My #postacstory

Leaving research was a little bit like leaving South Africa. It was an ending without a  beginning, but still rather exciting. The fact that it wasn't entirely my decision did cause some anxiety, but this was outweighed by the knowledge that I had to be with my Mother during the last few weeks of her life.

Three years on, and I was recently asked to participate in a survey about what research staff do next. I surprised myself with the the answers I gave to the questions. Surprised because although I had been out of research and science, the skills I developed as an academic were still very much in use.

Scientific research is not just about pipettes, and buffers, extractions and electrophoresis, endless gels and PCRs, number crunching and statistics. Research is about teaching, communication, critical thinking, independent working, problem solving and time management. Scientists are project managers, networkers, innovators and leaders. And these are all valuable transferable skills.

So, far from feeling let down about not being in research, I felt uplifted after completing the survey. I had insight, and it has given me confidence that my role as practice manager is worthwhile, intellectual and most importantly, it has a future.

My academic story lasted 22 years. My post academic story is just 3 years old. Sometimes, it takes a prod of conscience to appreciate the gifts we have.

If you want to find out more, click here.

Heart health takes more than just a donation to the British Heart Foundation

I support the British Heart Foundation (BHF). They have funded research projects I have worked on, and, locally, they provide vital equipment in our local hospitals. Their organisational size and the research areas they fund mean that they are an extremely powerful charity, with a high public profile. Being involved in small, local charities I know how hard it is to engage with donors, to get people to part with their pounds for a charitable cause. So I'm not surprised by the increase in ever more 'in your face' fundraising. It just doesn't sit well with me.

And so it was, that when I watched the latest BHF appeal on inherited heart conditions on TV, I felt deeply disappointed. Not because their appeal isn't worthy. Of course it is. It is simply misleading, causes worry, and doesn't say how to get help if you are worried. It's all about getting the donation.

Your doctor will tell you that these heart conditions are complex. There are several causes, more than one gene, and certainly more than one inherited condition. I would urge you to visit the C-R-Y website for a simple outline of sudden cardiac death, one of the conditions specifically referred to in the BHF appeal. A simple ECG screening test can detect if there is a problem.

Yes, do donate to research. Yes, the BHF funds world-class research and researchers are breaking new ground all the time.

But please, also understand what you can do for yourself and your family NOW, TODAY. Be informed. Look after your heart.

Gross Anatomy: the death of an inspiration

I was saddened to read of the death of Professor Phillip Valentine Tobias, one of the iconic South African academics of our time. He inspired me, and gave me a life-long love of science and the human body. How many young scientists can say that about their teachers today? 

RIP PVT.

This was first published on The Camel's Hump in April 2012, but it seems appropriate to reproduce it here as my tribute to Professor Tobias.

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Gross Anatomy

POSTED BY SHACKLEFORDLB ⋅ APRIL 18, 2012 ⋅ 6 COMMENTS

FILED UNDER  ANATOMY, DISSECTION, EDUCATION, MEDICINE, RESEARCH, SCIENCE

I went to Medical School in 1987. It was an incredible experience, crammed full of learning from inspirational Professors at the peak of their careers. My stand-out memory is the first day of Gross Anatomy. Faced with dozens of cadavers in shrouds, fresh-faced students in crisp, clean white coats, and that smell – I couldn’t wait to get started. Such a privilege.

Each precious body had been donated to medical research, to help train doctors, nurses and physiotherapists. We stood next to our allocated body, four students in a group, and recited a modified Hippocratic Oath. We were to dissect the body over the academic year, 565 hours of dissection, in detail, covering all organ systems, blood vessels, nerves and the brain. Our bible for the year was Man’s Anatomy by Tobias and Arnold, in three volumes. Professor Tobias and Professor Arnold were the big beasts of Anatomy. We were in awe of them. They were known affectionately as PVT and JCA (behind their backs of course)!

Getting started was a hand-trembling affair, guided by this illustration. Skin preserved in embalming fluid is very tough. But once you’re in, you’re in – and the delights of the human body were ours to explore. Over the weeks and months, we committed to memory all the arteries, veins, nerves and bones (oh, my poor parents had that box of bones in their living room); using mnemonics to remember the long lists. For example, Peter And Paul Masturbated So Much Their Balls Shrank refers to the branches of one of the thoracic arteries (I wish I could remember which one)! I can remember, though, that this one refers to the twelve cranial nerves: Oh Oh Oh To Touch And Feel A Girl’s Vagina Very Happily (or something very like it). The point is, we were drunk on anatomy for that year. We were walking encyclopaedia of lists of body parts, our text books were marked in wax pencil (I still have one I used in 1987), and nobody would share the lift with us because the smell permeated our clothes and hair. We knew it and we didn’t care. We were doing something that not many people ever get to do. It would shape our lives in the future. Some would go on to be world class surgeons, some physicians, sports scientists, pharmacists. I decided on a career in research.

Who knows how a career will turn out. I didn’t even do Science at school. I was expected to study Languages at University. I’m grateful to a Biology teacher for showing me something different, and changing my life. She asked me to help her clear out the cupboard in the lab. What we didn’t find in there. And lurking at the back, in a dark jar, was the most gorgeous pig foetus. We changed the preserving fluid, to reveal the tiny, perfect animal; when was he put in there, kept for me to find? I was hooked.

And so, standing in the dissection hall, several years later, in the basement at Medical School, I knew I was in the right place. I grasped the scalpel with both hands and made the first cut. Nine months later, the Technician was standing over the cadaver we had been working on. It approaching the final Lesson – the brain. He used a tiny, whirring saw to remove the cranium. He revealed a clean, shiny brain in situ. In order to complete the study, we had to remove the brain, with all the cranial nerves in tact. I had the smallest hands and I put them on either side of the brain, inside the skull. I tugged gently and felt around the base of the brain, to free the nerves from their restraints. A little more tugging, and I had the brain in my hands. We prepared the dissection and made 1cm slices through the brain, sectioning it in cross-section. I have never forgotten that moment. And neither will countless other medical students. That brain, sectioned, preserved and displayed can still be seen in the Anatomy Museum at Wits Medical School.

Gross anatomy? I don’t think so. Stunning, wondrous anatomy, is more like it.

Humane medical research

Finally, some common sense, good science news. The Dr Hadwen Trust for human research has announced it will be sponsoring research projects in cardiovascular disease, cancer and mental health. These projects will aim to reduce the number of animals used in medical research. I have previously written about the use of animals in science, and whilst I support well regulated medical science using animals, it will be a huge break-through to move away from animal models.

You can read a summary of the announcement at the Talkhealth Partnership blog.

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Ethics and consent in research

In general terms, we expect that people who ask our permission, who require our consent, will have the morals and ethics to respect our wishes. Recently however, I have seen a few examples where frankly the people concerned have the morals of a snake. I’ll say no more on that, but it prompted me to think more widely about these terms; ethics, morals, consent, permission.

In my own field of life science research, no research may be undertaken without a prior favourable ethical opinion. It used be ethical approval, which implied that a peer-reviewed process had taken place, and an important group of senior people had carefully considered the application and deemed it ethical to conduct the research. Now, it simply means that a committee has spent a few minutes of the agenda discussing the merits of the work, and no responsibility or blame can be put their way should the experiment turn out not to be ethical, either in its design or in the outcomes. A matter of semantics, perhaps, but important none-the-less.

Important because many of the subjects for my research are human volunteers who trust us, the scientists, to do the right thing. Now, I don’t want to put anyone off contributing to a research project; we do still need to do research using human subjects. But I do want to point out that the administration of the rules is not what it should be. To my knowledge, there is no enforcement of the consent. I have seen inspections. I have seen paper records. I know that biological material collected years ago is still lurking in the bottom of freezers in research laboratories. Consents and research records belonging to PhD students who have long-since moved on lingering on dusty bookshelves in study rooms. There is almost no way of knowing which material should be destroyed, ethical opinion and consents having long-ago expired. And that’s just in small university laboratories. Surely in large pharmaceutical and biotech organisations the record keeping and ‘policing’ of the research consents is more robust?

Well, yes it is, and that results in a different problem. Large organisations who embark on long term research require consent from participants to be able to follow up on the outcomes of the research over a very long period of time, decades in some cases. With changes in technology, particularly in genetic research, where even five years ago the cost of this work would have prohibited it, that is no longer the case. Cost are down, through-put is up. In short, scientists can analyse more data, more quickly, at much lower costs. If the material already exists, if the methodologies are the same, there are also no start-up costs. Results could be coming within days. That means that if you volunteered ten years ago, donated a tube of your blood, approximately 10ml, and gave scientists permission to keep cells, plasma and DNA, they will still have all those bits of you in storage and on file.

I mentioned genetic research, for this is where I am most concerned. When you donated that small amount of blood all those years ago, you were probably young, in your twenties (most lab volunteers are), and too young to be showing any sign of disease. Your parents would have been young too; too young in most cases to have cancer or heart disease. You wouldn’t yet have had children either. And now, what if you are told that scientists have just worked out that your DNA shows a variation recently found to be associated with cancer – would you want to know? What would you do about it? Cancer cannot be treated if it hasn’t formed a tumour yet. This is the proposal of researchers, owners of these so-called ‘bio banks’, because original research is too expensive and largely unfunded. Would you still give your consent for your material to be used?

I believe that material collected more than five years ago should either be destroyed or re-consented. Yes, that will cost money, but it keeps science honest and transparent. It makes sure that scientists’ personal ethics and morals are not tested. It introduces a check that the material we think is there, has been stored correctly and will be useful in the research. Very often, biological material degrades over time and is useless. Better then to destroy it.

And finally, I must reveal here that I never allowed my cells or DNA to be stored. I have never used my own blood, cells or DNA in any experiment I have conducted. I do not want to know that I have a particular genetic variation. Until scientists are clever enough to re-program my genetic material, there are some things not worth knowing. Of course, there are some conditions for which there are extremely good genetic tests, and with the correct counselling, it is very helpful to do these tests. But these tests have made the transition from research to clinical application. We can’t change what has gone before, but we can make sure that we are informed about the future. Research must be done, human biological material must be used for research wherever possible. Don’t take ethics, morals, consent and permission for granted in science.

Previously published at The Camel's Hump.
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Not sitting on the fence

Animal experimentation is always a sensitive subject, whichever side of the fence you sit. When I started out in medical research, almost twenty-three years ago, animals were used in all sorts of experiments, from radical surgical therapies to shampoo testing.

I personally witnessed some horrors in the name of science. It was fascinating stuff though, particularly the work done on developing novel surgical strategies for strokes, heart attacks and bone regeneration after motor vehicle accidents. I can’t say that I enjoyed seeing rabbits being used to test shampoo or make-up, and I’m happy that this rarely happens these days. I fully support campaigns against animal testing.

But, I also support those pioneering scientists who over the years have used animals big and small to test their hypotheses and make huge strides in science and medicine.

For example, life-saving surgery performed daily in many hospitals, putting a stent in a coronary artery, a main blood vessel supplying the heart, following a heart attack, would not have been developed if not tried in animals first. This surgery saves hundreds of lives every year. People who go on to live very productive lives after heart attack. Surely this is a good thing?

More recently, I have seen groundbreaking work carried out in genetically modified mice. These mice have been bred without a particular receptor (simply put, this is a grabber for chemicals such as drugs), which is believed to be key in addiction. This work describes how people are genetically pre-disposed to becoming addicted to cocaine or heroin. And it will help to provide strategies for treating a lost generation drug of addicts across Europe. The cost benefit of this treatment runs to millions of Euro’s.*

Photo caption : These cells are from a cell line derived from a human cancer patient, who died some time ago, but we have immortalised their cells to keep them going for research. They mimic human white blood cells in vitro.
Lesley Beeton (2004)

There is sometimes an argument for using alternatives to animal testing. I always prefer to use non-animal experiments. In fact, I have not worked with animals in twenty years, preferring instead to recruit human volunteers for my research. This is more difficult than it sounds. It often involves drawing repeated small amounts of blood from which I prepare DNA, the genetic material of life. And volunteers are understandably concerned about what scientists might do with that information. Consent is not required for animal experiments.

But ethics is required for types of experimentation. Morals and standards on ethics are required at all times. Public scrutiny is key to this as well, which is why I think it is important to talk openly about the work we do on animals. It is not sufficient to say that a committee of academics and vets approved the work, therefore it’s OK to do it. No, scientists must be called to account at all times.

The scientists who do this work conduct their experiments under the strictest conditions and scrutiny. Far from being hidden away, animal experimentation is a transparent necessity of science. The public has the right to know what experiments are being done in their name.

The problem is that there are some people who are so passionate about not using animals for science and research, that they endanger the lives of others. And that means that we cannot always talk about it openly. It’s a conundrum to which I don’t have a solution, just a plea to both sides. Maintain a dialogue, keep an open mind. Be respectful of each other. Scientists, especially in the UK, who use animals in their research are not evil people, taking over the world. I admit, there are less scrupulous researchers in other countries, but here in the UK, animal-lovers and concerned campaigners should be re-assured that the work is done with the very best intentions, in the best facilities, under the tightest regulations and conditions.

The sad fact is, that animal models are still needed for progress in many human diseases. Whilst it is true that whole animals such as mice or rabbits do not adequately represent the whole body situation in human beings, animal organ systems and cells are extremely useful for science and research. Non-animal models such as immortalized cell lines derived from humans, can only answer one question at a time, because these cells are taken outside the body and are not subjected to the same complex environment.

My mother died of cancer. She died from a form of lung cancer, for which there is no cure. She was sixty-six years old. She was too young to die. If scientists wanted to test a drug on animals, or design an experiment using animals to better understand the disease, I would be all for it. Wouldn’t you?

*Note: please understand that I cannot describe experiments in detail or identify scientists here.

This post was first published at The Camel's Hump.

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Accuracy and precision

This is an important distinction for scientists in all fields to understand. One of the first things I tell the undergraduate students, is to be precise in your experiments and accurate in your measurements. The definition of accuracy is 'the condition or quality of being true, correct, or exact;freedom from error or defect; precision or exactness;correctness.' Precision is 'characterised by or having a high degree of exactness.' (Collins English Dictionary – Complete and Unabridged © HarperCollins Publishers 1991, 1994, 1998, 2000, 2003).

For example, if the experiment is to measure the number of times a subject will jump if tapped on the knee for one minute, the experiment should be described precisely so that anyone wishing to reproduce the findings will carry it out in exactly the same way. The measurements, that is, the count of the number of times the subject will jump, must be accurate. If the subject jumps eleven times but the scientist records it as approximately ten times, that is not accurate.

I have simplified the example here to demonstrate the principle, but it matters in real life too. When making jam or confectionary, you need an accurate thermometer. Raymond Blanc says you need to weigh your egg whites precisely, or the macaroons will be pah!

And in a court of law, the barrister will ask you to be precise about your eye witness account, so that the court will be able to make an accurate assessment of the case.

So you see, accuracy and precision is more than just a phrase used by the boys and girls in white coats. It underpins many aspects of our modern lives, try it for yourself.

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What came first - Bioinformatics or Molecular Biology?

In this age of digital everything, it's easy to think that bioinformatics is a new discipline in biological science. It's trendy and uses the latest technologies to design, implement and analyse experiments. Molecular biology, on the other hand, was in use decades ago by the pioneers of biological research. Polyacrylamide gel electrophoresis was all the rage back then!

But what today's scientists might not realise is the groundwork for bioinformatics as we know it, was done by those pioneers. Those of us who learned to read a DNA sequence by hand and analysed polymorphisms by eye.

I fully appreciate the new skill set required by bioinformaticians, but feel a little sad that something is lost in the translation. There is a gap in the knowledge, of understanding how something was first described. That's progress for you!


To read more about science and the love of knowledge, click here.

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Comment : apartheid era chemical and biological warfare programme

I was twenty-two and worked as a life science rep in Johannesburg and Pretoria at the time. One of my customers was the now infamous Roodeplaat Research Laboratories. In the middle of nowhere, it wasn't the kind of place you could just drop in on. Over a couple of years, I built up a relationship with some of the workers there and had a tour around the facilities. Without knowing exactly what they were up to, what I saw was very upsetting. There were rumours of course, and reps were security checked. But then, that was common place at many labs at that time. I needed a security pass for the atomic energy corporation and the vaccine labs too. The common link between these organisations was that they were run by the Afrikaner elite, not government but definitely government sanctioned.

That's not to say that the science wasn't good. On the contrary, the science was exceptional, and produced quality research. Many of these scientists have since left South Africa and have prestigious careers internationally.

I once had occasion to meet Dr Wouter Basson. He was charming, quiet but powerful. He is a brilliant scientist. No surprise then that he is now a cardiologist. His past, however, is coming back to haunt him. And twenty years on, the dark secrets are out - again. It was talked about in certain circles back then, but somewhat hushed up. 

I watch with interest how the South African media will handle it this time. That this research was justified by the South African government of the time still makes me sick. That the results of the research is still being used by governments against their own people is more sickening.

Another reminder that in science the end doesn't always justify the means, and that all scientists have a duty to carefully consider how their research will be used.

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For the love of knowledge

Photo credit : Yousuf Karsh http://www.karsh.org/

Nelson Mandela said "Education is the most powerful weapon which you can use to change the world".


The St Stithian Foundation was set up to provide support for a Saturday school for pupils struggling to find a way complete their school education. It also supports teacher training. The Thandulwazi Trust is a Maths and Science Academy in Johannesburg, South Africa.


We are pleased to support this initiative, and yesterday we received a short film on DVD, following the success of three amazing people who attended Thandulwazi. It brought me to tears, just hearing their stories, and seeing how they want to use the education they have been given.


I am often asked why I left South Africa, and 16 years on, I honestly don't remember the exact reason. I know my husband and I were fortunate to receive an excellent education in South Africa and attended University there too. We wanted to be citizens of the world, use our education where it was needed. I'm pleased to say that for the most part, we have been successful in this. No matter what happens in life, nobody can take away your education.


Thandulwazi means for the love of knowledge. Wouldn't it be great if all pupils could go to school with those words in their hearts? Instead, I still see students in their final year of BSc working so hard to complete all the coursework, study for exams and write a dissertation, that they seem to have forgotten that they chose Science for the love of knowledge. They came to university full of excitement and promise and over the three years have been worn down to just wanting to get a 2:1. Some, of course, will always be enthusiastic and will want to know more than the syllabus dictates. They are challenging and fascinating people.


I had a brief exchange with a blogger from Nature News last week about the challenges facing UK universities in producing biomedical scientists who are equipped to face the changing environment of life science research. We have only just got them up to speed with basic molecular biology techniques and now the technology companies are telling us we need to train bioinformaticians. These are scientists who will spend their post doc jobs sitting at a computer, nowhere near a lab, analysing millions of digital data points. Where's the love in that?

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Publish or perish, then retract?

2011 saw some incredible breakthroughs in science and medicine, from the colour of meteorites to the secrets of ageing (in mice at least). It also saw two low points in the reporting of science. Sadly, the pressure to publish is a constant threat to researchers, and it can mean that research questions may not be stringently tested. The peer-review process of publication in reputable journals should be able to put the data through the ringer, but sometimes the work is so specialist it can be difficult for outsiders to follow.

My own research group is in just this position. We have done a good piece of work, which we know answers our research question, but which is so complicated in its analysis that we are finding it difficult to describe in a manuscript. The techniques used in our work are common place, but we adopted a novel method of extracting the data in order to account for the biological diversity of the region of genomic DNA we are interested in. The manuscript will almost certainly be returned for clarification. Indeed, our raw data is currently being moderated by clever scientists at Miamexpress. They have asked us some very in-depth questions about our experiments, which we must endeavour to answer before we submit our manuscript.

And the research groups who had to retract their manuscripts at the end of last year will have been just as thorough in their preparation. Unfortunately, that's not enough. Much of the data produced is digital, that is, there is no physical picture of the result for us to examine. And the nature of digital data is that it can be amended. I'm not saying that is what happened but if the data cannot be reproduced independently then questions will be raised.

The research papers in question at this time cover two exciting outcomes. The first is the finding that a murine leukaemia (or related) virus (MLV) was detected in patients with chronic fatigue syndrome. But, as the number of samples was limited and the data not reproducible, the authors had no choice but to retract their publication. That's not to say they aren't right. They simply need to find another way to prove it to their peers.

The second paper is arguably more topical, on stem cell lineage, published in the journal Blood. The researchers acknowledge that some of the data may not reflect the published data analysis. This paper, was published in 2008 and cited 13 times in other papers, so it may be argued that although there were errors in assembling the manuscript for publication, the authors stand by their findings and the interpretation thereof.

So, where does that leave the rest of us, struggling through to try and publish our blood, sweat and tears? I think it leaves us a little tainted in the public eye, and we must work harder to make sure our science stands up to rigorous scrutiny by our peers. As research funding decreases, the strongest research questions and protocols will rise to the top. Let's hope that exciting science does not drop away altogether.

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Painless PhD?

I believe it can be done. You need a solid research question, an open mind and an engaging supervisor. The first two requirements are easy - they're down to the PhD student. Finding an engaging supervisor is far more difficult. 

Many students choose the project first then try to fit in with the supervisor. Big mistake, but oh so easily done, when funding for studentships is fiercely competitive. How can you say no, that one's not for me.

A good student will always be offered more than one studentship, and that means you can interview the supervisors too. Remember, supervisors are human. Could that dismissive attitude be because her son is ill? Or needs picking up from school? Perhaps talk of money is uncomfortable. Academics aren't made of money either, so be realistic with your expectations.

But what if you aren't offered a selection of studentships? How do you make the best of the bad bunch? This takes an enormous amount of skill, time and effort. Managing your supervisor is the most important skill you need to master in the first three months of your PhD. 

Think before you go to see your supervisor. Can you solve the problem on your own? Do you really need their input at this stage? And when you do go, make sure you have critically analysed the problem, present it clearly with your thoughts on how to resolve issues. Be flexible with your availability too. Academic supervisors have all kinds of pressure on them - research, teaching, admin, not to mention grant writing.

And if it all goes wrong, it doesn't have to be the end of the line. Be open with yourself about what the problems are. Sometimes talking things over with a mentor or a colleague will show you that there is a way forward. Sometimes, finding another project is the only way. (I found this website useful, too).


But this doesn't have to be negative. Admitting you have made a mistake takes courage. Moving on and making sure you don't make the same the mistake twice takes strength of character. And most PhD students have both these attributes in buckets. Attaining a painless PhD takes a thick skin, determination, clear thought, fast reading and lots of fun. Good luck!

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Researchers say ...

How often do you hear the newsreader say those words at the beginning of a news item? Researchers say a lot of things. Sometimes, there are great breakthroughs to tell us about, sometimes its a non-story, or a re-hashed story, an attempt to re-ignite awareness, all part of the games they play to get research projects funded.

I am quite often amazed that some of these projects are funded at all; surely studies into gorilla behaviour is not as important as research into cancer? Perhaps that's a bad example, as cancer research suffers no shortage of funding. OK, what about research announced today that there is a large shallow lake on Jupiter's moon? Certainly, this is interesting research but will it enhance human life on earth today?

I must declare a conflict of interest here. I am an out-of-work scientist. The project I was employed on was a large collaboration across Europe, looking for novel gene variants which could be shown to increase the risk of cardiovascular disease, such as heart attack and stroke. The funding ended in September and there have been no new calls to fund this work. So, not only am I out of work, but three years of promising data from highly technical and skilled work will never find it's way to the public. And hearing the words 'researchers say' in relation to the prevention and cure of cardiovascular disease is a long way off.

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