Sunday, 17 June 2018

SF Science Exam Results

My second year exam results came out two days ago (Friday) during work, meaning I got very little work done that day. I was very very nervous about results -- worried about failing Chemistry and about getting a 2.1 or 2.2 that would leave me unsure about whether I'd get into Genetics.

Luckily, things went a lot better than I'd been expecting! My overall overall result was 86% which is a high first.

The highlights for me were:

  • high first overall
  • a first in every module
  • a first in every exam
  • getting high firsts even in the exams for essay subjects
  • not failing Chemistry
  • getting 100% in the Multivariable Calculus exam


Chemistry: 58%*
Cell Structure: 80%
Metabolism: 80%
Evolution: 65%
Microbiology: 80% (was very doubtful about this one)
Ecology: 65%
Behaviour: 65%
Genetics: 80%
Immunology: 80%
Multivariable Calculus: 97%
Statistics: 92%

Green highlight = prediction was lower than result
Orange highlight = prediction was higher than result

Results: (black bar shows First line)

I made these nice graphs using R and ggplot2.

Overall  Grade
Cell Structure
Multivariable Calculus

Genetics, weirdly enough as it's my chosen specialisation, is the only one where I did worse than I predicted (I predicted 80% and got 79%). Bit worrying but it's still a fairly good grade.

*After the exam I calculated this three ways: ‘Realistically but Conservative’, ‘Optimistically’, and ‘Negatively’ (the last one to see if I was likely to fail). I came up with 58, 71 and 51 respectively. Even my optimistic one, which I thought was far too optimistic, turned out not to be optimistic enough.

I got the same mark overall in my scariest subject (Chemistry) as my chosen moderatorship subject (Genetics), and even did worse in the exam in Genetics. To be fair, Genetics is an essay subject so they mark harder, but still disappointing from the Genetics perspective but great from the Chemistry perspective. Also, I did well in Evolution and that's an important part of Sophister Genetics. I was also disappointed in my Metabolism mark; I only got 79 in the Metabolism exam after using a Metabolism essay to get Schols back at Christmas, so I don’t know what happened there.

I’m not sure how good my grade is compared to the rest of the Genetics applicants; I know there’s a prize for the Genetics students who do well but I’m not sure if that’s for doing well overall or in Genetics and I didn’t do that well in Genetics, but maybe 79 would rank high, I don’t know.

I was very happy with my marks overall - 86 is a good mark, and there were some very nice surprises - especially in Chemistry, but also in Evolution, Behaviour, Microbiology and Stats. I was really impressed to have gotten grades above 90 in an essay exam, as happened in Cell Structure & Function and Evolution. There were definitely some shenanigans with Behaviour - my CA mark was 62% when the provisional marks were released but 95.3% by the time the final results came out, which is odd. 

I tried to do something I saw the Biology admin do at the start of the year, find the correlation between CA and Exam result for each of my exams, but that didn't really work with my marks; they were too clustered near the top I think, and once I restricted the bounds there was only a very small correlation of about 0.12. So I guess it works better applied to the whole class, maybe with a wider range of results. 

It was super cool to get 100% in one of my exams, Multivariable Calculus; especially after getting 56% and 59% in my maths exams last year, getting 100% and 93% is pretty cool. Learning! Improvement! Overall, my grade went up 24 points from last year to this year, from 62% to 86%. I'm proud of that. 

It was partly because I moved into a subject I like, and partly because I changed how I approached college and started sitting up front, asking questions, taking notes and writing them up right after the lecture. I'm proud of myself, and it also feels very satisfying because the college admin wouldn't let me move into 2nd year biology with no 1st year or Leaving Cert biology (I had to get the Students Union to argue my case, thank you Alice, but I worked hard like I said I would and did it and got Schols and a high first in the summer exams. A year of continuous hard work later I can finally relax. I did it!!!

Laidlaw Scholars Leadership Weekend 1

The first Laidlaw Scholars Leadership Weekend took place in Trinity on 8th and 9th June, with the 18 Laidlaw Scholars, Joel and Orla who run the show, and a collection of invited speakers and facilitators to run sessions. The Laidlaw Scholarship is a Research and Leadership Development programme that runs for two years teaching us how to lead and pays for us to do research projects over the summer.

I was really impressed with the weekend. In previous things I've been to, a lot of the advice would be stuff I already knew or not very useful, but I thought this stuff was good and they'd clearly put thought into it. Like Beth, I definitely prioritise the research aspect, but the leadership weekend very much seemed worthwhile. 

They also somehow managed to make this a really trusting environment in the space of two days - people were super open by the end of it and shared our thoughts with each other really easily; it was especially clear when hanging out with people afterwards, and I loved that. Maybe I shouldn't be surprised since they said from the outset that they wanted to do that, but they were really successful at it. It also helps that I know some of the Laidlaw Scholars from my other scholarships, so some are Scholars (of Trinity) and some are Naughton Scholars (I should make a Venn diagram of this), so I can see them there too. The Scholars are great, as I say below; they all seem super interesting.

Day 1: Friday

0900: Intro session: Joel and Orla told us about the weekend and taught us some leadership terms with examples of mission statements from various companies and institutions.

1000: Team building: We got into groups of 3 (carefully arranged so there was one girl in each group, as there are 12 guys and only 6 girls, or Laidlies as we've taken to calling ourselves) and did a really cool teambuilding challenge called 'SURVIVAL ON THE MOON', where you pretend you've crashlanded on the moon and need to either make it to an outpost 80 km away or stay put until you're found, and have to prioritise the items you'll take with you from a list of 15 (e.g. oxygen, water, food, liferaft, space blanket, map, compass, spacesuit repair kit). It was a cool challenge, one I hadn't seen before even though I've done a fair few bootcamps so I was very glad of that and especially glad it wasn't the Marshmallow challenge which seems to be a mainstay of these events.

Joel was funny; he said something like 'you've got the description there in front of you, but I'll read it through with you for dramatic effect.'

1100: Photos: Photoshoot time. Here's the photo they took of all of us:

1145: Research and Leadership in the Arts and Humanities: We went over to the Arts side of campus and Prof. Jane Ohlmeyer, Director of the Long Room Hub and Professor of Modern History talked to us about her experience through her career in research and administration and then invited us to ask questions. I asked about how research in the humanities compares to research in the sciences, for one. 

Something interesting she talked about was her work to digitise the 1641 depositions which are apparently very important but controversial documents about ethnic cleansing in Ireland, that she said Protestants have been using propagandistically for 300 years, and that she managed to get the UK government to pay loads of money for it by saying it was important for Anglo-Irish relations. In her answers to the questions she talked about a bunch of things like the high employability of arts graduates (but not in their field, so for example classicists get hired in financial, strategy and law sectors, ethicists needed for ICT and pharma), the number of international students vs the number of Irish people who don't get in, problems that can arise in teams, how Sofia is brilliant for maths because it was the tech hub of the Soviet Union, and how law and medicine shouldn't be undergraduate degrees.

We then had a tour of the Long Room Hub, which is a research institute for the arts and humanities.

1300: Lunch: We had lunch in the Science Gallery cafe and chatted.

1400: Research and Leadership in Engineering and Science: We had a lecture from AMBER (Advanced Materials and BioEngineering Research) about what they do. The presentation just seemed to be their pitch to investors since it was very slick and very much about their impact and metrics, so I'm not sure why it was shown to us - I'm not sure what we were to gain from seeing how many European Research Council Starter and Consolidator grants they have. They also pitched Trinity a bit which again was weird since we already go there. A second guy then spoke and talked about his job as a liaison with industry -- it was quite interesting to hear about how the process works and the sort of projects they're working on. I accidentally went full socialist by saying 'What if they just nationalised the pharma companies?' during the discussion. That side of me came out quite a bit during the weekend for some reason! It was interesting to hear about things like additive manufacturing and also upcoming projects with companies that I won't blog about just in case, although hopefully they wouldn't have told us anything confidential...

The second guy said that while doing his postdoc he somehow became President of the Singaporean National PostDoc Society because despite being shy for Ireland he wasn't considered that over there, and also that 99.5% of people who go in looking for academic jobs won't get one.
  • We then went on a tour of the place and that was quite cool, seeing what they're working on.
1530: Leadership Development Plans and Reflective Practice as a tool for self-development

I was not a fan of this session. We were given Post-It notes at the start and told to write one sentence starting with 'I' about what we wanted to get out of the session. The speaker refused to explain more so I just read the title of the session and said 'I want to learn how to begin a Leadership Development Plan' but when I read that out she said we wouldn't be covering that and when I said the words 'Leadership Development Plan' were literally in the title of the session on our timetable she didn't seem to get what I was saying or ignored it and it was very frustrating. The session just ended up being about reflection and I didn't like it at all; she talked about Bloom's Taxonomy of Learning as applied to the practices of being a student, where the first level, remembering, became 'did I remember the due date of that assignment to submit it?'. It seemed pretty useless and like a distinction without a difference. She also talked about reflection and different levels of describing/reflecting on something: 'Descriptive writing', 'Descriptive reflection', 'Dialogic reflection', 'Critical Reflection' with an example of describing walking the dog:
    • Descriptive writing: "I took the dog for a walk."
    • Descriptive reflection: "I took the dog for a walk and he trotted along beside me, wagging his tail." - apparently this shows 'evidence of deeper consideration'?
    • Dialogic reflection - "I took the dog for a walk and, as he seemed to enjoy and benefit from the walk, I will walk him more often" - this is fine I guess but I don't see what's special about it
    • Critical reflection - "I took the dog for a walk and it was obvious that the activity and fresh air is good for both the dog and I. His good nature reminded me that a reason I have a dog is for companionship ... so our daily walk is now on my 'to do' list." - this just seems like a far more verbose way of saying #3. Yes, they're now thinking about their own enjoyment of it too but it really seems to have been blown up into a bigger deal than it is and I don't see why they've formalised it like this. And I like reflection, that's why almost this whole blog is made up of reviews.
There was one thing I did take from it, which was the idea of being intentional about things; before sessions at conferences and things, think 'What do I want to get out of this?' and be deliberate about it. That seems like something i might do.

She also talked about how there are both conscious and unconscious competencies and incompetencies, and you can only identify the conscious ones by yourself so you need to use peer review.

She said that taking another's perspective is a very important attribute of a good leader, which was a bit problematic for the multiple autistic scholars there. Weird to say that if you're not going to offer alternative strategies for doing it to people who can't do it the usual way. 

1615: Building Your Networking Skills (How to Network without Cringing): 

Sinead English from Hilt Career Services talked to us about how to network, even for introverts. The session was mostly about informational interviews - it was described well and was useful information. I happened to pretty much know it already because I've picked it up slowly through experience over the last few years, but it was a good session and I can definitely see it being useful to someone who hadn't done it before. There were also a couple of new bits.

She had an interesting pyramid showing what employers do to fill vacancies in their company, starting with looking to promote or move someone within the company, then asking those employees for recommendations if there's no one to promote, then other things and then penultimately using jobs agencies and at the very end posting the job publicly. Apparently sometimes existing employees get paid if they suggest someone who then gets hired? She said that 30% of jobs are advertised. It seems a bit unfair honestly. I can see why you'd trust your employees' opinions of who might be good for the job but it definitely makes it hard for new people to get in and I don't think your chance of getting a job, especially one that doesn't really depend on people skills to a huge extent, should rely on being able to network. 

A nice quote on why you should be intentional about what you'll get out of going to a conference: 'There's easier ways to get a new pen'.

I also really liked how practical the session was; she talked a bit about the theory, which was fine, but did also give us tons of actionable tips so that was good.

Photo creds to Aaron.
Day 2: Saturday

1000: Elevator Pitches 

We spent an hour learning about elevator pitches and then coming up with our own. I thought we'd be doing it about ourselves but the way we actually did it was fun; we had to come up with an elevator pitch for a well-known company. Some groups did Hodges Figgis, Centra chicken rolls, and bottled water, and mine did Lego. 

I did the actual speaking and got grilled with questions like 'You said Lego has sold over 600 billion bricks. How do you justify the environmental impact of all that plastic?' and 'Is it possible to make it less painful to step on while still sticking together?' and 'How do you justify selling toy guns in your sets?', to which I replied something like 'We don't care about the environment, next', 'Nope, next', and 'We're actually sponsored by the NRA ... but good question and I actually don't support that'. So I guess there's a reason I'm not a company spokesperson! 

Also got an interesting question about why Lego doesn't expand to the digital space and I said it's important that we help kids develop manual dexterity (that said, they do actually have digital things like movies and video games but I had forgotten that). A lot of the pitches were really entertaining and people definitely got grilled. I love the Laidlaw Scholars, they all seem really smart/incisive/confident.

(Also, I was pretty proud of our pitch to be honest. Wasn't bad for having had a few minutes to prepare it.)

1100: Discovering your Personal Leadership Style

This was a pretty interesting 2-hour session on leadership vs management and the skills both require and when each is needed, the types of leaders (there are 6 apparently, including Commander, Affiliative, Pace-Setting, Coaching, Democratic and Visionary), and values. The Coach style seemed super interesting and is apparently about always trying to develop your people and help them grow (even if that's outside the organisation). I must say, the guy's slides were very fancy, and I liked the faces of each leadershpi style. He said democratic style is about managing expectations since you solicit opinions but aren't always going to follow them; visionary is about describing a future authoritatively; commander can be about being scary but can also be, when there's a crisis and no one knows what to do, stepping in and saying 'ok this is what we're doing, you take that side, you do this, I'll do this' and assuming that authority to sort of the problem, so it works better in the sort term; coaching is about noticing and conversations; and pace-setting just starts and doesn't really explain, and people tend to burn out after a while. The styles are best in combination.

The speaker described leadership as being about stepping into crisis, taking initiative, and going out to face the music. When going between management and leadership, it's important to be able to think 'Is this business as usual or is something different?'. 

It reminded me of that book I read a while back, Behave by Robert Sapolsky, about how weird it is that humans actually choose our leaders often (e.g. by elections).

Tidbits: apparently Anna Wintour is known as 'nuclear winter' in the industry; the iPad was ready before the iPhone. 

We were asked to think about how to define purpose, and that did make me think about how the words used for these things can be a bit ambiguous; my partner and I agreed that 'purpose' and 'vision' can be very interchangeable. An interesting question he gave us was 'If I was in a leadership position, how would my personal purpose show?' - purpose isn't just something internal, it should show through in some way. 

Tidbit: apparently IBM, 70 years after they started, having never laid off an employee, laid off 110,000 employees in a summer.

My socialist (or even just honesty-loving) side came out again in the 'values' part when I said I hate when for-profit companies publicise their values because clearly their main goal is money and as for-profit companies they will always prioritise that so it feels disingenuous to then say all these lovely things post-hoc when those aren't actually what you mean. 

That stimulated a lot of discussion (was quite scary to see all the hands shoot up!) and I do agree with some of the points people made, like that values are good as a signal of 'lines we won't cross' in pursuit of profit, but I still think far too many of the publicised values are post-hoc and not actually important to the company but just for PR purposes. Also, to be clear I'm using a fairly broad definition of 'non-profit' (which I think is fine to publicise values for) - they can make money, and their staff can be paid to do the work, but they should put excess money beyond a decent wage (which yeah can be difficult to define exactly) back into the work.

1300: Lunch

We had lunch in the same room in the Careers Service. I talked to Orla, the Director, and found out she has a very cool academic background. They did have vegetarian food, although it was largely leaves which was odd.

1400: Guest Laidlaw Scholar Beth from University of St. Andrews

Beth is an outgoing Laidlaw Scholar from a college with an established Laidlaw programme. She talked to us about her research (medical - palliative care I think) experience and how to make the most of the programme. She seemed cool and spoke well. A funny part was how she said originally she just wanted to get paid to do research and figured she'd just go along with the leadership part to get the research part, and Orla said 'I'm sure nobody here is like that...'. But Beth said that the leadership part did turn out to be good and that's been my experience too so far.

1430: Vocal Coaching Workshop with Cathal Quinn from The Lir

Our last session was a three-hour session with an actor from the Lir on public speaking. He starting by going around and asking each of us how many presentations we'd given before; most people said a few and then well I mean I wasn't gonna lie was I, so I said about 20. Which immediately drew attention to me. I thought I made some good suggestions for public speaking and so did a bunch of other people, which was cool. We did a lot of different things, from breathing exercises (have you ever been criticised on your breathing? it's an odd experience) to learning to project. We had one guy who spoke super quietly be gradually coached to get louder and honestly I felt so proud when he did in the end. We're friends now so that's cool. 

Cathal told us that a good idea is to take the work seriously and ourselves less so. One of the other scholars, Conor, said something helpful, which was to go through your presentation beforehand and mock it yourself in a safe environment maybe with friends, to see what's the worst that can happen and inoculate yourself against embarrassment.

Tidbit: apparently politicians speak past the ends of their sentences and are trained to become uninterruptible, i.e. saying phrases to get them past the expected full stop and into a new sentence without every officially ending their old one.


After the official programme had ended, we went to sit outside the Pav in the sun. Normally I'd have turned down that sort of invitation during the year as I was constantly studying, but I went and it was lovely - I finally felt like a real college student. I talked a lot to Sean, Luke and Mollie for about 4 hours. Such a good time.

Me, Luke, Mollie.

Also, just under a week after the Leadership Weekend, a group of us went out together to eat at the EatYard so yeah we've definitely bonded. Here are some pictures from there:

A nice candid photo taken by Luke.

Sunday, 10 June 2018

SF Behaviour

Really disliked this module, especially when exam time neared. I'd been excited to study it but there ended up being a ton of psychology which it turns out I don't like, and I couldn't really see the point to the whole thing. Like sure we can find this stuff out but why does it matter? I'm sure it matters to some people but personally I couldn't see the appeal with a lot of the course. It was fun during the actual lectures usually as the lecturer is very good, but the actual material did seem kinda pointless when I was studying it, though I did like the Conservation stuff. We were told Behaviour is like Evolution II but it seemed nowhere near as logical and cool. Learning about learning was also weirdly meta. The exam was also VERY MEAN DAMN DUDES.

Section 1: Psychology

  • the 'three kings' of ethology (Niko Tinbergen, Konrad Lorenz, Karl von Frisch)
  • learning
  • memory
  • cultural transmission - animals sharing information e.g. which foods are dangerous, which animals are scary, where to find food
  • imitation and what can be mistaken for it - this was a good example of what frustrated me about the course; we had to learn all the things that can be mistaken for imitation like emulation, stimulus enhancement, social facilitation, instrumental learning, and contagion, and honestly I was like so what if they're mistaken for it? It seemed like a bit of a distinction without a difference.
  • theory of mind & levels of intentionality - trying to figure out whether animals have theory of mind 
  • animal personalities and strategies
  • play - how we define it and how it happens - this lecture was actually tortuous because it turns out learning about play while being bored is awful. It was a long list of possible reasons play evolved and I mean long. It just felt weird to be academically studying play, though of course it is important to understand it for, say, teachers.
  • navigation - how animals get around, including simple rules to stay in environment, dead reckoning, compasses, maps, 'true navigation'

I disliked what seemed like an obsession with 'trueness' in animal behaviour, like 'true imitation' (not being one of the 5 things that can be mistaken for it) and 'true navigation' (knowing where you are without knowing how you got there, which admittedly is cool). 
obsession with trueness. It seemed like a lot of researchers arguing over whether an animal's behaviour is 'authentic' enough and yeah I guess I just didn't really care.

I joked about there being a slide on memes to my friends in physics but really I didn't like it, it felt a bit pointless. Interesting to discuss, sure, but weird in an actual module I guess. Glad I didn't do Arts!

Section 2: Special Lectures

These were an unusual addition to the course, and I appreciated the idea even if I didn't love all the guest lectures.

  • Neurobiology of behaviour
    • maybe my main issue is with how this is examined -- why do I need to know the number of neurons in Aplysia californica (it's 20,000 if I recall correctly)? Having to memorize that sort of fact was a hallmark of the Behaviour course that I didn't like at all. 
  • Parasitology 
    • quite interesting but some very gross examples
  • Hormones and behaviour 
    • I missed this one and unfortunately the slides didn't have much information but it seemed a bit weird, from defining what a hormone was to just giving random examples of hormones and behaviour so like 'corticosterone decreases amplexus [mating] in frogs whereas vasotocin increases it'. I think this lecture also had the Rhythms section about circadian, lunar, monthly and yearly rhythms, which came up as a full question on the exam and was exceedingly difficult to answer as it would say 'which type of rhythm would X animal doing Y activity have?' and there were like 10 animals and I didn't even know what kind of animal some of them were
  • Collective Behaviour
    • this was actually great, I loved it. It was about computer modelling of collective patterns like those of starlings flying, using rules about width of orientation zone, repulsion zone and attraction zone and getting a swarm, torus or directed shoal depending on width of orientation zone. Also stuff about how increasing your zone of repulsion gets you to the back of the group and how larger groups need a smaller proportion of leaders to set direction. In general it was about how you can get complex collective behaviours from small-scale local interactions and self-organisation rather than overall leadership.

Section 3: Conservation

  • Behaviour in Conservation 
    • how ethologists are useful in conservation e.g. finding accurate ways to count populations, dealing with the Allee effect on small populations, and trying to bring species back from the brink (like the kakapo, for which ethologists and biochemists worked together to synthesise the active ingredient from the rimu fruit, which made the kakapo want to breed but only fruited every few years, and to keep them strong while making sure they gave birth to females using evolutionary theory (they'd give birth to boys while well fed)).
  • Zoos and Conservation
    • problems captive animals face such as incorrect imprinting, stress, boredom and stereotypies, not learning to hunt or fear predators or move around correctly in the environment (apparently a load of monkeys or lemurs or something were released from captivity into the wild and then died because due to their steady structures in the zoo, they hadn't learned how to balance in trees and fell out), and zoos potentially favouring certain personalities.
  • Behaviour and Climate Change
    • climate change can throw everything out of sync; insects may be born before bud burst and starve, or at the wrong time for bird chicks to eat them, or birds may have trouble timing their migration so there'll be food at stopover points because different parts of the world are changing at different rates. 


  • zoo practical - had to go to zoo and observe various animal signals
  • collective behaviour - we all had to go to the gym and walk around in a crowd while being directed by the lecturer, then he showed us the video of it to illustrate points
  • David Attenborough videos - four videos on behaviour with quizzes (such long quizzes, like 40 questions each! I think)


I am glad the exam was all short questions as I had enough extra reading to do without having to do it for this course too, but wow the questions were mean. One this year, in the parasitology question, was 'Which African country had the highest [basic reproductive rate] of ebola in the recent outbreak?' which was at the bottom of a random slide. I don't see how that tests understanding of the material, which should surely be the point. Another was about climate change and conservation - we'd done an example in class of how increasing carbon dioxide leads to nitrogen starvation in leaves and the insects on those leaves actually cause more damage because they need to eat more to survive, and one of the questions was about specifically what type of bug it was, which doesn't seem much to do with understanding the principle and seems a lot to do with remembering the exact word on the slide. Would've been fine to ask 'what happens if you do this' or 'what do you think might happen if x changed' but this seemed a bit pointless. 

The exam was also stressful because a lot of it was 'pick the letter that goes with this number' and even though I checked a lot I'm scared I just put in the wrong letter even though I knew the answer and got everything wrong.

I'm also salty because I forgot to do a part of the CA, I just didn't realise that assignment existed, and did poorly in CA :( But I think my points still stand. There were definitely some interesting parts, but there was too much memorization, I didn't like the exam's method of assessment, and psychology is not my thing.

SF Microbiology

This was a second-semester module, as was Genetics, but sure who cares about order anyway.

I really didn't like this course while I was doing it and found it difficult, but once I had some time to study it from textbooks etc. I grew to like some parts of it, especially Genetic Switches and Viruses and that one Fungi topic on drug targets, and Bacterial Surface Structures weren't too bad albeit a bit boring. I ended up enjoying that it wasn't too focused on pathogenicity (Genetic Switches, for example, basically seems to study the systems because they're interesting on their own terms), and I found the superbugs parts some of the most boring, weirdly enough.

 The exam treated me well as I got that one nice Fungi question, and nice Genetic Switches and Viruses questions, so I hope I did decently. After studying and doing essay plans I felt a lot more prepared and happier with it, though to be fair I think that might be because I'd found it so hard, as I then set aside a disproportionate number of study days for it during the study period.

Here is a nice poster I made summarising the module:


Week 1: Bacterial Surface Structures

  • Bacterial Cells & Cell Division
  • Gram-positive and -negative cell envelopes
  • flagella, capsules, slime layers, extracellular polysaccharides, pili
  • peptidoglycan synthesis

Week 2: Toxins & Pathogens

  • Bacterial protein exotoxins
  • Hospital superbugs
  • Community-acquired infections
  • Respiratory infections
This one was pretty awful; the last three lectures involved just a list of different bacteria essentially and their characteristics, without much in terms of underlying principles. I did not do this part for the exam though I did try study it a bit because I wasn't gonna try learn the gram status, shape, (an)aerobic, method of spread, virulence factors (the most interesting part to be fair), motility and envelope properties of a bajillion different bacteria. 

The toxins lecture was fairly interesting though, and I learned why Clostridium tetani (tetanus) and Clostridium botulinum (Botulism and Botox) have opposite effects.

Week 3: Viruses

  • Diversity of viruses
  • virus replication cycle part 1: attachment & entry
  • virus replication cycle part 2: genome replication, protein synthesis, exit
  • viruses and preventing disease e.g. antivirals, vaccines, contact tracing, safe burials
This one was quite cool I will admit. We focused on influenza, polio, HIV and Varicella Zoster Virus and I also did some extra reading in Principles of Virology and managed to get that into my exam essay.

Week 4: Fungi

The first of these 4 lectures didn't go ahead so I'll strike that one out.

  • the fungal world: the good, the bad and the ugly
  • yeasts and their life cycles
  • introduction to yeast genetics
  • mating type switching in yeasts
Unfortunately I only went to the first one as 1) it was very gross, we were shown very graphic pictures of fungal infections in very gross places 2) (the main reason) the lecturer said that without extra reading you'd get a 2.2 and when I asked how we were supposed to have time to do so much extra reading on top of all our other modules and learning the (already difficult) course material, she replied dismissively which was upsetting because I was already stressed and burned-out from Schols and I was working hard. She also told me there were marking rubrics available for the Biology modules but when I went to the science course office and asked about them they said they didn't exist. I decided to not go to the remaining two lectures and just focus on the other sections of the course where I figured I could do better. Prioritising is important. Sometimes I feel like I should go to everything just to have gone but in that sort of situation there's not much point going to something if I'm not going to have time to actually study it properly and could put that effort to more use in another part of the course.

On the bright side, the first lecture had the 'fungal drug targets' part, which I learned well, and that came up beautifully in the exam so i won't complain on that front.

Week 5: Genetic Switches

  • the lambda phage lysis/lysogeny switch
  • the pap pili switch
  • the fim fimbriae switch
  • the P1 plasmid/phage and phage mu, and integrases vs invertases
I was totally bewildered by this course at first and it didn't help that the lecturer put almost no words on a fair amount of his slides so I couldn't make it up after the lecture. It turned out that they're just fairly complicated systems but actually really interesting, once I found a way to get the information after the lecture. For the lambda switch he'd recommended a book chapter called Phage Strategies from Genes X, which turned out to be perfect as it covered the topic in great depth and methodically, so I could understand it and even maybe get a little bit of extra information to throw in for my exam essay. For pap and fim I went through his slides (thankfully they had a bit more words) and read some papers to connect the gaps. It turned out that this (pap specifically I think?) is his research topic so I read a good few of his papers and also took some juicy facts from them to put in essays since might be good to cite his papers. Sadly pap didn't come up in the exam so I couldn't use it, but I preferred the lambda material anyway so I was happy to write about that.


We had 5 3-hour labs, one a week.
  • yeasts and moulds (looking at them under the microscope mostly)
  • yeasts (sampling our mouths and growing them)
  • various bacteria (again sampling our mouths and trying to grow things like S. aureus and Lactobacillus
  • observing things like bacterial swarming and doing the hanging drop test to test for motility
  • looking at viral plaques and using different methods to ID bacteria
In a personal triumph, I did manage to figure out how to use the microscope and focus it at 40x magnification, though I never did really manage to keep it focused at 100x with the oil lens. We did a ton of Gram testing throughout and I ended up with crystal violet stained on my finger for a few days after one of the labs. We were given 2% for presence in each lab and doing a worksheet, and then 15% (overall) from an MCQ at the end that was quite hard, much harder in my opinion than the Genetics one, to add up to 25% overall from CA.

Thursday, 7 June 2018

SF Genetics


Week 1: Molecular Genetics

  • DNA structure
  • DNA replication
  • RNA & transcription
  • Translation
I find this subject boring but I did really like how much experimental evidence the lectures included, and I actually ended up answering this question in the exam as one of my two essays.

Week 2: Genetic Engineering

  • Deciphering the genetic code (discovery of a continuous triplet code and matching amino acids to codons)
  • Recombinant DNA and PCR
  • Genomics and Transcriptomics
  • Genetics and Biotechnology (e.g. Bt insecticides, synthetic artemisinin against malaria, EPSP synthase inhibitors and genetically altered plants that can withstand them). 
The first lecture was interesting but unfortunately I missed it for some reason, and the slides for the other lectures were quite hard to follow. I think it is an interesting subject in general but I didn't love it here. 

Week 3: Mendelian Disorders

I was super excited about this week and ended up getting on well with the lecturer when I started talking to Aoife and at the Scholars' Dinner because I became a Scholar and he became a Fellor on the same day. Unfortunately I couldn't answer his question in the exam because I ended up studying a load of random extra stuff but neglecting significant parts of his lectures. I did write out the slides of course, but I didn't know them well enough to be happy with an essay on them so I didn't choose that one.

(I really love this photo. It's SO Hogwarts-y, with the feast, great hall, and gowns and hats that sort of look like wizard hats in this light. Trinity Monday was a fab day.)
  • Mendelian Genetics & Recombination
  • Mapping Mendelian Traits (linkage analysis, GWAS)
  • Genetics of mendelian diseases - autosomal dominant and recessive, and X-linked recessive
  • Quantitative genetics/heritability
  • Genetics of common diseases e.g. breast cancer
Week 4: Cancer

This was my favourite as I find cancer genetics really fascinating and I ended up doing a lot of extra reading on this (there was a good chapter on it in Lodish's Molecular Cell Biology and some other textbooks). It didn't really split evenly into four lectures though.

  • Cancer in general, mutations and the tissues cancer is most likely to originate in
  • Cancer as a multi-step process - the process of transformation e.g. overcoming the Hayflick limit and the limiting factors on cancer development, cancer being monoclonal (super interesting that this was discovered partly by looking at B cell cancers which would be unique because B cells produce unique antibodies), and the discovery of viral origins of cancer and v-Src
  • oncogenes like Ras and Raf
  • tumour suppressor genes like p53
Week 5: Genetic Regulation

This was a weird sort of module -- I guess I was expecting it to be more like metabolic regulation. But once I went home and studied the stuff in Lehninger I did quite like the genetic regulation stuff, and the genetic regulation week we did in Microbiology as well. 

  • The lac operon -- this was cool but it did have a ton from Jacob and Monod's experimental notebooks, which was cool but difficult to understand
  • Control of gene expression in eukaryotes -- unfortunately found this quite boring with the whole chromatin aspect, but might not be as bad if we dive into it, I think i just don't like the shallow-but-wide survey of things
  • Control of mRNA localisation and translation, and 3' UTRs (+ a lot of stuff about hox genes)
  • Control of mRNA splicing, sexual behaviour in Drosophila (fruit flies - we learned about gay flies), and master regulators

The funny thing is that while I am dying to get into Genetics, I actually didn't enjoy the Genetics module that much, although I did really like the cancer section and I found a lot of the extra reading I did really interesting. But I think I'll like the subject as a whole, especially since I really liked Evolution and sophister Genetics has a fair bit of evolution in it, and to be fair I was SUPER burnt out after Schols so that might've contributed to me not enjoying my second semester subjects as much. 


We had a lab each week. These included:

  • extracting our DNA and using PCR and gel electrophoresis to genotype ourselves for the PTC tasting gene, and comparing that to our phenotype (actually licking some). I'm a heterozygous Taster. I was originally worried it'd be ambiguous, like hmm does this actually taste bitter or is it just the taste of paper but OH BOY IT IS CLEAR. 
  • really cool Bioinformatics practical where we looked around an NCBI database at the taster gene and similar genes and had to answer lots of lovely thinky questions like 'how might these genes have evolved' (gene duplication) and looking at differences between human and chimp(?) sequences for the gene to see why chimps can't taste it (they don't have three mutations in the gene like us iirc, they're missing a start codon for the taste receptor protein).
  • looking at gene expression in plants under the microscope and finding that for example a gene involved in root development is, y'know, expressed in the roots
  • getting E. coli to take up an antibiotic resistance plasmid and express Green Fluorescent Protein (the antibiotic resistance so that we could grow them on rifampicin plates and make sure only successfully transformed ones grew, and GFP we could look at in UV light and see them looking all cool and green). 
  • do RT-PCR and look at whether actin and creatine kinase are expressed in brain/lung/skeletal muscle.

I really liked the labs because I learned a lot and they were generally interesting, and I felt they complemented the course well without overlapping too much. The assessment did annoy me though; it was by two lab reports and an MCQ, and while the MCQ was good, I was marked really badly in the lab reports - 61% in the first, because I wrote very concisely what we were told to (since they said to write concisely), and 79% in the second when I wrote tons and tons (of good quality I think). I feel like I wasn't supposed to take them literally? But I didn't know that. So then I ended up with only 85% in CA which is annoying but decent enough I guess.

Overall, it was a pretty interesting module though not my favourite, but I think the subject has potential especially when combined with Evolution and more coding, so I really hope I get into sophister Genetics!