Policy and Bright Club Cambridge

Alas my neglect for this web-site has been wanton and unmerciful, sorry little autapses. I am currently in Cambridge (UK) doing a policy placement at the wonderful Centre for Science and Policy (CSaP). Part of what they do is help civil servants network with academics to provide government departments with direct access to the best available research. Before I joined I did wonder why they couldn’t just use Google Scholar, but I quickly learned this was a fabulously naive point of view. Civil servants are often very busy, inexperienced with research, unable to devote the time to finding the best and most relevant information in the mountains of muck that populate the literature, and as a result of moving between departments have great breadth but not so much depth of knowledge. The direct links to relevant academics that CSaP provides are really important for getting good research knowledge into government.

Anyway, evangelism section is now complete, advertising commences: I will be “doing a bit” at Cambridge Bright Club at the Portland Arms tomorrow (Friday 14th June) evening, I think there are still some tickets left (just checked, yes there are, BUT NOT MANY). Professional funny people will be there to make you laugh, and six researchers will be there to try to make you laugh. At the very least, you may learn something.

More soon…

Complexity

The other day I finished reading Complexity: The Emerging Science at the Edge of Order and Chaos by M. Mitchell Waldrop (hilarious back-page plug: “if you liked chaos, you’ll love complexity!”). I’m not much of a bookworm usually, but very occasionally I will relentlessly read something from cover to cover in a short space of time, which I managed to do in this instance (this also happened recently with Robin Ince’s Bad Book Club [which is hilarious, and you should buy it immediately], so it’s not just a science book phenomenon). Complexity was written in the early 90s, shortly after the Santa Fe Institute for complexity research was founded. It serves partly as a documentary of the founding of the institute and its early years, partly as a biography of the key figures involved in its development, and partly as an introduction to the ideas of the new kind of science that the institute was trying to pursue. This works remarkably well – you get a good overview of the relevant scientific ideas, but almost feel like you’re reading a novel. The constant breathless excitement in the tone does begin to grate a little, but it manages to convey the passion of the researchers and the thrill of scientific discovery. It certainly rekindled my excitement with some of the ideas that made me interested in computational modelling and biological systems in the first place.

As the book was written at the height of enthusiasm of the scientists involved, it unfortunately lacks a critical view – no stories of the less successful avenues of research that were pursued, and little mention of criticisms by “mainstream science”. Interestingly, the Santa Fe Institute’s own history page mentions this kind of criticism in passing:

As the Institute’s research interests and reputation grew, so did its list of detractors. Exploring new scientific territory meant that some lines of inquiry failed to live up to expectations. Some researchers in mainstream science felt that complexity science was long on promise but short on results. The criticism culminated in a June 1995 Scientific American article by senior writer John Horgan that openly mocked not only the science of complexity but the scientists doing it. The article, today regarded at the Institute as a wakeup call, caused many in the complexity community to do some soul searching about their field.

I am definitely sympathetic to the approaches pioneered by the Santa Fe institute (amongst other places, of course), though. I particularly love the emergence of complexity in the behaviour of cellular automata – such simple rules can lead to such interesting behaviours. You can’t prove truths about the universe from such simulations, but I think they can give you very deep insights into problems that you just can’t get from other approaches. But that’s just, like, my opinion, man. Go and have a play with a game of life simulator, like this one, to see what I mean.

Anyway, I recommend it, but bear in mind it is quite un-critical, and quite out-of-date. If you want to have a hands-on play with some of the ideas of complexity theory and know a bit of programming, you could do a lot worse than pick up Alan Downey‘s book “Think Complexity” (available for free from his website).

I’m now onto an old software classic, The Cathedral and The Bazaar, which actually has some surprising parallels – complex emergent behaviour in software development processes, defying standard theory through the collective behaviour of individual programmers…

Postgraduate students are rich

I used the Institute for Fiscal Studies’ “where do you fit in” calculator the other day, which, given your household size, number of dependent children, council tax and post-tax earnings, calculates your income in relation to the rest of the UK population. Though the standard research council annual stipend of £13 590 doesn’t sound much compared to what other graduates are expected to earn, it is income-tax and NI free, and as a student I pay no council tax. I also live in the City of Dreams, where the cost of living is not so high as other parts of the UK (though the calculator doesn’t look at this). What are my results?

I live with one other similarly-funded student, so I entered a combined household income of £28 000 (a few hundred extra each per year for teaching/marking), 0 children and £0 council tax. This means my household has a higher income than 66% of the population (red bar in image below).

UK income distribution histogram

UK income distribution

Not bad for students eh? If we had one dependent child aged 0-14, the calculator estimates we’d have a greater income than 52% of the population.

Other thoughts: If I lived on my own, my household income would be greater than 49% of the population. If I quit now, moved into a flat on my own and got a graduate software development job at, say £30 000 a year (pre-tax), depending on my council tax (I’ll assume ~£2 000) and assuming I was making full student loan repayments, my household income would be more than 68% of the population.

Conclusion

  • Research council funded PhD students are really quite well off
  • Children are expensive

2012 in metal

If you’ve met me for longer than about 5 minutes, you will be well aware that I heart heavy metal very dearly. I enjoy most musical styles, but heavy metal occupies a particularly special place in my heart. I also enjoy lists, because nothing gets internet keyboard warriors as angry as a list that is CLEARLY WRONG. Therefore I present to you my Top 20 Metal (and related) albums of 2012, plus a few bonus mentions. I have also compiled the top 20 into a Spotify playlist for you, because I’m nice.

EDIT: list originally for the Snakenet Metal Radio 2012 Members’ Chart

01. Diablo Swing Orchestra – Pandora’s Piñata
02. Hail Spirit Noir – Pneuma
03. Devin Townsend Project – Epicloud
04. Napalm Death – Utilitarian
05. Jess and the Ancient Ones – Jess and the Ancient Ones
06. Sear Bliss – Eternal Recurrence
07. Gojira – L’Enfant Sauvage
08. A Forest Of Stars – A Shadowplay for Yesterdays
09. Killing Joke – MMXII
10. Deftones – Koi No Yokan
11. Witchcraft – Legend
12. Pallbearer – Sorrow and Extinction
13. Converge – All We Love We Leave Behind
14. Evoken – Atra Mors
15. Ihsahn – Eremita
16. Enslaved – RIITIIR
17. Baroness – Yellow & Green
18. Meshuggah – Koloss
19. Cauldron – Tomorrow’s Lost
20. Malignancy – Eugenics

Near misses (no specific order, asterisks by particularly good ones):
Dodecahedron – Dodecahedron*
Dawnbringer – Into the Lair of the Sun God
Vindicator – United We Fall*
Sigh – In Somniphobia*
Tenochtitlan – Sotvorenie Mira
Master – The New Elite
Wodensthrone – Curse
Blut Aus Nord – 777 – Cosmosophy
Unleashed – Odalheim
Paradise Lost – Tragic Idol
Gorod – A Perfect Absolution*
Hooded Menace – Effigies of Evil
Krallice – Years Past Matter
Borknagar – Urd
My Dying Bride – A Map of All Our Failures
Anaal Nathrakh – Vanitas
Dordeduh – Dar De Duh*
Katatonia – Dead End Kings
Nachtmystium – Silencing Machine*
Accept – Stalingrad
Overkill – The Electric Age
Christian Mistress – Possession*
Corrosion of Conformity – Corrosion of Conformity*
Orange Goblin – A Eulogy For The Damned*
Kälter – Ubuntu
Monolithe – Monolithe III*
Nile – At the Gate of Sethu

EPs that would have made the top 20 if I were including EPs:
Inverloch – Dusk / Subside
Orchid – Heretic
Deathspell Omega – Drought

Loved but not metal enough:
Storm Corrosion – Storm Corrosion
Kylie Minogue – The Abbey Road Sessions

 

I realised that I also have my lists for 2011 and 2010, so if you’re interested (duh, obviously you’re interested), then here’s how I felt about the heavy metal in those years, too.

2011:

01. Vektor – Outer Isolation
02. The Devil’s Blood – The Thousandfold Epicenter
03. Devin Townsend – Deconstruction
04. Opeth – Heritage
05. Beardfish – Mammoth
06. Blut Aus Nord – 777 Sect(s)
07. Blut Aus Nord – 777 The Desanctification
08. Blood Ceremony – Living With The Ancients
09. Mastodon – The Hunter
10. Krallice – Diotima
11. Thy Catalfaque – Rengeteg
12. Primordial – Redemption At The Puritan’s Hand
13. Dornenreich – Flammentriebe
14. Taake – Noregs Vaapen
15. Mitochondrion – Parasignosis
16. liturgy – Aesthethica
17. Arkan – Salam
18. Doomsword – The Eternal Battle
19. Symphony X – Iconoclast
20. Forefather – Last Of The Line

Honourable mentions (no order):
Aosoth – III
Burzum – Fallen
Cannabis Corpse – Beneath Grow Lights Thou Shalt Rise
Decapitated – Carnival is Forever
Esoteric – Paragon of Dissonance
Exhumed – All guts no Glory
Red Fang – Murder the Mountains
Rotten Sound – Cursed
Rwake – Rest
Sólstafir – Svartir Sandar
Absu – Abzu
Anaal Nathrakh – Passion

 

2010:

01. Deathspell Omega – Paracletus
02. Aborym – Psychogrotesque
03. Orphaned Land – The Never Ending Way Of ORwarriOR
04. Star One – Victims Of The Modern Age
05. Ihsahn – After
06. Todtgelichter – Angst
07. Triptykon – Eparistera Daimones
08. Ghost – Opus Eponymous
09. Enslaved – Axioma Ethica Odini
10. Kylesa – Spiral Shadow
11. Sahg – III
12. Melechesh – The Epigenesis
13. Impaled Nazarene – Road To The Octagon
14. Overkill – Ironbound
15. StarGazer – A Great Work Of Ages
16. Griftegard – Solemn. Sacred. Severe.
17. Nachtmystium – Addicts: Black Meddle II
18. Sigh – Scenes From Hell
19. Atheist – Jupiter
20. Finntroll – Nifelvind

Honourable mentions (no order):
Burzum – Belus
Gnaw Their Tongues – L’Arrivée De La Terne Mort Triomphante
Cathedral – The Guessing Game
The Meads Of Asphodel – The Murder Of Jesus The Jew
WolfP.A.C.K. – I
Slough Feg – The Animal Spirits
Rotting Christ – AEALO
October Tide – A Thin Shell
Leng Tch’e – Hypomanic
Lantlôs – .Neon
Keep of Kalessin – Reptilian
Kamelot – Poetry For The Poisoned
Immolation – Majesty And Decay
Galar – Til Alle Heimsens Endar
Electric Wizard – Black Masses
Agalloch – Marrow Of The Spirit
An Autumn For Crippled Children – Lost
Negura Bunget – Virstele Pamintului
Grand Magus – Hammer Of The North
Hesper Payne – Unclean Rituals
Alcest – Écailles De Lune
Celestiial – Where Life Springs Eternal
Deftones – Diamond Eyes

Oh, those gays and their “marriage”

Following the wonderful and happy Xmas messages from Archbishop Vincent Nichols* and the Pope**, we have judge and founder of pseudo-charity The Marriage Foundation*** Sir Paul Coleridge weighing in on the same-sex marriage “debate”:

“So much energy and time has been put into this debate for 0.1% of the population, when we have a crisis of family breakdown.”

A few questions:

  • Since when was it considered a chore to grant people equal rights? We could reduce the expenditure of precious time and energy by ignoring the people that the changes won’t affect (i.e. everyone arguing against same-sex marriage rights), but perhaps that would be considered “undemocratic”. Or “Orwellian“.
  •  What is the threshold percentage population that we should bother with when discussing equal rights? 0.11%? 1%? 6%?
  • If Sir Paul Coleridge had actually looked up the number of gay people in Britain, would he have used this to inform his percentage estimate, or would he have continued to make shit up****?
  • If same-sex marriage were legalised, would The Marriage Foundation then take an official position on it?

Visit the Coalition for Equal Marriage.

 

* in which we discover that the head of the Catholic Church in this country thinks that granting equal rights to minority groups means that we are living in an Orwellian nightmare
** fuck the pope
*** seriously, have a read of their aims*****
****along with Archbishop Nichols – 7:1 against gay marriage my balls
***** legal disclaimer: I’m not saying the charity is fake; I’m saying that I don’t consider an organisation dedicated to pushing a narrow-minded moral agenda to be worthy of charitable status******
****** though private schools manage to keep charitable status, so it takes all sorts*******
******* I enjoy this asterisk lark, as you might have noticed

Newcastle Skeptics in 2012

Newcastle Skeptics in the Pub have just had their final talk of the year (BUT DON’T FORGET THE XMAS PARTY/QUIZ ON 4TH DECEMBER!) so I thought I’d have a quick look back the year’s events.

January

We started the year with a visit from local MP Chi Onwurah, who spoke to us about innovation and science in Newcastle. SITP is very much not a partisan entity, but I think it’s good to be able to involve local politicians and make them aware of the growing interested in skepticism, science, and evidence-based policy across the UK. Chi has a very interesting background and it’s good to know that there’s a scientifically literate voice to represent the north east in parliament, even if her talk was naturally Labour-biased.

February

We continued with something a little different – a talk on tattoos and media perceptions of tattooing by Matt Lodder. It was good to get away from our usual science-oriented focus to a really interesting topic that I think most of us didn’t know much, if anything, about. Fascinating pictures of people donating their tattooed skin to art galleries, and an interesting discussion afterwards.

March

We had two events in March. Firstly, local academic Tom Joyce gave a talk on his research into failing metal hip joints, and the current licensing regulations on medical devices. Medical devices and drugs are regulated quite differently, and Tom gave a detailed account of how the regulations have allowed the current metal hip joint crisis to develop.

Secondly, we had an open-mic night, where several regular and not-so-regular SITP attendees gave short talks on a really diverse array of topics, from genetic algorithms to dodgy breast implants to energy saving buildings. Also I did a song. We’re pretty keen to do another one of these next year as it went down very well, so please get in touch (tweet @SITP_NCL or leave a comment) if you’re interested!

April

Mark Lynas ventured up north for April’s talk, talking about climate change, ocean acidification, nitrogen use, biodiversity loss, and several other global problems that currently confront us. Mark’s talk discussed potential technological solutions to these various problems, including making compelling cases for the use of technologies traditionally opposed by green campaigners like genetic modification and nuclear power. Plenty of food for thought in this one.

May

A very personal perspective on gender identity from Edinburgh Skeptics’ own Miss Twist, talking about clothing choices in law and culture, and how she manages to create such an excellent cleavage when wearing a dress. Definitely made me consider how I think of others’ clothing and self-image choices. I’d be very interested in hearing Miss Twist speak again in a few years time, to see how much her experiences/societies reactions change in the future.

June

Another month with two events. First off, the scandalous Rich Peppiatt, former Daily Star journalist and lover of Sierra Nevada Pale Ale, spoke about his experiences as a tabloid journalist, the agendas that drive tabloid news stories, and why he quite his job and leaked that letter to The Guardian. This was particularly interesting in light of the Leveson Inquiry, and I’d highly recommend going to see Rich’s “One Rogue Reporter” show if you get the chance.

Apocalyptic storms hit Newcastle on the very afternoon that Helen Arney was scheduled to entertain us with her unique brand of wonderful geeky songs. Fortunately Helen had arrived in Newcastle before all our transport systems failed; unfortunately, everyone else got stuck as all our transport systems failed, but we battled on and Helen put on a great show for the few of us that made it along. Just the thing to cheer us up on such a miserable evening.

July

Another non-science talk this month (she’s going to kill me for saying that) as Hannah Little gave us a talk on the evolution of language, a really fascinating topic that I knew very little about. Highlights: Hannah’s description of the Great Vowel Shift, and discovering that there existed an ape by the name of Nim Chimpsky. Hannah recently moved to Brussels to start a PhD in linguistics, good luck Hannah!

August

Back to science for August (sorry Hannah), with Keith Lindsey of Durham University talking about GM crops. I must admit I missed this one because of other pressing academic engagements in Germany, which is a shame as it’s a topic I find particularly interesting as there is so much emotive discussion about  it, but very little good evidence presented in the media. Hopefully I’ll get to hear Keith talk at a future event.

Yet again we managed to squeeze two speakers into one month (we are generous like that), with Alom Shaha speaking about his experiences growing up in a community of Bangladeshi immigrants, losing his faith in Islam, and how he deals with conflicts between science and religion that can arise in the classroom. Alom gives a great talk and it’s fantastic to hear from someone with a very different background from those in the New Atheist crowd talking about their lack of faith.

September

After a double-talk month, we unfortunately skipped September entirely as our speaker had to cancel at the last minute. We’re currently aiming to have Keir Liddle join us in 2013 instead, when he will discuss the Burzynski clinic cancer “treatment” affair.

October

Keith Laws from the University of Hertfordshire visited in October to speak about the use of Cognitive Behavioural Therapy in treating severe mental disorders. I was very pleased to see nurses and clinical psychologists in the audience, who stimulated a very interesting debate following the talk (which even continued on Twitter the next day…). Keith clearly explained the intricacies of meta-analysis and the details of how trials of talking therapies can be biased. Didn’t bring his synths along though, sadly.

November

Our most recent talk was by Caroline Fiennes, who spoke about how to assess the truth of claims made by charities. Far from being a charity-bashing session, Caroline has been a charity CEO and is obviously very much pro-philanthropy. She spoke about how charities can measure and maximise their impact (e.g. randomised controlled trials), about how good intentions can go wrong, and how to get charities to take this message on board (be more discerning donors!). She also has a very good answer to the perennial question “how much of my money actually gets to the people we want to help?” – read her book to find out.

We’re currently putting together a wizard-wicked programme of speakers for next year – any requests let us know! In December we will be having an Xmas Party Special Awesome Bonanza, including quiz and wonderous prizes. It’s on 4th December at the Old George. Hope to see you there!

Ridiculous thesis requirements: impact factors (again)

The thesis: a culmination of your years of hard toil as a PhD student, representing a significant original contribution to your field of study. So sayeth the dictionary (probably; I haven’t checked), but one can go about structuring a thesis in various ways. Some universities offer the option of submitting a collection of published papers, together with an introduction and conclusion to tie-together the various works, as an alternative to writing a thesis from scratch and having to reformat your data and ideas from your papers into a new entity that few will ever read. This seems like a sensible compromise to me – if you’ve proven that you can produce research of suitable interest and originality to be published in peer-reviewed journals, it seems somewhat superfluous to have to spend further effort writing a thesis (though of course there are good arguments for writing a separate thesis, which I won’t go into now because I’ll lose the impetus behind my indignant rant).

A friend of mine doing their PhD at a university in East Asia is allowed to submit a thesis in this form, and is currently finishing writing up several papers to include. However, the regulations from their university demand that the combined impact factor for the articles be 10 or more. The problems with impact factors have been well documented elsewhere, and it’s really worrying that this is being asked for as a requirement for a PhD degree when it makes little sense to apply impact factors for journals to individual papers from those journals, let alone to the researchers themselves. These kinds of demands are apparently quite common across universities in the country my friend is working in (apologies for clumsy anonymiserating…), resulting in instances of research fraud – I’ve heard of a supervisor who submitted a review article to a journal with their student listed as first author, though they hadn’t worked on the article, just to bump up the student’s impact for their thesis.

Hopefully my friend won’t have too any problems meeting this ludicrous requirement, as they are doing good research in a “high impact field”, but I wonder how many students, having published good work, can’t achieve this target simply because the good journals in their specialism don’t have comparatively high impact factors.

Guess the mystery device!

COMPETITION! Guess the mystery item at the bottom of the post. Prize available. See below.

Further neglect arising from a delightful holiday in Sicily and a 4 day course on FSL in Bristol. FSL is a tool for analysing fMRI, MRI and DTI brain imaging data, and it’s pretty nifti*. This isn’t really anything to do with what I work on, but it’s nice to have a bit more knowledge about the various tools and methods that go into these kinds of imaging analyses, especially for understanding imaging papers. Bristol is rather nice, too:

Bristol Cathedral

We walked past the Cathedral every morning, which was delightful

 

"Do NOT put chewing gum in the urinals - this causes blockages and flooding [and it ruins the flavour]"

Chemistry department toilets

This device is in the Bristol Clinical Research and Imaging Centre. If you leave a comment with an amusing guess, I may send you a prize. This prize may be good, or not. People that I’ve told the answer to, don’t spoil it. Also, no Googling. Points for creativity.

The Mystery Device

If you can guess what this is, I will give you a prize

 

*I’m sorry.

London Met international student ban insanity

Perusing the news this morning, I notice that London Metropolitan University has been banned from sponsoring non-EU foreign students because of its rather lax approach to visa enforcement, with 26/101 non-EU foreign students having no valid visa according the UK Border Agency (I also notice I’m a bit behind The Times, as they broke the story on 26th August. Shit, it’s almost September).

Firstly the timing of this, shortly before term starts, is ridiculous. The students that will be affected, legitimate or otherwise, now have a mad rush to find new courses before the academic year starts. Secondly, the general approach is all sorts of wrong. Why on Earth are legitimate, fee-paying students being punished for the failings of their university? Ashiqur Rahman nails it: the Border Agency could easily have banned the university from taking on any international students in the future, and allowed the current crop to finish their courses, thus preventing the massive upset to hundreds of legitimate students and the damage this may cause to UK higher education’s international reputation.

The government is setting up a task force to help deal with affected students, which is all fine and good and hopefully they’ll be able to do some damage limitation, but what a ridiculous waste of effort when the situation could have been avoided entirely by applying the rules with a little leniency and intelligence. Or am I missing something?

Measuring brain electricity

Ah yes, I was going to write about data analysis, but I got distracted by more data analysis. Anyway, here’s a bit of information on how we measure what’s going on in the brain, and how we interpret those measurements.

The brain generates and processes information using electrical signals, as far as our current understanding goes. For example, neurons in the eye respond to light by sending electrical signals to the visual cortex (via some other brain areas), where the signals are processed, interpreted, and distributed to other parts of the brain for integration with our other senses, further interpretation etc. These signals are very small, but measurable, even from the scalp – this is called electroencephalography (EEG). Each electrode of an EEG measures contributions from hundreds of thousands, perhaps millions, of neurons, so only provides a very coarse measurement of what’s really going on. At the other end of the scale, the electrical responses of an individual neuron can be measured by using a very small electrode to attach to its cell membrane, revealing the electrical activity inside it (or even to look at the currents flowing through individual channels in the membrane). This gives you information on what a single neuron is doing, but neurons never work in isolation, so you’re missing out on a lot of information about how the rest of the neuronal network is behaving.

Various types of measurement are available to bridge this scale divide. The type that I’m working with is from Utah arrays – 3.6mm square grids of 100 small electrodes that measure electrical activity from the space around neurons. This kind of measurement is similar to an EEG in that each electrode measures activity from many neurons surrounding it, but because the electrodes are placed so close to the neurons, spikes from individual neurons can also be picked up. The smaller scale allows the construction of a detailed picture of the local brain dynamics. Utah arrays are also particularly cool, because they are one of the only types of electrode that provide information on this kind of spatial scale that have also been approved for use in humans. They have already provided previously inaccessible information about epileptic brain activity in humans, and can be used to create brain-machine interfaces.

Utah array, source http://www.sci.utah.edu/~gk/abstracts/bisti03/

The faintly terrifying-looking Utah array. Don’t worry, it’s quite small.

The data I get is from less glamorous locations than behaving humans, but in future I may get my grubby paws on recordings from brain tissue that has been removed during epilepsy surgery. Currently I’m looking at how brain activity varies in space over the small scale that the Utah array provides, and trying to match a computer model to the information provided by the recordings. The idea then is to investigate aspects of the model that cannot be changed in an experiment, such as how neurons are connected together, in order to guide future experimental research into unhealthy brain activity.