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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?


Next S366 Prev S366

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.

Next S366 Prev S366

Saturday, 2 January 2010

S377: Book 1 - From Molecules to Cells

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.


Thursday, 17 December 2009

S366: Evolution - arrival

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.


Monday, 30 November 2009

S377: Molecular and Cell Biology - Arrival

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.