Review: Ricochet by Kathryn Berla

Rating: 2/5
Source: ARC from Netgalley for review
Date finished: 27 June
Pages: 328
Publication Date: October 8 2019

When seventeen-year-old Tati sends a saliva sample to a DNA ancestry testing site her results come back inconclusive. What’s wrong with her DNA? And what does it have to do with her unexplained seizures and the beckoning tunnel she sees during them? 

What Tati discovers is more than she could have ever imagined possible. Parallel universes exist and her abnormal DNA compels and condemns Tati and her other selves—shy Ana—privileged Tatyana—and on-the-run Tanya, to a lifetime of ricocheting between their parallel lives in the multiverse.

With knowledge of their existence a deadly threat in every universe, the only chance all four have to survive is to work together to take down the scientist responsible: their father. (Blurb from Goodreads)

I liked the premise, which is why I requested it on Netgalley. But my god the science. The science. My EYES. The reason she has these mysterious seizures and strange DNA is that her DNA was edited so that it's now got unstable vibrations or something that means she can travel between 4 parallel universes and meet the other versions of herself. After that it was a struggle to finish the book. I do not recommend it for the geneticist in your life. Either use something more related to universes, like some physical particle, or don't try to justify it scientifically at all! DNA editing changes a base from, say, A to C, not to plutonium!

Other issues:

The real action only got started around 90% and then it was all wrapped up stupidly. I usually hate it when books become series and I want to award it a star for not being a series, but it just was not wrapped up right at all. So it was a slog and then a weird rush.

I was also confused about some of the facts, like the identity of her birth mother. It took me a while to twig that Tati, Ana, Tatyana and Tanya are all different people but that could be my problem and it was a fairly cool realisation. In general it was difficult to get into, probably as a natural conclusion of the premise.

While I don't like how anxious I get for the characters in books, this lacked tension because you know Tati or Ana are going to be fine in their own realities - maybe if her dad had been able to chase her through them? And the ending! Awful.

One of the Tatis seems to wake up at the end and think it was all a dream! Argh!

In summary: 1-2 stars. I don't want to give it 1 because it had some positive qualities (such as how the genetic testing went), but there was just so much that annoyed me.

Visit to New York City

From 12th to 15th July I went to New York City from Friday evening to Monday morning and stayed with Carla, my post-doc friend from Brown! Here’s a quick rundown of what we got up to.

Friday evening

I got in around 9 pm, so we just walked through Times Square to the subway. Times Square at night is intense, exactly what I imagined from a Big American City but with more neon and so much advertising. The news ticker going along the side of a building made me feel like I was in a movie myself and about to find out about Patient Zero of a new pandemic. It’s funny that before I came I thought American cities were usually like this, when actually most of them are small and quaint, more like towns.

Saturday

Brooklyn Botanic Gardens

These were gorgeous. I liked that they had the plants arranged into a room for each biome, e.g. desert, tropical. Apparently Australia is temperate? I particularly liked the water plants – something about water makes looking at it very peaceful for me. I did have to keep taking breaks to sit in the shade, though – it was very hot.

I like this picture.

Brooklyn Library

Has hieroglyphic-looking pictures referencing famous books covering the front wall. Also saw an ad for a party for Harry Potter’s birthday.

Brooklyn Bridge

We walked across Brooklyn bridge, which took a very long time but gave us pretty views when we weren’t dodging cyclists barreling towards us.

Financial District

We didn’t go up the World Trade Center building, but we did walk around the area and get gelato, which is just as good and considerably cheaper. We also saw a monument to Alexander Hamilton, which I had to get a photo of in memory of my Hamilton fangirl days. We saw the Wall Street bull too.

Staten Island & Statue of Liberty

We then got the ferry to Staten Island, which is the most distant of NYC’s five boroughs and is basically beside New Jersey. That’s something I’ve noticed about the East Coast of America while I’ve been here – there are so many islands! They really do not shy away from building beside the sea or over or under rivers.

The ferry is free, which is nice, although it was less nice that while queuing the big neon sign in front of us boasted to potential advertisers of the captive audience they have for 25 minutes each way 24 hours a day.

Anyway, we got somewhat close to the Statue of Liberty and it’s actually quite a beautiful statue. It was interesting seeing Ellis Island – I keep thinking ‘see where my ancestors landed’, but considering I’m 100% Irish, not Irish-American, clearly those weren’t my ancestors, but my compatriots I suppose. A place of significance anyway, important in producing an Irish ethnic group of 80 million people despite there being only 5 million people in Ireland.

As is apparently common, we saw nothing of Staten Island itself apart from buying drinks in the shop/port and seeing a display about oyster conservation, because we turned right back around and got on the ferry back.

We then got the ferry home and by that time there was only an hour or so to wait before a free concert in a park right beside Carla’s apartment! (highlighting this because it's an event and I don't have photos for it, not for emphasis). 

Sunday

Meeting

I had my first in-person meeting with Nan, who runs the America’s Amazing Teens project I’m part of. It was good to meet her and Ann Makosinski in person for the first time, talk about the book I’m working on and find out what they’re up to.

The Metropolitan Museum of Art

This is a big place, so I didn't see all of it in the few hours we were there. I ran around the various European paintings (where they make you wear your bag on the front or on one shoulder, grr), saw the classical sculptures, and looked at art from different places like Polynesia (liked this one apart from the animal killing it glorifies - saw this in the Smithsonian as well amid statements I consider oxymoronic like 'they respected them' alongside 'they killed them'), Africa (why were so many of these sculptures terrifying-looking?!), and the Islamic world (some nice tiling and rugs like in my old house).




Carla, Clive and I got a nice photo on the roof of the building:

The real work of art in the Met museum (I KID).

Central Park
Just briefly dipped in here because it was apparently not to be missed. Going by the map it's huge - I've actually noticed America seems to have tons of greenspace. Have a photo.



Monday morning
Got up at 7.15 am, horror of horrors (it gets worse in July - the morning of the day I'm writing this I got up at 4.08 am) to get the 9 am bus back to Providence and got to work around 1 or 1.30 pm. Obviously this was not the plan but anyway. Carla came with me to the bus station because she's great. It was a fun weekend.

Monthly recap: June 2019

This is a rushed post, alas, being done towards the end of July while I struggle to get my work done before going back home.

Evolution conference

Happened towards the end of June and was pretty cool, apart from the odd horrifying realisation that the speaker doing this interesting study on birds killed them at the end and didn't even think it was wrong. Aaanyway, here are some things about it that I enjoyed:

Talks Relevant(ish) to Laidlaw project

* The speaker showed that using BUSTED, which detects selection, without accounting for synonymous rate variation across the genome, can give a huge number of false positives when there's no selection, and she made a version called BUSTED[S] that includes SRV.

* 'Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers' - the first demonstration of total sex chromosome dosage compensation in fish (possibly just teleosts)

* Talk: evidence in sticklebacks of sexually-antagonistic selection on a locus on a new sex chromosome

Talks relevant to my research at Brown

* 'The timing and geography of adaptive Neanderthal introgression in modern humans' - this is pretty much exactly my research topic but she did it completely differently which was very interesting, using ancient modern-human genomes. I had no idea there were so many of those.

* 'Leveraging both ancestral and derived information to detect local introgression' - this was done by someone in my lab, Lesly, who made a new version of the D-statistic called D+. Instead of using ABBA and BABA sites like D, D+ uses sites of shared ancestral alleles also so that the values don't swing as much from region to region just from not having many shared derived alleles. 

Other Interesting Things

* Poster: A professor from Brown was presenting on mutations in which the sign of selection changes with population size. I thought it was interesting but he said in his poster 'It thus appears that sign inversion always occurs because the sign of the selection coefficient acting on a mutation evolves from negative to positive'. But when I asked him what about cases where a mutation is beneficial when rare but deleterious when common (e.g. density-dependent selection, Batesian mimicry), he didn't have an answer. He said he'd thought about it but couldn't answer so I thought it was weird he put that on the poster. 

* Poster: genetic rescue with animals from other populations can introduce deleterious alleles because they were adaptive in the other location, not in this one (that wasn't the point of the poster, it just made me realise this)

* Poster: extending Fisher's geometric model to situations with conflict

* Poster: An example of a rock-paper-scissors evolutionary dynamic in one lineage in yeast, where ancestor A < B < C (final descendant) which is in turn < A. I thought this was interesting but it was assessed using competition assays and I would've been more convinced  it showed what he was trying to show (that evolution doesn't always proceed upwards) if he had also measured absolute growth rate. He said the error bars on that are too big though.

* Talk: In a species of wasp with individual recognition, selection on that trait seems to have been the strongest selective pressure on them recently, not immunity or anything else.

* Talk: high genetic diversity can contribute to extinction in small populations, because of recessive deleterious alleles from the larger population

* Talk: sperm is degenerating in an asexual species of freshwater snail that occasionally produces males, showing reduced selection on males

* Talk: the adaptive value of males in a self-fertilizing hermaphroditic fish is that they survive better in stressful environmental conditions

* Talk: a new sexual signal is developing in crickets which is harder for a parasitic fly to hear.

* Talk: 'Can females differentially allocate resources to offspring sired by different males?' They still need to do more work on this but it seems like females provision placental resources differently to males from different populations (their own vs other) in a mixed brood. 

* Talk: Exaggerated nuchal humps in Midas cichlids seem to be sexually attractive and also threatening to other males, but hinder swimming. It seems to follow Zahavi's handicap principle rather than Fisher's runaway process.

* Talk: 'Genomic consequences of UV sex chromosomes' - these are in moss, with males haploid V and females haploid U. I actually missed this talk but apparently the V has Ne twice as low as U and sexual selection is implicated (I'm interested in sex chromosome evolution, sexual selection and conflict, in case that wasn't obvious). They say they've made chromosome assemblies and RNAseq data.

Moving House
My aunt, who I'm staying with for the summer, moved house. That's been pretty chaotic with the viewings and actual moving, especially since that happened on Day 1 of the conference!

Leon's visit
Leon came over to visit for a week, which was great. We visited Boston together and saw the aquarium and Harvard (Trinity is much prettier). We didn't too much other tourism but that was okay because we got to hang out.

Duolingo 365

I hit a 365-day streak on Duolingo (but I did use 2 or 3 streak repairs on the way...yet somehow hit that on the same day as my one-year anniversary, strange. Possible a timezone issue)! For the last five years I've been doing French on it, and I recently started Hawaiian.

Work

Honestly couldn't tell you what I did in work in June, as I am unfortunately writing this on 19th July. I do know I spent two weeks doing the wrong thing after misinterpreting my supervisor and not asking for clarification! That said, I ended up using almost all of the techniques and skills I learned during those two weeks in my actual project, so not such a waste. Even the stuff I didn't use was good to learn about, like VCFs.
,
Here are some of the graphs I made and emailed to myself - no quality guarantees, and in fact I know now I made mistakes in these ones that mean the data isn't right, so don't try to derive meaning from them!





I also had to go to my J1 Scholar Orientation like 3 or 4 weeks after I arrived, which felt silly, but the speaker was good and gave us a lot of info about tax and such.


Writing

I wrote, if I've calculated correctly, 42182 words in June for my novel. 22669 were words on the actual draft, while 19513 were outlining/planning. I've been tracking for the 100-4-100 challenge. I've been doing a lot of outlining, as you can tell - one round because I was leading up to a tricky scene and one in the last few days to get ready for July's Camp NaNo, in which I am planning to write 40,000 words on the draft. I outlined the book on lovely colour-coded Post-Its today! (The image is blurred to prevent spoilers.)



Reading

I completed my Goodreads 2019 Reading Challenge of 26 books this month, less than halfway through the year! While my reading slows down a LOT during the academic year, this is cool because I set my 2019 goal to be the number of books I read last year, so I've improved.

Books I read this month:

• Bridge to Terabithia (finished June 3) - 4*
• Internal Medicine (June 4) - 2*
• The Hate U Give (June 8) - 5*
• Find Your Why (June 9) - 2*
• Planet Earth is Blue (June 11) - 3*
• Two Like Me and You (June 16) - 3*
• Ricochet  (June 27) -  2* - ARC from Netgalley for review 

Lablinn/Scicomm

Worked on contacting cool scientists to make videos about what they do for a talk to 8-12 year old girls with the Stemettes in London - thanks so much to everyone who contributed! Also worked with the mentor group on setting up a science fair Q & A service which is now, as of mid-July, live at reddit.com/r/AskAYoungScientist.

Child Abuse Post

Honestly not very keen on talking about this publicly again but anyway, the head of the Garda protective services division in Ireland saw my post and we' re going to meet in August when I return to Ireland, so hopefully things can get better. There's a chance.

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.