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SD429: TMA-4

2011-10-05T11:10:00.000+01:00

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

2011-09-20T18:37:00.000+01:00

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.

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SD329 - TMA3

2011-08-03T11:32:00.000+01:00

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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SD329: Book 3 Vision

2011-07-31T11:02:00.000+01:00

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.

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SD329: TMA-2

2011-06-08T20:54:00.022+01:00

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.

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SD329: TMA-1

2011-04-25T09:14:00.018+01:00

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.

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SD329: Book 2 - Hearing and Balance

2011-04-20T08:49:00.030+01:00

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.

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SD329: Book 1

2011-03-20T08:06:00.022Z

Book 1 actually contains the first two blocks. That is:

Block 1 - Introduction to the senses

and

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.

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SXR208: Day 7

2011-03-18T09:09:00.019Z

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.

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SXR208: Day 6

2011-03-17T09:08:00.044Z

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!

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SXR208: Day 5

2011-03-16T09:07:00.031Z

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.

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SXR208: Day 4

2011-03-15T12:04:00.046Z

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.

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SXR208: Day 3

2011-03-14T12:59:00.028Z

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.

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SXR208: Day 2

2011-03-13T12:57:00.058Z

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!

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SXR208: Day 1

2011-03-12T12:27:00.030Z

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.

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SXR208: The Preschool assessment

2011-03-02T09:35:00.001Z

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!

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

2011-01-17T15:30:00.001Z

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!

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SXR208: Observing the Universe

2011-01-13T11:47:00.003Z

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!

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Results - and a degree

2010-12-23T09:54:00.001Z

The results came out. Its now a week ago as I write.

I had predicted what I might get, and I was pretty close to the mark mostly. However evolution scored a grade higher than I expected, whilst the others were where I thought they might be. As such, this means I have all the courses and grades necessary for a degree. The OU web page popped up a link saying would I like to accept the degree, and I clicked on it - as I couldn't improve on it.

So there we have it - I got my degree, I can now call myself

B. Sc (Hons) Life Sciences (Open)

It's still sort of sinking in.

I was convinced I wouldn't get the results I needed (and it was a pretty close run thing), so I'd already signed up for another course, which I will do anyway - as it looks interesting (SD329). It's also the last year of the level 2 residential courses in science 2011, so I signed up for the astronomy residential. The last chance to take a trip to Majorca to stay up all night with a telescope for a week.

S377: The exam

2010-10-19T14:30:00.050+01:00

The exam - and one I have not been looking forward to.
There are just so many things that they can test you on here, it seems impossible to revise everything. Some things seems to come up regularly. Cancer, and cell structural proteins - but they are both quite big subjects.
Others seem to come up at random.

The format is to do eight questions out of 12 in the first part - all of these worth 10 points. Then answer questions on a research paper that you have been given beforehand for the remaining 20 points.

Q1 is about the microfilament network. I'm better on the microtubule network, but I gave this a go.

Q2 looked horrendous, asking you to draw a sketch graph of the activation energy of an enzyme catalysed reaction. After reflecting on it for a bit though - I decided this was really just the same as a normal chemical reaction graph that I'd done in S205. I'm hoping so anyway - so tried that too. Also covered SDM and catalytic sites.

Q3 was about membrane proteins and included secondary and tertiary structure questions. I tried this one too.

Q4 was about eukaryotic nucleosomes and apoptosis. I tried this, but really couldn't remember half the proteins involved (well half is probably an overstatement - I don't think I got any of them - until I was walking down the street after the exam!).

Q5 was about mRNA splicing and the removal of introns. It also covered RNAi methods - I tried this, but again couldn't remember the relevant proteins.

Q6 was about ribosomes, and I tried this working from first principles. I knew how they worked, but hadn't revised any of the details, so I sort of shot in the dark for the explanations they required.

Q7 was about RTK signalling receptors. I had revised this - but not quite in the form the question was asking. I scratched around - trawled my memory, and guessed at some of it.

Q8 was about apoptosis and necrosis, and a bit about tumour development. I tried this too.

Q9 was about tumour development - but I couldn't remember the techniques they asked about. I think I skipped this one

Q10 was about small G proteins, RAS and VEGF. I tried this one too.

Q11 was about ageing and mitochondria. I might have attempted this - I can't remember. I wouldn't have got far if so.

Q12 was about stem cells, intestinal cells and the WNT pathway. I couldn't remember enough detail to attempt this one.

The paper is a bit of a shock to most of us. Not so many of the common topics seem to come up, and quite a few oddities come out of the woodwork in the first part. Stuff that hasn't been on previous years papers and I think many of us were scratching around for things we could answer. In the end I did manage to find 8 questions to answer, but some of them rather badly. It was good in that the first question I could answer, but then as I scanned down the paper, circling those I might try, I'd got to the last question and only ringed about 3, and some of those rather hesitantly. At the end I attempted a couple more questions as I had lots of time spare, to see if I fared any better.

In contrast the research paper seemed a lot nicer - there were a couple of questions that had to be answered with knowledge from the course, rather than digging out figures and things.

So all in all - a bit of a shock and although it was never going to be an easy paper - it was harder than most of us were expecting I think.

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S366: The exam

2010-10-12T08:54:00.056+01:00

The exam - oh my!

So the exam comes around, as always a bit of a tense time. The exam consists of several sections.
The first section is 10 questions which comes in pairs. You have to answer 1 from each pair, plus two others. So 7 questions in total from 10, but narrowed down so you have to be able to focus on the topics within each pair.

Q1 concerns 5 statements, and you have to explain why each of them is false. From mutations to molecular clocks to the allometry of horses teeth.
Q2 picks pairs of definitions and you have to explain why they are related.
I did both of these in the end, despite not quite knowing what one of the terms was.

Q3 Is about area cladograms and vicariance. Two subjects that didn't stick with me, so I missed this out.
Q4 Is about mass extinctions and what can cause them. I attempted this one

Q5 Is about the neutral theory of evolution, and molecular clocks
Q6 Concerns the different type of selection, directional, stabilising and disruptive.
Both of these tried

Q7 is about birds and sexual selection, and life balance trade offs. I tried this one.
Q8 is about allopatric selection. I wished I could remember exactly what that was - on the day I wasn't certain enough to attempt it.

Q9 Is about chromosome counts and how breeding possibilities between near relatives such as horse and donkey. I tried this one
Q10 Is about morphological constraints and how they affect things - I think I skipped this one

The next section part 2 and mandatory, is usually a question on cladograms. You have to be able to draw one usually, and usually amend it. In this exam we had to draw the given one with state changes marked on it. Then redraw it in a different format, and see which version was more parsimonious. It concerned various birds and their ancestors. I found the cladograms easier to draw than I had on mocks for this one, although I messed up the definition of sister taxon, drawing a line parallel to its sister, rather than a branch. It became obvious when the two tree lengths were the same. After looking at it for a time, and checking all the transformation states twice, I spotted the branch and everything became better.

Part 3 is also mandatory and is to do with graphs and data associated with the breeding date of birds. You are then asked to relate these things to natural selection and say whats going on. Based on the results you found you then had to infer a few things about their histories.

Finally part 4 is about a paper that you are given before hand and have to read. Then the question asks various things about the paper, and the evolutionary concepts it relates to. The paper is one from Scientific American about the loss of hair in humans, the probable time it happened and the reasons behind it. I think this went ok - but its all a bit hazy now.

All in all, it wasn't a bad exam. I'm not sure I'll have done staggering well, but enough to pass I think. It was a fair test of the stuff learnt on the course, and seemed eminently achievable. I could have done better, I could have been better prepared for some of the questions - but that is always the case. In contrast to my other exam - this seemed like a breeze!

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S366: TMA-5

2010-09-15T08:38:00.026+01:00

TMA 5 - the final one! Three questions - but as usual, big questions with lots of sub parts.

The first question covers quite a few basic definitions of evolution, and what causes genetic variation. You are presented with various scenarios and asked to hypothesis what is going on to give the resulting diversity. It also contains a part where a mutual relationship between plants and ants is considered, and the hybridisation of two species. Finally it finishes up with a bit on Bats and the genes that have probably changed to give them their ability with questions about these concepts.

Question 2 gives you a list of scenarios a) - k) and then a list of possible answers and asked to match them up. There is not necessarily a one to one relationship between questions and answers, and also there is the additional option of "none of the above" and you can insert your own answer into the question. Its reasonably tricky, as in some cases you could easily use more than one explanation for a given event. I got most of them right, with one or two exceptions, and some of my explanatory notes were a little off the mark.

Question 3 you are given a paper to read, in this case one about the origination of dogs in the new world. Did dogs come with the settlers that had already been domesticated before, and then came across the bearing straits, or did they come over and domesticate wolves in the Americas? So lots of questions on the paper. Interpreting their cladograms, looking at the stats, trying to find out the conclusions and the supporting data.

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S377: TMA-4

2010-09-12T11:30:00.030+01:00

TMA-4 - the last one.

Question 1 - and we're back to ICAMs. This time interaction with other molecules and cells such as T-lymphocytes. It also goes into signalling with chemokines and things like that.

Question 2 - we;re into differentiation starting with embryos. This includes going through the different mechanisms and drawing a picture for asymmetric division. Then some discussion of how possible antibodies could distort the division and what its effect might be.

Question 3 looks at the enzyme G3PDH, two versions of it. One human the other lobster. First it has to be displayed with its active site visible and showing the interactions.

Then there is a list of comparisons to be done, to compare the amino acids between the two different forms, and show how much conservation there is in the structure. You also have to predict what effect changing some of the AA might do to the activity of the protein.

Question 4 and you have to write a report based on some virtual experiments. Its not quite the normal scientific paper I've come to know that they are asking for, but something similar. There are quite tight constraints on it though. Only 4 pages, a max of 800 word, max 1 table and 1-2 figures. So emphasis on conciseness.

Slightly better marks for this one - but overall lower than I'd hoped across the whole course.

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S366: The book - part 2

2010-09-01T13:28:00.040+01:00

The rest of the book contains the following chapters:

Section K - Genetic drift: Evolution at random
This is one of the few random bits of evolution, where mutations and other characteristics which aren;t strongly selected for settle out at random. Like blue eyes/brown eyes. Eventually they would settle out just by chance.

Section L - Natural selection and adaptation

Section M - The genetical theory of natural selection
Onto the genetics and the cellular level of natural selection.

Section N - Evolution under domestication and its relevance to the origins of natural phenotypic traits.
This is about artificial selection and what changes and traits can be preserved.

Section O - Conflict and cooperation
Symbiotic relationships, predator prey and paracitism.

Section P - Species
The rise of species.

Section Q - Speciation
Different models of how species can come about - through isolation mostly, but also through other ways such as behavioural isolation

Section R - How to be fit: reproductive success
Looking into the metric that is fitness, and how to measure it.

Section S - Coevolution: evolving interactions among species
How one species can affect another in its evolution.

Section T - Evolution and development
The whole evo/devo debate. I regret not being able to quote ontology recapitulates phylogeny in my TMA's and exam.

Section U - Macroevolution: evolution above the species level
How big changes happen - mostly small changes and lots of time.

Section V- Contemporary evolution
All about recent changes to humans, domestication and so o.n.

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S366: TMA-4

2010-08-25T08:20:00.024+01:00

TMA-4 - the project.

In this TMA you have to write up two reports, in the style of a scientific paper. Its a little weird as there is a limit of 2500 words split how you like between the two papers. This is not too bad, as there is a lot of basic stuff to write about in the first paper, that you can then reference in the second. Calculations and meaning of variables etc.

I did mine on the computer project, which was the analysis of a virtual populations of the Adonis blue butterfly. It was a lot of analysis of data. Analysing virtual gels of DNA of the microsatellite markers. Then there were lots of calculations to see how related populations are, and what this might mean. This meant quite a lot of quality time with excel. The calculations aren't hard, but there are a lot of them, and its easy to get so of the steps the wrong way around.

Then there are references to find, and conclusions to write. I got a little confused about some of the statistical texts, not sure how to see if they were significant or not, but in the end I did something that seemed to sort of read ok, and got not too bad a mark.

After many reads, I got a friend to also ready it, and based on comments I had, I went back and explained a lot more what the variables were and what they meant, which in turn made me understand them a lot better. So that was useful, but I did miss out a few key things in the report.

So - one TMA left.

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S377: TMA-3

2010-08-17T10:05:00.032+01:00

It's time for TMA-3.

So 5 questions to be answered.

Question one is about endocytosis. It gives you 5 different things that are endocytosed, and asks you for the different mechanisms they use. These are IgA, transferrin, influenza virus, apoptotic cell debris and cholera toxin - so there.

Question 2 looks at the cell surface ICAM-1 in rather more detail than I ever want to again. How it is glycosylated and how it is transported about the cell, and all the key proteins it comes into contact with.

Question 3 - more on ICAM this time on its signalling system. What class of receptor it is, how it might function and its processes within the system.

Question 4 is about caspases and death domains, apoptosis and the like. I can't help thinking of death eaters from harry potter for some reason all the way through this.

Question 5 we have another paper to study, about altzeimers and untranslated regions of the mRNA. It looks in detail about mRNA regulation, and that there are mechanisms to stop the translation of mRNA into protein that can react quickly to needs. Anyway, there is a huge number of questions on this - a) to m), and several of these having i) ii) iii) subparts. There are a lot of marks on offer for this (50%). I manage to lose quite a few here though, and nto through not understanding, just being slightly out of kilter with exactly what the question is asking for. I think several of my answers are sort of right, but not what is expected. Grrr. My worst score so far.

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S366: TMA-3

2010-07-25T12:14:00.023+01:00

The third TMA in this course. Three questions to answer - more conventional than TMA-2.

The first question has parts (a) - (h) and covers things from basic definitions of evolution, to matching up statements and definitions, interpreting graphs in evolutionary terms. designing experiments, working out F_ST numbers, molecular clocks and mutation effects. Phew! 40%

Question 2 is all about Hardy-Weinberger equilibriums and is just (a) - (f). It looks at a sample of mice in the wild and how closely it matches theoretical H-W models. 20%

Question 3 involves quite a lot of rather tedious measuring on a virtual experiment. It looks at the size of house sparrow bib markings and if they might give an advantage. (a) - (d) - some of them involving calculations, others speculating on how these markings might enhance or diminish an individuals prospects. It also looks at a variety of habitats and how this also changes the dynamics. 40%.

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SXR270 Tutor - Day 7

2010-07-23T22:48:00.000+01:00

Day 7 and the last breakfast. Some combination of the last few days...

Anyway - off to the final lab. Students doing things to bits of rat tissue. We have a few failures with oxygen electrodes, and I get the chance to see one being rebuilt. Who would have thought cigarette papers had such a use in research!

Lots of mixed results, the end of the week is in site, but the students battle on to get results.

Then lunch - chicken kiev and some more chocolate.

Final summing up lecture, I had out the written assignment to my group - then home! Mixed feelings. It was a great week, but it will be nice to be back to normality in some ways.

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SXR270 Tutor - Day 6

2010-07-23T01:17:00.001+01:00

Day 6, and breakfast starts again - 2 sausage and two types of egg. I think that's all the variations tried now.

To the lab - theme 2, energy. We start with the Manduca caterpillar. I'm in charge of the microscope section - having to brief on those. Not too bad - I know how to use a microscope more or less, but then so do the students by this time of the week. I also help with the ion transport experiment as things come back to me.

It goes not too badly, we get some results - which is about par for this experiment.

Lunch then - I settle for sandwich and a big slice of walnut cake.

In the afternoon its the oxygen electrode again! I had a run in with this during plants week. Luckily they are almost the same as I am asked to show the students how to calibrate them. I surprise myself by remembering most of the steps. They can be tricky, but I manage to get through it without too many hitches. Then its into the experiment. There are one or two people waving cyanide filled micro-pipettes around which makes me slightly nervous. However its all pretty successful, despite one or two machines breaking down.

Then - leaving the students to think about an experiment to do tomorrow, we go back for tea (salmon and lemon meringue) and I dash down the hill for a lecture on black holes, although I struggle to stay away all the way through.

Now back to the room, and a shower. Then some vague attempt at initial packing.

Now then, bar then disco? Probably.

So - yes - I went to the disco, yes I danced like someone undergoing electro shock treatment, yes there will probably be an inquiry, and yes there is evidence.... unless I pay

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SXR270 Tutor - Day 5

2010-07-22T00:29:00.001+01:00

Day 5 - and the sausages and bacon go with the mushroom - although only 3 of them.

Then off to the lab to do some cardiovascular work.
This involved using various heart rate monitors, blood pressure meters and stethoscopes.
The students planned a lot of their own experiments, from the effect of exercise on BP & pulse, to caffeine intake, to mental stress. Some clever ideas came out of the session.

Lunch was cauliflower and potato bake, and more chocolate stashed.

After lunch, they were given 2 hours to construct a scientific poster, and some very good ones were made.

It was a bit of a panic at the end. Then after they were all finished, I had to go and mark my groups, which was a bit of a responsibility. It took quite a time to read them all and examine.They all passed, and I wrote comments for them.

Then a mad dash back for tea (chicken and chocolate pudding), in rather muggy weather. A shower was needed before I went back to the room to give feedback and forms to the students.

Then back up the hill once more, and to the bar. I bought a disco ticket, and decided to leave earlier as tomorrow could be a late night.

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SXR270 Tutor - Day 4

2010-07-20T23:33:00.001+01:00

Breakfast, two sausages, eggs and tomato.

Then off to the lab once more. Today a new theme, which starts with a glucose assay. However two students had forgotten lab coats so I had to run around and find them ones to borrow to start with. All part of the service. The students have to make up 42 different tubes of assay samples - so there is a lot of pipetting going on. The glucose turns a shade of pink - depending on how much there is present.

The group gets some very accurate graphs - not down to my influence I hasten to add. Then its a break for lunch, and a chance to stock up on chocolate. I had the steak, and got 3 bars of chocolate.

After lunch we went on to metabolic rates, where you have to analyse expired air collected in a huge bag thing - called a Douglas bag.

There is a chance to design your own experiments here, and some tried the effect of different exercises, others the effect of hot and cold. Seeing them wrapped in blankets with only noses poking out, or sitting in front of 5 fans was amusing to say the least.

Then to tea - the korma again for me, though it could have been anything I think. The apple pie was nice though. Not that I really need any more food at this point.

Now another set of tutorials to sort out, before the evening finishes, and a "blue parrot soiree" invite for tutors. Slightly nervous!
Well the tutorials went ok I think, I'll have to see. Then some cokes, yes I said cokes, in the bar, as I think I hit the wall on this marathon.

Then to the blue parrot thing - which turned out to be a VERY blue cocktail, looking rather too much like anti-freeze for my tastes, and with a fearsome reputation. Anyway - chatted with a few of the tutors, nibbled some cheese, and then eventually retired.

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S377: Book 4 (The Interactive Cell)

2010-07-20T13:09:00.012+01:00

Book 4 - the final book in the course.

It starts with a short chapter (15) on cellular interaction. Just a few pages long and a sort of introduction.

Then onto chapter 16 about Cell Migration and Adhesion. Looks at the various cell adhesion molecules, cell movement, chemotaxis and control. Also disintegrins and a few other bits and pieces.

Chapter 17 is about differentiation, how a single cell can grow into a multicellular organism. What different ways growth and differentiation is controlled, and how nerve systems and other organs develop.

Chapter 18 is the other end of the cycle so to speak. It looks at cell death, ageing and damage. It looks at a number of ways ageing may occur, and concludes it is probably multi-faceted.

Chapter 19 is the last part, and looks at tumorigenesis. This sort of brings lots of things together, becase for tumours to come about a number of the pathways and mechanisms have to fail. So some of the pathways get stuck in the on position. Some of the checks get switched off. Cells migrate away from their location spreading the tumour. They have to avoid the apoptotic signals that would otherwise kill them, become immortal and grow without limit whiles maintaining blood supply. So a lot of things have to happen to get to the final part.

So - I suppose its a good round up, but not always the sort of thing you want to read about.

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SXR270 Tutor - Day 3

2010-07-20T00:14:00.001+01:00

Day 3 starts - and I choose the scrambled egg - not very memorable.

Then off to the lab. On the way we have to wander into a copse of trees to grab a sample of lime leaves - some shaded, some in bright sunlight. It's one of the rituals apparently. It's also one of the experiments the students will be doing later.

Getting to the lab, its the leaf disc experiment, and it all goes pretty well - if you exclude the results. They have to subject leaf discs of various plants to radioactive carbon-14 to see how much is taken up by different surfaces and colours of plants.

About 5 different plants were tested including the huge maize plant.

Note the cameo role of the air conditioner next to it - which probably isn't doing it a great deal of good. There is a lot of radioactive marker tape around, and we have to take extra precautions. Special lab coats so as not to spread contamination, gloves and goggles, and a special fume cupboard with lots of admin sheets to account for all the radioactive material.

Most of the results were the exact opposite of what they should have been, oh well - that's science - something I had to say more than once today.

The afternoon brings the presentation skills, and the students have an hour and a half to put together presentations to present to the rest of the group. Then its off to a very large lecture theatre where they get to present them to the group (only 18 people). All very successful. Then a tutor debrief as we prepared to hand over to the next theme.

Then back for tea (pork and various veg, bread and butter pudding).
Then to be with my group as they get introduced to the next theme, and to help out with the poster design workshop.

Then, I think I see the bar in my near future! Oh karaoke.... hum. Its OK - but you can't hear people talk or hold a conversation. Just the one tonight then.

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SXR270 Tutor - Day 2

2010-07-19T02:15:00.002+01:00

The first full day in the lab. In truth I'd forgotten a lot of the first experiment, but it all came flooding back once it had been demo'd. Managed to remember most of the details, and by listening carefully to the theme tutor I picked up some useful details to pass on. I felt quite confident at points, then I was put in charge of the cronky old 1970's era centrifuge, and it took a while to get that to go. However it all came out ok, the students got their chloroplast suspensions, and were able to proceed with the experiment.

I got lost finding the coffee bar first time, and nearly led a large group of students to the wrong exit to the cafe. However we got there in the end, a good Sunday lunch of roast beef and Yorkshire puddings. and I'm up two mars bars on the day!

This afternoon both tutor groups combined to do one bigger experiment on stomatal openings. It went pretty well to, although the actual results were pretty marginal.

Then back for tea (chickeny thing in mushroom sauce & apple pie) after picking up the materials I'll need for tonight's talk. Then I got talked into a quiz - actually it didn't take much talking. And then after we didn't win, we went back to the bar just in time for last orders, and sat drinking in the garden until late.

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SXR270 Tutor - Day 1

2010-07-17T23:05:00.000+01:00

First day as an SXR 270 tutor. Well, no ones run off screaming yet anyway!

So - what was my day like? Well 12:00 a briefing on the course with the other tutors, and a chance to meet all the team. I knew at least a couple of the other tutors, so that was good. No real surprises at the meeting.

Then off to the labs to go through the equipment - that was OK too. Most of it came back to me eventually. Some of it more quickly than others.

Then off to hear the course directors introduction talk, followed by taking the group up to the lab for introductions. We split the group into two, and I had my 10 students. I then had to do some ice breaking, and a quick talk on keeping a lab book. It all seemed to go OK, although I wasn't sure.

After that its time for tea after the walk back from the medical school - they are building AGAIN! Tea - was a repeat of last Saturdays menu - I turned down the mushroom rice thingy I had last week (risotto I think), and went for the chicken instead.

After that, I had to give a talk on the scientific method and formulating a hypothesis. I seemed to go through the material quite quickly, even though I'd brought along some of my own slides.

Then to the bar - to have some drinks with my group, and a few other friends I knew from previous courses. I decided on an early night at about 10:30 as tiredness is a real possibility, and other nights might not be so easy to sneak away.

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SXR375 - Day 7

2010-07-16T16:49:00.000+01:00

The last day :-(
Today no labs - we just have to give presentations. Breakfast - and wonder of wonders - you're allowed 5 items today!!! I only had 4, as I could hardly believe it!

Then we had an hour to tinker with our presentations. Ours was all finished, but I did have one addition. The only person who had published a paper on our plant, I'd sent an email to the previous day, asking him what pigments he'd found. He lives in New Zealand, but even so I thought it worth a shot. He replied in time for me to include his answer in the presentation. So I quickly inserted a slide in to show his thoughts on it. He hadn't found specific pigments, so we were one better than him. Of course he'd found other details that we referenced, so it was a good trade.

Anyway - then me being the computer geek, I took over the lecture theatre computer and got every ones presentations loaded up, in order and ready to go. I also had my handy dandy laser pointer which everyone used for advancing the slides and pointing things out.

The presentations went very well, and we finished in just over two hours. No one really had a problem, despite most people being full of nerves, and it was a really good session.

Then we had a quick last talk in the lab about the ECA and what was required, then back for our last lunch (fish and chips).
Then it was a few good byes and the whole thing was over. Slowly real life starts to fade back in. I went back to my room, because I'm in the same place next week - being a tutor on a different course. I made a start on the ECA (well just the headings - so a good 15 words from the 2500 required!) - hey its a start.
Then - pickup time for a nights sleep in a proper bed, then a similar thing to do next week!

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SXR375 - Day 6

2010-07-16T00:02:00.002+01:00

Last day in the labs today. Breakfast first - the usual mix.

Then down to the labs, to complete our last few bits and pieces. We had a go at the full pigment spectroscopy, but with mixed results. We tried a couple of times, really grinding the leaves up hard with abrasive sand, but it always came out as a green colour and the spectroscopy showed a classic chlorophyll curve.

The the tutor gave us another idea, to mix in acid to try and release the attached molecules, and suddenly we got our nearly flat black spectrum that we wanted - hooray!

Now we had the full story. So we finished off and went up to start work on the presentation.

We broke for lunch with about half of it done (sweet and sour chicken).

Back down to the lab for a quick briefing on what happens next, and we then worked some more on our presentation. Soon had it finished and then we went to try it in the big lecture theatre.

A few more tweaks, then printed out the slides and went back to write some notes for the talk around the slides.

Tea coming up (lasagne and lemon meringue with ice cream - no soup), then - to disco or not to disco - that is the question?

Well in the end, we sat in the bar, drank and laughed a lot about presentation skills. It was a release I think from the weeks work.

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SXR375 - Day 5

2010-07-14T23:58:00.001+01:00

Day five - project start day. We get to do our own thing a bit more now.
Breakfast, and at last the mushrooms make an appearance.

Then down to the lab - and to decide on the project. Our team of three want to investigate the black leaved flowers and see what they contain. We started off with an ambitious three pronged attack, wanting to measure photosynthetic activity of green v. black leaves, the pigments in the black leaves, and whether the flowers had any insect attractants. After a few false starts with the oxygen electrode we decided to leave that bit. It looks a bit fiddly, and our initial tests were a bit difficult to understand.

We go and fetch some fresh leaves and flowers and set to work. We do chlorophyll extraction first, to see if there are extra pigments there. However nothing unusual shows up.

Then we set to work extracting the other pigments. Anthrocyanins and flavinoids.

The pinky one is from the flowers, and the darker red from the leaves. We leave them evaporating and go and get some lunch (chicken fajitas - pretty good i have to say).

The afternoon brings mixed results. We get very poor TLC plates for the pigments - although the flavones come through. We rerun them a number of time but a smear is the best you could describe them as.
We attempt to use the UV spectrophotometer, but it appears to be a cranky old beast and ignores our best attempts. Then we notice that the visible light spectrophotometers dip into the UV a bit, and they are far easier to use in comparison. So we do a few runs of that, and get something we can talk about I think.
In the end - it looks like we have the data to talk a story, but there is one more thing that would help, and I ask Andy about full spectrum of the pigments.
He told us how it can be done, so that's one more thing for tomorrow.
Tea time (mushroom soup - good, beef steak - ermmm passs, chocolate sponge - not the best ever). Then another two tutorials. One on our upcoming presentation to the group, and then another on our final piece of written work, and where the marks will be.

We were all a little tired now, and trudged back up the hill. The bar called, and most of us answered.

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SXR375 - Day 4

2010-07-13T23:04:00.002+01:00

Another day. Another breakfast - much the same as all the others. This 3 items thing does make the plate look a little empty. Anyway - onwards. Its raining again on the walk down to the lab.

We start the lab by doing assays of chlorophyll and protein in the chlamydamonas that we used yesterday. This will help us plot our curves - although really we need a miracle for any curve to come out of ours!

We head for lunch (baked potato with cheese and ham) and then all meet up to go off to a garden, to look at some plants - with the ulterior motive of selecting species to do our projects on. I find some of my black leaved plants in there, which I'm considering doing a pigment analysis on.

After that - its back to the labs for some to finish up assays - collect data and do graphs and things. We do extensive surgery on our graphs - they still look awful, its a very noisy circuit we have so very difficult to pick out data.

Tea - crunchy minestrone soup (interesting idea - not sure it will catch on), chicken korma with rice and nan, and a rather good rhubarb and ginger fool (no not me).
The back to the lab in the pouring rain to discuss the last three days work, and see what data we have for the end of course assessment write up.
Then to the bar, for a light evening avoiding an impromptu quiz.

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SXR375 - Day 3

2010-07-12T23:54:00.001+01:00

Day three. Another breakfast (fried egg, bacon and veggy thingy), and its started to rain.

The morning brings experiments on single celled green algae (Chlamydomonas reinhardtii). We want to get some of them, shine light through them and see how much oxygen they make at different light intensities, including none at all.

Well its a bit of a disaster really, and we're trying to recover some data. First the water bath wasn't switched on, so we had to wait for that to come up to temperature. Then something went wrong with our calibration of the oxygen electrode, so we had to wash it all out and redo that, about 15 mins gone. We then eventually got results, but the electrode gave very spikey traces, and the results were not really what anyone was expecting, except in general terms.

So lunch, and then we'll try and get some useful data out of the noise (pasta of some sort)

After lunch things were no better - our graph looked like a roller coaster.

Everyone elses graphs were perfect.

Oh well - there is always the bar to drown our sorrows... oh after tea (something vaguely porcine) a tutorial or two...
Now done, and some sorrows drowned. Tomorrow is another day.

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SXR375 - Day 2

2010-07-11T23:24:00.002+01:00

Day two. A patchy breakfast, fried egg or scrambled, sausage and tomatoes. I was reliably informed by others on the table that they doubted anything organic went into the scrambled egg, so my choice of fried seemed good. Still cereal and toast is ok, and coffee was welcome.

Off to the lab, and our first task was to grind up some leaves. We chose petunia leaves, other groups did tobacco, pak choi, coleus and others. We then extracted the pigments in acetone and diethyl ether. Then we did some thin layer chromatography, try to separate out the pigments such as chlorophylls, lutein, violaxanthin and neoxanthin. Some nice bands separated.

We then tried to take some of the bands - and analyse them in spectrophotometer. FIrst time it didn't work - we had the tube the wrong way round. Second time looked better, but one of the peaks was in the wrong place.

Then just time to put some flowers in to stew in HCl before a break for lunch.

After lunch, we came back and did similar procedures with the extract from flowers. We were looking for flavones and anthocyanins, using similar techniques. We had a hitch when we put our first TLC papers in the solvent, which turned out to have too much acid in, and they all dissolved into mush! Anyway - after coffee break we redid things, and they worked much better.

More chromatography, and some absorption spectra helped us isolate pigments from the various plants we'd looked at. We collated the data - wrote it all down and then went to tea (roast beef and yorkshire pudding).

After that I attended a tutorial on photosynthesis and plant pigments, and another on giving presentations.

Then - to the bar!

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SXR375 - Day 1

2010-07-10T14:32:00.011+01:00

Its a hot day. with the help of the family I've got registered, found my room, and unpacked just a little.

The family were with me, and they helped me label by books and name tag.

The room has a fridge in it, a desk and a bed. A few other things like a kettle and so on.

Still - I won't be in it a lot. Lots of time in labs, tutorials, eating, or in the bar.

We had a walk around the campus to locate the biology building.

Then the family left, and I sorted out my things. The course started with an introductory talk which covered various administrative things, and then we went down to the labs. We were introduced to the courses tutors and formed up into small teams. I found two others who thought I would at least not cripple their efforts. We then had a look at the range of plants they had on offer, which tomorrow we will be extracting chlorophyll and other pigments from.

After that - back to the hall for lunch and a coffee to keep things going.

Next there is a guest lecture on pesticides, so I'm off to that.

This was good - with a good discussion of issues involved in feeding the world, GM crops, organic produce and so on. We then retired to the bar, where I started a table that grew to about 8-9 people discussing a variety of topics. It was a good evening - hope the alcohol intake doesn't disrupt tomorrows labs!

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SXR375: Plants and Pigments - CMA

2010-07-07T13:03:00.003+01:00

There is a CMA that has to be done before attending the school. You have to score 35% or more on this, to stand a chance of passing the course. Sneakily, although you can see why, you don't get the results until after the residential school.

Its 20 questions, all multi choice. However some are "choose the correct answer", some are "select up to 3 true statements", some are "find the two false statements" and some require work to be done, graphs to be plotted to get the answer. A few of them are based on research papers which we have a copy of, that we have to dig the results out of.

All in all, its not too bad. I think some of the questions are a little ambiguous, but I think I'll pass OK. One question that insults my sense of logic is "Select three correct answers" and we have A-F to choose from... except F's answer is "All of A-E are true". So if you choose this, doesn't that invalidate choosing 3?

I have a slightly freaky moment, when on the last 4 questions, I realise I've been using last years question paper rather than this years! Ooops - good job I spotted that.

Anyway - its gone now! Time to pack now - and remember to take my new white (well it is currently) lab coat!

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S377: TMA-2

2010-07-07T09:06:00.007+01:00

So TMA-2 of the course. Five questions.

The first one is about mitosis, and the anaphase part. You have to draw a diagram of a cell on the verge of splitting its chromosomes. Then talk about the proteins involved in the separation and the conditions required to bring about the separatation. Then a bit to answer on what happens if any of the mechanisms fail.

The next question is about DNA replication and how it happens, what speed it goes at and how it differs between eukaryotes and prokaryotes. Also a classic experiment on the process is investigated to explain how it works.

Question 3 is about transcription. It considers the TATA box, and how transcription factors are involved. Then the epigenetic DNA modifications and how they are preserved.

Question 4 you have to investigate a zinc finger transcription factor and look into the structure of it. How the metal ions are held, and how it interacts with the DNA molecule. Finally you have to show part of the model with some parts highlighted in colour and labelled.

Question 5 you have a paper about a membrane bound protein, and there are a whole load of questions on it. Some is stuff from the course, other is data from the paper. There are a lot of questions, and I found it easy to get out of step answering a little too much in a) and then not including some of the data in b) so losing marks.

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S377: Book 3 - The Dynamic Cell (Vol 2)

2010-07-06T11:27:00.022+01:00

Book 3 which is confusingly entitled The Dynamic Cell - Volume 2 carries on from the previous book.
There are just three chapters in this, although some of them are pretty big.

Cpater 12 Transport and Compartmentalization: It starts with a chapter on transport and compartmentalisation. This covers how the cell moves stuff around, how signal in the code are recognised as labels to send the packages to the correct destination. It also looks at hte transport network, which moves these vesicles around. It covers endocytosis (bringing stuff into the cell) and exocytosis - the opposite. 64 pages in this chapter!

Chapter 13 Signal Transduction: The next chapter is about signal transduction. How signal are recognised on the cell surface and how they trigger cascades. Also some words on the different receptors and ligands that are in common usage.

Chapter 14 Cell Death: The final chapter is on the subject of cell death. All cells have the ability to commit suicide, either on command or if they detect things are going wrong. So this chapter covers some of the mechanisms that trigger these events.

So 180 pages or so in this book. Some of it is pretty heavy going, but interesting.

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S366: TMA-2

2010-06-12T08:50:00.001+01:00

TMA 2

This is a bit of a weird one. Its one of 5 pieces of coursework for this course, but this only counts 5% towards the total of assessed work. You have to pick a sort of project thing to do that explores evolution a bit There are 4 projects on offer.

Bird Predation Project -this is where you bake little bits of coloured pastry and look to see if there is selection of the bait favoured by the birds coming to feed on it in your garden.
Conservation genetics project -Looking at two different species of tree or flower and making measurements.
Hybridisation project -A computer based butterfly project, where you look at microsatellite information to see what populations of butterflies exhibit and how related they are.
Snail shell project -collecting common garden snails and looking at the banding on them. This is an extension of the S170 work.

I chose the conservation genetics project, as I like computers and am fundamentally lazy!
Anyway - apparently this TMA is a forerunner for TMA-4 which counts for 30% of the marks, and requires you to write up two experiements for the project. So this TMA is for you to make mistakes in, and mess up calculations and graphs so it can be corrected.

I spent a long time on it though, far longer than the 5% justified. However I hope quite a lot of it will be reusable for the TMA4.

The TMA also has a proforma like thing where it tells you what data to put in, what calculations to make and what questions to answer, so it is fairly easy to tick all the boxes.

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S366: The book

2010-05-27T11:53:00.002+01:00

As I've said, this course is a combination of two books. The text book that comes with it, and the companion text which tells you which bits to read. Sometimes this directs you to read a whole chapter, sometimes just bits and the companion text then has lots of text to read that replaces or supplements that in the text book. So what do we do in this course? Well here are the first few chapters. All labelled with letter of the alphabet.

Section A Evolutionary biology - this is an introduction to evolution. Where it stands, what its principles are, how secure it is etc. Sets the scene nicely.

Section B Adaptation - here we look at some examples of adaptation. It includes a DVD video on Adaptation in Svalbard reindeer. Some reindeer that are unique to a small island, which has influenced their evolution.

Section C The Tree of Life: classification and phylogeny. Lots of stuff on constructing cladograms, and phylogenetic analysis. Several exercises to do here, some stuff for TMA 1 too.

Section D Patterns of evolution - more on phylogeny, and a look at trends and adaptive radiation.

Section E Evolution in the fossil record - some examples including the origin of feathers and the ancestry of birds. A look at fossil trends, punctuated equilibrium, and this is where the brachipod stuff fits in.

Section F A history of life on Earth - From Earth’s earliest life, through evolution in the precambrian to evolution in the more recent eras.

Section G The geography of evolution - looking at geographical influences, barriers, climates, ecologies.

Section H The evolution of biodiversity - which looks at how to quantify taxonomic diversity, mass extinctions, and so on.

Section I The origin of genetic variation and Evolution of genes and genomes - here we look at genes and genomes, how mutations occur and the randomness of it. Also things like recombination, the origin of new genes and then some parts on the phylogenetic processes applied to genes.

Section J Variation - Distinguishing sources of phenotypic variation, some work on population genetics, molecular markers and qunatative traits. Some maths involved here.

So - thats about half the course.

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S377: Book 2 - The Dynamic Cell (Vol 1)

2010-05-25T11:18:00.004+01:00

This is the 2nd book of the S377 course.

We start to get into a lot of the cellular stuff here. The chapter numbers follow on from the first book - so it starts with Chapter 7.

Chapter 7 - Introducing the Dynamic Cell is quite brief, and is an introduction to the cell and its contents. Nothing particularly new here, but it sets the scene.

Chapter 8 - The Cell Cycle is much more in depth. We cover the mechanisms of mitosis, the cell cycle meiosis and cell division. However this is in quite gory detail. I'm sure many people have seen videos of chromosomes lining up and then separating to opposite ends of the cell. All very nice, I've even seen it under the microscope, although of cells caught in the act rather than dynamic. However you have to ask here, how do the chromosomes move around, how do they pair up, how do they line up? What causes them to separate and how does the cell arrange for it to happen without error.

Chapter 9 - DNA Replication and Repair - again something I've covered many times before. However not in this detail. The typical animated image shows DNA unzipping and getting copied just like that. However its a lot more complicated than that. For instance as the strands separate under the influence of a enzyme, the twisted nature of DNA means that further up the molecule it starts to get all twisted and under tension . Its like unwinding the strands of string, as you pull them apart if starts to ravel up further down. DNA is also often packed up into compact structures, which have to be unpacked before you can even start the replication. Then there is the problem of replicating the lagging strand, the fact that to replicate something like human DNA in any reasonable time you have to have lots of replication at the same time doing different bits, that then all have to get joined together. Yes - its complicated. Then there is repair...

Chapter 10 - Gene Expression - this chapter is all about how genes are switched on and off. Lots of stuff on operon, enhancers, silencers and so on. The infamous Trp operon is considered.

Chapter 11 - Translation and Protein Turnover - the last chapter of this book. Considers how the ribosomes work, how they match the tRNA to the mRNA, and how the tRNA gets the right amino acid attached to itself - again something normally skated over. There is also alternate splicing, mRNA regulation, post transcription modification, nuclear export - lots of details here.

Some fascinating stuff here - and some stuff that is not too well understood.

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S377: TMA-1

2010-05-09T17:29:00.004+01:00

The first TMA of the course - and its a long time until the submission date. Given I started the reading before Christmas, the April submission date is a long way in, and I've read past most of the relevant material, so some rereading is required.

So there are 5 questions to answer.

Question 1 is about enzyme structure. It looks at a kinase and you have to make some general comments on structure, domains and function.

In Question 2 we have to look at a 3-d molecular model and identify and measure parts of it. There are also tasks to perform. Also required is to include an image of the enzyme active site.

Question 3 simply gives you some concentration data and asks you to work out the equilibrium dissociation coefficient of a ligand and its receptor. The question is a little sparse as it doesn't really give much guidance on what is wanted in the answer except the value.

Question 4 is about SDS-PAGE and requires you to run gels on the computer simulation with a number of kinases and antibodies to work out what the results tell you.

Question 5 is all about reading scientific literature. You are given a piece of writing and then have to make sense of it and answer a number of questions about what its conclusions are.

Not a bad TMA in some ways - but a little disappointed with the mark I get.

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S366: TMA-1

2010-04-17T12:00:00.001+01:00

So - time for the first TMA. Its quite a long way into the course, so you have a lot of time to devote to it if you want - or alternatively to ignore it!
So whats in this TMA?

Well - first thing to say is its big! Its 12 pages long, and for 3 questions thats quite a lot.

The first question is all about phylogenies.
First you have to identify a range of features in a sample, preparatory to doing an analysis on it.
Next you have to look the cladogram of these species and pick out some features in it.
Then you have to indicate the most parsimonious transitions on the diagram, which means finding the transition points for the 10 different features being considered.
Then there is more commentary required on the shape of the cladogram, and what this says for the inter-relatedness of the species.
The next step is to input the characteristics into a program, and perform your own cladogramatic analysis.

The next question is about statistical analysis - and it brings in the home kit.
A while lot of work is required to analyse some given data, and relate it to the data you have worked out from the home kit. There is a log of statistical manipulation required here. None of it is hard, but one figure feeds into the next, and its easy to make a mistake - subtract rather than add, or pick the wrong figure to divide by.
A couple of graphs have to be drawn or amended, and then commentary has to be made on the results and what they show of the species and now they are related. Whether their growth patterns are similar. You also have to make some predictions on what this might mean if you found new samples.

Finally question 3, which is 10% of this, is a SWOT analysis of each of the potential projects that need to be undertaken for the next TMA. It also includes a risk analysis section, which I struggle to take seriously, but complete through gritted teeth!

The course team reckoned 5 hours to complete the TMA, I wouldn't like to think how long I spent on it though.

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SXR375: Plants and Pigments

2010-04-15T14:29:00.005+01:00

So yesterday a parcel arrived - it has in it the material for my next residential school coming up in July.
This is a 3rd level course investigating plants and pigments.

It arrives with

A folder
A folder insert
A course description
Some prereading material
A DVD

The school is all about analysis of plants and the way they use pigments to control their photosynthesis and manage energy and light issues. There is a computer marked multi choice paper that has to be done before hand (online) which you have to pass to complete the course.

Then there is the school itself, which includes presentation of results, and then a write up to do afterwards. Looks to be fun, and this time I have to take my own lab coat, so have ordered one.

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S366: The brachiopods measure up

2010-02-07T09:50:00.004Z

So - with the arrival of the practical kit, and the appropriate part of the course reached. Its time to do some practical stuff. So here we are - presented with 30 plaster casts of various brachiopods, all from the same era.

My task is to measure them with the supplied calipers. They are accurate to about 0.1 mm although I suspect most of the error measurements comes from how you actually attempt the measurement. For each of the 30, I have to measure and record the length, width and thickness of them. Now you might think this is simple enough, and I suppose it is, until that is you offer up the first sample to the jaws of the vernier calipers. Width is perhaps the easiest, as there is really only one width, and the only trick is making sure the sample is perpendicular to the jaws to get a true reading. Length is next easiest, but you have to do it in the right orientation otherwise off axis sticky out bits tend to make it seem longer than it is. Thickness is more tricky, as the thickest bit on one side is not opposite the thickest bit on the other. Therefore you have to make sure the "seam" is appropriately flat to the jaws and you haven't got the whole thing crooked.

All simple enough really, but rather than sitting down at a table in a good light with sharpened pencil and pad, I find myself sliding into the event sitting on a settee with the TV on (Horizon) and dispensing with the pencil altogether and recording straight into excel. Is laziness ever a virtue I wonder? Its certainly much easier to read my writing back afterwards, so maybe it is. I'd planned the well lit desk I think, but just somehow drifted into the first measurement, oh well...

With the results recorded there is now a whole heap of stats to apply to the numbers to see if there is a correlation at all, if there is a relationship between the three dimensions, and then finally how they compare with some brachipods from a slightly different era. The calculations are not hard really - as either excel or a supplied program can do them, but they are fiddly. There are quite a number of them, and its quite easy to divide one number by the wrong one at some point which means the final answers are way out of line. It takes another night, and a fresh look at the calculations to have any confidence that the chain of about 20 results really do end up with something sensible. I mean, does -6.2 sound about right to you?

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S366: Evolution - first steps.

2010-01-08T09:00:00.001Z

Well two things have happened since the original S366 materials arrived.

I've started working through the course, which involves quite a lot of cladograms and phylogenies. Making by hand, by computer and so on.

I find the course difficult to get to grips with in some ways, but this is mostly the way it is constructed. There is the very solid book Evolution by Futuyma, at 540 odd pages, but then there is the commentary on it written by the course team at over 300 pages that directs you which pages to read. So its read 2 pages of the course guide, which tells you to read 4 pages of Futuyma, and then run a program to generate a cladogram, or maybe watch a DVD.

I like to get stuck into the reading and absorb stuff, but the chopping and changing of books I find a bit disruptive. I mean they are big and heavy enough you can't just balance them somewhere while you flip to a page in the other. So I'm running a 3 bookmark system - one the place in the course guide where I'm at, another in Futuyma and another at the back of the course guide where the answers to the inline questions are.

The second was the exciting arrival of the practical kit. This comprises of a lot of fossils casts and some vernier callipers to allow you to measure them.

That at least looks fun. Though I suspect when it comes down to it, there will be a fair bit of tedious work involved.

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S377: Book 1 - From Molecules to Cells

2010-01-02T17:18:00.007Z

Book 1, being the first book therein, is, as indeed is conventional, is the first book in the course. So its where you start into this course. At just over 300 pages its a reasonably large book - but one of four that make up this course. So - plunging in what do we find inside.

Chapter 1, Evolution of the cell, is really a sort of introduction, but describes the probable evolution of the biological cell. It's a nice short chapter with plenty of familiar terminology and concepts - so is a reasonable introduction into things.

Chapter 2, The foundations of life, is a tad more involved. It considers a lot of chemistry that makes up the cell, including the chemistry of water, biological carbon compounds and ions. There is a fair bit on different types of bonding, chemical equilibria, stereochemistry, pH and pK factors, and the interaction between molecules. There is also a section on molecular modelling and getting you to use the 3-d programs that display molecules to become familiar with it and its abilities. So quite a lot of chemistry in this chapter, which would be a lot of new things to contend with if I hadn't done the S205 course.

Chapter 3, Proteins, goes into a lot of detail about proteins. It looks at electrical interactions of the side chains of amino acids, protein domains and families. There is more on molecular modelling 3-d program too and its ability to show the tertiary and quaternary structures of proteins - as well as the atoms.

Chapter 4, Thermodynamics and Bioenergetics, looks in detail at some of the thermodynamic principles as to whether reactions will proceed or not. This culminates in discussions of Gibbs free energy and entropy/enthalpy, which is second nature after S205 - although the application to biological molecules is a little more complex.

Chapter 5, Nucleic acids and chromatin, considers the key genetic molecules and spends some time looking at their structures. DNA can be found in its traditional double helix, but also in two other forms. It also looks at other forms of the nucleic acids and how their packaging in increasingly complex structures which reduce potential damage. Again some chemistry comes into this as it looks at energetically favourable states.

Chapter 6, Membranes, looks at the structure of membranes and the various components they can be made of. It considers the different types of fatty acids and what they bring to membrane structure. It also looks at the proteins that attach to membranes in their various forms.

Also at points in this book you are directed to read some scientific papers, including the original Watson and Crick DNA paper, and their follow up which gives detail of the proposed structure.

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S366: Evolution - arrival

2009-12-17T12:57:00.006Z

Well guess what arrived just now! I checked the site only yesterday, and it said it wasn't scheduled to start being delivered until next month, but here it is - and a heavy box full it is too!

So - what do you get in this box?

Text book - Evolution by Futuyma - which accounts for most of the weight!
A companion book to the text book
A bookmark with some handy diagrams on
An introduction and guide to the course
A practical booklet
A TMA form - hoping these are eTMAs.
A DVD pack
Checklist and Welcome note

Its quite a tome is old Futuyma, I don't know how much of it we'll have to read!

Anyway - something to do over the holidays, as if Christmas, kids parties and stuff weren't enough.

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S377: Molecular and Cell Biology - Arrival

2009-11-30T14:46:00.005Z

The next course arrives - it doesn't start until February, but I'm doing two courses together, so I'm glad of the head start. This is only the first of two mailings, but has some good stuff in it.

What you get is:

Book 1 - From molecule to cell
Book 2 - The Dynamic Cell (Vol 1)
A Bookmark with some useful data about amino acids on
A ring binder
A ring binder insert with pretty picture and title
A set of folder dividers
A glossary
An introduction and guide
A study skills pack for books 1 and 2
A DVD containing molecular modelling programs, movies and other bits

Notable by their absence is a calendar, TMAs and the normal OU computer disk.

All looks nice and shiny, and I'm ready to go having not had any assignments to do for the last month or so. However as the course site doesn't open for a while yet, there are no assignments to contemplate, just books to read and exercises to do.

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S283: The Exam

2009-10-22T14:04:00.004+01:00

It has to be done - another exam. Why do we go through this I wonder?
Well I'll tell you - well actually, I'll tell you why I think its good to do an exam.

This is where the course really comes together. There is no avoiding it, you have to confront your weaknesses. You can't go back to the books in the exam and reread a subject and go "Oh yes, I must have skipped that the first time around". I find a lot of things become clearer when you have to be prepared to answer questions on it.
You feel validated. I have this nagging feeling that others may be able to do the course, just by reading from the books and repeating stuff without understanding it. I expect this is not true, but if so - well you can't do that in exams. So though its stressful, you feel having done it you understand the subject.
For those few weeks of revision - you are a real expert on the material. Sadly it fades sooner or later after the exam, but for a while, should someone make the mistake of asking you a simple question on the topic, they'll find themselves pinned to the wall for an hour or more as you hold forth.

What I don't like about exams is:

Memory stuff. In this exam for instance, you really need to know the distance of the planets in AU for the exam. That's just wrote memory test, not much more.
That feeling when you open the paper, read a question, and realise you don't know anything about this.
All that revision

Anyway - this exam consists of
Part A - 8 multiple choice questions

Q1 is about Venus, how far is it from the sun and whats in it atmosphere
Q2 is about the structure of planetary bodies
Q3 is about the structure of an unidentified planet.
Q4 is about the orbit of an asteroid, and needs some of Keplers laws.
Q5 is about the requirements for life.
Q6 is about Titan and its environment
Q7 is about Doppler spectroscopy for detecting exoplanets.
Q8 is a graph you have to identify.

Part B - About the solar system and stuff - answer 3 questions from 4.

Q9 gets you to normalise rock samples based on mineral components and plot a graph.
Q10 is more an essay question about how planets form, where you have to write some of the steps in their formation.
Q11 is about some craters on Mars, and how they form. Again you have to describe mechanisms.
Q12 is about meteorites and their inclusions.

Part C - Astrobiology and the search for life - again 3 from 4.

Q13 is about evolution, the requirements for life and Panspermia.
Q14 looks at Europa and gets you to label images and say what is going on in resurfacing terms.
Q15 is about habitable zones around stars, and is maths based, which you then have to comment on.
Q16 is exoplanet detection using doppler and astrometry. Then follows this up by exploring what else you might find out.

I've had worse exams, I've also had better ones. I think I passed, but possibly not as well as I might have hoped. Oh well, nothing I can do now.

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S283: TMA-4

2009-10-21T09:51:00.003+01:00

The last TMA. I need a big score to up my OCAS average on this one. Alas not to be, despite spending far too long on it, repeatedly reworking it. I'm just not putting what is in the marking template apparently.

Question 1 is about evidence for water flow on Mars. You have to download a paper discussing recent evidence for water flow on Mars and compare the paper with details in the book.

Question 2 concerns rainfall on Titan, and the atmospheric structure there.

Question 3 concerns the Drake equation, and asks you to calculate civilisations based on some given numbers.

Question 4 is about extra solar planet detection using the Doppler method. It also includes details about transit detection, what its probably density is in comparison to Jupiter, and so what sort of planet it is. Also how it might have got there through migration.

Question 5 is all about suitability for life based on IR and light spectrum. Discussing possible spectra and what they might tell you, and what you would hope to see in some cases. Also reasons the planet might be habitable but still nto show up on the spectrum results.

Last TMA, not the mark I was hoping for, and in general the marks for this course have been hard to get compared to all the other courses I have done with the OU. I still got reasonable scores, but found it very difficult to get a good score on a TMA, as it seems very picky about minutia of detail. If you answer is right, but not what is wanted, you score less than otherwise.

Anyway - now just the exam.

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S283: TMA-3

2009-09-18T08:26:00.006+01:00

Well, my worst TMA of the series (so far). One stupid mistake which probably accounts for a couple of lost points, and several questions where I miss the point.

So
Question 1: This is about ¹⁷O and ¹⁸O ratios, and what they say about stars. You have to calculate a few quantities and the rest is interpreting the results.

Question 2: Is about geochemical data for asteroids, and looks at rare earth element ratios. You have to calculate some data in a spread sheet for 3 different sample, and then plot it on a graph. You also have to do the same thing with δ¹⁷O and δ¹⁸O ratios. Then armed with this data make a case for the origins of the various samples.

Question 3: This looks at possible biological molecules, asks you to identify the general type of molecule, its use as a biomarker. Then you have to draw the chiral equivalents of them in a chemistry program.

Question 4: This asks you to discuss the habitable zone around a star, and also looks at habitable zones around larger planets and similar.

Question 5: This is about the martian meteorite ALH 84001 and the possibility that it shows evidence of microbial life on Mars. You have to discuss the evidence for and against. Finally it asks you to critically evaluate the evidence for the emergence of life on earth, but says you should do it in 50-100 words - which to be indicates a short answer. The sample answer contains a number of points that I missed.

Anyway, there it goes, hope to do better in the next one.

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S171: Empire of the Microbe

2009-09-06T10:17:00.003+01:00

So another short course, to fill in a 10 point degree shaped hole.
This is a new course, first presentation. A scary prospect if there is an exam involved, but this is just the normal ECA so I feel confident.
What you get is

Empire of the Microbes course book
A DVD with a digital microscope flashg application and some videos
A study guide
An assessment handbook
A how to get help guide

All the rest is provided online, which due to a late sign up and some gremlins I've only been able to glimpse a couple of times before it declares me persona non-gratia. Anyway, the book looks up to the usual excellent OU standard, but with a TMA, an exam, and the S170 course to do, its getting scant attention so far.

S283: Book2 - An introduction to astrobiology

2009-08-20T10:54:00.008+01:00

Book 2 starts to get to some biology, and leave behind some of the geophysics, so its more in my comfort zone.

Chapter 1 starts by looking at the origin of life on earth. What it needs in terms of components, how it might have started and the clues left behind both fossil and molecular.
Chapter 2 looks at environments for life, and considers the habitable zone around the sun.
Chapter 3 is all about Mars, and the various attempts to find life there, including the notorious Martian meteorite.
Chapter 4 looks at the possibility of life on icy moons such as Europa and other places.
Chapter 5 is devoted to the moon Titan.
Chapter 6 is about exoplanets, those planets orbiting other stars and mostly about how they are detected.
Chapter 7 looks at exoplanets as possible habitats for life, and some of their properties that may aid or otherwise life development.
Chapter 8 looks at the potential to detect life on exoplanets from Earth, and the technology required for that to take place.
Chapter 9 considers SETI and CETI, interaction with extraterrestrial civilisations and how we haven't had any, and why that might be.

Whilst I found the first few chapters interesting, and the exoplanet chapters happened to coincide with a IYA lecture locally that was excellent, I found the book rather seemed to fizzle out at the end., or maybe it was me that fizzled out.

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S170: Darwin and Evolution

2009-08-16T11:10:00.003+01:00

Its been a while since I did a short course, but I have 20 points of hole in my degree and this is one way to fill it.
So I signed up, and its arrived. What you get is

An S170 Study guide - a booklet that tells you where stuff is and how to get to it. Increasing the material is online now.
Help with short courses leaflet
The 99% Ape book - looks good - not too bad at 244 pages. Lots of colour pictures and diagrams, so looks good.
S170 DVD, Darwin and evolution. It includes episodes from the series Jimmy Dohery in Darwin's Garden on it.
Assessment handbook

As with most short courses, there is only one written assignment, but it's not yet available as the course hasn't officially opened. Anyway, onwards with it (once I've finished my other course that is - oh maybe just a peek then...)

S283: TMA-2

2009-06-26T13:30:00.003+01:00

TMA 2 comes around, and there is more work to do on book 1 in this one. It has just the 4 questions.

Question 1 is about atmospheres. You have to start by discussing techniques for analysing atmospheres. This is followed up by some calculations on partial pressures and what sort of conditions could make for frozen carbon dioxide on the Earth and Mars.

Question 2 is about Keplers laws. It starts by getting you to state them, and then apply them to an asteroid. Based on this and some other data you then have to work out what sort of asteroid it is, and whether it is a potential threat to the Earth.

Question 3 is an essay! Its 600 words comparing and contrasting the atmospheres, structures and properties of Jupiter and Neptune. Well 600 words is either a lot, or not much depending on how much you have to cover. In the end, with some diagrams and tables and a couple of photos this turns into not too bad an account, but its when do you declare it finished!

Question 4 you are asked to discuss various theories of solar system formation. Based on the latest exoplanetary observations, it seems fairly clear that the current models are inadequate, but anyway to get the marks you have to describe what the books tell you.

Not too bad a TMA, and a lot better mark than the last one.

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S205: The Exam

2009-06-20T19:12:00.005+01:00

So the exam day dawns. I generally try to work through as many past papers as I can before an exam. Usually going through them 2 or 3 times.
The first time through is very slow, as I usually can't do or get stuck on nearly every question, or have nagging doubts about the answer. Either way, it means rereading sections of the books.
By the second time through, I've usually got better and can answer some of the questions without help, and others I still have to look up and check.
By the third time through, I'm no longer doing all the questions and only focusing on the areas I want to do. By this time, I'm starting to remember the answers anyway, so there isn't a lot of point going through them again.

So this plan worked well, although I quickly realised I just wasn't going to do much on book 9 - there is just too much seemingly random stuff in there to learn. I found the kinetics and molecular modelling and NMR/IR all quite good - but they are often in the same section so end up mutually exclusive.

There are 4 sections to the exam:

A is short answer questions - you answer 8 out of 12
B, C, D are long answer questions, and you do 1 from each section out of 3.

A questions are from all over, some can be answered in a couple of words, or with a simple diagram, others require maths of explanations. So its good to pick out the really short short answer ones, and build up some time for use later.
B is usually organic reactions and synthesis. Usually a retrosynthesis with analysis and some of the forward steps required. The rest are more conventional diagrams, but lots of curly arrows required (I took in a green pen just to draw curly arrows with).
C is typically kinetics, molecular modelling and NMR/IR stuff
D is often VSEPR, symmetry, and maybe some spectroscopy, thermodynamics (mainly Born Harber cycles) - and something on book 9.

Once the exam was a couple of days away, I sat down and did a timed exam using the sample exam paper they provide. This is good for showing up weaknesses, but very good for working out how much time you will have for different sections.

Anyway, in this exam I found a reasonable 8 I could do - I know your suppose to read the paper and digest, but I rushed straight into question 1, its nearly always of the same form. Fill in an orbitals diagram from an element. A nice easy 5 marks, as long as you get it right! In my mock I filled in 16 electrons when it asked for 14.

Question 2 was also so easy - I happened to know the answer, that I just wrote it down. You had to identify a compound from 4 possible options, and it happened to be very similar to a past paper - so although it was a book 9 question - I just knew it (or hope that is the case!).

Then I had to pause, and flicked through the whole paper.
I sorted out the ones I could do in the A section, and picked a couple of likely looking long questions. I worked through the A questions, leaving the thermodynamic one to the last, as that although fairly easy (and you can often check you got the right answer in the data book) it takes a little time and is easy to miss out a 1/2 or similar bit.

As usual, there is one that you can answer most parts of and one bit you can't, should you do this question or pick another one?

In the end I did about 10/12 from A, just in case (as they take your best marks). Also 5 long answer questions. I hope it's enough.

Prev S205.

S205: TMA-6

2009-06-15T11:55:00.004+01:00

Last and final TMA, and one that gave me considerable heartache! Its mostly on book 10 which is full speed organics.

Question 1 is about the production of biodiesel. On the face of it, this looks a nice simple question. However the mechanism is basically a transesterification, related to saponification (soap making). Now both those words sound long and complex, but actually the reaction is really very straightforward. There are two parts to the question, the first is to predict the products of the reaction.
The second is to draw the mechanism.
Well firstly, I usually need to draw the mechanism to be sure I know what the products are, but thats OK I can do the second bit first. The real issue though is there are 6 marks for the first part, and 19 for drawing the mechanism. Even if I do it in painful detail, I can really make more than 2-3 maybe 4 steps out of the whole thing. For 19 marks, this sounds warning bells that I've misunderstood the question. I returned to the question time and again looking for the missing part, even donwloading a research paper on the topic - but no it appears it really is that simple!

Question 2 is some basic organic reactions to extend alkane chains. One part you need to pick appropriate reagents, the other part two different directions for the same reagent. Fairly striaghtforward, but after drawing the mechanisms of the two reactions, I've got a lot more diagram than Q1, and this is only worth 15 marks for the whole question.

Question 3 is on radical reactions - rather scary reactions that have been tamed in recent years. Gives me a chance to draw fishhook arrows, but its basically derived stuff from the appropriate chapters.

Question 4 is on retrosynthesis. You have to undo the reaction to find the products and a way of bringing it about. It leads you through the steps as part of the questions quite nicely, provided you get the right bits. There are some comments on steroechemistry, and on reagents you might need to bring about the final results. Just a case of working through it really.

So - that is all the coursework done! Just the exam to look forward to :-/
(However - I ended up getting the best mark for this TMA out of the whole course, so Q1 must have been "just that easy").

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S205: TMA-5

2009-05-28T09:50:00.002+01:00

Last but one TMA. Not one I'm looking forward too as much. Its got essay like things in, and its so easy to lose marks in these. Oh well, after all the biology essays I've done, and skating quickly over the archaeology ones, I ought to be used to this sort of thing, so hey ho.

Question 1
In this one, you have to prepare an overhead transparency for a 1 minute talk. Of course almost no one uses overheads these days, they use powerpoint or similar. Gone are the days (hopefully) of getting acetates shrink wrapped around the photocopier drums. You have to prepare the overhead, on the subject of "The use of VSEPR to predict the structure of tellurium tetrachloride". You then have to write a script that when read aloud will take 1 minute to read in a normal voice and taking breaths etc. Apparently in some previous versions of the course, you actually had to record the talk and post a tape with it on, but thankfully that isn't required now. Your tutor has to read it and decide if you are within the time limits. You can annotate the script a little with markers to show where you are pointing to on the slide.
Anyway, not too bad a question - the topic is fairly striaghtforward, and a few graphics help spice up the slide.

Question 2
This is about book 9 - p-block materials. You have to identify an element given a few facts about its appearance and its reactions with flourine. Then a bit about its oxidation states, and then its reactions with acid and alkalis.

Question 3
Some entropy sneaks back in, as you have to compose a formation reaction for BCL₃. Then draw a lewis structure for it.
Thats followed up by a full blown thermodynamic cycle for the construction of it so you can work out the molar enthalpy. Finally an equation for the formation of BCL₃ from boric oxide and phosphorous pentachloride.

Question 4
More identification of solids and solutions based on some reactions. Some reactions are described and you have to predict what will be formed, then these in turn react and so on. Of course if you get step 1 wrong, your a bit lost for the rest of the question.

Question 5
Its essay time. "The chemistry of bromine can be predicted from its position in the Periodic Table". A report of 600 words explaining this. You can include graphs, diagrams, pictures, tables etc, and I throw in quite a few of these as it helps give me something to do rather than just writing words, and it also breaks up the structure a bit. Even a picture of dear old Dmitri Mendeleev helps give it a bit of colour.
You have to do all the usual stuff, introduction, conclusion, references etc. Anyway, after a lot of tinkering with it, I get something I'm not altogether happy with, but can't see how to improve it in the time and space available.

So - just one more to go, then the exam looms on the horizon.

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S205: Book 10 - Mechanism and Synthesis

2009-05-19T14:55:00.001+01:00

Book 10 - the last real book. There is a Book 11, but its more of a pamphlet and discusses how to write essays and make presentations and stuff like that.

Anyway, Book 10 is all back to organics and synthesis.

First there is a whole section on carbonyl compounds and reactions - those things with a C=O in them somewhere. I guess you either like this sort of stuff, or not. I'm rather less than impressed with it all, although the rules seems straight forward there seem to be a lot of them.

Then the next section is all about organometallic reactions. Grignard reagents. Despite not really knowing how these are made, they seem awfully useful for glueing bits of molecules together.
It starts with magnesium compounds, then we move through into sodium, lithium and copper compounds. Then it finishes up with organoboron.

Section 3 looks at radical reactions - where you get compounds with single electrons lieing around. These use to be so rapid and violent to be unusable, but recent times they have found ways of taming them to make a useful way of doing things.

Section 4 is about retrosynthesis mostly. So knowing what you want to make, how can you work backwards to find a way to make it from everyday molecules. Basically there is no right way or wrong way, but some rules help you to break up compounds to make it easier. It seems a combination of science, experience and a touch of art.

The last section looks at biosynthesis, which rather puts chemist in the shade. Making complex molecules at room temperature and pressure without breaking a sweat.

Finally, there is a case study on polymers.

Phew - all done - finally got to the end of what has been a long course squeezed into what seems too short a time!

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S283: TMA-1

2009-05-12T09:41:00.002+01:00

Well compared to the chemistry I'm doing alongside this, I find this TMA reasonably easy. Possibly too easy as I get a less than expected mark for it. That will teach me!
Lets see - what does it have in store?

Question 1 is about the formation of the solar system. When it formed, why rocky planets are in the inner and gas giants in the outer. Stuff about ring systems and density, and the asteroid belt. Not too bad for a start.

Question 2 is geology. What the structure of the earth is, what the layers are, how they are defined and stuff like that. Some bits on mineralogy and seismic data, and rounded off with xenoliths and what they can tell us about the structure.

Question 3 looks at various moons, and gets you to fill in a table. How old is the surface of each, what if any caused the resurfacing, and what was it made up of. Then you are given data about two imaginary satellites, and asked to work out from density and other information what sort of body they are likely to be.

Question 4 is about volcanism and cryovolcanism. What basalt is so common, what makes it so and so on. More geology...

Question 5 is interesting, as you are given a picture of part of the moon, and have to work out various dimensions of the craters pictured, and then determine if they are simple or complex craters. I found acrobat reader has a great tool for this sort of measuring. Then you have to make various observations and hypotheses about the craters such as age and relative order.

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S205: TMA-4

2009-05-11T20:00:00.002+01:00

Another TMA - and they are coming thick and fast at this point. Two TMA's due in the same month! This TMA is a bit of a monster, but turns out to get my best mark so far, so maybe something is sinking in - although I suspect its just how it goes.

Question 1 is about analysis. You are given some weights of elements found in a compound and asked to work out the empirical formula for it. Its really not too difficult, as its sort of like the S103 stuff, but a bit more complex. A nice surprise after some of the nightmare questions!

Question 2 is all about identifying struture. Youy are given IR and NMR spectroscopy data, and based on this and the molecular formula, you have top work out what the structure is. I find the NMR pretty good to do. The IR is a little vague, but you can answer it pretty much just from the NMR data, and use the IR for confirmation.

Question 3 is NMR from the other direction. Given a particular structure, you need to predict what NMR peaks and troughs it should give you. Its not too bad - once you get the idea of carbon equivalence.

Question 4 is looking at oxoacids, and working out their strengths. Its fairly straightforward if you can relate it to Paulings rules and coefficients.

Question 5 is to write an essay plan for the essay that has to be written for TMA-5. An essay - in chemistry, I never thought I'd see the day! Oh well...

As I said, not a bad TMA - which I think is more down to the absence of complex organic reactions than anything else.

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S205: CMA-2

2009-03-25T13:03:00.005Z

So - there is another computer marked assignment to do. There are 35 question to be done, and they vary a lot in format. Some you have to work out a number and type it in. Others require ticking boxes, and so on. These have their strengths and weaknesses. Firstly its a computer marking your efforts, although the questions are reviewed by the course team. This does mean you can sometimes get what you think is the right answer only to be caught out on a technicality, like typing 2.0 when it is expecting 2. Mostly though its pretty good at taking reasonable answers - but of course can't apply the same common sense a human can.

You generally get 3 attempts at an answer, unless its a true/false type one. A couple of them I got completely wrong. One was on the symmetry of SeOCl₄ using VSEPR - which even after 3 attempts I still got wrong, and couldn't work out why. My tutor suggested some possibilities given I knew the answer (it tells you once you get it wrong). I also checked it out with a chemistry lecturer friend and she came to the same conclusion as I had. After taking it up with the course team they explained (after the deadline) why their answer was right, but eventually they zero'd out the question as it was rather ambiguous. Even given the answer I couldn't see how you could come up with a definitive structure based on just the course notes - there simply wasn't enough data to cover these weird edge cases. The trouble with issues like this is that I find it suddenly undermines my confidence. Its not a silly mistake, its something I've thought about and still got wrong. I suppose whatever doesn't fail makes me stronger, but in reality it tends to lead to a certain fear of similar questions.

The other question I got wrong I could eventually see I'd just made a silly mistake. Its a bit weird doing these things, you tend to get CMA blindness. For instance I'd take all the data given, do all the calculations and come up with an answer - I'd probably check it too - and then look at the screen and see if my answer was there. If it was, I'd tick it, if not then I clearly need to try again. However often you get one of these calculations where you end up doing a load of steps and then the final one is to multiply by 2 -- or is that divide by 2... after due consideration you decide its multiply by 2, see the answer is there, tick and go. Wrong answer. My immediate reaction is not to do any more work (because I'm lazy by nature) but to assume it was divide by 2, and the answer is there to, so tick that and resubmit immediately without rechecking things. Wrong again! This is where you're 3rd chance comes in, and where you should sit down and rework the problem again - rather than phoning a friend or asking the audience.

Anyway - that was the last of the two CMAs in this course.

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S205: Book 9 - Elements of the p-block

2009-03-10T12:41:00.006Z

Oh no -its another vast book - 242 pages about lots of stuff - its information overload, and I'm not really sure what you are suppose to take away from this book. There seems far too much to learn, so in the end I just end up reading the book and hoping some of the concepts sink in ... hummm.

It starts off of, by looking at oxidation states and how you can work them out from various rules. That's not too bad.
The next chapter starts to look at acids and bases, and in particular extends the definition to Brønsted acids - which are compounds that can donate a proton or hydrogen ion.
So having just got the idea of a new type of acid, we have another new type in the next chapter - the Lewis acid. This is a substance that can donate a pair of electrons. Okkkayyy - just about getting that.

Next chapter is all about the chemistry of hydrogen - what it can do and how it can form hydrides and things like that. I'm sure there is some general message here but it seems like just a large number of different reactions.
Next we look at halides, and all manner of ways that the halogens can form compounds. Again a confusing number of different reactions.
After that - a real walk on the wild side as we look at those most unreactive of elements, the noble gases and the various compounds they can form. Its a bit like being told there is no Santa Claus that compounds of the noble gases can form compounds. I mean - the one thing you generally learn in chemistry is that compounds struggle to form bonds to make noble gas like electron shells. Then along comes xenon, and starts disrupting these well rehearsed truths.

After a brief foray into some trends in second and third row elements (which is also covered - better for me - in a dvd accompanying the book), we launch into group 3. Boron, aluminium and so on. Boron is plain weird, it eschews the eightfold way and is happy to make compounds with only a shell of 6 electrons. Its all rather disconcerting.

Then its time to look at group 4. Carbon, silicon and their ilk. It seems we've been doing precious little other than looking at carbon for most of this course, but here it is again.
Follow this up with a look at group 5 nitrogen, and phosphorous, and all they can do. Then its on to oxgen, sulphur and its pals.
Finally another look at trends and the book is done, except for a case study look at acid rain.

So much information, so many reactions - my head is spinning. How can anyone possibly remember a 10th of this stuff.

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S205: TMA-3

2009-02-28T17:24:00.001Z

Time for TMA-3 - and a bit of a disaster for me, despite thinking I'd done it almost perfectly!

Question 1 was about molecular orbital theory, and drawing diagrams and putting electrons in for a molecule of PS. Most of this was fairly easy, except for the last part where you had to work out how it would decompose. Despite questioning my tutor, I couldn't grasp exactly what this was asking, and got almost no marks for this part. I'm still not much the wiser.

Question 2 concerned semiconductors and the doping thereof. Some more diagrams to be drawn and some theory to be expounded on.

Question 3 was about organic reactions, and mostly to do with carbocations and yet more stereo-chemistry. I don't think I have the patience to do some of these reactions, and it shows in the marks I get! Some of the latter part of the question was on synthesis techniques, and how to get from one compound to another.

Question 4 was full on synthesis. How to move around from one molecule to the next, what sort of thing you needed to add to it, and what conditions this might happen under and so on and so forth. I think I did ok on this one, but it was a struggle.

This TMA is probably the low point so far for me, as I didn't do nearly as well as I thought I would, and it sort of leaves you wondering if you understand the basics or maybe you're just not cut out for the subject. However this seems to happen in most of the 60 point courses I've done, so its probably just a psychological hump. I hope so!

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S283: Book 1 - An Introduction to the Solar System

2009-02-25T17:08:00.001Z

Book 1 is a fairly weighty tomb, but about the size of the S282 books, and similar to the 2nd book in the course as it happens. Its 412 pages in total, and split into 9 chapters.

Chapter 1 is an introduction to the solar system. We briefly visit all the major bodies of the solar system in turn and look at the general layout of things. It gets you oriented into whats where and what will be looked at in the next few pages.

Chapter 2 looks at terrestrial type planets and their internal structure. There is a fair smattering of geology in this part, and stuff about tectonics and inner cores and stuff like that. There is also some parts on what happened over its life as the rocks were 'cooked' and changed.

Chapter 3 looks in depth at volcanism. So there is a lot about volcanoes and eruptions of lavas and what that can do to surfaces. It also considers cryovolcanism, where water and ice errupt in the more frozen worlds giving similar results.

Chapter 4 looks at planetary surfaces and in particular at cratering and what it can tell us about what has happened. We go into quite a lot of depth (NPI) on different types of crater and how they can be recognised.

Chapter 5 looks at plaentary atmospheres - for those lucky enoguh to have them. It also looks at clouds, and atmospheric motion, and the different layers that they tend to split into.

Chapter 6 looks at the gas giants, and what they're structure might be.

Chapter 7 is concerned with the more minor bodies of the solar system. So things like asteroids, comets, the Kuiper belt and even interplanetary dust.

Chapter 8 looks at how the solar system was formed, and what that was all about.

Chapter 9 ends up looking at meteorites and what they can tell us about what happened at various stages in its evolution.

So - that was quite a tour, but in some ways it wasn't as detailed as the earlier planets course I did. Many of the mechanisms we gone into in a lot more depth, but I didn't come out of it feeling I knew a lot more about the planets, but knowing a fair bit more about their formation.

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S205: Book 8 - Separation, purity and Identification

2009-02-23T16:57:00.004Z

Book 8 - and quite a thin one for a change. However the euphoria of that swiftly departs towards the end. Anyway, the first part is all about practical chemistry, something we don't do any of in this course, other than read about it!
We have some chapters on separation of products, by using suitable dissolving agents and the like goes with like rule. Then there is a chapter on how to find out how pure the substance you made is, and then some stuff about identifying the compound you've made.

Then, just as you think the book is about finished, we move onto IR spectroscopy and NMR. There is nothing written about this in the book, other than directions to work through a whole set of videos and computer aided learning on the accompanying DVD.

So there are a number of exercises to work through to find out what NMR and IR are telling you about things. After working through IR and getting the idea you can find some stuff out, the NMR comes as much more of a revelation as it gives you much more information in general.

Finally the book ends up with a case study on forensic science and what chemists can do to aid the search for truth.

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S205: Book 7 - Alkenes and aromatics

2009-02-06T23:41:00.004Z

Book 7 - and its more organic chemistry. This time is starts by looking at addition reactions. That is part 1 of this book, and doesn't have anything fantastically earth shattering as we've been looking at similar sort of mechanisms for a while
Part 2 goes on to look at aromatics, benzene rings and stuff like that. In particular Freidel-Craft reactions which show you ways of sticking stuff onto these rings. Its all a bit complex as there are all sorts of ways of adding stuff in depending on where you want it to add up, but by the end you can sort of see how some of the ideas of synthesis come about.
Then it is part 3, which is solely about synthesis, and ways of getting from a starting compound to where you want to end up. Its one of those topics that I can follow along, but would be completely lost if asked how you go about synthesising something new.
Finally the book ends up with a case study looking at petrochemicals and what sort of separation and other techniques are useful there.

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S205: TMA-2

2009-01-27T08:30:00.003Z

The second bit of coursework looms - and its name is TMA-2.
Four questions to tackle, based on books 4 and 5.

Question 1 is all about thermodynamics. You have to calculate a number of entropy, enthalpy and other things about substances. You also have to draw a diagram of a Born-Haber lattice energy diagram and work out lattice energy for GeI₄ a substance.

Question 2 concerns kinetics. You have to come up with an general reaction rate equation and then it starts to drip in information that eventually allows you to solve it bit by bit.
You also need to use the computer program provided (kinetics toolkit) to plot a graph of the reaction rate.

Question 3 is about S_N1 and S_N2 reactions. You are presented with some reactions and told what they might produce, and from this you have to deduce if it is an S_N1 or 2 type reaction. You then have to draw the reaction diagrams with curly arrows showing where the electrons are moving around. Then it goes on to get you to consider the enantiomers produced and which might be dominant.

Question 4 is similar to question 3, but with different molecules, and we are looking at elimination reactions rather than substitutions.

I managed to get completely wrong on the last one and follow it to its logical conclusion but starting from a false premise.

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S205: Book 6 - Molecular modelling and bonding

2009-01-08T12:32:00.004Z

This book is a book in itself, in that for once it isn't split into sections and parts, but does basically what it says on the cover.
It looks at the theory of electron clouds and how bonds form between atoms. It goes into all the detail about orbitals and hybridisation. It looks at what happens to bonds between atoms of the same type, and between different types. It also has a quick look at what is happening in semi-conductors, which is a little bit of a detour, although there is a relationship I suppose.

The part I don't really follow is the whole bit about symmetry. I can see some of the symmetries, others are a little harder to spot. I'm not too sure why they are important though, and to what extent the rather complicated rules for classifying the different symmetries are useful.

Finally there is a case study that looks at drug design and how knowledge of the bonding sites can allow enzymes and drugs to be designed.

Chemistry seems increasingly to be a collection of complex categorisation rules and quite a bit of maths. The maths I can cope with, but there seems a lot to remember otherwise. Oh well, judging by the book count, the course is over half way through now!

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S205: Book 5 - Chemical kinetics and mechanism

2008-12-22T21:46:00.003Z

Book 5 is all about reactions and how they work. Yet again its a split book.

Part 1 is about rates and involves a lot of graph plotting and analysis. We get to use some graph plotting software which makes finding gradients to curves nice and easy, but you have to plot quite a few graphs of varying stuff.

Part 2 looks at substitution reactions, and we get to look at nucleophhilic reactions and how they work. This is quite interesting as it shows right at the molecular level some of what is going on when two things react, and how electrons move around the molecule. Some of them work in single steps, and some in more complex steps, and often you can work out whats going on by looking at rates and products.

Part 3 then looks at elimination reactions, which have some similarities with the substitution ones.

Finally there is a cased study on zeolites and what they can do for you and makes for interesting reading.

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S283: Planetary science and the search for life starting-

2008-12-22T21:40:00.007Z

In 2009 I have a few things going on, so decided not to complete the 3rd level courses I was planning. Instead I decide to go for the S283 course which will complete me a certificate in astronomy, which would be good.
S283 is called Planetary science and the search for life, and seems like a fun course, although its alleged to have a certain amount of geology in it, my least favourite of the hard sciences. Anyway, I signed up and the books arrived in short order! Very similar sized books to the S282 course.

What you get is:
Book 1 - An Introduction to the solar system
Book 2 - An Introduction to astrobiology
A course handbook
A study calendar
A guide to submitting electronic assignments
An applications CD.
A DVD specific to the course

The books are very similar in layout to the S282 - lots of pictures and quite readable, and I can't help starting on them despite the ongoing chemistry assignments!

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S205: TMA-1

2008-12-17T22:59:00.004Z

Time to tackle the first TMA in this course, of which there are a number.

There are 4 questions in this TMA, each at 25%, so nice and simple.

Question 1 has a-d sub parts and is about identifying a couple of mystery elements. You are given some details about them, such as the electron shell configuration and you have to identify them. Then draw lewis diagrams of their bonding with F and Cl, including some ionised variants.
Following that, you have to use VSEPR theory to say what sort of shape the molecule would appear as in 3 dimensions. Then finally, draw the structure of the 3-d molecule using flying wedges.

Question 2 is about crystals and has parts a-g. You are given a molecular picture of pyrite, and have to measure various properties of the unit cell. This I find rather hard to pin down the unit cell, but eventually I come up with something. You then have to measure angles and interatomic distances, comment on the coordination number of the atoms, count the number of each atom in a unit cell (more tricky than it sounds as most of the atoms are shared between multiple cells). Finally, given the atomic mass of the atoms, the distances and the atom counts you are in a position to work out the density of the substance.

Question 3 - organic nomenclature - oh my!!! Two parts, firstly name 4 molecules they have drawn for you. Tricky - particularly those with rings and chains, which do you start with??
Then part two - the opposite, they give you some names, and ask you to draw them. Some of these are chiral so flying wedges are important.

Question 4 - you are given a two chiral center molecule, and have to label each chiral carbon with the appropriate R/S tag. Then give it a systematic name with thje appropriate chiral bits.
Next you have to draw an entaniomer of this molecule, and then draw a diastereomers of it.
For the last two parts you are asked to consider the optical activity of the system in various mixtures of the various molecules given and drawn.

Well done, and posted now!

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S205: Book 4 - Metals and Chemical Change

2008-11-26T10:35:00.006Z

So book 4. This one is all about why reactions happen. Why do some things when you mix them together react, some require heating, and some just never bother.
It has the potential to be a very boring book, as it discussing a lot of stuff about entropy, enthalpy and Gibbs free energy.
There are a number of videos that accompany the book and help bring it to life a little. Some of the chemical equations and calculations I find a little confusing, especially around metal ions. The crown ether stuff is also a little esoteric I found, but in the end with a bit of practice its possible to make some sense of the calculations.
Its quite interesting to see that given all this detail you can make some predictions about what reactions are possible and which aren't.
However all thats said there is a lot of equation manipulation in this bit - all relatively simple but there are enough steps that its really easy to miss off a coefficient here, or a plus sign there.

The book wraps up with a case study on batteries which is quite interesting. Going into the details of dry cells, NiCd and so on giving the design decisions around each.

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S205: Book 3 - The Third Dimension

2008-11-14T11:40:00.006Z

Book 3 is a little weird, it is actually two books it seems to me.

Part 1 looks at crystals in some depth.
It goes through the various forms of crystal structures that can be made, and looks at ionic bonding that is prevalent in crystals.
I found this quite hard going, there is a lot of 3-d visualisation to get the ideas, but its not always easy as there is a lot going on in some of the structures. Trying to work out the common patterns is not easy, and I found the 3-d visualisation software though good, didn't really help as it lacks a good perspective. You get to make one or two models too, which sometimes helps, but the complex ones can't be made. There are a number of videos also showing you how they are constructed, so you can't fault them for trying - but really none of it made much sense to me until the tutorial.

Part 2 looks at stereochemistry, and chirality.
First it starts by looking at the effect double bonds can have on structure. Because double bonds stop the free rotation of molecules, you can have two different forms of the same molecule, and then you get into the whole "how do you name them" discussion. Having worked through this and got some rules on exactly how to name things which look different but have the same components, you get into chiral chemistry. This is where typically a carbon has 4 different things attached to its different bonds, and this allows two possible configurations of the molecule. These structures also have interesting optical properties as they rotate polarised light.
However it doesn't end there, as you can have molecules with more than one chiral center, and then things get really complicated with stereo isomer, diastereomers, entaniomers, and meso formations. If crystals gave you a headache, well you haven't felt anything yet!

Finally the book finishes up with a case study on liquid crystals.

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S205: Book 1 and 2

2008-11-10T09:29:00.004Z

I have to say the chemistry books are slightly confusing at first.
Book 1 and 2 for this course are actually two sections of a single physical book.
Book 1 - or sub-book1 - is entitled "A prologue to the course" and is more or less what it says. Its presumably designed to suck you into the chemical world as it describes the great successes and progress that has been made in chemistry over the last few hundred years.
It covers diverse applications from forensics to ball lightning and mostly its just an enjoyable read - nothing too heavy anyway.

Then the second half of the book is "An introduction to the molecular world" gets into more details of chemistry. It looks at periodicity, electron configuration, VSEPR, bonding and reactivity. Its not too heavy, but the course has definitely begun in this book. Some of the topics covered, such as the VSEPR theory and the different types of bonding are useful. The idea that a noble gas configuration is not always required is a little disturbing in some ways, but one of the deeper truths that you have to contemplate.

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S282: The exam

2008-10-17T08:39:00.002+01:00

Time to face the decider, the exam for this course where all hopes and aspirations live or die.

After getting to the exam centre in plenty of time, and finding my seat and unloading all my stuff on the desk, and then having forgotten my watch and had to go back to the bag dumping ground to fetch it, I started on the admin tasks of filling in all the ids and stuff on the answer book.

Then one of the invigilators came over to the two of us taking this exam and gave us a couple of corrections to the exam paper. Basically a couple of the multi choice answers were telling you to pencil in the wrong rows.

Then it was time to start. Eight multiple choice questions that all have to be answered. Some of them are ok, work out a value and tick the right box. Others are much more tricky given eight statements and pick out the two right ones or two wrong ones. These are tricky as sometimes it all hinges on one word. Some most of the sentence is correct, but a small word somewhere like always can make the whole thing untrue.

Then part 2 - four questions, answer 3 - mostly on the life and death of stars, and often something specific about the Sun.

Part 3 - four more questions, answer 3 - this time on galaxies and cosmology.

I got through the multi choice in about 20 minutes, the paper says to allow 50, but there were 3 of these that I wasn't very sure about and didn't have a good answer, so I left them hoping inspiration might strike.
Then I did 3 of part 2, and followed by 3 of part 3. Then back to part 1 again and this time narrowed it down to at least the right number of answers. Some of them I just couldn't get to gel, and had to guess between two possibilities. Then I still had 30 minutes time, and as they take the best marks from section 2/3 (allegedly anyway) I did the two question I hadn't done, as it filled in the time.
I got stuck on one of them, when I couldn't find the equation for rotational mass/velocity to derive the weight of a black hole. I tried first working it out in terms of an unknown which you needed for the next part, so it would end up as something like 3.4 * M (where M is the answer I couldn't work out for the previous part).
However at some point the equation more of less jumped into my head, and after working the numbers the result didn't look out of place, so I went with it and gave a figure for an answer.

So now - over to the markers - hope they can read my scrawl!

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S320: The exam

2008-10-13T07:45:00.004+01:00

Well, the day finally came. It was an afternoon exam, which I find the worst. You are pumped up with adrenalin but nothing to use it on for most of the day. I decided after a few attempts at abortive studying to just relax, and watched a film instead. That worked quite well.

After lunch it was off to the exam room. We waited in the hall until the invidulator called us to come upstairs and sit down. There was a wall chart showing a seating plan, and after a false start I found my desk, and unloaded pens, pencils, rubbers, rulers, sharpeners, and calculator. Also my passport for identification, and the exam allocation letter. Not all the seats in the hall were full, but I think all the S320 ones were.

Whilst waiting for the official start, we were allowed to fill in our identifiers and other details like calculator make. I requested a second answer book, as I wanted to put down an essay plan if possible. Then the fatal time came and we all turned over.

I turned straight to the final question, and read up the title. It was a comparison of MRSA and C.diff asking why C.diff was doing so much better. I started to unload all my facts into a quick plan in note form on the 2nd answer book and planned to add to these as the missing facts hopefully drifted in during working on the other questions.

That done, I turned back to the start of the paper and read through the 16 questions, of which we had to do 10. I circled a few likely looking candidates and got eventually to 9 I thought I could do ok, and scratched around for a 10th.

Then I set off answering 1 per page. They went ok and I was doing OK for time, I generally find either I can answer them, in which case I can write down the details in a minute or two, or else I can't so thats that. I finished the 10 in just over an hour, and you are advised 90 minutes, so I was a bit ahead of the game.

Then the part B data analysis question, and a bit of a suprise. It was based on data we had used in TMA-1. It was nice to feel at home a little with that, although there was still pause for thought. The question had also come up in a past exam paper, but I didn't quite think it would occurr again!

Then onwards to the essay, and I skipped the title and abstract and wrote the main body of the article, with conclusion and intro. I managed to draw a reasonable graph of some statistics about the diseases, and a less than average cycle diagram of infections which I don't think worked very well. I finished off the title and abstract (10 and 40 words respectively) which are quite tricky to think up something relevant in that tight a word limit.

I now had about 40 minutes left, and started to check back through my part A answers. I always struggle with this, getting rather bored doing it. I know its important but by now I've about had it with the whole thing! I added the odd sentence here and there. Suddenly decided my answer to one of the questions was probably not answering it at all.
On quiet reflection, I thought there were a couple of other questions I could answer at least part of - so wrote something for those. Even asking for another answer book.
Then it was just checking all the admin was filled in, the number of answer books reported, everything tied together and then the exam was over, and in the hands of the markers.

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S282: CMA

2008-10-01T09:34:00.003+01:00

This is the last bit of coursework for S282, and it doesn't actually matter. Its informational to give you practice in filling in a Computer Marked Assignment, which is what will have to be done in the exam.

There are 12 questions in all, each with several possible answers - typically A-H. Sometimes there is just one right answer, sometimes two or three. The questions vary across the whole spectrum of the course, and are pretty tough in places.
Some get you to do a calculation and see if there is an answer that matches. Sometimes these are a little tricky, like working out energy and some of the answers are in joules, and some in electron-volts. So you have to calculate both potentially.
Others try and catch you out - asking you which is a true statement out of the 8 given. However at first glance at least 4 of them look correct, and then its looking for detail words like all, or always. These are sometimes a giveaway like "All stars of the mass of the Sun have the same luminosity".
Anyway, it takes a while but it got there. So now - just the scary exam.

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S282: TMA-4

2008-09-22T15:21:00.003+01:00

Its the last of the TMAs for this course. This is probably one of the more scary ones, as I found the first book much easier to digest in terms of concepts and ideas than book 2. Anyway, onwards...

It starts, conventionally enough, with question 1.
This consists of an image of a galaxy, and a spectral diagram of the same, and then there are a variety of questions on it. Firstly, just from the image you are asked to work out if you think this is a regular or active galaxy. Also what galaxy classification would you give to it?
Then there is a collection of data which has to be plotted as a graph to give the spectral signature of the galaxy. Again you have to discuss whether this looks like data from a normal or active galaxy.
The next part asks you to pick between a radio-loud and radio-quiet active galaxy, so rather giving the game away!
Next you have to make some more connections about a small part of the spectrum which is given to you as a graph. Looking at broadening of spectral lines and so on to work out what each shows.
Then some calculations on the broadening values to try and determine velocities.
Finally all the information has to be put together to determine what classification this galaxy is.

Question two is all about cosmology, and FRW models. It starts by getting you to define some FRW assumptions, then to imagine a universe with some given properties, and sketch out how the scale factor would change with time.
Then some algebra and stuff to work out if the curvature of space in this universe is negative.
A couple more calculations of other quantities such as the deceleration parameter and so on.
Then the last part throws in another observation and gets you to refine the model in the light of this new data.

Question 3 is only 5% and just asks you how you plan to revise for the exam. Not really any wrong answers here, although according to the tutor some interesting ideas are forthcoming!

This was a ratehr tough one for me, as cosmology is probably the weaker subject for me, and there hasn't been a lot of time for it to bed down in my mind. Still - its done now. I have a CMA to practice on - which is marked but not assessed, and then its just the exam left.

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S320: TMA-3

2008-09-19T11:00:00.004+01:00

The last TMA of this course, and its a big one. Its big because it counts double, so you can easily win or lose on this one. Its also big because there is not really a question to answer, but a paper to write.

So what you have to do is write 1500 words on a given topic, and include plenty of references and notes about it too (1500 again). There are also some constraints that you have to take care of.

First - the word limits are hard limits - in that you should not exceed them, and there are penalties if you do.
Second - you need a punchy attention grabbing title of up to 10 words. 10 words!!
Third - an abstract of 40 words. Again quite mean.
Then the usual introduction, conclusion, content, and some diagrams/tables/graphs.

There are several topics available, and this year its one of

The spread of West Nile virus in North America
Outbreaks of E. coli infection in the United Kingdom
The emergence of multidrug-resistant pathogens

In this case, I picked the third one, and focused on MRSA and C. difficile as two pathogens that are resistant to drugs. It took a while to read up what was current and what the literature said and how medical professionals are dealing with the outbreaks.

Eventually it was all put together, and sent of, with not a little crossing of fingers. Now it's just revision - however there is one extra thing. The exam includes an essay to be written on a topic disclosed in the exam. However the general subject of the essay is given ahead of time for you to research. This year its something to do with C. difficile - so that was lucky!

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S320: Book 7 - Treatment and control

2008-09-03T13:01:00.004+01:00

So the final book and its a bit bigger than the last one. This one looks at various options for the control and treatment of infectious diseases. It starts off by looking at simple strategies for controlling disease. Then it moves onto chemical attacks - looking at things like selectivity of chemicals and the development of them. After that we are into vaccination and how to make successful vaccinations. The next chapter looks into public health issues and how disease can be controlled from that aspect.

Finally there is a case study on the rather gruesome guinea worm which is one of the targets to be eradicated.
Its a good wrapping up book - now there is just a double weighted TMA to do, and the exam to revise and research for.

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S282: Book2 - Chapter 8

2008-09-03T08:09:00.005+01:00

The last chapter of the book, and it is here where we are treated to some ultimate answers, although as it turns out they are not ultimate answers. However after several chapters of "this constant might be this" and "space might be flat or might not" its nice to have something a little more solid feeling.
Anyway it discusses such topics as

What is of dark matter
What is dark energy
The horizon and flatness problems
Where did structure come from
Why is there matter and not antimatter
What happened at the big bang
The anthropic Universe

So actually there is no real answers - just best guesses and ideas, but its nice to know these abstract things we've been looking at may become more concrete. Anyway - that's the end of the text books.

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S205: Starting - Oh no!!

2008-08-12T19:51:00.005+01:00

So with the end in sight for my current courses, and the exams to prepare for, thoughts turn to next years study. For the first time, the S205 chemistry starts in September and runs to June, rather than the more normal Jan to Sept. So I've been thinking about this for a while, my chemistry is weak, and it would be nice to get more familiar with this stuff so I can understand molecular biology better, so after some vacillation, I decide to sign up. I expect the books will arrive some time in Sept, and hopefully the first TMA will be after my exams.

So I sign up on a Thursday, and come the following Monday morning there is a large box on my front door step! Already? - You haven't given me time to hide!!

Unpacking the box is a mixture of excitement and fear. There seems an awful lot in this first package, have I really done the right thing? Lets see - what do you get?

A DVD called Molecular Science - Physical Methods
A DVD called Molecular Science - Periodic Table
A DVD called The molecular World - Pack 1
A set of bookmarks for the first 3 books
Book 1-2 (both in the same volume), A prologue to the course, and Introducing the Molecular World
Book 3 - The Molecular World - The Third Dimension
Book 4 - Metals and Chemical Groups
A calendar for the course
A course guide
A course index
A course glossary
A data book full of weights, measures and so on
A leaflet about transferable skills
A molecular model kit (looks like fun!)
A document describing how to make molecular models
A document describing how organic chemicals are named
A royal society of chemistry guide to Getting the message across
A ring binder (with no pocket for insert!)
A ring binder insert?
A set of 4 TMA submission forms
A guide to the videos
An online applications CD-ROM

Wow! That does look a little on the scary side! The good news is the first TMA is in November, so I will have time to do my exams first before tackling that, so that's good. Well it will have to stay mostly on ice for now, as I have to finish these current courses (well OK I might have a little peek and really scare myself).

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S282: Book 2, Chapter 5, 6 and 7

2008-08-04T18:27:00.003+01:00

In these chapters we get deep into cosmology, and I find it quite heavy going at times. There are the various models of the universe, based on FRW parameters. From these and some other stuff various things are calculated theoretically. This includes the echoes of the big bang, whether space is curved, how fast the universe is expanding and if it is decelerating or not.

Some of this stuff is ok, some is a bit mind blowing. Lots of calculations that you are lead through to predict things like the proportion of hydrogen to helium predicted by the big bang theories.

Then in chapter 7 it considers attempts to measure the Hubble constant, the Hubble Time, the deceleration parameter, the cosmological constant, and the various density parameters.

My head hurts!

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SXR376: Summer school Day 7

2008-07-18T19:39:00.004+01:00

The last day dawns - and there are now labs. There is only the presentation to do, and it has been worked on hard, and is foremost in our minds!
We finish up the writing and last minute adjustments in the lab, and it is a work of art I have to say. Dave has put a lot of work into the formatting, but we're all a little nervous.

The fats people go first, and there is a usual mix. Some people are good, so people not so good - and some just go on too long! Then the plants people did there bit, and overan a little so there were no questions as we needed lunch. Mark remarks over lunch that he was wondering if his presentation was too short, but then decided there is no such thing as a too short presentation at this sort of event - and that is very true!

After lunch it was our turn. Again we had some good and bad bits, but the presentation did look good. By the time it got to my bit we were running behind schedule, so I spead through my slides mentioning only a few salient points.

We wrapped up, and the week was done. We got our attendance slips, collected our luggage, said our goodbyes and left. Suddenly we were back in the real world - how weird!

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SXR376: Summer school day 6

2008-07-17T23:54:00.009+01:00

Its the last but one day, and the last day that we can complete our experiments.
We start by getting the tray out of the fridge and washing off antibodies, before adding more. Its quite a time consuming job to go through the procedure to get everything stuck to everything else - although of course we can't see any of this happening and are just hoping its going to come out well when we look at it under the microscope!

Anyway, when it is finally washed and incubated in all the different solutions, we have to extract the cell coated cover slips from the wells we've been using. This is no mean feat, with them being almost invisible and fearsomely difficult to get out of these wells.

Then they are mounted on the slide and we take them over to the microscope to see what we've got. Has the two days spent washing and dousing these cells with various chemicals been worth while or not. At least there is a clear brown hue on the ones we want - the positive controls and the ones dosed with the ligand. They look rather similar though by eye!
Time to have a look.

Positive control, negative control, and experimental data.
Its difficult to say if the experiment worked, and it takes a while with the tutors to understand what we are actually seeing. Anyway, we have some data for the presentation at least.

The rest of the afternoon we spend on the presentation and doing some practising in the lecture theatre. The time for tea, and no tutorials tonight. there is a disco, but I decide with a few others to give it a miss, and we have a good time in the bar going over the weeks events! Now its just the final presentation to finish and then present and we're done!

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SXR376: Summer school day 5

2008-07-16T18:40:00.005+01:00

Well - as today dawns we start a new set of stuff. We've now finished all the core activities, and we need to go on and look at the further experiment set. In this there are a number of topics which you can pick, although they want all areas to be cover by someone. We elect to do an experiment involving immuno-cytochemistry. This is basically about attaching antibodies to the surface of cells using some amplification to get them to show up.

There are quite a few steps, but each of them after the first few take an hour or more to wait for the incubations. So by lunch time we discover that we didn't have enough time in the rest of the day to finish the procedure, so the tray was put in the fridge and left while we did some graphs and stuff. We also took a few other readings and prepared some slides for the upcoming talk.

There was a tutorial after tea on presenting a talk, and then on dividing up the talk. After that we went to a tutorial on the ECA itself, so we'd know what to write up.

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SXR376: Summer school day 4

2008-07-15T17:33:00.008+01:00

Day 4 dawns, and it looks initially like a bit of a rest day. We are to run PCR machines and then look at DNA tracks in gels. These are apparently much easier than the SDS-PAGE gels to get right, and the initial stuff goes well. There is some really tricky diluting, we have to pipette one micro-litre of DNA - which is almost impossible to see if you have anything at all in the pipette!

While the mixture we make up is in the PCR machine, we poured out the agarose gels to let them set. These are quite easy to do, the liquid is at 60C and you pour it smoothly, move any bubbles that appear to the side out of the way, and then leave it to set. As it has a flourescing agent in it - it has to set in the dark so it doesn't bleach.

After lunch, we came back and loaded up the gels with DNA to see what we'd got. After running them for a while, we took a look at them in the UV viewer, and we had only very faint bands. In fact they were practically useless. So we decided to rerun the procedure and see what we could do. We ran out of time, but luckily the demonstrater was able to finish it off and the results were good this time - very clear.

After tea - another tutorial. We swapped partners and had to prepare a quick talk on a given topic to do with the procedures we had used. We did a quick poster on paper and then had to present it to the group. This was clearly practice for the main symposium on Friday. After that there was a quick chat about the ECA we will have to do, and then a review of the data we had collected, followed by the further experiments.

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SXR376: Summer school day 3

2008-07-14T17:28:00.008+01:00

Its day three already, and we continue on with the gel stuff. SDS-PAGE is harder than it seems to do the first time - but luckily enough has been salvaged from the first day to make progress.

The gels were run and blotted overnight by the tutors after our small disaster and we actually got some reasonable results. We managed to get all the stuff off the gel, and then stained it for what was left and despite it tearing a little, we actually got something recogniseable.

Then we set to work on the blotted paper to see if we could use antibodies to pick up CCR5 and CD4 on them, and after a while we got that too! It takes a lot of washes and other stuff to get there but we could see bands in it.

What's more they almost make sense.

At the same time as all this was going on, we made up an ELISA dish with a number of standard protein concentrations and also put in our three cell lines at different dilutions and then after adding all the reagents, popped it into a machine which produced a set of results, in seconds!

After this, there was much plotting of graphs and interpolation to try and find out what we had got. Then it stopped for tea.
After tea we had two more tutorials, one on HIV infection methods and its life cycle, and the 2nd on how to read a science paper - which went rather quickly as we were all too tired to do much with the material we were suppose to be interacting with.
And so to the bar...

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SXR376: Summer school day 2

2008-07-13T17:28:00.011+01:00

Day two - and the first real lab day. We are going to be doing some western blotting and protein analysis from some sample T cells. We're going to be looking for CD4 receptors as a control, and CCR5 receptors to see if different cell lines have different amounts of that receptor.

We started by getting our samples out of deep frozen state into a form we could work with. This involved some washing and centrifuging, and then some extraction buffers to break down the cells to get at the proteins.

After that we had to make up a polyacrylamide gel to do the runs on. In this we had a bit of a disaster, as we made our first gel up OK, but the stacking gel on top vanished when we pulled the comb out. So we had to start again which put us a couple of hours behind everyone else. We managed to get the second gel to work, and start to run, but then we had to leave the lab, and hope that the tutors could do the transfer and other stuff that we didn't have time to do.

After tea, it was time for a tutorial. The first was on HIV and the genetic susceptibility of various groups and associated issues, given by our tutor Chris. The second was by the course directory on presentation techniques for the final presentation.

Retire to the bar to discuss the day and drown our sorrows!

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SXR376: Summer school day 1

2008-07-12T18:48:00.006+01:00

Day 1 at the summer school on "The molecular basis for human disease".

After turning up with the family (its only 10 mins from our house) and registering for the course, we walked around the campus a bit to find the lab and other things. We found the biology building and even wandered around it a bit looking at the set of various animal skeletons they had. Also found the lab I'll be calling home for the next few days.

At 4:10 we all went into the lecture theatre to learn about general things about the week. Then we split up into the three different courses (SXR374 and SXR375 are in the same building) and met up with our tutors and assistants. We went off to our lab and had briefings and lab manuals handed out and picked up lab coats and stuff like that. Then we did a bit of practice pipetting with the automatic pipettes wearing gloves and safety goggles. You can set these up to deliver various sizes and we tried dispensing droplets of water of the appropriate amounts.

Then, back to the hall for a spot of tea, and some time to ourselves until a lecture on GM crops.
This was very interesting and very well presented and we all enjoyed it with a number of question and answers going on. Then to the bar, where I got to meet a number of the people involved in the residential school informally as well as meeting up with some old, and new friends.

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S282: TMA-3

2008-07-10T10:36:00.004+01:00

It can't be put off any longer - another TMA to submit.

Question 1 (25%) looks at stellar evolution and reactions - and its in three parts.
Part a) gives you 6 nuclear reactions and then asks a number of true/false type questions. However the joke in the pack is that if you think it is false, you have to give a reason why it is false. So this means getting your reasons in order.
Part b) is similar, in that you are given 8 statements, and told to pick out two that are false, and then explain why they are false. All the questions concern binary star systems in one way or another.
Part c) is another list of 8 statements about stellar evolution, and again pick out the true ones, and explain why the false ones are incorrect.

Question 2 (20%) is split into a-c with subparts for each.
Part a) looks at the stability of stars and you need to draw a diagram showing the forces in balance in a star, then to consider what forces are important in various sized stars.
Part b), with 4 subparts, looks at the collapse of a stellar remnant to a white dwarf and a neutron star and what conditions each are formed in.
Part c) takes the part b) further and introduces black holes into the mix and you have to do some calculations on back hole radii.

Question 3 (18%) looks at supernovae, and its just 4 subparts. Its based around a given table and you need to consider what type or supernova each represents, what they can be used for, and what would happen to the remnant left over.

Question 4 (22%) is a little different in that you are given a spreadsheet of cepheid data from M81 and you have to calculate various equations and end up with a value for its distance. There are a few formulas to rearrange and some averaging to be done, and then some general questions about the results.

Question 5 (20%) is again different in that you have to read one of three recent articles published on the website and then write a short account of its significance

Its not too bad as there is a bit of variety in amongst it, although I found the first question dragged on a bit as I trawled through various pages looking for clear refutation of this point or that.

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