Wednesday, 10 July 2019

The case of the disappearing gene

Yesterday, I needed to add something to my code to account for genes that were unannotated by GO Term Mapper, but that broke things so I went back to my unedited code to make sure that was working. 

At some point, I think shortly prior to things breaking, I had saved my output dataframe to a file to protect it, which let me see when I reran the unedited code that something had changed - one gene, OAS1, was missing. But the code didn't seem any different, so how could this gene have gone missing?

I checked OAS1 was indeed in the saved df - yep. 

I tried to check in my other dataframe, which stores overlapping Neanderthal haplotypes with genes, for it, but OAS1 had never been in that dataframe because it has no overlapping haplotypes so that didn't help. This also meant I wouldn't be able to confirm what the right gene was by comparing the overlap lengths to the saved df (apart from checking that they're all zero/NaN in the relevant columns). 

I checked that my inputs to the call to biomaRt were still asking for OAS1 as before, and indeed they were - yet it wasn't coming back from biomaRt. 

Then, to check it wasn't a problem with my code or using biomaRt from R, I went to the browser and the Biomart website and manually typed in OAS1, OAS2 and OAS3 as my gene filters - that just returned results for OAS2 and OAS3. So the gene was missing from Biomart and thus presumably Ensembl.

I searched on the Ensembl website for OAS1 and just got random things like an antisense transcript over OAS1, 2 and 3, whereas when I searched OAS2 I got the OAS2 gene. 

So then I thought maybe I had the wrong name for it (even though that wouldn't answer why it was there in the dataframe I made max a few days before) - but I looked at HGNC and OAS1 is apparently its approved symbol. 

I also tried searching Biomart for OAS1 as symbol rather than gene name, but still no dice. HGNC listed OIASI and IFI-4 as alternative symbols for OAS1 so I tried those too, but still nothing. 

Finally, just googling 'OAS1 ensembl' and clicking on the top link, a link to Ensembl with the title 'Gene: OAS1' and the stable ID, redirected me to a page with the gene called 'AC004551.1'. 

I satisfied myself this was the right gene by:

  • modifying my code to replace 'OAS1' with 'AC004551.1' in my call to Biomart and seeing that the output dataframe now had the right number of rows (4968 vs 4912 before) because the number of rows a gene gets depends on the gene (which GO term categories it's in). 
  • seeing it was not in the overlaps dataframe
  • calling all.equal() on the new dataframe's categories for the gene AC004551.1 and the old df's categories for the gene OAS1. 
  • calling all.equal() on the new df's start position for that gene and the old df's start position for OAS1.

So that leaves me with the conclusion that Ensembl changed the gene name silently within a few days. So that's a thing that can happen.

Learnings etc:

  • Now that I think about it, to make sure it actually exists in Ensembl and find the name Ensembl is calling it, I probably could've searched by its coordinates, which I had from my saved df. 
  • Turns out I need to use human genome build 37 instead of 38 because that's what my haplotype data is based on, and the gene is called OAS1 in 37 anyway, but there you go. 
  • Perhaps I should've used the stable IDs, but everything else I'm using uses gene names and I guess I preferred not to have to convert those. 
  • Ensembl seems to change gene names without warning. If you have another explanation, shoot me an email at loughrae/@/tcd/./ie!


Is this the most boring blog post of all time? Quite possibly. Oh well.



Friday, 28 June 2019

Review: Two Like Me and You by Chad Gibbs

Two Like Me and YouRating: 3/5
Source: ARC from Netgalley for review
Date finished: 16 June
Pages: 298
Publication date: May 20 2019

Summary: 

A teenage boy breaks an old man with dementia out of his nursing home and smuggles him to France in search of the man's long-lost liver, and in hopes of getting famous to convince his famous girlfriend to get back with him.

Negatives: 


I found this book difficult to get into - it was one of those books where I read a few pages, then put it down for weeks, then once I picked it up again when I'd nothing to do in a bus read the rest in two days. 

The narrator is a perv - are teenage boys just like that? He keeps talking about ogling random girls, and his goal is fairly creepy in general. He was also very reactive, which honestly was fine as a reader but I hear you're not supposed to do that. 


Finally, I didn't find the ending satisfying. There was something in there that I'm pretty sure was supposed to be some grand metaphor but I'm afraid I did not get it. 


Positives:

Once I got into the story, it was a fun adventure, a romp through France with lots of nice little details. It was also solidly funny, and the relationships in it were pretty heart-warming and wholesome, especially the protagonist's relationship with his best friend - a heartfelt male friendship! Amazing! 

While Parker (the girl who drags him into this adventure) was kind of a Manic Pixie Dream Girl, she had her own problems and her own goals in life, which I liked. 

In summary: If you can stick with it through the first few pages, a fun and pretty wholesome story.  It wasn't one of those books that stick with me or make me strongly identify with the characters or feel very deep, but it was an enjoyable read.





Friday, 14 June 2019

Book Reviews: May 18 - June 13

I've read 8 books between May 18 and today, and like last time with the books from May 1 to May 17 I've decided to do bulk reviews because that'd be a lot of individual reviews to write!

Le Petit Nicolas - Goscinny & Sempe

Le Petit NicolasRating: 3/5
Source: Bought for Kindle app on iPad
Date finished: May 18
Pages: 167

This is the first French book I've ever read. It's a children's book and is, I am surprised to find out, only 167 pages long. It took me weeks to read because I read one chapter (about 5%) a day. But hey, it's in a different language. So that's pretty good. And the stories were grand.



Coders: The Making of a New Tribe and the Remaking of the World - Clive Thompson

Coders: The Making of a New Tribe and the Remaking of the WorldRating: 3/5
Source: Local library app
Date finished: May 23
Pages: 448

An interesting anthropological history of the emergence of tech culture. Quite a few interesting insights (e.g. about women in tech, AI) I may write more about later. I knocked off a star because he said he was surprised to find out someone had Asperger's because he had liked them!




You Can Change the World! Everyday Teen Heroes Making a Difference Everywhere - Margaret Rooke

You Can Change the World!: Everyday Teen Heroes Making a Difference EverywhereRating: 2/5
Source: ARC from Netgalley for review
Date finished: late May?
Pages: 240

A variety of stories written by teenagers around the world about inspiring things they've done. Felt it was false advertising as it was really about things like overcoming adversity, being yourself etc more than changing the world. It was also pretty rude about non-teenagers and formatted terribly, even for an ARC. Full review here (I reviewed this one in full because I got it for review). 



Bridge to Terabithia - Katherine Paterson

Bridge to TerabithiaRating: 4/5
Source: Local library app
Date finished: June 3
Pages: 128

A beautiful little story about a 5th-grade friendship with a devastating ending. I found it hard to get into at first because of the narrator's dialect, but it's really quite gorgeous.




Internal Medicine - Terrence Holt

Internal Medicine: A Doctor's StoriesRating: 2/5
Source: Brown University bookshop
Date finished: June 4
Pages: 288

A collection of essays about life as a hospital doctor. I love these stories, except this was ruined because he says at the start that none of the stories are real - not even the narrator is really him. I understand changing patient names, and while it ruins it a bit if you change details of their diseases, fine - but he said he fully amalgamated patients so as not to profit off anyone's suffering. Noble ideal, but why write it in that case? There was also a completely fictional story at the end with some moral I couldn't understand. 

On the bright side, it was compelling and I read it from the evening of June 3 into the evening of June 4. And it was pretty cheap, around $6. First physical book I've read in a while. That day I also bought Planet Earth is Blue even though it was physical and ridiculously expensive because I wanted to support the autistic author.

The Hate U Give - Angie Thomas

The Hate U GiveRating: 5/5
Source: Local library app
Date finished: June 8
Pages: 444

This book was amazing. I'll list my few gripes first:

  • the AAVE dialect bothered me a bit, especially them always saying 'out the' instead of 'out of the', but I get why it was used. Just hard to get used to.
  • No idea why Starr didn't get arrested for one of the things she did in the book (not that I think she should've, morally, necessarily, but it seems like something you'd be arrested for)
  • I felt uncomfortable criticising the book because I'm white, which is not ideal.
  • Starr seemed rich (e.g. her dad owns a shop and she goes to a private school, albeit with a scholarship) and felt somewhat estranged from her black friends since she goes to the white school - I wondered whether this was done to make her more palatable. My gripe is that she says in the book something like 'X is white, I'm black. X is rich, I'm poor' when she's not poor!
Now back to the good stuff. It was seriously great. It's about Starr's friend, Khalil, being shot by the police while she's in the car with him, and her subsequent choice on whether to speak out and try to get justice for him. It was so compelling and really made me empathise with her situation (and feel angry that police departments get to investigate the crimes of their own officers?! Does that happen in real life?!). But what's really impressive is that even without the topical, compelling subject, this book was a great YA and reminded me why I love YA so much. It's hard to put your finger on, exactly, but it's the way you get up close to the narrator and feel their life around you. Also, the scenes with her family were super adorable, same with her boyfriend, and her little brother's name, Sekani, is cool. 

Find Your Why: A Practical Guide to Discovering Purpose for You and Your Team - Simon Sinek, David Mead, Peter Docker

Find Your Why: A Practical Guide to Discovering Purpose for You and Your TeamRating: 2/5
Source: Local library app
Date finished: June 9
Pages: 256

I like the core concept, which is that finding your WHY (he always bloody capitalises it) means looking for your origin story: what are the threads that go through your life experiences and show you what motivates you to do what you do. I may try to find out, though I dislike how he keeps saying you need a partner and can't do it by yourself - maybe that's true, but maybe he's trying to sell his workshops.

Apparently the process is to think of a load of specific childhood stories and figure out why they're important to you, then draw out themes from there. 

This was one of three leadership books I just took out from the library - the Laidlaw Scholarship have got their claws into me apparently! Our Laidlaw workshops and other entrepreneurship stuff I've done have talked a lot about the importance of vision but I've struggled a lot with articulating mine, so I read this book. I'm glad I picked this one instead of the first book, START WITH WHY, because I would've been frustrated without practical instructions I think. I know I struggle with leadership - maybe it's because I'm autistic but I really find it very difficult. I am a leader in the sense I take the initiative to do new things, but I'm not good at working with teams and I want to be, both as an ordinary member of the team and as the leader of a group. One issue is that I do not naturally hold much authority or gravitas, so I got a book about leadership when not in a position of authority and another one about communication.

Now for my many gripes: 
  • He gives the template of a WHY statement as 'to ________________ so that _________', with the first blank being your contribution and the second its impact. All okay so far. But he gives many examples of supposedly good WHY statements throughout the book and nearly all of them are utterly shite! 
    • To innovate relentlessly in order to create opportunities for everyone*
    • To believe in people so that they can, in turn, believe in themselves
    • To provoke people to think differently so that they can be awakened to new possibilities (I guess this one is ok)
    • To bring people together to savor life (the company makes coffee machines)
    • To enable people to be extraordinary so that they can do extraordinary things
    • To propel people forward so that they can make their mark on the world
    • To provide for people so that they thrive and feel empowered to always do the right thing
The only good one I remember was about a guy wanting to promote sustainability to leave the Earth a better place for future generations. 

  • He says everyone has a WHY, and that the WHY must include helping people - this just seems unlikely. There have to be some people in the world who are not in fact driven by helping others. 
  • He says everyone has one WHY, and that the reason your colleagues, friends and significant other love you are all the same, which I doubt. He also says that the contribution you make to your family is the same as the contribution you make in other areas of your life, which is obviously false. Maybe this is why so many of the WHYs above are so vague. Or maybe it's that their jobs are to do this WHY training so it's very meta. 
  • Misuse of biology - reading this kind of book (what is it? It's not even pop science - pop psychology?) does put a biologist in danger of annoyance, but ugh. 
  • One of the tips is to think of a day where you left work and thought 'I'd do that for free' and figure out what it was about that day that made you think that. But I mean, I think that about most days at work (I would still like to be paid, thanks) and I don't think it's necessarily connected to some deep inner purpose. I do find biology fulfilling but I don't see what that has to do with helping others (it's not for medicine), and one major reason I say I'd do that for free is that I spend most of my day coding and doing data analysis and I do exactly that at home as a hobby. The money helps me stick with it through the tedious and tough moments. And also I need to eat and otherwise service my corporeal form.
Planet Earth is Blue - Nicole Panteleakos

Planet Earth Is BlueRating: 3/5
Source: Bought from Brown University bookstore
Date finished: June 11
Pages: 240


I bought this book even though it was non-digital and very expensive because I wanted to support the #actuallyautistic author writing about an autistic person. I'm not sure how I feel about the book. The narrator had a very, VERY childish voice even though she's about twelve, which I didn't really enjoy. I liked it talking about the people who did and didn't believe in her because she couldn't speak, and it was accurate to the parts of the autistic experience myself and the character share. 













Monday, 3 June 2019

Recap: May 2019

It's been a good month! The big event is of course my journey to America to start my 11-week J1 internship doing computational biology at Brown University in Rhode Island. 

America

I've been here for three weeks and am really enjoying it so far. The flight was very uncomfortable, as if American Airlines was punishing me for being an Economy class pleb, but at least I love the exhilarating feeling of flying. 



I'm in Providence, which is a city, but contrary to my expectations of America the area is actually quite quaint. The weather is nice and not too hot so far, and I've done a little bit of tourism to see the Rhode Island statehouse, downtown Providence, and Newport.  I also went to the Providence Public Library, where they're selling seeds for some (cool) reason.






Providence is absolutely gorgeous and there are trees and ocean everywhere. As in, ocean two feet from the road, everywhere. There are also lots of cool new (to me) flowers.



This picture is so calming all by itself.

I haven't actually done a full week at work yet because I started on my second Monday but that day was for admin and then this week's Monday was Memorial Day. I'm staying with my aunt, which is great because we're getting to talk lots. 

 

The public transport here is pretty awful - no buses to where I am after 8 pm - but on the bright side RIPTA (the transport organisation) has a cool app where you can buy tickets and use them instantly on your mobile device (do you hear me, Dublin?) - and I found out this week that my bus travel across the whole state is free with my Brown University ID card!

I have, in my opinion, been good about trying new things, which doesn't come naturally to me. I've been trying a fair few different food places around work. I've also been doing a bit of 'involuntary tourism' by getting lost on the way back from work to the bus!

I joined some Meetup groups to make sure I have social things to do, and have gone to one event so far, a meeting of the Providence Data Science group.

I am so relaxed, which is very rare for me. It's great! Especially because I was apprehensive about coming. Thank you Trinity Genetics Department for the scholarship :) 

(Look - they made me a sign!)



Work - the science part
I'm working on timing adaptive introgression between modern humans and Denisovans and Neanderthals, i.e interbreeding events that gave us beneficial alleles. I like it!

I spent my first two weeks figuring out how to run someone's program for all combinations of parameter values (grid search) and graphing my results (can you believe I get paid to graph?! I saw graphs in a paper and knew immediately they'd been made with default ggplot2, and then later - couldn't believe my luck - my supervisor asked me to recreate those graphs!). Obviously, there have been annoying parts like breaking my code, and I've been nervous meeting new people, but I've been feeling really happy and bouncy coming home from work. I normally spend most of my time stressed, but I am genuinely happy here and now. Summer is great.

Work - gallivanting

My walk to work is up two unbelievably steep hills, but I kinda like it because I need the exercise and the place is gorgeous.
This is not the hill.


The people are fun, and we do lots of outings. In my first week we all went out to dinner to say goodbye to Carla, a lovely post-doc who unfortunately left at the end of my second week. Then this week just gone two people brought their dogs in (a bunch of us went out for an hour during the day to walk one of those dogs), I went to a party and hung out with a snake, and we went to a gardening shop and out for ice cream waffles. 





People in my lab/department out for icecream waffles!






Perhaps the best part, though, is that nearly all of the walls in our fancy office are WRITABLE!



Reading

I read a lot this month, though it has definitely dropped off since I started work. I read 8 books between May 1 and May 17, mini-review of which you can find in this blog post. Briefly, they were (K = bought for Kindle, L = library app, N = Netgalley):

  • Simon vs the Homo Sapiens Agenda - L
  • A Thousand Perfect Notes - K
  • Bad Taste in Boys - K
  • Craic Baby - L
  • Losing Earth - L
  • The Unexpected Everything - K
  • This is Going to Hurt - K
  • The Mathematics of Love - K
Later I finished Le Petit Nicolas (K, a kids book in French), and read Coders (L, an ethnographic study of programmers) and You Can Change the World (N, review here), and am currently reading Bridge to Terabithia (L). I started Tamed (L) by Alice Roberts but didn't like it so let it expire. After these, I have two Netgalley books to read and I'm also interested in reading an #ownvoices book about an autistic girl, Planet Earth is Blue, if I can get it for Kindle. It's probably a good thing that there's no internet on the buses here so that I don't waste my journeys on bloody social media.


Writing

I have returned to writing a novel that I did most of the first draft of five years ago, when I was 15, and I am loving it! I'm participating in the GoTeenWriters 100 words for 100 days challenge, which started on May 20th, and every day since then I've written 1000 words! I do it at night right before midnight and it really makes me happy. I've also noticed that since I've started actually writing I'm getting ideas way more often. It's so much fun doing this creative work. 

Junior Sophister Results

I got my overall results for my third year of college and first year in the specialised Genetics moderatorship. I got 78% overall, which isn't as good as last year's 86% but it's a good First and keeps me in the running for a Gold Medal. Damn hard markers. Also, I'm just much more relaxed about grades this year in general. I still worked very hard, but in second year I did nothing but study, probably because in second year I was doing Schols and then had to compete to get my place in Genetics. Now I feel more secure. Then again, this year's results actually count towards my degree - 20%. A low enough number that before each exam I could calm myself down by saying 'this is only 1.6% of your degree'.

Anyway, the results:



I did best in Data Handling (Python, terminal use and statistics, 94%), Evolutionary Genetics (89%) and Neurogenetics (81%, I bet this is because I wrote a 6-page essay on heritability with all the material I didn't get to use in the Medical Genetics exam the day before). I did worst in the Molecular Genetics lab (68%), the lit review (70%) and jointly the Analytical Genetics lab and Eukaryotic Molecular Genetics (72%). I got one 2.1 whereas last year I got all firsts. Still grand.  

Family & Friends

Leon and I spent the first 12 days of the month together, before I flew over here. I was definitely sad to leave him but he is coming over to visit soon, so that's something. I also visited my family before coming over, and they'll be coming here too.

Misc

I published a very scary blog post about child abuse and shared it on Twitter. People were very nice and supportive, and I'm hoping to turn my experience into something good by getting some change in child abuse policy from the government. 

I started learning some Hawaiian this month and kept up my French, so got to roughly a 334 day streak in Duolingo French by the end of May.

I made a quick dataviz out of a concept I'd had in my head for ages and it got to a peak of #3 on r/dataisbeautiful! The viz itself isn't very good and I didn't make the diagram from scratch but used sankeymatic to do it, but I think the idea is fun.



Like I said - a good month!

Sunday, 2 June 2019

Review: You Can Change the World by Margaret Rooke


You Can Change the World!: Everyday Teen Heroes Making a Difference EverywhereRating: 2/5
Source: ARC from Netgalley for review
Pages: 240


Summary

A collection of vignettes, each a few pages long, from about 50 teenagers to inspire fellow teenagers to take action in the world, get through adverse experiences or turn their lives around. 

The Good

There was a variety of stories, and some of them were indeed inspiring, like the girl who got Tesco to agree to stop selling eggs from caged hens or the guy into fashion design who makes clothes for the homeless. 

It wasn't just famous people. There were a lot of people I know or know of from the teen activism/science fair circuit but there was only one of them here. Whether that was because the author couldn't get a piece from them or chose not to talk to them, I don't know. It would've been interesting to hear from, for example, Greta Thunberg and Jamie Margolin. However, it was good to give these lesser-known activists some publicity. And the fact that these teens seem relatively normal, not at the exalted heights of Greta Thunberg or Malala Yousafzai, might make it easier for reading teenagers to relate and feel inspired.

I noticed there were loads of autistic people included, which makes me wonder whether we're drawn to activism or whether the author is drawn to us! 

The Bad

My main issue is that this book was false advertising. It's called 'YOU CAN CHANGE THE WORLD' but only a small section of it is about campaigns to address issues in the world, while the rest are to do with things like coping with a parent's death or bullying. Those are good things and deserve recognition, and perhaps the author means to express the idea that change on a small scale changes the world too, but that did not get across. 

Something that really annoyed me was the insults towards non-teenagers. So many of the contributors to the book said teens are more flexible, creative, etc than non-teenagers. It really annoyed me because the way it was written made me feel ancient when I'm only twenty! I'm one year done with being a teen but they made it sound like I'm basically dead! That said, it did have some fair points like that teens have a unique ability to make change through social media and in school because of the way teens socialise, and that teens are impulsive and more likely to take risks, which is often bad but can be necessary to make changes.

Then there's a general issue with any sort of book like this, which is: how do they decide what's 'good'? Presumably they want to encourage teens to change the world for the good, but that's a very ill-defined concept. For example, I think all the teens here used non-violent (and not even mildly disruptive of business at all) means, but I think violently liberating a concentration camp would be considered good. And if a cause is mainstream enough to be celebrated in a mainstream book, maybe it doesn't need to be fought for. For example, years ago when being gay was widely considered immoral, smaller, fringe gay activist groups agitated for rights while the mainstream wouldn't support them. So maybe the people who really need our help are the people we aren't hearing from yet. 

Personally I had some problems with what was celebrated in this book and didn't agree with everything the contributors were saying. Someone was talking about how we should understand other cultures, like how their African friend wasn't comfortable with a couple sitting together. There was also a guy who was 7 feet tall at ~15 and after playing basketball for a bit got scouted for a team - what is the moral there? Be born with immense genetic privilege? (It's probably to make the most of the talents you're given, and the guy seems nice - it just reminded me how much of success in sports and other elite fields is due to innate genetic talents). And someone trying to help disabled students in their school by getting everyone to wear sunglasses for a day to 'understand what it feels like to have autism' (???).

The ARC was also formatted terribly. Obviously, the whole point of an Advanced Readers Copy is that it isn't finished, so you're not supposed to comment on exact quotes or formatting, but this was done to a far lower standard than any of the many ARCs I've read before - lots of 'insert ending here' or 'insert illustration here' and pictures in the middle of sentences. 

Recommendations

What I hoped for from this book was a collection of stories with different methods of changing the world, but it only gave me a couple, like petitions and fundraising. The book even says at the end that it has a list of tips for changing the world, but they're not very useful.

The book is probably good for inspiring young teenagers to make something of themselves, but doesn't live up to the promise of the title. 

Saturday, 18 May 2019

May Book Reviews (May 1 - 17)

Turns out I've read 8 books in May so far, which is a pretty huge jump from usual - I read 8 books in the previous 4 months put together! It is fabulous being off for the summer, and in particular these last 3 weeks I've been completely off so they've been my best chance all year to get reading done, and I'll probably slow down a bit once I start work on Monday. Also, I've been intentionally reading a lot of short books because that's what I feel like at the moment, so not that impressive. All pagecounts below are from Goodreads even if they weren't the exact amount in the edition I read.

Simon vs the Homo Sapiens Agenda - Becky Albertalli

Simon vs. the Homo Sapiens Agenda by Becky AlbertalliRating: 3/5
Source: Local library app (Borrowbox)
Date finished: May 3(?)
Pages: 303

Blurb
Simon is a gay highschooler who's being blackmailed by someone threatening to tell the school he's gay, while conducting an online flirtation with a mystery guy in his school over email.
Review
This book was pretty cute and funny, but the main character is a bully who makes fun of people for being weird, and it's not acknowledged, so I can't support that. You can't do that just because you're gay. He's also bizarrely friendly with his blackmailer so the stakes didn't feel super high. 

I liked that he was kind of private and so was his boyfriend, not super campy (which is fine, obviously, etc), even though I'm the type to be open about my sexuality.
A Thousand Perfect Notes by C.G. Drews

A Thousand Perfect Notes - CG Drews

Rating: 4/5
Source: Bought for Kindle app on iPad
Date finished: May 5
Pages: 282

Blurb: Beck spends most of his days practising piano, which he hates but is forced to do by his abusive mother who is making him into a piano prodigy so she can live vicariously through him. The abuse keeps escalating but he has no hope until he meets a girl called August at school. 

Review: August was absolutely a manic pixie dream girl, so that was annoying, but having experienced it myself I can say the abuse was good representation - contrary to those who said it was unrealistically brutal, except perhaps at the end - and I liked the book. 


Bad Taste in Boys - Carrie Harris

Bad Taste in Boys by Carrie HarrisRating: 3/5
Source: Bought for Kindle app on iPad
Date finished: May 7
Pages: 201
Blurb: When a high schooler discovers the coach is giving the players illegal steroids, she investigates and discovers that they're turning the players into zombies and there's now an epidemic spreading through the school. She has to sort it out. 
Review: This was a fun, short book (read time only 2 hours). I really liked that the heroine was a scientist, but I hated that she loved dissecting animals (aka murder) so that really knocked my enjoyment. Also, the writing was significantly flawed - far too many plot-convenient decisions not to tell someone about the zombie epidemic and trick scares making it seem like zombies were attacking when it was just a cockroach/a haunted house/someone being normally sick. Unless it's a sophisticated story about what happens to someone's mind under pressure?

Craic Baby - Darach O Seagdha

Craic Baby: Dispatches from a Rising LanguageRating: 2.5/5
Source: Local library app (Borrowbox)
Date finished: May 13
Pages: 268

Blurb: A meditation on the place of Irish, with random Irish words and phrases shoved in. 
Review: I really liked his essays, especially about his daughter, and would gladly have read more of those, but found the lists and boxes of Irish words gimmicky - maybe they help sell the book, since they're found on the cover. A lot of them were very tenuously inserted, like he'd say X, not to be confused with [Y that doesn't sound at all similar to X], and I didn't like the chapter on Hiberno-English. But I really did enjoy his essays and musings, on Irish and other things. 

(I did get a nice word for 'bad inheritance' though.)

Losing Earth - Nathaniel Rich

Losing Earth: A Recent HistoryRating: 3/5
Source: Local library app (Borrowbox)
Date finished: May 15
Pages: 224

Blurb: The story of the decade from 1979-1989 during which climate change was a bipartisan issue that came tantalisingly close to a global accord to solve the problem, and how it all fell apart. 

Review: Pretty good, and less depressing than I had expected (which is why I delayed reading it), probably because of the very historical tack. The author takes a very intense tone at the end, though, vilifying those merchants of doubt who deny climate change and continue to destroy earth, or at least humanity's chances of a future on it. A weird book to read, but better to be informed hopefully. One of its most interesting points is that pretty much all the science has been known for 50 years - which, come to think of it, reminds me of this infuriatingly true Onion headline: 

Image result for the onion scientists global warming politely clean energy technology


The Unexpected Everything - Morgan Matson

The Unexpected Everything by Morgan MatsonRating: 4/5
Source: Bought for Kindle on iPad
Date finished: May 15 
Pages: 519

Blurb: Andie is the daughter of a congressman and is used to being the perfect daughter, never doing anything to jeopardise her dad's career, and having her medical career path mapped out. But when a scandal means Andie's dad steps down from his job and she loses her prestigious summer internship, she is cut adrift. This incredibly Type-A personality ends up walking dogs all summer, in the meantime meeting the mysterious, adorable Clark, spending the summer with her tight group of friends, and actually seeing her Dad for the first time in years. 

Review: This book was too long, but really sweet and touching. It's frustrating how self-destructive Andie is (in terms of not trusting people enough to be vulnerable with them) but it's a good arc. I'm very fond of all of the characters and thought it was fleshed out really nicely and made into a sweet, realistic coming-of-age story. A really nice book for some summery warm-and-fuzzies with depth.

This is Going to Hurt - Adam Kay

This Is Going to Hurt: Secret Diaries of a Junior DoctorRating: 3/5
Source: Bought for Kindle on iPad
Date finished: May 16
Pages: 256

Blurb: Adam uses diary entries from his years as a doctor (all the way up to senior registrar level) to show what life was like and just how ridiculously punishing life as a 'junior' doctor is. He throws in a lot of humour throughout.

Review: Fundamentally, he makes a very important point, and I don't know how on earth people survive that or why we do that to doctors (seriously, why the masochism in the profession?!). I do feel however that he leaned too much on crude jokes (since he was a gynaecologist, he had a lot of those anecdotes) and the fact that nearly all of it was told through page-long diary entries meant that it was very choppy and didn't have much of an overarching narrative structure. 

The Mathematics of Love - Hannah Fry

The Mathematics of Love: Patterns, Proofs, and the Search for the Ultimate EquationRating: 3/5
Source: Bought for Kindle on iPad 
Date finished: 16 May
Pages: 128

Read this one in one sitting in the early hour(s) of this morning, more for the maths than the love. It was a bit cheesy in that way pop science authors can be when they're really trying to make it not scary, but the maths things in it were really interesting (seems unfair to call them maths really, rather than game theory or something...) and I might write a blog post on them or think of some biology projects I can do with them! 

It touched on the following. I've bolded ones I didn't already know about.

  • discrete choice theory
  • Nash and Pareto equilibria
  • stable-marriage problem & Gale-Shapley algorithm
  • OKCupid's matchmaking algorithm - was particularly interested to see that it asks your answer for X, what you want their answer to be for X, and how important this is to you for weighting
  • being polarising (in how people rate your beauty from 1 to 5) is better for success on dating sites than being a consistent 4
  • sealed bid auctions & second-highest bid winning (did this in the Harvard thing, can't remember the reasoning now though)
  • Iterated Prisoners Dilemma and Tit for Tat
  • network analysis and why the hub is so important to the spread of diseases (most likely to get infected AND most likely to pass it on), and how to best distribute vaccines
  • optimal stopping theory
  • making wedding guest lists
  • organising seating plans to maximise happiness

Also, a great quote: 'Love consists of overestimating the difference between one woman and another.'


Also, I only realised halfway through the book but I am so thankful that the book with this title was not just a list of stats, because I could totally see someone just making a book called The Mathematics of Sex and filling it with random trivia like 'the average person has sex X times'. Which, I mean, this book did have, but it was mostly concepts with just the occasional stat. 














Thursday, 9 May 2019

What Could Have Helped Me Escape Child Abuse Sooner

I was abused by my mother for the majority of my childhood, including frequent beatings and neglect. We were eventually taken away by social services and my Dad was given custody when I (the oldest) was 17 -- and we were lucky, because we had Dad (who lived elsewhere) to go to rather than having to go into care. 

I think about a decade of child abuse is too long and so, three years after escaping the situation, would like to share some reasons I think it went on so long and some potential solutions that could've helped.  This isn't my field, of course, and hopefully many solutions are being worked on or even available at the moment, but they weren't there or known to me, so here are my suggestions for what could have been better.

Reason 1: I was too scared to report. 


I feel bad about this, but I guess it's pretty understandable, especially since we were frequently coached on what to say ('tell [babysitter] you got X for dinner last night') and guilted for 'bitching' about her (when she caught me telling my friends about her hitting me the previous day). 


What factors, apart from her behaviour, caused me to be afraid to report? 



  • I didn't know what would happen. Change is scary. Even though the situation was pretty bad, change could have been worse and the unpredictability made it too scary. We could have been separated or (before Dad left) put into care or anything. 
  • The possibility of being punished if I reported and nothing happened. This happened; the police came to our house quite a few times and Mam even got in trouble for kicking Dad's door in, and one time when I was about 16 we were even sent to a friend's house for a night and Mam had to get counselling - so many false starts. It's hard to articulate how terrifying she was - of course I didn't want to risk it getting worse. 
  • Life wasn't all bad. This is real life - she wasn't hitting us every day. Sometimes, especially when I was young, we did nice things, and I do have some good memories with Mam. I think it would've been easier to report and think about leaving if she was a one-dimensional villain, but she isn't. 
  • I thought it wasn't bad enough to get help. I would only see stories in the media of sexual abuse or of people near-murdering their children, so mine seemed not too bad in comparison. I also heard that it only counts if it leaves visible marks and since this only happened in some of the beatings I thought it didn't count. Now, I thought it was plenty bad enough for me, but the issue was thinking other people wouldn't care and help. Which wasn't completely unfounded. 


Potential Solutions 


1. A website and service where kids can get information on what will happen if they report to social services or the police. The website for general information, and also an advice textline/online chat where the child can describe the details of their situation (e.g. X of the kids still in school, whether there's a relative available, the kind of abuse) and be told by a social worker how to report and what the possible results are of that given the details of the child's situation. (Failing that, a set of checkboxes they can tick to describe their situation and get an automated response from the website.) Most importantly, there must be a guarantee that nothing will come of it unless the child wants that. 


There are some possible issues with that, such as: 


  •  the social worker can't know for sure how things will turn out (that's ok, it doesn't have to be a guarantee, but to the best of their knowledge what the possibilities are and how likely each one is) 
  • the social worker may be mandated to report this once they know there's a child in harm's way. I believe they shouldn't, because if I thought there was a chance they'd report me when I came to them for advice I would just never ask for the advice in the first place.  What I would've wanted in that situation was reassurance - clearly I wanted to report, but I couldn't do that until I had a good idea of what would happen. I know that feels unpalatable, and maybe it's not how we should do it with young children, but I do think it would have helped me.
  • how to make sure the information is true, and not just what's most likely to make the child report


And perhaps something like this already exists, but I looked when I was in that situation and didn't find it, so if it does it needs to be advertised more. 
 

2. More communication and a sense of agency for the child throughout the process

This was decidedly lacking in my experience, in which after about a decade a switch finally tripped and suddenly everything happened at once, with no information about what was happening or what was going to happen. Stressful!

I was just told while on a sleepover with my boyfriend that Mam had been reported and the week-long holiday we were on with Dad was being extended for an indeterminate period, so I never got to say goodbye to my home and I really miss it. I went back once or twice to get books - did I mention it was March of my Leaving Cert year when this happened? - but I didn't know it was the last time. I'm not sure what could be done to fix it except perhaps the abuser should be removed from the house and the kids get to stay, rather than the other way around? 

Also, I told a guidance counsellor about the abuse (really didn't mean to, just wanted to talk to her about my anxiety and mentioned 'volatile home environment' as one of a list of bullet points) and she promised me she wouldn't tell but she did. I'm not saying it was the wrong decision, and I'm glad we got out, but it was a betrayal of my trust. She did buy us bags of food for a two-week break from school when she heard we weren't being fed much, so she did help. 

I also thought for a while that I'd be able to spend half the week with mam and half with dad, but after I organised that I was told I probably couldn't do that. There were lots of incidents like that, and overall I would REALLY have appreciated being kept up to date by the social workers on what was happening and what I could expect. This could be done by the social worker talking to the child regularly and perhaps with a supplementary book or website on what to expect in general.

Change is hard enough as it is without being completely in the dark about everything changing in my life and having no agency whatsoever. 


3. More nuanced media portrayals or PSAs of child abuse, showing that an abuser is not a one-dimensional monster to help children recognise abuse.

4. More prompts and opportunities to report.

In school, this could be teachers being more willing to ask if something was up at home (see Reason 2). This is also important in hospitals and similar places. I remember fantasising a lot about a beating sending me to the hospital and me reporting there but even in these fantasies I would typically say something stereotypical like 'I walked into a lamp post' in hopes they'd catch the hint. Even that would be risky because if I didn't convince Mam I was a bad liar she'd know I was trying to report her. For this reason, I think there need to be more opportunities for privacy away from parents for a child so that a doctor or nurse can ask the child if they're being abused. The combination of privacy AND prompt is important. 

Reason 2: I got good grades and was well-behaved at school.


I've always been very academically-inclined, and I came to view school as a safe haven despite the bullying I experienced there, especially when I started getting free school meals. I was even winning prizes in national competitions and travelling to speak at conferences.  So I was nerdy and well-behaved, apart from latenesses and not having my uniform right. I wouldn't disrupt class or start fights, and I think those are seen as signs of something not right at home. The irony is that part of the reason I was so fond of school and participated in so many activities was that it meant I got away from home. The fact that I participated in the BT Young Scientist meant that the teacher who organised that would drive 40 minutes round trip to bring me to school when Mam wouldn't because she was angry at me, so while I enjoyed those extra-curriculars I also needed them. 
I often didn't like school breaks because I was relying on school for breakfast and dinner and sometimes even toilet paper. 

Potential Solution 
Teachers shouldn't assume that just because a child excels academically and doesn't disturb class or act violent that everything is fine at home. Some teachers would give out to me for not having money in for a class trip (when I was too scared to ask for it) or not having my PE clothes (partly because I'm autistic and disorganised, yes, but it is hard to have everything organised when many mornings are chaotic events of being yelled at and beaten), instead of just asking if everything was OK.

Reason 3: Ineffective (and Sometimes Harmful) Interventions from Social Workers and Gardai


As I said above, the guards came multiple times, yet they only talked to Mam and when she cried and said she was just stressed, they usually believed her and left her alone. 


A guard came to the house when I was about 16, after Moya had texted Dad that I was being hit and Dad had called the guards, and handled it terribly. First they came and banged on the door and threatened to break it down if I didn't open it. I was terrified because Mam would now see that it had been reported (even though I didn't know about it until the guards were called), but I opened the door. Then it got worse - the guard proceeded to interrogate me and my sister, asking if we were being hit, in front of Mam! We said no and then she shoved a phone in our face as proof that someone had called the guards. We continued to not say much and look uncomfortable until she finally sent Mam out, but Mam was still just sitting on the stairs right outside the room. I presume Gardai get some kind of training on dealing with victims of child abuse or crime in general, so what the hell was this? 

I remember being so annoyed Moya had told Dad (we normally never reported it at all) because that night was pretty mild - I was cornered in my room and kicked a few times - and because it was probably the one time I'd ever stood up for myself instead of just saying yes sorry Mam it's my fault for not cleaning your room/not wanting to set up your dating profile/touching the mouse on your computer when trying to show you how to do something, so I was a less 'sympathetic victim', even though all I'd done was contradicted her when she said I should be grateful to her for my all-expenses-paid trip to Seattle (which I won in the BT Young Scientist and brought her along on for free, and during which she continued to abuse me a little, like pinching me if I walked on the wrong side of her). You might think this is an unreasonable concern, but it wasn't, because as that garda drove me and my sister to our friend's house for the night, the garda told us that all mothers and their daughters have fights and made it out to be no big deal. If I recall correctly she even said that she'd give her daughter a smack too. 


Potential Solutions 

1. Better training for gardai in dealing with victims of child abuse (or better garda hiring)
I had several bad experiences with guards during the abuse, and while I can't say for sure that it's not just my local area's guards that were the issue, I think there might be a need for better training. A whole bunch of guards didn't take it seriously enough, and that particular beangarda (a) interrogated the terrified victims (b) in front of the abuser and (c) then trivialised it. 

2. Actually treat child abuse like the crime it is. Take it seriously.
I wouldn't necessarily want to testify (writing the victim impact statement was upsetting enough), and I don't even know how I'd feel about prosecution in my particular case, but I would really like the guards to at least take it seriously as a potential crime rather than just a parenting decision the state should stay out of. Recognise the serious impact it has on people's lives, and not just when it becomes life-threatening. Also, I frequently see news about trials for child sexual abuse but that isn't the only kind of child abuse that matters. 

I'm glad a law was passed to remove a defence for hitting kids in 2015, but it is still so bizarre to me that hitting an adult is assault but hitting a kid is considered (by quite a lot of people) parenting. 

Fun fact: I had to actually google whether physical child abuse and neglect are illegal, because I so rarely see prosecutions.

3. Less focus on keeping the family together (especially if the child has loving relatives they can stay with), more focus on listening to the children. 

Seriously, why did nobody interview us until the very end? Why were they content to listen to the perpetrator's description of events? It's not like we were tiny children and thus arguably unreliable - for much of this there were two teenagers plus two preteens. 

4. Reporter protection
I don't know why nobody did anything for a decade, but if I could've trusted them to take action then reporting would've been less scary. The issue was that if we reported and they came but then left us with Mam, she would know we had ratted her out and hurt us more. That obviously discourages reporting by traumatised kids. As one concrete example, that beangarda should not have said in front of Mam that one of us had reported her to Dad, especially since she wasn't taking us away to somewhere safe. I remember in school I was being bullied and threatened and I told a teacher, who got an older student to tell the bully they'd seen them and to cut it out. That's a brilliant technique and I really appreciated it - why didn't they do something like that? 

Reason 4: Signs of Abuse and Neglect are Not Always Obvious

Mam wouldn't hit me in visible places. She'd rain down blows on my head (hidden by hair) and kick me in the legs, sides and belly (hidden by clothes). Half the time when she hit or kicked me or threw things at me it wasn't hard enough to leave a visible mark but it still hurt and was terrifying - and even some really hard kicks that made it hard to breathe wouldn't leave bruises if they were on certain parts of my body like my solar plexus. Sometimes when I was on the ground and she was still kicking me in the diaphragm I genuinely thought I might die (perhaps dramatic, I don't know) but a day or two later when it was time to go to school it wouldn't be noticeable. 


[Something that annoys me: it's hard to describe all this perfectly - like 'did she hit my head with a closed or open hand?' - because while she was doing it I usually went into my head and sort of dissociated so I didn't feel it as much. Sometimes I couldn't do this as she would make me tidy while hitting me. Also, it was a pretty long time ago.] 

However, there were signs. I got kicked out the door with a kick to the tailbone, and then another about six weeks later while it was still healing, and I remember not being able to sit straight in a hard chair in school for ages. I also had big round bumps on my head from being hit there. I was thin, weighing 43 kg at age 17 when we moved to Dad's (at one point I had a BMI <15), as were my siblings (the photos below are all from when I was 14 before I started getting fed in school, with friends cropped out for their privacy). And sometimes my little brothers were only getting a slice of bread or two for lunch. It's weird that no one even asked if we were OK.










Also, she took precautions. She would every so often go stand outside and get the four of us to scream as loudly as we could. Now, I don't know why this was - I thnk she said it was in case there was an emergency to make sure the neighbours could hear us. But it might have been to make sure the neighbours couldn't hear us crying when she hit us. And once we had to stay inside in my attic room for I think a month during the summer and babysit our brothers because she was always away at court or at work or something and didn't want the neighbours to notice we were home. 

I'm sure there are other reasons - perhaps that she's a woman, not an alcoholic or drug user, has a successful professional career. But those are the main suggestions I have and that I really would've liked someone to know. In summary:



  • give the victims information and agency
  • stop stereotyping who can be an abuser and a victim
  • ask if kids are okay (in privacy)
  • train gardai and social workers to take it seriously and think about the consequences of their actions (such as telling the abuser the victim reported and then leaving the victim with them)
P.S. Thank you to my friends who let me stay with them or cheered me up when this was going on, and to my teachers who helped (especially Ms. O' Regan and Ms. Connell, and Dad, Mary, Nana, Glenn and Barry).