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

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.

Diseases
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.

Identity

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.

THE BAD & THE UGLY

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.

OVERALL

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 

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. 

April

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. 

May

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

June

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 (lablinn.com/team, 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

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

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


September

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


October

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

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. 

December

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. 


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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 lablinn.com, 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?


YOUTH PLATFORM & BUDAPEST

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. 

READING

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. 

LAUNCHPAD 

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. 

WILLIAM CAMPBELL TALK @ ROYAL IRISH ACADEMY

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. 

PHYSOC 

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. 

Thursday, 23 November 2017

Youth Platform Autumn Meeting in Budapest 2017

Hello from (presumably) somewhere over the Irish Sea! I’m currently on the flight back from my trip to Budapest for the ETSN Youth Platform’s autumn meeting, so here’s a bit of a rundown on how it went.

Image may contain: 3 people, people sitting, table and indoor

Conference-Related Stuff
  • *      We had a talk on the funding and legal matters of the YP
  • *      We tried out a ‘3D Virtual World” which was really more like a video game that had your documents/stuff from the internet/links incorporated into it. That was pretty technically impressive, to be fair.
  • *      The Council decided we need to have one of us be a supervisor for each project so I chose the blog project and have been helping them out.
  • *      We heard about ECHA 2018 in Dublin and discussed what we’ll contribute to it. Mad how much more expensive Dublin is than most European cities.
  • *      We had lots of time set aside for the project leaders to make progress on the projects. Beforehand, they presented to us about their progress so far or lack thereof and what they’d found challenging or needed help with, and after the project work sessions we had a debrief where they talked about what they’d done. So it was definitely the most practical, work-focused, concrete meeting we’ve had so far, which I appreciated.

General Abroading Stuff
I have some things to say to Hungary/Budapest/the hotel.
  • *      To whichever receptionist had this wallpaper on your computer: nice Image result for sleep all day party never

    • *      Why did you freak out when I said I’m a vegetarian, and give me fish instead, and then be confused about why that wouldn’t work? Why did you then proceed to give me literal slabs of grilled cheese for future meals? Apparently this is a thing lots of continental Europeans eat. Personally I think the bread/other substrate is an important part.
    • *      Budapest, you need more pedestrian traffic lights, for real. Had some very stressful experiences running down entire long streets to find a crossing in the dark/while running late for flight.
    • *      Why did the hotel have a dentist? Or at least a sign for a dentist?
    • *      Please do not change the stops on your bus route when it goes in different directions. I guess I should’ve believed Google Maps when it didn’t give me the same route back as it had on my way in, but oh man why did the airport shuttle bus stop somewhere I connected to on the way from the airport but then not stop there on the way to it? Very confusing, and led to lots of stressed-out getting lost and arriving to the airport only an hour before my flight when I’d meant to arrive 2-3 hours before it.


    • *      I had great fun getting Anna (from Greece), Marco (from Italy) and Robert (from the Czech Republic) to try to pronounce Irish names like Caoimhe, Siobhán and Sadhbh. They concluded that Irish sounds nice but looks awful and is very inefficient with its letters. It really was amazing fun though, like chocolate for my brain.


    Things I Learned
    • *      Italian is a beautiful-sounding language, oh my God. I got Marco to read out the first verse of TS Eliot’s The Love Song of J. Alfred Prufrock (which is in Italian) and honestly it was amazing.
    • *      Hotel staff can be super helpful. I’m always really dehydrated in hotels and this year I’m super broke so couldn’t buy tons of water bottles, so I went down to the bar and they filled up my empty bottle for free. Also, they printed my boarding pass for me at the desk.
    • *      If you’re lost in a country with a different language (maybe in general to be honest), go into a hotel and ask a receptionist. They’ll generally be able to speak English.
    • *      Czech people (two of them, at least) don’t know that the backwards peace sign means ‘fuck you’ in Ireland.
    • *      Greek has a letter that literally just looks like a curly bracket.
    • *      If you’re really unhappy about something, speak up! You might succeed and change the thing for the better, or you might fail and get impeached/resign and then at least you don’t have to be associated with and work on a bad thing anymore. Win-win when you kick the fear out. Also, if you’re feeling it, chances are other people are too but also don’t want to speak up. So just be open.
    • *      The Hungarian government is intense and oh boy funding has strings attached.
    • *      Survivorship bias is a hell of a drug.

    Personal Development Payoffs
    • *      Having learned in Ireland over time that buses going in different directions generally have their stops on the opposite sides of the same road really helped when I needed to find the bus from the shuttle bus to my hotel without being able to read Hungarian.
    • *      I realised that I’ve actually picked up a lot of knowledge and experience in my five years of blogging and was able to help and advise people with actual good, actionable advice.
    • *      All my public speaking practise has definitely made me more articulate and better at thinking on my feet.


     I am very much in Dublin finishing this post ten days later, in case you were concerned that I've been in an airplane for that long. But yeah, there's a quick rundown on the meeting. You can watch a video one of the project leaders made about it here.

    Thursday, 2 November 2017

    Review: October 2017

    Hi guys! I've been hella busy this month but just with college and studying mostly, not with a ton of super exciting events like last year, oops. Have been generally happy though, so that's cool. I'm gonna talk about the modules I've been doing (next week I'll have a blog post on each module talking about what I've learned in the first six weeks), Lablinn, pals, Physoc, conferences n things, Harvard grades, going outside, Hurricane Ophelia and other miscellany.

    COLLEGE: EVOLUTION MODULE 

    This is probably my favourite module. It covers the mechanisms of evolution (natural selection, genetic drift, founder effect, bottleneck effect, allopatry/sympatry/parapatry, polyploidy and hybridisation, etc), the evolution of animal behaviour (co-evolution between predators and prey including arms races and mutualisms, Batesian and Mullerian mimics, sexual selection and dimorphism, cooperation (including mutualism, reciprocal altruism, kin selection, the evolution of intelligence and more)), endosymbiotic theory, biogeography, genetic evolution (genotypes and evolution, phylogenetics including tracing the origin and evolution of HIV, and upcoming lectures on human evolution, evolution of development, and disease genes). 

    I know I just listed all the stuff we've studied, hope you survived that paragraph, but anyway it's so fascinating and fun and I'm learning so much while having a blast. The practicals are also all really creative -- they're all self-directed, which is pretty challenging, and one was to go down to the Trinity Botanic Gardens and answer a ton of questions about plants there and their evolutionary relationships, one was to go to the Zoology Museum and build phylogenetic trees of animal lineages based on morphological characteristics, and for the upcoming one we have to test a theory of altruism by designing and completing our own experiment out in the world. Surprisingly challenging, but very cool. Also, the lecturers have in general seemed to love their subject and be friendly and positive, and all around it's just a great experience that I'm delighted to get to experience. 

    COLLEGE: BIOCHEM I MODULE

    This is a strong contender for favourite module; it's a lot of work because of the module structure, and it's harder, but it's super interesting. It's taught as a flipped classroom, meaning we're given recorded lectures to watch and take marked (for continuous assessment points) quizzes on before attending the lecture, and then extra material is covered in the lecture or we get more quiz questions in the lecture via clickers, which are great because we can answer the MCQs on the slides without having to risk shouting out an answer and being wrong, and also the lecturer can see what percentage of the class picked each answer so they know how much we understand. 

    Because we often have two or three presentations and quizzes to do per lecture, it can mean that we essentially have 12 Biochem lectures a week instead of 4, but I do like it because it makes sure I stay on top of things and because we get the results of each quiz and I generally get 100% so (a) I know it's contributing lots to my CA marks (b) I know that contrary to what members of college admin said, I am in fact capable of doing this subject despite not having done it for first year or Leaving Cert. They really wore down my confidence despite all the work I'd done to get up to speed but this is a really nice means of validation and of seeing that I am in fact capable of doing well/getting 100% instead of failing like they acted like I would. So I like how this module gets me to work hard but does reward me for it. 

    So to get to the actual stuff we cover:

    • Eukaryotic Cell Structure (cell anatomy and means of transporting molecules in and out of organelles; the cytoskeleton i.e. how things are transported around and arranged in cells; DNA, RNA, Transcription and Translation; the Cell Cycle and Apoptosis i.e. programmed cell death)
    • Proteins (Amino Acid Chemistry; Protein Purification & Analysis; Protein Folding)
    • Enzymology (Michaelis-Menten Kinetics, Briggs-Haldane Kinetics; Enzyme Inhibition modes; Enzyme Regulation)
    • Neurochemistry (chemical synthesis of neurotransmitters; action potentials and signal propagation through nerves; neurotransmitter reuptake and degradation; medical applications including Parkinson's and depression medications)
    • Signal Transduction (upcoming)
    I didn't really like enzymology but acknowledge that it's important so will learn it. The other stuff has on the whole been fascinating -- there are so many disease-related applications, for one (imagine how excited I was learning how Triple Therapy for Parkinson's works and being able to understand why), and just getting to learn so much and understand so much about how life works. It's an intense course with the essentially 8 to 12 lectures a week thing but it's meant I've learned an incredible amount. I never thought I'd be able to understand this much after just six weeks of college (and a lot of work over summer) and it makes the hard work so worth it. 


    COLLEGE: CHEMISTRY

    Chemistry has been my least favourite module this year but it's been alright. We had a week of Kinetics, which was very intense and squished into fewer lectures than it should've been, and since then it's been Inorganic Chemistry (Coordination Chemistry of Transition Metal Complexes and Molecular Orbital Theory). Our Inorganic lecturer is good with creative analogies, and I did like Crystal Field Theory and the associated field splitting diagrams. My appreciation for them isn't really because they helped me understand stuff that much, it's more just that I got them quickly and like making logical diagrams and populating them according to logical rules. 

    COLLEGE: MATHS (MULTIVARIABLE CALCULUS)

    Maths has been way better this year, mainly because we have a really good lecturer now and also some stuff seems to have clicked because I had to finally learn them for the summer exams, like finding a vector product using matrices and using the various techniques of integration (I can't believe it took me until after the first of the summer maths exams to just learn that stuff properly). 

    There have been some things I haven't understood but I've generally felt comfortable asking the lecturer during or after class because she's really approachable and cheerful, so that's been really helpful. The maths can get pretty crazy though -- look at this from today:



    LABLINN

    We've been working hard over at Lablinn. 



    • We held a Training Day to train the team members in holding workshops and worked out logistics for going out in pairs to schools. Also did all the associated things (there are so many associated things) like refining the presentation, writing a script, minutes, FAQs, templates...
    • We have a workshop organised for a school in Meath next week, and two more being organised at the moment. 
    • We have an interview underway with APOPO, the organisation behind the HeroRATs that detect TB and landmines.
    • I've drafted Lablinn's themed weeks, which run every two weeks, from November until May. Next week is Diagnostics week, so we'll have our APOPO interview and some articles from me on nanodiagnostics and the relevance of diagnostics to antibiotic resistance. 
    • Daniel, a Gaeilgeoir member of the team, is heading up a project to get some of our material translated into Irish so we can talk to Gaelscoileanna as well. 
    • Ella wrote an article for the blog about presenting her research at the Young Scientists' Journal conference.
    • Members of the team have in general been really great at taking the initiative and coming up with e.g. interviewees to contact and articles and ideas for developing Lablinn.
    • I've been invited to speak at Twitter Dublin about our work next week. 
    We're also doing a bunch more that I'll share later but yeah, I'm really loving the momentum we have going. Lablinn team is cool. 


    HURRICANE

    Hurricane Ophelia hit Ireland so college was cancelled for a day. It was pretty windy out. That's it really -- we had prepared to lose electricity but we were lucky and didn't even though thousands of people near us did. So a pretty chill hurricane on our end. I did see a tile fly off a roof and over my head and smash on the ground in front of me though, which was pretty cool. 

    HARVARD GRADES 

    I got my grades back from the Harvard Business School thing I did over the summer -- got 100% (800/800) on the Statistics exam, 96% in Economics and 93% in Accounting, which was cool. Kinda funny since I don't like business but in fairness I do like stats so. 




    OUTSIDING

    I went outside sometimes! Climbed the Sugar Loaf (a mountain, for the unacquainted) on the bank holiday we had off college with a bunch of college pals. Here we are.




    LEON

    Have been officially living with Leon for a month and a half now. It's pretty good. This month we went to the cinema to see Maze, which was about an IRA prison breakout, and bought a new board game to play together called Forbidden Desert as a Halloween treat. We've mainly been playing Magic and Carcassonne this month, which are both fun. We were playing Pandemic a ton (epidemiology? yes please) and he got sick of it so  "accidentally" left it behind when we moved out. 

    PHYSOC

    I'm Physoc Secretary this year, which as an exec position actually has some responsibility attached. I quite like being Secretary; my responsibilities are to write the weekly email to our members and take minutes at meetings. I stress a bit about having the wrong information in the email but generally it's worked out pretty fine and I like it, it feels like I have my own domain which is nice. 

    SPEAKING

    I've been invited to speak at a Twitter-UNICEF event on Thursday November 9th at Twitter Dublin HQ about my work with Lablinn and "raising your digital voice", so that's a thing.

    CONFERENCES N THINGS

    I'll be off in Budapest 10th to 13th November at the Youth Platform's annual meeting there. 

    IN GENERAL

    In general, I've really buckled down over the last few months after transferring to a subject I love and am doing fewer conferences and superficial things and more just keeping my head down and putting the work in. Conferences are fun and I'm open to doing some if asked (see above), but I'm not seeking out that sort of thing quite as much and am instead studying a lot and working away building Lablinn up. It feels really nice and wholesome and fulfilling. 

    I should have significantly more blog posts in November I think because I'll be writing about my impressions of each of my modules after six weeks, Budapest, Twitter, and maybe some stuff about Lablinn. If you want to keep up more with Lablinn, you can check out the website or @LablinnTeam on Twitter.