The brain as a network – a new hypothesis?

The BBC News Sci/tech section recently ran a few stories about neuroscience and technology that I considered to be a bit oversold. There was one article in particular I wanted to write about: Brain works more like internet than ‘top down’ company. The article refers to a recent study in PNAS that used injections of dye to trace connections between brain areas. The article claimed that it demonstrated that the brain is an interconnected network like the internet, counter to the apparently prevailing view of the brain as a hierarchy. The technique could also apparently lead to a map of the brain. Now, I was initially going to take the BBC to task for what seemed to be another oversold and rather general piece of research. However, after having a read through the paper, it seems that the authors may, to some extent, have oversold the novelty of the implications of the work, and the groundbreaking-ness of their technique. The line of reporting by the BBC only compounded the problem.

Sunday Links #6

Apparently it was SharkWeek on the Discovery channel recently. C6H12O6 has a guest spot about the biology of sharks, which is quite frankly amazing. If you can find Channel 4′s Inside Nature’s Giants, I recommend you watch the shark episode of that too (as well as all the others).  For starters, a sharks’ jaw bones evolved from their ribs, and they lunge forward when they bite. The footage of the goblin shark has to be seen to be believed.

Zombies+science=WIN. In so much as you can apply science to animated corpses, Cracked.com details 7 reasons why a zombie outbreak would quickly fail. (Specific zombie franchise not specified)

Colin Schultz at CMBR provides tips for young science journalists. Ideally, I guess it should be tips for all science journalists, but they tend to be quite stuck in their ways. It includes such unfortunately necessary science journalistic tips as “don’t just accept what your told, be a journalist”.

On a related note SEEDMagazine asks how do you avoid scientific miscommunication?

Following on from my discovery of the concept of open lab books, a 15 minute video explaining what they’re all about.

What is the social impact of science? A post at Sciencebase about a paper on how it has changed over history. The paper itself is unfortunately behind a paywall.

Can dogs and humans communicate? Thoughtful Animal reviews a recent paper from the journal Animal Behaviour. Unfortunately also behind a paywall.

And finally, something light to finish on (!). Sam at Skepchick reviews The Nature of Existence, a documentary by Roger Nygard exploring people’s ideas about why we’re here and what we should be doing while we are “at an enjoyable lay level”. There’s a trailer to watch too.

http://www.cracked.com/article_18683_7-scientific-reasons-zombie-outbreak-would-fail-quickly.html

Looking back on my PhD

Now that I’m in the hopefully fairly short final straight of my Phd, I’m feeling a bit reflective. Whilst I’ve been writing up, I’ve been reading around the science behind my project in some depth, and only really now starting to get a grip on the theory behind the experiments. Unfortunately in some cases, this has meant that I’ve learnt that some of the experiments I’ve done probably weren’t going to work the way we intended, and probably weren’t worth the struggle. I always knew that when you came out of a PhD, you were supposed to be an expert in that tiny subfield. With this in mind, I started to wonder whether when my supervisor set me on an experiment, I was supposed to go away and understand the problem before I even started on it. What I usually did was understood the problem enough to see the rationale behind the experiments, did them, then went to my supervisor with the data. It’s only now with reading and writing up I can see all the potential problems.

I’ve been worried that I’ve left what feels like the bulk of my PhD to the end. The experiments were just things that I did, but the learning and understanding is what the PhD is about, surely? I felt like I’d missed something. It’s made worse by the fact that I came to a neuroscience PhD with only AS-levels in biology and chemistry, straight from a psychology bachelors degree unfortunately lacking in in-depth neuroscience content, without any intervening masters. I was fortunate to be ably taught how to do extracellular electrophysiology by a patient post-doc who started in the department at the same time as me (thanks Lio!) who was replaced by his partner in crime from his PhD, who was equally helpful (thanks Nico!). But I was worried I’d skipped the theoretical fundamentals behind neuroscience and electrophysiology.

Fortunately I’ve been reassured by older colleagues that  it’s pretty common to have reached the end of a PhD before you have learned enough to realise that you should have done things differently, and that a large part of a PhD is learning where your strengths and weaknesses lie, and not knowing them at the start and be done with them by the time you’ve finished. I feel a bit happier about it all, but like with many things in life, I still sometimes wish I could do it all again with the benefit of hindsight. Sometimes I wish I’d come to the PhD from a neuroscience skewed biology degree instead of psychology, but then I wouldn’t have been in the right place at the right time to have the fantastic opportunity I have had.

I envy the guys in the States who do PhDs for something like 7 years, with lots of studying before getting stuck into a project. Three years seems pretty inadequate compared to that. Cardiff seem to have it down too, their neuroscience PhD program consists of three years of experimental project, but first a year of study which is half modules explicitly teaching you how to do a neuroscience PhD (the nearest thing at UoS – MSc Cognitive and Computational Neuroscience – seems to try to cover too many bases at once) and the other half completing three practical lab rotations. I tried to take some second year undergrad biology neuroscience modules as extra credit, but I was told that they had to be masters level or above to qualify. This is in spite of the existence of accredited modules which are designed for the extra credit system which involve taking a first year undergrad psych module, or even having a discussion group about your PhD in a coffee shop…

Ignoring the green-eyed academic in me, I’m glad I know what the educational known unknowns are for me. I’m just dying to make them known knowns, and I hope I get the chance to do it.

Just when you think you have things figured out…

I was talking to someone at work the other day about how in the natural sciences (and probably most other sciences), if you think you have a stone cold fact about the way something works, no matter how low-level or fundamental you think it is, it’s probably a generalisation and doesn’t exactly describe how things actually are. Like you can describe electrical conduction using basic laws, but sometimes the laws don’t work how you might expect, and it turns out your wires do funny things at extreme temperatures. It’s the reason error bars exist. What might seem like random variation in data might partly be the result of experimental error, but some of it will be due to not knowing all the factors involved or not being able to measure every tiny variable.

I’m rambling a little. Hopefully an example I found today might help.

Neurotransmitters are released by neurons. They tend to be released when the neuron fires an action potential, but not always. The amount released might be modulated by how much has already been released, or the input of other neurons, or lots of other factors and their effect can be modulated by changing the receptors in the cell membrane of the target cell. I know that the cause and effect of neurotransmitter release is a complicated business.

What I didn’t expect is that the mechanism of neurotransmitter release itself is not a passive process. I had assumed that the ‘instructions’ to release were received and vesicles of neurotransmitters were carried to the synapse, exocytosed, and the neurotransmitter was released. I knew that the pre-signalling instructions were modified by all sorts of factors, and the effect of the released neurotransmitter was modified by all sorts of factors, but I just saw vesicles as little packets being carried to their destination. Apparently, however, the microtuble cytoskeleton, which provides scaffolding to the cell, and along which vesicles travel, is actively modified by, and modifies the neurotransmitters being released.

Despite accepting that there are probably unknown unknowns in descriptions of natural systems at every level, they’re still surprising. Those little blips and outliers in your data? Keep an eye on them, they might not be the random errors you think they are.

Gardiner, J., Overall, R., & Marc, J. (2010). The microtubule cytoskeleton acts as a key downstream effector of neurotransmitter signalling. Synapse [Epub ahead of print] doi:10.1002/syn.20841

Referrers

I’ve got lots of one-off referrals from unrelated junk blogs, advertising sites and sites that just seem to trawl the web for new posts. Is there any way to filter some/all of them from by blog stats, or stop them registering as referrals? I want to see where my traffic is actually coming from.

Lab books

It’s probably quite late in my PhD to finally take this on board (I’m at the end of my final year now), but I’ve realised that my note taking for my experimental lab book is pretty poor. I might have a future career in academia which means I can make use of this new attitude to my organisational skills, but I’m going to at least make the most of it in my last few months.
It’s not that I don’t write enough down for me to remember what I’ve done throughout my PhD, but if I ever need to come back in 10 years, or if someone else needs to understand my notes, especially if they don’t have the first clue about my experiments, they won’t be easy to understand.
To be fair to myself, I don’t seem to write much more or less detail than most of the people I work with. Recently, however, I read some example lab books as part of a guide to successful academia and even little things like writing the date out in full in case you move from Europe to US to Canada seemed to make sense. Mostly though, I realised that my notes a) make the assumption that you know what the study is and why it’s being done and b) sometimes only make sense if you follow the ‘story’ over the course of a few experiments.

It’s a late lesson to learn, and it’s not a big lesson, but if I’m going to be pro-open-access science, I guess openness should begin at home.

EDIT: I’ve just tripped over a Wikipedia article on Open Notebook Science, based around the idea of full openness with data, described in a blogpost by Jean-Claude Bradley. There’s a list of active open notebooks, which might be interesting.

Does emotional abuse make you ROFL?

Hello again! I’ve got a bit more organised with my blogging recently – setting aside times to work on posts outside of/as a break from work hours rather than spending all morning procrastinating on it. I’ve also started to list links to issues which aren’t really funny/interesting links to put in the Sunday Links digest, but aren’t enough to do a long post on. The result should be little posts like this that I can knock out over lunch, and hopefully as a result more frequent posts. Anyhow…

Does emotional abuse make you ROFL?

I’m usually quite amused by the NCBI ROFL blogs at Discovery magazine. It highlights the weird, wonderful, and sometimes incredible subjects that is available on the NCBI database PubMed, and bills itself as “real scientific articles with funny subjects”. Now, I hate the mocking of legitimate research as nonsense, which usually results out of a misunderstanding (such as Sarah Palin dismissing the entirety of fruit fly research, or a popular free public transport based newspaper taking one sentence of speculation out of a molecular neuroscience paper and presenting it as the major finding in a “press release from the department of the bleeding obvious” segment), but I do have a sense of humour about weird research, which NCBI ROFL seems to share. Sometimes they pick seemingly fairly normal subjects, like ethological studies of behaviour, but whatever.

However, the Thoughtful Animal’s post on their recent choice of “Exposure to parental verbal abuse is associated with increased gray matter volume in superior temporal gyrus” or NCBI ROFL: Belligerent berating builds bigger baby brains!.

There’s nothing funny about child abuse. Perhaps a better name for the blog would be NCBI WTF, rather than ROFL, or perhaps they should just stick to actually funny stuff. To be fair, they conceded that they don’t consider it funny, but it’s odd that they defend their choice with “who would think to look for a correlation between getting yelled at as a child and brain size?”. Moving beyond their characterisation of verbal emotional abuse as “getting yelled at”, the paper details how severe verbal abuse is a traumatic event which can have long-lasting psychological effects. These effects might have an underlying neural pathology. It’s hardly a bizarre leap to make…

By all means have a sense of humour about people spending their time debating whether Gollum has schizophrenia or MPD, but don’t mock legitimate, albeit esoteric research, and certainly don’t do it to serious research into serious subjects.

Are online archives restricting what we cite?

I recently read article at Code for Life inspired by a post from fellow science blogger Isis about an apparently increasing tendency to cite recent research papers on a topic that stretches back much further, and researchers publishing ‘new’ discoveries or techniques which had already been made. The suggestion was that the availability of recent papers online has made us less willing to cite older work. It made me think about my own referencing habits, and whether I was measuring up.