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@sweden recap

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So, a couple of weeks ago I tweeted from the @sweden account. This is a short recap of some things that were said, and a few links that I promised people. Overall I think it went pretty well. I didn’t tweet as much as some other curators, but much much more than I usually do. This also meant I did spend my lunch and coffee breaks looking at my phone. My tweets are collected here, if for some reason you’d care to read them.

Of course, tweeting from a rotating curation account is very different from the way I normally use Twitter. First, I read much more than I write. One of the main purposes of Twitter, for me, is to get a steady stream of links to read. That doesn’t really work on an account that follows much more and entirely different people. A lot of what I wrote was prepared monologue, but I don’t think that’s necessarily a bad thing. I follow a lot of people on Twitter for their monologues. Also, thankfully, a lot of people asked me questions! Another thing that struck me is that so few people were unpleasant. There were a few extreme right folks who wanted me to retweet their racist tweets, but only a few. Then, a few felt the need to tell me that I’m utterly boring, which is fine. Someone lamented the fact that all curators are uneducated about the proper use of Twitter (it’s probably to build your personal brand or something). Also, a certain Swedish celebrity got put on ignore so I wouldn’t have to see him tagging each tweet with ”@sweden”. But that was pretty much all.

I talked quite a bit about my research. I spent more or less a full day on the chicken comb as a sexual ornament and genetics of comb mass. We discussed domestication as an evolutionary process, tonic immobility, and how to measure gene expression for eQTL mapping. I also wrote about Kauai feral chickens … And what I actually do in a day nowadays, that is: writing R code.

I got a question about what to say to your creationist friend. I think this depends on what the creationist friend believes and what their objections to evolution are. Unfortunately, I don’t think there is a simple knock-down argument against all forms of creationism, except that evolution works really well and has a lot of evidence going for it. I certainly don’t think it will do to rely on methodological naturalism and say that ”creation would be a supernatural event and outside the scope of science”. First, because I don’t think that is how science works. Say if unicorns, miraculous healing, and species popping into existence without relation to other species were actually part of the world, wouldn’t we want to study that? Second, that will never convince anyone, except of the irrelevance of science to their worldview.

But I think there are a handful of things that creationists often take issue with. First, some don’t believe in sequence variants creating new functions. This is often described with slogans about information, and how it cannot be created by random mutation. I don’t think ”sequence information” is a particularly useful concept, and would much prefer to talk about function and adaptation. That is what is important, after all, organisms acquiring new adaptations. It turns out, new functions arising can be observed, particularly in microorganisms. Some really fun and well-studied example occur in the Long Term Evolution Experiment; see Richard Lenski’s blog which has explanatory posts and links to papers.

Second, the formation of species come up a lot in these discussions. This is a bit tricky, because it’s not always clear what constitutes different species. The definition most people have heard is probably that individuals belong to different species if they cannot have fertile offspring. But just think of asexually reproducing organisms. There, individuals belong to different species if they’re sufficiently different. So we already have what is needed to understand the formation of species in the evolution of new functions. When it comes to sexually reproducing organisms, there are examples of the evolution of reproductive isolation — cases where it seems to be ongoing or to have happened recently. (See for instance this paper on hybrid incompatibility in Mimulus guttatus; I have blogged about it, but only in Swedish)

Third, there is the question of relatedness between species. In particular, some creationists really hate the idea that humans are apes. I think it is important to emphasize a couple of things that evolution does not say about humans and other apes. By the way, this isn’t just confusing for creationists, but for everyone. Evolution does not mean that humans descend from extant apes. Look at this phylogenetic tree from Perelman & al 2011. This is just like a family tree, but of populations: we see how chimps and humans have a recent common ancestor population. This is different than claiming that we would descend from extant chimps. Of course, chimps have also changed since the common ancestor, although not in the same ways as humans. (Again, I’ve written about this before in Swedish.)

journal.pgen.1001342.g001

Speaking of unicorns, I of course celebrated unicorn Friday:

Someone asked whether you can keep fruit flies for amateur genetics at home. That should be quite possible, and I don’t see any real problems with it either. The fruit fly community has really strong culture of classical genetics with crosses and stocks. I don’t know if stock centres would deliver to private customers, but I don’t see why they wouldn’t — except for transgenic flies. It turned out, however, that transgenic flies was actually what the person asking was after. And of course, I can’t recommend that. I must say, I have mixed feelings about do-it-yourself biotechnology. On the one hand, some home molecular biology should be possible and rewarding. On the other hand, a lot of things routinely used in molecular labs are actually really dangerous if misused, and not just for the user. For example, when making any type of construct in transgenic bacteria, antibiotics and antibiotic resistance genes are the standard screening markers. They are used to pick out the bacteria that have incorporated the piece of DNA you care about. This is not the kind of stuff you want to use without proper containment. So, in the fly example, you would not only have to handle the flies, but also transgenic antibiotic resistant bacteria safely and legally. Then again, a lot of the genetics I care about does not involve any of that, and could very well be done in a basement.

The @sweden account caught me under a teaching week; otherwise, all of my photos would’ve been my computer, my pen and my coffee mug. Now I got to walk the followers through agarose gel electrophoresis and a little transformation of bacteria:

And, finally, Swedish spring:

Written by mrtnj

4 maj, 2015 at 19:45

Morning coffee: @sweden

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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.

Written by mrtnj

15 april, 2015 at 07:05

Dagens rekommendation: Hans Rosling

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TED talks är ofta inget vidare men det finns lysande undantag. Hans Roslings tal är några av dem. Ed Yong, som jag rekommenderade häromveckan, ett annat.

Se inte bara den här videon, utan leta runt lite på Youtube.

Några saker att lägga märke till:

Rosling använder inte vilken visualisering som helst; han använder en visualisering som är en polerad variant av ett enkelt diagram med prickar.

Han drar slutsatser från modeller, inte bara grafik. Dels lutar han sig på demografiska modeller, som såvitt jag förstår är mekanistiska modeller över hur populationen av människor kommer växa. Dels extrapolerar han trender i sina diagram. Utan att han säger det skulle jag tro att det skulle motsvara linjära modeller.

Förutom att han uppenbarligen funderat mycket på vilka illustrationer han ska använda, så är han bra på att kalibrera sina jämförelser och ställa dem i relation till begripliga saker. Det är inget som kommer ur siffrorna, utan en fråga om tolkning.

Och, viktig: Rosling tolkar sina modeller som orsakssamband, inte bara som associationer. Han är intresserad av frågor om vad människor borde göra och vad som kommer hända då. Det är inte heller något som går att utläsa ur siffrorna. Det kräver tolkning och antaganden om orsakssamband, men är en oumbärlig del av Roslings argument.

Written by mrtnj

29 april, 2014 at 19:52

Publicerat i med mera

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Bibliometrics and I

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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.

Written by mrtnj

24 april, 2014 at 18:05

#blogg100, språkförbistring och etologens topplista

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Jag måste säga att jag är ganska nöjd med att det gått över 50 poster i #blogg100 innan jag skriver en post om #blogg100. Överhuvudtaget tycker jag att det fallit ganska väl ut så långt. Har lyckats avsluta och publicera ett gäng poster som legat och väntat ett bra tag. ”Åtminstone tre sorters osäkerhet”, till exempel, är ungefär ett halvår gammal. Jag hade väntat mig att komma på mig själv med många sluga knep för att dela upp poster på flera dagar, men jag har inte gjort så många dumheter, mer än posta korta länktips, rekommendationer och citat. Jag har i alla fall ingen intention att fortsätta om jag inte har något vettigt att säga, så det är mycket möjligt att jag lägger av innan etthundrastrecket och återgår till vanlig takt.

Min blogg lider av en viss språkförbistring (vilket jag skrivit om på engelska här). En del saker vill jag skriva på engelska så att eventuella icke-svensktalande läsare kan förstå. Samtidigt vill jag inte driva två bloggar. Någon måtta får det vara. Jag har ingen aning om ifall språkblandningen jag håller på med nu är en bra idé eller inte, men det får vara så tills vidare

Hur som helst är det inte bara jag som ägnar mig åt #blogg100-galenskaper. En annan deltagare med biologianknytning är Johan Lind, docent i etologi, som gör en topp 100-lista över djur med egna fotografier. Mycket fint och allmänbildande! Om jag gjorde en topplista skulle den bli betydligt kortare, men hönan skulle i alla fall komma på plats ett. Titta till exempel på nummer 98, mindre havsnål och nummer 83, Chromodoris reticulata!

Written by mrtnj

22 april, 2014 at 18:04

Publicerat i med mera

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Dagens rekommendation: The Dog Zombie

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Naturligtvis är jag, som är en doktorand som bloggar, svag för att läsa doktorander som bloggar. Jessica Perry Hekman är en sådan och jobbar dessutom också med domesticering och beteendegenetik. Hur mycket bättre kan det bli?

Läs till exempel den här posten om Belyaevs rävar (något jag själv borde skriva om också) eller den här om Dias & Resslers studie om epigenetiskt arv och lukt (min post här).

Written by mrtnj

20 april, 2014 at 12:57

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Från undervisningslabbet

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IMG_20140409_135104 IMG_20140408_201345 IMG_20140409_160510 IMG_20140409_160455 IMG_20140409_151733 IMG_20140409_151721 IMG_20140409_151552 IMG_20140409_151444 IMG_20140409_140901 IMG_20140409_135115

Written by mrtnj

19 april, 2014 at 10:58

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