Saturday, 26 May 2018

Review: February 2018

Very long time no see but here I am since exams are finally over, to record what little I can remember of the past few months. 

COLLEGE: In February I had 4 modules going on: Genetics, Microbiology, Behaviour and Statistics. I really liked some parts of Genetics and wasn't as interested in others, didn't like Microbiology at all, found Behaviour OK but sometimes boring, and loved the idea of Statistics but definitely did not like the way it was taught as our questions weren't answered and the lectures and homeworks were very theoretical whereas the exam was quite practical and seemed very different to the lecture material. Anyway, I'll have a post up on each module in a bit.

STUDY: I was doing a bit of study for the exams by this point and made an Excel spreadsheet with my plan to do a chapter of extra reading from some textbook each night up to exams (I ended up sticking to it quite well). Unfortunately because of Schols and getting straight back into studying I never really got a break and was quite burnt out and unhappy through second semester.  

SUMMER JOB: I was really trying to sort out my summer job by this point. Ideally I wanted to do research but I at least needed to get something because y'know, I gotta eat and have accommodation. I reapplied to work where I worked last summer, and made a long list of pharma companies to ring to apply to. I also emailed Trinity Careers service asking them to put me in touch with one nearby company that only interacts with students through their Careers service, but they were unhelpful and just said Trinity doesn't do that. Another email was to the Senior Tutor asking what to do since some jobs wanted a letter from my college tutor but my one said she doesn't write recommendation letters, her job is just to get me through college, and didn't get a reply. 

BUT things ended up great on the summer job front overall -- I'd been put in touch with Prof. Aoife McLysaght, a very awesome genetics professor in Trinity, by Dr. Shane Bergin who I know from conferences and things, back in November, and we'd arranged to meet in February. I was super scared of the meeting as I thought it'd be typical businessy interview questions like 'talk about a time you solved a problem' or 'tell me why I should hire you' which I find really difficult and nervewracking, but it was brilliant! I just went in and we sat on couches and talked about biology! Apparently it was impressive that I'd 'read and understood' her papers, I kinda thought that was the bare minimum but yeah it was great and we just had a really fun conversation talking about biology so I wasn't even nervous, and then she said she'd be happy to have me! She also got me an exemption to be allowed do genetics without the prerequisites just because she thought it'd suit me!

Towards the end of the month I applied for funding for it from the Wellcome Trust with Aoife's help. 

CODING: I worked on my programming skills by doing a course in R on DataCamp. Did you know R uses <- instead of = as the assignment operator? Weird. I'm certainly not fluent in R but I did learn enough to use it to check bits of my Stats homework for the rest of the semester (because R is a stats language). 

CHEMISTRY BROAD CURRICULUM: That bloody group project continued into March (imagine a 14-person group project that lasts 6 months) with the presentations. Our team, which was doing the Chemistry of Solar Panels, made it through the semi-finals (which were actually very good, I was really impressed by everyone's presentations, they were genuinely interesting even though I heavily dislike Chemistry) and into the finals, where unfortunately we didn't place (there were some significant technical issues and other things at the start). Surprisingly I did win one of the Best Speaker prizes and also got a goodie bag for being Secretary. The goodie bag contained, oddly, several types of glue: superglue, Pritt Stick, sellotape...

READING: I finished reading Behave, the tome on all the (neurological, evolutionary, psychological, cultural..) reasons for human behaviour by Robert Sapolsky, and What Makes Biology Unique by Ernst Mayr. 

SNOWSTORM: Towards the end of the month and into March, Storm Emma and the Beast from the East arrived and we got a Red Weather Warning and had to stay inside as the whole country went into lockdown from 4 pm! It was very exciting and also very pretty seeing the blizzards from the comfort of inside.

Here's a photo of our balcony and the ground below covered in snow. The shape there is an empty Quality Street box we left out there that got filled to the brim with snow and was icy for ages afterwards.

Wednesday, 28 February 2018

Review: What Makes Biology Unique: Reflections on the Autonomy of a Scientific Discipline by Ernst Mayr

Ernst Mayr was a huge figure in the modern evolutionary synthesis and was referenced a ton in books I read for Schols (both negatively and positively). I have mixed feelings on him myself but was interested in the idea of the autonomy of biology in the face of physicists and chemists claiming it's within their subjects, so I read this book. 

Mayr talks about different kinds of science, and how it's not just experimental science but also what he calls 'historical science', often employed by evolutionary biologists, where you come up with a hypothesis/historical story for how things happened and see how well that matches up with the available evidence. 

He distinguishes between functional biology, which talks about how things work and in his mind can be reduced to chemistry and physics, and historical biology, evolution and ecology, which is his field. He says functional biology mainly asks how, historical biology why, and they use different methods. He mostly only defends historical biology, but some of his arguments apply to both. 

Physicalist ideas he says don't apply to biology:

  • Typology -- in biology, there aren't a limited number of things, where all things of each type are the same (e.g electrons); instead, evolutionary biologists go for population thinking, which acknowledges that organisms even within one species or population vary, and means that, to borrow a lovely phrase I got from Ridley's Evolution textbook while studying for Schols, means that even though sparrows vary in size across North America, 'all sparrows are equally good sparrows'.
  • Determinism -- even if you know the position and momentum etc of everything, you can't predict biology with certainty into the future. Physicists realized that a while after Laplace said you could, but it's especially important in biology where chance drives the variation needed for evolution to occur. 
  • Reductionism -- the idea that if you know what each component of a complex system is and what its function is you can understand and explain the whole system. Whole chapter devoted to this so read on.
  • Universal natural laws -- don't really apply in evolutionary biology, so Popper's falsificationism doesn't work. He says biological theories are based more on concepts than laws, and then showing that he seems to think all of biology is just evolutionary biology, says: 'Examples of concepts that became important bases of theories in various branches of biology are territory, female choice, sexual selection, resource, and geographic isolation.' 
Autonomous features of biology:
  • Complexity of living systems
  • Evolution
  • Open systems in regards to entropy
  • Dual causation -- controlled not only by natural/physical laws but also by genetic programs. 
Chapter 3: Teleology

He also talked about a bunch of philosophical issues like teleology (goal-directedness of something), which he resolved by splitting the broad word teleology into five types e.g. teleonomy and saying four are proven by science while the fifth, cosmic teleology (everything leading to a cosmic purpose/for god), doesn't exist. In his chapter on Analysis vs Reductionism, he talked about how physicists like to break everything down to atoms and quarks but in biology the way things are arranged is as important as their parts and is an emergent property, and often in biology it's not actually any more helpful to go below a certain level e.g. you can understand cell signalling well just from molecules and the odd atom without understanding quarks, since the link from quarks to atoms and atoms to molecules is already built by physicists and chemists. I agree with that, although he did caricature physicists and reductionism a bit. 

In Darwin's Influence on Modern Thought, he talked about how people say Einstein's relativity revolutionised how people think about the universe but it didn't -- only strong physicists really benefitted from it or felt the revolution. In contrast, he says, Darwin's theories (he says there were five, including evolution, natural selection and common descent) really did change the way the public thinks about the world. 
In Do Thomas Kuhn's Scientific Revolutions Take Place?, he argues that Kuhn's idea of a  cycle of paradigm change ('revolution') followed by a period of 'normal science' doesn't apply to biology, which has mostly seen steady progress as we gain more knowledge and understanding. He makes the important point that most philosophers of science are really philosophers of physics, which rang true from my experience. I've only read about a couple of philosophers of science (mainly in the book The Meaning of Science by Tim Lewens, review here, which discussed Popper and Kuhn among others), but their work does seem to have been based on physics, at least in the examples they gave. 

He has a whole set of chapters on evolutionary theory, which were ok but not what I read the book for. I had to force myself to read his 'another look at the species problem' after studying that as the Schols special topic, and similarly with his other evolution chapters I already knew most of it from Schols study. The 'origin of humans' chapter wasn't great bu I generally just find that topic really boring, even in lectures. 

He randomly has a chapter 'are we alone in this vast universe?' about aliens, in which he basically says we shouldn't look for them and they wouldn't be sentient, and gives out for a while about SETI. As another reviewer said, it'd have been better if he'd written something about what discovery of alien life would mean for evolutionary theory and how interesting that would be. 

General Criticisms:

  • he doesn't really introduce concepts, though he does have definitions in the glossary
  • loves sound of his own voice -- that said, the book is short, which I appreciate
  • distinctions can seem pointless, as between some of the types of teleology
  • so many squabbles in evolutionary biology! 
Overall it was a fairly interesting read, but only a few of the chapters were on what the title promised, and he only seems to view evolutionary biology biology, with molecular bio just chemistry. 

Sunday, 4 February 2018

Review: January 2018

Not sure I did much this month but anyway let's go. 2018? Whew. Year-names haven't sounded real since 2012 ended. 

New Year's: Watched Die Hard with Leon and Gráinne and then spent the actual first day of the year lounging about with them. Also was impressed by the Irish show for it with people in laser suits flying around above the Liffey.


The first week of January was the last week pre-Schols so I spent it reading over all my Speciation, Evolution, Biochemistry and Cell Structure notes and cramming Immunometabolism 12 hours a day as was habit at this point. 

Then it was time for the exams. I'm working on a whole post about Schols so I'll have lots more detail about that shortly, but basically the exams went better than I'd expected overall in the stress of the final week of study, in that it turned out I knew sooooooo much information. Unfortunately, my downfall was that this was the first set of Biology essays I'd ever written and so my time management was absolutely disastrous. I wrote about 3 excellent (in my opinion) essays out of 8, and the others were either middling or totally messed up by running out of time. So that'll probably have decked my chances at actually getting the scholarship but it, and the fact that my exam technique visibly improved over the four days (#4 was an issue for other reasons) and my essays got much better, bodes well for my summer exams. And it's nice that I know the material. The annoying thing is that because they're essays I have zero idea of how good they're supposed to be or what they're supposed to be like, so for all I know they could be amazing or trash, but sure we'll see. 

The y-axis on the chart (should be labelled, yes) is in pages. 

It's so weird that Schols were the second week of January -- when I was thinking about this blog post I didn't originally include them because it feels like they happened forever ago. It's definitely a weird feeling to be finished after studying nonstop for them for six weeks, and to have to be a functional human again. 


Back to college for Hilary term and into Statistics, Genetics, Microbiology and Behaviour (Ecosystem Biology & Global Change and Infection & Immunity are later in the term). So far I don't like my biology subjects this term as much as I liked Metabolism (Biochemistry) and Evolution, but then I really loved Metabolism once I started studying it properly from the book for Schols. And the modules are pretty interesting. It's definitely a change from last year when I consider a module that's fundamentally interesting but has some boring lectures 'not great', when last year I wasn't interested in pretty much anything we did. Biology is cool yall. 

Also, our Genetics labs have been cool. Maybe they're collecting our samples for government surveillance with that and our Microbiology labs though -- so far we've sampled and been analysing our DNA, fingerprints, tongue and nose. Suspicious.


Have been doing a lot of conceptual work on Lablinn and figuring out what our core goals are. Have decided on this: 

We aim to facilitate civic engagement with science and help people lead citizen science projects in their communities to expand the reach of science and help improve the world.

So we've got a lot of exciting work now to bring that to fruition, and have started on some means to achieve it. Watch this space. 


In January, I read Endless Forms Most Beautiful: The New Science of EvoDevo by Sean Carroll, The Future of Life by Edward Wilson (both for Schols), and The Gene by Siddhartha Mukherjee. I also started Behave by Robert Sapolsky and What Makes Biology Unique by Ernst Mayr. 

BT Young Scientist:

I went to the Young Scientist and saw some cool projects, including a mentee and a friend I met there years ago who's now Individual Runner-Up, which was super cool. There ended up being a lot of controversy over the winner, it was weird seeing the YS actually release a statement over it, really made it seem like a big deal. 

That's about all, I think. Leon also convinced me to play Pokémon on his DS. It's quite nice. 'Til next time.

Saturday, 20 January 2018

Review & Recap: The Gene by Siddhartha Mukherjee

The Gene is a follow-up to Mukherjee’s amazing Emperor of All Maladies: A Biography of Cancer, and unfortunately doesn’t quite live up to it. It has lots of interesting information and repeats his customary style of intimate history, tackling a huge subject’s scientific, personal, historical and cultural factors by bringing the reader to the scene of the action. On the negative side, it doesn’t seem as natural to the author as the first book (presumably because he’s an oncologist and has more personal experience with the subject), the personal subplot felt unnecessary, and it has some factual errors and misrepresentations that I can’t look past. Let’s look at some highlights first (this part is super long, so if you want to see my complaints about it scroll to the end).

The book was split into six sections, dividing the time between 1865 and the present into the discovery of the concept of a gene and heredity (The "Missing Science of Heredity" (1865-1935)), the discovery of the physical material of genes and how they work … and also eugenics  (In the Sum of the Parts, There Are Only the Parts (1930-1970)), genetic engineering ("The Dreams of Geneticists" (1970-2001)), genetics as applied to understanding humans and the Human Genome Project (“The Proper Study of Mankind is Man” (1970-2005)), what the Human Genome Project has shown about our genome (“Through the Looking Glass” (2001 - 2015)) and genome editing (Post-Genome (2015 …)).

That said, the sections still aren’t very clear -- for example, eugenics features most of the way through in scattered chapters -- so I’m just going to talk about individual highlights.

The Gene Concept

The gene was first discovered as a concept long before people knew it had a physical form, never mind knowing about the double helix. The ancient Greeks had various ideas like that all the information to make a baby was in the man’s sperm, and the woman’s womb was just to provide nurture, and then ideas didn’t really advance much until Mendel, who did crossing experiments with hundreds of thousands of pea plants across seven different traits (wrinkled/smooth seeds, flower colour, tall/short, etc), and discovered various laws like the Laws of Segregation and Independent Assortment. One important thing he did was show that genes are particulate and inheritance is not ‘blending’ (i.e. when two people had a kid their babies were a blend of the parents’ traits and so eventually all traits would blend together and variation would disappear). He crossed true-breeding i.e. homozygous plants with two opposite alleles for a trait (e.g. wrinkled vs smooth seeds) and counted the proportions of the phenotypes (appearances) that resulted. This cross would be WW x SS and would result in all offspring being heterozygotes i.e. WS. Smooth is dominant so all of the seeds would be smooth. But when he crossed these heterozygous offspring with each other i.e. WS x WS, he’d get SS (smooth), 2 x WS (smooth) and 1 x WW (wrinkled). This showed that inheritance doesn’t blend because the wrinkled trait emerged unscathed after a generation just as wrinkled as ever.

Interestingly, Mendel failed his biology exam to become a teacher twice and that’s why he ended up doing the pea experiments in the monastery. I don’t blame him -- I would’ve hated biology at the time, when it was mostly about memorization (natural history) of different organisms and being able to name and classify them. Luckily he failed and contributed to the much more mechanistic and lawful biology we have now.

This section also talked about Darwin and Wallace and their conception of the idea of evolution by natural selection. One big issue with that was that at the time people thought inheritance worked by blending. Variation is needed for the theory of evolution by natural selection because without it there are no mutants for selection to act on via them surviving or reproducing better or worse than others.  Mendel’s discovery was thus very helpful for the theory of evolution, but unfortunately despite being contemporaries Darwin and Mendel never talked and Darwin doesn’t seem to have been aware of Mendel’s idea.

People also used to think people could inherit acquired characteristic a la Lamarck, so Weismann cut the tails off five generations of mice and showed that the baby mice were still born with tails. Pretty cruel way to do it but it worked I guess.

It also features Francis Galton, Darwin’s cousin, who badly wanted acclaim and ended up becoming a biometrician (got a ton of family histories and measured various traits to show that human traits tend to come in bell curves) and eugenicist.

During this period, genes were thought of as units of heredity -- not necessarily something with a physical basis, just a unit of information transfer between generations.

What are Genes?
An early clue that genes are physical things came from linkage. Some genes violate Mendel’s law of independent assortment, i.e. these genes for different characters are not passed on independently (e.g. gene for eye colour and one for nail texture). Experiments on flies determined that this was because these genes were beside each other on chromosomes  and that you could actually map the position of genes on chromosomes relative to each other by how independently they were inherited. Genes right next to each other are most likely to be passed on together, while recombination can occur between genes that are further apart and they’re more likely to be passed on. If genes could be physically near each other, that meant they had to have some physical basis and location.

Griffith’s transformation experiment showed that injecting a non-pathogenic live bacterial strain mixed with a heat-killed pathogenic strain resulted in a pathogenic strain that killed mice -- this was the ‘transforming principle’, where something from dead cells had passed to live cells and changed them. Poor mice. Apparently Griffith was very shy and his friends would have to force him to go to scientific meetings by stuffing him into a cab with a one-way fare. He published his results quietly in the fairly obscure Journal of Hygiene after some delay  "God is in no hurry, so why should I be?".

So the next thing was to figure out what the genetic material actual was. Originally scientists thought it must be proteins because there are so many different proteins and the incredible variation in them would make sense as genetic material because they could make all the different body parts of organisms. Nucleic acids like DNA surely couldn’t be it because they only have 4 bases (A, C, G, T) that repeat themselves, and how could they give all the diversity we see in organisms? Turns out it’s all in their order, and DNA is indeed what makes up genes. Experiments that used the transforming principles showed that using things like chemotrypsin and ribonuclease that break up proteins and RNA didn’t affect it, but things that break up DNA did.

Once DNA was accepted as the genetic material, its structure and way of working had to be elucidated. James Watson, Francis Crick, Rosalind Franklin and Maurice Wilkins were pivotal in discovering the double helix, and Watson and Crick figured out that A and T and G and C base pair with each other using Franklin’s crystallographic measurements. They also observed that this base-pairing immediately suggesting a way DNA could replicate itself. The central dogma was born soon after: DNA → RNA → protein.


Eugenics was a prominent theme; American, German, Austrian and British. It started with American eugenics and places like the Virginia Colonies, where social undesirables like prostitutes, orphans and poor people were deemed ‘moral imbeciles’ and sterilized to prevent their having kids and creating more imbeciles. One woman was deemed to be a hereditary moral imbecile because of prostitution and because her young daughter (who was doing fine in school) wrote notes to boys in class, and when her daughter had a child a social worker was sent to say the seven month old was an imbecile even though there was no way for her to know that. But the court nevertheless ruled that they were hereditary imbeciles and had them sterilized.

In Germany, before the much more famous genocide of Jews, there was Aktion T4, where disabled people were killed and many others sterilised. As detailed in Neurotribes specifically about autistic children, children were taken from their parents to ‘relieve the burden’ and then starved to death or gassed. Their families were told they died of a variety of causes -- one was said to have died from ‘warts on her lip’. By 1934, nearly 5000 adults were being stabilised every month in Germany, and there were 400,000 forced sterilisations between 1933 and 1943.

Genetic Engineering

The book details how academics and  companies like Genentech discovered how to express genes from other organisms like frogs and humans in bacteria so that the bacteria could pump out insulin, human growth hormone, alpha interferon (to treat blood cancers) and recombinant TPA (blood thinner) to treat human diseases without having to take e.g. the pancreases from millions of sheep as they were doing before.

It also has some pretty interesting stuff about scientists self-regulating as they realised the power of their new abilities to completely alter the traits of organisms and inject, say, a dangerous virus into a bacterium that typically lives in human intestines and could find its way in there easily -- the Asilomar conferences that put strict rules on genetic engineering.

The story of AIDS is briefly told, and something I found interesting was that apart from the well-known cases of gay people and IV drug users getting HIV, haemophiliacs very commonly were infected because due to their lack of functional clotting factor VIII they had to get blood transfusions with factor VIII derived from blood from tons of different people, and it was enough for one of them to have HIV.

The part on tracking the Huntington’s gene was interesting. The person who started it had a family history of Huntington’s so was very invested in it. She wanted to figure out where the gene might be so needed a bunch of affected family trees but it was too rare in America to get that so she went to a village in Venezuela where 10-20% of people carry the Huntington’s gene (have or will develop it), i.e. about 2000 people in total in that one village. Something particularly interesting was a phenomenon called anticipation, in which Huntington’s onset comes earlier with each affected generation. It seems to be caused by a gene repeat, and the first person in the family to have it might have 30-40 repeats, but then some of these Venezuelan kids had 70-80 copies because the number of repeats increases with each affected generation and were developing the disease aged 12.

A footnote discussed ideas on why cystic fibrosis has not been selected out of the population and is in fact quite common. One factor is that it’s recessive; another, related one is that humans with one copy of the CF gene are partially protected from the worst effects of cholera thanks to a slightly diminished ability to lose salt and water through their cell membranes. This may have protected them during the Middle Ages and caused the gene to persist.

A really creepy aspect was the concept of ‘wrongful life’ -- parents suing a doctor on behalf of their child for not telling them their child would be born with a severe disability, saying that they would have aborted the child and it should never have been born. These cases don’t typically win because people say a disabled life is better than no life at all, but sometimes they do. I get wanting money because it can be very expensive to raise a severely disabled child, but it must feel awful for the child to hear their parents saying they should never have been born, and so I find it pretty creepy.

Sort of on that note, a quote from Francis Crick, co-discoverer of the double helix: 'no newborn should be declared human until it has passed certain tests regarding its genetic endowment'. Also, man, so many Nobel Laureates in the sciences were huge eugenicists. Okay I’ve read quote like that from like two or three, but that’s still a lot for humanity’s ‘best and brightest’.

The Human Genome Project

I learned that the project to sequence the human genome (all genes) involved competition between the government-sponsored scientists and Craig Venter’s startup called Celera. If this company had achieved it faster, it would’ve been a PR nightmare for the government, so Bill Clinton, who was president at the time, send an aide a note saying ‘Fix this!’ and the heads of both projects were brought to dinner and convinced to agree to announcing the completion of the project together whoever finished it first, and publishing their papers back-to-back in the same journal (due to further spats over Venter wanting to commercialise parts of the genome the second part didn’t end up working out).

It was also interesting that they got one of their computer scientists (James Kept) 100 desktop computers so he could run his code simultaneously on all of them, and had him icing his wrists every night from all the work.


This section was quite interesting, talking about the relation between genetics and various aspects of identity like race, gender identity, sex, sexuality and human evolution.

The first chapter, on race, was about the book The Bell Curve and how African-Americans consistently have an average IQ of 85 whereas whites have an average IQ of 100, even when these studies were carefully done outside the South and only taking results from after 1960. A typical explanation, and one I would have believed before, is that this is due to socioeconomic disparities (since poverty decreases performance on IQ tests), but the gap between average black IQ and white IQ (in America) actually widens at the top of the income bracket apparently. One explanation is that IQ tests are not actually good measures of intelligence, and that changing the weighting of different subtests within them dramatically changes results; another is that there seems to be some psychological/internalised racism factor affecting performance, because African-Americans do badly on IQ tests when told it’s to test their intelligence but do fine when told it’s to test a new electronic pen or to refine the test.

On human evolution, Mukherjee discusssed Mitochondrial Eve, a woman who lived 200,000 years ago in Africa to whom we can all trace our mitochondrial ancestry.

I found the sex determination stuff interesting. It wasn’t known for quite a while what determined maleness. Eventually the Y chromosome was discovered, but how did it work? What were the genes for ‘maleness’? It seems that the SRY gene is a master regulator for maleness: two illustrative lines of evidence are that forcibly activating SRY (by putting it into the X chromosome) makes mice with all XX (female) chromosomes that develop a penis and testicles and mount females. Women with Swyer syndrome are chromosomally male (XY) but have mutations in SRY and develop with a female phenotype.

Interestingly, XX mice that are exposed to a drug that blocks signalling of ‘femaleness’ to the brain have all the anatomical and physiological features of femaleness but are behaviourally male including mounting females.

The chapter on sexuality was interesting mainly for the quotes showing the extraordinary vitriol people have shown towards gay people. A psychiatrist in the late 1960s is quoted as saying:  'the homosexual's real enemy ... is not so much his perversion but [his] ignorance  of the possibility that he can be helped, plus his psychic masochism which leads him to shun treatment"; another, in 1956: 'permanent homosexuals, like all perverts, are neurotics'.
Dan Quayle, Vice President, in 1992 said: 'homosexuality is more of a choice than a biological situation ... it is a wrong choice"

A (gay, as it happens) scientist later showed that there is a chromosomal region associated with homosexuality (he carefully checked it wasn’t ‘sissyness’ or other things it could be confused for, and was very thorough with his experiments according to the book). The Daily Telegraph then said that now that the ‘gay gene’ was known: 'science could be used to eradicate it'. The scientist was attacked by both gay activists for fuelling people’s ideas of eradicating homosexuality via in utero testing, and by anti-gay activists for giving a biological ‘excuse’ to homosexuality. It’s just absolutely bizarre how hateful people are and especially were towards gay people. Like, obviously they don’t need treatment.

Epigenetics - how the environment affects our genomes

I was shocked to discover that during the Dutch Hongerwinter at the height of the famine they were down to 400 calories a day, or the equivalent of three potatoes. Someone said about that that a human being is ‘a stomach and certain instincts’, which I guess shows how intense it was and how dehumanising, when you’re so hungry you can’t think about anything else or really think much at all.

Children born to mothers who were pregnant during the Hongerwinter grew up more obese, as if their systems had figured they’d need to hold onto every piece of food it could get, and so did their children -- so clearly some chemical memory had been left of the event.

Gene Therapy

I found two of the gene therapy stories really compelling. The first was Ashanti DeSilva, a small girl with a non-functioning adenosine deaminase enzyme causing a form of Severe Combined Immunodeficiency resulting in severe damage to her T cells and frequent life-threatening infections. Some of Ashanti’s T cells were removed, had the functional gene inserted and were injected back into her, and the treatment seems to have worked -- but we can’t know for sure, because she was allowed to continue with the usual treatment of injecting the enzyme once a month, which confounded the results. The really sad part of that story is the quote from Ashanti, aged 4: “Mommy, you shouldn’t have had a child like me”.

The other story was that of Jesse Gelsinger, a teenager who lacked ornithine transcarbamoylase, a crucial enzyme in the urea cycle and thus couldn’t metabolise ammonia properly. He had a ‘mild’ variant of it -- he ‘only’ had to take 32 pills a day to keep his ammonia levels in check to stay alive and functioning, and when he broke his no-protein diet and ate a peanut butter sandwich he went into a coma -- because his gene mutation had occurred in one of his cells as an early embryo and gone into all the mitotic descendants of that cells so he was a human chimera and only had the deficiency in some of his cells. But still, y’know, pretty bad. So he was happy to volunteer for gene therapy to try to insert the OTC gene into his genome. The researchers wanted to use a virus to insert it and needed it to not be dangerous, so they used a stripped-down version of an adenovirus, the type that causes flu, since that type is well understood and not very harmful. Unfortunately, they didn’t do their due diligence and didn’t realise that precisely because this virus was so common it was an issue -- when they injected it, Jesse’s body raised antibodies against it and after an overwhelming immune response he died.

A more successful story of gene therapy is in the treatment of Haemophilia B; they used a virus to insert the gene for the missing clotting factor IX and were able to restore the concentration of factor IX to 5% of its normal value, which was enough because it resulted in a 90% decrease in the haemophiliacs’ bleeding episodes and requirement for injected factor IX.

Genetic Screening

I’d never heard of preimplantation genetic diagnosis before -- it involves screening IVF embryos for certain disorders before implantation to not only prevent disordered babies being born, but to prevent the need for even an abortion -- to prevent them from even growing in the womb at all. An example of this was a couple where one had a family history of X-linked ‘mental retardation’ and the other had a history of an X-linked immunological syndrome, both of which only affect males, so they screened the IVF embryos and selected only female ones.

Mukherjee makes the point that the largest ‘negative eugenics’ (killing or sterilising the undesirable; ‘positive eugenics’ is encouraging the ‘best’ to procreate with each other) project in history wasn’t the Holocaust; it’s the 10 million girls missing from adulthood in China and India due to abortion, infanticide and neglect of daughters.

He also discusses the criteria for genetic screening and intervention: highly penetrant genes (that gene has a strong effect and someone with that gene has a very high likelihood of having the negative phenotype); high suffering; justifiable interventions (aborting a foetus with Down Syndrome and performing a double mastectomy on someone with the BRCA1 gene, which makes your chance of breast cancer around 80%). It was kinda chilling how he just casually put the bit about Down’s in there; I don’t know if he’s reflecting his own beliefs or just describing the consensus, but it seems like a weird example of something when there are other things that would less controversially be considered ‘justifiable interventions’.
environment incongruity.

He describes the interesting concept of a ‘previvor’ e.g. someone who’s discovered that they have the BRCA1 gene knows they will most likely develop breast cancer but it hasn’t actually started yet, and someone with the Huntington’s gene knows they’ll develop Huntington’s later -- but for now, they’re previvors.


First of all, a small gripe -- he didn’t have a table of contents with the chapters in it? It just had the six sections and their pages, not the many chapters within each. Anyway, onto the more important stuff.

Firstly, he says something that I’m not certain is correct, though I could be wrong. He says 'most evolutionary biologists agree that sex was created to enable rapid genetic reassortment" when from my study for schols everyone says the origin of sex is a mystery, and the rapid genetic reassortment argument (in which sexual organisms do better because they can more rapidly combine multiple good mutations in one organism rather than having to wait for each mutation to come up sequentially in the germline) only works if positive mutations occur  frequently enough that it actually makes a difference, which is not certain. There’s a whole literature on this but yeah seemed weird that he didn’t qualify that statement much.

What annoyed me the most was his treatment of autism. Some quotes:

  • 'polygenic illnesses -- schizophrenia or autism, say' autism is not an illness
  • 'Shockley...afflicted by a syndrome of paranoia, aggression and social withdrawal that several biographers have suggested was a form of high-functioning autism' suggested by others, yes, but this isn’t representative of autistic people and since he gives so little representation anyway I think he should’ve chosen not to include it
  • Said most autistic children are peeling their skin off or smearing shit or something but some ‘rare’ children might maybe even possibly be ‘functional in most situations, and possibly hyperfunctional in some (a chess game, say, or a memory contest)' this is promoting stereotypes of what autistic (including Aspergers) people can do. Out of the ones I know, I’d say most of them actually prefer arts to the stereotypical maths/computer science tropes, and I’ve never met any who are typical ‘savants’. That’s not to say they don’t exist, but to say they are very much less common than they’re assumed to be, and autistic people are much more variable than we’re given credit for. This is especially irritating because he writes it in a way to suggest that this is the very pinnacle of what autistic people achieve. It’s in a section about how illnesses are actually about a mismatch between genetics and the environment, so it had the potential to be very woke (I subscribe to the social model of disability when it comes to autism) but he lets himself down by using stereotypes.
  • Said high-functioning autists might do well in an environment that required the ‘sorting of objects by the subtlest gradations of color’ probably the least bad here because it does at least have some truth to it in terms of autistic sensory characteristic, but not exactly aiming high when that seems to be the point of the section.
I looked in the acknowledgements and his source on autism is a researcher whose lab looks for genetic ‘risk’ factors for autism and is explicitly looking for a cure. Why didn’t he consult autistic people instead, or in addition? Of course he was going to get a skewed picture of autism if he only consulted someone who wants to eradicate them.

Finally, I wasn’t a huge fan of the family thread he wove through the story. He inserted a couple of random chapters about his family history of schizophrenia, about his mother being a twin and about his family during Partition in India. They were fine, and the first chapter was pretty good, but they felt unnecessary since I was there for the science. They could also be very overdramatic; he describes his father and uncles spending all day solving a puzzle in the most incredibly dramatic way, with a lot of unnecessary metaphors. Maybe other people liked them though.


There was lots of interesting information here, and Mukherjee is talented at making us feel like we’re right there where it happened -- but a small bit of factual error and bad representation of autism make me dock it to 3 stars out of 5.

Tuesday, 16 January 2018

2017 Review

Yo. I've just finished my Schols exams so here I am, back at the blog. Here's how 2017 went down for me. 

January 2017

In January I went back to college for my second semester of first year and experienced this:

Hung out with the gang a bunch, including ice skating at the RDS: 

worked on a precursor to Lablinn, visited the BT Young Scientist and read Superintelligence by Nick Bostrom, Bad Pharma by Ben Goldacre and The Social Animal by David Brooks. 

February 2017

I kicked off February by going to the Trinity Science Ball:

Then I went to UCD to run a workshop with Shane Bergin's Science Ed masters students on antibiotic resistance education:

I started dating Leon on the 11th of February and celebrated Valentine's with him on the 14th (obviously).

I spoke at Dublin Tech Summit (for some reason on a panel about entrepreneurship?) shortly afterwards:

I also spent a lot of time in February working on a book proposal I'd been commissioned to write about citizen science. 

At the end of February, I went with Leon and the gang to Edinburgh for the Physoc trip:


March was pretty busy. It featured the end of the Physoc trip, submitting my book proposal, being featured in two documentaries. learning to code in (and becoming obsessed with) Ruby, cool dates with Leon including seeing Hidden Figures and visiting the Real Bodies exhibition, participating in a workshop on implementing the Bratislava Declaration of Young Researchers in Ireland, celebrating Leon's birthday with a weekend trip to the seaside, running for Secretary at the Physoc AGM and getting it, starting work on Lablinn's website and interviewing people, and going to Budapest to run the European Youth Summit. 

The documentaries were the Outbox Incubator documentary -- my feelings upon watching it were: "It was really nice to see, and it felt awesome to be featured prominently. It was very weird seeing my name come up at the end in one of those typical documentary "Elle is now ...." with a picture of my TEDx talk because I'm used to that exact formatting being in documentaries about actual famous people. "  -- and a documentary about the Women on Walls project in the Royal Irish Academy, which I'm in for 2 seconds at the end by accident because I attended the launch. 

Budapest is beautiful -- here's a photo by Lukas Frankl, one of the attendees of the conference. 

Through the Bratislava Declaration meeting I got to put some ideas on inquiry-based learning in pre-tertiary education into the recommendations document released from the meeting, which was cool because of the possibility it could have an impact. It was funny because when accepting my invite I had to register and the closest box I could tick in terms of career stage was 'Pre-PhD student'. 

March review is here. 


In April, I had the last day of the European Youth Summit in Budapest, was selected as one of 100 people under 40 from around the world to be a Young Global Changer and attend the T20 Summit in Berlin in May to come up with ideas for world leaders, got a job, signed up for Harvard Business X CORe, studied for my annual college exams, started realising that I really liked Biology and should probably be studying it, interviewed someone for Lablinn, consolidated my various open science and outreach things into Lablinn, and booked some workshops for the antibiotic resistance talks. 

April review is here. 


I had my 6 annual exams, talked to six classes of students (three primary, three secondary) about antibiotic resistance: 

published the Lablinn website, went to Berlin as a T20 Young Global Changer, and had fun playing board games with Leon. 

I wrote this about the Berlin experience: 
  • Cool speakers included Nobel Laureates George Akerlof and Joseph Stiglitz, Sweden’s Minister for Finance who was awesome, and other big economists including Jeffrey Sachs and Lord Nicholas Stern
  • Berlin was HOT. The minimum night-time temperature was 18 C.
  • I met so many awesome people from all around the world there and learned so much about different cultures. Such an incredible learning experience. For example, here’s a photo with five people from five different continents: Europe (Ireland), Asia (Vietnam), Africa (Ethiopia), South America (Venezuela) and Oceania (Fiji). "
It was super cool, met a lot of interesting people and am glad to have been given the opportunity. T20 was awesome even though there was no one my age there (I was the youngest by like 6 years). 

May review is here


In June, I started my job as a Teaching Assistant at CTYI and met my lovely Instructor colleague Belinda, gave antibiotic resistance workshops to around 170 students, recruited the Lablinn team who are very cool (, check them out), hit 100,000 blog visitors and celebrated my 5 year blogiversary, researched degree paths intensively and tipped to favouring Biology, did the first third of the Harvard course, read/reviewed 4 pop science books and moved out of digs

June review is here


July was mostly taken up by my job at CTYI (which was pretty enjoyable but definitely hard work and involved 16-hour days including commuting), hanging out with Leon (including lots of board games, Brooklyn 99 and a nice trip to Glendalough), working on Lablinn and getting to know the team, making 30 pages of Biology notes from Campbell and loving it, doing half of the Harvard course, and reading two popsci books

July review here


August was pretty busy and involved visiting three different countries, which was cool. At the start of the month I went to London (thanks Stemettes) for a Lablinn-related business trip, then the next day to a work reception back in Dublin:

Then I put in my new subject choices (biology), and the day after had my six month-iversary with Leon and my 19th birthday (on the same day) -- unfortunately I spent it crying because the Biology department in college were refusing to let me switch to Biology (despite meeting the prerequisites) because they thought I'd fail and after all my research and study I'd realised it was all I wanted to do and I'd have to drop out if I couldn't do it. That extremely stressful situation went on for a month managing to ruin my whole month and two holidays before, through drastic measures, I finally convinced them to let me in (I now have an average above 90% in the Biology modules I've got marks for, so there). Thank you to the students union for your advocacy for me though. 

I went to Prague to visit Lukas from the Youth Platform:

Then to Brno: 

Then to Vienna to visit Lili from same: 

The trips were definitely a strain on my finances but I only had to pay for flights so I managed it and they were pretty cool.

I finished up my Harvard course, had a photoshoot for the launch of TEDxDrogheda, and read Sapiens, Superbug, and Brave New World. I also went to LeakyCon, the Harry Potter convention, wrote nine blog posts, studied Biology and worked out how successful I'd been with my 14 August 2016-July 2017 goals:

  • Dropped (realised not a priority): 2
  • No significant progress: 3 (organise a college science fair, do a research project, open 3 open labs -- these goals were a little unrealistic)
  • Significant progress i.e. halfwayish done: 3 (reach 1000 students with antibiotic resistance talks, get a first in college, publish 20 paid freelance articles)
  • Complete: 6 (exercise 30+ mins 90% of days, read 15 popsci books, write 52 blog posts, speak at 6+ events, run two youth platform projects, complete Nobel Physics blogging project). 
Blog post about progress on the goals here, and August review here


I did my Harvard exam on the 1st, went to another day of LeakyCon, moved into my new apartment with Leon, womanned the Physoc stand for Freshers Week, started back at college, organised a Lablinn team workshop Training Day, wrote 8 blog posts, read 3 books, finished writing my 100 pages of notes from Campbell biology and....developed Tennis elbow from studying too much (and without proper arm support). Never realised how much I used my arms and hands til doing anything with them was paaaaain. D'oh.

September review here


College really got started in October and I got to experience studying Biology in college which is a m a z i n g -- you should totally read the October review for info on my experience of each module, but basically they were awesome. I was even better at Maths and Chemistry just because being in a subject I loved made me so engaged and happy. 

We did a bunch of stuff at Lablinn including a Training Day for the team, interviews and booking workshops. Hurricane Ophelia hit, I got my Harvard grades back (passed with Honours, got 100% in Stats, 96% in Economics and 93% in Accounting), and I went outside and climbed a mountain with college pals (not all on the same day):

Leon and I played a bunch of Magic: the Gathering and Carcassonne, and saw an IRA film in the cinema, and I did various Physoc secretary things. Overall though, I mostly studied because I had a lot of work and it was really fun. 

October review here


November was mostly spent studying as I'd signed up for Schols, Trinity's super hard optional scholarship exams, in four Biology papers. I was also continuing to love college, finding Maths interesting, being fascinated by Biochemistry and not even minding Organic Chemistry. 

Apart from that, Lablinn was super active (held workshops with 120 students and booked some more, published a bunch of articles and an interview with the very cool APOPO HeroRATs on the site, and had me do a talk about Lablinn and enroll on a Launchpad mentoring scheme for it), I spoke at a TwitterxUNICEF event at Twitter Dublin HQ, I went to Budapest for a few days for a Council of the ECHA Youth Platform meeting, went to a William Campbell talk in the Royal Irish Academy (he won the Nobel Prize for discovering a treatment for river blindness) thanks to the Naughtons, and did the usual Physoc stuff plus going out for dinner with our speaker Shane Bergin, which was fun. 


I had my first meeting with my mentor for the Launchpad program at the start of December. College ended in mid-December and from then on I upped my Schols study to 12 hours a day so I really had time for nothing else -- I couldn't even think about anything else my brain was so full. I learned so much but it is nice to now have a little bit of brain space to think about well, anything else. I celebrated a little bit of German Christmas with Leon's family and then went to my own for Christmas day, then back home to the apartment and celebrated New Year's by watching Die Hard with Leon and Gráinne. 


All in all, it was a good year. Switching to Biology was one of the best decisions I've ever made, because I adore it and am getting 90-100% so it certainly seems like I can do it. It's so fascinating and I love studying now whereas last year it was just like an obligation. Over the summer, thanks to Leon, I learned how to embrace the concept of fun rather than just working myself into the ground -- I still subsequently worked myself into tennis elbow, but at least then it was doing something I enjoyed rather than just working out of workaholism. He even got me into playing board games and then, slightly, video games (the horror). In general me and Leon had a lot of happy times and have now been living together for four months (although we were effectively doing so for many months before that). I stepped back a bit from conferences as the year progressed so I wasn't actively seeking them out anymore but did still go to some cool things I was invited to. I learned a huge amount by being engaged in college and it  was awesome. Lablinn grew from having only been piloted in one school to having reached about 700 students, gained an international team and a website, and lots of other cool stuff that I'll talk about in a blog post shortly. There were definitely some bad times too, but I'm happy about the progress made and especially about making the right decision to switch to doing what I really love rather than what I felt was expected just because I thought it was illegal or whatever to have fun -- I'm really loving what I'm doing at the moment. Here's to a good 2018 :) 

Saturday, 9 December 2017

Review: November 2017

Hi all! Long time no talk, I know. I'm currently in bed listening to Christmas songs, and taking a study break to write this post. I've been studying a lot so that's most of what I've been up to, but here's some other stuff:

COLLEGE: I've been incredibly engaged in college this year, it's awesome. I spend a lot of time studying and also pay much more attention to the lectures and it's great. I feel super immersed and scholarly, and I've learned so much. Multivariable Calculus continues to be interesting and I'm learning a lot of stuff I didn't even realise I didn't know; we did Organic Chemistry in the Chemistry module and despite my usual dread of organic chemistry it was fine, especially since we concentrated on stereochemistry and the lecturer linked it to biological uses a lot; Metabolism, the second Biochem module and only biology module I have during this part of term, is tough but really cool and interesting, much cooler than it looked from the description I read over summer. It's so crazy that the admin were so resistant to letting me switch to Biology. Contrary to their expectations, things have been even better than I imagined. As my friend Will said (possibly paraphrasing slightly?) "Elle, you love Biology more than I love some close family members."

LABLINN: Lablinn was super active in November. We:

  • held workshops with about 120 students in Finglas and Meath, demoing our new cooler workshops with me, Sarah and Daniel delivering the workshops.
  • had Diagnostics Week on, featuring articles on nanodiagnostics and the importance of diagnostics for antibiotic resistance, and a really exciting interview with Lily from APOPO, who train HeroRATs to safely clear landmines and diagnose tuberculosis. 
  • had Ella write about speaking on a Stemettes panel (something from our collaboration with the Stemettes was just released at the start of December!)
  • had me speak at a TwitterxUNICEF event on digital advocacy about Lablinn - more on that below
  • organised workshops in two more schools for December, with Laura delivering.
  • had me get a mentor from Social Entrepreneurs Ireland for Lablinn through Launchpad (see below)

TWITTERxUNICEF #DigitalYouth17

I was invited by Twitter's EMEA head of third party policy outreach, Ronan Costello, to speak at Twitter HQ as a young person using the internet for advocacy/cool things alongside three other young people with cool stories. So that cancels out all the time I've wasted scrolling Twitter, right?


My term as a Council Member of the Youth Platform of the European Council of High Ability (what a mouthful!) continues, so I've been doing the usual work for that and also went to Budapest for a few days over Reading Week for our autumn Council meeting. 

Did lots of work, and had time to confuse people with the pronunciations of Irish names like Saoirse and Sadhbh, so a good mix.

SCHOLS (...and learning how to #hackthelibrary)

I've signed up for schols in all the biology papers, which is kinda hilarious because I didn't even do biology last year. For non-Trinity readers, schols are super hard optional exams you do in January of second year and if you get a first in them you get free accommodation, free dinner and various possibly mythical things as well for five years. You also get to put 'Sch' after your name but I think it's generally seen as a bit obnoxious. Since I'm going in with a bit of a disadvantage, I'm not expecting to get them, but apart from the pressure I am really enjoying studying for them. I just counted and I've written almost 60 pages of notes for the extra biochem study and typed a good few pages for the evolution paper in the last 3 weeks, which was a pleasant surprise. It's really interesting stuff. 

As part of that, I've learned how to #hack the library and by that I mean (a) find out whether books I want are there and where they are using Stella search (b) get them from the section only some people (including me) can access for various reasons like being registered with the Disability Service, so I can take out a whole 8 books and keep them for 4 weeks without renewing rather than 1. So I currently have 7 books out of the library. Even if I don't get schols (it really depends what kind of paper I get), I'm loving being all scholarly and reading a ton and am glad of the skills I've picked up studying for it. 

The annoying thing is the pressure, and how the papers seem very hard to categorise or prepare for in a way I can be reasonably confident of -- so I'll need to get lucky as well. We'll see -- for now I'll just use it as an excuse to learn cool stuff. 


I've mostly been reading as part of studying (so lots of the biochem book I'm using), but I did read Maryn McKenna's book on the Epidemic Intelligence Service of the CDC, which was interesting. The last book I read is The Selfish Gene by Richard Dawkins, and I'm currently reading his book The Blind Watchmaker. Apart from that, lots of papers on evolution. I also bought an evolution textbook (Skelton) on a whim because I found it online for 75 c (75c! for a textbook!) not including postage, but still under a tenner in total. 


I've enrolled in Launchpad's Women Who Wow mentoring programme and been assigned a mentor, Sara, from Social Entrepreneurs Ireland, to help me develop Lablinn. The launch event was in late November and we had our first meeting in early December. 


The Naughtons got us Naughton Scholars tickets to hear Nobel Laureate William Campbell talk about his discovery of ivermectin, a life-changing treatment for river blindness and similar diseases in tropical countries, in the Royal Irish Academy. In an awesome turn of events, Belinda was there and we talked a bunch. 


I continue to be Secretary of Physoc. It's grand. Probably the best part so far was taking Shane Bergin out for dinner before his talk with us on The Scientist as Advocate -- it was great to see him again, we had very interesting chats. 


That's about all I can think of. The vast majority of this month has been attending college and studying, and honestly it's been cool.