Tuesday, 30 April 2013

What's it really like to do a PhD?

I'm currently in that peculiar limbo of having handed in my PhD thesis and waiting for my Viva (oral exam which decides whether or not I'm doctor material). This has given me some headspace to reflect on the whole PhD process, so I thought I would write a piece dispelling some myths, and possibly shedding some light in the whole PhD process. As one quick caveat, this only applies to a science PhD, since I've no experience of any other kind. 

The first thing to address is why you might choose to undertake 3 years of research into one tiny subject. The most obvious motivation is that of wanting to pursue an academic career, for which a PhD is pretty much essential. By extension, any career in a science- or knowledge-based subject would be substantially enhanced by having a doctorate. As well as the qualification itself, the skills learnt during this period are greatly marketable in these fields, namely (but not exclusively) evaluating evidence, critical thinking, experimental design, independent research, and effective communication of this research. On top of these are the personal motivations: the desire to test yourself academically, to see if you are up to the challenge. Also, let's face it, everyone likes the idea of getting a posh title. 

To effectively explain what a PhD studentship is, it's important to dispel a few preconceptions as to what it isn't. It is not the same as being an undergraduate. There are seldom lecture courses to attend, and there are no long university holidays. You are essentially a paid researcher, expected to turn up every day and do your job. While there may be flexibility regarding your hours, there are still deliverables to be met and supervisors (both academic and corporate) to be satisfied. In my case, I was expected to both produce academic papers (I've published 3 out of the 4 so far) for my department, and also produce and present to sponsors (www. protexin.com) research which they could use in both formulation of and publicity for their products. This tends to fly in the face of people's preconceptions of a PhD student as being just another university-based layabout, but my experience suggests that such a studentship is more akin to a low-paid job than 3 years on the booze. 

While on the subject of preconceptions, it is worth mentioning those that the student himself might bring to the table. It is certainly not an easy alternative to hitting the job market, not least since you will have to do that afterwards anyway. In the meantime there are long hours in a lab (in my case a lab which was regularly filled with the smell of fermenting faecal samples) to be put in. Nor is it a continuation of the undergraduate process, either in terms of doing very few hours per week, or in terms of regular feedback. This latter can be a real issue. Without constant quantitative feedback in the form of marks for assignment, it is possible to spend much of your time wondering whether what you are doing is any good or of any use. Publications help this situation somewhat, but these are relatively scarce occurrences, and tend to happen at the end of the process. A good relationship with your supervisor can also help with this uncertainty (and I couldn't have had a better supervisor), but even now waiting for the final verdict, I can't help wondering sometimes if my thesis passes muster. In this I can only assume that if it weren't my supervisor would not have let me submit. The other preconception is that you will spend your time changing the face of your field forever. My experience of research suggests that you spend plenty of time doing work that produces no results (frustrating at the time, but certainly a legitimate part of the learning experience), and that there is barely ever a definite answer to a hypothesis. At best, you are likely to produce an answer of "err, well, maybe, if I've interpreted my data correctly." Oh, and you will at the end likely be working for free. A PhD takes 3-4 years, they almost all run over the 3 year mark, and typically you are only paid a salary for the 3 years, so any overrun leaves you somewhat financially stranded. Worth bearing in mind when thinking about undertaking this process. 

So what of the process itself, this arcane mechanism by which ordinary graduates become "Doctors?" Typically your first year is spent doing quite a bit of floundering, and feeling like everyone else is confidently getting on with their research. In the midst of this, there is the need to write a literature review. This is where you read, analyse and criticise all the research in your field (narrowing this down to what is actually relevant is a big challenge in itself), with a view to finding the gaps in knowledge, and hopefully how to investigate these gaps to produce something new. One of the main criteria of PhD-quality work is whether it adds something new to existing knowledge, which speaks to the importance of this literature review. Once this is done, hopefully you have a good idea of what and how to research. At this point it is worth pointing out the variety in PhD projects. Some, such as those funded by large research bodies such as the BBSRC, are very regimented, giving a timetable as to what needs to be done and when. Others, such as mine, are more along the lines of "go and research this subject area." The relative merits of each are a subject for very lengthy debate, but my opinion is that the latter type give the researcher more scope for proper independent research, although they can leave them feeling somewhat lost if they arrive at a dead end.

At the end of the first year, you have to undertake the Transfer process, where you provide a report on your work so far, and a plan on how you will proceed. You are then interviewed by 2 academics from your department to ensure that your work is of the right standard for you to proceed. Despite the fact that failure at this point is relatively scarce, this is still a nerve-wracking procedure, although ultimately the chance to write up and review your work is very useful in informing how you will proceed. 

Then real research begins, typically involving long hours in the afore-mentioned smelly lab, collecting numbers in a lab book. Eventually, you get to the point where you need to do something with those numbers, and then realise that although you loathe statistics, you have to use the ones you did as an undergraduate and forgot about as soon as you left the exam hall. Statistics done, you need to then ponder the significance of your results to your field and possibly wider. At this point, hopefully you have enough data to write a paper. That's one down. You need at least 3 of these, plus your literature review and supplementary chapters to form your thesis. At 35,000 words, mine is regarded as comparatively short (although I prefer the terms concise or efficient!). Towards the end of the whole process, if you're unlucky or disorganised you need to write up the whole lot, necessitating you casting your mind back to work you did 3 years ago to try and remember why/what/how you did this. My department at Reading has a policy that you write up and publish as you go. This makes far more sense than writing it all up at the end; the publications mean more prestige for the department, and let the researcher know that their work is of the right standard. It also avoids the memory-strain mentioned above, and makes the final few months less stressful, since you only need to write one paper and a brief concluding chapter, bringing the whole body of research together. 

Assuming your thesis is up-to-standard, it is then submitted to the university and your Viva is arranged. At this point you need to "defend your thesis" - nice, hostile term - in an interview with an expert academic from another university, as well as one from your department whose role it is to make sure the external examiner does their job correctly. After this 2-hour grilling, several outcomes are possible:

- outright pass (i.e. your thesis is perfect as it is - you can imagine how rarely this happens);
- pass with minor corrections (you have 3 months to make changes to your thesis agreed upon at the Viva);
- pass with major corrections (12 months to make major changes, potentially including more experimental work);
- recommend that you are awarded MPhil instead;
- Fail (let's not go there).

So that, in 1,500-odd words is what it's like to do a PhD. Would i recommend it? I'm honestly not sure. For certain careers, you just have to get one, so it's a rite of passage. My own experience has been one of real ups and downs, a reality TV clich├ęd "journey." I have gained the skills mentioned above as well as others, and certainly learnt a lot about myself. But I have also experienced feelings of isolation and hopelessness in the process, and according to my wife have been hell to live with. I don't necessarily feel like I have scaled any intellectual heights, but then a friend of mine, doing a PhD in business management, said to me that doing a PhD is not for the smart, but for the stubborn. He has this spot on - at times you do feel like you are hitting your head repeatedly against a brick wall, and making no indentation. Having said all this, reading my thesis in preparation for my viva, I do feel some pride in having done a decent piece of research and communicated it effectively. I also feel some pride in having produced a thesis at all, given the number of times I wanted to give the whole thing up (I don't believe any PhD student who says they have never thought about quitting).

Besides, won't it all be worth it when I have to change all my cards and documents so they say "Dr. C Chapman?"

Friday, 19 April 2013

Everyone loves a curry...

This recipe of mine has appeared on my friend Liz’s Fit & Fun at Home Facebook page, so I thought I’d share it here too. As well as requiring no specialist skill or equipment, nor a vast list of ingredients which it takes hours to buy, this curry is very tasty, and packed full of beneficial ingredients:
·         I’ve previously mentioned the benefits of eating oily fish such as the salmon here, which could just as well be replaced by trout;
·         The cauliflower and spinach both contains high levels of compounds called glucosinolates, which may have a protective effect against certain forms of cancer. Studies have shown that they can block the initiation of tumours.1
·         Quercetin found in the onion is a powerful antioxidant, and studies have linked high intake of it with reduced risk of heart disease; 2
·         Sweet potatoes are a great source of vitamins A and C, and are a source of low GI carbohydrate, which will not give your blood an insulin spike, keeping energy levels more constant.

Ingredients (serves 4):
1 tablespoon olive oil
1 medium white onion, chopped
1/2 jar curry paste (Patak's Tandoori works well here)
1 can of coconut milk
4 medium sweet potatoes, peeled and cut into 1" cubes
1 cauliflower, cut into medium florets
4 salmon fillets, skinned and cut into 1" think slices
1 bag of spinach

Cook the onion in the oil until soft but not too coloured. Add the paste and sweet potato. Stir and add the coconut milk. Bring to the boil, put on a lid, and leave to simmer for 10 minutes. Add the cauliflower, and simmer with lid off for another 10 minutes. Throw in the salmon, then the spinach, cover and cook for about 8 minutes, until the fish is cooked and the spinach is wilted. Serve sprinkled with coriander leaves if you have them.
Eat with naan bread to mop up the sauce, unless you're on a gluten-free diet, in which case just tip the bowl up and slurp up the sauce!

A bowl of this will give you the following nutrients:
Energy: 616 kCalories
Protein: 33g
Carbohydrates: 39g
Fat: 33g

To change things up, this would work equally well by substituting any white fish or prawns for the salmon, or broccoli for the cauliflower. A garnish of chopped fresh chilli would give a metabolism-raising hit of flavour.


1     Navarro, S. L., Li, F. & Lampe, J. W. Mechanisms of action of isothiocyanates in cancer chemoprevention: an update. Food Funct 2, 579-587, doi:10.1039/c1fo10114e (2011).
2          Davis, J. M., Murphy, E. A., Carmichael, M. D. & Davis, B. Quercetin increases brain and muscle mitochondrial biogenesis and exercise tolerance. Am J Physiol Regul Integr Comp Physiol 296, R1071-1077, doi:90925.2008 [pii] 10.1152/ajpregu.90925.2008 (2009).

Thursday, 18 April 2013

Don't believe the hype


As a real chocoholic, I make no apologies for the crowd-pleasing subject of this post. It seems that you cannot go a week without the press carrying a miraculous headline that a food previously-labelled as bad for you now has health-giving properties, making it seemingly alright to consume as much as you wish. The two main commodities in question are arguably the two most attractive, alcohol and chocolate. This post will deal with the latter, and hopefully clarify some potentially misleading headlines.

The reason for a product so full of fat and sugar having possible health benefits comes from a group of chemicals called polyphenols, which are the result of metabolic reactions within the cocoa plant (theobroma cocoa, Latin fans). It seems that these polyphenols are often created to help a plant survive natural stresses such as extreme heat, and that these protective properties sometimes have similar benefits to humans when ingested. In the case of chocolate, the main polyphenols whose health benefits have been studied are called flavanols, proanthocyanidins and anthocyanins.1

Study evidence suggests several main health benefits of chocolate:
1.      Antioxidant content. Free radicals are a by-product of many natural reactions within human cells. These free radicals are very reactive, and as a result can cause damage to healthy cells. Antioxidants can “mop up” these free radicals, reducing the potential for cell damage, and related conditions such as cardiovascular disease. Studies have shown that long-term dark chocolate consumption can increase the antioxidant capacity of blood plasma, and decrease the oxidation of LDL cholesterol (a major contributing factor to heart disease)2, and that flavanols from a cocoa drink can inhibit oxidation markers within the blood.3
2.      Reduction of blood pressure. Dark chocolate high in flavanols have been shown to reduce blood pressure4-5. However, 2 things need to be borne in mind here. Firstly, these studies used chocolate that was especially formulated to be high in flavanols, and as we will see below, not all chocolates are created equal. Secondly, as a food chocolate is high in fat and sugar, both of which can contribute to raised blood pressure anyway.
3.      Arterial reactivity. Dysfunctional arteries with reduced flexibility are an important marker for cardiovascular disease. Arterial function is promoted by the production of nitric oxide (NO), and flavanols within chocolate have been linked with increased production of NO, resulting in greater arterial reactivity and consequently reduced risk of heart disease, stroke and related conditions.6 This study found a dose-dependent effect, i.e. the more you take in the better the effect. However, as above, greater intake of a fatty food has been linked with adverse effects such as increased CVD risk, so this result should be taken in the context of the whole diet, rather than an “eat chocolate and you’ll reduce your heart attack risk” blanket message.  
4.      Other reported benefits of cocoa-derived polyphenols include increased circulation of blood to the skin,7 increased oxygen saturation in blood to the brain during cognitive tasks8, and reduced incidence of brain disorders in long-term consumers of cocoa.9

However, these health benefits need to be taken in context for several reasons. Firstly, several of these studies use chocolate which has been specially formulated to include especially high levels of polyphenols, rather more than your average bar of Dairy Milk. Other studies have given subjects chemically-isolated polyphenols rather than whole chocolate, meaning that you can draw conclusions as to the effect of the polyphenol, but not as to its effect when taken is as a component of the whole food.

In fact, the food matrix appears to be of great importance when it comes to health benefits of chocolate. Not all chocolate is equal, with great variety in the amount of epicatechin observed in fermented beans from different regions.10 Another related issue stems from the production of chocolate from its raw bean state. The roasting, fermentation and other steps in the chocolate-making process can result in up to 85% of the polyphenols being lost or changed into unusable forms.11 With the health-giving properties of cocoa flavanols being big news, producers are trying to find new processes to increase the polyphenol content of their chocolate, but these not in general use by the industry.
Many of these studies used cocoa drinks rather than chocolate bars, and there seems to be a greater effect when the flavanols are delivered in this way rather than in the solid form. It also appears that the milk proteins in milk chocolate can bind with the flavanols within the chocolate, which can reduce how much of the flavanols you can actually absorb. This has led to the common conception that dark chocolate is the one that is “good for you.”

So what can we conclude from the wealth of scientific evidence about chocolate? We have gone from the Chocolate is GOOD for you!!!! headline to the reality which is that chocolate contains compounds which, as long as they survive the production process and are consumed in the right concentrations from the correct food delivery system without you eating too much fat and sugar, might be able to reduce your risk of certain conditions. Not as snappy or sales-orientated, but it does have the benefit of being closer to the truth.


1          Wollgast, J. & Anklam, E. Review on polyphenols in Theobroma cacao: changes in composition during the manufacture of chocolate and methodology for identification and quantification. Food Research International 33, 423-447 (2000).
2          Baba, S. et al. Continuous intake of polyphenolic compounds containing cocoa powder reduces LDL oxidative susceptibility and has beneficial effects on plasma HDL-cholesterol concentrations in humans. Am J Clin Nutr 85, 709-717, doi:85/3/709 [pii] (2007).
3          Flammer, A. J. et al. Dark chocolate improves coronary vasomotion and reduces platelet reactivity. Circulation 116, 2376-2382, doi:CIRCULATIONAHA.107.713867[pii] 0.1161/CIRCULATIONAHA.107.713867 (2007).
4          Grassi, D., Lippi, C., Necozione, S., Desideri, G. & Ferri, C. Short-term administration of dark chocolate is followed by a significant increase in insulin sensitivity and a decrease in blood pressure in healthy persons. Am J Clin Nutr 81, 611-614, doi:81/3/611 [pii] (2005).
5          Grassi, D. et al. Blood pressure is reduced and insulin sensitivity increased in glucose-intolerant, hypertensive subjects after 15 days of consuming high-polyphenol dark chocolate. J Nutr 138, 1671-1676, doi:138/9/1671 [pii] (2008).
6          Monahan, K. D. et al. Dose-dependent increases in flow-mediated dilation following acute cocoa ingestion in healthy older adults. J Appl Physiol 111, 1568-1574, doi:japplphysiol.00865.2011 [pii] 10.1152/japplphysiol.00865.2011 (2011).
7          Neukam, K., Stahl, W., Tronnier, H., Sies, H. & Heinrich, U. Consumption of flavanol-rich cocoa acutely increases microcirculation in human skin. Eur J Nutr 46, 53-56, doi:10.1007/s00394-006-0627-6 (2007).
8          Francis, S. T., Head, K., Morris, P. G. & Macdonald, I. A. The effect of flavanol-rich cocoa on the fMRI response to a cognitive task in healthy young people. J Cardiovasc Pharmacol 47 Suppl 2, S215-220, doi:00005344-200606001-00018 [pii] (2006).
9          Bayard, V., Chamorro, F., Motta, J. & Hollenberg, N. K. Does flavanol intake influence mortality from nitric oxide-dependent processes? Ischemic heart disease, stroke, diabetes mellitus, and cancer in Panama. Int J Med Sci 4, 53-58 (2007).
10        Kim, H. & Keeney, P. (-)-Epicatechin Content in Fermented and Unfermented Cocoa Beans. Journal of Food Science 49, 1090-1092 (2006).
11        Visioli, F. et al. Chocolate, lifestyle, and health. Crit Rev Food Sci Nutr 49, 299-312, doi:908817344 [pii] 10.1080/10408390802066805 (2009).