The Belly of the Beast: Inside the Mass Spectrometer

As my lab work draws to a close I realise I have learned a surprising amount about running and fixing lab instruments, such as the Delta XP mass spectrometer (mainly when things go wrong as they often do with such high precision instruments). This post is more about the inner workings of the CosTech Elemental Analyser, used for analysing my stable isotopes of Carbon and Nitrogen from feathers.

The Delta XP in the foreground. The Costec furnace (with the blue stripe) for
Carbon/Nitrogen analysis and the tall red Vecstar furnace for Hydrogen in the
background

Inside the CosTec:

Not a tube of festive decorations, but a spent
reduction column filled with copper shot.
When new all the copper was grey, as in the
bottom of the column. 

A used and new combustion column with the 
handy ruler to guide column packing.
This is the column where the sample is burned.
Note the build up of ash from the tin capsules
in the used column.
    (QW= Quartz wool)

Inside the Mass Spectrometer:

The furnace has 2 reactor columns, 1 where the burning takes place (flash pyrolysis), the other is a reduction column that scrubs out unwanted compounds from the sample gas before it is carried by helium to the mass spectrometer which "counts" the number of isotopes of different weight in the gas. Simple!

Inside the Delta XP mass spectrometer

Even deeper inside the Delta XP. The Source  -if you see this then something has
gone very wrong and the mass spec has been opened up. It takes a few days for
it to return to vacuum and for atmospheric moisture to be removed.
So seeing the source means delays in lab work. Fixing it requires a steady hand,
tweezers and a tiny screw driver. 

I have only seen the ion source (known simply as The Source) 3 times during my 4 years of mass spectrometry as a Masters and PhD student. The ion source converts the sample in to charged particles (ions) which are then passed to the magnet. The magnetic field deflects the particles by differing amounts according to their mass:charge ratio. The detector then counts the relative abundance of the different ions based on their mass:charge ratio. I am measuring the ratios of 12C:13C and 14N:15N, the heavier form being rarer. 

Iberia is dominated by C3 photosynthetic pathway plants with an average 13C of -27 parts per thousand (per mil), where as in Africa in the savannas of Senegal, most plants are C4 pathway plants with an average of -13 per mil. All living things take up these isotopic ratios through diet and they become fixed in tissues like feathers. In this way if I select a Lesser Kestrel feather likely to have been moulted in Africa I can tell from the isotopic ratios whether an individual migrated to Africa or whether it wintered in Iberia. Really fascinating science!

Quadcopters -non avian flying things for a change!

I have submitted an application for funds to buy one of these Phantom quadcopters for White Stork research (fingers crossed), so I jumped at the chance to do a short course: Aerial Photography for Fieldwork using UAVs (Unmanned Aerial Vehicles). 

Also, it looked too much like pure good fun!

Meet the Phantom Quadcopter. With its glowing lights it is sometimes mistaken for an alien spacecraft!
Red is the front, green is the back -not so easy to see when it is a distant speck in the sky above you.

In the last few years quadcopters have suddenly become easy enough to fly and cheap enough to be in the range of even the more humble research budgets. Whilst mostly used by snowboarders and skateboarders to film stunts (and most of the aerial footage in Top Gear is filmed with UAVs), they can also be used to help answer a whole variety of research questions.

Fitting the GoPro camera

This particular quadcopter is mainly used to map changes in mountain sides and valley floors before and after volcanic eruptions or erosion events in Ecuador, the Caribbean and other amazing places. The images can be overlaid on to terrain or elevation models to create amazing 3D images of changes over time. 

The Sainsbury's Centre, from the pilots view... 

...and what the quadcopter saw.
Structures from Motion. One of many hundreds of images that we will stitch
together to make a 3D model of the Sainsbury's Centre.

Mission complete. Good catch!
UAVs were all developed by the military so it is full of
military termimology. A flight is called a Mission -of course!

Investing in a quadcopter is much cheaper than purchasing a satellite image -and they are far more versatile and reusable! 

Uses include:
-Vegetation mapping
-Monitoring changes over time, eg slopes prone to rockfall or mudslides; or to detect patches of illegal logging in rainforests. 

-The camera can easily be modified to thermal or near-infra red imaging to look for nesting birds, or assess plant health (by detecting chlorophyll levels). In this way farmers could target fertilize crops rather than treating whole fields. 

-Fire fighters have used UAVs in controlled experiments to to assess how fire takes hold as it burns across a field, and to look for thermal heat patches that may signal fires in a building before any smoke is detected. 

-Or it could simply be used to view high or dangerous to reach places, like me checking number of eggs in inaccessible stork nests. 

The number of possible applications of UAVs in research will only increase as technology improves. I'm sure it wont be long before university degree courses feature modules in piloting UAVs and the post-processing of image data.

Quadcopter cam view from ground level.....
Mission: to map the UEA Broad. Lift off imminent with me at the controls.
Karen holds a GPS to log various control points round the broad.
After we have cropped and merged together a selection of images
into one photo this can then be geo-referenced and digitalised by
overlaying it on to a map layer in mapping software packages, such as GIS.

...and the Quadcopter's view of the UEA Broad.
You can just see a blue spec holding the white box -thats me
at the controls.

The Phantom flies in winds of over 30mph
and flies itself to some extent. It was amazing
to see it leaning against the wind to maintain
position as it hovered. 

Dont worry, nothing died: my favourite talk from the SPEA conference

It was a talk about how nothing died -quite rare for biologists because biological science is seemingly most interested in death and explaining why things died!

In an nutshell, Ricardo Tome and team are using radar and field observations to minimise collision deaths of soaring birds as they pass through wind farms -in fact they have done better than that, they have reduced the number of deaths to zero in their study site: a wind farm in south west Portugal.

I found myself sat opposite him and some of his colleagues over one of those long, tasty, boozy, cafe lunches during the SPEA conference (Birdlife partner for Portugal) that I was talked about in my last blog post. He was a very humourous and entertaining lunch companion as he explained his project in more detail.

As a flock approaches the wind farm, the radar and human observers (placed at some distance around the site), track the flock and decide if the huge sweeping blades of the wind turbines should be stopped. If the flock continue inbound, the turbines are briefly halted, just long enough for the flock to pass through safely. Stopping is near instantaneous and apparently it is quite something to see the wind farm suddenly shut down in unison.

During the whole study period no birds were killed by collisions with wind turbines and there was minimal impact on electricity generation. This seems like a win-win situation to me and captured my imagination, especially because I am an East Anglian lass living on the border of the North Sea in sight of many new off shore wind farms and important coastal areas of birds.

I encourage you all to follow this link and hit the "translate" button -if you dont speak Portuguese
http://www.cienciahoje.pt/index.php?oid=54734&op=all