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Thursday, 23 December 2010

Results - and a degree

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.

Tuesday, 19 October 2010

S377: The exam

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.

Tuesday, 12 October 2010

S366: The exam

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!

Wednesday, 15 September 2010

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.

Sunday, 12 September 2010

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.

Wednesday, 1 September 2010

S366: The book - part 2

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.

Wednesday, 25 August 2010

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.

Tuesday, 17 August 2010

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.

Sunday, 25 July 2010

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 FST 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%.

Friday, 23 July 2010

SXR270 Tutor - Day 7

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.

SXR270 Tutor - Day 6

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.
video

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

Thursday, 22 July 2010

SXR270 Tutor - Day 5

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.

Tuesday, 20 July 2010

SXR270 Tutor - Day 4

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.

S377: Book 4 (The Interactive Cell)

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.

SXR270 Tutor - Day 3

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.

Monday, 19 July 2010

SXR270 Tutor - Day 2

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.

Saturday, 17 July 2010

SXR270 Tutor - Day 1

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.

Next SXR270tutor

Friday, 16 July 2010

SXR375 - Day 7

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!

SXR375 - Day 6

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.

Wednesday, 14 July 2010

SXR375 - Day 5

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.

Tuesday, 13 July 2010

SXR375 - Day 4

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.

Monday, 12 July 2010

SXR375 - Day 3

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.

Sunday, 11 July 2010

SXR375 - Day 2

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!

Saturday, 10 July 2010

SXR375 - Day 1

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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Wednesday, 7 July 2010

SXR375: Plants and Pigments - CMA

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

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.

Tuesday, 6 July 2010

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

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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Saturday, 12 June 2010

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.

Thursday, 27 May 2010

S366: The book

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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Tuesday, 25 May 2010

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

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.

Sunday, 9 May 2010

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.

Saturday, 17 April 2010

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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Thursday, 15 April 2010

SXR375: Plants and Pigments

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.

Sunday, 7 February 2010

S366: The brachiopods measure up

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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Friday, 8 January 2010

S366: Evolution - first steps.

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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