conjugate that is injected is a hybrid of Dtx:Antigen, and the immune response will be raised against the pneumococcal antigen with a bit of help from the toxin.

The conjugate vaccine “take” (efficacy at eliciting an immune response) has been shown to be 97% effective in phase three clinical trials, and much more effective at producing protective antibody in infants and the immunosuppressed than the original polysaccharide vaccine, and as such was licensed for use in the USA in 2000, and routinely given to children at 2-3 months in the UK from 2006. Since its US introduction, there has been a 69% decline in invasive disease in young children, and a variable 8-32% decline in adults, depending on age. So effective is this vaccination campaign, that even unvaccinated adults were conferred some level of protection. How on earth can that work??

There’s this pretty cool phenomenon in disease control called Herd Immunity. If enough of a population is vaccinated, then even those individuals who have not been vaccinated will be protected. This is because in order for an infectious agent to persist in a population, it must have a large enough pool of susceptible hosts to keep an infection going, and this cannot happen if herd immunity is present. Let me explain.
If I were to catch measles tomorrow, I would become very ill for a few weeks, and I would infect all of those around me that I could. Say I’m sitting in a lecture theatre, and I infect all of the people in the front row where I’m sitting. Eventually my infection would run its course and I would get better, and the measles virus would no longer be present in my body, but the infection would live on in the other people I’d infected. They might then pass on the disease to the second row, thence to the third, fourth and fifth row. In other words, the infection PERSISTS in a population.
Now let’s change the situation. I’ve been very unlucky, and have visited my friend on the other side of the country who gave me measles. Upon my return, I’m sitting in a lecture theatre but virtually everyone in that theatre has been vaccinated against measles; all apart from a few scattered diffusely throughout the theatre. Now, because everybody on the second row has been vaccinated, my measles cannot be passed on to anybody – they’re all immune. So, try as the virus might, it can’t infect anyone new. So, the infection will run its course and I will get better, but crucially, the infection will die out from the population and will not be able to persist because there simply aren’t enough people for it to be passed on to. As such, those few individuals in the lecture theatre who were not originally vaccinated will still be immune because there is nobody around them to give them the virus! Make sense?
As you can imagine, herd immunity is a pretty useful phenomenon for vaccination scientists, and it is a bit of a bonus if a vaccine is able to bring about herd immunity.

As I said earlier, the two types of vaccine that are available for Meningococcus are also a polysaccharide vaccine and a conjugate vaccine. The same kinds of problems were encountered with the polysaccharide vaccines as were encountered with the Pneumococcal polysaccharide vaccines, and subsequently a conjugate vaccine was developed following the success of the conjugate Pneumococcal vaccine.

There are three types of conjugate vaccine:

• MenC – monovalent, protects against the group C Meningococcus serotype. The usage of MenC has been routine in UK children since 1999
• MenA/C – bivalent, has not yet been licenced for use in the UK, and is still undergoing clinical trials
• MenA/C/Y/W-135 – tetravalent, licenced in the USA and used in various other developed countries.
• MenAfriVac – an affordable form of MenA, which was especially developed for use in developing countries, where Group A Meningococcus are the most prevalent. It is manufactured in India, and, unlike the usual $7 MenA used in the developed world, MenAfriVac costs only 5p a dose.

Now, if any of you were on the ball, you might have noticed that the notorious, worldwide tyrant, Group B meningococcus were missing from any of the above vaccines. The reason for this is that Group B conjugated vaccines don’t work. Why? Well, the type of polysaccharide which is found on group B Meningococcus is called N-acetylneuraminic acid (NANA for short) The problem with using this in a vaccine is that this NANA is also found on the body’s own tissues.
Your body has got some beautiful mechanisms to ensure that its immune system doesn’t respond to its own tissues. The result would be catastrophic. Diabetes, Arthritis, Multiple Sclerosis, Rheumatic heart disease....all of these are the result of the body’s erroneous destruction of its own tissues. Bad news.
So, going back to our vaccine, one of two things could happen if you injected NANA. Either, nothing would happen at all – your body has eliminated all of the potentially dangerous cells in the immune system, so nothing would happen, OR...you’d start attacking and killing all of the cells that have got NANA in them. SERIOUSLY bad news – if that happened, you’d probably die of clinical Shock within hours. So yes, as yet we’ve not come up with a way around this little problem. There have been some ideas for using different antigens from Meningococcus B, but as yet, they’ve not been hugely successful.

Haemophilus influenzae also likes to live in the upper respiratory tract. There are six types, A-F, and type B (Hib) causes 90% of H. Influenzae infections. Haemophilus influenzae is not only an important cause of meningitis, but also of pneumonia, for which it is much more commonly associated.

There are three vaccines for Hib are all conjugated to different proteins. All of these vaccines were introduced to developed countries in 1992, and all show extremely high – 90% efficacy. As such, their use has virtually eliminated invasive Hib disease in the developed world, and furthermore, due to the TYPE of immunity that they induce, has also massively reduced pathogen transmission within the community. What this means is that if an individual is unfortunate enough to catch Hib, they will be much less likely to pass it on to immunised individuals, as their immunity decreases chance of infection.
I bet you’re thinking, well, surely that’s the point of a vaccine, is it not? Well, not exactly...A vaccine is merely an agent to prevent outright DISEASE - not infection. It is possible to have an infection without disease, even in vaccinated individuals. A vaccine usually just prevents the infection from turning into disease. However, the Hib vaccine is what is known as a “sterilising vaccine”, which prevents infection as well as disease. There aren’t very many of those around at present, and it’s a major area of research.

So given that the Hib vaccines are so fantastically effective all round, why are they only used in developed countries, and not in developing countries where the burden of disease is much, much greater? The simple reason: Cost. It all comes down to cost, sadly. The pharmaceutical companies who manufacture the vaccine simply cannot afford to give away vaccines for free, even though the value of human life is supposedly more important.
The Hib vaccine is extremely expensive, costing $7 for a whole vaccine course. By comparison, a full course of vaccinations for measles, polio, diphtheria, pertussis, tetanus and tuberculosis costs $1 COMBINED. It is hardly surprising that still the burden of disease from H. Influenzae in these developing countries is still astronomically high.

Maybe one day they will think of better ways of administering and developing vaccines to third world countries – but they’re still a long way off. Indeed, vaccinology, as a science, is still very young, so potentially in the future injecting little bits of a dangerous pathogen into a susceptible individual may seem as old-fashioned as drinking pus to prevent bubonic plague...

Procrastination: Oh the worst of all the human characteristics

March 16th, 2010

Why is it that the worst thing about work is starting? I mean, I can get into almost anything once I've started, regardless of how I feel or what better things there are to do, but these latter parameters always seem to affect my ability to start in the first place. I don't really understand why.

This morning, I got up with the rest of my family at around 7am, ready to start work as soon as I had got dressed and had breakfast. Great idea, it seemed. Well, it would have been, except that now it's 8:48 and I'm STILL not started. Instead I have managed to occupy myself with various other menial and pointless tasks that "just need to be done first" before I get down to the lever-arch folder's worth of work that is waiting for me.

This morning, in order to avoid putting off work for just that little bit longer, I have:
- Emptied the dishwasher
- Filed away all of last term's work
- Made 4 cups of coffee
- Had a Facebook friends clearout
- Tidied my Mum's desk

Of course, all of these jobs just HAD to be done right this second; my ability to work greatly impaired until they were all out of the way. Admittedly, the last on the list was the closest to actually being necessary - I indeed did need to clear it before I start work, but to make a big deal out of it such as I did was just nothing but a pointless, procrastinatory exercise.

My favourite time-wasting activity is making cups of coffee. I drink a LOT of coffee, and consequently I am nurturing a tremendous caffeine addiction. But I don't make coffee necessarily because I love the taste: I make it purely to waste a little bit of time so that I don't have to work. "I'll just go and make a cuppa, then I'll be able to work properly".

As I have six weeks until the final exams, I really really really ought not to be wasting as much time as I am doing. I have procrastinated and wasted away almost all of this term, and now have so much work to do in the last six weeks that it is going to take a miracle to get it all done. So why, WHY can't I just sit down and do it?

Procrastination is one of those universal human characteristics; we are all guilty of it, albeit to varying degrees, although only when it becomes chronic - grave to a point where one gets nothing done but fritters away all available time in which to do a task - does it become a problem. I guess that if you put off a task for a long time, someone else may eventually do it for you, but if you have a task which only you can do, then putting it off is both nonsensical and futile. Procrastination serves only to shorten the amount of time available to do a task, rendering it therefore exponentially more difficult with the more time wasted. (Unless, of course, that the reason for your procrastination is not to delay a difficult task, but only to delay an ODIOUS task, when wasting time before starting serves only to heighten the anticipation of the odium and therefore, indeed, worsen its extent).

I would say that the task I have before me, however, falls into neither of these categories. I guess that the idea of working all day at something I find less than enthralling is an ARDUOUS task, but not necessarily difficult or odious. But that's what I mean by heightening anticipation - the IDEA of working all day is no doubt going to be far worse than ACTUALLY working all day. And here I arrive back to my original point, that the worst thing about work is starting.

Procrastination takes strange forms, it seems. Usually I find unneccesary, thoughtless tasks to occupy my time, although today I have acutally written this note to waste time. WHY did I do that? These notes take a fair bit of thought, so I have actually done some work in order to avoid doing work. Oh GOD! See what I mean about chronic procrastination?!

Right, now that I really have wasted enough time, I am just off to make a cuppa, then I will get started!! (But not before I have de-scaled the kettle).

Brazil nuts

February 27th, 2010

It's been quite a long time since I last checked in with my faithful readers. Indeed, this particular note - or half of it - has been sitting on my hard drive for a very long time, I've just never found the time to finish it. I've at long last found the courage to trawl through all the pseudo-scientific and woefully inaccurate claptrap out there and search for the elusive information that I couldn't find the first time I
attempted to write this, and at long last, I've found it. Anyway, the finished result is here, even if it IS nearly two months since Christmas! :-)

Ahh, Don't you just love Christmas?? All the turkey, the family, the carols, the chocolate, the university holidays...ahh, yes. I doubt I'd be alone in saying that Christmas is one of my favourite times of year.

A lot of people say that after Christmas dinner, they feel so uncomfortably full of turkey and Christmas pudding that they literally can't move, and feel inclined to then slump on the sofa in front of the fire, watching the "Christmas day special", whatever it may be, on BBC1 for the rest of the afternoon. A peculiar ritual, is it not! Okay, so I am just as lazy as everyone else on Christmas day, and I confess my family and I did sit down and watch TV all afternoon. However, there is one aspect of this lazy afternoon that I do not generally participate in: the uncomfortable over-fullness. Personally I HATE the feeling of being over-full, I really do. I simply can't bear it, it is one of my biggest fears and something I hate more than I can ever describe to you. True to this, I usually avoid this feeling at all costs, rarely eating large meals, but snacking frequently throughout the day. Even at Christmas, this is true. Christmas day this year I had a normal-sized portion of "cow pie", as it is affectionately known in our family, mushy peas and a bit of sweetcorn. How lame! I can hear you cry! But actually, I much prefer this to a great big blowout meal with all the trimmings, because this is just simply too much food for me.

Despite this, I did manage to put on a few pounds over Christmas - not anything I'm worried or particularly care about, but it intrigues me that every year, people see Christmas as a time to stuff their guts with all the foods which they would normally keep to a limit. I attribute this weight gain not to the QUANTITY of food I was eating, but rather to its sheer calorific value. I wish I could say that I objected to my house filling up with enough chocolate to make even Richard Cadbury feel embarrassed, but I love chocolate, and the child in me was secretly grinning from ear to ear. Chocolate. Mmm, chocolate. Inevitably all of my usually healthy-ish snacks (yoghurt, fruit, cereal bars, etc) got rather rapidly replaced with chocolate, wine and dried fruit/nuts.

It is the last of these foods that claims the attention of the rest of this piece. When I was at my parents' house just after Christmas, I was forraging around in the cupboard and came across a bag of Brazil nuts. Bad news! Whoever brought those into the house made a fatal mistake - nobody can resist them! I was just selecting a few juicy specimens from the packet when my Mum came in and caught me red-handed. Holding one up to me, she said "D'you know, there's enough energy in one of these to boil a test tube full of water"...

As much as I would have loved to come up with a devastating, smart-arse retort or a flawless biological anecdote to refute this claim, alas I could not, and just stood there looking sheepish and somewhat embarrassed as I was forced to accept this bothersome little fact. I simply wasn't able to deny it; indeed, I've done the very experiment myself, and if you don't believe it to be true, check out this video:

http://www.youtube.com/wat ch?v=r5hBjKeIcfU

As I'm sure you will appreciate, when you are about to eat something that you know is horrendously bad for you, HEARING about how bad it is about as welcome as a turd in a swimming pool. But anyway, I have been thinking of this ever since, and things that get me thinking usually make for amusing reading.

At first thought, to me this seems a biochemical impossibility. hy? Well, a Brazil nut weighs virutally nothing, and it just doesn't feel big enough to contain enough energy to boil water.

A paradox that has to be resolved, I feel.

Fat is the most calorific of the biological molecules. Because I'm a nerd, I happen to know that fat contains nine kilocalories per gram. By comparison, sugar and protein - the second highest in calorific value - each contain four kilocalories per gram. Now, I imagine that these raw numbers mean very little: Let me put them into context.

- A penny weighs 2.5g.
- 1ml of water weighs 1 gram (by very definition)
- The lid of a biro weighs a tiny bit less a gram
- A Brazil nut weighs 4g, give or take a bit.

A calorie is defined as the amount of energy needed to raise the temperature of one gram of water by one degree celcius. Just ponder that for a moment. That is one hell of a lot of energy. Raising the temperature of anything requires a lot of energy, because you've got to give the particles that make up the substance more energy to move around. That's what temperature IS - a measure of the average
movement of all the particles in a substance.

So, nine thousand calories - the amount of energy in one gram of pure fat - is enough to raise the temperature of nine kilograms of water by one degree. Or, if you prefer, of one kilogram of water by nine degrees. Ok, so this is getting confusing! (Nine kilograms of water, by the way, is nine litres - about half a bucket). By these comparisons, when you think about it, packing NINE THOUSAND calories into so little of a substance is a hell of an achievement, and it is easy to see why eating fatty foods quickly piles on the pounds.

Right, now let's get back to my original problem. A bog-standard test tube can hold 15ml of water (or indeed, of any liquid!) One of the requirements, it seems, of being a biologist is a total ineptitude at mathematics or arithmetic, so give me a second while I dig out my calculator...

15ml of water weighs 15g. (Ok, so I did that bit in my head - honest) So, to raise its temperature by 1 degree, I need 15 calories. Room temperature is about 20 degrees celcius, so in order to raise the test tube to boiling point, I need to increase the temperature by 80 degrees. 80 x 15 = 1200. Therefore, I need 1200 calories to raise my test tube to boiling point. So, by that calculation, a Brazil nut must contain AT LEAST 1200 calories.

I know this is getting boring, stick with me, it gets better I promise!

Wikipedia reliably informs me that a Brazil nut is, by weight:
- 0.72g protein
- 0.052g carbohydrate
- 2.76g fat
This, unless you don't trust me and are fastidious enough to want to calculate for yourself, is a total of a little bit over 29800 Cal - or if you prefer it, 29.8Kcal. (2880 of which come from the protein, 2080 from the carbohydrate, and 24840 from the fat).

Remember I said that you only need 1200cal to boil the test tube full of water? Well there are nearly twenty-five times more calories than this in our old Brazil nut - there's our answer! THAT's where the energy comes from! This also explains why, if you watched the video, the brazil nut continued to burn for another three minutes after boiling the water.

I am hoping you're still with me, but I imagine you're bored as hell and that what I say in this next sentence is going to decide whether or not you keep reading. If Brazil nuts are indeed SO calorific, then why on earth do health experts and the like say that they're good for you? Truth is, they contain a
variety of trace elements (including selenium, phosphorus, zinc, copper, manganese, magnesium, etc) which are all required in very tiny amounts for various bodily processes. In particular, Brazil nuts contain a particularly high concentration of selenium (which, if you're interested, is involved in the action of anti-oxidant enzymes in most body cells).

So, was I right to feel guilty for eating the Brazil nuts on Boxing Day? I like to think not. In order to put on "a few pounds", I would need to eat around 7,000,000 cal (the amount of energy contained within about two pounds of body fat). To gain this number of calories, by a simple calculation, I would have needed to eat 235 brazil nuts. I only ate about six. Hmm, nothing to worry about, I don't think. They can't have added that much to my weight...

Now, here I confess...
When I was writing this a few nights ago, I spent an embarassingly long time pulling my hair out and tapping random combinations of utterly irrelevant numbers into my calculator in order to try and work out exactly HOW much weight these six Brazil nuts added. YES, I am THAT sad! It just had to be found out!! After about an hour, I finally admitted defeat and phoned up Sarsie on her mobile at about
midnight to do the calculation for me. I'm "a big retard", apparently - the calculation really isn't that difficult! Arithmetic ineptitude? Big Retard? Guilty as charged! In my defense, I'd had had rather a lot of wine, and I think that at the time I would have struggled with even my two times table - she'd never believe me though - one-nil this time, Sarsie! She also made me promise to credit her in this note!

Basically, Sarah finally worked out for me that six Brazil nuts would have contributed 23.17g of my 2lb weight gain, if ALL of the energy that was contained within these Brazil nuts had gone straight to my waist. That's quite a lot, I was surprised! However, it is of course highly unlikely that ALL of those calories were deposited as fat. Why not? Let me tell you a bit about the way that the body uses the energy that's available to it; I find it quite interesting.

The body's first choice molecules for obtaining energy are carbohydrates (sugars) which are used for short term, immediate energy-requiring processes. If I were to get up now and go and make a cup of coffee, (something I fully intend to do when I get to the end of this sentence), I would be using energy
gained from glucose sugar. Likewise, if I were to go and run up the stairs a few times (which I most certainly do NOT intend to do any time soon), I'd be using energy from STORED sugar in my liver. The liver stores this sugar as a long string of glucose molecules; a polymer called GLYCOGEN. Basically, every time some energy is required, glucose molecules are removed from the end of this great big glycogen molecule and burnt to free up some energy. Make sense?

Okay, the liver only stores a finite amount of glycogen, and this is quickly depleted following physical activity. What happens when it's all run out?? If there is no carbohydrate available to it, the body will start using its fat stores. Fat from adipose (blubberous, muffin-top, does-my-bum-look-big-in-th

is tissue) will be broken down into its component parts which then enter the bloodstream and can be used by cells for energy. Thing is, like I mentioned earlier, fat contains one HELL of a lot of calories, so if you're trying to burn off enough to make a significant difference to your waistline, you gotta work it, babe!!

Now, although I said earlier that protein contains just as many calories per gram as does carbohydrate, proteins are far too precious to be broken down for energy. They're involved with millions of other body processes instead. Virtually every single process in the body is controlled at some level by proteins. Proteins are only broken down for energy only in states of severe starvation. It's the body's last-ditch attempt to save itself from death if it's not getting any sustenance. Now, I'm talking SEVERE starvation, here, When your body has virtually NO ADIPOSE tissue left on it. Think African famine victims. When this happens, the body will have no choice other than to start using protein in order to get its energy. First, non-essential body proteins will be broken down, including those biceps that you guys have spent ages building up, and girls, all the protein that makes your hair and nails grow shiny and strong. Then, as a REAL last-ditch attempt, you'll start wasting away other muscles and proteins that ARE essential. The most obvious of these is the heart muscle, which as you can imagine, hugely increases the risk of heart attacks. By the time starvation has got this far, it is a REALLY dire state of starvation that won't last much longer.

So, in light of all that, I think it very unlikely that ALL of the calories in my Brazil nuts went straight to my waist. I think I was certainly far from starving on Boxing Day - certainly not starving enough to break down proteins! I do, however, think it was quite likely that I was storing the fat away, as I did manage to eat quite enough chocolate over the whole Christmas period to provide me with enough sugar to keep me going for several months! The fat and sugar in that alone was probably MORE than enough to make me gain 2lb! I will never be able to look at a Brazil nut in the same way again, but maybe it's the chocolate that I ought to be more concerned about!

It's okay, I've given up junk food for Lent. (Well - sort-of!)

The 12:22 service to Stansted Airport will depart from platform 1…

February 1st, 2010

It’s been ages since I last posted anything; I’ve just not been having the inspirational vibes recently. Incidentally, this is exactly why I am currently sitting on the Stansted Flyer from Birmingham New Street, in the hope that a week at home with my mother might be the thing I need to get me motivated enough so that I don’t fall spectacularly over the last hurdle before graduation.

I must confess, I haven’t really got a focus for this note, I’m just rambling because I am going to be stuck on this chronically slow-moving train for the next three hours and need something to stimulate my brain cells. Gazing out of the window is just not doing the job – the scenery on the way out of Birmingham falls painfully short of the word ‘breathtaking’. I suppose it would be unjustified to call Birmingham the worst place on earth, but you can certainly see it from there.

The train today is unusually empty; most of the time I am lucky to get a seat, but today I even managed to get a forward-facing window seat all to myself! Feeling very happy about this, I was just about to spread all of my stuff all over the adjacent seat when, not a moment before the train was supposed to leave, a heavily panting and rather overweight lady asked if she could sit next to me. Of course I wasn’t going to object, taking up two seats is just greedy. But then, not a moment later, the foul, pungent stench of garlic pervaded all the air around me, offending my nose and instantly extinguishing all of the pleasant feeling of good fortune that I was previously enjoying. After a short while I did become a little bit more accustomed to the revolting smell, athough I still seized an opportunity to move to the other side of the table after it became vacant (I went to go and “get” something from my bag – I most definitely didn’t just fiddle with the zips a bit then return to the opposite seat). Either she noticed and was grossly offended by my conspicuous seat-change, or maybe it was just her stop, but either way, she got off at the next station.

Why does this always happen? I’m sure I’m not alone in the view that it doesn’t matter WHERE you sit or where you are, be it on trains, buses or aircraft, there is ALWAYS somebody who makes your journey that little bit less tolerable. Maybe it IS just me being completely intolerant of others’ annoying idiosyncrasies, but seriously, it’s almost as if the train companies plant these annoyants in the carriages for their own personal amusement.

I must say, sitting next to someone with smelly breath is a new one for me; it’s usually the person who tries to read my magazine over my shoulder, or the older fellow who keeps talking at me and telling me tales of back in the day, or the suit-clad business man who unfolds a the Financial Times broadsheet right in my face and rustles the pages in a loud, “I’m very busy and important” way. I’d say that on a scale of one to annoying, these people are probably somewhere in the middle. I do think, however, that the award for most annoying HAS to go to the boy with heavy metal blaring out of earphones loud enough for the whole carriage to hear – today, thankfully, he’s not sitting next to me (he’s sitting behind me, and it’s not heavy metal but a rather peculiar type of what I can only identify as Irish Folk music, although with a weird time signature). The reason he’s the most annoying is because he annoys everyone in the carriage, not just the poor sod that has had misfortune enough to have to sit next to him.

I’ve finished moaning now, I promise. We’ve just pulled away from Oakham station, and I’ve just looked out of the window and seen a brown road-sign reading “Lands’ End”... deary me, I clearly need to consult my atlas – I’ve been under the illusion all these years that Lands End is in Cornwall! Apparently I stand corrected, it’s in Oakham! Where even is Oakham, anyway?!

To my mild amusement, the ticket inspector has just come round, and the woman opposite me looked all flustered, went bright red and nervously giggled, “ohhh, I forgot to buy a ticket, silly me!” Yeah, right...you thought you were gunna get away with it, dincha!

I’m now at Peterborough, which is about half way through my journey. I’m not going to bore you with finding interesting things to fill up this note with for another hour and a half – I’m sure you’re getting a little bored. But before I go, I do have a rather funny story to tell you.

Most modern trains now have these automatic toilet cubicle thingies – you know the ones, those with the electronic sliding door and the “lock door” button that you have to press once you’re inside. Well, I have a morbid fear of them and would rather wet myself in my seat than use one of them. Most phobias are, by definition, completely irrational, although I wouldn’t say this one is, as in the past I have been rather unfortunate in my encounters with electronic toilets...

A few years ago, I went to use one of these toilets and shortly after I went in there and pressed the “lock” button, the door began to open because someone had pressed the button on the outside – I found out the hard way that the “lock” button wasn’t working. The train was literally packed to the rafters and there was what looked like the entirety of a male rugby or football team standing in the area just outside the loo. I don’t think I’ve ever been more embarrassed. Really. I just wanted to evaporate. As I remember it, it was only a few weeks before that when the very same thing happened to me – on The Strand in London; of all the unfortunate places. I couldn’t find a loo anywhere except this one on the street that you pay 20p for, so begrudgingly I paid up. Not a few seconds after the door locked, the whole thing sounded a loud alarm that nearly made me jump out of my skin, and to my horror, the door began to open and water began pissing out from somewhere under the floor. I can only concede that its cleaning time was on a timer, and that cleaning was initiated at this time regardless of the occupancy or not of the cubicle. I guess I was just very unfortunate. So I had to go into my interview (the reason I was in London in the first place), all red and flustered, with wet shoes and feeling murderous. Somehow, I got the job.

It’s a very loser-ish thing to laugh at your own jokes, but the guy sitting opposite me keeps staring at me as I’ve been periodically sniggering whilst I’ve been writing this note, followed by bursting into full, uncontrollable laughter as I wrote the previous paragraph. I love it when that happens, especially when it’s in the most inappropriate of places...

Anyway, I shall leave you with that thought! Ely has just passed me by, I’m nearly home, so thankyou for making my journey more enjoyable. And don’t forget to take all your personal belongings with you when leaving the train.

A bone to pick

January 6th, 2010

Boredom is, at times, a wonderful thing. Those of you who've seen any of my Facebook Statuses (stati?) over the last few days would have good reason to think I''m going barmy; after all, I do complain of being bored rather a lot. However, I quite like the frame of mind one reaches on being SO bored that your mind starts to wonder about peculiar and random things that usually you just accept without question, such as why teaspoons are teaspoon shaped, how they make paperclips, or if pandas like the taste of bamboo. A lot of my most innovative thoughts have spawned from serious boredom, and, happily, today is no exception.

Although I've been back in Leamington for quite some time now, I've not yet had the chance to go shopping, and I don't have much in the way of food in the house. As most of you will appreciate, rooting through a student freezer is always a risky business; I imagine some of the stuff in there is so old that it would take a team of dedicated forensic scientists to identify it. But anyway, I was hunting around to see what surprises I could find for my tea and I came across a salmon fillet that I'd bought a few weeks ago on my usual prowl around Somerfield for all the reduced delights just before closing time. I love salmon. It's probably one of my favourite foods, so I cooked it up with some rice and peas. Delicious.

There's only one problem with salmon, which I guess you're already anticipating before I say it: those pesky little bones. In today's average-sized fillet, I picked out no fewer than thirteen little bones, which, I must say, rather tainted my enjoyment of the whole thing. I mean, what on earth are they there for?! Maybe somebody put them there just to be annoying. After all, surely they're far too small and bendy to provide any kind of support to such an enormous fish as a salmon. I couldn't help it; I simply had to find out...

As I've already said, salmon are big. HUGE, in fact. Some of the seven species of salmon (namely Chum and Chinook) can grow up to a metre in length and weigh up to 25lbs. THAT'S ENORMOUS!! By comparison, that's about the weight of the average 2 year old, or of about 65 spuds! Yeah, they're pretty hench. Surely those daft little bones can't make a huge amount of difference to such a massive body. So what ARE they for? Indeed, as I found out, their purpose is NOT primarily to confer structural support to the fish; they're actually involved in movement. To make it easier to explain, let me first tell you a little bit about muscles.

When we eat fish or meat, it is muscle tissue that we are eating; a fact that, when I first discovered, temporarily startled me. I don't really know why; it just felt a bit weird. Muscle, as you probably already know, is tissue which brings about movement. I know a lot of biology, but I have to say that the way that muscles work is probably one of the most fascinatingly simple mechanisms that I have ever come across, and one that never fails to amaze me. Indeed, it is finding out things like this that makes me remember why on earth I am still studying this stuff after three years. So yeah, muscles. They're really cool.

The very fundamental unit of muscle in humans is called a sarcomere, and muscle cells are packed full of parallel sarcomeres. A whole muscle contains thousands of interacting sarcomeres which, when all stimulated simultaneously, bring about muscle contraction and movement.

As with most biological systems, sarcomeres are made of protein. Two different types of protein, to be precise, called actin and myosin. Within a sarcomere, actin and myosin fibres interlock with each other, and it is the sliding of these filaments over one another which is the basis of muscle contraction. Let me explain. Essentially, muscle contraction starts when the muscle cell is stimulated by an electrical impulse from a nerve cell. This electrical impulse causes calcium to be released from stores inside the cell. Calcium causes changes in various other associated proteins which allows the myosin and actin to interact (with the help of a bit of energy). The muscle fibres then slide over one another and interact further, which decreases the length of the sarcomere. That's the key point! This sliding DECREASES THE LENGTH of the sarcomere. When this happens in many hundreds of sarcomeres in a muscle, the length of the whole muscle decreases. Muscles in humans are anchored to bones by tendons, so contraction of muscles causes the movement of the bones that they're attached to.

In fish, the basic unit of muscle is the same as in mammals, and it contracts in the same way. However, in fish the muscles are not anchored to bones via tendons. Instead, blocks of muscle run all the way along the fish's body separated by tough sheets of protein, known as myosepta. These sheets run right from the core of the fish (where they are attached to the skeleton) to the outside (where they are attached to the overlying skin). The fish moves by passing a wave of contraction from the head to the tail along one side of the fish, then along the other side, which causes the fish's body to move from side to side, which produces force which propels the fish through the water. Make sense?

Effectively, this wave of contraction is like a mexican wave in a football stadium.
Imagine that the blocks of seats in a stadium are the muscle blocks, and that the staircases between them are the myosepta. A mexican wave might start at one block and move all the way across all of the blocks until it reaches the other side of the stadium. However,if the people at the edges of the blocks are a bit dopey, it might take them a while to realise that the previous block is mexican-waving, and they woudn't notice that a wave is going on until it's right at the edge of the previous block. This means that the next block won't start waving until the previous one is finished. This is the same in the different muscle blocks of the fish: The myosepta serve to separate the blocks of muscle so that the side of a fish is not just one continuous lump of muscle from one end to the other. If the myosepta didn't exist, then the fish wouldn't be able to create this sequential wave of contraction. Instead, all of the muscle along
the side of the fish would contract simultaneously, and the fish wouldn't be able to move elegantly through the water; it would just be flailing around looking stupid while being laughed at by all his speedy fishy friends.

Ok, so now I have digressed unashamedly from my original point, I feel it's high time to return. The pin-bones in fish are also known as inter-muscular bones, and, as the name suggests, are found in between the blocks of muscle, within the myosepta. They are what are known as "floating bones", which means that they are not attached to the main skeleton. (This explains why they are able to elude capture even after the fish is filleted). As I said before, They are not involved in structural support; certainly not to the fish's structural integrity, anyway. It is thought that their purpose is to further stiffen the myocommata, which unifies the rate of contraction between the individual sarcomeres in each muscle block, and helps direct the muscular forces among them. What I mean by this, is that by stiffening up these dividing sheets, it means that the forces that are generated by the contracting muscle are hugely amplified, so the fish can generate forces with up to a huge magnitude if it needs to swim really quickly. Clever, innit.

On a relatively minor point, the bones are not as soft in a living fish as they are when you unsuspectingly bite into them; If they were, the only purpose they would effectively serve would be to ruin my dinner! They certainly wouldn't help the fish in any way! I can't find any direct information as to WHY they become so soft, but I speculate that it's just because the cooking process causes a loss of all the minerals in bone that are there to strengthen them. Bones are made of primarily two components; protein and calcium phosphate, along with a few cells and other components thrown in for good measure. The protein is there to make bones resistant to snapping, stretching, or otherwise being distorted or broken, and the calcium phosphate is there to harden the bones and make them really really strong. Without the protein, bones become really brittle, and without the calcium phosphate, bones become bendy and soft.

So these little pin bones are highly variable amongst different species of fish, and salmon are estimated to have around forty. Sometimes it seems that some fillets have more than others, although this is almost always down to the filleting process, not anatomical differences between the individual fishes. Call me a snob, but I don't think it's very classy to serve bones in food (whaddya know!) so many high class fishmongers will remove the pin-bones before the fish is sold. However, cheaper fillets and mass-produced supermarket fish often have them left in. You would probably have good grounds to shoot the cook if you found pin-bones in your £50 fillet in a swanky London restaurant (actually, maybe shooting him might be a bit of an overkill), but I think the presence of pin-bones in a run-of-the-mill, £2.99 jobbie from Tesco's is probably as certain as me tripping up the steps on graduation day.

Anyway, to end, let me just say this. Pin-bones are just a fact of life that must be accepted. If they really put you off your succulent salmon fillet so bad that they simply HAVE to be removed before cooking, or if Gordon Ramsay's coming for dinner, you could always use your toenail tweezers to get rid of them... now there's a thought to put you off your dinner!

Oh, that is so cliched

December 22nd, 2009

Don't you just hate those irritating, cliched things that people say when you are feeling, for what ever reason, miserable or upset? You know the ones I'm talking about; all the: "no, you're way prettier than she is"

"It's his loss, not yours"
"You really have nothing to worry about"
"It's probably not as bad as you think"
"There are plenty of people worse off"
"Never mind, better luck next time"
"Aww, there's plenty more fish in the sea"

Yeah, you get the picture. The last of these particularly irritates me, not least because it contains an egregious grammatical error, but anyone whose situation is likely to invoke the usage of this cliche by the well-meaning friends and family is probably feeling like their life has just ended, and that it doesn't matter how many fish are out there, none have colours as bright as the one that has just been lost. It is also among the most insensitive, belittling and isolating things one could possibly say to someone such a situation; You might as well say "Oh well, just get over it". (and that really would be considered abominably insensitive). Although masked by an annoying piscine metaphor, that IS exactly what you are saying.

Whenever I hear the words, "there's plenty more fish in the sea" or, "There are plenty of people worse off", that just makes me feel so much better! I mean, what do you know! I've been deluding myself all this time, I guess there really ARE loads of other fish out there! I'm just going to pick myself up right now and forget about all my troubles just like that, and I feel so much better for having heard an age-old, worn-out, pointless cliche, thankyou so much! And as for the second...frankly, as cruel as it may sound, when I'm feeling low, I don't give a monkeys about anyone else right at that minute. "Yeah, I've just been dumped/lost my job/failed my exam...but it's OK, there are LOTS of people who've got it bad, so it doesn't matter that I feel lousy because OTHERS FEEL WORSE!"

In case you're wondering what has provoked my writing of this latest cynical, negative musing, I was just thinking about a text conversation I was having earlier today with a friend of mine. After employing one of the choicest cliches ("Awww, it wasn't as bad as you think it was, you have nothing to worry about"),I stopped, remembering that a few weeks ago when I was in a similar situation, the endless cliches and unhelpfulness just made me cross, lonely, and feeling like no one actually cared or actaually was even listening to what I was saying. I rephrased the text, in my OWN words (and avoiding sources of mis-interpretation that is the curse of modern-day electronic communication), and the text I eventually did send was much more heartfelt and like I'd actually put some thought into what I wanted to say. I think my friend appreciated it, for she said she felt better.

I guess I don't really have a point that I'm trying to make here, other than that cliches are not cool and not helpful - care ought to be taken before using them in anything other than jest. Anyway, I implore you, next time one of your family or friends needs your support or empathy, don't just idly cast aside their feelings by spouting off an unmindful cliche - try and think of something worthwhile to say.

One of my favourite quotes:

"The friend who can be silent with us in a moment of despair or confusion, who can stay with us in an hour of grief or bereavement, who can tolerate not knowing; not healing, not curing... that is a friend who cares".
--Henri Nouwen

Happy Christmas!

The purpose of sore throats and tickly coughs

December 16th, 2009

Why, exactly, is it that the virus that causes the common cold – rhinovirus – causes sore throats and coughs? Why? What’s the point? What earthly advantage does an irritating, tickly cough convey to anyone? Just WHY? WHY do I have to suffer weeks of dull, grouch-inducing pain every time I try and swallow anything (oh haha guys.) Why, why, WHYYYY??

As you might be able to tell, I have been suffering from a cough and sore throat for a good week now, and I’m more than just a little bit tired of it. A lovely new addition is this semi-acute earache and intermittent headache, exacerbated immeasurably by looking downwards or at bright lights.

I’ve not caught a cold for a very long time; I thought I’d escaped the (almost) inevitable Freshers’ flu this year, but it seems it finally caught up with me. Literally the moment, the very moment my ought-to-be-illegal viol of pure menthol for injecting into one’s face every 30 seconds (Vicks “First Defence”) ran out, and before I had time to replenish my stocks, I caught the mother of all colds. Running a temperature of nearly 39°C, it floored me for a few days; it prevented me from getting out of bed, and made continuing with any aspect of my life temporarily impossible.

Now that I’m out of bed, I’ve doped myself up on every legally-available analgesic I’ve been able to get my hands on, and have been periodically swigging cough mixture out of the bottle (it seems the credit crunch hits all areas – the bottles no longer come with a plastic spoon). Clearing the backlog of work that didn’t get done this term has only just begun, yet progress is still being seriously impaired by the savagely bad mood that the tail end of this cold is eliciting.

When I started this piece, I fully intended to create one of my nerdy discussions about the exact cause and purpose of cold symptoms, but my brain just isn’t working. I think, in the case of the particular rhinovirus serotype that is currently resident in my upper respiratory tract, some additional symptoms include brain disengagement, lack of ability to apply intelligence, and severe aprosexia (that’s lack of attention-span, for those of you imagining any seedy, après-coital activities).

Unlike the sore throat and tickly cough, I can at least see an advantage that the latter three symptoms might convey to the virus. Perhaps the virus knows that if I study the relevant immunology, I might stumble across the key to ridding myself of the cold, which is certainly not in the interests of the virus.

If, indeed, the virus is as intelligent as herein I give it credit, then surely it must have considered the possibility that by giving me a bad cough and sore throat, all it is likely to do is put me in a bad enough mood to make me want to stay indoors, wearing hideous tartan PJs and a man-sized cardigan, wrapped up in a duvet and sipping chamomile tea through a straw while watching girly movies. Oh! Fancy that! That’s exactly what I’m doing! Indeed, the virus ought to FURTHER know, that by making me want to stay indoors wearing hideous tartan PJs and a man-sized cardigan, wrapped up in a duvet and sipping chamomile tea through a straw while watching girly movies is NOT particularly conducive to spread of virus, which, surely, is the whole point of an infection in the first place, n’est-ce pas?

So actually, despite my temporary lack of ability to apply it, I can rest assured that I am the possessor of superior wit over my friend rhiny. I don’t think she’s very happy. Maybe she’s trying to get her own back. Maybe THAT’S the reason behind the otherwise utterly pointless but insanely irritating sore throat and tickly cough!!

With brains like that, one day I’m going to be a professor.

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