The Toilet Door

So I've been playing around a bit with LaTeX because I like the idea of what it can do. It sorts out all the tricky formatting depending on how you want to present your work. It's not ideal for collaborative editing though. Microsoft Word wins in that department with comments and tracking changes.

One of the ways I'm going to investigate using LaTeX is with some custom tags. This xkcd comic illustrates which characters interact with each other as a function of time over a story. Now that was produced by reading the books, and manually going through and making note of which characters are where and with who at each time. Ideally though, if that information is put into custom tags at various chapters or at points in the story it can be invisible to the reader, but a simple program or script could extract the information and produce a plot like that. Similarly, if we could generate one for characters, we can also do it for action, or emotional content.

Having the ability to produce graphs to demonstrate the action during a story or comedy say gives an author new tools with which to view the overall story. Is the front action heavy? Is it too dry? Is there enough story progression? Humans are visual creatures, so I'm hoping I can make something to produce these graphs, so that when I begin writing, I have a large number of tools available to guide my story.

Well 2 days in a row followed by a long break isn't too bad. At least I remembered enough to feel guilty about not doing it.

Can't think of anything great to discuss at the moment. I'm finishing off my next paper to be published. It's a different kind of writing, significantly more restricted and a whole lot of editing to ensure the correct meaning comes across. I guess it's the same as any writing and communication though, you may have the ideas in your head, but unless you can communicate them clearly, efficiently they are worth nothing. Scientific writing requires one to be explicitly precise and at the same time, concise. This limitation poses significant challenges. Typically one could do the following for example.

The machine was left on overnight and there was a spill. It was fixed by turning it off in the morning.

With a sense of context, it is obvious the spill was not turned off. It, is referring to the machine. We could make this sentence more ambiguous by removing a part

The machine was left on overnight and there was a spill. It was fixed in the morning.

Here, we are left unsure if the machine being left on is the problem, or the spill is the problem, or both. Obviously avoiding ambiguity is what good writing should always aim to achieve. However, it can quickly become very verbose, especially when describing unnamed objects.

The brown machine was left on overnight and there was a spill that affected the black machine. The black machine was fixed, the brown machine was turned off and the spill was cleaned up in the morning.

In scientific writing however, items don't have simple or small names such as the brown machine or the black machine, they often have long, awkward names. This is partly due to the nomenclature used to describe molecules. It is insufficient to simply write glucose, there are two isomers, so we write D-glucose, but even then, there are two forms, so we write α-D-glucose. In regular writing, it would be sufficient to simply introduce it as α-D-glucose and then refer to it as glucose from that point on, only adding clarification if you later introduced a different form. As science papers are rarely read by scientists in order, it is a necessity to ensure that if a reader picks up the paper and starts reading from a given figure, that it remains unambiguous.

It is taking me a while to get used to writing in a style where each sentence I write must be able to stand on its own, such that a reader with some scientific knowledge can make sense of it without being confused by attempts to reduce the number of words on a page. Basically, nomenclature is really important. I'm definitely looking forward to being able to write freely

So after the better part of a year trying to set up this experiment. I've finally managed to get a respectable amount of signal at my detector.

Basically the optical fibre that was meant to couple the signal into the detector was damaged or cracked somewhere. Which resulted in very poor signal to noise ratio.

I've since moved the detector onto the table and reconstructed the beam path so I now couple the fluorescence directly into the detector. Even with a fairly unoptimised alignment I'm getting massive amounts of signal. Which makes sense since I can visibly see the fluorescence coming out all over the shop.

To quantify the improvement. Previously using the damaged fibre, it took me about 5 minutes of collection at max power to get an intensity count of about 160,000 or so.

Coupling the light straight into the detector. It is taking me about half a second to get just as much. That represents an increasing in signal by about 1000 times.

Things are looking good for me

Also forgot to mention. With the fibre I needed all the room lights off and the sample and detector covered from as much ambient light as possible. With the detector on the table, I can do it with the room lights on! (obviously I wont when trying to collect publishable data on samples with much lower quantum yields)