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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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.