Tag Archives: research

The ten plus ten (plus a few more) commandments of how to be a successful student and scientist

*Update from June 2017: I have added a few extra ‘commandments’ from Twitter and Facebook friends at the end**

This week, three Honours students and one PhD student are starting in my lab. In the back of my mind I have always wanted to pass on my accumulated “wisdom” at the start of their research careers. I haven’t got around to it until now. Earlier this week I put the word out via Facebook and immediately got a response from an old friend that inspired me to write this. Professor Darren Griffin from the University of Kent, UK put together ten commandments for succeeding in academia.They outlined, succinctly, virtues such as persistence, imagination, strategy and just being a decent human being.

I concur and took the liberty of adding another ten – numbers 11 to 20.Many thanks to colleagues past and present including Drs Jane Loke, Nick Wong, Sara Hassan and Joe Sarsero, for their inspirations and suggestions.

11. Network, network, network

Talk to people from outside your group at the water cooler, tea room and at work functions. You will make friends, but importantly, they will be contacts who may be able to help you out some day (see Commandment 12).

12. Beg, borrow or “steal”

You never really run out of a reagent or broken piece of equipment. If you know the right people, you will be able to beg or borrow it when you need it the most. And return the favour when the boot’s on the other foot. And no, don’t steal; it just sounded like a good phrase 😉

13. Say ‘No” to plagiarism

A good idea is worth developing but good text should act as inspiration only. If you like it so much, paraphrase it. If you want to know more about plagiarism and how to check for it, see Turnitin.

14. Write early and write often

It is never too early to start writing your Honours/PhD thesis or your manuscript. Start with something simple such as Materials & Methods. Get feedback and write some more. I also strongly recommend writing the odd blog post. There is no good and bad; there is only read and widely read. Try IFLScience and The Conversation for inspiration. And even Tweeting can sharpen your writing skills.

writer
From PhD Comics http://www.phdcomics.com/comics/archive.php?comicid=333

15. Ask

Never be afraid to ask questions, whether of your supervisor, Postdoc or in a seminar. Lab heads respect and notice those who ask questions and there really aren’t any stupid questions. On the subject of seminars, try going to ones that don’t match your area of interest – you may be pleasantly surprised. If you are not, you could always play Seminar Bingo.

16. Discovering why an experiment didn’t work is almost as satisfying as getting it to work first time

Self explanatory.

17. Be honest

If you break something, always ‘fess up. You will be respected much more than if you don’t.

18. Ask not what your institute/department can do for you, ask what you can do for your institute.

Try volunteering at an institute or departmental event. If you ever go asking for funds for a project or a student group and they don’t know you from Adam, you will have less chance at success. Furthermore, volunteering is good for your health.

19. Find a good mentor apart from your supervisor

Whether a shoulder to cry on or just general advice, get yourself one of these. In fact, get 2 or 3. They can be Postdocs, lab heads, inside or outside your institute.

20. Last but not least, look after yourself

Make sure you top up regularly the three things that could save your life one day: exercise, a healthy diet and spending time being mindful (such as taking part in yoga, meditation or prayer). They all change your epigenetics for the better.

diet3
From PhD Comics: http://www.phdcomics.com/comics/archive.php?comicid=582

21.The Black Jack

Yes, you will hear that being a researcher is not a financially rewarding career and comes with little job security. Both of these can be true but following these commandments should help you be resilient and stay near the top of the pack.

Have a happy and healthy research career!

 

And a few more from Twitter buddies

  1. Your supervisor is your supervisor, not your boss – Dr Emma Beckett @synapse101
  2. Run your own race, everyone has a unique PhD experience – Dr Emma Beckett @synapse101
  3. Push the boat out as far as it will go, and always be guided by 2 Qs: Is it true, and who cares? – Clare Llewellyn‏ @Dr_C_Llewellyn
  4. Don’t rely on anyone handing you answers on a silver platter. Be curious, ask questions and seek answers beyond the ivory tower. – Nathalie Martinek‏ @Chitananda
  5. You’re LEARNING, everyone knows this, no one is judging you. Seek help as you need it. Don’t wait. – Kristal Sorby‏ @KrisDoesEcology
  6. Be self-reliant ! You’ll need to be … 😉 Belinda Weaver‏ @cloudaus
  7. Always question the ‘facts’ stated by your supervisor – Terence Pang PhD @seriouspalates
  8. ‏ Depending on the topic, read Been Goldacre’s Bad Science. Also do a timeline – Felice Jacka @FeliceJacka
  9. Get into habit of putting together a slide for each paper they read that will go into your lit review – Felice Jacka @FeliceJacka
  10. Read the article ‘A PhD is not a Nobel prize’ – Fiona J Clay (via Facebook)

 

Advertisements

Science: uncovering Nature’s secrets

It was a wet Saturday afternoon and I was sat in a dark room looking down a microscope. Then I saw it – something that no-one had ever seen before. This was my “Eureka” moment and encapsulated what it’s like being a scientist of the natural world.

The Ancient Greek Homer knew a thing or two about science; he said that it was the knowledge of nature, true for every community, as opposed to local customs and superstitions. Since that time, science has gradually uncovered more of nature’s secrets one by one.

This uncovering of secrets using science is basically detective work. We sit and watch nature for hours, days, and months. Maybe we see nothing for a long time; maybe we see more than we bargained for. And at the end, our equivalent of a defendant being found guilty is the publication of your research findings that results following peer review.

science-10For my first job interview, one of the panel asked me whether I liked to do crosswords. Funny question, I thought, but a lucky one, as I had started to learn about how to crack cryptic crosswords. I said yes and got the job. The interviewer was really asking whether I was patient and did I have the deductive thought processes to progress though a scientific investigation.

You don’t have to be a working scientist to do science. When I was a child I kept mini worm and butterfly farms and made unwritten observations every day. When I was at high school, this came in useful when I had to think of a biology project. I stuck a brick in our garden at home, monitored what I found underneath it every day and called the project “Life Under a Brick”. I won.

The scientific study of nature can take many forms – from chemistry to physics and biology. With medical research, we use all three, but mainly biology, to uncover how humans develop and age and what can go wrong and result in disease. In my area – the early origins of disease – we have found that the time spent in the womb in the most formative part of life because our bodies are at their most vulnerable. Together, those who study our DNA and the proteins that it codes for, work together with doctors who see the patients, collect their samples for study and return the favour by applying newly-discovered treatments.  

A few centuries after Homer, another ancient Greek, Archimedes, stepped into his bath, saw the water rise and realised that he had found a way to measure the volume, and hence the density of a gold crown that a friend of his had suspected wasn’t pure gold. This thought caused him to yell out “Eureka!” (“I have found it”) and promptly ran to see his friend, not realising he was naked. For scientists, the thrill of discovering new things is the same. When I had my microscope moment, I immediately ran (with my clothes on) to tell a colleague down the corridor. Today, I guess, I would have Tweeted it. There are other ways to celebrate a discovery. A colleague wanted to make her mark on the gene she discovered and called it “RING” – short for “Really Interesting New Gene”. This gene is now known to be part of a family of genes all sharing a particular characteristic in their protein called the “RING finger”. Scientists do have sense of humour too.  

Archimede_bainEureka moments can also come before the discovery. They can be the time when you put together your thoughts with those of others and come up with a hypothesis that can be tested. In a way, this was similar to Archimedes’ experience.

Back to my specific area of research. Like all my colleagues at the Murdoch Childrens Research Institute, I want my research to lead to the detection, prevention and treatment of childhood disease. Maybe it was seeing my sister cured of childhood leukaemia that inspired me to start my career in medical research? It certainly made me aware that every step of her journey, from her diagnostic blood tests, right through to her chemotherapy were all products of medical research. In the end, “breakthroughs”, such as the dramatic increase in survival for childhood leukaemia, mostly come from years of work by many researchers. I want to be among the number.

keep-calm-and-do-science-25

Why I will again be shaving my head for leukaemia research

Update, February 2015 – Bid for a solar system necklace

Before you sponsor me to shave my hair off for leukaemia research and read the blog below, a generous donation from Alistair of Bentley and Hope, Queenscliff, means that I have two (yes two) of these silver-chained solar system necklaces for people to bid for. The two necklaces will go to the people who sponsor me the two highest single amounts (and who tell me you are doing so on the sponsor site, via @DrChromo or via jeff.craig@mcri.edu ). RRP is AUD45 (GBP25). Bid away!

Necklace
The unique, limited edition silver solar system necklace made locally in Melbourne

Here is the original article:

Every year since 1998, hundreds of thousands of Australians have shaved or coloured their hair in the annual Leukaemia Foundation’s World’s Greatest Shave . Why do they do it? Why have I done it this year?

Image

My sister Sarah developed leukaemia as a teenager. I can remember, almost thirty years ago, peering through the door of my sister’s isolation ward and all I could see was her bald head. She had just been through aggressive rounds of chemotherapy and radiation and she looked so fragile. These treatments  target all rapidly dividing cells, which includes cancer cells but also ‘collateral damage’ of cells lining the gut and hair follicles. If this sounds a little like chopping your hand off to get rid of a spot on your finger, you are correct, but research is slowly making treatments more specific for cancer cells. For those of us that haven’t been there, it is impossible to describe what treatment for leukaemia feels like. The closest I have come is reading about it in Paullina Simons’ book The Girl in Times Square, in which the main character experiences something similar.

Sarah was treated successfully because of a combination of aggressive treatment and a transplant of fresh bone marrow from my brother Jim. She also survived because of previous successes in leukaemia research . Successes that have come about through years of research into finding the best way to treat and cure people with leukaemia and other blood cancers and through years of trying to discover how and why people get leukaemia. As a result, cure rates have increased annually over the past thirty years. For example, the average survival rate for all types of leukaemia  has risen from 12% in the early 1970s to 44% in 2005-2009.

However, in recent years, the success rate for obtaining research funding from the Australian government has generally decreased, causing leukaemia researchers to look to other sources of funding. This is where the Leukaemia Foundation and other such organisations around the world such as the Leukaemia & Lymphoma Research in the UK have helped to fill this gap.

Importantly,  the Leukaemia Foundation also provides financial support for families of those suffering from leukaemia, which can involve extensive travel to hospitals.

Image
Many women also take part

It’s always hard asking for money, as anyone who’s ever had to rattle a tin can tell you. In the case of the World’s Greatest Shave, it helps that a coloured or bald head can act as a ‘selling point’. Reactions from others are manifold, from people who look the other way to those who donate and engage. OK, many already give to their own favourite charity; I understand that. But I like the engagers; they make life interesting.  This year, one sponsored me for a mohawk haircut then another to get everything shaved off. No problem.

Image
Yes, even George Bush shaved for leukaemia

So that’s why some people show solidarity with those living with blood cancers such as leukaemia and this is why I have chosen to do so this year. In remembrance of someone who, through the benefits of leukaemia research, gained an extra twenty nine years of a rich and fulfilling life, including marrying and giving birth, and all the time staying positive.

Image
Sarah with son Matthew

Postscript: It’s not too late to donate donate

Epigenetics: from Greeks to geeks and leaks

Epigenetics, a word that seems to have stirred up disagreement between scientists for so long, is currently experiencing a rebirth and may have applications for the prevention of many different human diseases.

Starting at the beginning, the word ‘epigenesis’ was coined by the Greek philosopher Aristotle over 2,200 years ago because he was sick of the theory current at the time that we all start out as microscopic versions of our adult selves. He believed that all complex creatures grow from a simple fertilised egg or seed though to a mature organism through stages of development and differentiation: out of the simple comes the complex. This idea is widely accepted as true today.

Aristotle Jump forward just over 2,100 years and we come across a man with possibly the longest name in scientific history: Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck. Let’s just call him Lamarck. He proposed that the way an organism adapted to its environment would somehow be passed down the generations. Two generations later, Charles Darwin liked Lamarck’s idea and went further, proposing an idea of his own – ‘gemmules’ – minute granules that are ‘thrown off’ by our tissues. Gemmules, he proposed, could multiply and travel to our eggs or sperm sex cells through which they could be passed on to future generations.

lamarckDarwin

 Step forward another 75 years and followers of Darwin thought they knew it all – evolution occurs by natural selection through random changes in our DNA that have enabled us evolve and adapt over millennia. And that’s that. Then Conrad ‘Hal’ Waddington came along and stirred things up by turning ‘epigenesis’ to ‘epigenetics’, which he used to describe the way in which our genes interact with their environment to make us what we are. In this sense, epigenetics means literally ‘the factors on top of our genes’. Waddington was a man before his time.  Between then and now, arguments have raged about whether nature (genes) or nurture (environment) are more likely to influence our health and behaviour. The truth, exemplified by a recent book by Matt Ridley entitled ‘Nature via Nurture: Genes, experience and what makes us human’ is, like Waddington suggested, a combination of the two.

waddington2Today, epigenetics now describes the set of small molecules that sit ‘on top of our genes’ and choreograph when and how they act. This in turn directs our development from the zygote to the grave. Epigenetic molecules can be encoded by our DNA and they can be added or removed in response to our environment. Nature via nurture. Another way of looking at it is that in the symphony of life, epigenetic molecules are the musicians that play the genes as instruments and together they make up a huge orchestra of thousands of working genes. Alone, genes are silent; they need musicians to play them.

orchestraHowever, controversy still exists about what we can actually label as ‘epigenetic’. Some say that epigenetic changes need to be long-term, lasting for many cell generations, while others have shown that some epigenetic marks can change within a single cell’s lifetime. Some geeks say that the epigenetics should be tightly linked with its molecular definition and others that it should be loosely applied to how an organism adapts to its environment.

Arguments aside, epigenetic changes are most likely lie behind a recently recognised phenomenon call the Developmental Origins of Health and Disease. Known in short as ‘DOHaD’, the idea is that our experiences in the womb and early childhood can ‘program’ our future health. It is likely that epigenetics is part of the programming language involved. An oft-cited example of this in humans is that sixty-year-olds who were in their mother’s womb at the time of the Dutch Famine in the Second World War, not only had poorer heart health than their siblings but also had an epigenetic imprint of this experience stamped on a handful of their genes.

Animal studies reveal a similar story. In rats, a mother’s licking and grooming behaviour influenced subsequent stress levels in the offspring, mediated by an epigenetic change to a gene involved in stress response. Newborn rat pups whose mothers spend time licking and grooming them grow into calmer adults, whilst pups who receive little maternal attention tended to grow into more anxious adults. Grooming altered the pattern of epigenetic marks, which in turn altered gene activity of the stress regulator gene. Critically, when neglected rats were treated with a drug that alters these epigenetic marks, both their anxiety and the accompanying epigenetic changes could be reversed.

Such findings have huge implications for medicine, the largest being that if we can reliably detect epigenetic changes that in early childhood signal a risk for diseases such as cancer, heart disease, autism or diabetes, we can start to prevent these diseases by intervening early. This is the area I find most exciting, but we have a long way to go to the clinic for most of these. However, we can take heart from cancer research, which has already supplied a small number of epigenetic tests that can predict severity or response to treatment in some cancers.

Finally, it seems that in principle, Lamarck and Darwin may also have been on the right track after all. There is accumulating evidence that the environment our mothers and even our fathers encountered before we were a twinkling in their eye may be passed onto us in the form of a risk for conditions such as obesity, diabetes or anxiety. Studies of a remote Swedish village have shown that food abundance in grandparents correlate with the health of their grandchildren. Another found that sons of men who smoked just before puberty were more likely to become obese. However, neither of these has yet been linked with an epigenetic change. Could it be that epigenetic marks can ‘leak though’ to us via eggs and sperm? There is recent evidence that this can happen in animals that has people in some very high places invoking Lamarck.

NN lamarckWe still need to discover how such factors could pass into the eggs and sperm and how these changes would survive two major life stages at which the epigenetic ‘whiteboard’ is wiped almost clean. This usually occurs just after fertilisation when a newly-formed zygote wants to shed its sexual origins and become a new human being and when the opposite happens, when a group of cells early on in development want to put on the sexual cloak and become eggs and sperm. However, I said ‘almost clean’, which leaves the door open in principle for these barriers to be breached. An attractive, emerging idea borrowed originally from plants is that small epigenetic molecules, in form of the “messenger” genetic material – ribonucleic acid (RNA) – can be shuttled into eggs or sperm and be inherited by the next generation, and survive the epigenetic cleaning. Watch this space.

 

Epigenetics resources

Web sites

Epigenetics Genetic Science Learning Center, University of Utah

The Nova documentary on epigenetics originally aired in 2007

Instant expert: epigenetics’ from New Scientist magazine

Epigenetics explained‘ by Scientific American

Awesome animations and short documentaries

The epigenome at a glance‘from the Epigenetics Genetic Science Learning Center, University of Utah (01:46)

Lick your rats‘ interactive game from the Epigenetics Genetic Science Learning Center, University of Utah (takes about 5 mins to lick a couple of rats)

Insights from identical twins‘ from the Epigenetics Genetic Science Learning Center, University of Utah (04:41)

‘X inactivation and Epigenetics’ by Etsuko Uno and Drew Berry from WEHI TV (11:04)

Epigenetics Overview‘ by Cell Signaling Technologies (02:14)

Epigenetics: what makes us who we are?‘ from Begin before Birth (04:10)

What happens in the womb can last a lifetime‘ from Begin before Birth (02:24)

Epigenetics‘ – a short documentary from the Science Show on DNATube (09:26)

Resverlogix movie about epigenetic drug RVX-208 (03:32)

Charlie’s Story – can we improve crime rates by supporting vulnerable women during pregnancy and the first 2 years of their baby’s life?‘ from Begin before Birth

Articles – basic

Epigenetics’ by Brona McVittie (2006)

‘Evolution, Epigenetics, and Maternal Nutrition’ by Asim K. Duttaroy (2006)

‘Why Your DNA isn’t your destiny’ from Time Magazine (2010)

Epigenetics: promising field delivers (2013)

Articles aimed more at undergraduates

Epigenetics: the sins of the father’ from Nature magazine (2006)

‘Taking a chance on epigenetics’ (2014)

Books

epigenetics revolutionorigins2genome generationidenitcally different

Further learning

Marnie Blewitt’s Coursera online course on epigenetics

Epigenetics 201: the four Rs

Can we compare scientists to rock stars?

Yesterday I was promoted to the level of Honorary Associate Professor and for some reason it got me thinking about the parallels between scientists and rock stars.

You can’t see it? Let me explain. Most musicians start out by learning an instrument, by training their voices and by learning about music in general; most scientists learn train within in a specific area of science while learning about the broader field. A musician may join a band early on, just as a scientist will join a lab pre- and post-PhD. Most musicians start out writing and releasing songs without recognition; some may be classics, but most are average quality. Most scientists start out by writing scientific papers; some may be citation classics but some wallow in obscurity for years garnering single figure citations. And maybe being awarded a platinum disc for selling a million records is like reaching 1,000 citations?

However, we all know that rare case of a musician or scientist seemingly coming out of nowhere and zooming meteorically up the charts with their first release/paper.  Often such people are lauded and sometimes, hype creeps in. Some may continue at that level, others crash and burn.

What other parallels are there? Is finding a good music manager akin to finding a good lab head or mentor? Do young scientists ever get ripped off by a lab head “borrowing” their ideas. You bet, although a great synergy between a mentor/lab head and young Postdoctoral researcher can really bolster their career and help them navigate “The Business”.

How about salary? Well, surprisingly there are parallels there too. Both musicians and scientists are mainly in it for the love of it and often settle for a pittance and on rare occasions may be financially rewarded for performance. When they make it big and play large stadiums or  lecture halls, they may get their fares and hotel paid for. I even once saw a scientist trash their hotel room.

Recognition? Here are where things start to get a little different. Rock stars are recognised wherever they go by a broad section of the public. Top scientists get recognised only at their specialised conferences. Very rarely, your Sir Richard Dawkins or your Baroness Greenfield will be recognised by many, but even then, at levels much lower than rock stars or sports players.

Finally and almost inevitably, some rock stars and scientists drop out of the field because of disillusionment, burn-out or lack of funds. Coincidentally, both seem to end up rather unexpectedly as school teachers. But we all know the true heroes of science – the Mick Jaggers and the Leonard Cohens of the field. They have triumphed despite rough beginnings and bad living. Let us celebrate the whole span of the scientific career and aspire to be as they are, for one day, someone may just stop you in the street and say, “I know you, you’re… that old science guy/gal”.