Electronic Lab Notebooks

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Every time I have to write a report, prepare a presentation or meet with my boss, I curse the fact that I can’t just “+F” through my lab book and find those conditions/results/images that I’m looking for.

Of course, with an electronic lab (note)book (ELN), that would be perfectly possible. I see that there are plenty of options; purpose-built or general, local or web/cloud, free or commercial.

At the moment, I’m contemplating a locally hosted WordPress blog, because it is what I know already and it’s easy to set up, but I’m totally open to other solutions. All I know is that I’d like it to be both local and free.

Does anyone have any experience with using Electronic Lab Notebooks and have any advice or preference? I’m all ears.

Also, how about image tagging, like iPhoto or Lightroom but for micrographs? I can’t count how many times I’ve looked for “the kinda round one” or “the one with the weird speckles”…

Joining professional societies

As a PhD student in the life sciences, there are plenty of professional/scientific societies vying for me to join them. These range from the very general, covering all science such as the AAAS, through the general biology (Society of Biology) down to specific fields (Biochemical Society) or techniques (Royal Microscopical Society). Most seem to come with a student rate, subscription to the society’s journal and some obscure postnomial letters. Perhaps most importantly, becoming a member often entitles you to apply for travel funding, as hapsci pointed out.

On the other hand, joining a society requires outlay of some (normally small for student) membership fee, pestering your PI to sign a form stating you are student of a relevant discipline and for the travel grants, anticipating when you want to travel as some societies require you to have been a member for some time prior to asking them for money.

So I’m putting it out there; is it worth joining these societies as student, and if so, how many?

Corsican Panoramas

A little while back, I wrote about experimenting with panoramas. I’ve since become firmly convinced that they are the best way to capture a landscape. I think a lot of people have come to the same conclusion, given the number of point-and-shoot cameras that offer some panorama creating feature, including my own, which allows you to “record” as you pan across a landscape and then stitches the panorama together on-board.

With this in mind, here are 2 panoramas from Corsica, taken recent on my summer holiday:

Calvi Harbour

Porto

The town of Porto

Is using an academic title automatically an ‘argument from authority’?

We are bombarded with ‘expert opinions’ every day in the media, both printed and broadcast, and many of these people are presented to us with their title: Prof, Dr, PhD, FRS and the like. An example might be this recent story on sleep deprivation and stroke from the Guardian, which is followed throughout.

My questions are: does including their “rank” in the scientific hierarchy automatically say to the audience “you should believe this person for they are more qualified than you“, is this committing an ‘argument from authority‘ and does this even matter at all?

The first question translates basically to whether or not an academic’s title is optional. On the one hand, they’ve earned the degree/accolade by working pretty damn hard and deserve to be called by it. In 3 years time, when (hopefully) I finish my PhD, I’ll be pretty cheesed off if ‘Dr’ doesn’t get written down in the right places. On the other hand, within science (certainly biology/biochemistry), people don’t much use their titles. At the institute where I work, titles are basically relegated to the telephone directory and a handful of email signatures. They certainly don’t appear on published papers, so why in the press release and press coverage. (As an aside, this is different in the medical world such as the BMJ, The Lancet and NEJM, where author qualifications are published). If they aren’t on the paper itself, I think that says to me that they aren’t needed in the press coverage, but I’ll admit that it’s an open question.

Does the inclusion of these titles confer authority on to whatever quote their holder is giving? I think they probably do. This might not be the intention in science reporting but it has that effect. Why else would people be so keen to use the title Dr, if not to be accepted as an expert in a field?

A better question is whether worrying about presenting a well-qualified expert as an authority figure actually matters? As noble as the Royal Society’s motto might be (nullius in verba – On the word of no-one), equally nobody has time to fact check everything, and qualifications and titles are often a pretty good heuristic for reliability. As Paul Nurse (or perhaps “the Nobel laureate Sir Paul Nurse PRS) recently put to James Delingpole (3m30s), when you go to a doctor, you trust their clinical judgment. You might do your own research and disagree with the consensual position, but that would be a very unusual position to take.

The problem – as there is with all such rules of thumb – is that it is open for exploitation. I alluded earlier to those who ‘pass off’ having more qualifications than they have, often in order to lend their opinion legitimacy, often for monetary gain in the form an endorsement by an expert. Weirdly, this means that every time a title such as Dr is used legitimately, it adds weight to all those using the same title illegitimately. A reverse problem can also occur – someone with a legitimate qualification, in a relevant field presents a maverick view rather than scientific consensus and can be spectacularly wrong, but still taken “on authority”. Think Andrew Wakefield and the disproven MMR/Autism link for an example.

On balance, I’m not sure that there is a right answer to the use of academic titles. To me they are a mark of respect and achievement, not authority and certainly don’t mean that everything the holder says is true and sacrosanct, but I’m not sure that is always how they are taken.

“James Streetley BSc (Hons) MRes

“Justin Lee Collins: Turning Japanese”

Five just aired the first part of three in this series where Justin Lee Collins checks out Japan. You can catch the first part here as well as find the promotional material and synopsis. I was always going to be interested in this as I have an uninformed fascination with Japanese culture and have recently taken up learning the language, despite skeptical about what the comedy persona of Justin Lee Collins would bring to it. The blurb starts off well:

Justin arrives in Tokyo on a mission to learn more about the people and customs behind Japan’s often baffling image

However, I think the programme potentially added to the “baffling image” by focussing on what would appear to be quite bizarre aspects of Japanese culture: meeting a man with over 100 sex dolls, costing over £250,000 and sending Justin Lee Collins out to be a host in the city’s Red Light District, where a single night can cost the customer >£1000. I could be totally wrong here and that is pervasive behaviour across Japan but it seems unlikely to me, not least because of how much it costs.

There were some genuinely interesting and troubling moments when the programme visited a sex doll showroom and saw child sex dolls, but this is interesting because it doesn’t need to be presented as “normal” for us to find it shocking and it was spoiled by rest of the programme which seemed to dress up fringe activities as normal.

Frustratingly, I think they skirted around the actual issue they were discussing. The lessons on meeting people, the sex dolls and the host bar were all lazily hung from an interesting point on population decline in Japan that could have been treated in more in-depth way whilst still fitting in some of the kookier aspects which presumably sell the programme.

I would like to see a proper, genuine comparison of both similarities and differences across these cultures, rather than programmes such as this and Beckii: Schoolgirl Superstar at 14 which play into stereotypes rather than challenge them.

Science is Vital

Supporters at the rally

Supporters at the rally

Yesterday, I attended (and helped marshall, as evidenced here) the rally for an important campaign called Science is Vital. It is a campaign against any proposed cuts to the science budget, when the spending review is published later in the month. I urge anybody who hasn’t already done so to: check out their website which details all the reasons why continued investment in science is a necessity, sign their petition and write to their MP about the campaign. It was a fantastic afternoon and great to meet up with so many people that I’ve heard about or briefly tweeted @ them but never spoken; even if it was under unfortunate circumstances with the prospect of cuts hanging over all our heads.

This campaign is more than just a self-interested group getting antsy about a policy they don’t like. Yes, many of the people who have signed the petition are scientists who are understandably worried about their own careers. I am also worried about what the state of biomedical science will be when I start looking for my first position after finishing my PhD in 3 years time.

This is about more than that though. We are saying

We already don’t have enough money to do all the research we need, with only around 20% of grant proposals finding funding, and yet we greatly ‘punch above our weight’, in almost any metric you pick; number of World-class universities, citations per researcher, papers produced against spend. We can’t get more efficient. We are already at the limit.

And it isn’t the scientists that will be the biggest losers in this. They can move to other world-leading institutions in the US, Japan, India, Australia, Germany and others. It is society that loses out, as we have to become reliant on the work of other countries to fulfil our scientific, technological and engineering needs.

The Campaign for Science and Engineering has plenty more on the economic reasons why science funding is a poor judgment, so if you like facts and figures, head here. The Science is Vital campaign has also collated photos and other reports from the event and the Pod Delusion has podcasts of all the speakers and some reporting from the rally. The rest of my own photos from the event can be found in this Flickr set.

Regulation of Old Wives’ tales-type medicine?

Handing out diplomas

This morning, Voice of Young Science stood outside the Department of Health on Whitehall, assessing passers-by and awarding them diplomas in “Traditional Medicine of Old Wives’ Tales”.

The reason for this is a little bit protracted, but bear with me and I’ll explain why they were doing it, and why it is important to take notice. The story started over a year ago when the Department of Health published this document, a consultation on the statutory regulation of a number of Traditional Medicine Systems. This seems to have sent alarm-bells ringing for a number of people, for a number of reasons:

  • the proposed registration scheme doesn’t require a practitioner to have any training
  • the scheme doesn’t require evidence of efficacy (that the treatments work), merely that they are traditional
  • registration from a Government body such as the Department of Health or a subsidiary implies endorsement and legitimises these treatments.

These concerns are found in the Sense about Science submission to the consultation (from October 2009) and in the flyer for today’s event.

It is the first point which VOYS have taken the most issue with: lack of training and the implication that “[traditional] practitioners have the knowledge, skills and attributes of qualified medical practitioners”. This leads on to today’s exploits, which aim to show just how little knowledge is required to proclaim Old Wives’ Tales-type traditional medicine – so little knowledge, that even I got a Diploma:

My traditional medicine Diploma

I’m not entirely sure what the significance of today is, as other than the original consultation, I haven’t been able to find any more on the matter from the Department of Health, not even a response to the consultation. There has also been a little bit of criticism over the choice of “Old Wives'” as the type of traditional medicine portrayed here, as ageist, sexist and failing to take account of historical context, when conventional medicine wasn’t exactly evidence-based. I also think that the way today’s event was done, it looked more about the ease of obtaining a qualification rather than about regulation in traditional medicine.

However, none of these snaggles should stop us from being seriously worried at the point made today though. Regulation and accreditation of alternative medicine only serves to legitimise this sort of pseudoscience and helps it to gain another foothold in society, similar to the platform that traditional medicine courses in universities has provided. We must make every effort to ensure that money isn’t wasted on regulations that could ultimately hinder medical care.

“Beckii: Schoolgirl Superstar at 14″

I’ve just watched Beckii: Schoolgirl Superstar at 14 on the BBC iPlayer (originally on BBC Three last night). It chronicles the fortunes of Rebecca Flint/Beckii Cruel, her family and finding global fame.

There are plenty of things that are really interesting about the documentary; from the way the Internet can make stars of people, the concept of multiple identities across different cultures and the conflict of interest between parent and offspring. (That last one may just be some unsympathetic editing towards her father, Derek, but even so, it made me think about childhood success and the parents wanting “in”).

The aspect I really want to talk about is the fandom, or inappropriate fandom that the girls received.

The film devotes much of the middle section towards this, but mostly parries it off as being a “cultural difference”, especially when her manager is asked about it. My question is: just because another culture allows a fixation with young, female teenagers, does that make it acceptable? Or to spin it around, because British (Western? I hate that word though) culture doesn’t allow it, does that mean it is wrong? For sure, I got a slightly uneasy feeling watching parts of that film, but of course I’ve internalised the British view.

Incidentally, I think Beckii has an amazingly level head on this, perhaps more so than her parents and manager. Her piece to camera after she receives the bass guitar is very considered, and her take on the “cultural difference” is equally sensible, where she talks about making sure she is happy (31mins in on iPlayer).

I think working to get away from the sexual side , that’s why we’ve turned down a lot of offers for [?] magazines and everything because we don’t want to do that and I never want to do that. I mean I’m 14 years old and even if [?] “oh, its just a different culture”, even so, I’m a British person with a British mindset and I think it is wrong so, yeah.

My basic problem is that if we assume that 14-16 year old girls getting attention from 45-54 year old males (27mins) isn’t a problem but part of the culture, then why are is it important to make sure that the girls clothing is so carefully checked (29mins and 10mins) and that their “look” (from 9mins) of large eyes, chiselled chin is so important. From 9-14 mins is particularly illustrative of this.

To me, printing photobooks of a 14 year old girl – where the girl is the product, not like a clothing catalogue – and making out that it isn’t sexual/objectifying doesn’t quite add up. Part of me wonders if someone, somewhere, is ignoring the “elephant in the room” on this.

That is not to say that printing her photobooks and other merchandise is necessarily wrong. I want to explore why and if behaviour of those consuming those materials and generating that market is acceptable. I mean surely she should be able to publish whatever materials she wants, and it is up to those consuming them to be responsible in the way that they contact her and behave to her. Pragmatically however, should she censor herself to minimise the risk of unwanted attention?

Obvious follow-up questions are: is there ever an age for objectification as above?  Is this solely a problem for girls (cf. Justin Bieber)?

Maybe I’m coming at this with too much of a gender and culture bias? Anyone else have thoughts?

Update: I just had this conversation with @Tom5mith on Twitter, about our take on the ‘moe‘ and ‘idol‘ culture. Relates strongly to our attempts as Brits to see through the cultural difference.

Cycle Hire Experience – 1 week on

I awaited the Barclays Cycle Hire scheme with interest. I live within the covered zone (approximately zone 1 + a bit) and make around 2-3 return trips a week by bus on routes that I could cycle. I’d also been considering cycling for a while, but wasn’t sure if I’d like it (or even if I still could) and I don’t own a bike.

In other words; I’m definitely part of the target audience for the scheme.

When registration day came around, I duly registered (with a glitch or two) and was sent my membership key in advance of the bike release day.

Bike docking station outside the office

Bike docking station outside the office

My first trial wasn’t good – I attempted to give one a quick go around Russell Square from the rack just outside my office, but instead got an amber light and horrible juddering noise. Instead I had to walk to the next rack along, on Bedford Way, where I took my first 8 minute ride.

I can confirm and corroborate the general opinions on the bikes. Yes, they are quite heavy, but not overly so. The gear range is terrible. I’m not a strong cyclist, or fit in any way, but even uphill only the highest gear was of any use. First or second just leave you pedalling like a maniac without actually moving. And if your bag is too small, it will just fall sideways out of the basket, unless it is large enough to be bungee’d in.

The real test came on Saturday, when I took one to and from work (having invested in a helmet and reflective backpack cover). Other than highlighting how unfit I am – panting and sweating after a 15min cycle, it was totally fine. I even cycled home at 2am in the morning and found the lights to be adequate and the experience perfect. The scheme was actually perfect, as there is little in the way of public transport from Goodge Street to Farringdon/Sadler’s Wells, but there were docking stations almost door-to-door. Spot on!

Monday night, I got even braver and tried Russell Square to Victoria during the rushhour, and took advantage of being able to dock the bike and forget about it; using it to cycle to the pub, have a few drinks and get the bus back, not worrying about leaving my own bike somewhere overnight.

I’ve now used the bikes to make seven journeys that I would normally make by bus or tube, and it has been both fun and useful each time. Only once have I been over the 30 minute limit (by 34 seconds), so I’ve saved at least £6. 15 more weeks until I’ve paid off the £45 annual membership and the cost of the helmet and backpack cover!

The only scary moment I’ve had was cycling down Oxford Street. So many buses, bus stops and rickshaws that all seem to be out to get you. I shan’t be making that mistake again any time soon. The other thing that is quite strange about cycling around London is my propensity to get lost. I know my way around places that are walking distance from home and work, and I know the buses and tube for places further away, but actually having to cycle to places I’d normally take public transport too was surprisingly difficult. It isn’t like being on foot, when you can just stop any time, or turn around and because you are moving faster, there is less time for contemplating the route. It is funny though, because I don’t have that feeling in the car. (Probably to do with the sat-nav…).

Any way, so far I have loved the scheme and I hope I continue to use it beyond its current novelty.

SciencePunk – A critique of skepticism

And so it is the beginning of another month, which means it’s time again for Westminster Skeptics in the Pub. This month, it was the turn of the SciencePunk, Frank Swain, to address us with a talk entitled “A critique of skepticism”. Here, he basically told us where skeptics (or the skeptic “movement”, if that exists) are going wrong in engaging with others. I think most of us probably have an uneasy feeling about things we have seen done in the name of skepticism and how we are perceived by “non-skeptics”, such as my first thoughts on skeptics insular nature last month.

In a way, I think Frank was putting out there our own “inconvenient truth”, that we dimly recognised before. The genius was in his delivery, which was a well-illustrated, persuasive and coherent argument. I’ve said this before, but it is a mark of great speaker at SitP, when we carry on discussing their talk long after fact, because it has been that thought-provoking.

What follows is just a few of my favourite quotes from the presentation. I never take enough notes for a full round-up and there are many who are better at it than I anyway.

What are the KPIs of skepticism?

  • Who are you talking to?
  • Who is listening?
  • Whose mind is changed?

I’m pretty sure anything I’ve written hasn’t changed any minds. Why? I write for those who already think like me. Not on purpose, but because actually challenging someone’s opinion, in writing, is difficult. What is worse is that I hadn’t even considered this until last night.

“A Facebook group or Twitter hashtag is not a campaign.”
It shows a groundswell of support from those already in the know, but it doesn’t change minds or engage. It is people agreeing with their mates.

Undeniably true.

I think this is also the time that Frank introduced the “Mum” test: how would you explain it to your mum and would she care? A useful teaching technique that should be applied to skepticism more. To me, that indicates a danger of talking down to people and coming across as superior – a point that is later addressed.

Facts do not speak for themselves. We have a fetishism for facts.
How many people have heard or used “the plural of anecdote is not data”? *many hands go up* – “instead it’s a convincing argument”.

Whilst we can ask for evidence until we are blue in the face, it only convinces people that make evidenced-based decisions. Anecdotes persuade a lot more people. Frank’s example here was; user reviews on Amazon – many of us use them to make purchasing decisions based on anecdote, because we trust others. Also, how many of us can prove that the Earth orbits the Sun? I guess anecdotes/non-first hand evidence is more pervasive that we’d like to think.

Arguing from facts is cowardly. You’re going in with the knowledge that you’re right. Arrogance will show. (I didn’t note this verbatim, so relied on a tweet for wording)

I struggle to agree with this, because people don’t go into arguments knowing they are wrong. Each party tends to believe (to the extent that they know) they are right. However, I can definitely buy the idea that arguing arrogantly doesn’t work.

This is why I have a problem with the concept that skeptics are teaching or enlightening people. It implies a hierarchy where skeptics are above those they are talking to, who are in turn in some way stupid or primitive.

That leads on to what I think was the take-home message; just because you have evidence, doesn’t mean you are better, or even right.

In no way was that a complete report of the talk. It is only the bits I found most interesting and challenging (and the bits I had notes for). Most notably I missed out all of the coverage of the recent Twitter mess regarding Gillian McKeith and the level of skeptic vitriol that was shown.

I will link here to any more complete reports as they become available: