To ask or not to ask? What is the question? A guide for asking questions at the end of a scientific talk

Author’s note: this blog is aimed at junior research scientists, although it can apply to anyone in any type of seminar, class or lecture.

Tense, nervous headache at the end of a seminar? Are you afraid to ask a question? Do you think it may make you look silly? You are not alone. But fear not.

Q2

Firstly, speakers want questions; it makes their talk or journey worthwhile and questions help them hone their talk for next time and may even inspire a new research direction. You will also be given ‘stored credit’ by your supervisor/Group leader/Department Head for asking a question; it will shown that you can think and engage – two qualities that will be recognised as essential for a career in research. Kudos in a competitive market will give you the edge.
So, what kind of question can you ask? Well, first let’s build up to that moment. For a visiting speaker, find out a little bit about their work beforehand. Read the talk abstract or their web site blurb. This is how the professionals do it and it’s not rocket science (unless the talk is on rocket science).

Secondly, take notes during the talk. It crystallizes what the speaker has said and it’s a natural way to form questions. Write questions down as you think of them. I usually start a line of notes with a ‘Q’ to make it easier to find at the end of the talk. During the talk, rewrite the question if necessary and rehearse it in your mind and don’t be afraid to read it from your notes. Tweeting instead of note-taking is also a way to formulate questions. If others are tweeting at the same talk, then you can even run a potential question past them.

Q3

Still no idea for a question? Once you consider the variety of possible questions below, you will never lack a question again.

The honest question. Maybe the speaker didn’t explain themselves properly (consider yourself a typical audience member). Maybe they forgot something or had their facts mixed up? Ask the question you want to know the answer to.

The knowledgeable question. A variation of the ‘honest question.’ If this is your field, you are starting at an advantage; you will be excited with the topic being presented and questions are much more likely to come to you.

The technical question. Ever been frustrated by not enough information? ‘What did the error bars on that graph signify?”, “What were the units on the X axis?

The staple question. This is the best category as this type of question requires no knowledge of the speaker’s field, and doesn’t matter if you haven’t been paying attention. Typical questions are:
“What are the strengths/limitations of the method you used?“
“Could this technique be applied to the study of….?”
“How do your findings compare with others in the field”
“So far, what kind of reception has your work had in the field/by scientific community in general/by the general public?”
“I’d be glad to know about the evolution of your thinking on this topic. Who do you see as the people/papers that inspired you in the first place?”
“Do you have any unanswered research questions you still want to address?”
“Would your method be suitable for another application/organism”?

The “please explain” question. Did the speaker say that they chose not to go down a particular avenue or did they say that a certain technique/topic was too difficult? If so, ask why. A speaker may say that they don’t have time to cover a particular aspect of their work. In this case, they often have some secretly-prepared slides after the end of the talk that they would be most delighted to share with the audience, thanks to you.

Q4

Finally, the elephant in the room: the “silly question”. Well, it may sound clichéd, but there is no such thing as a silly question. If you really think your question is silly, frame it in one of the following ways:
1. “I may have missed something but…?”
2. “This may sound like a naïve question but…?”
3. “Can you please clarify what you mean by…?”
4. “Can you explain a little on what you said about…”?
5. “I am thinking on the run here, but…?”
6. “I am not familiar with this area, but…?”

Some final tips: do be polite to the speaker (“that was a great talk…”); don’t ask a question that simply demonstrates your superior knowledge, don’t confront your speaker, don’t make a statement instead of asking a question (although a comment together with a question is sometimes acceptable).

Armed with this toolkit, there will be no stopping you. Good luck!

 

Sources
• Personal experience
“How can I ask better questions in seminars?” from MetaFilter
Ask questions like a pro: questions you can ask at any scientific seminar
• “Guidelines for the Preparation of Scientific Presentations”

 

 

 

 

 

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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?

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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.

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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.

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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.

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Sarah with son Matthew

Postscript: It’s not too late to donate donate

Epigenetics 201: the four ‘R’s

Want to know a little more about epigenetic marks; what they are and how they come about? Read on.

Epigenetic marks are all small molecules, some examples being the methyl group (-CH3) and the acetyl group (-COH3). Many different marks can bind to histones – the proteins that are responsible for packaging DNA into the two metres of genetic information found in every nucleus. Histones are shaped like commas and most epigenetic marks bind to the tail of the comma. However, only a single mark – the methyl group – binds to DNA and only then, to one specific sequence – cytosine-guanine (CG) – often referred to as CpG, the ‘p’ denoting the phosphate ‘backbone’ of the DNA double helix. Together with other packaging molecules and RNA, they make a substance called chromatin. Chromatin can come in many flavours depending on how tight it is packed, from ‘open for business’ to ‘closed for the season’ and states in between. At any particular gene, combinations of different epigenetic marks combine to influence its structure and function. Generally speaking, when regions regulating gene activity contain DNA with CpG methylation, the gene is inactive. Conversely, if the CpG methylation is removed, the gene may be activated. This is, however, a very simplistic interpretation because it ignores all the other epigenetic marks but it fits most situations.

NIHepi2

How do epigenetic marks get added and removed from our genes? This is when the ‘four Rs’ come in: epigenetic Recruiters, wRiters, Readers and eRasers. In the figure below, a strand of DNA located at a gene’s control region is illustrated with, for clarity, only four groups of histones.

JC1The first stage of epigenetic change involves the addition of sequence-specific Recruiter proteins or RNA, illustrated by the coloured symbols.

JC2Next, epigenetic wRiters, often called transferases, attracted by the recruiters, add an epigenetic mark, for example, acetyl (Ac), methyl (Me) and phosphoryl (P). Note that the first three marks are added to histones and the final, methyl mark, is added to DNA.

JC3Next, a combination of epigenetic Readers specific for each epigenetic mark bind in tandem in a way analogous to a key in a lock. Each gene or group of genes can have its own specific combination of marks, writers and readers.

JC4This ‘opening of a lock’ is akin to opening up the structure of the gene for it to be expressed.

JC5To reverse this process, a set of molecular eRasers specific for each mark can strip the mark off. An example of such an eraser is the deacteylase group of proteins.

JC6Which, when all marks have been stripped off, brings the gene back to square one.

JC7Further links and a more basic description of epigenetics can be found in my Blog “Epigenetics: from Greeks to geeks and leaks”

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