This blog hasn’t been active for a year now, but it’s still generating hits, so welcome to you! Feel free to look around. 

I now write on a new blog, called Memetic Drift. Hopefully you’ll enjoy it 🙂 


Hey. This blog hasn’t been active for a year

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Posted by on May 5, 2013 in Uncategorized


Bristol 24-7 article: influenza virus and ‘censorship’ in science

Just a link to my Bristol 24-7 article summarises the current situation on the controversial H5N1 research in mammals, which side I stand on in the discussions, and why my own view surprised me!

Have a good day!


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Posted by on March 5, 2012 in Uncategorized



The influenza virus – molecular shapeshifter extraordinaire

I’m planning to write an article for Bristol 24-7 in the near future about the controversy of censoring science for the benefit of public security, specifically in relation to a couple of studies where scientists managed to artificially increase the ability of Avian flu virus to transfer easily from animal to animal. Should the methods used and the full findings of experiments like this be published or censored, and what are the real risks? This is something I’ll be exploring soon.

I’ve enjoyed some great lectures on the topic during my Biochemistry degree, and here on Sciamour I’d like to explain some background of the influenza virus, particularly we’ve been unable to kick it out of existence so far. It’s a fair bit longer than my newsy articles but hopefully still of interest, especially if you’ve suffered the flu before!

1918 was a bad year for the people of Earth. Not only was the First World War still raging for most of it, but it was the start of the most widespread and devastating disease pandemic of the century. WWI killed nine million people, yet the Spanish flu following on from this set back the population between 50 and 100 million. Nearly a third of the entire world’s population got infected in three years.  

Spanish flu was caused by a subtype of the influenza virus called H1N1, a form which returned in 2009 as “swine flu”. Only a few years before then, there was fear of a H5N1 pandemic, known as avian flu. As it turned out, both these strains were lacking features which the Spanish flu of 1918 possessed to make it so deadly. Swine flu was highly infectious but the symptoms were generally mild and mortality was around 0.01% according to WHO data up to August 2009. Avian flu, had a very high mortality rate, killing nearly everyone who caught it, but was very rarely transmitted from human to human. Hence cases have been low in number and restricted to people who spent large amounts of time around infected poultry.

 The names of the viral subtypes (e.g. H3N2) are derived from two protein molecules found on the surface of the virus, which are needed for the virus’ reproduction cycle and infectivity. Hemagglutinin (HA in Figure 1) protein studs the outside of the virus, recognising and binding to specific sugar groups found on the cells it’s going to infect. The animal cell will take up the virus in a compartment called the endosome, where an attempt to destroy it with acid is made.


Figure 1: structure of an influenza virus. Note the haemagglutinin (HA) and neuraminidase (NA) molecules studding the surface of the virus, and the genome being divided into eight separate sections.

Image Copyright 2005 Nature Publishing Group, Horimoto, T., et. al., Influenza: Lessons from past pandemics, warnings from current incidents, Nature Reviews Microbiology 3, 591-600

Unfortunately for the host, lowering the pH is exactly what the virus needs to execute the next stage of infection. Low pH causes hemagglutinin to undergo a massive shape change, making it open like a flower bud to reveal a molecular “spike” which stabs into the host cell membrane, locking virus and host together. Viral RNA is then released loose into the host cell, where it is replicated.

The other protein found on the viral surface is neuraminidase (NA in Figure 1). This is an enzyme which allows newly formed viruses to bud off from the dying host cell, so that they may infect the next. Because of their presence on the surface, hemagglutinin and neuraminidase are useful components of vaccinations. As with all vaccinations, if you can raise antibodies against a specific viral component, when you face that virus again, your body is able to fight it off with hugely increased swiftness and force (see here or here for animated explanation of how vaccinations confer immunity). If only it were that straightforward, influenza might have gone the way smallpox did. However, hemagglutinin and neuraminidase are molecular shapeshifters evading the immune system. This might seem like a “tactical” move, but of course as a non-sentient, (not-even-truly-alive!) bundle of molecules, this is impossible.

The evasion, called antigenic drift, is actually caused by a sloppy replication mechanism which makes the viral replication a fairly haphazard and error-prone process. In our cells, poor checking of replication contributes to cancer development, but for viruses, it means antibodies which would work against last years’ influenza may not bind properly to this years’ form. Along with the fact there are so many different types and sub-types of influenza, this is one reason why people can get flu time and time again.

The reason why seasonal flu vaccinations don’t always work is because they have to be made in advance to virus mutations, so the manufacturers must attempt to predict which mutations this season’s influenza will make; a very difficult task.  Howver, influenza can do something worse, something which is pretty much impossible to predict.




Figure 2: Infection cycle of an influenza virus. See text for main points to note.

 Image Copyright: G Neumann et al. Nature 459, 931-939 (2009) doi:10.1038/nature08157

The diagram above shows the infection cycle of a flu virus. Note that influenza’s RNA genetic material is divided into eight independent tracts, and for a time, this RNA is “loose” in the cell (middle right). The eight sections are then packaged into the new budding virus coat (far right). This provides opportunities for exchange and reassortment of RNA pieces if two or more type of influenza virus were to infect the same cell. This process, called antigenic shift (not to be confused with antigenic drift!) is thought to be the way 2009 H1N1 swine flu arose. Scientists who sequenced the genetic information of this virus noted that it contains sections from previous human, bird and pig flu. This rearrangement most likely took place in a single pig, because they act like an intermediary between human and bird influenza. Although these two cannot be directly transmitted, both of them may infect pigs.

This forms an interesting argument in favour of laboratory-grown meat, which Dutch scientists have recently demonstrated may be possible soon. Antigenic shifts are far more likely to occur in areas of close contact between humans and animals, such as factory farms. Remove the farm animals, and the likelihood of pandemics devastating the population, as well as many other zoonoses will be vastly reduced.

Will we ever be rid of influenza? It’s not yet possible to tell, but it’s not looking promising yet. Forms of influenza have shown resistance against every drug made so far. However, by looking at viral proteins which don’t mutate so readily and are shared between all forms of influenza, the National Institute of Allergy and Infectious Diseases (NIAID) is working on a universal vaccine. Despite pandemics past, present and future, it never ceases to amaze me how viruses, such a small amount of genetic information wrapped up in just a few proteins, can cause so much misery and bafflement in the world.

Emily Coyte

Twitter: @Sciword

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Posted by on March 2, 2012 in Uncategorized


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Why are childhood vaccinations controversial?

This is an article I wrote for my cousin’s blog on her business website which is specialist physiotherapy for pregnant women and new mothers. I’m posting it here because it links in with some things I’m working on at the moment for Bristol 24-7 and here on sciamour as well. Stay tuned 🙂

Vaccinations – what’s the fuss?

Starting off life as a new mother is full of decisions. Which school do I plan to send him to? Am I feeding her the right amount of the right type of food? Should I vaccinate them?

A lot of people are concerned about vaccinations. A quick look at and other sites for parents shows dozens, if not hundreds of threads from people worried about making the wrong choice for their new child. It is a shame that such a brilliant innovation in science and medicine has caused such worry amongst people.

To demonstrate what vaccinations have achieved for humanity: we’ve totally eliminated the smallpox virus (google image if you have a strong stomach) from the wild in an amazing feat of international participation and co-operation. The crippling disease polio is also on the way out – but as I reported in a previous article, resistance to vaccination some certain members of certain countries mean there is a risk of resurgence. Every vaccinated child provides a dead-end for the viruses, preventing their spread. If your unvaccinated child only comes into contact with other vaccinated children, the risk of infection is very low, but if too many parents opt out, we could see a big rise in infection rate.

So where have these worries come from? Talking to my own mother, she explained how she is of the age where children were pretty much expected to catch measles and mumps, and she remembered how horribly unpleasant they were for her. Due to the overwhelming success of the MMR (measles, mumps and rubella combined) vaccine, which are also available separately, these diseases are so much rarer now, so new parents will  probably not have felt the pain of these potentially debilitating diseases. This can make the threat seem quite distant, but the high rate of complications associated with catching the diseases (see here for the complications associated with mumps) are far higher than the chances and severity of side-effects associated with the vaccine, which are listed here.

Vaccinations were also the centre of one of the biggest scandals in science of the decade. Very bad research was done by Dr Andrew Wakefield, who claimed there was a link between MMR, autism and bowel disease. He is now banned from practising due to the unethical nature of his study and his unscientific approach. A huge number of other studies have been done which disprove Wakefield’s findings and show that the vaccinations we use today are safe and good for the public. Even if this man’s name has been forgotten, the murmurings that vaccinations are somehow dangerous are still being passed around. The Public attitudes to Science survey 2011 shows that 5%, or one in every twenty people, thinks vaccinations are more dangerous than beneficial. I really hope that number goes down in the next few years.

There are a lot of resources out there on the Internet, see here, here and here. Of course, no information you find on the Internet is a proper substitute for a conversation with your GP. They will be happy to talk to you about it with relation to your child in particular. 


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Posted by on February 20, 2012 in Uncategorized



Adult and embryonic stem cells

Note: I wrote this back in November 2011, before I started writing for Bristol 24-7. The editor told me he couldn’t publish it because it read too much like an academic essay and, looking back at the content I’ve made since, I’m really inclined to agree with him! I can only blame the fact I was fresh out of uni where essays abound!

I’ve been busy writing blog posts for other people, as well as being horribly ill with a throat infection, so this will have to suffice for now. Sorry about the slightly stuffy tone and hopefully you’ll learn something about stem cells!


What potential do adult and embryonic stem cells have for the future?

Stem cell research has been given all sorts of good and bad press, but the field has vast potential for modern medicine and human health. What defines a stem cell is the remarkable ability to change themselves into other cell types, a process called differentiation. Bristol University (where I graduated from) made the headlines in late 2008 for their successful contribution of a world-first technique using stem cells to heal a woman whose windpipe had been severely damaged by tuberculosis. Adult stem cells were used to create a new, fully functional trachea which could be surgically inserted without risk of rejection, saving her the dangerous alternative of removing the entire damaged lung.


The differentiation process is especially important right at the start of our lives. It has to be – we start off as a small ball of cells and somehow turn ourselves into working human beings with brains, muscles, layers of skin, blood and bones. But consider this: the DNA within every one of our cells is essentially identical, if we exclude mutations acquired throughout our lifetimes. A heart cell and a nerve cell have the same core genetic information concealed within the nucleus, but it’s never all used at once. The cells differ in appearance and function because they activate and use different genes at different times, making proteins which further alter the way genes are expressed.  So much of our useful DNA actually codes for proteins which regulate the expression of other pieces of DNA! The genetic information is the blueprint for what the cell is physically able to produce, but the initial instructions which tell a stem cell what it should become are determined by position and communication. Like gossipy old neighbours, cells love to chat to each other. They secrete all sorts of chemical signals telling anyone that cares to listen what is going on inside them, and at the same time they listen out for what their neighbours are doing, changing their behaviour and expression patterns accordingly.


Embryonic stem cells (ESCs) are special because they are so ready and able to transform into any human cell type.  Perhaps it’s worth noting that the cells are obtained from IVF clinics rather than from inside a woman, although it’s still easy to see where the controversy begins. Adult stem cells are more limited in the cell types they can become. For example, the stem cell reservoirs deep at the base of our skin are somewhat undifferentiated but may only mature into skin cells. These still have strong medical implications; collecting these special cells from burn victims can be used to create effective skin grafts which are guaranteed not to be rejected by the patient.


The reason transplants frequently fail is that our bodies are very good at identifying and destroying objects seen as “non-self”. This is a marvellous defence against pathogens like deadly bacteria, but natural selection could never have accounted for the practise of deliberate transfer of human material into another human, so organs from another individual are seen as foreign objects which need removing. Adult stem cell research can totally bypass this problem because the body will happily accept its own cells back even after being shaped and differentiated while in the lab.


Although adult stem cells are more limited in what they are able to become compared to their embryonic counterparts, they have the great advantage of being personal to the patient and will not get rejected. What’s more, some cells can now be made to revert back to their “original” state of pluripotency if bathed in the right mix of chemicals. This is called induced pluripotency. If we are able to find ways of reliably generating induced pluripotent stem cells from a patients’ own body, then we will have made many steps forwards towards personalised medicine and treatment. 

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Posted by on February 15, 2012 in Uncategorized



What will sciamour do for me?

Hi, welcome to Sciamour. 

I derived the blog name by mashing around some latin root words after exploring them in my twitter account @Sciword. The Sci- is latin for knowledge, most obviously found in “Science”, the main topic and indeed point of this blog.

Amour is love, passion. The latin root amor- might have worked but I had a think about it and I’m a little too protective of English quirks to exclude a “u”. Plus it sounds more french and romantic that way, right?

I think knowledge is sometimes undervalued in this society and that it should be celebrated rather than hidden away as a guilty secret. Be proud of what you know and always seek to discover more. Always.

As for me, I’m a biochemistry graduate and lifelong lover of science and what it can do for Earth and for humanity. Sciamour will be dedicated to exploring topics with scientific relevance and about the inner workings of the scientific method, including some of its problems and limitations. I should warn you I’m also a firm advocate of free-speech (fired at the moment by ACTA/TPP/SOPA/PIPA) so I might spill into a bit of law and politics if I need to get something off my chest or want to raise awareness! But I’m all about the science.

I hope you like what I’m going to do here.

Love Knowledge; Sciamour 

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Posted by on February 2, 2012 in Uncategorized