Y12 Suggestions for planning your own EPQ

Education has its roots in a word used to describe the development of a child (leading away from naivety, would be my interpretation). In schools and universities education is generally considered to be a formal process through which a student develops his/her mind. At school in England, this is achieved primarily by teachers delivering "The National Curriculum", a series of topics that are both required and optional. The topics and levels of challenge are linked to the Key Stages (KS), with KS5 being the highest level, typically leading to qualifications (associated with learning pathways) including A levels and BTECS. The decision to place a student on a particular pathway is reached following an evaluation of each student's aptitude, suitability and academic track record. Once you enter Y7, it is the priority of a school to support their cohort of students, enabling each one to achieve their potential; and more besides!

But education isn't a passive process. It is a shared experience, in which each student assimilates taught material and builds on it with independent study. Students are also encouraged to develop their own personalities, both mentally and physically, through activities ranging from chess, through playing a musical instrument, to the many different types of sport. When you leave school, you will be a product not only of your family and home life, but your experiences at school(s) and your own personal achievements.

This is where Extended Project Qualifications (EPQs) come in. I assume there are at least a few things that you really like in the National Curriculum? I became fascinated by enzymes when I was in the sixth form: my Chemistry teacher gave us an "off curriculum" lesson on the properties of enzymes in Y12, and I just had to go away and find out more. In those days, that meant a trip to the local library. This is the beginning of an EPQ. First identfy a topic of interest and then pose a question. The topic can come from any of the following general areas of study, which include:

Arts [Music, Art, Literature, Classics]

Humanities and Social Sciences [History, Geography, Linguistics and Language, Societal Issues, Philosophy, Psychology]

Healthcare [Medicine, Dentistry, Veterinary Science]

Engineering [Mechanical, Electronic, Civil, Chemical, Automotive, Aeronautical]

Science [Chemistry, Biology, Physics, Mathematics, Psychology]

Here are some ideas to get you thinking.

Arts

Why has the contemporary electric guitar become such a key instrument in popular music?

Should music be considered a computer language?

Why do some people prefer instrumental music over music accompanied by the human voice?

How can you compare the aesthetic appeal of Michelangelo with Lucian Freud?

Compare the media used by artists over the centuries

What motivates artists to interpret the world, from the wonder of Nature to the brutality of War?

Choose an author and discuss how their work(s) have had an impact on the world. (You could choose Dostoevsky, Shakespeare, Dickens or more contemporary authors like Orwell, Tolkien or Rowling).

Humanities and Social Sciences 

Choose a period you like in history and dig deeper and use the knowledge to address a contemporary issue. 

How has modern Britain (or Liverpool) been shaped by its History and its Geography?

Are there lessons that we can still learn from reading Plato?

Has the experience of Covid-19 changed your perspective on the world?

Has the experience of Covid-19 highlighted any shortcomings in our global society?

Should we all learn more than one language? If so, which ones?

Healthcare

The cost of Healthcare in the UK is getting increasingly difficult to fund through taxes, but why does the human race care so much about sick people? 

The 1918 Spanish flu killed around 5 million people worldwide. Have we learnt lessons from it? Focus on the challenges faced and met by New York in 1918.

How strong is the evidence that supports the culling of badgers as a means of controlling TB in cattle?

Some people believe fluorides should be added to tap water: some do not. What are the pros and cons for dental health?

How can we make the world a better place for people suffering from dementia related diseases?

Engineering 

Discuss the role played by engineers in supporting space travel and communications (both or one) in the future.

Covid-19 has shown that we all live and work too close to each other. How could you design schools to meet the challenge of a world threatened by viral infections?

Science

Choose a difficult topic and describe how you would explain it to the public through a range of different "channels" (podcasts, blogsites, infographics etc)

Take a topic of interest and find out what challenges science faces in this area

Molecules to Market project: develop a business idea around a particular science idea/concept

These are by no means meant to be the only EPQ topics, they are just ideas that I thought of while writing. 

I would invite you to suggest an idea/topic and then we can discuss it and develop it, in a way that captures your enthusiasm and at the same time enables you to produce a thought provoking narrative.

Understanding Covid-19 . I Definitions and Origins

This is a short series of science oriented posts on the current Coronavirus pandemic. I intend to release them in bite-sized narratives and so there will be 3-4 to follow. All questions and comments welcome, but I should make it clear I am not a virology expert.


The subject on everyone's lips (hopefully metaphorically and not physically!) is the Corona virus pandemic. With a tsunami of information everywhere, I thought I would provide some background to the issues that have cropped up in my conversations with colleagues, students and friends. My emphasis will be scientific and not behavioural, but hopefully it will clarify some misconceptions and provide the facts as they relate to other historic viral epidemics. At the end of each post I shall provide a glossary to ensure you have a good working definition of key words (which I shall highlight in bold at the first mention). Ideally, these posts will serve as a resource and please feel free to post questions, which I will do my best to answer in a timely way. I shall begin with some generic properties of all known viruses and then I shall focus on some of the well known examples.


Let's begin with a the word virus itself, originating from Latin, where it was used to describe a poison from an animal such as a snake's venom. It was then in 1900 that medical researchers recognized that some infectious agents or particles could be selectively removed by simple filtering procedures. This provides the dictionary definition below with the reference to virus dimensions (20-300nm). Interestingly Google's Ngram analysis identifies the 1980-1995 period as the period of most frequent printed use of the word virus (I am betting this will be overtaken by 2015-2025, when it gets analysed!). My favourite definition is given below and was obtained from www.dictionary.com

A virus is an ultramicroscopic (20 to 300 nm in diameter), metabolically inert, infectious agent that replicates only within the cells of living hosts, mainly bacteria, plants, and animals: composed of an RNA or DNA core, a protein coat, and, in more complex types, a surrounding envelope.

Let's unpack some of these terms. Ultra-microscopic implies that the virus cannot be "seen" using a conventional "light microscope", used routinely to look at bacteria or human blood cells (for example). An electron microscope is required for direct visualization, and the image on the right was taken by researchers at the University of Hong Kong. The scale bar shows the virus (looking like a crown or corona from the Latin again, or ancient Greek for a wreath (classical scholars among you will be familiar with the Olympic victor's wreath, made from olive branches) entering a human cell prior to its reproduction. The white scale bar shows the diameter of the virus as approximately 500nm (slightly larger than the dictionary definition). The virus genome will be discussed later, but the term metabolically inert refers to the fact that viruses of this kind are absolutely dependent on the host for providing energy (in the form of ATP) for their reproduction (often called replication): they cannot produce energy from food: they "steal" it from the host. The terms RNA, DNA, protein (coat and envelope) describe the classes of macromolecules associated with information (RNA and not DNA in the case of covid-19), structural and catalytic components (proteins) and the "protective shell" or envelope surrounding the virus particle.

In short then, covid-19 is an RNA virus capable of infecting humans primarily through a respiratory route (nose and mouth). It is around 500nm in diameter (a typical lung cell has a diameter of 8000nm: assuming viruses and cells are perfect spheres, what would be their respective volumes and what would be the capacity of each cell for virus particles?). It is an enveloped virus surrounded by a lipid membrane, into which a number of major "spike" proteins are embedded. It is these spike proteins that establish contact with respiratory cells prior to invasion of the cell itself (as shown above). The spike protein will assume importance in subsequent discussions of vaccination strategies.

The leaf on the left is healthy, but the one on the
right has been overwhelmed by a TMV infection

The first detailed analysis of any RNA virus was the subject of the 1946 Nobel Prize awarded to three protein scientists, including Wendell Stanley for his work on Tobacco Mosaic Virus (TMV). In a seminal paper published in 1935 (yes 85 years ago!). Stanley purified and crystallized this cylindrical virus and demonstrated that the pure preparation could elicit the biologically common infection of tobacco plant leaves as shown in the image on the left. In 1935, proof that DNA was the genetic material was unavailable, and moreover, methods did not exist to easily identify and characterize RNA molecules. Today we know that some of the major pathogenic viruses are encoded by RNA and not DNA genomes.

The diagram on the right, compares the structural features of covid-19 (left) and TMV (middle)  alongside another well known pathogen, the norovirus. These three viruses share some things in common, but covid-19 (like HIV) is an enveloped virus: the other two have capsids not envelopes and importantly, alcohol gel is ineffective in eradicating norovirus, but effective at inactivating covid-19. In general hand-washing with soap is the best way to reduce viral transmission, since the viruses we are likely to encounter could be of either type. All RNA viruses that infect eukaryotic host cells (plant or animal) must either express their genes from the injected RNA by direct transcription, or by first converting the RNA genome into DNA, through the action of the enzyme Reverse Transcriptase. With the viral genome now in the form of DNA, the host cell machinery that converts its own structural genes into first mRNA and then proteins, is hijacked by the virus genome. The result is a rapid accumulation of the building blocks needed to make more virus particles. When the cell capacity is exceeded, the infectious particles are released and the host begins to mount an immune defence. (I shall discuss this process in the light of the recent work published by the Australian virology group, but I do like this NYT graphic summary).

To end this first installment, one question I have been asked is "how does covid-19 compare with small-pox virus"? By the end of the eighteenth century, smallpox was responsible for killing around 10% of the world population..... and then along came Edward Jenner (here is one link that looks at the historical eradication of smallpox). The origins of variola virus (the cause of small pox and cow pox) are unknown, but certainly date back to the third century BCE. Variola viruses are unlike covid-19 in one important respect: they are DNA viruses. Why is this important? Viruses encoded by DNA genomes are less likely to mutate than RNA viruses, since the process of viral genome replication is less "error-prone" in DNA viruses and therefore the equivalents of the "spike proteins" in variola viruses present an easier target for vaccine production. For this reason, unlike flu vaccines, which are produced seasonally, smallpox vaccines can be stockpiled through the agency of the World Health Organisation (a valuable resource in all ways). There are over 30m shots of vaccine in deep storage, just in case this disease, which is in fact the only disease to have been completely eradicated globally, should ever re-surface. Clearly the successful vaccination against covid-19 is a priority and... 

I shall discuss vaccines in the next installment...

Glossary of Terms (in order of appearance in the text)

Epidemic and pandemic (from the US center for disease control)

Occasionally, the amount of disease in a community rises above the expected level. Epidemic refers to an increase, often sudden, in the number of cases of a disease above what is normally expected (this called endemic)  in that population in that area. Outbreak carries the same definition of epidemic, but is often used for a more limited geographic area. Cluster refers to an aggregation of cases grouped in place and time that are suspected to be greater than the number expected, even though the expected number may not be known. Pandemic refers to an epidemic that has spread over several countries or continents, usually affecting a large number of people.

Filtering is simply a process by which small and large particles are separated. It is a slightly more sophisticated form of sieving in which a liquid is passed through a barrier (such as paper or a plastic mesh). The holes in the filter can be manufactured to allow (in this case) particles of less than 1000nm diameter through (the viruses), leaving the cells on the filter itself. 

RNA, DNA protein (these are discussed above), but formally, deoxyribonucleic acids differ chemically  from ribonucleic acids by virtue of a single oxygen atom per sugar (see RHS). One of the consequences of this difference is that DNA molecules form Watson and Crick based paired double helices, whereas RNA molecules form heterogeneous mixtures of helical regions and single-strands. In both bacterial and mammalian cells Francis Crick proposed the central dogma of molecular biology which states that DNA makes RNA (the process called transcription) makes protein (the process of translation). In the case of retroviruses, by definition, the genomic RNA must first be turned into DNA (through the action of the enzyme Reverse Transcriptase) before the proteins that make up the viral coat can be expressed in the host cell. 

Replication is the term used to describe the duplication of a genome. In the case of DNA genomes, the enzyme DNA polymerase (which varies considerably in its complexity, from bacteria to man, but is renowned for making very few mistakes) catalyses the copying of DNA to generate new chromosomes. In the case of viral replication, many copies of the viral genome must be replicated to be packaged into the viral capsid (protein shell) or envelope (protein and lipid coat). The original concept of replication was suggested by Watson and Crick in 1953 and through the pioneering work of (Arthur) Kornberg and Meselson and Stahl, we now have a good understanding of the molecular basis of DNA replication as shown diagrammatically on the left. If the genome is made from RNA instead of DNA, replication is much more like transcription and since he transcribing enzyme, RNA polymerase is more careless than DNA polymerase, mutations arise more frequently in RNA viruses.

Thanks for the request from Anudhi regarding the specifics of replication in corona viruses, here is a summary of the properties of the Replicase gene. Like many RNA viruses, the proteins encoded in the RNA are expressed as a poly-protein which requires processing by a protease prior to assembly of the functional protein: in this case the replicase. The two replicase proteins combine to catalyse both transcription of the viral genome and replication in order that the genome can be packaged following assembly of new virus particles. The genome is just less than 30 000 nucleotides and an overview of the related SARS corona-virus can be found here for those of you who want more details.

Planning and writing your final EPQ document

Following our discussions last week, I thought I would try and help with your writing. To begin with, there is a deadline looming: the 24th February, approximately 5 weeks! Again as we discussed this means that you should be aiming to produce around 1000 words per week: at approximately 500 words per page, that's two pages of printed text per week. The key to ensuring you get through this process is planning. The main sections of every report will be organised as follows:

1. Title (10 words)
2. Abstract [optional, but recommended] (150 words)
3. Introduction and background (1000-1500 words)
4. Main content [this depends on the type of EPQ: experimental or literature based] (2000-2500 words)
5. Discussion (1000-1500 words)
6.Bibliography (Exclude the references from your initial word count)

The EPQ should also contain Figures which enhance your message. For experimental projects this will typically include data in the form of graphs and photographs. Exclude the Figures from your word count, and we will review this prior to final submission. Now let's look a little closer at each section and the differences between experimental and library based EPQs.

Title. This should be concise and informative. This must create a strong first impression. Some good and bad examples are below:

Good. Exploring the role metal ions in the active site of the enzyme catalase  

Bad. Experiments on the rate of reaction for the enzyme catalase.

Good. Developing a novel methodology for efficient DNA extraction in high yield

Bad Work on the extraction of DNA from tissue samples

Good. The contribution of Robert Bunsen to the British Chemical Industry

Bad. The life and times of Robert Bunsen

Good Can the UK Fashion Industry help Britain overcome the challenges of Brexit?

Bad A study of the UK fashion industry

Good  Are the scientific metrics used to determine the rate and impact of Global warming fit for purpose?

Bad How strong is the evidence for Global warming?

Why are some good and others bad? First of all, by bad, I don't necessarily mean that the titles are inappropriate: at this stage in your education, I expect the titles to be reasonable (which they all are). However, the better titles should whet the appetite of the marker. They should also convey to the marker that there is a sense of purpose to your EPQ and that it isn't just a well written summary of facts and figures. By "lifting the spirits of the marker," you will improve their assessment: this may not be written down anywhere, but from years of examining student work, I believe it is true. It's human nature to respond favourable to first impressions, but as you can see below, they are not the ONLY thing that will get you the marks (or the job) you want!

Abstract. This is a summary of the entire content and conclusion(s) of your EPQ. A good abstract will use words economically, judiciously and will be engaging. As with the value of a good title, a good abstract can provide a marker (or reader) with a short-cut to a good mark. If I am reading a scientific paper, I scan the abstract as a means of triaging (or filtering) my reading priorities. Below are two related abstracts for different research papers on a similar topic. Don't worry about the detail! I think you will agree, the first is too dense and specialised, the second beckons me to read on and the third is a more detailed abstract, which presents some perspective rather than being simply factual. You should consider the style of the last two examples when you come to write your own.

Abstract 1

The DNA polymerase from Thermus aquaticus (Taq polymerase) is homologous to Escherichia coli DNA polymerase I (Pol I) and likewise has domains responsible for DNA polymerase and 5' nuclease activities. The structures to the polymerase domains of Taq polymerase and of the Klenow fragment (KF) of Pol I are almost identical, whereas the structure of a vestigial editing 3'-5' exonuclease domain of Taq polymerase that lies between the other two domains is dramatically altered, resulting in the absence of this activity in the thermostable enzyme. The structures have been solved for editing complexes between KF and single-stranded DNA and for duplex DNA with a 3' overhanging single strand, but not for a complex containing duplex DNA at the polymerase active-site. Here we present the co-crystal structure of Taq polymerase with a blunt-ended duplex DNA bound to the polymerase active-site cleft; the DNA neither bends nor goes through the large polymerase cleft, and the structural form of the bound DNA is between the B and A forms. A wide minor groove allows access to protein side chains that hydrogen-bond to the N3 of purines and the O2 of pyrimidines at the blunt-end terminus. Part of the DNA bound to the polymerase site shares a common binding site with DNA bound to the exonuclease site, but they are translated relative to each other by several angstroms along their helix axes.

Abstract 2 

High resolution crystal structures of DNA polymerase intermediates are needed to study the mechanism of DNA synthesis in cells. Here we report five crystal structures of DNA polymerase I that capture new conformations for the polymerase translocation and nucleotide pre-insertion steps in the DNA synthesis pathway. We suggest that these new structures, along with previously solved structures, highlight the dynamic nature of the finger subdomain in the enzyme active site.

Abstract 3 

Among the trending topics in the life sciences, stem cells have received a fair share of attention in the public debate - mostly in connection with their potential for biomedical application and therapies. While the promise of organ regeneration and the end of cancer have captured our imagination, it has gone almost unnoticed that plant stem cells represent the ultimate origin of much of the food we eat, the oxygen we breathe, as well the fuels we burn. Thus, plant stem cells may be ranked among the most important cells for human well-being. Research by many labs in the last decades has uncovered a set of independent stem cell systems that fulfil the specialised needs of plant development and growth in four dimensions. Surprisingly, the cellular and molecular design of these systems is remarkably similar, even across diverse species. In some long-lived plants, such as trees, plant stem cells remain active over hundreds or even thousands of years, revealing the exquisite precision in the underlying control of proliferation, self-renewal and differentiation. In this article, we introduce the basic features of the three major plant stem cell systems building on these facts, highlight their modular design at the level of cellular layout and regulatory underpinnings and briefly compare them with their animal counterparts.

Introduction. This is your first substantive section and can be broken down into several sections. I favour the use of numbered sections eg here is an example of an Introductory layout that I have made up.

Title The relationship between DNA structure and the mechanism of DNA replication in bacteria.

Abstract

Introduction

1.1 Background to the project.

Watson and Crick published their iconic paper on the double helical structure of DNA over 60 years ago (Watson and Crick, 1953), and since then it has remained largely unchallenged. The DNA double helix comprises a complementary pair of polynucleotide strands that suggested to the authors a simple mechanism for replication that would retain the sequence of the bases in the genome as one generation produces the next. Etc....

1.2 The molecular structure of the Watson and Crick double helix

Fig. 1

DNA was shown by Avery, MacLeod and McCarty (1944) to provide the information needed to produce a living organism. This provided Watson and Crick (and others) with the justification for determining the three dimensional structure of DNA. Armed with the pre-publication data of Franklin and Wilkinson (1953) and the earlier X-ray data from Astbury's (1938) group, the proposed model for DNA, which is shown schematically in Figure 1, comprises.....

1.3 The enzymes involved in DNA replication in E.coli.

Arthur Kornberg was the first scientist to investigate the mechanism of DNA replication. He selected the emerging model organism as his choice of experimental system and began a period of investigation that lasted for over 5 decades. During this time he would identify the DNA Polymerases, win a Nobel Prize and then others would prove that his enzyme (DNA Polymerase I used to be called the Kornberg Polymerase) was not in fact essential for DNA replication......

The use of sections allows you to build a structure, to write "bite-sized" narrative and is VERY EASY to mark!

Finally 1.12 Aims of the project

Here I will demonstrate that the experiments performed over 50-60 years ago require some revision in the light of new technological breakthroughs. I shall establish what features of the original Watson and Crick model remain correct and how the structure provides an elegant solution to its replication, but also what barriers it presents in the light of the need to package the DNA genome into a highly compact three dimensional space in the cell......

The introduction should provide a basis for the research question. It should provide the reader with a collection of facts that relate to the topic and should be written in a succinct way, illustrated where possible. You MUST incorporate key references in the correct way (see resource files) and finally summarise what your aims/questions are and how you will address them. 

Main content

In this section let us consider a project that relates to Robert Bunsen. In the introduction you will have given a biographical sketch and explained who he is and what he is known for (if you didn't know, think Bunsen burners!). Here you are going to explore how he influenced the development of the Chemical Industry in Britain at the outset (around 1840-1890).

Robert Bunsen was a pioneering chemist, specialising in analytical methods (flame tests to determine the composition of matter) and the development of instruments to facilitate analytical and preparative chemistry. I shall consider first his direct contribution to the science underpinning the major chemical processes that would form the core of the UK (and German) chemical industry sector. In the second half, I shall consider the scientists who received their academic training from Bunsen, and how this group of extraordinary individuals, including Ludwig Mond, went on to shape the British Chemical Industries until their decline in the last half of the twentieth century......

Again use sections, for example:

2.2 Bunsen's published academic work

Robert Bunsen published a significant body of work between the years....

2.3 Bunsen's views on patenting

Unlike most scientists, who were pioneering process development .....

Discussion

Fig.2

The British Chemical Industry formed a major part of the overall  UK economy from 1840 until 1900 (See Figure 2), when competition began to emerge from ..... 

In this section, you MUST incorporate your critical insight. What do you see as important, unimportant etc and use evidence to justify your opinions. This is an important section since it LIFTS your project to an encyclopaedia account, in which the facts are distilled and re-presented, to a critical evaluation of a complex issue. Which is exactly what an EPQ should be all about!

Bibliography

Here, you must list in full, all of the references cited in your EPQ. There are instructions provided in the Google Classroom folder. Importantly, you must be consistent in your referencing. You can use numbers as in:

Narrative Watson and Crick [1] were the first authors to correctly interpret the X-ray data produced by a number of different research groups, including Wilkins and Franklin [2,3] and Astbury [3-9]. 

1. Watson, J and Crick, F.H. (1953) Nature 171, 737–738 Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

Alternatively, you can cite the authors in the narrative and then list them alphabetically at the end.

Astbury, W. (1938) Nature 162, 235-237 X ray diffraction of the sodium salt of Deoxyribose Nucleic Acid I

Astbury, W. (1939) Nature 167, 435-442 X ray diffraction of the sodium salt of Deoxyribose Nucleic Acid II

Astbury, W. and Jones, G. (1938) Nature 168, 2-9 X ray diffraction of the sodium salt of Deoxyribose Nucleic Acid III

This will hopefully help you get underway! Any questions, come and find me.

Approaching the first draft of your full EPQ

The submission deadline for your draft versions is looming (Tuesday 10th December), with feedback scheduled for 7 days later (17th). The timetable has been arranged to give you and me the first opportunity to see how you have managed to organise your thoughts in a comprehensive manner. The feedback should help you finalise your EPQ in advance of your January presentations and your final EPQ submission for internal and external assessment. Please come along and see me or email me today if you need any advice in meeting these deadlines: we are now at a critical phase in the process.


Let's take stock for a moment and ask yourself if you have fully taken on board the points below. 

1. You have all settled on a title for your EPQ and submitted a detailed proposal and work-plan and feedback has been provided in return. (This is a completed stage and is formally assessed). 

2. You have provided me with examples of your narrative and you have responded constructively to my suggestions (this is true for some of you, but not all and is an advisory intervention rather than a formally assessed stage).

3. You have been keeping a diary in which you log your EPQ associated activities and collate your sources and/or any data. Again, those of you who have chosen to provide me with documents or have discussed this with me have hopefully benefited from my direction. Again, this element was introduced to support you in completing your EPQ and some of you have chosen to exchange materials and discuss issues, while others have not. The submission of an activity log, does form part of your final submission, and so this is a mandatory task and one that will be assessed, independently.

4. You have been asked to provide a sample of narrative containing appropriately cited references. Again, the aim of this exercise is to reassure you that the format and style of presentation, meet the expectations of a high quality EPQ. Those who have chosen to provide me with material will have received constructive suggestions, if you have not, I assume you are confident that this is something that you are already familiar with. That's OK, just make sure you familiarise yourself with the formal methodology of citation of publications: both paper and virtual.

5. The resources folder in the Google classroom contains material to help you with all of the above. It is a little like a past paper for an exam and if I am right, while past papers can be incredibly useful, there is some benefit in discussing the various requirements face to face or by email. Please make sure you get in touch if you have any concerns.

Establishing Credibility and Authenticity: key skills for Life

The most interesting part of researching and writing an EPQ is digging into an academic field in detail to find hidden "treasure". When it comes to writing the report, you may be a "natural" at writing (unlike me), or like me, you try your best to apply the standard rules of English (in our case) to produce a logical and well organised document. However, one of the fundamentally important aspects of any research report (or any factual publication, news report or TV documentary etc) is to be able you say that you "got your facts right". If your chemistry teacher says that sodium has a higher atomic weight than potassium, you write it down without a second thought. If the TV announcer says that your favourite programme will begin an hour later than usual, you feel like you should check to see if he/she is correct; just in case you miss it. You might check online, just to be sure. This is called verifying a fact and it is a critical part of any academic writing or broadcasting. But why do we do it sometimes and not others. Well simply, it depends on the importance to us, of being correct. 

In academic writing, a piece of work stands or falls on the quality and accuracy of its sources. In the world of invention, where the currency may be filing a "patent", the patent office will check to make sure there are no earlier patents that have already claimed a similar invention. This is referred to as "prior art" and is the term used by patent lawyers to ensure the invention is novel: a key element of a patented invention.

When you write that "most people in the UK own a mobile phone", it sounds believable. Maybe you are the new Prime minister trying to raise taxes from mobile phone owners to help pay towards the NHS. Then you think, how many people are over say 20 (the age when most people start paying taxes) and how many people are over 65 (many of whom, don't pay taxes) but who may have a mobile phone? Now you see why you need to verify the information. I consulted the Industry Regulator's web site (Ofcom), who regularly survey providers and phone users. In August 2018, they reported that 78% of all adults own a smartphone. There are around 16m people under 20 in the UK, and the population is around 60m, then Ofcom quote that 78% of 44m adults own a mobile phone. Finally since only 16m out of 60m are 65+, you can see that the proportion of adults who own a mobile phone and who are also eligible for taxation, needs to be verified carefully. Even though 78% of adults own mobile phones, only 50% approximately, will be tax payers. And so it goes on: the reliability of the information should be directly linked to the application of that information: if it is critical information: it must be reliable.

You may ask, why do I "trust" Ofcom's data? I would say that primarily because it is a government regulated authority, which immediately gives me confidence in its authenticity. But maybe I do not completely trust in the data. I would really like to be able to verify the data using another reliable organisation. It might be the results of a survey of users carried out by University researchers: where they have no "vested interest" in the outcome of the survey. It probably would not be the association of mobile phone suppliers, who might want to "accentuate the positive: eliminate the negative" as the American songwriter, Johhnny Mercer once wrote! Where possible "get a second opinion" and use sources other than individuals, unless they have a good track record in their field.

It is not easy to validate completely, but you should try your best. Basing your ideas or conclusions on a single publication or source, which is not corroborated by other papers or sources, is a risky strategy. It is always good to see how many times a paper or resource has been "cited". This is not totally reliable, but it improves the confidence in the source. Reputable sources include learned journals (eg Nature, Scientific American or the Biochemical Journal etc.) and professional organisations and societies. Newspapers are NOT reliable: if you cite them, always check the primary source of the information: a good newspaper will cite this. 

These are the processes you need to comment on when you cite a source. You can come up with a shorthand to indicate how a source was validated: but I'll let you devise one of your own.

Filling in forms and answering examination questions: two sides of the same coin!

One of my colleagues at Sheffield, a yeast geneticist, once said to me that "experimental scientists stand and fall on their ability to write". At first I didn't get wheat he meant, but then I realised he was absolutely right. If I want to carry out a piece of original research (as with your EPQ), I need to persuade a group of experts that my idea is sound, and that it meets all of the criteria required for them to award me the money to carry out the project. (FYI a typical project in Science will cost around £150 000 per year to carry out). I don't get the opportunity to meet any of these "experts" (or peer reviewers as they are known), I don't even get to know who they are! I am also given specific instructions on what to write and how much to write. If I don't follow the rubric, they don't even read my application.

Assuming my idea does get funded, when it comes to telling the world about my results and conclusions, I can attend scientific meetings and give talks about the work, but it is the written publication that appears in a respected and (yes, here we go again), peer reviewed journal, that gets recognised. And this is what then enables me to apply for more funding....and so it goes. I think you will agree: he was absolutely right! Of course, in between writing, we do carry out some experiments!

When I am given a form to fill in, like the EPQ Project Proposal Form, I fill in the simple stuff and then I look carefully at any guidance or indications of what is expected in a particular section. For example: Section Two is where you explain why you have chosen to work on a particular topic.

Reasons for choosing the project (eg, links to other subjects you are studying, personal interest, future plans, knowledge/skills you want to improve, why the topic is important)

What are they looking for in your response? This is very similar to an examination question in which the setter provides some direction on what to consider in writing your answer. If you ignore these guidelines, you may well misjudge the question. A road which can only lead to disappointment! So ALWAYS follow the guidelines! IN this particular situation, this is what they are looking for. Let's say you have chosen to investigate the topic:

Is it the responsibility of the individual, the restaurant or the Government, to ensure that individuals who have a peanut allergy are not placed at unreasonable risk when they choose an item of a menu?

Reasons for choosing the project?

I recently saw an item on TV in which the courts fined a restaurant over £100 000, because an item on the menu, that was not clearly labelled as containing nuts, was eaten by a young girl, who subsequently died. Was £100 000 enough compensation for the family who have lost a child tragically? Should those people with allergies be expected to ask if a product contains nuts? The fine led to the closure of the shop with the loss of 3 jobs: I didn't think this was fair on the staff who were just following orders. For these and other similar reasons, I wanted to understand all of the factors involved in this, since my brother is allergic to peanuts.

I hope you can see, I have provided the examiner with a good reason, it has plenty of details and illustrates how my mind works and considers such issues.

Links to other subjects

I am studying Biology A Level and taking a Business Studies BTEC. As a Biologist, I am fascinated by the body's response to allergens like peanuts (because of my brother), but also medicines like penicillin. I am also thinking about the difficulties in running a business, and how much of a factor "regulatory compliance" is , in making a business profitable, while avoiding adverse publicity. 

Again, I am providing information about the legitimate choice of project topic and something about my academic background and aspirations.

Future Plans

I have mentioned my subject interests earlier: I am interested in studying Biotechnology at University, but I would like to run my own business, rather than work for a large company. This project should give me early insight into some of the challenges faced by start up companies, in particular how things like Health and Safety, can be critical for establishing a viable business.

New skills


In carrying out this project, I hope to learn more about the application of my Biology knowledge in the "real world". I also feel that I need to look at a specific case from a legal perspective: as an individual affected by a policy decision faces a battle for compensation with a major Food Company and restaurant chain.

Again, I am trying to demonstrate that the project takes me away from the Curriculum and applies my  knowledge in such a a way that will give me greater insight into sustainable business planning.

Time management skills

One of the most transferable skills that will have an impact on almost every aspect of your lives, is your ability to manage your time judiciously. Try and think of it as a way in which you get the most out of an opportunity, rather than meeting someone else's agenda. So being asked to attend a meeting or interview at 9am, may seem harsh, but it gives you the opportunity to be one of the first people to be interviewed. It gives you enough time to take an hour to prepare any last minute thoughts or go through any paperwork etc. It also means that you can act on the outcome of the meeting in the same day; something that is more difficult if the meeting is at 4pm. If the meeting is scheduled for 4pm on the other hand, travel is cheaper, and people are often a little more relaxed at the end of the day, so you need to wake everyone up! Again the way you approach meetings and interviews (in this example) should be viewed as an opportunity.

When in school, at university and eventually in the work place, deadlines are a regular occurrence. In my experience, there is never any situation where meeting a deadline comfortably (by hours, days, weeks, depending on the timescale of notice), does not help. You will have the chance to remove silly writing errors, to relax a little instead of being rushed, to check your files can be accessed and viewed, etc etc. And the only way you can be sure of meeting deadlines is to plan properly. 

As soon as you are given a deadline, write the date in your diary/calendar and also add a reminder of the deadline a week before (if you have more than a week's notice). It may be an examination deadline or submission deadlines for coursework, for example, whatever it is, you must work out how much time you need to meet that deadline. Here are some average times taken to do things.

• Reading 1000 words takes around 5 minutes

• Walking a mile takes around 20 minutes

• Writing 500 words should take no more than 2 hours, depending on the content.

• Producing a detailed diagram can take around 4 hours.

These are relatively easy time-scales to predict, but how long does it take to memorise a Shakespeare sonnet, or the lyrics of the National Anthem? These are much more difficult to predict on an individul basis, just as it is difficult to estimate how long two Science students will take to master the concept of differential calculus. Sometimes we have to estimate as best we can, and then make allowances for things that take longer than expected. In another example, if I plan to drive from Liverpool to Sheffield, I would beging with an estimate of 2 hours 15 minutes. However, if I set of from Liverpool at 8am, I can add up to  2 more hours, making the journey time over 4 hours. The same would be true if I set of at 4.30pm. If you assume it will take 2 hours, and you set off at rush hour, you will miss your appointment and an opportunity will be lost.

The first piece of work required to meet the EPQ deadline of November 11th is a completed Project Application form and an example of your activity log (see my earler post). They can both be loacated in the Classroom Resources folder. Read through the document and establish what they require you to do (not what you would be rather be doing: remember half an hour spent reading through the document will pay dividends. When you open the document, you will see that Mr. Crabtree has annotated it heavily to guide you through completion.            

So remember....take the opportunity to plan well.

Royal Society Partnership Award 2019

Directed evolution of Nickel and Iron binding sites in the synthetic, chimeric NiFe protein 

This is the title of the project for which we have secured competitive funding from Britain's Royal Society. According to the Society's literature, "the Royal Society was formed over 350 years ago by a group of people who wanted to share ideas about the natural world by using experiments and observations". Today, the Society is renowned for its prestigious cohort of "Fellows of the Royal Society"; distinguished scientists who have been elected on the basis of the impact their research by leading experts from across the world of Science. Famous Fellows from the past include Sir Isaac Newton, Robert Hooke and Charles Darwin and from their annual announcements every January, last year included Manjul Bhargava for his work on number theory, Veronique Gouverneur, for her work on fluorine chemistry and  Jack Szostak, for his work on molecular genetics and in particular DNA replication and evolution. The current The current President of the Royal Society is Dr Venki Ramakrishnan, who received the Nobel Prize for his work on determination of the structure of the ribosome. 

Partnership grants are awarded to provide school students with an opportunity to explore a research problem alongside a University research group. In this case, students will be mentored by Mr Blackham at the NLA and Dr. Dyer at the UTC. The project is an ongoing research problem that has been investigated by two Masters Level students, James Florence (now a PhD student in Professor Hornby's lab at the University of Sheffield) and Alex Wakeman. The protein called NiFe is encoded by a small gene which has been made by chemical synthesis and combines a Ni binding domain (NBD) from the human transcription factor nonO and the complete sequence of the Fe binding electron transfer protein, rubredoxin. The N terminus of the nonO protein, sometimes called p54nrb, is Glutamine (Gln,Q), Proline (Pro, P)  and Histidine (His,H) rich as you can see below. The His residues coordinate the Ni ion, and often this property is utilised by adding six consecutive His residues to the N or C terminus of a recombinant protein, to facilitate its purification on a Ni chromatography resin (the most popular is called Ni-NTA).

MQSNKTFNLEKQNHTPRKHHQHHHQQQHHQQQQQQPPPPPIPANG 

The function of the NBD is unclear, but it allows us to explore the ways in which metal ions, which are widely used in Chemistry as catalysts, join forces with proteins (polypeptide chains) to enhance the catalytic and redox properties of proteins early on in the evolution of Life on Earth. A possible 3D model for the complex with Ni can be derived from a related crystal structure (below), discussed in a review of Ni binding proteins found in E.coli. This will form part of the project.

 

The Fe or iron, binding domain (IBD) is derived from the rubredoxin redox protein from thermophilic microbe, Thermotoga maritima. It has a structure shown below (from a closely related species (PDB Ref to add), and a polypeptide sequence shown below the image, following on from the p54nrb sequence.

MEQSNKTFNLEKQNHTPRKHHQHHHQQQHHQQQQQQPPPPPIPANGQQASSQNEGLTIDLKENLYFQGELHMKKYRCKLCGYIYDPEQGDPDSGIEPGTPFEDLPDDWVCPLCGASKEDFEPVEGGSEFE

These are the synthetic proteins, but what are the questions? Here is a taster, rather than a comprehensive programme of work. Darwinian evolution is based on an intrinsically error-prone process that copies gene sequences from one generation to the next. When a selective advantage arises that promotes the advantage of a particular mutant within a population, that mutant will begin to dominate and eventually replace (in some situations), the parental gene (or genome). We have developed (James's PhD thesis) a mutant form of a Polymerase Chain Reaction enzyme that introduces errors into any gene, allowing us to "evolve" our NiFe protein in the test-tube: thereby compressing evolutionary time from many years into days. Can we use this process of molecular evolution to change NiFe into CoFe for example?

The second strand of the study is to understand the mechanism underlying metal ion catalysis of reactions such as the decomposition of hydrogen peroxide. Ions like manganese (in a number of oxidation states) are able to catalyse the decomposition reaction very efficiently. So why did catalase evolve? Does it make a metal ion better or does it use a different catalytic pathway? What are the chemical and physical parameters that confer catalytic power on metal ions in solution (and in the solid phase)? How does our understanding on the coordination of metal ions in solution help us understand catalysis? And what is the connection between catalysis in chemistry and biochemistry to the quantum mechanical models of atomic orbitals?

I hope you can see we have an opportunity to dig a little deeper into the science behind catalysis in both the test tube and the cell. I will begin to populate the blog site myself and then I will hand over to you!