ack abstracts some highlights from the chapter on electricity generation

So.. chapter 11 is exciting to me, not just because it begins to address my persistent questions about HOW molecular motors do what they do. I understand its focus to be free energy transduction: biology creating electricity “out of nothing”!

At first when I read the Benjamin Franklin quote at the start, I scoffed and thought that so many other things in science are better than plain old electricity at making “ a vain man [sic] humble”!! But then I decided that Nelson hadn’t put that quote there to remind us that electricity in and of itself is a marvel- rather, that the marvel is the super efficient generation of electricity by (/in/through?) biological systems. And this, I think, really is a great example of “natural” biophysical reality doing a much greater job than humans at something humans value.

I also like the way this chapter talked about structure, function AND property, but connected those three things in a different way to the standard “structure THEN property THEN function” narrative we tend to use when talking about investigating proteins. For example, Nelson talks about the function of “some busbar” connecting respiration pathways and ATP synthesis machinery before he identifies the busbar structure as a mitochondrial inner membrane. (Have I managed to make sense? If not, someone pull me up about this is class please.)

Last but not least!: I’d like to mention oxygen as another reason I liked ch 11. It’s possibly something human movement students learn early on, but I’d never thought much about anaerobic vs. aerobic energy production. I think it’s fair to say I now have a greater appreciation for the significance of O2 on earth (hooray for being able to couple the energetically “uphill” phosphorylation of ADP to the energetically favourable oxidation of the product of glucose glycolosis! [which I've learnt is called pyruvate]). Is there an analagous "environmental factor" that helps boost energy production in anaerobic organisms?

Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon

Because not all of us are members of physics-all :
"Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon"

Remainder of semester schedule

Hi all,

I was supposed to post this schedule for us all to see. As Kristen has already posted a reminder that this week was chapter 11, i will continue from week 10 after the hols:

week10: Chapter 12 / presentations (?)

week11: Neural Networks / 2 x presentations

week12: Photophysics / 2 x presentations

week13: Structure, property, function relationships / presentations (?)

...something like that. We have a bit of probably necessary flexibility in presentation times at the moment.

I have been a bit crook this last week, think i pushed the molecular motors too hard? haha

Also, my Biochem prac during "teaching free week" and I think I get my break at 1pm, so I might miss you all unfortunately tomorrow.

Cheers, Alex.

Michael Mulls over Machines in Membranes Meticulously

I’m not sure if any of you are the same but I have found it difficult to know what to say when blogging. If it is before I have done the reading I obviously don’t know the topic yet and if it is after the reading my head usually hurts =P. I find it difficult to just post questions on the blog as I think better when bouncing ideas off people and often better understand the answers I get if I can hear them in person and clarify what people are saying. It is also easier to realize you don’t quite understand something when talking a topic through with someone.

This said in an attempt to make blogging something I can do more successfully I am going to do a running blog as I go thought this week’s reading writing my thoughts as I go. This means either this post could get very long or the more likely option this post will be heavy with content from the beginning of the chapter and slowly decrease as my stamina dwindles.

Machines in Membranes

Initial thoughts from intro: Oh good I have done quite a bit on this subject before but I wonder what slant this chapter will take on the topic.

The brief historical recap is quite interesting and left me wondering if I would have going into science if I have been born back in those days.

11.1.2 is good to know but at the same time I have done a lot of it before and no offence to the authors but how can they manage to make something which is interesting and rather simple in principal soooo boring. – on an side note I was most disappointed when I eventually realized many of my subjects were talking about the “squid giant axon” and not the GIANT SQUID AXON which my mind had hoped for.

11.1.3 Surprisingly the term Donnan equilibrium doesn’t pop to mind when I think about this topic and I don’t really remember it being mentioned in other subjects. From what I understand it is due to charged macromolecules trapped within cells and is a description of an equilibrium state which could be representative of non neuronal cells…? We can talk about this in the tute.

N.B. Considering the number of times chapter 11 references chapter 7 maybe it was a bad choice to skip it hehehe =P.

11.2.1 Wow just found the section talking about osmotic pressure providing plants with their rigidity really cool! I would also not have remembered to say this if I had written this blog later on. I really haven’t done much plant biology mostly animal maybe I should. Then I can create some SUPERHUMAN PLANT HYBRID harnessing the POWER of OSMOSIS . . . oops side track.

I like the phrases “equilibrium is not life; its death”, and the one I want to see in a movie “Entropic forces can kill.”

Like I predicted, despite this method creating a better blog entry it has taken me a couple hours to get only half way through the chapter. Realizing this I just read ahead without blogging every thought. The rest of the chapter is also quite cool, the way in which the body really does function as a factory on so many different levels. This is a concept I am quite familiar with from my biochemistry courses so not many things caught my attention.

With that I think I might end this post as it is taking up an A4 page in word and I imagine it will be significantly larger than that on the actually blog.

See you all on Tue. Michael.

Reading this week

Hi all,

Just a reminder - at the tutorial on Tuesday, we decided that we'd all read Chapter 11 in Nelson for next week.

next assignment

Due tuesday 23 september

chapter 9 people

Problem 9.1 and 9.2 in Nelson
and any two of 9.5, 9.6, 9.7, 9.8, 9.9, C9.12, C9.13 9 (see pages 594 ff.)

chapter 10 people

10.1, 10.4
and any two of 10.5, 10.6, 10.7, 10.8, C10.10 to C10.14

Modelling complex systems

I'm yet to finish my Chapter 9 reading, but I thought I would post an idea from Chapter 9 which is probably more widely applicable.

At the beginning of Chapter 9 of Nelson, it is argued that when studying a system which has a large number of constituents which are allowed to interact - such as a biological system - the analysis of the system can be greatly simplified, using just a few degrees of freedom to effectively describe a system's behaviour.

So when you have a large interacting system - our analysis can be made more simple if we first stop to think about what are the parameters that we can use that will more widely describe the bulk behaviour of the system. I think that at times this might seem like an oversimplification, but I think when analysing a large complicated system, we need to think about what questions we're really trying to answer, and what parameters are the most important that will allow us to answer that question. If you tried to take everything into account, then at times it's going to take far too long and will be far too complex to model, when some of the minor details may not matter when trying to answer a particular question about your system.