Month: October 2019

Week 13 – Late nights during the final week

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Mistakes in my data file

Over the weekend I hoped to get some rest before my final week at Bristol. Unfortunately, during our data analysis we saw some data points that seemed to be very strange. When we checked the data I had collected we found some possible mistakes so my job over the weekend was to re-check the data.

This meant I was soon back to the tedious work that took up most of the previous week – remeasuring skulls, checking the formulas and so forth. But finally as I went into the office Monday morning I was sure my data file was ready for a final data analysis.

Our contour plots showed Lystrosaurs that survived the PT extinction may have had strong dorsal neck muscles

Monday and Tuesday was mostly spent adding in further codes so that we could produce disparity plots through time and contour plots. My disparity plots through time took into consideration all the functional characters to show how much they vary through time. For example, after the Permo-Triassic extinction we see a dip suggesting low cranial variation within anomodonts. On the other hand, contour plots were made for each functional character. The plots are the similar to the morphospace diagrams except these plots show areas of high and low values of the functional character within a morphospace plot.

However, just as I felt things were coming together there was yet another problem with my data file. For some of the species, I had taken measurements from different specimens. Although the calculations for my functional characteristics used data from the same specimen, I was told I needed to rescale. At this point many things ran through my mind. I was angry that I had made so many mistakes with my data file.* But more than that I was worried that time was running out. I had to go back to London on Wednesday for some commitments meaning I only had two full days left.

Handling stress

At such times of distress, I think it’s important to stay rational rather than let your mind wander about in panic. Firstly, its important to remember that ‘Our doings are not so important as we naturally suppose; our successes and failures do not after all matter very much’ (Bertrand Russell-Conquest of Happiness). Remembering this prevents us from getting too attached to our own ego. Secondly, there is no point in worrying about a matter when one is no position to do anything about it. Thus, as I attended to my commitments in London I stopped thinking about the project and when I had time to fix the rescaling issues I did so. This meant I didn’t get much sleep on Wednesday night but it did mean I had rescaled the measurements and on Thursday and Friday we could focus solely on making the figures even better.

Another discovery?

At our final meeting. From left to right, my supervisors Professor Benton, Armin Elsler and Suresh Singh

And so we did. On Thursday, we were able to add another functional characteristic that showed the relative development of the dorsal and lateral neck muscles (referred to as the OI). When we ran our contour plot for this functional character we found that the morphospace occupied by taxa which crossed the P-T boundary were in areas of high OI which meant they had well-developed dorsal neck muscles. This corresponded to feeding on higher vegetation which stumped us as it is an established fact that there was no such vegetation during this period. Consequently, myself, Suresh and Armin (who had both been helping with the coding) launched into a discussion on why this could be. In the end we came to an agreement that the strong dorsal muscles could have been used to uproot plants by pulling back on them.

Despite the data analysis coming to an end, Thursday was yet another late night. For the past week I had been going into the office at 10am, as I normally would, but getting back home at 8pm. Strangely though I did not feel drained. Being able to see how the hard work was leading to new theories and a window into a world 300 million years ago was enough to keep me going so when I got into my office for the final time on Friday I was slightly sad things were coming to an end.

Giving back

Nevertheless, Suresh, Armin and I had one last meeting scheduled in the afternoon with Professor Benton so I had to get some figures ready to illustrate our findings. The final meeting was just like all the others – casual, happy and informative. And just like all the previous meetings I left it with a greater confidence in myself. To show my gratitude, while I was in London I brought some presents for my supervisors along with a card. Unfortunately, I couldn’t find anything related to anomodonts so I had to give into dinosaur souvenirs!

The final day

The rest of the final day was taken up by transferring the code onto my laptop so I could use it after I left Bristol. This took a while as R had to be updated and the code had to be run again to check it worked. In conjunction with the past week, we found a few more issues and went late into the night to fix them.

The presents and card I gave to my supervisors at our final meeting

By the time the code was fixed it was just Armin and I in the office. Suresh, who had helped me with most of the coding, had gone home. It was around 10:30pm when we finished. The whole building was empty and darker than usual since some of the lights had been turned off. As Armin escorted me to the buildings exit we talked about the next steps. He repeated what was said in our meeting with Professor Benton – that the project could be published and had the potential to be a high impact paper. He also reassured me that if I couldn’t write it up by the deadline, which we had decided to be April 2020, that I was to inform him so that they would be able to write it. The only drawback would be that I would no longer be the primary author. Then we talked about staying in touch via Skype and email. After that we said our goodbyes and I walked out of the Life Sciences Building in Bristol for the final time.

*Later on, when I got back to UCL, I found out that its normal to re-edit the data file many times over the course of a project.

Week 11 and 12 – Returning to Bristol, coding, the thrill of discovery and dinosaur memes

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Measuring skull traits

A morphospace plot. Each colour denotes a family. Triangles are Triassic taxa, squares are Permian taxa and the circle is a taxa which survived the PT extinction

I hadn’t done too much work during my trip in India. My aim was to start the measurements as soon as I arrived at the office. For this I needed to make sure I knew what traits I was going to record. So when I had some spare time in India, I refined the list of skull traits I had decided to measure. The big challenge was trying to understand where a certain measurement started and ended – e.g. the length of adductor muscle attachment on the mandible. To do this I had to read through the literature to see if there were any consistent points on the skull I could use to start and end my measurements. Unfortunately, I did not finish this during my time in India and had to carry on with it in Bristol.

Fortunately, this did not take up much of my time and I was able to get my supervisors up to date with my progress and start the measurements. This was a very tedious task. I was aiming to be done with the measurements by the end of the week but I soon found that was an underestimation. The trouble was that the skulls of anomodonts are not the same so the points of reference I was using for my measurements would sometimes be absent or not so clear. As a consequence, it took me a while to get used to recording the measurements. On average for each of the 148 species I had to measure 20 traits. Of course, some species had images that didn’t show a certain view of the skull or no specimen images at all. For these I had to miss out all or some of the measurements. Despite this it still took me a few days to get into a flow and in the end it I finished the measurements a week and a half later.

Coding

Finally we could start coding. I say ‘we’ because the coding required for the analysis was beyond my skillset. My supervisor, Suresh, was the man for this as he already had some coding from a prior project which we could use as a template for mine. Surprisingly, this was very exciting for me. I say surprisingly because coding is not one of my strengths but since I had Suresh to help me things were made much easier. And when the first morphospace diagrams loaded up the results were not disappointing. Before I could process the figures Armin and Suresh were going back and forth on what the figures could mean. I can’t pretend to know what they were discussing although I did get the general gist of what they were saying. To put it simply my results seemed to contradict Professor Benton’s hypothesis that the P-T extinction event created an anomodont bottleneck from which they never completely recovered. This thrilled my supervisors which I found quite funny because it reminded me of the reaction of when friends beat each other in a video game. In the end most palaeontologists do their job for the same reason someone may play a video game so perhaps such a reaction shouldn’t be surprising!

One of the more tamer memes from the facebook group

Dinosaur memes

This can be seen in simply what post-docs and PhD students talk about in their spare time. During this week, as part of the Benton lunch group we went to a nearby restaurant called Beerds where we ate some pizza. Most of the students there were involved in Palaeo. One, a published author named Vicky Coules was conducting research into Palaeoart. She has been blogging her experiences here. Therefore, a lot of the conversation was around how dinosaurs had been represented in the media. At certain points in this conversation, one student Steven Zhang started making statements as if he was quoting from something. The statements themselves weren’t strange but the manner in which he said them were peculiar. I looked at my supervisor Suresh and his expression was as though of a person who had heard a bad joke. He explained to me that Steven was repeating lines from the Walking with Dinosaur series. Although this was perhaps the nerdiest thing I had heard of (this coming from a big fan of the Walking with… series), I did find it funny. However this was only the start as Steven started showing everyone something on his phone which he clearly found hilarious. He showed it to me and low and behold there was something I never thought I would see. It was a ‘Walking with dinosaur…’ meme. In fact, it was a whole private facebook group dedicated to memeing the series. Again nerdy but funny and refreshing. I say refreshing because back at UCL I’m not friends with anyone that has the same fondness of the series as myself although I must say quoting lines from the series during lunch perhaps goes too far.

At the time of writing this I have joined the esteemed facebook group  and I can confirm the memes are as cringey and funny as they seemed when Steven showed them to me!

Week 6-10 My holiday in India – family visits, religion and culture

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My cousins getting a bit too excited before watching the Lion King

Prioritising family

Although I was relieved to be able to split my internship into two parts and still go on holiday, I was slightly disappointed that I would have little time at home in London during my summer because the plan was to return to Bristol after getting back to England.

Furthermore, holidays in India with my family aren’t completely relaxing for me. We normally visit India once every two years for 3-5 weeks with the sole intention to meet and spend time with family.  There are two main challenges with this. Firstly, in our culture we tend to stay in touch with more distant family members – some are so distant that I sometimes forget their relation to me. Secondly, as time has gone on these family members have become more dispersed within the country. Consequently, this means that we have to do a lot of travelling within a short space of time so we never stay in one place for more than a couple of days.

Despite this, I still very much enjoy going to India since its nice to be reminded that there are so many family members who care about my family and I, which is a sharp contrast to London where my family is limited to just my brother and parents. Hence, emotionally the trip is quite refreshing but physically the climate and the travelling can be quite taxing.

A pregnant and bored macaque in Bangalore

Within the 5 weeks I was there, I visited 6 places of which most are within the state of Tamil Nadu.  Chennai, Hyderabad, Bangalore and Thanjavur are probably the most well-known places I visited. Chennai is the capital of Tamil Nadu and had been in the news in recent years because of water shortages and flooding. Hyderabad and Bangalore are in a different state and have a much cooler climate than Chennai but like Chennai are big well developed cities. Thanjavur is also a city but not as well developed as Chennai. It is most famous for a 11th century temple constructed by RajaRaja – the emperor of the Chola empire and I have been fortunate enough to visit it several times. However, prioritising family visits means there is never much time for sightseeing.

Differing ways of life

Nevertheless, going to visit family in India over the years has allowed me to experience different ways of life. Of course it is impossible to ignore the poverty in India. Visiting India over the years I’ve seen much development in technology and infrastructure but I never seem to see the levels of poverty get any better despite what the statistics say.  Similarly, the state of public education seems to be on the decline with classes getting bigger and the number of teachers getting smaller. Even though hearing and observing such struggles are always difficult it has and continues to make me more grateful of my life in England especially through difficult times.

Differing attitudes

As a consequence, many of my relatives have different priorities when it comes to choosing a career. The stereotypical idea is that Indians want their children to be either one of two things – a Doctor or an engineer. If these aren’t possible then a career to do with computer or software engineering will suffice. To a great extent this stereotype is true. I believe this is because these jobs generally offer a good pay and for a people who have generally grown up without much wealth, like my parents, a good salary was desperately needed to support their family. Unfortunately, this attitude still exists among those who have obtained this necessary wealth. Hence, I still find it quite apprehensive to explain to my relatives what I study because I know invariably the next question would be ‘What job could that get you?’ followed reliably by the question ‘Will that be good pay?’ In academia, at least in the beginning, the pay is not proportionate to the working hours. So I know if I answer these questions honestly I’ll be met with disappointment.  It could be said that this could lead to an interesting conversation about how much we should pursue money in our lives and what is a happy and worthwhile life but I’m not sure how fruitful that conversation would be. On my part, I believe we should pursue money as much as it gives us ‘leisure with security’ (Bertrand Russell-Conquest of Happiness) and if the job I’m doing is something I find fun then I don’t think I would need much leisure to be happy.

The role of religion

At the RajaRaja temple in Thanjavur

Another obvious difference between London and India is the role of religion. From my experience, for the average person in London religion has almost no role in daily affairs but in India it does. Most of my family there are religious. Of course, some are more strict than others. When I was much younger I always wondered how some members of my family, could be firm atheists and get along so well with strict theists. In turns out there is nothing special to it. My Dad calls it ‘a matured theism and a cultured atheism’. He, along with his brothers, were brought with a ‘healthy theism and nourishing atheism’. They would be taken to temples, would sing religious songs and celebrate religious festivals despite their father being an atheist. This prevented their atheism from being blind to the attraction of religion such as its ability to give meaning to peoples lives. Likewise the religious members of my family are not blind in their belief and in some conversations have accepted the limitations in their religious systems. I believe it’s this humility and honesty combined with some common sense in practical affairs that has led to this tolerance. I’m not usually inclined to feel pride but I do feel proud of my family (both immediate and extended) on this matter. Something which I cannot say for India as a whole at this moment.

Who, who is God? You, me are God

This life is a penance, where Love is God

For the people who believe in God (theists), God is love

For the people who don’t (atheists) but preach goodness, love is their God

(Translated lyrics from a Tamil song called Anbe Sivam)

 

Week 5 – The stressful end to Part 1 of the internship

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Increasing pressure

For the first time, things were getting quite stressful. Originally the plan was that I would be finished with the image collection by the start of the final week so I could complete the measurements before I going to India. However, I had only collected half of the images I needed to. This was not because I was being lazy but more so to do with how I naturally work. I usually take my time with my work and when the task was to sift through seemingly hundreds of papers to find on average 5-6 images per species it took longer than I expected. Moreover, overtime the names of the species and specimen number can change so a paper in 1920 of a species could be different to the present day.

Dorsal views of the mandible were difficult to find

An additional problem was with the mandible. Most of the traits I would measure were related to the mandible but while I was collecting the images there were quite a few specimens that did not have a mandible. Particularly, a dorsal view of the mandible which was needed in order to measure the extent of propaliny.

I had to accept that I would not get onto the measurements during the final week so I told my supervisors about the delay and expected them to be worried that I would not finish my project. But to my surprise they accepted it without a problem and Professor Benton was even able to extend my internship to the end of September meaning I would have a few extra weeks after coming back from my holiday. This did ease my tensions and I was able to solve my concerns about propaliny measurements by consulting with Professor Rayfield who said I could use lateral views of mandible instead.

Many specimens like this Repelinosaurus were missing the mandible. Image taken from Olivier et al 2019

Problems with some skull traits

Nevertheless, mentally it was getting tiring. Spending long hours in front of a computer screen searching for images was starting to take its toll but fortunately I was getting quicker at it. And finally by the end of the week I had finished with my image collection but looking at the type of images I had collected made me realise certain traits could be a problem to measure.

For example, I thought calculating the mechanical advantage would be difficult since I could not figure out what references in the skull I could use to make the measurements needed for the calculation. This meant that during my holiday I had to look at the literature and see if I could find any features in the skull that I could use as a reference for the beginning and end for the measurements. However, I had another five weeks to do that so I wasn’t too worried and was ready to go on my holiday.

Week 4 – The Benton lunch group and Bristol zoo

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The tedious part of the project

Finally I was able to meet my supervisor, Suresh, who had been in the US for the past few weeks.  Fortunately, he had done a similar project but on a wider group of vertebrates so he had gone through a lot of anomodont skulls hence I was able to ask him some questions on measurements.

Week 4 consisted mostly of me collecting images for the near 150 species  of anomodonts. This was a tedious task but I understood that this was all part of science. Since the task did not require deep thought, I was able to listen to a few audiobooks to help me get through the boredom.

Fortunately, there were also a few social events to keep me entertained. We had another tea and cakes social. This time more people showed up and I found out that I was the only intern being paid. One intern I met had come from Italy and was trying to find another place to stay. He had taken up a job at a Chinese restaurant to pay for his private accommodation. Realising how fortunate I was made me more determined to stay diligent with my project since I felt the boredom from the task was a small problem compared to the difficulties other interns were facing.

Benton Lunch group

In addition to the tea and cakes that week, on Thursday I was invited to the Benton lunch group. Although any graduate student could join, the group consisted mostly of Professor Benton and the students he was supervising. Even during our lunch most of the conversations were about Palaeontology but it was interesting to hear what the other students were up to. One student was being supervised by Dr Adrian Lister to do a project on Mammoths. Apart from that, a good portion of the conversation was akin to academic gossip where we talked about other Palaeontologists.

Bristol zoo

But overall the whole week was uneventful in terms of work. However, I still had the weekend to look forward to. It was my birthday on Saturday and my parents, from London, and I planned to go to Bristol zoo. If possible, I recommend going to the Zoo. Its the world’s oldest provincial zoo. Its has a few stand out features including the twilight zone where they had the aye aye which many other zoos don’t have. Although it was nice to see a few extant animals for a change, I had to get back to my airbnb on Sunday as there was still a lot more measurements to be done and only a week left to do them.