Wednesday, 5 October 2011

SD329: TMA-4

The final TMA.

Three questions.
The first one is the big one though, as it has 50% of the marks. We have to write an essay, of no more than 1500 words(!) on mechanoreceptors and their use in proprioception. Also it needs to include body image and body schema. I don't like essays much. This seems to have been reflected in my marks, although I think I made a fair stab at it.

Question 2 - we look at some images of rat glomeruli, when labelled with radioactive substances, and look at the uptake when exposed to three compounds. We have to comment on the similarity and differences in the compounds, the patterns shown in the glomeruli, and then bring it together by saying whats happening here with known mechanisms of odourant coding. I found this one a bit difficult to answer well. Not really sure what was being looked for outside of the obvious.

Question 3 - pain - and how Ibuprofen, codeine and amitriptyline work, where they work and what side effects they have.

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Tuesday, 20 September 2011

SD329: Book 4 - Touch and Pain, Smell and Taste, Integrating the senses

The last book contains the final three blocks of the course.

The first block (block 5) is about touch and pain.
It starts by looking in detail at touch and the various sense receptors used to detect touch, pressure, and so on.
Then it looks at the integrated perception of touch, and how it is perceived. This is followed by the sense of proprioception - which is how you know where your arms and legs etc are without actually looking at them.
Its an important sense, as a video of someone who lost it shows, they are unable to walk or even sit in some cases.
Finally we look at pain, how it is sensed, how its passed and what various drugs can do to stop pain.

Smell and taste are block 6, and it seems there is still a lot to learn about the exact mechanisms that work here. It starts by looking at smell and how the structure of molecules and the sense of smell don't always seem to be correlated. Then there are the usual nerve pathways to consider, and theories on how exactly smell works etc.
Taste is similar in a way but much less complex as there are only 4-5 basic tastes.
Then a quick bit on combined taste/smell.

Then finally a rather short block on the integration of the senses. Things covered include the focus of attention and connection between sight and sound, and things like motion sickness.

Phew - another course that I've read to the end of.

Wednesday, 3 August 2011

SD329 - TMA3

Course work 3. Three questions.

Question 1 is the biggest. In this we have to perform a home experiment, and then write it up as a proper experimental write up. The subject is the Pulfrich effect, which is an oddity in visual processing. You view a pendulum in this case or other moving thing using both eyes, but with one eye slightly obscured by a filter making the scene less bright. The brain interprets the slight lag in a similar way to seeing things moving in 3-d, so the pendulum which is swinging back and forth in front of the subject, starts to apparently take on a elliptical path moving closer and further away at the peak swing. What's more you can measure this using a pointer stick and work out where apparently the object comes to its closest point. From all this it is possible using a bit of trig to work out what this means in the delay in neural processing.  Myself and my daughter set this up one Sunday morning as my variation on the experiment was to see if the difference in ages affected the processing speed.
I used a tin of beans attached to the curtain rail, and a handy dog as backdrop. We were supplied with

Anyway - the experiment went ok, and the write up too. 1500 words or so with references and so on.

Question 2 is a short essay for the layman, describing visual processing contrasting bottom up and top down processing. This wasn't too bad, after the marathon first question.

Question 3 was much easier for me anyway - it was about focal lengths and whether a person was short sighted or not, and what was the nearest distance they could observe etc. Some basic maths and a few definitions.

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Sunday, 31 July 2011

SD329: Book 3 Vision

On to the most complex of the topics - Vision.

To begin with it starts with an examination of light. What light is and how it is composed, and then how the eye interprets if. Looking at the science of colour and intensity. Colour is very much a product of how our eye perceives it, and we all see it slightly differently.

The continues by looking at the eye itself, the structure and function of the bits. All the bits that bring the image into focus, including some rather detailed physics of how the cornea is transparent despite being made of proteins. Also something about visual defects such as short and long sightedness, then onto the retina, colour vision movement and adaptation. There is a lot of processing done in the retina itself, to aid things like edge detection, colour constancy and other things - its a big topic.

After that we follow the signals from the retina to the visual cortex, taking in such structures as the optical chiasma, the lateral geniculate nucleus and ending up at the visual cortex.

Then its a case of looking (NPI) at visual processing, how we recognise shapes, scenes and people, including a whole chapter on recognition of writing. Lots of theories and experiments, but still it seems little in the way of solidly understood detail.

Wednesday, 8 June 2011

SD329: TMA-2

The second coursework. I haven't finished book 3/block 4 - vision - its a pretty big subject as you might imagine.

So - what's in TMA-2?
Q1 is a research questions. It starts by asking "Can regular drug intake or exposure to chemicals increase the risk of hearing loss?". In particular drugs such as aspirin, paracetamol and the like. Can regular taking of these affect hearing? We are given a paper where there is a claim to that effect. We have to do lots of internet searching to find articles for and against the position, and to determine what we think about each source - how trustworthy it is etc.
There are three parts to the question focused around the two sub questions

1. Is there a proven link between use of either painkillers and hearing loss?
2. Is there any evidence that a particular group within the general population is more at risk or that a particular drug or chemical is any more, or less, risky?
We first have to compile our bibliography of information, together with criticism of the sources.
Then we have to argue to each of the sub question above
Finally we have to describe our search strategy - how we found the items, what we searched for etc.

For question 2, we have to write a summary of one of the detailed chapters in the hearing section. So condensing several pages and diagrams into 400 words.

Question 3 is about hearing directly. First we have to define pitch and intensity. Then we have to describe how both pitch and intensity are encoded, with two possible mechanisms for each.

I found this TMA somewhat easier, although the first question is quite open ended, depending on how much searching you want to do.
Anyway, much happier with the mark for this one, more up to my usual standard.

Monday, 25 April 2011

SD329: TMA-1

Time for the first piece of coursework.

There are three questions on this.
It starts with the first question - where we have to write a brief essay (600 words) on the structure and function of the neuron. It's been a while since I had to write an essay, but the format comes back to me. We have to mention things like dendrites, axons, neurotransmitters and so on. All in just 600 words. It appears conciseness is a virtue in this course.

Question 2 is a bit about sensory inputs, and how they are detected, encoded and received. We also have to describe lateral inhibition.

In question 3 we are given a paper to read all about the McGurk effect, which you can see an example of here. There is a lot of detail in the paper, and several images of brains. We are asked a number of detailed questions on the scope of the paper and the results. By the end of this, I'm beginning to find I no longer wish to hear or see the McGurk effect again!

Anyway, first TMA posted, and a rather poor score for me. If we had a cat I would probably kick it.

Wednesday, 20 April 2011

SD329: Book 2 - Hearing and Balance

Book 2, Block 3 is all about hearing and balance.

It starts off discussing what sound is, and how it is quantified. It looks at waveforms and analysis of sounds, and what filters do. So with the basics in place, the process of hearing can be discussed.

The next chapter discusses the structure of the ear. The three major components, outer, middle and inner. Also what are the vital parts of it, and what goes where. Several diagrams and more than a few Latin names for tissues.

Next we're on to how the sound is received and processed. How frequency is discriminated, how intensity is encoded. You have to remember that nerves only fire on or off, and so there are various schemes for encoding what you hear. Frequency or pitch can be encoded by phase locking to the signal and the nerve firing on every cycle. However this can only work for a small range, as the nerves themselves have a limited firing rate - therefore the position from cochlea to brain is preserved to allow placement to mark frequency. Similarly for intensity, although it all gets a bit complicated. Then there is the whole subject of processing - how do you know a sound is coming from the left or right, front/back, up down.

Finally as a wrap up to sound a chapter on the perception of sound.

All this is supplemented by another book full of essays about each topic that you are directed to read at the appropriate time, which go into far more depth on the subject.

The last chapter looks at the sense of balance, and how that works. Detection of being the right way up, and acceleration and how that is linked to other senses, such as turning your head towards a sound (very useful if you are potential dinner). It will come up again linked to vision where there is a special circuit to keep your eyes focused on something despite moving your head.

A very interesting book and topic.

Sunday, 20 March 2011

SD329: Book 1

Book 1 actually contains the first two blocks. That is:
Block 1 - Introduction to the senses 
Block 2 - The sensory nervous system.

The first block is a general introduction to the senses, it goes through the senses in overview and gives a taste of what will be coming up in the course. It coves a number of optical and other illusions that show how our senses can be fooled, a theme that reoccurs throughout the course.

Block 2 is more detailed, and goes into how the nervous system works. From the basic functioning of nerves and neurons, to the sensory apparatus that triggers things like touch and pain. It also covers the general layout of nerves in the body, what goes where, how they are interconnected. Afferent and efferent, which I'm destined to get mixed up through the rest of the course.
It then finishes with a chapter devoted to imaging the brain, which takes us through the basics of EEG, SQUIDS, PET and fMRI.  So Not a bad introduction, and a taste of what's to come.

Friday, 18 March 2011

SXR208: Day 7

Day 7 - wrap up

Nothing special today except for a wrap up meeting in the hotel at 2pm. So a chance to catch up on sleep until then with no project reading to be done. I think by now we were all pretty tired, so the chance of sleeping in until late was good. We ventured out for some breakfast/lunch at about midday, I can't remember what we had.

Then we went to the bar area to meet up for the final briefing. Here we had to get the final details, and also let them know what project we were going to write up.

Finally a photo by the swimming pool - I don't think anyone had ventured into it, but it made a nice foredrop.

I could go on to tell you about the drinks in the local bar that night, the um slightly odd "live" music they had in the bar, and those people who stayed there till 4am and nearly missed their flight, but I won't bother.

Thursday, 17 March 2011

SXR208: Day 6

Day 6 - CMD of clusters

 The last proper lab session tonight - and looking like the skies are clearing too. If so this could be a really good session. We have to look at clusters, two open and one globular. This was our final night and would be assessed from beginning to end.

We started by selecting 3 different choices of nebula, with a couple of backups. We hoped to get M35, M67 and M3. We then worked a plan of observing together with our darks, flats and biases we would need.

We then set about the task of getting the nights images. What cloud there was seemed to be quickly fading and things were looking good.

We took our calibration frames quickly and then searched for a reference star nearby the target to synchronise the telescope to. We had to wait for the cloud to shift, and at the same time the team in the labs were producing finding charts for the object chosen so we'd know it when we found it.

We found our first target and took several images of it, in both the V and V bands using filters for M35.
We were going to try our second open cluster, but to our horror found it was right next to the full moon. So we skipped that one for now and went on to look at the globular cluster, M3.

We got some good images of this, in both bands, and sent them off for analysis by the team in the lab.
We then had our midnight snack, and by now the moon had moved a bit, and we wondered if we might get our final target. It looked a little close, but we gave it a shot, and it worked out OK.

We were then going to try for one of our secondary targets, but the telescope went a little weird, it reset itself and decided it was now midday in 2002 so all our coordinates were off. This despite being equipped with GPS. The course director took a look at it, but decided it couldn't be fixed right now - seemed to be an issue with power sources. Anyway, we had enough data, so we all joined in on the analysis.

After gathering data from lots of selected stars, and plotting them on a graph, we were able to make a reasonable Hertzsprung Russel diagram with a part of the main sequence and the red giant turn off arm. This allowed us to estimate the age of each of the clusters, although our error bars were pretty huge.

However it was a very successful night, and with more data and more processing time we could have got a better estimate. A very positive end to the weeks observing. Back to the hotel and a quick walk on the beach at 5:30 in the morning - it was empty! The skies were a little light polluted too - so we could only see the main constellations, and the moon we'd hoped would be nestling over the water had set. So we all went to bed!

Wednesday, 16 March 2011

SXR208: Day 5

Day 5 -Photometry

After getting up late again - there was breakfast to be found - although it was lunchtime. Later I found some cake and coffee with a friend before starting the trip to the observatory.

Today we'll be looking at some key stars to try and work out how bright they are and what effect the angle ot looking at them has on the amount of light. This is called the light extinction plot, and gives you a simple equation that relates the angle you are looking at the star to the amount of light absorbed at a couple of wavelengths. In this way you can compensate for the angle you're looking at a star for and get a much closer idea of its real magnitude.

We had our planning session and picked two stars that we might go for, despite the weather looking pretty unspectacular.

The night was cloudy so we didn't get any real data, although we went through the usual procedures of setting up and parking the telescope.

We had to look at stars in both B and V bands and do various calculations on them. There was also a lot of work on errors that we had to work through.

We had a good time - but what with the error calculations and cloudy skies it wasn't my favourite investigation, although chatting with the tutor who was a professional astronomer was well worth while.

Tuesday, 15 March 2011

SXR208: Day 4

Day 4 - Spectroscopy

Today we hope to take spectrographic images of stars. It is quite amazing what you can do with a spectrum fo a star. You can work out what its made from, how big it is, which direction it is moving and all sorts of other things, which rather puts the final nail in the quote 
"On the subject of stars, all investigations which are not ultimately reducible to simple visual observations are ... necessarily denied to us. While we can conceive of the possibility of determining their shapes, their sizes, and their motions, we shall never be able by any means to study their chemical composition or their mineralogical structure ... Our knowledge concerning their gaseous envelopes is necessarily limited to their existence, size ... and refractive power, we shall not at all be able to determine their chemical composition or even their density... I regard any notion concerning the true mean temperature of the various stars as forever denied to us."
— Auguste Comte,

Waking up around 11:00, we headed toward the beach in search of food, and found a rather good paella, with lots of sea food in it. The sort that sticks out and looks at you.
Then after reading up on the evenings project, I met with some of my group. Some of the group wanted pre meeting planning to get things ready for the planning meeting. I arrived late, but joined in, and then it was soon time to board the bus. Another talk in the planetarium and then the planning session, where we again identified stars. Then off to get some food - very nice it was all week.

Then to the work in hand. First we had to calibrate the spectrometer. So this was done with a He-Ar lamp which produces a well defined spectrum. We took an image of this and then went off to the lab to make a calibration graph so we would be able to analyse the spectra we were to take.

Then the team I was in went off hunting around the sky for our targets. The first two were nice and easy to find, Arcturus and Regulus. We managed to get these stars onto the diffraction grating slit without too much trouble, but still made a couple of mistakes, but we had time as the clouds drifted by. We stopped for the midnight snack and lots of coffee.

Then it was onto a fainter object, BD+31 2750 - trips off the tongue! Finally Saturn just before the clouds rolled in and we had to stop for the night.

We managed to extract a few spectra, but some of our graphs seemed to be off by about 4nm. Something we couldn't explain despite redoing the calibration. We had a debrief with Andy which went pretty well, we decided we needed more data really. This was our first experience using real data, and we were all quite excited to have done something real.
The bus at 4:30am, and back home to bed at about 5:30 and make sure those do not disturb signs firmly attached.

Monday, 14 March 2011

SXR208: Day 3

Day 3 - Binary Stars
The pressure steps up as today we do real projects, projects that are assessed. We started with a lunch/breakfast at Jaime's. A simple baguette of ham and cheese, but with salad and a fried egg in it - unexpected but yummy!

Today we're doing binary stars, trying to detect the presence of one star orbiting another. The weather looks foul, so I think we'll be working with archive data.
There was an initial talk scheduled, but a power cut at the site put pay to that for a while, but soon power was restored and we got going again.

We first had to have a planning meeting where our team decided on what star to look at from a list of candidates, what exposures and so on.

We first had to process the images, to subtract dark, bias and flats. Then we had to do some comparative photometry. Comparing the target star to a reference star to see if it changed in brightness. A couple of check stars were also included to check that the reference star wasn't varying too.
Luckily Maxim DL does a lot of the hard work for you here.

We then exported the collected data into excel and plotted a graph, and wow, it looked as though we had detected something.

There we have it - clear evidence of a periodic dip in brightness. We then had to go off and do protracted calculations to work out from this the period, and using some other data how massive the two stars were as a result. Pretty impressive stuff.
We then again went through the motions of setting up the telescope and taking the requisite basic images - as, like the tutor said, you need to be quick at doing this, because if you get clear skies tomorrow it will save you time to have practised.

We then finished off our data, and then met up at about 4:00am to discuss it with our tutor. Then home to the hotel and crash out until tomorrow.

Sunday, 13 March 2011

SXR208: Day 2

Day two of the residential, and the first full night scheduled.

Today we get to play with telescopes, and start getting into the rhythm of the course.

It's a bus at 4:30 to get us to the observatory at about 5:30, we then have a talk in the planetarium. Tonight's was about the software we would be using, Maxim DL and excel. How we would be taking bias, flats and dark frames to allow better processing of the science images that we would take later.
Bias frames are a dump of the CCD detector to sense the effect the bias voltage on the chip has, this can then be subtracted from the full images.
Dark frames are exposures taken for the same time as the science frames, but with the shutter closed. This allows an estimation of the thermal noise that would occur on the image, and again can be averaged across several frames and subtracted.
Finally flat frames are images taken on a lit white image (a big round target held up to the telescope lit with a lamp) that allowed for vignetting, dust and other oddities of the optics to be taken into account and subtracted.

We spent the first half of the night in the lab, occasionally looking outside at the clear skies. We did some Maxim and excel processing of data, and my partner for the night and I were both pretty computer literate, we zoomed through the tasks. We finished with over an hour to spare, and the course director suggested that as there was a telescope spare we could have a play with it. We got it all set up and ready to run, and focused on Saturn, when they had a breakdown in one of the other domes, and kicked us out! So close.
Midnight, and after our snack session and quite a lot of strong coffee, it was our legitimate time in the domes. However the sky had clouded over and nothing was visible now. So we went through the motions of setting up the telescope, taking darks, flats and biases, and then went through the shut down procedures for parking the telescope. Then after a bit more time in the lab, we went back to the bus at 4:00am for the ride back to the hotel. There we had to attract attention to get the main door open, and then to bed. Everyone had to remember to hang the "Do not disturb" signs on their door, as no one wanted their room cleaning whilst trying to sleep!

Saturday, 12 March 2011

SXR208: Day 1

Day one of the residential school in Mallorca.

I'd arrived the previous day, an early flight meant getting up even earlier to get to the airport (2am) so it seemed sensible as the first night was scheduled to end after midnight to arrive the previous day and at least get some sleep.

The formal part of the day started with registration at 4pm, and then some sitting around in the bar area waiting for the bus to arrive to take us to the observatory. It's about a 50min journey into the middle of the island, down increasingly tiny roads to get to the observatory. We were about half way there, where the bus broke down. Overheating apparently, but they said there would be a replacement in 20 minutes. Much to everyone's surprise, they were good to their word, and we reached the observatory just 20 mins late.

We arrived in the pouring rain, and the nights scheduled stargazing look like it wasn't going to happen. We split into groups and went for a tour of the site, with coats on in the rain. We got familiar with where the various buildings were and how to get between them, in the dark "No running and use torches" was the mantra drummed into all of us.

We got given our documents, a clipboard, a notebook and a planisphere set for the local longitude. We had a good lunch and then went to the planetarium for a show, and ended with stargazing in the dome, given the inclement weather.

The night ended at about midnight, and the trip back to the hotel, uneventful this time.

Wednesday, 2 March 2011

SXR208: The Preschool assessment

Its nearly time to go to this, its come around quite quickly.

Before you can go though, you have to complete a pre school assessment. This is based on the text book provided with the course, and consists of an online test with, in this case, 28 questions.
I thought the questions might be quite easy, but I struggled to answer more than a couple without referring back to the book.
It has questions on the following
  • Positional Astronomy (5) - this is things like right acension and declination, local zeniths and so on. How to find stars and the celestial sphere. Apart from one nasty question where a labelled star was rather ambiguous, and I picked the one to the left of the label, when it should have been to the right, I did ok on most of these.
  • Astronomical Detectors (5) - focal lengths, resolution of telescopes, all covered under this topic.
  • Spectrographs (3) - use of the grating equation, and other details to do with interpreting spectra of stars comes under this category.
  • Photometry (5) - Things to do with light, star magnitudes and relative brightness under this.
  • Interpreting images (5) - Here you are given pictures of craters and similar on other planets/moons/asteroids. You have to interpret the features, based on light angles and also measure the features given the scale of the image.
  • Experimental uncertainties (6) - How to deal with errors, ending with an absolute stinker of a question where you need to combine experimental errors in an equation involving powers and multiplication to work out what sort of error in one parameter requires in the measurement of another. I did quite a bit of algebra on this, and amazed myself after getting thoroughly confused doing it twice, adapting an equation rather freely, but coming out with a number that was marked correct.
  • Meade Simulator (1) - In this question you are provided with a computer simulation of the Meade Telescope control software, and have to calibrate it and then slew it to a couple of stars and end up with a result that the software then checks. I got it wrong the first time, because I forgot to turn off all the handy feature which projects a map onto the sky! Not very realistic!
Anyway - for most of them you get 3 attempts - and a hint if you get it wrong twice. Your score is reduced if you don't get it right first time.  My results were:
  • 1 where I took the full 3 attempts (that dratted labelled star in the first set)
  • 5 where I had a second go - so correct at the second attempt. Some through stupidity, and some were a fair cop.
  • The rest I managed on the first attempt - after much checking in some cases.
Anyway, so now I'm ready to go - in just over a weeks time!

Monday, 17 January 2011

SD329: Signals and perception: the science of the senses - Once more unto the breach

Another year another course. I'm addicted!

As I've now got my degree, this is a just for fun. So of course I'll take it easy and not really try .... as if. There is something about a piece of coursework that these days stirs my competitive spirit. I recall in school doing more or less just enough to get me through,

The web site has opened - I have PDFs of the materials, and even the first bit of coursework (oh no - it has an essay question in it!!). However we're all still waiting for our books to be despatched. The course doesn't officially start until February though, but its good to get ahead. Its easy to waste time if you get ahead, less easy to catch up!

Thursday, 13 January 2011

SXR208: Observing the Universe

Its the last year for many residential courses in the science faculty. Something we'll all miss badly.
So I've always wanted to go on this course, and this year I'm not doing too many other courses, so as it is the last year, I'm grabbing it.

It's a week in Majorca, at an observatory, sleeping by day, doing astronomy by night. The first set of materials have arrived which includes the course book, a PT3 form, and an introductory booklet telling you what you need and advice on how to get there. You have to get your own flights, but hotel is included, as is the bus to the observatory.

The book covers lots of things, from basic telescopes, to equations used in astronomy, use of CCD sensors and how they are applied. Also things like teamwork, working out sources of errors, graphs and a few other bits and pieces.

I'm due there in March, and am quite excited about the whole thing. There is the book to read, some coursework to do beforehand, and a write up to do after. Although Majorca is more or less in the same time zone, I'm expecting jet lag from the shift in daily routine!