Bayes and Girls

2533475728_a0dcfd4524_zYou have long hair, never miss the Great British Bake-off and are particularly good at multitasking. You also work in Parliament. So are you more likely to be a man or a woman?

Well, some pretty lazy stereotypes aside, we may believe that the initial description is more likely to be female than male. The cliches certainly push us into thinking that way.

But, we should also consider the under-representation of women at all levels in British politics, a fact which has been highlighted in the news.

So, ignoring the introduction spele, if we were simply asked what is the chance that someone picked randomly from Parliament is a guy or a doll, how could we go about answering this? Well, let’s think in terms of the proportional representation of these two groups. Chances of picking a fella is certainly going to be larger. We can reasonably then go and place our stack of chips with the chaps.

What happens when we also consider the multitasking, baking-lover characteristics? These are things that stereotypically we would associate with the fairer sex so, we may reason, this person is more likely to be female. The result is a conflict between these two guesses.

7204293066_1866f0488a_zHow many men have long hair, like baking shows and can pat their head and rub their stomachs at the same time? Actually, probably quite a few. Maybe not proportionally as many as women but if we then include what we already know about the relative population sizes in Parliament, there may well be, in absolute terms, more men who fit this description. Simply by the prior fact that there are so many blokes in parliament, this may well weigh the answer in their favour.

This example is a different take on a common example of something called decision heuristics which can lead to cognitive bias. That is, rules-of-thumb that you and I use to take mental shortcuts, focusing on one aspect of a problem rather than the whole thing. It involves presupposition and is an example of where our intuition can lead us astray. The description of the person’s characteristics seduces us into imagining a woman but the baseline gender ratio, which is sneaked-in afterwards, is probably a better indicator.

What this little example can show is how we can go about combining two separate bits of information to get an overall, rational answer. In statistics this can be done formally using something called Bayes’ theorem.

In general terms, Bayes’ theorem takes what we already know- called the prior- and combines this with what extra information or data we observe- called the likelihood. As a result, we then have an answer- called a posterior- that is influenced by both of these things. How much it is influenced by each depends on the strength and conviction of the prior belief or data respectively. If they agree, then the answer is more certain than it would have been if we had used only one of them in isolation and if they are conflicting then the answer represents this too.

In the British politics example above, the prior could be what we know about the proportion of men and women and the extra data is the description of the employee. Like a tug-of-war, these two bits of information pull us in different directions. For example, we can not simply go along with the description in isolation and bank on a broad. The conclusion could be that, before hearing the characteristics, we are fairly sure we would get a gent at random and, even after hearing the profile, we may still think this is the most likely outcome, although we’re less sure about it.

5985805174_bd5e2cfe98_zKnowing that the mystery person has long hair moves us towards thinking that it is more likely to be a woman compared to before we knew anything about their hair-do but it’s just not enough to overpower what we already know about the parliamentary gender bias. That said, even though the flowing locks may not actually change our mind, they would introduce more doubt. Bayes’ theorem could help quantify this doubt.

Bayes’ theorem has applications far and wide, including spam filtering, internet search engines and voice recognition software. Originally, its statistical fundamentals were thought a little shaky, so have been extensively discussed and argued but it is fair to say a lot of progress has been made and the theorem has attained acceptance in most fields. That said, It has some way to go before it’s nearly as popular as the Great British Bake-off.

Post by: Nathan Green

Aaahh!! Real Monsters!: How parasites and pathogens colonised fiction.

After the recent torrent of zombie everything and anything, it might feel like science fiction is all about done with weird parasites and diseases.  But the mystery and power of organisms sometimes invisible to the human eye has inspired fiction for decades, including some of the most famous Sci-Fi monsters. I’d take a wager that we’re still a few undead away from total eradication of fictional parasites.

Settle in, pull on a hazmat suit and a facemask, and we’ll delve elbow deep into the parasitic ooze of film, television and video games to take a good look at some of the best parasites and pathogens Sci-Fi has to offer.

Xenomorph or Alien – Alien franchise
Best get the big guns out right away. Alien is one of my all-time favourite films, centred around one of cinema’s most iconic and terrifying Sci-Fi monsters.

Xenomorphs they steal resources from their host from within the host’s body, so we can call them endoparasites. They’ve got a pretty complex life cycle: some life stages needing a host and some able to live in the environment. This mixture of host dependency is seen quite often in real parasites, in human-infective worms such as the roundworms Schistosoma and Ascaris, and flatworms like Fasciola. Like the Xenomorph, these worms use their human host as a place to reproduce or develop, whilst the free living stages search through the environment for new hosts to infect.

 Putting my well-practised, “parasite-life-cycle-specific” drawing skills to good use even years on from all of my undergraduate exams.
Putting my well-practised, “parasite-life-cycle-specific” drawing skills to good use even years on from all of my undergraduate exams.

Real parasitic worms are fairly scary too, responsible for a huge burden of severe and chronic disease especially among the world’s poorest populations. Although we can at the very least be grateful that their method of exiting the host as eggs in the faeces is a little less violent than the “chestbursting” exit of the Xenomorph.

 Ooh hello! Alien, Brandywine productions. Still taken from Backwoods Horror.
Ooh hello! Alien, Brandywine productions. Still taken from Backwoods Horror.

Genophage – Mass Effect video game series
Some of our fear of pathogens is really a result of our fear of our own misuse of them, as bioweapons. Genophage is a phage-like virus in the Mass Effect universe used against the Krogran race to control their population by the Citadel, an intergalactic governing body.

Phages are small, simple viruses that infect bacteria. In doing so, they are able to insert genetic material from themselves or other host cells, into that of their current host. The modus operandi of the genophage virus is not too dissimilar, as it inserts a specific mutation into all the body cells of Krogans that prevent pregnancies carrying to term.

Phages have the power to turn the fairly unpleasant Escherichia coli bacterium into a thoroughly horrible and occasionally fatal O157:H7 form. Scientists are now trying to harness this ability, but for much less nefarious purposes. It’s hoped that modified phages could provide a new mechanism of delivering vaccines or medical treatment against certain infections: seriously cool stuff.

Ceti Eel – Star Trek II: The Wrath of Khan

As a complete non-Trekkie, my one-time viewing of 1982’s The Wrath of Khan didn’t give me a full idea of the wonderful world of Star Trek zoology (TRIBBLES. LOOK AT THEM).

 TRIBBLES. Star Trek: The Original Series. Desilu productions. Still taken from Wikimedia Commons.
TRIBBLES. Star Trek: The Original Series. Desilu productions. Still taken from Wikimedia Commons.

From that one film I was introduced to Ceti Eels, fantastic parasites that set off my love for the gory and gruesome in a manner only paralleled by real parasites on the level of loaiasis and Chigoe fleas. After incubating in the body of its parent, the developed Ceti Eel enters a host through the ear, worming its way into the skull cavity and attaching to the cerebral cortex. As you can imagine this is hugely painful.

The Ceti Eel then unveils its crowning weapon: mind control. Or to be more precise, the infected are left susceptible to suggestion – fantastic news for the enigmatic antagonist, Khan.

Mind control must surely be confined to Sci-Fi? Not so. Both Ophiocordyceps fungus and Dicrocoelium fluke worms can manipulate their host’s behaviour to suit their own ends. The juvenile stage of the fluke is released by snails as cysts in their slime. Ants eat said slime for its moisture. Once in the ant, one key worm gets up to the central nerve structure of the ant, and convinces it to climb to the top of a blade of grass and clamp down, waiting right on show to be accidentally eaten up by a cow or sheep. The worm drives the ant to get itself eaten. The real mind-controlling worm is even better at its job than the fictional eel!

Why are there so many parasites in Sci-Fi (and why are they all so damn cool)? Art and culture are vital for exploring and communicating the world around us. This stands just as true for science fiction, and just as true for the gory and the weird that nature likes to throw at us. The strange and exciting parts of nature are what take our piqued interest, and drive us to fascination and awe. So, while the current zombie tidal wave might just be past its peak, I reckon as long as we have fantastic, powerful, utterly disgusting parasites from which to draw inspiration, we’re going to be telling stories about them for a long time to come.

This post, by author Beth Levick, was kindly donated by the Scouse Science Alliance and the original text can be found here.

References: fictional
http://en.wikipedia.org/wiki/Alien_%28creature_in_Alien_franchise%29
http://masseffect.wikia.com/wiki/Genophage
http://en.wikipedia.org/wiki/Khan_Noonien_Singh
http://en.memory-alpha.wikia.com/wiki/Ceti_eel

References: better than fictional
http://en.wikipedia.org/wiki/Helminths
http://en.wikipedia.org/wiki/Bacteriophage
http://news.nationalgeographic.com/news/2014/10/141031-zombies-parasites-animals-science-halloween/
http://en.wikipedia.org/wiki/Dicrocoelium_dendriticum
http://en.wikipedia.org/wiki/Ophiocordyceps_unilateralis

What’s going on in your head?: The science behind our inner voice

As a neuroscientist, one aspect of brain-science that has always intrigued me is the idea that we may never know exactly how another person experiences the world and whether their experiences differ from our own. I know what the red ball (pictured right) looks like to me but how do I know that you’re seeing same thing? In fact, I’ve often wondered what it would be like to see the world through the eyes of someone whose perceptions differ from mine, for example someone with colour or face blindness.

Sadly though, I’ve always assKarl_Pilkington_2008-02umed that my own experiences are disappointingly mundane and ‘average’. That was until ‘life guru’ Karl Pilkington taught me otherwise…

A few months ago, during a particularly long experiment, I was passing time listening to old exerts from the Ricky Gervais show when I came across the following dialogue:

Reading from Karl’s diary: “While I sat listening to The Kinks on my iPod, I wondered if everybody thinks in their accent. I know I do.”

Stephen: What’s this? What are you talking about?

Ricky: How do you know you think in your accent? Tell me a typical thought

Karl: I thought “that’s weird innit?” not “that’s weird isn’t it?” and I thought “I actually think in my accent”

Ricky: No, but, when I think I don’t think the sentence as like I’m saying it, it’s just a thought, the thought appears, it’s conceptual and it’s already there. It’s not like I go, “Rick?” “What?” “Just err… looking at that fella over there were you?” “Yeah, I was yeah. Erm, I was think he looked a bit weird” “Oh, so was I”, I don’t think out whole sentences…

Stephen: Is that how your mind works?

Karl: In a way, yeah

Ricky: Brilliant, it’s great, he has to think out whole sentences!

Stephen: That explains a lot!

This sparked my curiosity since, as far back as I can remember I’ve always thought in complete sentences, often to the extent that I have conversations with myself inside my own head – I just assumed that this was a pretty normal thing to do!

So, I decided to do a bit of my own research into this ‘inner monologue’. This research began life (as many eminent and respected studies often do) on Facebook, where I asked a number of friends:

“What is it like to climb inside someone else’s head? – I’m researching for a post on the inner monologue and, although I think in words like I’m narrating my own life, apparently there are people who don’t…what’s it like inside your head? and if you don’t think in complete sentences, how do you think?”

From this question I got some pretty interesting answers – In brief, most people who responded had some kind of inner voice but few regularly thought in complete sentences or engage this voice in conversation. Some interesting answers included:

“I think in pictures like I’m watching a silent film. In order to submit things to memory I have to have visuals as i struggle to remember audio descriptions. So most of my memory is made up of pictures and that’s how my thought processes work!”

“I sometimes imagine a highly adapted version of something I’ve read or watched – featuring me – and tailored to my real life situation of the time. Less actual words, more images, but like I’m an outsider observing myself observe my situation.”

“I think I only think in words when I’m either a) questioning something (“why’s that there?”) or b) making a decision to do something (“cup of tea!”). I often say such things aloud too when I’m alone.”

“I was wondering about my very minimal inner monologue after talking to my husband about it earlier this week. I find it incredible how most people seem to constantly be thinking in words/sentences. It sounds exhausting to me. I think in actions, visualizations, feelings, impulses and only really have a proper inner monologue when reading or writing. I never know internally what I’m about to say out loud (unless I force myself to do so, or if I’m nervous about talking in specific situations). Often my mind seems blank with no thoughts. I find meditation very easy.”

“I have narrated my life for as long as I remember. Sometimes, when something is particularly challenging, I sort of Parkinson interview myself, as if the problem is now in the past, and I’m discussing how I overcame it….I’ve done that since I was a teenager!”

So, it seems like people experience a huge spectrum of inner ruminations –  from short sharp assertions “cup of tea!” to long complex “Parkinson style” inner interviews.

But what do scientists actually know about this inner voice? Well, unfortunately it seems that this is one topic that’s been neglected by modern science. However, inspired by the theories of L. S. Vygotsky, modern research has now again picked up the baton and started to delve into the inner workings of the verbal mind.

Where does the inner voice come from?:

16931172632_0f1676a803_mVygotsky believed that inner speech starts to develop in early childhood, evolving from a phenomenon known as ‘private speech’. Many young children talk to themselves while playing – I remember I used to talk to myself, I’d also sometimes have conversations with inanimate objects (perhaps a downside of being an only child?). Vygotsky called this dialogue private speech and suggested that it comes from social dialogues with parents which, in later childhood, becomes internalised as inner speech.

This would imply that inner speech relies on the same biological mechanisms as those used when we speak out loud. Interestingly, we know that inner verbalisation is accompanied by tiny muscular movements in the larynx – it’s as though audible speech is almost produced but is then silenced at the last minute. If anyone’s like me, they may have experienced the phenomenon of externalised inner speech: when I’m deep in internal thought I’ve been known to accidentally say things out loud which should have stayed in my head.

Neuroscientists have also found that an area within the left inferior frontal gyrus, known as Broca’s area, is active when we speak out loud and also during inner speech. Intriguingly, if this region is disrupted using magnetic brain stimulation both outer and inner speech can be altered.

And, to answer Karl’s question….It has been suggested that, assuming inner speech derives from childhood verbalisations, the voice you hear in your head should sound like your own voice – as Karl would say “everybody thinks in their accent”.

Screen Shot 2015-10-10 at 17.01.37Interestingly, studies of limericks suggest that this is indeed the case! Ruth Filik and Emma Barber from the University of Nottingham asked participants to read two limericks silently in their heads, these being:

1) There was a young runner from Bath, Who stumbled and fell on the path; She didn’t get picked, As the coach was quite strict, So he gave the position to Kath.

2) There was an old lady from Bath, Who waved to her son down the path; He opened the gates, And bumped into his mates, Who were Gerry, and Simon, and Garth.

All participants were native to the UK, some having northern accents and others southern. In the UK there is a strong regional divide in the pronunciation of the words bath and path, with southerners rhyming bath/path with Garth while northerners rhyme bath/path with Kath (this being the correct way to pronounce things). By tracking participants eye movements the researchers were able to tell when they were reading a rhyming or a non-rhyming sentence. From this they found that both groups appeared to read silently in their own regional accent (although this is not always the case).

So, what does inner speech actually do?

4929178358_dac74312b0_zVygotsky thought that inner speech may help people to perform difficult tasks. Thinking a task through in words may make it easier to accomplish – there are definitely a lot of words going through my mind when I’m building Ikea furniture. Actually, a number of studies have found that people tend to perform worse on tasks which require planning (like playing chess) if their inner voice is suppressed while performing the task.

Recent studies have also found that inner speech often has a motivational quality. In fact, one of my friends offered this example of her inner voice: “I tend to ask myself questions and then think through the different answers. Also I cheer-lead myself along- ‘Right, ok, you can do this!’”.

The self reflective tendency of the inner monologue may also allow us to reflect more on who we are as individuals. Indeed, Canadian psychologist Alan Morin suggests that people who use inner speech more often also show better self understanding: “Inner speech allows us to verbally analyse our emotions, motives, thoughts and behavioural patterns,” he says. “It puts to the forefront of consciousness what would otherwise remain mostly subconscious.” This idea is further supported by a study of neuroanatomist Jill Bolte Taylor who reported a lack for self awareness after a stroke which damaged her language system.

But, I doubt my friends who reported the lack of an inner voice suffer from any associated lack of self awareness. Therefore, I’m sure that there are still a number of individual differences which remain unaccounted for in these studies.

The dark side:

2967650878_1f436efd1c_zJust as your inner voice can be your own personal cheerleader giving you a boost when you’re feeling low, it can also be your worst enemy. Alongside my Facebook friends, I also posed my question to a group of individuals who, like myself, have been or are currently struggling with depression and/or anxiety. I was intrigued to find that, of all 30 responses, only a couple of people reported not having an internal monologue and most said that their inner voice was conversational (like my own). Not just this but most also said that their inner voice was ‘nasty’ and ‘cruel’ repeating phrases such as “you are useless” or “you aren’t good enough”.

There are a number of studies which support this observation, specifically suggesting that depressed older people rely more heavily on negative internalised speech than social communications when constructing their view of reality (giving them a negative outlook on life). Indeed, the backbone of cognitive behavioural therapy (a commonly used tool in the treatment of mental illness) relies on teaching individuals to re-frame or alter negative thought processes like those mentioned above – “I can’t do it” may become “it’s a challenge but I’m capable given enough time”

Researchers are still not sure how the inner monologue, negative thought processes and social isolation interact in the case of depression. It may be that withdrawal from social interaction leads to a greater dependence on internal processes or perhaps disordered negative thoughts breed the need to withdraw from society. Whatever the case, a better understanding of the mechanisms behind our inner critics may help understand and treat those suffering from depressive illnesses.

Researchers from Durham University found that around 60% of people report that their inner speech has the to-and-fro quality of a conversation. So, despite Ricky and Stephen’s surprise, it seems that Karl perhaps isn’t that abnormal after all. With inner speech being such a wide-spread phenomenon and knowing its possible links with mental health, perhaps it’s time scientists paid a bit more attention to the little voice in our heads?

Post by: Sarah Fox

A Spinal Emulator for Medical Training

The complexity of the human body requires medical practitioners to have an astute working knowledge of anatomy and physiology. It’s no surprise then, that pursuing a degree in medicine is challenging and costly pursuit!

One of the most enigmatic and challenging regions of the anatomy to diagnose is probably the spine. To diagnose problems with the lumbar (lower region) of the spine, a doctor will lay a patient flat on his/her stomach (to achieve what’s called a lordotic spine shape). The doctor will then use the pisiform (bony region at the bottom of the wrist) to apply pressure to each of the lumbar vertebrae. By feeling how the vertebrae respond, the stiffness and how far they move, an experienced doctor can diagnose problems. In case you can’t visualise that, check out this demonstration.

To become competent at this takes time. In fact in medical circles it’s seen as a skill that takes years of practical experience, rather than something that can be picked up in an three hour workshop… But back problems are becoming pretty commonplace, especially with our increasingly sedentary lifestyles, so this is not a skill that should be in short supply!

But why is it such a difficult skill to acquire?

6dcf55_b9902d2be5924629ba07c2cf267ea78a.jpg_srb_p_410_410_75_22_0.50_1.20_0.00_jpg_srbWell, currently medical students learn to diagnose spinal problems by practising on lifeless, unrealistic plastic models.

That is, pushing down onto plastic vertebrae that don’t move or feel anything like a real spine. Following this medical students will then continue to try it out on each other. But, how can you teach students exactly what, for example, a degenerated disk feels like? Short answer, you can’t learn the realistic feel of it without trying it out on a real patient.

Not only that, how can a professor teach his students how fast or hard to press down on the spine, without knowing exactly how hard or fast a student is applying pressure?

My solution

The crux of this problem is that we’re currently using ‘low tech’ to teach this method. This project involves using some simple, low cost technology to create a spinal emulator, that a student can use to learn this method by simulating both a healthy and an unhealthy spine.

Something like this, which I have designed as an initial prototype…

6dcf55_2e9f95631a554ab8be075aca7723d1c4.png_srb_p_630_347_75_22_0.50_1.20_0.00_png_srb

At the top of this model are five lumbar spine vertebrae, the sacrum and the coccyx. Four of the lumbar vertebrae are mounted on flexible metal bars to provide passive “springiness”. But one of the vertebrae (Lumbar 3) is not. This vertebrae is mounted onto a linear actuator (basically a motor system that can move up and down – it’s the black thing in the design above). Underneath the linear actuator is a load cell, a sensor that can measure force.

So we have a system where one of the vertebrae can be electrically moved, and the pressure applied can be sensed. Hopefully you can see where I’m going with this. We can use some embedded electronics to move the vertebrae up or down, according to the amount of pressure being applied to it. With some control algorithms, we can essentially simulate what a real vertebrae would feel like, by simulating a force-displacement ratio (stiffness ratio). We can go further, and simulate varying stiffness profiles to correspond to specific spine problems. In other words we can, in theory, simulate any spine problem in theory.

Why are we only simulating one vertebrae?

Simple answer: cost. This is just a prototype, our budget is small, so it’s a proof of concept. If it works we’ll be looking to create a fully actuated spinal emulator.

So will it work?

Hopefully. But the real value of the system will be in how well it can simulate the real feel of a human spine. And that depends a lot on the algorithms I use… Seems I’ll need to learn the method before I can even attempt creating software to simulate it – any volunteers?

Guest post by Josh Elijah: @yoshelij

aBs7TWXT_400x400Josh is an electronics engineer with a passion for robotics and control systems. He is currently working on a range of projects at Manchester University before embarking on a PhD.