Shotton Hall Academy – Where can my maths take me?

Last week I was asked to go into a Peterlee academy (Shotton Hall), and they asked me to give a talk about maths in the workplace. Obviously the field that we study in uses a LOT of maths that most other fields don’t so the school were keen for me to come along and impart some of my knowledge. During the day I spoke to about 100 students, giving a half hour talk and answering any questions they had. I covered some basics of maths in science, such as statistics that are needed, and how any scientific job (and in fact, pretty much any job) massively benefits from having a good mathematical grounding.

I then went into a bit more detail about my own specific research, showing the kids some of the David Attenborough 3D footage from micro monsters (the teacher was pretty scared of the 3D tarantula!) and talked the students through the different angles and geometries involved in creating 3D footage. The teachers said that the kids were all engaged and even talking about Maths in the break, so I must have done something right! I enjoyed myself as well, not very often I get to talk for half an hour about my work without interruptions!

Paul explaining 3D maths to children at SHS

Paul explaining 3D maths to children at SHS

The children paying attention as I go through the details of 3D angles

SHS thanking paul for his talk

SHS thanking paul for his talk

I even got tweeted my thanks!

British Science Festival

This has been an exceptionally good and fun week doing the British Science Festival. Lisa had set up a workshop all on camouflage and mimicry and during all the lab helped out (although kudos to Lisa who managed to do every session with a big smile on her face!). There were lots of different activities to do during the workshop including a load of real life creepy crawlies that were all experts at camouflage. My task was to take the children through some posters and do some questions on a quiz sheet. The first question was to do with mimicry. I explained that a hoverfly pretends to be a wasp so that it doesn’t get eaten by birds and we had three example hoverflies from different species trying to mimic a wasp. The children had to rank them in order of ‘most waspishness’ and everybody agreed one was rubbish, one was good, and one was OK. They found it very interesting that birds actually saw our OK mimic as a good mimic and our good mimic as an OK one, and some even ventured a guess that it meant birds see things differently from ours.

Next up on the quiz was aposematism. For those that don’t know, aposematism is the act of being very bright and colourful to warn predators away from eating them, we had examples such as a bee (black and yellow, ‘I’ve got a stinger leave me alone’), a poison arrow frog (Black and yellow patterns ‘don’t eat me I’m poisonous’) and the bombardier beetle (red and black ‘don’t eat me or I’ll spray you with a horrible stink, the kids particularly loved this one!). As a group we then discussed other aposmatic creatures. I had some very interesting answers, of which most were brightly coloured but more to stay camouflaged (tiger, zebra and clown fish). I had some that were mimics or dangerous in their own way (milk snake and sea anemone) and some really good answers (ladybird, skunk, wasp, ringed octopus).

The final two questions involved matching the creature to the type of camouflage it was using, and then guessing which out of 14 butterflies were poisonous and tasty. After the quiz was finished the kids rotated and did something else in the room (which you will probably hear about in other blog posts) and I started again with the next group.

The entire workshop was a great success and I really think some kids took some real knowledge and interest away from the day, and I heard more than one say it had been the best one they had seen yet. Very pleased I volunteered to help out with the event!

Tying up some loose ends

While I wait to begin construction of my next experiment (assessment panel approval pending) I have been working hard on various different bits and pieces. My paper for the oblique angles study is almost ready for submission (bar the inevitable red pen from Jenny, and a results section that is still half-written as we finish analysing the results) and I am pleased with the progress. With the analysis we have constructed various models to try to map the data, with my personal favourite being a combination of two Gaussian curves, and others including absolute values (which means the magnitude of the number only, not the sign, for example the absolute value of -2 is just 2) and polynomials (terms with powers, such as squared and cubed etc.).

Jenny and I are discussing these later this week, to decide which is the best to model the data. We have assessed the significance using SPSS already so all we really want is a nice smooth model to represent the data well. I am thrilled to announce we do have significant results however, which is something scientists always like to hear! While I don’t agree with the practice it seems to me a trend in journals is that significant results get published much more. Probably because significance proves something, where a lack of significance, by definition, proves nothing.

For example if you spin a 5 coloured spinner and say ‘it is definitely red’ – then you have a result (red). However if you say ‘it is not definitely red’ you cannot say anything about the results. It may in fact be red. But even if it is not you have no idea what colour it really is.

I can see the argument for such papers (definitely red) getting preference but I do believe scientific research would develop much quicker were all the non-significant tests and results published, even somewhere open access like wikipedia. If only to check nobody has already tried what you’re thinking of and failing. Such a site may indeed exist but I haven’t heard of it. Some non-significant result papers do make it in if they are well written or have original methodology, but the habit of selecting significant papers is one I think sometimes hinders scientific development. Just my opinion.

Wow got a bit sidetracked there! So while waiting for my next experiment to be approved and set up I have also submitted my paper on oblique angles to IC3D to see if they would like me to present (still waiting to hear from them) and I am presenting a poster twice in the space of a week! Once at an internal ION event (postgraduate poster evening, should be fun) and NEPG2013 (6-university wide event where postgrads can submit, and I was selected. Much more formal and a bigger deal!) So I am looking forward to that.

Lastly I have assembled my team of supervisors properly for my PhD. Tom Smulders, who did animal behaviour with me in my MRES year, and Vivek Nityananda, a member of the lab, will join Jenny in making sure my PhD goes without a hiccup!

British science festival, modelling and good time management

It is the British Science Festival (known from here as BSF) next week in Newcastle so the institute is very bustly over the last few days. Lisa on our team has done a tremendous job of organising not 1, not 2, but three timetables and stands for the BSF for our lab and affiliates to run. I’m heading up the poster and worksheet team, and hence working on it every day next week when it is on (mon – thurs). So if anybody does want to come and see the brilliance that is pure science and learn something new, come on down! I’ll be the guy with a big smile getting far too into the role.

In amongst that this week I have started the task of juggling my PhD. I say and really mean juggle, as even though I am only one month into a 36 month process I currently have two papers on the go, a mathematical modelling code to simplify, a student (Pramod) to keep an eye on for a long term piece, an online survey to collect data, a journal club to attend and various other equally important but not massively time consuming things to consider. Anybody who wants to get into science needs to have the focus and attention to concentrate on one problem for weeks on end, but also the ability to chop and change quickly between jobs and problems. How my supervisor Jenny copes is beyond me, as she (being the PI) is juggling the jugglers! that’s like juggling squared!

The modelling is taking up a lot of my time. The oblique angle study that I did for my MRES needs some statistical analysis before we can submit it to Journal of Vision, and that involves a lot of complex mathematical conversations with Jenny, something I properly enjoy! It does also require some serious matlab and more than a little bit of concentration. We have two normal (or Gaussian curves) centred around perpendicular viewing, and also on the angle for which the person is actually sat at, and we weigh the two curves accordingly, then optimise to fit the data. This is both very finicky (exact character matching and just missing a colon or a bracket brings everything falling apart) and time consuming. However it has been fun and the end is in sight. We have two options to pursue: an addition of the weighted curves or a multiplication. Looking at the fitted models in the graphs to me it appears that the addition route will give us a better fit. We then test this using bootstrap resampling (take all the data we collected, put it all together and mix it up, pick some data and random and go again) to determine how well the fit really is quantitatively.

Next week is all BSF, and hopefully a little bit of advancement on a paper on illusions I have written for the Leicester conference.

OpenGL and NEPG

Last weeks debugging finally came to fruition on Friday, with Jenny and myself knocking our brains together for the past 3 days and coming up with the solution to the problem. After altering the viewing frustum using some mathematics and then changing the code with loading identity matrices and rendering the texture we got a perfectly lined up, textured, solid cube in openGL which mapped perfectly onto the points already worked out previously using vector mathematics and trigonometry. So the next step (which is going to be the majority of this weeks work) is to implement it into a matlab program to allow it to be ran and the experiment to be done and recorded. Some images of the cube lined up against a perspex proof are shown here. We put the coordinates of one of the faces in at a funny angle of both rotation about the perspex and the table, calculate the coordinates in world space (in cm) and put them into the code. Open GL recreates the same points perfectly on the screen for the viewpoint. A laser was used to make sure the origin was lined up correctly on the screen (you can see the red laser crosshair on the chinrest on one of the photos) and a laser distance measurer was used to judge the distance from the screen.


This week I am also submitting an abstract to NEPG, which is the North East Postgraduate Conference, a coming together of many northern universities (from Edinburgh to Leeds) to present data and information. I hope to be given a spot to present in, or a poster place. Either way it’s an exciting prospect to hopefully present up here for my peers to see what it is that I am doing. Regardless of acceptance or not I look forward to seeing other works and attending talks.

To finish off the week I am giving a talk in Leicester on Friday titled ‘an illusion using 3D technology’. Which will be my first time presenting my data to anybody. While I am not in any way nervous yet I imagine I will be come 9:15 when I open the talks of the day as the first speaker. Wish me luck!

Slow and Steady wins the race.

I have spent the entire week battling with OpenGL. OpenGL is a graphics program that is supposed to make life easier for you by doing much of the hard calculations to project an object correctly onto the screen. Unfortunately this is the exact opposite of what it is I want to do, as I’m doing oblique angles instead of frontoparallel (straight on). The advantage that OpenGL has however is that it is very good with figuring out what should be able to be seen at any one moment. So in this program the back of my cubes aren’t visible when they shouldn’t be, which is exactly why we opted to use openGL for phase 2. Unfortunately I now need to reassess how to work out the oblique warping all over again. Fortunately I intend to use previous thinking as a ‘roadmap’ to avoid any of the pitfalls I suffered before.

I now have 7 weeks until the project is supposed to be finished. If I can get the cubes working in the next two weeks I’ll have more than enough time to run through some volunteers and collect some results. How do I know I have 7 weeks left? My wedding is the Saturday after the project is done. Which is altogether much more scary than science!

Kids Kabin in Walker

The time certainly does fly when you’re busy! Since my last blog post I have worked hard on the stimuli to get them to work as we hope they would, and have sorted out an occluder (something to block the edges of the screen from the viewer, so they can’t gauge the orientation of the screen). And I am now in the process of recruiting volunteers and running the experiment.

On Monday I helped out at an ION outreach programme at the Kids Kabin in Walker, an after-school club. School classes have been visiting the centre during school hours to learn different things not seen in a classroom such as pottery, cooking, and including a session on the brain ran by ION. In this session the children (varying age) are taught about how the brain works and how the different parts of the brain handle different tasks. They are engaged in activities they wouldn’t see normally such as the Stroop task (reading out the colour of the words font, rather than the name of the colour, for instance BLUE RED YELLOW would be RED GREEN BLUE and also wearing some custom made glasses which warp the view the of the world the child sees, which are worn and a simple task, like throwing a ball into a basket, is attempted. The emphasis of the classes is to teach the various regions of the cortex and how they work together to perform even simple tasks. The day was good fun for the kids and for the grown ups! Looking forward to going next week!

Graphs are good

All week Lisa’s been a bit gloomy about the behaviour of the mantids. Apparently they have not been cooperating well, doing defensive postures at the screen or even jumping off their perch. But she’s plugged doggedly on with true PhD student grit :). Anyway, we just sat down and created a script to load up the Matlab files and graph such data as she has managed to collect. And it’s great! Really beautiful, does exactly what we expected, demonstrates our protocol is sensible and suggests it’s worth while proceeding to more interesting stimuli. Just goes to show, you don’t always have an accurate sense of how good your data is as it comes in.

In other news, Paul has taken delivery of a 3D Dell laptop. Having a few teething problems getting it to display in 3D, but I shall be very interested to see the results. MSc computing students Mike and Nick are starting their projects in the lab this week, and James is back from holiday. So it’s going to be a nice diverse lab meeting this Friday.

Completed my first ever report!

The mouse experiment has finished and went exceptionally well, with the mice all being very well behaved and doing what we hoped! I have now finished my first ever report, being from a maths background, and I think it is pretty good! We had to do a quick presentation on our results and me being very loud lent itself to me doing most of the talking which also went well. Good chance to flex my R muscles as well. In other aspects I have been continuing my taught material, and trying to hit the ground running with my research question in February. I have looked at some matlab code and I am still wrestling with it but it is still coming along and I have some ideas! Christmas round the corner means that I am even BUSIER than normal, with house renovations, uni work and christmas stuff, it’s amazing I get time to sleep!

Starting to seriously pick up speed!

My workload has started to increase and while I feel the pressure I like to believe I am positively thriving off it! I have never enjoyed university as much as I am now. Over the last 2 weeks I have attended many lectures, mostly on visual systems, which I have found helpful and interesting. The way we as a species have developed trichromacy and the complex way we reach the visual cortex and what happens IN the visual cortex is all very fascinating. I have also attended a lecture on mitochondrial diseases, and a couple of optional lectures Jenny herself ran on physiology (fortunately it was the eye, again, so more area covered). I have begun work on a behviour experiment with mice involving object recognition, which I am finding quite exhilarating and working quite hard on. And Jenny and myself have had a good chat about the research question I will be looking at in semester 2 and 3. Rather than looking at compensation mechanisms with 3D viewing alone we are going to look at the compensation mechanism involved when motion is also induced on the object and see if this affects the level of compensation (we hope it will!). personally over the fortnight I have got the keys to my house and started all the repairs needed on it, beginning with the physical jobs of tearing out carpet and ripping down walls, all very macho! Still very much enjoying the MRes and long may that continue!