Blogging by Candlelight

For me, Cromer Is SO Bracing kicked off today.

I forwent last night’s fish ‘n’ chips in favour of sibling-ly support of the Minotaur Theatre Company’s Cabaret

Today’s happenings have been documented in the friendfeed room but in summary:

This morning I completed the Cromer Is SO Bracing complement at the Cliftonville Hotel, where two hours of intensive brainstorming coerced a plethora of ideas into something of a storyboard. We ventured to the Gee beachhut for tea and contemplation and have now retired to the Maison des Girrafes where a veritable industry of sea-creature-crocheting has been set up at the Gee dining room table.

With a table booked at the Cromer Curryhouse for this evening, tonight promises more fruitful discussion. Tomorrow’s plans include a full day of scriptwriting, science and drama culminating in the masterpiece that will be Cromer: Darwin’s Lost Weekend.

A guide to the best 100 blogs was the cover story in the Sunday Times Culture Magazine today

The accompanying article gets off to a good start – the opening sentence reflects the opinion of at least one NN blogger. Bryan Appleyard attempts to capture the spirit of blogging, contrasting it with other forms of publication. I think that he explains what blogging means to him. I don’t think that his perspective can be generalized to all bloggers.

The article rounds off with a list of The Best 100 Blogs, by catagory:

• World affairs
• Celebrities
• Style
• Words
• Cult
• Original thinkers
• Comic relief
• Domestic politics

• Visual aids

I like to think that we have all of those covered here on Nature Network.

Last week saw the launch of the RCSU Imperial College Science Challenge 2009

The Challenge? To write an 800-word response to one of the questions set by the panel of judges, competing for a share of the prizes including cash prizes of up to £5000!

This year’s four questions set by their respective judges are:

• What might we learn from the Large Hadron Collider project?

Prof. Tejinder Virdee, CERN

• What can be done to ensure an informed and balanced debate of Science and Technology?

Dr. Martyn Sené, NPL

• Will Homo Sapiens continue to evolve? If so, how?

Prof. Armand Leroi, Imperial College

• Hydrogen is key to tackling the world’s rapidly increasing demand for energy. Discuss.

Duncan Macleod, Shell

The Science Challenge is judged in two categories – Imperial College students, and school-age students in years 11-13 at any UK school. School-aged entrants compete for bursaries to study at Imperial College, and Imperial students compete for cash! In addition all winners are invited to take part in some money-can’t-buy science experiences:

• A day shadowing Lord Robert Winston
• A trip to CERN, with a guided tour of the facilities
• A trip to NPL, with a guided tour of the facilities

• A trip to one of Shell’s laboratories

So, if you have contact with Imperial College students (ahem) or school age children in Years 11-13, encourage them to have a think about the questions and, if they feel so inspired, to construct their essay and to send it in.

You never know where it may lead.

Most students and followers of Synthetic Biology will be familiar with the repressilator

(If you’re not a student of Synthetic Biology, you can become one. The Synthetic Biology Community has a strong ethos of open science and you can find course materials on OpenWetWare (including the course I took).)

Towards the end of last year, I blogged about a fast, robust and tunable synthetic gene oscillator and the difference between this oscillator and the repressilator.

In this week’s Nature, another biological oscillator makes an appearance. In contrast to the two aforementioned synthetic biological oscillators, this one is constructed in mamallain (CHO) cells. Again a different circuit design is used – this oscillator makes use of sense-antisense transcriptional control to construct positive (using the sense strand) and negative (using the antisense strand) feedback loops.

The accompanying News and Views article considers how in silico and in vivo studies have made apparent the role of positive and negative feedback loops in biological oscillators. The authors of the News & Views article draw parallels between our current understanding of biological oscillators and the seventeenth century’s replacement of the water clock with the pendulum. The say

Advances in generating biological oscillations are similar to those made in the seventeenth century that led to our widespread adoption of the pendulum clock.

Is this an optimistic view of the current state of our understanding? Together, the three papers I mention here describe improvements including new and more detailed mathematical models and the design of more robust, tunable oscillators. However the heritability of the oscillations between parent and daughter cells is partial and the oscillations die out over time.

I was not around in the seventeenth century to witness the establishment of the pendulum clock as the de facto standard for timekeeping, so I cannot say whether the current stated of play in Synthetic Biology is analogous with the progress and pitfalls of the first pendulum clocks. Synthetic biology has plenty of scope for learning from mathematical models and natural oscillators (such as those that track circadian rhythms). But since their invention in the seventeenth century, pendulum clocks have been replaced with atomic clocks, and whilst natural oscillators are remarkable in their robustness to variation in extrinsic conditions, it will be a long time before we establish a Synthetic Biological clock with the precision demanded by today’s time keepers.

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How do you answer the simple question What do you do?

When the (semi-)joke Me? Oh, I’m just an eternal student!

is met with the inevitable Oh…studying what?

but Bioinformatics…and Theoretical Systems Biology…

returns a quizzical look:

(_Bio – informatics?_)

Where do I go from there?

I typically resort do – It’s like computers, but for biologists. I’m a biologist, so this year I’ve got to learn computing.

If my new acquaintance’s eyes have not yet glazed over, and they want to know what you can do with bio-, bio-, bio-what-was-it-you-said-again?, my favourite example is

You know those whizzy 3D pictures you see of proteins, or viruses, or molecules, sometimes on the news, or in the paper?

(For an example, see the ‘cool bit’ on Stephen’s video)

Figuring out what those structures look like, from what we know about proteins, now that is a classic problem in bioinformatics.

I’m not sure that this doesn’t leave some people with the impression that I’m some kind of graphic designer.

But other summaries of what bioinformatics is, or what bioinformaticians do, don’t seem to get it right either.

We deal with big biological data sets.

We use computers to study biological problems.

Perhaps it will be easier to explain (although perhaps harder) once I am working on a project, not preparing (or trying to prepare) assignments in Java or Python.

Or perhaps I should adopt the strategy favoured by him indoors.

I just say I’m a pilot.

Some recent articles from the blogosphere and further afield:

From the New York Times Magazine, Steven Pinker piece on his participation in George Church’s Personal Genome Project.

A number of journalists and writers have recorded their experiences of genetic testing (see, for example, Mark Henderson, Richard Powers and Ben Hammersley). With multiple reports of the same experience, we might think that each genetic `testee’ will have little to add to what has already been said.

But what comes across in these articles is the unique perspective each writer has as he encounters his genome. Pinker connects his participation in the PGP to his opportunities as a psychologist to subject himself to a battery of tests to discover more about himself. He considers what makes us who we are from the perspective of a cognitive psychologist as well as from a genetic point of view, mulling over the relationship between genes and behaviour.

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From PNAS and a companion blogpost by PZMyers at The Panda’s Thumb, a neat rebuttal of creationists’ celebrations of the concept of latent evolutionary potential (in this case, the capacity for organisms to increase in size) being realised as the environment changes. Having spent last term grappling with the concepts of neutral evolution and contingency, I welcomed Myers’ amusing analogy of random genetic drift with drunken Australians.

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And finally, if the gloom of British winter is getting a bit much, contemplate emigrating to Australia for The best job in the world.

(HT: JL)

Do you ever read a piece of research and wish you could take that idea and run with it?

As part of their special collection on Education & Technology, Science published a report Why Peer Discussion Improves Student Performance on In-Class Concept Questions.

In a lecture theatre containing tens or hundreds of students, individuals are reluctant to speak up when the lecturer addresses questions to the audience. Interactivity can be introduced by providing each student with a clicker and posing a multiple-choice question. The audience responds via the appropriate buttons on the clicker and the combined results can be displayed and discussed. (This technology is used to Ask the Audience on Who wants to be a millionaire?).

In the report, Smith et al used this technology to test whether peer discussion could improve student performance on in-class questions, even when none of the students in the discussion group knew the answer. According to their findings, discussions were useful even when none of the students in the discussion group answered correctly individually.

Examinations are looming large in my mind at the moment. I have long maintained a wish for the opportunity to collaborate in an exam setting – I remember cursing that at A-level, my peers and I could not check each others’ maths papers for those trivial errors that often trip me up.

I would be more than willing to use my upcoming exams to extend Smith’s investigation. If we as a study group were allowed to discuss our answers, I hypothesize that we would be able to cobble together an answer to some of the problems, even if each of us alone were stumped.

Having said that, coursework this past term was the focus of several desparate fruitful discussions and between us we managed to formulate some reasonable responses to the problems we were set in class. We can hope that what we learnt in those late nights in the pub computer lab will have rubbed off when we turn over the paper.

There have been a number of posts around the blogosphere and elsewhere about the merits of taking a break

As the end of term approached a couple of weeks ago, some of my friends at college were alarmed when I explained that I had to do some studying over the holidays. This term’s lectures for the MSc course I am taking are examined in the first week of January, which strikes me as somewhat brutal, seeing as term doesn’t start until the 10th.

Other students were less surprised…one commented that he would be in the lab over the vacation, another had a report to prepare for January, and a third, although she was getting away, was printing out a stack of `bettering’ reading to pile by her bed.

Even in the absence of imminent deadlines, Jenny has blogged about how scientific thinking follows us in our daily lives. Even my Christmas gifts were related to what I do. (Thanks Dad! 🙂 )

From the number of us who spend our days, evenings and nights reading about, writing about and doing science, it is a wonder that we seem to get so many other things done. (Example.) Having taken a few days off slobbing out in front of the telly I am fighting a tide of festive distractions, trying to get my brain back into gear and do some past papers. I recall a snippet from the Guardian that I read in the run-up to undergraduate finals. Sometimes – or so the article claimed – you need to hang work-life-balance, and to immerse yourself in your deadlines until the pressure has passed. I must gird myself for the coming week and leaving my new Christmas reading until the dark nights of January.

Perhaps once he has had enough of complaining about advertising-equivalent exposure and Britney Spears’ breasts, Ben Goldacre could take a look at this article.

The lengthly title, Discrepancies in sample size calculations and data analyses reported in randomised trials: comparison of publications with protocols belies the simple and slightly alarming findings.

This “research about research” considered seventy published randomised controlled trials, comparing the protocols and the corresponding publications of results. The authors considered the proportion of protocols that did not provide information about sample size calculations and statistical methods, and the proportion of trials with discrepancies between information presented in the protocol and the publication.

The authors find numerous such discrepancies in the protocols and resultant publications, from the framework of the study to the methods of statistical analysis chosen.

Does this matter? Well, yes – different statistical methods explore the raw results in different ways, and can give different impressions of the outcomes. If these statistical methods are not specified in advance, choosing which tests to include could potentially be influenced by explaratory analyses of the data. The authors end their piece with a call for documentation of sample size calculations and full plans for data analysis before a trial gets underway, and faithful adherence to this published protocol, or necessary amendments to be explicitly described.

Only with fully transparent reporting of trial methods and public access to protocols can the results be properly appraised, interpreted and applied to care of patients.

Just as Richard wonders if anyone takes that junk seriously, we can question whether clinicians (and researchers, journalists and the public) read, or will begin to read, reports of randomised controlled trials with the scrutiny that this article suggests is warranted.

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A.-W. Chan, A. Hrobjartsson, K. J Jorgensen, P. C Gotzsche, D. G Altman (2008). Discrepancies in sample size calculations and data analyses reported in randomised trials: comparison of publications with protocols BMJ, 337 (dec04 1) DOI: 10.1136/bmj.a2299

Journalist Ben Hammersley tries out 23andMe ‘s services.

” The test has added, apart from curiosity, nothing meaningful. ”

I believe that the download will be available for a week; after that, you’ll have to listen again by finding the program in the Analysis archive

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