SD329: TMA-4

The final TMA.

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

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

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

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SD329 - TMA3

Course work 3. Three questions.

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

I used a tin of beans attached to the curtain rail, and a handy dog as backdrop. We were supplied with

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

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

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

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SD329: TMA-2

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

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

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

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

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

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

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SD329: TMA-1

Time for the first piece of coursework.

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

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

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

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

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S366: TMA-5

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

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: TMA-4

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

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

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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S377: TMA-2

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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S366: TMA-2

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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S377: TMA-1

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

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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S283: TMA-4

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

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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S283: TMA-2

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: TMA-6

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

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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S283: TMA-1

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

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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