chemiluminescence
I just found a copy of my IB Chemiluminescence project! Feel free to download the .pdf (including all of the data) and have a read but I make no apologies for the mistakes and dubiously explained chemistry within. This was back when I was 17 so it’s a source of nostalgia for me.
I’m finally getting round to using my Raspberry Pi for something useful. I’ve got a whole load of various files that are sitting on portable HDDs that I need to transfer to a NAS. I’m going to use my R-Pi for this as it can sit there copying files happily plugged in somewhere rather than me having to have my laptop on all the time.
Headless Raspberry Pi set-up:
Installed the latest Raspbian (2012-12-16) on a generic 2GB SD card using win32diskimager, as per R-Pi SOP.
Then I simply booted the R-Pi attached to my router as SSH is enabled by default now.
Now I don’t need the GUI for this but I thought since its there I might as well make use of it. So I installed tightvnc on my win7 machine and installed the server on the Pi (http://www.penguintutor.com/linux/tightvnc).
So then I mounted the disk I wanted to copy from. The NAS I’m using is a Buffalo Terastation. Massive thanks go to http://buffalo.nas-central.org/ as there’s so much info there to play with the frequent troubleshooting required for this thing.
I installed “screen” onto the R-Pi to let me start the copy, then close the ssh and get on with other things. I then installed cifs-utils before mounting the terastation:
sudo mount -t cifs //192.168.x.xx /path_to/mount
I think that’s all I needed to do… I wonder if I’ve forgotten something.
Finally I installed rsync and started synchronising.
There are many misconceptions about the wonderfully complex mix of chemicals and microorganisms that we call bread. I don’t wish to delve into the depths of bread science here as this is just a Sunday morning rant. A lot has been written on these topics and bread people know this already. Here are some clarifications:
Sourdough /= soda bread
Sourdough /= yeast-free
Spelt /= wheat-free
Considering so many people out there are confused, I thought the easy to digest (sorry) message above would be useful.
For a slightly deeper clarification, let me explain: sourdough is leavened bread. The producer of the CO2 gas is yeast. Now the difference between “sourdough” and ordinary yeasted dough is that the yeast used is wild. Not a single defined strain and it’s in presence of other organisms such as lactobacilli. Sodabread is a leavened bread. The CO2 gas is produced by a bit of simple chemistry. NaHCO3 (sodium bicarbonate) is neutralised by acid. The acid can be anything, usually buttermilk is used. Buttermilk contains lactic acid (as does sourdough) but this does not mean they are analogous.
The main difference between sour- and soda bread is time. Soda bread is a quick bread as the CO2 is produced rapidly. As soon as the ingredients are mixed, the reaction begins. The bread must be baked very soon after mixing or it will collapse. Just like a cake. In sourdough the CO2 is produced slowly. This is crucial as it increases the time that the dough sits in an acidic environment. This means that hydrolysis reactions are occurring while it sits there proving/rising. The gluten has time to “develop”. The long gluten protein strands organise themselves into a cohesive network that gives it strength so that it can hold its shape even though its been hanging around for hours.
Spelt is a type of wheat. It is quite different from normal wheat. But it seems that a lot of people think it’s some kind of magic grain. It’s nice certainly but don’t eschew excellent “ordinary” wheat breads for mediocre spelt breads. Both grains can be used to make excellent loaves. And, no, I’m not forgetting about rye. I think that all grains are awesome for something and we need a variety of grains as they all make different types of breads/cakes/foods.
I’m at the Aalto FabLab in the DIYLILCNC session as part of the Open Knowledge Festival (#OkFest on twitter).
Basically I, like a lot of people, am pretty interested in 3D printing, CNC and other manufacturing techniques. Mostly I’m interested in these in the sense that I want to be able to use them cheaply and preferably in a local facility or at home. This is why hackerspaces are so cool. People have been talking about using these to make various bits of lab equipment. Not reaction vessels or anything but better clamps and things to make life easier. Even peristaltic pump parts as these can be quite expensive and could be used to make cheaper flow chem set-ups perhaps.
Anyway, I want one and they are making one of the DIYLILCNC machines here at the fablab, so I’m pretty excited.
I forgot to add a link to a bit of underwater video from Shelly Beach a few months ago. I’ve been extremely lazy in editing a whole load of GoPro free- and scuba dive footage. I’ll try to get more of it up in the not too distant future!
(Test post from the phone)
I received my Raspberry Pi at the end of last week. I’ve just set it up for the first time using the instructions provided without a hitch. I had planned on writing some further instructions here, but they really aren’t necessary. I used the recommended Win32 image writer to write the debian “squeeze” (19-4-2012) distro onto a Verbatim class 10 SD card. I plugged it into our ancient TV and it booted up fine. I’ll probably use it via VNC though.
My friend Oleg prompted me to read this article about analysis of mobile phone data and its implication in treatment of malaria. Nathan Eagle has been using (anonymous) mobile phone user data in developing countries to attempt to identify disease outbreaks through monitoring of the movement of people. The study was reportedly used to try to identify if it was viable to attempt to control malaria by localised elimination of the parasite. The conclusion was that elimination of the parasite would not be effective because the high mobility of people rendered it ineffective.
I wonder how useful this data would be in the prediction of where drug resistance is likely to appear next? If the data can be correlated with known areas of resistance and mass movement of people are observed to new areas, could this information be used to inform drug regimes for treatment of disease? For example switching to alternative medication regimes when resistance is suspected.
Artemisinin (Wikipedia)
Artemisin resistant malaria is scary (one of the reasons that we’re working on things to help combat this) and on its way. It would be great to track the data of people movement from areas such as the Thai/Burma border but I doubt their respective govs will be happy to share the movement of their border populations and crucially of troops operating in the jungle.
I’m always amazed by the price of some bits of lab equipment. Things like aluminium heating blocks are way overpriced and as a result most academic labs make do with oil baths. Obviously these have a number of problems that are highlighted by suppliers but their arguments still don’t justify spending 300 GBP on a heating block for a single round bottom. They argue that they pay for themselves over one or two years due to the price of silicone oil. I don’t know how often they think the oil in baths gets changed but I hadn’t found a single chemist who would agree with this.
Having said that, I’m not a fan of oil baths. They are a real pain when carrying out small scale reactions in parallel. At the beginning of my last year of my DPhil I somehow found time to learn how to turn and mill metal thanks to our in-house workshop and friendly engineers. I made myself a heating block to hold 8 CEM microwave tubes. This thing made life so much easier. No more slippery oil coating and contaminating everything. All for 2 hours of work and a chunk of scrap aluminium worth about £20.
Now our workshop here has made me a heating block to hold 25 mL vials as disposable reaction vessels. I also asked them to turn some B14 to vial adapters so I can attach condensers or any other quickfit glassware to them. Andrew in the workshop designed a beautiful thing made from 2 pieces of PTFE. Connected to the vial it easily hold a vacuum <1 mmHg, so vacuum purging and inert atmospheres are all good (not that I'd recommended using vacuum on parallel sided, non vacuum rated vessels without a proper shield).
Anyway this is the prototype and the heating block is getting anodised. It's going to be beautiful. I would encourage anyone to get to know your lab workshops if you are lucky enough to have them.
A few months ago [I just checked, this was in June 2010! Time flies!], while sitting around in Oxford Cycle Workshop talking with my friend Jonty and an idea popped into my head. Bike speedos are mostly ugly plasticky things, so I though I would add another project to the list: Make an analogue speedometer for a bike that fits in a nice case. I sketched some rubbish down in my notebook:
The trusty Moleskine
Today, Jonty pointed me toward the people at Redfish have basically drawn up what I was thinking about but with much fancier graphics.
I got as far as looking up prices for stepper motors, clock movements, etc etc before I pretty much gave up and got on with writing my thesis. I hope RedFish gets much further than that.
Over the years that I’ve been involved with synthesis the solvents I’ve used for reactions and work-ups have changed quite drastically and, unfortunately, I seem to be going backwards according to the solvent selection guide.
Just a scribble graph of solvent use over time.
My “gateway” solvents (heptane, toluene, acetonitrile, ethyl acetate) seem to have led me on a downward spiral towards the environmentally nasty DCM. This is a result of a combination of lazyness and necessity. While at Pfizer, I simply didn’t use any halogenated solvents except for CDCl3 and very very very occasional DCM for sample prep. It just wasn’t hanging around on the bench and the rotavaps were perfectly capable of taking off toluene and ethyl acetate, unlike some found in academic labs. The process solvent choice thing hung around with me through my masters project but I did resort to DCM for some reactions and work-ups. Through the DPhil, my main reactions were carried out in 1,2-DCE but this accounted for a small amount of solvent per reaction. Methodology work with usually only 1-2.5 mL of solvent doesn’t work out to much even when you’re doing hundreds of reactions. Later on we did change this to propylene carbonate which is a solvent that I really enjoyed using. It is probably worth trying out in more reactions and recrystallisations. I did still try to use more benign solvents for most of the starting material synthesis. With no 2-Me-THF, TBME, or MeCN about (this was around the time when acetonitrile production stopped for a while), THF and diethyl ether became the general work horses.
I’ve always been one to avoid columns if I can possibly help it but of course I do need to use chromatography. My column solvents changed from ethyl acetate/heptane at Pfizer to EtOAc/60-80 petrol to ether/40-60 petrol to pentane. Switching to lower bpt solvents mostly to get rid of persistent solvent residues in the annoying oils/gums that I was producing at the time. Column waste is something that is particularly rife in academic labs. People generally use way too much silica for most separations and then use inappropriate solvent systems and then complain that their columns take so long.
Now I’ve somehow slipped into using DCM pretty regularly. MeOH/DCM is being employed too readily but at least my DCM squeezy bottle isn’t around anymore.
Yes yes, DCM is cheap and a great solvent but it’s disposal isn’t. Do any (academic) departments out there charge disposal costs to the individual research groups depending on use?
[I just noticed this topic has recently been discussed over at Org Prep Daily]