Martin Johnsson

Martin Johnsson
is @Sweden

Hello!

I’m a PhD student in genetics at Linköping University. I’m interested in how genetic variation causes differences in shape, behaviour and sexual ornamentation of animals. Therefore, I do genetic research on chicken domestication. I use molecular methods and computers to learn more about the genetic basis of domestication traits. This may or may not sound technical, very lofty or slightly wrongheaded. If so, let’s talk about it this week!

Usually, I tweet about my life in science, and that’s what I’ll be doing this week as well. I’m likely to write about genetics in general, chicken genetics in particular, evolution, data analysis, the joys and woes of research and teaching, my pet peeves and hypotheses, my plans and worries about continuing to work in science … And a little something about poetry and cocktails might sneak its way into the feed as well.

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.

My twitter most weeks: @mrtnj.

@Sweden april 18, 2015 21:20

I’d love to post a few more I’d my favourites from the Swedish scene, but are you OK with a bunch of poems in Swedish?

@Sweden april 18, 2015 19:57

Short version: the chickens sound, look and have mitochondrial DNA that suggest that they are a mixture of wild and domestic.

@Sweden april 18, 2015 19:17

So there are chickens all over the island. Google it to see the pictures! There are two hypotheses or stories about where they came from.

@Sweden april 18, 2015 12:24

As for Herzog, it’s true that a lot of other animals are not as clever as humans. But that is no excuse for an attitude of contempt.

@Sweden april 18, 2015 12:21

But I think it’s within the realm of science to the same extent as knowing what other humans are feeling and thinking.

@Sweden april 18, 2015 11:50

It’s used as one of several tests of fearfulness in the chicken. One puts the chicken on its back and measures the time it stays immobile.

@Sweden april 18, 2015 10:22

For reasons that elude me, some folks think it’s a very clever joke to point out that it sounds like female chicken in English.

@Sweden april 18, 2015 10:20

It’s a gender neutral (and sex neutral) pronoun, I’d guess most understand it by now and it’s in the vocabulary by the Swedish academy.

@Sweden april 18, 2015 10:08

The figures are of course for a manuscript, as manuscripts are one of the practicing scientist’s true obsessions.

@Sweden april 18, 2015 09:59

This weekend I need to read a chapter of population genetics, make a couple of figures, and clean my home a little. The rest is all twitter.

@Sweden april 17, 2015 22:38

You can probably tell that I’m not that thrilled about the title of that news item, but quantitative genetics is fun.

@Sweden april 17, 2015 21:17

But maybe for developmental reasons there can’t be a horn in that position. Maybe I’d know if I’d read the freaky horn transplant paper.

@Sweden april 17, 2015 21:12

(Again, I don’t know how my keyboard turned ”don’t” into ”doubt”. I’ll just have to embrace the awful English.)

@Sweden april 17, 2015 12:29

We tried to connect Walt Whitman, the industrial small town, the strong pink rock and metal in Finspång, and the bookend.

@Sweden april 17, 2015 01:08

I arrived at mum’s house around eleven. Both were tired, but for some reason we talked for two hours about the molecular basis of disease.

@Sweden april 16, 2015 22:27

Imagine starting a new population from a random sampling. The composition might change a lot, especially with a small sample!@DMRI05

@Sweden april 16, 2015 18:02

The pink stuff is DNA labeled with a fluorescent molecule. We stick it on a glass slide that contains DNA probes matching known genes.

@Sweden april 16, 2015 17:23

Others are caused by variants that change how much a gene is expressed. That’s the kind that eQTL mapping can find.

@Sweden april 16, 2015 17:21

Some heritable differences between individuals are caused by changes in gene products, like changes to protein function.

@Sweden april 16, 2015 16:35

If you hadn’t caught me during a teaching week, all of my pictures would’ve been of my desk. I’m in a writing period now.

@Sweden april 16, 2015 15:00

We put plasmid, i.e. circular DNA with the genes we want (here: not much, since it’s for demonstrating the principle) into Escherichia coli.

@Sweden april 16, 2015 10:31

This year I’m going to the ESEB (evolutionary biology) in Lausanne and IBANGS (brain and neural genetics) in Uppsala.

@Sweden april 16, 2015 10:26

Scientific conferences (I go to about two a year, one Swedish and one international) are some of the highlights of being a PhD student.

@Sweden april 16, 2015 10:07

”We were somewhere around Barstow on the edge of the desert when the debates about an extended synthesis began to take hold.”

@Sweden april 15, 2015 22:19

I think I’m going to have to make Saturday paper day, where I find and link all papers I’ve promised people or hinted about. :)

@Sweden april 15, 2015 17:23

Sat down to tweet and the students at the next table were loudly debating casual inference. Sometimes I just love the university. #liu

@Sweden april 15, 2015 12:16

People use this to search for parts of the genome that have been recently selected, looking for regions of reduced variation.

@Sweden april 15, 2015 11:52

There are also cases like frequency dependent selection that can maintain variation, if say rare variants have an advantage.

@Sweden april 15, 2015 11:39

Say that the propensity for some kind of behaviour is heritable in humans. Does that mean that the behaviour is adaptive?

@Sweden april 15, 2015 11:37

It seems pretty common to believe that the fact that some trait has a heritable component means that it’s an adaptation.

@Sweden april 15, 2015 11:32

Another thing I could’ve brought up among common misconceptions and confusions is the connection between genetics and selection.

@Sweden april 15, 2015 08:43

That there is genetic variation in comb size is pretty clear from selection experiments, mapping and the wild/domestic comparison@Feuerz3ug

@Sweden april 15, 2015 07:40

I suspect that this is a side-effect of selection for other traits such as egg production and early sexual maturity.@cmbsweden

@Sweden april 15, 2015 07:34

Also, we find associated regions of the genome, but the resolution isn’t that great. There can be hundreds of genes in these regions.

@Sweden april 15, 2015 07:32

All practical mapping studies will miss variants of small effect. When this occurs in human genetics it’s called ”missing heritability”.

@Sweden april 15, 2015 07:30

First, we already suspected that comb mass, like most interesting heritable traits, I’d affected by lots of genetic variants.

@Sweden april 15, 2015 07:26

Now, a few technicalities about this method, called quantitative trait locus mapping (because it maps quantitative traits to loci, duh).

@Sweden april 15, 2015 07:08

For some reason, comb mass has been affected by domestication. Domestic chickens have larger combs, even relative to their bigger bodies.

@Sweden april 15, 2015 06:37

(Obviously, this doesn’t apply to Swedes who are native English speakers, nor to other exceptionally fluent individuals.)

@Sweden april 15, 2015 06:33

So I suspect that when Swedish writers think their English poetry sounds better,it’s often because they don’t see the tired cliches in.

@Sweden april 14, 2015 23:39

There is a similar thing going on with poetry. How often have you heard a Swede claim that they write better in English?

@Sweden april 14, 2015 23:37

The problem is that expressions and phrases that sound good and clever to me in English often sound stupid in Swedish.

@Sweden april 14, 2015 23:09

The hard thing about writing about science in Swedish is not the technical terms, because they’re mostly the same.

@Sweden april 14, 2015 23:03

But I’ll note something about speaking English, as someone who goes around sounding like a robot all day at work.

@Sweden april 14, 2015 23:00

And I’m sure you already know the Swedish word for drinking coffee, and that we sound like robots when we speak English.

@Sweden april 14, 2015 20:52

Long DNA molecules travel slower through the gel. Therefore, the size of the fragment is reflected by how far the DNA gets in a given time.

@Sweden april 14, 2015 20:50

And then we wait. The gel contains a fluorescent molecule that binds DNA so that we can see the DNA under a ultraviolet light.

@Sweden april 14, 2015 20:29

We have copied up some DNA sequences (last lab, with PCR) and now we want to compare their lengths. Gel electrophoresis is good for sizing.

@Sweden april 14, 2015 20:16

By the way, working in a lab has given me a lot more passion for cooking. And for cocktails, but that’s maybe a topic for another day.

@Sweden april 14, 2015 20:12

To show that all this technical stuff comes down to doing things that are (for molecular biology) a bit like working in the kitchen.

@Sweden april 14, 2015 16:49

Teaching time! Lab practical in molecular genetics. I’ll try taking some pictures, and then we can have our own little MOOC later.

@Sweden april 14, 2015 12:43

One thing lots of people do is to use some kind of network or clustering method on gene expression data.@partielldiff

@Sweden april 14, 2015 09:11

Plasticity, in this case, means that individuals with a certain genetic makeup may still show a range of trait values.@EKantis

@Sweden april 13, 2015 19:31

We’re also interested in feralisation, which is like reverse domestication in some sense. Our latest paper was on the Kauai feral chickens.

@Sweden april 13, 2015 19:28

I’ve been looking into bone traits, comb mass (an ornamental trait in chickens), fearful behaviour and gene expression.

@Sweden april 13, 2015 19:21

Therefore, we (the people in the lab where I work and quite a few in the neighboring labs as well) work on wild x domestic chicken crosses.

@Sweden april 13, 2015 19:09

And wild animals are still there, and can interbreed with the domestics. That sets the stage for genetic mapping of domestication traits.

@Sweden april 13, 2015 13:14

Right now I’m making some tables and figures for a manuscript I’m working on. Hopefully, submission time is Pretty Soon(TM).

@Sweden april 13, 2015 10:16

That means I pretty much only have one interest right now, which is science. Consequently, that’s what I’ll tweet about, more or less.