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.

This week's Reading

Just a reminder about the reading for this week:

We decided at the Tuesday tutorial that we wanted to be able to have time to cover topics outside of Nelson, and we knew that Alex wanted to cover some of the Enzyme material on a week when he'd definitely be able to make it. To that end, this week we're reading Chapters 9 and 10 of Nelson. Since two chapters is a lot of reading, Ack and myself will be reading Chapter 9 and Tomas, Michael and Alex will read Chapter 10, and we'll get together and teach each other any material we've missed out on at the Tuesday session.

Ross and Seth - I'm guessing you guys could just pick whichever one you found more interesting.

Kristen

Physics Colloqium this week

Just in case anyone here was interested, the Physics Colloqium for this week is titled "Nonlinear dynamic phase contrast microscopy for microfluidic and molecular biology applications". The abstract for the talk can be found here. It will be held Friday (11th September), 4pm in 7-222.

Biofilms and quorum sensing disruption

Further to Tuesday's brief discussion of biofilms and their effect on urban water supply networks, I came across the publication Biophysical controls on community succession in stream biofilms (citation). For those wanting more info on biofilms, this article (citation) is dated but a good read. (L. Sly is still at UQ, and I'm sure would answer any questions on biofilms, water quality and the SEQ supply network.)

New biophysics research prize

The McAuly-Hope prize is a new award for original biophysics research. So if you come up with something novel and fantastic during the course of PHYS3170 - and happen to have been an ABS member for two years - this could be for you...

(If you aren't interested in the prize itself, the autobiography quote on the web page is worth a few seconds.)

Supplementary Reading for Stat. Mech. in Biochem.

Hi All,

If anyone decides that they just can't go on living without more Statistical Mechanics reading, another good place to look with a Biochemistry/Mol. Bio. focus is the book by K. Dill and S. Bromberg "Statistical Thermodynamics in Chemistry and Biology".

-Seth

Thoughts on Chapter 6

I have to sympathise with Kristen as I too found the initial portion of this chapter rather dry. At the time I found it frustrating as I felt I understood most of the concepts yet continually had to think my way through equation after equation. That said it was actually the equations which helped me to better understand many of the concepts by the time I finished the chapter.

Despite my initial disapproval I did find the chapter useful although perhaps not the most interesting thing I have ever read. That said I hope someone can pull out some interesting application for this weeks discussion as I'm currently a bit light on for ideas.

Comments on Chapter 6 so far...

I have found the beginning of Chapter 6 to be very dry. To me it seems like it presents a lot of formulae all at once, and had I not seen some of that material before, I don't think I'd be able to take it in all at once. To that end, to anyone who is more interested in learning more about statistical thermodynamics I would recommend having a flick through the relevant chapters from Physical Chemistry by Atkins (any edition) or An Introduction to Thermal Physics by Schroeder. Having said that, we've probably already got a lot to digest!

It strikes me as odd in that in the entire Chapter 6 of Nelson, there is no mention of the equipartition theorem (where you have 1/2 kT of internal energy per degree of freedom in your system), but it is implied when Nelson presents a lot of results about ideal gases. I would have thought that it would be important to explain how you get, for example, the internal energy of an ideal gas, rather than just presenting the results and using them to derive other results. Perhaps it's more of a physicist thing to be concerned about the equipartition theorem - do 'biophysicists' not care about it as much?

Posts on chapter 6 to read

I just put a couple of posts on condensed concepts.
sorry, I wont be at the tuesday meeting.
Hopefully, I will see lots of other posts before then.

Recap Discussion Sept 2

To recap my impressions - one day later - from this week's discussion, we established some important points.

1. The Reynolds number gives the relative importance of inertial vs. viscous forces for an object moving through a fluid.
2. The small Reynolds numbers experienced by bacteria (and even more so, biomolecules) means that their mechanics are very different from objects on our scale (a car, for example).

One of the consequences of observation 2 is that is is incorrect to think of the energy from a chemical event (ATP bond breaking, for example) at a given site in a protein is the "same" energy that is used to accomplish something at a distant part of the protein. This would be an inertial transfer, which cannot happen in water on the scale of molecules. Rather, molecular motors work through a "Brownian Ratchet" action, where the energy is used LOCALLY to make a change that alters the energy surface on which the system is diffusing. The energy that is harvested at a distant location is not the "same" energy as was originally liberated, it is harvested instead from the thermal motions, which now occur on a BIASED surface.

En route to explaining this, we reviewed Feynman's "thought-ratchet" and his result that you cannot harvest fluctuations with a ratchet if the entire ratchet - both the handle and the ratchet itself - are in the same bath. You can harvest energy, however, if the handle and the ratchet are in different baths. This helps explain why membranes are so important to biology - they separate baths with different states, and allow energy harvest.

-Seth

Key concepts in thermodynamics

As much as I love Nelson's book I prefer to approach teaching thermodynamics and particularly entropy without introducing microscopic notions such as ensembles, probability etc.
The first ten of these slides I use in PHYS2020 to give a succinct view of the key concepts in thermodynamics. Here entropy is a macroscopic concept associated with irreversibility.