Blogging by Candlelight

Today saw the launch of the RCSU Science Challenge 2010 – featuring an addition to the options for entrants which should please the new-media types. (More details below.)

As I blogged last year, the RCSU Science Challenge is an annual competition which

aims to promote scientific communication and creative thinking amongst some of the country’s most talented young individuals; the same individuals that will eventually shape our future over the years to come.

The competition has been running since 2006, but entry is restricted to students at Imperial College. A parallel competition, with the same questions and entry criteria as the Imperial College competition, is open to secondary school students in years 11, 12 and 13. I would encourage those of you who know potential entrants to point them in the direction of the Challenge’s website, with the suggestion that they start to mull over the questions.

In common with previous competitions, this year’s panel of judges include representatives from research, industry and media, as well as an Imperial College native.

I have reproduced the questions below, but this year the most exciting development is the change in the criteria for entries. In addition to the essay format, which is still welcome, media entries will be accepted. The competition’s organizers encourage creativity in producing a short (up to six minutes) video. [1]

The Questions:

Mark Henderson, Science Editor of The Times
How will genetic advances change medicine and society by 2020?

Andrew Harrison, Fuel Innovations Manager, Shell
The Climate Change Act 2008 commits the UK to an 80% reduction in greenhouse gas emissions by 2050- can technology alone deliver road transports’ share of this reduction?

Athene Donald, FRS, UNESCO 2009 Woman scientist of the year
Can renewable energy sources solve the UK’s energy problems?

Sir Keith O’Nions, Acting Rector of Imperial College
What are the prospects for finding life on other planets?

The prizes are significant, including £4000 cash and opportunities to gain insight into the circles in which the sponsors and the judges move. The Grand Final is a black-tie affair (in common with previous years, when venues have included the Science Museum and the Ritz). Tickets, I am assured, are selling fast.

¹ Unfortunatly, the outcome of CISB09, at ten minutes, falls fowl foul of the entry criteria. Besides, team entries are not permitted. Back to the drawing board…

Is it always this difficult to propose?

The third milestone¹ in the PhD process here at Imperial College is to submit a research plan. Similarly, once a supervisor has been agreed, the funding body supporting my PhD studies requires that a proposal be submitted.

The plan for College does not have to be terribly long (four pages); there will be substantial overlap between the plan I write for college and the proposal sent to the funding body. A number of people has assured me that it is likely that my plans will change during the PhD, such that the planned work in the proposal is not that which I end up submitting.

I am extending some work which formed part of my MSc, and as such, my supervisor and I have talked at reasonable length about what work I will do over the next three years. We have met with my second supervisor and talked about applications of the methods we will develop.

Then why is actually getting the plan down on paper so hard?

According to my student handbook, the research plan “should demonstrate a sound understanding of the research to be undertaken”.

So then for me, the difficulty arises when I attempt to explain with some degree of fluency the background to my study. I am new to the field of statistical genetics, or at least, the statistics part. When it comes to the concepts relating to genetics, I feel at home; however, and I am not a statistician. Trying to express with some degree of fluency the statistical concepts which do not (yet) trip off my own tongue feels laborious.

I was advised to write a lot of waffle keep the proposal general and non-technical. With my biologist’s mind, I interpreted this as “do not put any maths in”. However, if my PhD studies are going to cover statistics, I can see that learning how to waffle using mathematics express basic concepts clearly and succinctly is going to be a necessary skill, as it is likely that I will have to write the background to my study many times.

The current draft of the proposal reads like a hotch-potch of other people’s descriptions of what I am going to do, where I have taken a line from the introduction to a paper here, a series of equations presented in a textbook there. My handling of statistcal concepts feels clumsy, and I plead with my supervisor to proof-read my work carefully because the errors might not be obvious to me.

At the minute, putting together a coherent proposal feels extremely challenging. At different stages of an academic career, I imagine that the that the difficulties are different. As one gets more familiar with the field that one is proposing, do the challenges change?

Continue reading →

In February of this year, my supervisor at the time circulated to the members of his group Professor David Nutt’s article (*pdf*) Equasy – An overlooked addiction with implications for the current debate on drug harms [1].

At the time, the Equasy article made us chuckle!

Commentary on the article’s publication made it into the press and I followed the story for a time, including the carefully worded apology given by Nutt in response to the (then) Home Secretary’s demands.

I was surprised by the news, which I first read last night but which is in today’s papers, that Professor Nutt has been asked to resign from his position as Chair of the Advisory Council on the Misuse of Drugs (ACMD).

The ACMD is an “independent expert body that advises government on drug related issues in the UK”. It seems to me that the government did not like the advice. The call to resign is prompted by the publication of Estimating drug harms: a risky business (*pdf*) [2] by the Centre for Crime and Justice Studies at King’s College London.

The article is an edited transcript of a lecture given by Nutt, which I suspect contributes to its narrative clarity. In the article, Nutt introduces the many factors influencing legislation concerning drugs, acknowledging that the advice of the ACMD is but one voice in a debate subject to media influence, public perception and political opinion. Findings relating public perception and media influence are presented, and the interrelationship between these, and their affect on policy decisions, is discussed. Nutt also presents the scale published (*pdf*) in The Lancet in 2007 [3] in which he and his colleagues attempted to parametrize and summarize the risk associated with use of drugs both legal and illegal, resulting in a table that seemed at odds with current drug classification.

Nutt acknowledges

In recent years the whole process of determining drug classification has become quite complex and highly politicised.

What I suspect prompted the call for Knutt’s resignation is his criticism of the government’s approach to drugs legislation that is not based on an assessment of harms. He summarises

A fully scientifically-based Misuse of Drugs Act where drug classification accurately reflects harms would be a powerful educational tool. Using the Act in a political way to give messages other than those relating to relative harms undermines the Act and does great damage to the educational message.

It is a shame that, given his acknowledgment that the scientific voice was unlikely to be the deciding one in legislation, his attempt to offer a more rigorous and honest perspective has been squashed, and that what his findings have to offer was are not acknowledged for what they are – information that could be used to usefully inform decision-making in a tricky and emotive legislative area.

¹ Nutt DJ (2009). Equasy– an overlooked addiction with implications for the current debate on drug harms. Journal of psychopharmacology (Oxford, England), 23 (1), 3-5 PMID: 19158127

² Nutt D (2009). Estimating drug harms: a risky business? Centre for Crime and Justice Studies

³ Nutt D, King LA, Saulsbury W, & Blakemore C (2007). Development of a rational scale to assess the harm of drugs of potential misuse. Lancet, 369 (9566), 1047-53 PMID: 17382831

So, I made it through to the end of my MSc. There was an 100% pass rate among the students this year – celebrations all round!

In a previous post I was trying to decide upon a supervisor for my PhD studies. The advice I received here and elsewhere mirror that offered to Anna Vilborg in her post on trying to decide where to do a post-doc – don’t do what I did!

I got on well with the supervisor of the third MSc projects from the outset, and, of the three projects I had to complete for the MSc, this was by far the one I enjoyed the most. The supervisor and I agreed that the MSc project can be considered a preliminary or preparatory study and that I can work on this topic for a PhD.

So after a fortnight’s break, I am back at my desk, writing my PhD proposal, preparing a paper on one part of my MSc project, and writing some code to use for the PhD proper.

Inevitable induction sessions took place early in the first week, including a welcome by the graduate schools. I have blogged before about my penchant for self-help guides. My collection of Imperial’s trio of in-house publications has been completed with my copy of Learning to Research . In common with the transition from taught to research study, Learning to Research has a less softly-softly approach than its predecessors, and includes a comprehensive description of the rights and responsibilities of both student and supervisor.

Whilst it does not make its way formally into the Code of Practice for Students and Supervisors, the phrase A PhD is not a 9-to-5 was reiterated during the welcome session, both verbally (video link) by the Director of the Graduate School for Life Sciences and Medicine and in a written summary of what PhD students and supervisors should expect.

Students are expected to

Work Hard – PhDs cannot be accomplished with only a 9-5 effort.

If I am honest, I am a little intimidated by this.

Professor Morley claims that

_hard work placates supervisors.
It makes us happy when you are here long hours and weekends_

There is one sense in which science never leaves me. I cannot be alone in taking papers home, to read in the evening, because they are not strictly related to my PhD topic, but they are interesting nonetheless. Often, often, the solution to a problem that I have spent half a day staring at hits me when I am walking across the park, or ploughing up and down the swimming pool, or doing the washing-up. If someone asks me what my PhD is in, I can quickly get excited about it and try to explain it, and what I am going to do next, and what it means.

In that sense, my studies are not 9-to-5, they are more like 24/7.

I appreciate that self-doubt is common among postgraduate students (and scientists at any stage of their careers), but the reinforcement of the above expectation has me thinking, do I have it in me to work hard enough? I like my work, but I have many other things I like to do too. Some are science-related, but some are not.

There are many valid work patterns, and to relentlessly evaluate how hard I am working against my perceptions of my peers’ efforts is unlikely to be accurate, but that doesn’t negate the nagging question.

I reassure myself that I have made it this far, with my own study habits and my own way of working, that I have adapted what I do as I go to meet the demands of the courses. My work-life balance over the next three years is not set in stone – I can change my schedule as I need to. Maybe such a flexible approach does not come naturally to a scientist, but I don’t think anyone is able to tell me that if I am in the office at this time and leave at this other time, that will be “sufficient”.

The flexibility of the schedule is both a perk and a burden of research. I hope that someone will let me know, though, if I am not getting anywhere fast enough.

It is coming up for a year ago that I attended my first conference.

I was aware, when I registered for SciBlog08, that this would not be a conventional convention. From being asked what should be discussed to a slightly unusual social programme

Someday, all conferences will be like this

SciBlog08 was certainly a Web2.0 gathering.

But the next two events I attended did not fit with what I imagined a conference would be like, either.

There was the relentless enthusiasm of the iGEM 2008 Jamboree. Then there was Bayer ‘s Press Forum, Perspective on Innovation, at which I witnessed the nature of questions from the floor when they come from those with a journalistic, rather than a scientific, motive.

Since then, I have been to a couple more meetings, both at home and away.

There are some elements that these conferences have in common. There is being starstruck at seeing someone whose work you admire presenting. There is struggling to follow some talks, and being captivated by others. There is conference paraphernalia and there are nametags, which for some inexplicable reason I retain.

What’s my name again?

I feel privileged to have attended what I believe is 2009’s most exclusive gathering, which came with what is undoubtedly the best conference hospitality I have witnessed in my short conference-attending career to date. The programme was infinitely flexible, incorporating local cuisine and culture.

The freebies were exemplary. And, being among friends, no nametags were needed.

I like “how to study” guides. I don’t mean syllabus synopses, useful for cramming though these might be, but general counsel for academic survival success.

Imperial produces its own materials for students. There is Learning to Learn, a booklet distributed to new undergraduate students during their first year. Written in an informal and friendly style, its advice encompasses reassuring quotes from previous undergraduate students. I remember

Even with good A level results I felt I was at the bottom of the pile compared to those around me.

ringing particularly true for me.

Such snippets are combined with practicalities. The tips for how to get the most out of lectures gave me some food for thought.

My undergraduate degree was a return to study after a two-year break. During the first term, having been disappointed by the feedback on my first essay, I was determined to make a better job of the second. However, I was perplexed as to how one was supposed to hand in 1500 words on a topic that had only briefly been touched upon in lectures. I sought some support, and found it in the form of the reassuringly titled “Write Great Essays!” (note the jubilant exclamation mark!) and its cheery series partner “Sail Through Exams!”.

From the promotional sticker on the cover, I surmise that Waterstones Gower Street was attempting to entice anxious students such as myself.

I turned to the plain English, common sense and practical advice in these texts time and time again throughout my degree. A friend of mine commented that she never found these books helpful – “Don’t they just tell you what you already know?” – but I find the step-by-step suggestions stopped me floundering, and the tips that didn’t seem relevant, I discarded.

Moving on from undergraduate study, Learning to Master was produced by a group of Masters students who were frustrated that there was nothing similar to Learning to Learn available to them. The booklet itself points out that it does not repeat the material in Learning to Learn. It is much shorter, and the central tenet seems to be “Work hard. From the beginning. Hit the ground running, and be organised.”

Another book I have referred to in recent months has been How to get a PhD by Phillips and Pugh. I read the advice on applying for postgraduate study over a year ago, and as my course is a four-year program, I now turn to the section on choosing a supervisor. The book is replete with worrying case studies detailing the many and varied reasons for students’ failure to complete the PhD or to pass the viva, some of them due to problems with supervision.

It seems to me that good communication between the student and the supervisor is a crucial aspect of a successful supervision.

Do Nature Networkers, many of whom have completed PhDs or worked in research, have any advice for me and others in my position?

One of the requirements for my most recent project was that our findings were presented in the form of a website.

This format was intended as a reprieve from the standard report-and-presentation method of assessment. I, however, was nonplussed at the prospect. I know how to write, and to present, but I only know the very rudiments of HTML. Colleagues made a number of suggestions (“use CSS“, “it’s easy, use Dreamweaver“), and I dutifully read the manual and did some tutorials on both these topics. However, with a stack of predicted protein structures in one hand and a blank webpage in the other, I was not much the wiser about how to put the two together.

So I am grateful to one helpful person who pointed me in the direction of Andreas Viklund, a Swedish Web Designer and Music Producer. On his website are some elegant website templates which I was able to download, complete with accompanying CSS, and use to build my site.

I made use of a number of open source and free to use tools in the course of my project, and I am grateful for all of them. But I feel I owe Mr Viklund a particular thank-you, for allowing me to give my website a more professional finish.

It was coming up to a year ago that I last really thought about Biochemistry, the title of my undergraduate degree. Of the timescale I am certain, because despite College being closed for the undergraduate vacation, the library is packed. Colleagues who are where I was one year ago count down the days of revision remaining until their finals in agonising, procrastinating Facebook updates.

After my finals, I moved, by way of a computational final year project, towards Bioinformatics and Theoretical Systems Biology. This year, a term of taught courses preceeded three lab rotations. The report describing the first of these was completed, bound and submitted two weeks ago.

For my next trick project, I have been dispatched to the Centre for Molecular Microbiology and Infection in the building next door. Needing someone with bioinformatics skills to tackle a particular problem, the group leader advertised for an MSc student who was to make this question their project.

Today, Easter weekend over, I venture into the (busy!) library to get stuck into the background reading. As I tackle, highlighter in hand, the half-dozen papers I located via PubMed this morning, I face a dizzying reminder of the essay I came across during my first foray into Systems Biology. It’s not just that, in the papers I consider, “Algorithm details” have reverted to “Materials and Methods”. Back in the territory of cleavage sites and cell walls and proteases, I just don’t feel certain which side of the Bioinformatics/Biology fence I belong.

What with the recent celebration of International Womens Day 2009 and the forthcoming Ava Lovelace Day I have been thinking about what it means to be a woman and a scientist. And I am certainly not alone. This week, a book review in Nature was a variation on a theme, and I met a celebration of 100 Women in Science every time I entered college.

Twice recently, in conversation with people older and wiser than myself, came up the question of belief in one’s own abilities. A number of my peers struggle, like me, to internalize the fact that they are able. We surely are able. We would not have been awarded a degree, would not have gotten a job, would not have been offered a place on the course if we were not able.

When I described this incongruence between the evidence and the feeling, the feedback was “yes, but you are all women.”

Which brings me to the above quotation, which caught me by surprise when I was listening to the (typically PG-rated) Guardian Tech Weekly Podcast. In an edition entitled women in technology, Alex Krotoski [1] quoted Leah Culver in a panel at SXSW 2008.

(Fast-forward to about ten minutes in.)

I had thought that this lack-of-self-belief was a function of being at the beginning of a demanding course, with its workload and its ups and downs. Can it, at least in part, be attributed to being female?

And is there anything practical that can be done? After all, even good science faces knockbacks. Academia is a tough environment to be in. Are there any practical steps that can be taken towards toughening up?

¹ From Alex’s profile, she is a PhD student too. I hadn’t realised that.

Whilst by day, Cromer Is SO Bracing, this weekend I am resting my head in the house where my brother lives in nearby Norwich. (Thanks, Ant!)

Ant explained to me that I was free to stay in his flatmate’s bedroom but asked

“You don’t mind sharing with a tortoise, do you?”

Mind? Mind? As I am in Cromer to celebrate all things Darwin, it seemed entirely appropriate!

Welly, who turned three years old last week

Welly might bear a closer resemblance to a giant tortoise than anything in the Jardin des Girrafes, but I didn’t feel that this would justify kidnapping her for the afternoon’s filming, so a photo had to suffice. Whilst Welly might look giant in the picture, she is actually the size of your hand, so a close-up was needed.

Henry has documented elsewhere yesterday’s happenings, complete with photo-diary. Much chaos filming took place, along with some a substantial amount of science, all fuelled by superb catering from Mrs Gee ’s Location Catering Services ^TM

Thanks to one and all for the opportunity to take part in Cromer Is SO Bracing. Like the rest of the blogosphere, I await the finished article with interest.