A year ago in Lund: the panel discussion at Evolution in Sweden 2016

This meeting took place on the 13th and 14th of January 2016 in Lund. It feels a bit odd to write about it now, but my blog is clearly in a state of anachronistic anarchy as well as ett upphöjt tillstånd av språklig förvirring, so that’s okay. It was a nice meeting, spanning quite a lot of things, from mosasaurs to retroviruses. It ended with a panel discussion of sorts that made me want to see more panel discussions at meetings.

The panel consisted of Anna-Liisa Laine, Sergey Gavrilets, Per Lundberg, Niklas Wahlberg, and Charlie Cornwallis, and a lot of people joined in with comments. I don’t know how the participants were chosen (Anna-Liisa Laine and Sergey Gavrilets were the invited speakers, so they seem like obvious choices), or how they were briefed; Per Lundberg served as a moderator and asked the other participants about their predictions about the future of the field (if memory serves me right).

I thought some of the points were interesting. One of Sergey Gavrilets’ three anticipated future developments was links between different levels of organisation; he mentioned systems biology and community ecology in the same breath. This sounded interesting to me, who not so secretly dreams of the day when systems biology, quantitative genetics, and populations genetics can all be brought to bear on the same phenotypes. (The other two directions of research he brought up were cliodynamics and human evolution.) He himself had, earlier in his talk, provided an example where a model of human behaviour shows the possibility of something interesting — that a kind of cooperation or drive for equality can be favoured without anything like kin or group selection. That is, in some circumstances it pays to protect the weak, and thus make sure that they bullies do not get too much ahead. He said something to the effect that now is the time to apply evolutionary biology to humans. I would disagree with that. On the one hand, if you are interested in studying humans, any time is the time. On the other hand, if the claim is that now, evolutionary biology is mature and solid, so one can go out and apply it to help other disciplines to sort out their problems … I think that would be overly optimistic.

A lot of the discussion was about Mats Björklund‘s talk about predicting evolution, or failing to do so. Unfortunately, I think he had already left, and this was the one talk of the conference that I missed (due to dull practical circumstances stemming from a misplaced wallet), so this part of the discussion mostly passed me by.

A commonplace that recurred a few times was jokes about sequencing … this or that will not be solved by sequencing thousands of genomes, or by big data — you know the kind. This is true, of course; massively parallel sequencing is good when you want to 1) make a new reference genome sequence; 2) get lots and lots of genetic markers or 3) quantify sequences in some library. That certainly doesn’t cover all of evolutionary biology, but it is still quite useful. Every time this came up part of me felt like putting my hand up to declare that I do in fact think that sequencing thousands of individuals is a good idea. But I didn’t, so I write it here where even fewer people will read it.

This is (according to my notes) what the whiteboard said at the end of the session:

”It’s complicated …”
”We need more data …”
”Predictions are difficult/impossible”
”We need more models”

Business as usual
Eventually we’ll get there (where?)
Revise assumptions, models, theories, methods, what to measure

Nothing in evolutionary biology makes sense except in the light of ecology phylogeny disease

Everything in evolution makes sense in the light of mangled Dobzhansky quotes.

(Seriously, I get why pastiches of this particular quote are so common: It’s a very good turn of phrase, and one can easily substitute the scientific field and the concept one thinks is particularly important. Nothing in behavioural ecology makes sense except in the light of Zahavi’s handicap principle etc. It is a fun internal joke, but at the same time sounds properly authoritative. Michael Lynch’s version sometimes seems to be quoted in the latter way.)

Linköping–Edinburgh–Uppsala

If you are the kind of person who reads the lists of decisions from Formas, you may already know this. In March, I’m starting a new postdoc position, in collaboration with John Hickey’s AlphaGenes group at the Roslin Institute in Edinburgh and Dirk-Jan de Koning’s group at the Swedish University of Agriculture in Uppsala, funded by a mobility starting grant for young researchers from the research council Formas. Hurrah!

The project involves using huge datasets from livestock animals to search for genes and variants underlying quantitative traits. In that sense, for me, this is both a new direction (animal breeding research) and a natural continuation (the genetic basis of quantitative traits). So, in the coming years I anticipate, among other things, learning a ton about computational quantitative genetics; meeting and working with great people; travelling more than ever (relative to my relatively low baseline); writing a poem or two about the scenic environs of Edinburgh and the Royal Mounds of Uppsala; figuring out the across-borders relationship thing; discovering new and useful things about quantitative traits; and hopefully picking up a bit of a Scottish tone in my otherwise Swenglish accent.

Linköping has been very good to me, and so have my colleagues in the Wright lab and AVIAN Behavioural Genetics and Physiology group. So, naturally, I’m both happy and sad to leave. Friends in Linköping, we will meet again.

Also, happy new year!

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(Me holding a sign that says (in Swedish): ”Thank you, Formas! I will do my very best.”)

Some things that happened last year (in pictures and links)

Some things happened in 2015. For one thing, I defended my PhD on the 18th of December. I’m still waiting for some paperwork so I can get a nice diploma, but dear reader, for most intents and purposes, I’m a doctor of genetics! How did that happen? Here is a short chronicle of the year in mobile phone pictures. Enjoy!

In May I went to the conference that is either called the IBANGS meeting or the GBB; I’m not sure which is the proper name, actually. Regardless, it is the meeting of the International Behavior and Neural Genetics Society, and last year it took place in Uppsala. One must take the opportunity when the meeting is in Sweden. I had a poster about some of our work on behavioural genomics under chicken domestication (Johnsson et al. 2016) and also featured on a couple of posters about dog behaviour.

I’ve mostly been to genetics and evolution centric conferences before, so themes and perspectives were a bit new to me. There was quite a bit of neural circuitry and addiction studies, but also a big chunk of genomics-type research. I was surprised by the relative lack of quantitative genetics. I had expected more of that, particularly from the human side. Maybe psychiatric geneticists go to other conferences.

Summer and time to write my dissertation. In fact, since the dissertation was a compilation thesis under the Swedish system, it consisted of a bunch of papers stapled together with a summary (”kappa”, which think comes from the Swedish word for overcoat, not from the Greek letter). Since the papers were either published or quite close to being submitted at this time, most of the writing actually lay behind me. Anyway, I decided to go to some place without distractions for a few days to write. I went to Östersund, where I don’t know anyone, had nothing else to do, and wrote the draft while sitting on cafés and in the candle-lit (!) hotel dining room.

And in August: ESEB! The European Society for Evolutionary Biology meeting took place in Lausanne. That picture with all the greenery, by the way, it’s from the campus!

I gave a talk about our work with the Kauai chicken population (Gering et al. 2015, and unpublished stuff). I remember looking at the list of symposia early in the year and thinking that they looked less interesting than previous years … I don’t remember why, though, and it turns out that I was all wrong, and ended up overwhelmed with talks to go to. As usual, and as it should be. Also: my travel laptop died on me (of course!) and I took this picture with a trash can. Good times.

Speaking of silly selfies: here is me in the chicken house and in the lab. The hammer is the actual RNA isolation hammer; we’ve found that for a lot of frozen tissues, dipping the piece in liquid nitrogen, putting it in a bag and hitting it with a hammer is a good  way to quickly disrupt it before putting it into a homogenizer. The pink tube contains Tri (acid phenol) extraction for RNA isolation. It’s one of the most photogenic steps (one of the few where what’s in the tube isn’t just a colourless liquid).

Winter and time to print and defend the dissertation. Alexander Hultberg made the pretty chicken on the cover. Apparently I took two photos from my defence: one of the opponent, Dirk-Jan de Koning, explaining QTL mapping, and one of his summary slide.

I got a hat. The middle picture shows Dominic Wright giving a speech. I felt very touched.

Finally, Linköping University in winter, and a picture of my sister’s dog, because you know: dog.

I may eventually get back to regular posts about science, or not. In the meantime, here are links to new papers that came out in 2015 (or early 2016) and I had something to do with. Apparently, this was also a year when a lot of stuff went from pipeline into print.

Johnsson M, Williams MJ, Jensen P, Wright D. (2016) Genetical Genomics of Behavior: A novel chicken genomic model for anxiety behavior. Genetics.

Johnsson M, Jonsson KB, Andersson L, Jensen P, Wright D. (2016) Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken. G3.

Fallahsharoudi A, de Kock N, Johnsson M, Ubhayasekera SJ, Bergquist J, Wright D, Jensen P. (2015) Domestication Effects on Stress Induced Steroid Secretion and Adrenal Gene Expression in Chickens. Scientific reports.

Johnsson M, Jonsson KB, Andersson L, Jensen P, Wright D. (2015) Genetic Regulation of Bone Metabolism in the Chicken: Similarities and Differences to Mammalian Systems. PLoS Genetics.

Persson, M. E., Roth, L. S., Johnsson, M., Wright, D., & Jensen, P. (2015). Human‐directed social behaviour in dogs shows significant heritability. Genes, Brain and Behavior.

The paper on the genetics of open field behaviour made the rounds a bit in the media, which was fun. I’m a bit surprised to say that an article in The Daily Mail had the most interesting take … There was also a Nature News feature from collaborators’ field trip to Kauai in the fall, complete with a looping video of my supervisor Dom Wright and collaborator Eben Gering trying to catch a chicken. This is a must-see.

Richard Gray. Forget calling someone a chicken! Farm birds have BRAVERY genes that make them less anxious than their wild cousins The Daily Mail.

Ewen Callaway. When chickens go wild. Nature News.

Last year in Marseille and the EBM18 book

The EBM in Marseille was about a year ago (September 2014), but I don’t mind a bit of blog anachronism. I post this from the European Society for Evolutionary Biology conference in Lausanne. If you happen to be here, you can see me talk about signatures of selection in feralisation in Symposium 20 on Tuesday afternoon.

If you saw a bearded man carrying a pink bag scrambling towards Gare de Marseille Saint-Charles (pictured below; an incredibly beautiful train station) while eating boiled potatoes from a plastic bag, you may have witnessed my stylish departure from Marseille. This was during the Air France strike, and I had just learned that I could catch a train to Nice and go from there. In a moment of brilliance or cheapness, I also decided to spend the night at the airport Nice Côte d’Azur.

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The conference itself was nothing short of wonderful. There were many interesting talks, but it was small enough that everything fit in one track, and there was plenty of time to meet people. The conference also ended with the nicest social activity at any conference I’ve been to: a group of participants went for a walk around Marseille with Pierre Pontarotti and his cute little dog. Myself, I presented our comb size work (2012 paper, 2014 paper and some new stuff). I felt like it went rather well. It seems someone else in the scientific committee thought so too, because I got invited to write a chapter for the book with meeting participants that they make each year. The invitation was to write an overview of the field we talked about, so I wrote about ”The genomics of sexual ornamentation, gene identification and pleiotropy”. One can have a look at the chapter on Google Books. The chapter goes through genomic studies (mostly QTL mapping and gene expression microarrays) on sexual ornaments, and some of the problems and promises.

I am not really sure when the book came out; I saw it popping up on Google Scholar the other day, but I haven’t seen the final version of my chapter. I assume a book is on it’s way or waiting for me when I get back from ESEB.

Pontarotti Pierre (Ed). (2015) Evolutionary Biology: Biodiversification from Genotype to Phenotype. Springer.

Morning coffee: @sweden

This week, I’m tweeting from the @sweden account. It is a rotating account with a new Swede every week. I honestly have no idea who could have nominated me, but I’m flattered and happy. So far I think it’s going well. As I wrote on curatorsofsweden.com:

I’m unlikely to present any great insights about the nature and meaning of Swedishness, but I hope I may be able to give you a new appreciation for the chicken comb.

I think I could probably just keep the week going by answering questions and comments, because there have been many good ones! We’ve been talking about domestication (of course), programming languages for data analysis, the bright but possibly distant future when quantitative genetics and systems biology come together, common misconceptions about genetics, what to say to your creationist friend etc.

R in genomics @ SciLifeLab, Solna

Dear diary,

I went to the Stockholm R useR group meetup on R in genomics at the Stockholm node of SciLifeLab. It was nice. If I had worked a bit closer I would attend meetups all the time. I even got to be pretentious with my notebook while waiting for the train.

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The speakers were:

Jakub Orzechowski Westholm on R and genomics in general. He demonstrated genome browser-style tracks with Gviz, some GenomicRanges, and a couple of common plots of gene expression data. I have been on the fence about what package I should use for drawing genes and variants along the genome. I should play with Gviz.

Daniel Klevebring on clinical sequencing and how he uses R (not that much) in sequencing pipelines aimed at targeting the right therapy to patients based on the mutations in their cancer cells. He mentioned some getopt snippets for getting R to play nicely on the command line, which is something I should definitely try more!

Finally, Arvind Singh Mer on predictive modelling for clinical genomics (like the abovementioned ClinSeq data). He showed the caret package for machine learning, with an elastic net regression.

I don’t know the rest of the audience, so maybe the choice to gear talks towards the non-bio* person was spot on, but that made things a bit less interesting for me. For instance, in Jakub’s talk about gene expression, I would’ve preferred more about the messy stuff: how to make that nice gene-by-sample matrix in the first place, and if R can be of any help in that process; also, in the other end, what models one would use after that first pass of visualisation. But this isn’t a criticism of the presenters — time and complexity constraints apply. (If I was asked to present how I use R any demos would be toy analyses of clean datasets. That is the way these things go.)

We also heard repeated praise for and recommendations of the hadleyverse and data.table. I’m not a data.tabler myself, but I probably should be. And I completely agree about the value of dplyr — there’s this one analysis where a couple of lines with dplyr changed it from ”argh, do I have to rewrite this in C?” to being workable. I think we also saw all the three plotting systems: base graphics, ggplot2 and lattice in action.

Bibliometrics and I

Dear diary,

I’m attending a course about scientific publishing, and the other day there was lecture about bibliometrics by Lovisa Österlund and David Lawrence from the Linköping University library. I don’t think I know anyone who particularly likes bibliometrics, but I guess it makes sense that if one needs to evaluate research without trying to understand what it is about there are only citations, the reputation of the publication channel and the cv of the researcher to look at. I imagine it’s a bit like reviewing a novel in a language one doesn’t know. A couple of things occured to me, though.

What to do when different instruments of evaluation give different results? Take the two papers (so far) published during my PhD: they both deal with the genetics of chicken comb size; one is published in PLOS Genetics and one in Molecular Ecology. If we look at journal impact factors (and we shouldn’t, but say that we do), PLOS Genetics comes out ahead with an impact factor of 8.5 against 6.3. For those that do not know this about it, journal impact factor is the mean number of citations for papers in that journal the last two years calculated by Thomson Reuters in their own secret way. However, Linköping University has for some reason decided to use the Norwegian index for evaluating publication channels. I don’t know why, and I don’t think it matters that much for me personally, since the system will change soon and I will finish in about a year and a half. In the Norwegian system journals are ranked as level one or two, where two is better and is supposed to represent the top 20% of that subject area. According to their database, Molecular ecology is level 2, while PLOS Genetics is level 1. The source of the discrepancy is probably that PLOS Genetics is counted as biomedicine, while Molecular Ecology is biology, according to the Norwegian database.

They also mentioned Altmetrics, and I don’t know what to make of it. On one hand, I guess it’s good to keep tabs on social media. On the other hand, what do numbers of tweets really tell you, except that one of the authors has a Twitter account? One of the examples in the lecture was the metrics page for this paper that I happen to be a contributor to. It is actually pretty strange. It shows three tweets or 11 tweets, depending on where on the page you look. Also, when I accessed this page earlier today it linked a blog. Now it doesn’t. That says something about the ephemeral nature of internet media. Regardless, when I first saw the page I thought perhaps the metrics page had picked up on my post about the paper, but that was not the case. I don’t know how altmetric.com define a ”science blog”, maybe the blog has to be listed on some aggregation site or another, and I’m not pretending my post is particularly insightful or important. Still it’s a little strange that the altmetrics page doesn’t list a post by one of the authors about the paper, but listed a post that referred to the paper with only two sentences and was mistaken about the conclusion.