PhD done, moved to Okinawa

April 1st, 2014 § 1 comment § permalink

Special Breath Chewing Gum

Hello everybody!

I realise I haven’t done a post since last September, which I believe is long enough to declare this blog legally dead. Fortunately I am trained in internet CPR and am able to kickstart the heart of this here blogging enterprise using my natural guile, expert medical training, and the WordPress “add new post” button. In my defense, I have been finishing off my thesis, which has now been submitted, scrutinised, corrected, resubmitted, re-scrutinised, and finally deemed worthy by the Powers That Be, which means I am now officially Dr. Richard Tömsett, PhD.

In more interesting developments, I have moved away from the City of Dreams to the wonderful island of Okinawa to start a 1 year postdoctoral research thingy at OIST (many thanks to the Japan Society for the Promotion of Science for moneys). I’m lucky enough to have been to Okinawa before, in 2011 when I did the Okinawa Computational Neuroscience Course. They have a beer vending machine. Insanity. Anyway, a big attraction of Okinawa is the beaches and sunshine, but of course it’s been raining pretty much since I arrived so far. The university itself is pretty sexy though.

There are already plenty of pictures of how sexy and nice Okinawa is so I thought I’d mainly post pictures of things that tickled me about Japan. Behold, the chewing gum that, when you put it in your mouth, gives you “special breath”:

Special Breath Chewing Gum

Your breath, it will be special

As I haven’t posted for ages, you get the bonus treat of the magical toilet that has a sink on top of it, so when you flush, you can wash your hands and not waste any water! Ingenious

Wrong studies: is this how science progresses?

September 18th, 2013 § 6 comments § permalink

An article by Sylvia McLain in the Guardian’s Science Blogs section yesterday argued against John Ioannidis’ provocative view that “most scientific studies are wrong, and they are wrong because scientists are interested in funding and careers rather than truth.” The comments on the Guardian article are good; I thought I might add a little example of why I think Sylvia is wrong in saying that prevailing trends in published research (that most studies turn out to be wrong) just reflect scientific progress as usual.

There is a debate in the neuroscience literature at the moment regarding the electrical properties of brain tissue. When analysing the frequencies of electrical potential recordings from the brain, it is apparent that higher frequencies are attenuated more than lower frequencies – slower events show up with more power than faster events. The electrical properties of brain tissue affect the measured potentials, so it is important to know what these properties are so that the recordings can be properly interpreted. Currently, two theories can explain the observed data: the high-frequency reduction is a result of the properties of the space around neurons (made up mostly of glial cells), which result in a varying impedance that attenuates higher frequencies; or it is a result of passive neuronal membrane properties and the physics of current flow through neurons’ dendrites, and the space around neurons doesn’t have an effect. Both of these explanations are plausible, both are supported by theoretical models, and both have some experimental data supporting them. This is a good case of scientific disagreement, which will be resolved by further more refined models and experiments (I’ll put some links below). It could be that aspects of both theory become accepted, or that one is rejected outright. In that case, the studies will have been shown to be “wrong”, but that is besides the point. They will have advanced scientific knowledge by providing alternative plausible and testable theories to explore.

The kind of “wrong” study that Ioannidis describes is quite different. His hypothesis is that many positive findings are results of publication bias. High profile journals want to publish exciting results, and exciting results are usually positive findings (“we found no effect” is rarely exciting). Scientists are under pressure to publish in high profile journals in order to progress in their careers (in some cases even just to graduate), so are incentivised to fudge statistics, fish for p-values, or just not publish their negative results (not to mention the problems inherent in null hypothesis testing, which are often ignored or not known about by many study designers). Pharmaceutical companies have further obvious incentives only to publish positive results from trials (visit www.alltrials.net !). This doesn’t lead to a healthy environment for scientific debate between theories; it distorts the literature and hinders scientific progress by allowing scientists and doctors to become distracted by spurious results. It is not – or should not be – “business as usual”, but is a result of the incentive structure scientists currently face.

Hopefully it’s clear why the second kind of wrong is much more damaging than the first kind (the first is healthy), and that’s why I think Sylvia’s Guardian piece is a bit wrong. Changing the incentives is a tricky matter that I won’t go into now, but as an early career researcher it’s something I don’t feel I have a lot of power over.

REFERENCES
Note: this is far from comprehensive and mostly focuses on the work of two groups

References in support of the variable impedance of brain tissue causing the low-pass filtering of brain recordings:
Modeling Extracellular Field Potentials and the Frequency-Filtering Properties of Extracellular Space
Model of low-pass filtering of local field potentials in brain tissue
Evidence for frequency-dependent extracellular impedance from the transfer function between extracellular and intracellular potentials
Comparative power spectral analysis of simultaneous elecroencephalographic and magnetoencephalographic recordings in humans suggests non-resistive extracellular media

References in support of intrinsic dendritic filtering properties causing the low-pass filtering of brain recordings:
Amplitude Variability and Extracellular Low-Pass Filtering of Neuronal Spikes
Intrinsic dendritic filtering gives low-pass power spectra of local field potentials
Frequency Dependence of Signal Power and Spatial Reach of the Local Field Potential
In Vivo Measurement of Cortical Impedance Spectrum in Monkeys: Implications for Signal Propagation (this is, as far as I know, the most recent direct experimental study measuring the impedance of brain tissue, finding that the impedance is frequency-independent)

Bright Club audio

September 17th, 2013 § 0 comments § permalink

A little while ago I posted about doing Cambridge Bright Club – well here‘s the podcast from that event, which includes excellent pieces from the other performers. I’m on first.

Anti-optogenetics 2

September 7th, 2013 § 0 comments § permalink

This is a response to John Horgan’s response to the responses to his original anti-optogenetics-hype article what I blogged about. The comments section is worth reading, but I thought I’d respond to a couple of points here, too.

Neuroscientist Richard Tomsett says one of my examples of hype—a TED talk by Ed Boyden, another leader of optogenetics—doesn’t count because “the whole point of such talks is hype and speculation.” Really? So scientists shouldn’t be criticized for hyping their research in mass-media venues like TED—which reaches gigantic audiences–because no one is taking them seriously? Surely that can’t be right.

I perhaps wasn’t clear enough here – my point was that it seemed silly to refer to a TED talk as an example of hype when all TED talks hype their particular topics. Scientists certainly should be criticised for hyping research, but this is a problem with the TED format rather than optogenetics.

…the abysmal state of health care in the U.S. should have a bearing on discussions about biomedical research. I’m not saying that journalists, every time they report on a biomedical advance, need to analyze its potential impact on our health-care problems. But knowledge of these woes should inform coverage of biomedical advances, especially since technological innovation is arguably contributing to our high health care costs.

I agree, but again this is not a problem with optogenetics, or even the scientists that try to hype it.

John’s posts touch on an issue with the way that science is funded, which (in the UK at least, and I assume elsewhere) requires an “impact” assessment to try to ensure that research spending isn’t a waste of money. This is a big problem because it can be very difficult to predict what impact most research will have in the short term, let alone the long term. The most obvious way to demonstrate “impact” in neuroscience is to refer to potential treatments for brain disorders, though such treatments might be years or decades away. The brain is so complex that it’s impossible to predict how a particular piece of research might impact medical practice, but you are compelled to spin your case because of this demand for “impact” – hence why all neuroscience press-releases will refer to potential treatments, no matter how relevant the research is to medicine. I completely agree that if scientists want to justify receiving public money then they need to justify their research to the public, but the current incentives promote hype – particularly medical hype. Note that I don’t offer a solution to this problem…

As I said in the previous post, there are good points to be made about the hype surrounding optogenetics (as in this post), it’s just unfortunate that John instead went for criticisms that could be leveled at any hyped science. Rather than attacking a particular field with some quite shaky points, it would have been much more interesting to address why scientists feel the need to hype their work in the first place.

Anti-optogenetics

September 1st, 2013 § 1 comment § permalink

I read an article that annoyed me a bit. It’s a rant by John Horgan against optogenetics and why the author is vexed by breathless reports of manipulating brain functions using light (optogenetics is where you genetically modify brain cells to enable you to manipulate their behaviour – stimulating or suppressing their firing – using light. This is particularly cool because it allows much better targeted control of brain cells than using implanted electrodes or injecting drugs, the other most precise methods of controlling the activity of many cells). I love me a good rant, and here is a nicely considered article about the limits and hype over optogenetics [NB: I am not an expert in optogenetics], but this was neither good nor considered.

The first half of the article raises a complaint about the hype, which might have been legitimate if it had not misrepresented said hype. It grumbles that articles about optogenetics tout its therapeutic potential for human patients, but we don’t know enough about the mechanisms underlying mental illnesses to treat them with optogenetics. While this latter point is certainly true, it’s a straw-man: read the articles linked-to in the first half and see which ones you think are about human therapeutic potential (I’ve included the links at the bottom*). They all clearly report on animal studies, though of course make reference to the potential for helping to treat human illnesses (not necessarily using optogenetics directly, but by better understanding the brain through optogenetics). Indeed, this point was made to John on Twitter, so his article now includes a clarification at the end admitting as much, but still making some unconvincing points, which we’ll come to later.

The second part of the article addresses John’s “meta-problem” with optogenetics: he “can’t get excited about an extremely high-tech, blue-sky, biomedical ‘breakthrough’-involving complex and hence costly gene therapy and brain surgery-when tens of millions of people in this country [USA] still can’t afford decent health care.” Surely this is a problem with all medical (and, indeed, basic) research that doesn’t address the very largest problems in the health system? I agree totally that this is a massive problem, but it is entirely socio-political, not scientific. Moaning that optogenetic treatments will be expensive is like criticising NASA because only a few lucky astronauts get to go into space.**

John has been good enough to add some “examples of researchers discussing therapeutic applications” to his post. Briefly looking through these, we have a 2011 article in the Joural of Neuroscience, which uses optogenetics to study the role of a particular brain area in depression (doesn’t mention therapeutic optogenetics in abstract, only as a potential avenue for further research in the conclusion); a 2011 TED talk (the whole point of such talks is hype and speculation); this press release from the University of Oxford (which alludes to possible therapeutic use “in the more distant future” in one paragraph in a sixteen paragraph article); a 2011 article in Medical Hypotheses (a non-peer-reviewed journal whose entire point is to publish speculative articles that propose potentially fanciful hypotheses); and this article in the New York Times (I can’t argue with this – there is a fair bit on therapies for humans; John’s main gripe here, from his comments about this article, appears to be with the military funding that one of the several mentioned projects is receiving).

In the second amendment to the article – labeled “clarification” – John admits that he “overstated the degree to which coverage of optogenetics has focused on its potential as a treatment rather than research tool”, which is nice, but then criticises the potential insights from optogenetics research, saying:

But the insights-into-mental-illness angle has also been over-hyped, for the following reasons: First, optogenetics is so invasive that it is unlikely to be tested for research purposes on even the most disabled, desperate human patients any time soon, if ever. Second, research on mice, monkeys and other animals provides limited insights–at best–into complex human illnesses such as depression, bipolar disorder and schizophrenia (or our knowledge of these disorders wouldn’t still be so appallingly primitive). Finally, optogenetics alters the cells and circuits it seeks to study so much that experimental results might not apply to unaltered tissue.

Regarding point one: this is still about therapeutic, not research, uses of optogenetics; it also ignores that many patients undergo invasive surgery for epilepsy (which involves actually cutting bits of brain out – surely optogenetics could be a bit better here?) as well as for deep brain stimulation to treat severe depression and Parkinson’s symptoms. Regarding point two: this is a criticism of using animal models in any kind of research rather than optogenetic research in particular – it is valid, but totally besides the point. Regarding point three: if we’re looking to modify the cells in therapies anyway, why does this matter? Stimulating cells with electrodes or drugs changes the way they behave compared to “unaltered” tissue, too!

TL;DR – read this article instead, and don’t pay much attention to this one. It could have made some good points about optogenetics-hype, but didn’t.

*Links from the original article:

OCD and Optogenetics (Scicurious blog)

Implanting false memories in mice (MIT technology review)

Breaking habits with a  flash of light (Not Exactly Rocket Science blog)

Optogenetics relives depression in mouse trial (Neuron Culture blog)

How to ‘take over’ a brain (CNN)

A laser light show in the brain (The New Yorker)

** yeah I know, tenuous analogy – but let’s face it, all analogies are pretty shite

Policy and Bright Club Cambridge

June 13th, 2013 § 0 comments § permalink

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

March 29th, 2013 § 0 comments § permalink

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

February 7th, 2013 § 0 comments § permalink

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

January 22nd, 2013 § 0 comments § permalink

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”

December 27th, 2012 § 0 comments § permalink

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