MethylCal: Results published in FASEB

New results from our interdisciplinary work are now online.

The recently published article, entitled “Transcriptomic and epigenetic regulation of disuse atrophy and return to activity in skeletal muscle“, by Dr. Andrew Fisher, Dr. Robert Seaborne, et al., investigates the transcriptome in response to the recovery of muscle after disuse and the associated epigenetic mechanisms that may function to modulate gene expression during skeletal muscle atrophy or recovery, since physical inactivity and disuse are major contributors to age-related muscle loss.

The investigation used experimental tissue samples from laboratory rats. The tibialis anterior muscle in rats was silenced with tetrodotoxin to reduce the muscle mass over different periods of time and then allowed to recover, such that the fraction of restored muscle mass after seven days of recovery, during which the rats resumed habitual physical activity, could be measured and compared to a control sample. A transcriptome-wide analysis demonstrated that 3714 genes were differentially expressed across all conditions after disuse-induced atrophy. The most differentially expressed genes after microarray analysis were identified across all conditions and were cross-referenced with the most frequently occurring differentially expressed genes between conditions. Transcript expression of these genes and another specific gene (Fboxo32/MAFbx), of interest due to a known link with disuse atrophy, were analysed to identify which genes showed significant changes in gene expression during recovery. In fact, some genes demonstrated significantly decreased DNA methylation at key time points after disuse-induced atrophy, that corresponded with significantly increased gene expression. This is the first study to demonstrate that skeletal muscle atrophy in response to disuse is accompanied by epigenetic modifications that are associated with alterations in gene expression, and that these epigenetic modifications and gene expression profiles are reversible by returning to normal activity.

Part of the data analysis was performed with MethylCal, a bespoke Python-based program designed to aid the analysis of such experiments in epigenetics. MethylCal determines the calibration solution between the known concentration of methylated DNA in standard laboratory samples and several observed properties, and then applies this calibration to the experimental DNA samples, enabling us to trace the level of gene expression. Examining the varying methylation concentrations of experimental samples exposed to different conditions therefore allows us to determine the important factors affecting gene expression.

In this recent work, MethylCal was used to analyse the results obtained via high-resolution melting (HRM) and hence determine whether some gene tests were sent for further follow-up using a more sophisticated method of determining the methylation concentration: pyrosequencing. This method allows the methylated regions of a sample to be sequenced and gives a more quantitative calculation of the methylation calculation for a specific site of the gene region, rather than a global percentage methylation concentration for the entire region. (For my colleagues in extragalactic astronomy, consider it like measuring the star formation rates in individual HII regions within the disk of a galaxy, rather than integrating everything across the disk to obtain the global star formation rate.) Samples that showed no methylation with the HRM analysis were excluded from further study, whereas those with some level of methylation were sent for pyrosequencing.

The article is now available in The FASEB Journal, or you can download the PDF.

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Award of the China-Chile Fellowship

I am truly honoured to have been awarded the China-Chile Fellowship.

This joint fellowship award from the Chinese Academy of Sciences (CAS) and the National Commission for Scientific and Technological Research (CONICYT) of Chile grants me numerous, exciting opportunities to continue to contribute to advancing our knowledge of galaxy evolution whilst developing skills in observational astronomy. Though I will still be primarily based in my current office at the Institute of Physics and Astronomy of the University of Valparaiso, my host institute in Chile, I will also be a Fellow of the School of Astronomy and Space Science at the University of Science and Technology of China. I aim to strengthen ties between the Chinese and Chilean astronomy communities via my proposed research program to be conducted at these two institutions.

The research itself will be a continuation of my recent work with the Valparaíso ALMA Line Emission Survey (VALES), focusing on my two main projects. One is to further study the calibration between the dust continuum luminosity and the molecular gas content of galaxies using direct measurements from ALMA observations, instead of the indirect estimates of the dust continuum used in my most recent paper. Whilst this project will utilise the global, integrated measurements for a sample of galaxies, the second project aims to provide a complimentary study (also with ALMA) of the dust-to-gas ratio on spatially-resolved scales across the disks of three star-forming face-on galaxies. The award of the fellowship and the recent acceptance of the ALMA proposals central to these projects will hopefully provide the highly-desirable combination of data plus resources that will allow me to do some exciting science! In addition, I’m also aiming to publish my analysis of the physical conditions in the interstellar medium via the modelling of emission lines observed by the Herschel Space Observatory.

I really, really appreciate the chance to spend the next two or three years as a Research Fellow, doing what I love. I’ve already had a very successful and rewarding time as a researcher in Valparaíso, and I aim to keep building on this success. I want to publicly thank CASSACA and CONICYT for this award. I also thank the people who have supported me on my adventures in astrophysics: my supervisors and mentors Luca Cortese, Maarten Baes, Edo Ibar and Yongquan Xue, and my friends and colleagues around the world (you know who you are). I could not have made it this far without the love and support of my family. Thank you.

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Observing at APEX (Run #2)

Check out these 360 degree views of the APEX site on Chajnantor Plataeu!

I took the images during my second observing run at APEX using the Google Street View app for the iPhone. You basically have to stand on one spot and use the iPhone camera to photograph the entire 360 degree sphere. I couldn’t take many photos because the cold at high altitude really drained the battery fast, allowing for only three attempts. I was hoping to use them for public outreach events with Google Cardboard, but they didn’t turn out so great.

I also took a load of 360 photos on a recent trip to Punta Arenas and the Torres del Paine area. Click here to see all of my Google contributions, but my favourite is this one of the view of the towers in Torres del Paine:

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The Valparaíso ALMA Line Emission Survey

During my time in Chile, I’ve been working on a new survey.

The Valparaíso ALMA Line Emission Survey (VALES) is a sample of main-sequence and starburst galaxies selected from the Herschel Astrophysical Terahertz Large Area Survey (H-ATLAS). The idea is to characterise galaxy populations at “intermediate” redshifts to act as a reference for future studies at higher redshifts. Although the survey will be predominantly based on observations of spectral line emission with the Atacama Large Millimetre/submillimetre Array (the ALMA in survey name), we are also pushing an observational campaign using APEX/SEPIA, VLT/MUSE, etc., to obtain both integrated measurements and high spatial resolution maps of various emission lines.

Fun fact: the survey was almost called the Herschel-ALMA Intermediate Redshift Line Emission Spectroscopic Survey, but this suggestion was too bald. Ahem.

At the moment, we have three submitted papers (two awaiting the referee report and one accepted for publication) based on ALMA Cycle 1 and 2 observations – the quality of the data is incredible – with hopefully more observations to be delivered during Cycle 4. These studies are summarised as follows:

VALES I (Villanueva et al.)

We present the ALMA Band-3 CO(1–0) observations for the first time, using them to study the molecular gas content in a sample of 67 normal star-forming galaxies. After describing the data reduction process, we calculate CO luminosities, the optical to CO size ratio for the spatially-resolved galaxies, the global Schmidt-Kennicutt relation, and study the gas content and star formation efficiency as a function of redshift. As the paper was only just submitted, I’ll write more on this later.

VALES II (Hughes et al.)

This paper, now accepted for publication and available on the arxiv (see also the talk I gave at this year’s SOCHIAS meeting), studies the physical conditions in the interstellar gas via the comparison of the ALMA CO(1-0) and Herschel [CII] observations to a photodissociation region (PDR) model.

We determine the gas density, surface temperature, pressure, and the strength of the incident far-ultraviolet (FUV) radiation field. The majority of our sample exhibit hydrogen densities and experience an incident FUV radiation field with strengths (when adopting standard corrections) that are consistent with local, normal star-forming galaxies and non-starburst nuclei.

A comparison to galaxy samples at different redshifts indicates that the average strength of the FUV radiation field appears constant up to redshifts z~6.4, yet the neutral gas density increases as a function of redshift by a factor of approximately 100 from z=0 to z=0.2 (quite an intriguing result) that persists regardless of various adjustments to our observable quantities.

Whilst this evolution could provide an explanation for the observed evolution of the star formation rate density with cosmic time, I think the result most likely arises from a combination of observational biases when using different suites of emission lines as diagnostic tracers of PDR gas. The interesting part to this, though, is that whichever way you make the comparisons to avoid the biases (VALES versus the low-z sample, or VALES versus the high-z sample), the increase in gas density with redshift seems robust.

VALES III (Hughes et al.)

In this paper, I am presenting the calibration between the dust continuum luminosity and interstellar gas content obtained from current VALES sample of 67 main-sequence star-forming galaxies at 0.02<z<0.35. I’m using the ALMA CO emission to trace the molecular gas mass and estimating the dust continuum luminosity from MAGPHYS modelling of the GAMA Survey‘s far-ultraviolet to submillimetre spectral energy distribution (see example below).

We then provide relations between continuum luminosity, molecular gas mass and total ISM mass for different combinations of the VALES and literature samples, and adopting two different values of the alpha CO factor (that converts the CO luminosity to a molecular hydrogen mass estimate). I’m pushing for these relations to be published in time for ALMA Cycle 5 proposal deadline, as they may be useful for estimating the gas content from the continuum emission from high redshift systems.

This brief overview is just a taster of the first few papers that are almost ready to be released into the wild. There are many more studies possible given the quality of the data in hand, with more on the way. Watch this space!

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Atacama Large Millimetre/submillimetre Array

I was thrilled to finally explore the ALMA Array Operations Site!

The high site was high on my bucket list for Chile. Although I had already seen the ALMA Operations Support Facility, the base camp at 2900 m, a number of times as either a professional visitor or a tourist (I highly recommend their free public tours if you ever find yourself in San Pedro de Atacama on a weekend – book early!), it wasn’t enough to satisfy my curiosity. After spending the last year as an ALMA postdoc, proposing for ALMA time, working on ALMA science, analysing ALMA data, publishing ALMA results, I obviously really, really wanted to go and visit the actual array itself up at 5100 m on the Chajnantor plateau.

On the day of my visit, the array, composed of 66 12-metre and 7-metre diameter antennae, was in the most compact configuration for low resolution observations, meaning most of the antennae were in the central cluster of pads by the AOS Technical Building that houses the array Back End and the Correlator.

Click on each image below to see the full size version.

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Observing at APEX (Run #1)

In December, I spent a week collecting photons with the Atacama Pathfinder EXperiment.

As a co-investigator on an approved proposal, I volunteered to join a small team of four astronomers that would use APEX during the scheduled Chilean observing time to carry out observations for the Chilean community. APEX is a 12 metre telescope built as a prototype ALMA antennae. I was hugely appreciative of this fantastic opportunity to gain experience observing in the submillimetre regime, for which the varying projects required different instruments and pointing/mapping modes. I was also especially thankful after having to miss a previous opportunity for observing at APEX because the schedule perfectly conflicted with my brothers wedding and, as they say, blood is thicker than water interstellar gas.

Arrival at Sequitor base camp

On arrival at Calama Airport from Santiago, we met the other Chilean astronomers, telescope operators and other support staff, and were transferred via a minivan through the desert to San Pedro de Atacama. The operations base of APEX is a small compound located just outside of San Pedro comprising a remote control room, administration offices, a conference room, residences for staff and visiting astronomers, and a dining room (compliments to the chef, the food was great!). I attended a handover briefing with the ESO astronomers who were finishing their observing run, and spent the first evening familiarising myself with the control room computer terminals, the projects we would be observing and the data reduction scripts.

Acclimatisation at Chajnantor site

Due to the high altitude, I spent the first day acclimatising at the observatory site. The APEX telescope itself is situated at around 5100 m on the Chajnantor plateau in the Atacama Desert, the location of the highest observatories in the world.

Working at high altitude presents certain risks, partly due to the lack of oxygen. In order to observe at APEX, I required a medical exam to get a certificate for working at high altitude – a whole other story in itself, as I spent an entire morning in a clinic navigating the procedures in my broken Spanish. The eye test was more like a Spanish test, as I had to describe to the nurse what images I could see, and I accidentally took most of my clothes off for what was just a simple chest x-ray. After much embarrassment, I finally got my certificate of good health.

Prior to this trip, I had been to high altitude at 4100 m during an observing run on the UK Infrared Telescope (UKIRT) on Mauna Kea, Hawaii. I distinctly recall how, after taking some photos at the true peak of Mauna Kea, I was rushing back up a ridge to the observatory control room. In my haste, I nearly blacked out on the ridge from the lack of oxygen (and a regular gym routine). I also remember it being very easy to get out of breathe simply climbing the stairs up to the dome. Even considering this solid experience of observing at high altitude, I was still nervous at the thought of having a bad reaction to the conditions at 5100 m that would somehow cut short the trip for me, mostly because of how much I had been looking forward to using APEX.

The first time I went up to Chajnantor, finally seeing ALMA and getting inside APEX was fantastic. An engineer took me up and let me shadow him whilst he replaced a component in the instrument room, which is actually behind the dish itself (by the platform in the picture). I got a good look at the instruments, of which I was particularly interested in SEPIA and the Band 5 and 9 receivers that are being tested for use on ALMA, and had a wander around the site. Despite the nervousness, I only felt out of breathe once when lifting a heavy box containing the engineer’s replacement component. Apart from that, I felt no bad affects whatsoever and all nervousness was completely switched with excitement. And the observing hadn’t even started yet!

Professional observing

Our support astronomer for the Chilean run, Diah, very kindly gave us the day shifts meaning that we would be observing at the high site from the telescope control room rather than remotely from the control room at Sequitor base. I had the morning shift. Each day, we had a morning briefing at 5:15 am before heading up at 5:30 am. The journey took approximately one hour from Sequitor along the gravel road that passes the ALMA OSF and up to the plateau, a distance of roughly 40 km. The sun would just be rising to start the shift.

Inside the control room, which is kept oxygenated, I would then decide what projects to observe based on the scheduling priority, positions of targets in the sky, weather conditions, water vapour, etc. At submillimetre-radio frequencies, the atmospheric transmission is most affected by the precipitable water vapour (PWV), which absorbs and attenuates submillimetre radiation, that is typically around 0.5 to 1.0 mm during good conditions. I would edit the scripts to perform the observations that were then executed by the telescope operator. We ended up mostly observing CO transitions and some fine structure emission lines using the SHEFI receivers, though our own project required SEPIA Band 5 observations. Performing a quick on-the-fly reduction of the data and seeing emission maps take shape, or the 5 sigma detection of a line emerge from the noise, was very satisfying.

When observations required longer integration times, I would sometimes have a wander around site just to experience the climate and feeling of isolation on the plateau. Every shift was so much fun, quite relaxed and passed by way too quickly.

And some amateur observing

A DSLR camera capable of astrophotography with my Meade 14 inch telescope has been on my Christmas list for a long time. Having some plans for some interesting trips in the near future, especially this observing run in the Atacama, finally pushed me to splash out on an entry level DSLR and tripod. During my time at Sequitor, I would sleep during the day, wake up at sunset to do some amateur observing, and then head off at sunrise for my professional observing. I’m still learning how to use my new toy for astrophotography, but my best effort from my experiments is below. It was taken with the Nikon D5300 with 18-55 mm kit lens of 20 times 10 second exposures stacked with Deep Sky Stacker ( I’ve more sequences of exposures still to process and will post the better attempts in future. Still, this was my first proper look at the Magellanic Clouds – great to see!

Overall, this was my most rewarding experience of observing to date and, since I have been awarded more time from another APEX proposal (targeting the CO SLED in star-forming galaxies), I hope I have another chance to go again in the near future.

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[NII] 205 μm line emission as an SFR tracer

My paper presenting the [NII] 205 – 24 μm correlation is now on arxiv.

My original aim for this work was just to produce a short research note to support part of the methodology in my recent paper on the edge-on spiral galaxy NGC 891. In this previous work, I exploited an empirical relationship to predict the [NII] 205 μm line emission from a higher resolution MIPS 24 μm image. Although this technique allowed me to expand my analysis, I disliked that section of the study because the underlying nature of the correlation was still unknown, mostly because of the uncertainties when dealing with high inclination systems. Integration along the line-of-sight through an edge-on spiral galaxy will include a range of physical environments, from active star-forming [HII] regions to diffuse ionised gas, making it difficult to interpret the origin of the relationship. I therefore wanted to test whether the [NII] 205 – 24 μm correlation had a physical origin or, in the most extreme case, was just an artefact of line-of-sight projection effects in an edge-on disc.

We combined Herschel and Spitzer observations of face-on and interacting galaxies in the Very Nearby Galaxies Survey – M83, M51 and the Antennae galaxies, NGC 4038 and 4039. The four panels above show black contours of constant 24 μm continuum emission superimposed on the SPIRE FTS maps of the [NII] 205 μm line emission for each galaxy. We found the same [NII] 205 – 24 μm correlation in these face-on systems, but also that the line emission correlates with the local star formation rate. Interestingly, offsets in the correlations between the ‘normal’ star-forming discs and the starbursts in M83 and NGC 4038/9 could be interpreted by a simple Starburst99-based model as differences in the gas heating efficiency and how recently the stars were formed. We present a general relation between the [NII] 205 μm line emission and the SFR density, but I would be cautious in using this line as a SFR tracer given these offsets.

The article is now available on astro-ph, or you can download the PDF here. I’ll be using these results in a continuing project to analyse the Herschel far-infrared photometry and spectroscopy of NGC 2403, similar to my treatment of the NGC 891 observations. I’m also working on a new draft presenting my work to constrain the physical conditions in interstellar gas for higher redshift galaxies based on ALMA observations of their CO and [CII] 158 μm emission – watch this space for updates!

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MethylCal: Results published in Biogerontology

The published results from our interdisciplinary work are now online.

Led by Dr. Adam Sharples at RISES-LJMU, the study focuses on whether muscle tissue retains a ‘memory’ of inflammatory periods.

Experimental tissue samples, pictured left, are exposed to a cytokine involved in inflammation (TNF-α) at different times and compared to the growth of the skeletal muscle myoblast (traced via myoD, a marker for the fusion of muscle cells to form muscle i.e. differentiation). We demonstrate for the first time that myoblasts that have previously received a dose of TNF-α will typically have reduced morphological and biochemical differentiation upon a subsequent administration of TNF-α.

In other words, skeletal muscle tissue that has once been inflamed will thenceforth show less and less growth with each subsequent inflammatory episode, basically leading to muscle wasting.

Part of the data analysis was performed with my bespoke MethylCal program, designed to aid the analysis of such experiments in epigenetics. Specifically, MethylCal determines the calibration solution between the known concentration of methylated DNA in standard laboratory samples and several observed properties, and then applies this calibration to the experimental DNA samples, enabling us to trace the level of gene expression. Examining the varying methylation concentrations of experimental samples exposed to different conditions therefore allows us to determine the important factors affecting gene expression.

The article is now available in Biogerontology, or you can download the PDF. The next step in the project is to repeat the experiments using different markers of muscle differentiation. A comparison of all the different available markers would be very interesting for verifying our conclusions.

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How to Move Institutes in Five Easy Steps

I’m finally back to work after moving from Belgium to Chile.

I’m thrilled to start a new position as an ALMA-CONYCIT research associate at the Universidad de Valparaiso. Even with the help of past experience, this time moving countries took a considerable amount of effort to accomplish, and I thought I’d write about the journey here. First, let me be clear: written below are just the facts of what it took to move institutes. I’m just going to be frank and honest about the experience, what was expected of me, and what I did. The key motivation was simply to keep working in science.

1) Temporarily switch countries to make bureaucracy easier

I loved my time in Gent. I was a very happy and productive worker. During the two years, I was able to double my first and nth author publications, present my research at numerous conferences, attend a number of collaborative meetings and went observing. The research group was great. Things were going great. However, the position had a limited lifespan due to my Herschel-related funding from BELSPO (set by the demise of Herschel, I think) and I needed to pursue other avenues of funding to continue research in Belgium. I made applications, they were rejected, and the funding ceased at the end of 2014. At this point, I didn’t have any concrete offers for another postdoc position – I was clearly wishful-thinking (or possibly under the influence of delicious Belgian beer) that we could stay longer in Ghent.

Regardless of where we would end up, either staying in academia or leaving to become a data scientist, physics teacher etc., any future bureaucracy or visa applications would be much easier dealt with from my permanent home in the UK. After all options were considered for moving, my wife and I decided to first travel back to the UK via the Eurostar, from where I could easily hire a van for moving everything out of our rented apartment. One weekend in February, my parents and I drove from Birmingham to Ghent, packed up all our belongings and furniture (affectionately known as the portable Ikea showroom) and drove it back to the Birmingham. I hired a storage locker and organised everything for the possibility that we may need to shortly ship it elsewhere.

2) Find a job

Finding a job is a brutal process; it’s uncertainty can be crippling and the rejection utterly depressing. I was spending many days in Tamworth Library writing grant applications, postdoc applications and applying for data science courses/internships, since I think this would also be a very rewarding area in which to work. I was also exploring the possibility to become a secondary school teacher – the UK seems desperate to fill positions for good physics teachers from candidates with STEM backgrounds.

Whilst I don’t want to share too much information about our personal lives, in the end, several factors including my wife’s UK visa status, our current financial situation, and support from my family, meant I chose to pursue another postdoc position as a researcher at the University of Valparaiso, Chile. I think it was one of those once-in-a-lifetime opportunities to do exciting science (with ALMA!) whilst exploring another part of the world, that fortunately appeared to fit our situation at the time.

After receiving the offer of the position, I decided to go and check out the institute and the local area (I distinctly remember once considering moving to China “blind”, but those days are over). My wife had to return to China to see her family but also collect some paperwork that I correctly guessed she would need for the visa application. We had one of those rom-com moments where we both flew from the same airport at the same time yet going in opposite directions, Rongrong to China and myself to Chile.

Valparaiso itself was a huge shock at first. Following the calm, quiet and mostly clean streets of Ghent, Valparaiso’s mess of dilapidated buildings, covered with graffiti, that line the dog-mess-covered pavements, took some getting used to. (EDIT: I’ve now fallen in love with the place.) The institute itself was nice and welcoming, and it was exciting to talk about research again. After many Skype calls, talking things through, I eventually accepted the position. Flying out to Chile to check out the place was a huge gamble, risking losing a lot of money, so in hindsight I’m very relieved that I liked the place. However, whilst I should have been celebrating the new job, something that took months of effort and doubt and uncertainty to secure, I simply could not. I’ve moved countries enough times to know that the journey was just beginning and the decision always comes with even more pressure and uncertainties; Could I handle the work? Could I beat the bureaucracy? Could we afford to live there? But it’s completely expected that, if you are passionate about a career in science, then you keep publishing and move institutes every few years. So I bottled it all up and we started the move.

3) Apply for a work or residence visa

One would naively think that after applying for so many visas over the years, they get easier, but for me this has not been the case because each application has been for a different country and a different situation (e.g. work/study/tourism, single/married, transit/residency).

For Chile, we required a one-year temporary resident and an accompanying dependent temporary resident visa. This required a police certificate (£50 each), a health certificate from a doctor (£150 from a private health clinic), a legalised document (constancia) from the University to say I will be working, and our marriage certificate. Acquiring these documents took three weeks, then we submitted the application online and waited about 6 weeks for the visas to be approved.

In mid-July, we travelled down to London to spend a whopping £1200 on the visas (for reasons, UK passport holders pay a grand more than the Chinese). One thousand pounds for a work visa. I’ve held a couple, and that is by far the most expensive I’ve encountered. But, we were free to fly to Chile and start working! Our only problem: the flight tickets at the time were also £1000 each and by this point my credit card was hurting badly. We were advised that the relocation costs would be covered by the grant money associated with the position, so this wasn’t a huge deal for me at the time.

So, we booked the cheapest flights possible, leaving in September (£500 Birmingham-Santiago return, try beating that!). I took the cheapest option to ship our furniture from our storage locker in Birmingham to Valparaiso, loading up a 2 m^3 container. This was made possible thanks to Ikea, absolutely amazing – we shipped a bed, two comfy chairs, two wardrobes, ironing board, laundry basket, four dining chairs, a dining table and coffee table, plus other household essentials, that all fit into just a 2 m^3 box!

4) Find a temporary job to pay for the move to the other temporary job

If Ikea helped make shipping everything possible, then Argos helped make the first month of science in Valparaiso possible. During the first half of 2015, it felt like we were bleeding money. Imagine the total cost of Eurostar tickets, weekend van hire, storage space, visa application fees, flight tickets to China, flight tickets to Chile, hotels, shipping costs… makes my heart heavy just thinking about all those costs just so I can continue to be a professional astronomer. My tight budget to move two people across the world was very tight, but my all my plans were extremely well-organised, and I thought that, once we arrived in Chile, the reimbursement of our relocation expenses plus the affordable cost of living would help cover most of our costs and we could return to normal life again. To help ease our financial worries, I took a job as a van driver at Argos, helping them set up a new home delivery process to compete with the likes of Amazon and other retailers. During the summer, I traded with them 600 hours of my life for roughly £3000, and was very thankful for both the opportunity given by, and the understanding nature of, the store manager. I hope my academic colleagues reading this now understand my slow response time to emails – I was working, just not researching!

5) Safely arrive at your new institute

After all this, in September we finally made it to Chile. We immediately applied for our RUT cards (like a national identity number, you need it to do everything), headed to the institute, got tear-gassed twice by the police during nearby rioting, and moved into a temporary apartment rented via Airbnb (highly recommend Ignacio’s place!).

Practically, we were very lucky, most things went according to plan and finding an apartment was very easy. Our portable Ikea showroom was delivered after much help from colleagues. I now have a desk and am finally back to doing research.

Unfortunately, the Registro Civil – the government office responsible for giving our RUT cards – has been on strike all month, so we haven’t been able to get the cards, and so cannot open bank accounts, sign my employment contract with the University, or sign our rental contract. On top of this, I’ve also been advised I cannot claim back any of our relocation expenses and also won’t be paid for the first month here, as the contract will start from October.

So, although making very rational and logical decisions, we return back to the same situation as when we were in Ghent, unsure of our finances and employment situation. The great news is I’m now analysing ALMA data and doing science!

Sure, this situation is not normal and just an unfortunate coincidence with the government strike. But I’ve found the last five or six years in academia to be terribly inefficient for doing science: moving countries to a new institute, taking time to adjust and be productive, and saving up just enough money to afford the next move to the next institute. In all the commotion and uncertainty, it’s obviously difficult to concentrate on work sometimes. However, in the current academic system it is expected and encouraged that a postdoc should jump through all these hoops whilst continuing to publish. I greatly admire those researchers who have also been able to start a family.

Bonus tip) Be honest about the postdoc experience

As I said above, these are just the facts of our recent move, this is not a rant, just a testament about the system itself. You make a decision to do research, be a scientist, and you open yourself up to financial uncertainty, job insecurity and a lot of stress. We should be honest about these issues with aspiring students. I’m not sure whether other postdocs share similar experiences as documented above, or I’ve just been (un)lucky with each move, but I find the system bizarre: surely there has to be a more efficient way we can do things?

Yet, I stand by my decisions to pursue a career in science. Ultimately, I wouldn’t trade these experiences for anything. Despite the tear-gassing, earthquakes, government strikes and financial mess, so far I am very much enjoying living in Valparaiso and fully appreciate the opportunity to continue with research. The position is only for two years and, if I have learnt anything from leaving China and leaving Belgium, I should soon start making plans for the next stage of my career.

Wherever that will take me.

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Solar Eclipse 2015

Today the Universe treated us to a superb view of a partial solar eclipse.

The only solar eclipse I had previously witnessed was in August 1999, where the path of totality crossed Europe, the Middle East and the Indian subcontinent. We were on holiday in Majorca at the time, where only about twenty percent of the Sun was obscured, yet the startling image of the Moon partially blocking the Sun remains a powerful memory. Needless to say, I was very excited at the chance to see this rare phenomenon.

Although I knew the solar eclipse was approaching, my visit to Toravere Observatory almost immediately followed by a brief trip to Ghent, meant I had no time this week to properly organise my observing strategy. Of course, you can’t observe the sun directly and must take precautions to avoid damaging eyes and camera lenses, but by Thursday it was already too late for me to either make a custom solar filter or simply buy one, and rushing round the local supermarkets to find some eclipse glasses proved fruitless. Defeated, I resigned to instead try out the telescope projection technique or just view reflections in water.

This morning started off overcast, yet after many prayers to the great sky gods asking for clear skies, the clouds completely cleared and I raced to set up my telescope. As I’ve wrote before, I love my 12-inch Meade LX90GPS but the overlapping region of the Venn diagram depicting “At Home In UK”, “Free Time”, and “Clear Skies” is extremely small, leading to a highly limited amount of usage. Fortunately, I was in the right place at the right time, and quickly set my scope up to project the Sun’s image onto a piece of white card.

From my location in Tamworth, the eclipse started at approximately 8:26 am, reached maximum partial eclipse at 9:30 am and ended at around 10:40 am. I crudely calculated that 90% of the Sun was obscured at maximum eclipse (with a few percentage error). Without a proper solar filter, I didn’t dare try connecting the camera to the eyepiece, but I managed to take some nice images of the projected images. I’ve included some of my favourite images representative of the different stages of the eclipse below. A couple of the eclipse images also include the active sunspots.

I’m pretty thrilled Birmingham received near-perfect clear skies to witness this event in full, especially given the long wait to the next partial solar eclipse in the UK, due in August 2026. However, the impatient can head to North America in August 2017, where observers will be treated to a total eclipse.

Click on each image below to see the full size version.

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