Archive | June, 2013

My Problem with Latex

29 Jun

If you do any sort of scientific publishing, Latex is indispensable. Its advocates say who nice it looks (only if you agree that it knows best). How easy it is to use (once you learn how to use it). I’m sure they say other things, but I really can’t think of them. Oh, how nice all the cross referencing is and BibTex (well I’ll give them that mostly). Really Latex is nice if you let it assume that it knows better than you.

But what if you want to do something slightly offbeat. Like say have subfigures in a paper that has a particular style guide that conflicts with the packages you use to do so. Or keep up with the most valid packages: is there anywhere that states what are the msot recent version of each “package” that you should use? Since they are all user generated a package is often succeeded by a different package and you are left not knowing which one is the right one. Ccaption or just plain caption? Or even caption2? As far as I’m ware it is caption, but the paper I’m working on at the moment style uses ccaption which clashes with caption, meaning I can’t relabel minipages as a table (and I’m using minipages as I can’t use subfigure either).

What latex really needs is a governing body. Somebody that says “This is what you will use” and “Oh you want to add this functionality? Add it to this package, don’t produce a whole new one”. The closest thing at the moment is Ctan, which as far as I’m aware is more a repository of Latex packages.

I really can’t see this happening though: it would involve academic from many disciplines actually agreeing on something. The only chance of it happening is if a whole lot of journals, like Elsiver, got together and insisted on standards. But once agian, cooperation. 


The New Prime Minister

27 Jun

This title is reminding me of the first chapter of Harry Potter and the Half Blood Prince, “The Other Minister”, they are even somewhat related.

The Australian Labor party finally decided what they are doing yesterday and voted Kevin Rudd as their new leader, dumping Julia Gillard. Their policies are not significantly different, however, all in all I prefer Gillard to Rudd. This is not purely because of Rudd’s reputation of making unreasonable demands of his staffers and I’ve heard (via a friend of a friend) that when giving an award to a female PhD student he commented “So you are one of those women not having babies”. Gillard just seems to have done more stuff: the NDIS is in, the mining tax and the carbon trading scheme. Rudd did have the education revolution, but Gillard was the education minister for it. The only other thing I can think of Rudd doing was the apology to the stolen generation. Having said that, not that Rudd has come in support for gay marriage, something might be done there. Gillard seems well liked by her party and her minions, even if they did vote her out. I think the only real reason they voted her out was because of the public perception of her.

My initial reaction to this news was annoyance, “Why are they fucking around with this, when no one really cares if the leader is Rudd of Gillard?”. Turns out I was wrong. People much prefer Rudd to Gillard, but it might be the new and shiny speaking. Either way, still not likely that Labor will win the next election, BUT with a new leader they have a chance to change some policies around. I would love to see Rudd just run with a completely populist and anti-everything-Abbot-says campaign. Make gay marriage an election issue. Promise another stimulus package. Promise that he will never appear in public in speedos. I just want to see Abbot try to come up with some policies of his own.

On the plus side to everything,   Stephen Conroy has resigned (the whole cabinet has) and now Penny Wong is leader in the senate.

Mathematical Modelling: Part 2

26 Jun


Continued on from Mathematical Modelling: Part 1

How do you Model?

Modelling is really  more of art than a science. There is no perfect model. There is no right way to create a model. Anything interesting really depends on having some sort of insight and/or creative thought. But there are ways to guide your thought process.

Whenever I’m trying to create a new model I think:

  • What am I trying to do? Many problem specifications are so vague that you really need to think about what your actual problem is. Before you start doing anything, work out (at least roughly) what you want to be able to do: does it need be able to predict things quickly? Then you want to avoid a problem that takes 3 months to predict tomorrow’s weather.
  • What data do you have? Data could be empirical data or general information like “Weight is relative to height”. Anything that you know straight up to be true (at least in the context of the model)
  • What are the unknowns? I’m including independent variables in here. You might want to model what your wage is in respect to hours worked, make time a independent variable. You might have more than one independent variable.  Besides, chances you have other things you don’t know and need to consult with others to find out. Your model will nearly always have unknowns
  • How can I relate my unknowns and knowns? This is really the essence of modelling, finding some relation between them. What the relationship look like (formula, markov chain, IP….) depends on what you are trying to do (does it it need to be modelled in excel?).
  • What assumptions do I need to make? This comes hand in hand with the previous point. Sure, you try to make do with the information you have, but sometimes you need to make assumptions. Just make sure these assumptions are well justified.


So after all of this, hopefully you will have a model. But just because you have a model, doesn’t mean it will be correct. You need to check you model. Questions to ask yourself:

  • Does my model actually model the problem? Cause if it doesn’t, what will it be used for?
  • Does it fit ALL the data I was given? Models are meant to reflect the data, they don’t work if they are not consistent with each other.
  • Did you model all the data? If you left some out, was it for a good reason?
  • Is it written in a usable way? Your model is meant to be used. If people can’t use it, what is the point?
  • Do the predictions make sense? Does it make sense to have a car tire circumference of 1.2km? Nope, if your model says that, you should rethink your model.

Really if any of these are the case, you need to rethink your model.



Keep in mind there is now right model. There are good models that do what they are meant to and do it well. There are bad models which, well don’t. The only way to get there is to keep on trying.

Mathematical Modelling: Part 1

25 Jun

I’m giving a talk to year 9/10 students (~15-16 year olds) this evening on mathematical modelling. So  I thought I would write a summary here so my thoughts are in order before I give this evening’s talk.

What is mathematical modelling?

A description of a system that uses mathematical concepts and language (Thanks wiki). The keys things in this definition is:

  • ..description.. a model is just a description. The difference here is that the description isn’t just words, we have the whole language of maths available to us
  • system… the description has to be of something that has some sort of order in it. Which is, admittedly most things. But not all. Think  xkcd055 (ueseless):
  • uses mathematical concepts and language: As I pointed out initially, the description is in maths. And not just the maths you see in high school . We like using graph theory, group theory and pictures to get out models across as well. And all the other maths

What are some examples mathematical models?

  • e = mc^2 : this models the relationship between energy and mass.
  • Modelling the vibrations of a molecule. Compounds have their molecules ordered in a stuctured way. Due to the structure, there is certain ways the molecules can move. We use group theory to model the symmetries of the molecules in order to determine the vibrations
  • Road networks. The roads become the edges of a graph, the locations become the nodes. Now that we have a nice graph we can use well known algorithms like Dijkstra’s to find the shorted route between two locations.

What type of models are there?

  • Empirical vs. mechanical models. For an empirical model we collect data and try to fit a model to it. Mechanical  models we take something we already know, and try to adjust it to fit some other problem.
  • Discrete vs. continuous models: Discrete models only take in given quantities, continuous models take all values. Population growth is normally a discrete model: we don’t want to model the population down to the very second. On the other hand, modeling the leak in a tap is normally continuous.
  • … There are really heaps more. I could go on forever if I had to list them all
  • I’m going to focus on discrete models

What do we use models for?

  • To help explain a system. Mathematical models are often very concise, so it is much easier to see what is really happening.
  • To make predictions. Understanding how a model works means that we have a better idea on what will happen in the future, meaning we can make more accurate predictions.
  • To assist in making decisions. Since we can now  make predictions, we can make decisions. Big business loves making accurate predictions

Next post! Actually doing some modelling.

Obesity is a disease

24 Jun

In the last week the American Medical Association recognised obesity as a disease. Cue out rage from body acceptance blogs. I don’t normally frequent body acceptance blogs as I find them somewhat hypocritical. They promote “health at every size” and get upset when people define them by their size. But now that obesity is classified as a disease, they are upset that they are a disease. So they don’t want to be defined by their size, but as soon as a medical organisation classifies their size as a disease, they are suddenly defining themselves by their size. Bizarre.


A disease is an abnormal condition that affects the body of an organism. Does obesity effect the body of an organism: yes. So it is a disease, at least with that definition. In the same vein, anorexia is also a medical condition. Actually, I think that obesity would be better classified as an eating disorder, similar to anorexia as in both cases they have an unhealthy relationship to food. Why can people who aren’t eating be forced fed, whereas the obese cannot have food withheld?

And those promoting “health at every size”. I think you are delusional. Read this. Yes, your blood work might show you are healthy. But the fact you have 10cm of fat between the outside and your vital organs will make it that much harder to perform any surgery. You might be healthy right now, but how will you be in 10 years time.

These are facts. It is also true that your weight doesn’t define you. If you are 150kg, but can do everything you want to, I just don’t care.  Stop trying to make your size define you.

Book Review: Porn

21 Jun

I bought myself a kindle the other week. Mostly so that when I travel I can take a decent amount of books with me. I wasn’t planning on doing much day to day reading on it as there is a good library near me that gives me good books for free. Which is better than paying dollar for some classic or $10 for a more modern one.

But then I remember the euphemistically called erotica section. The local library doesn’t have a good erotica selection, surprisingly enough, but there are plenty of people publishing erotica on the kindle store. So my kindle really should be called “Rachel Porn device”.

So the first book I read on it was “Mr. Benson“. Written in the 80s (I think) this is a fairly heavy unrealistic slave/master gay sex. It has good sex scenes and I find the relationship between the two main characters quite sweet. Based on the recomendations for Mr. Benson, I read Power Exchange and Safe Word. Both these were definitely had more on the plot and less on the porn (Mr. Benson has a really bizarre plot that suddenly comes in 2/3rds of the way in that the author seemed to suddenly decide he must have). Power exchange has a better plot than Safe Word, but still enjoyable enough. The characters actually have dimensions and the draw, at least for me, is seeing how the characters cope with the events that occur in the book.

Which brings me to  the book I read night. It was a recommendation  based on Power Exchange/Safe Word. It had 4 stars. Even better it had a 100% discount (was $5). Wow that was bad. While I don’t mind my porn being unrealistic, this was just not believable. And had way too many uses of the word “hot” and bizarre run verbal diarrhea sentences full of cliches. Things like “Fortunately, or unfortunately, his tailbone took the brunt of the fall” and “..and wanted to do something useful with his passion”.  Essentially what my writing is like, but I’m not crazy enough to publish it. It really was like a more pornful version of Vampire Academy (which had the excuse it was written from a 14 year old girl’s point of view. As she got older the writing got better). I have no idea why it got 4 stars, I gave it 2, not sure why I didn’t give it 1.

The best thing I can say about it was that it was free. I now need to find some proper erotica so that I’m not rolling my eyes constantly throughout a book.

Powerful Woman

20 Jun

Australia has been a fun place in the last week if you are interested at all in gender relations. The first female prime minister has had a menu written about her “Small breasts, huge thighs and big red box” and been questioned if her de facto partner is gay. This is after she was called “deliberately barren” (when she was opposition  health minister) and had signs saying “burn the witch” brandished at a rally attended by the opposition leader. Not to say she hasn’t come out fighting. There is her excellent misogyny speech.

The interesting fact about being questioned if her partner is her gay, it was on the premise that he is a hair dresser. So at first glance it seemed to be some homophobic stereotyping coming out. But Helen Clarke (NZ ex-PM) has been questioned about her husband’s sexuality, as has Helle Thorning-Schmitd (Danish PM).  So while it still might not be direct misogyny, there are still people in position of influence who can’t understand that a straight male can be a partner of a powerful woman.

This has gotten me thinking. Will people be looking down at  my partner if I get a high-powered job? Its not that I mind people thinking that he is gay (they are wrong, but its not like being gay makes sense as an insult), its that people think less of him because of something outside his control.

I’m really hoping that this is mostly just the older generation and that they will die out soon. Somehow though, I don’t think we will be so lucky