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Ewan Birney
@ewanbirney
, 5 tweets, 1 min read Read on Twitter
One of the most jaw dropping bits of serendipity in molecular biology (enabled by the free and open sharing of data) was the discovery in the early 90s that the malaria parasite - Plasmodium - is actually an ancient algae. Yup - you read that right.
Sometime ago Plasmodium and its cousins decided to pack in its freeliving autroph/mixtroph life style (mixotroph - a bit of photosynthesis, a bit of feeding) and become an outright parasite, and these nasties have parasitised everything from humans to snails
Here (elifesciences.org/articles/49662) Jan Janouškovec wrestles more of the apocomplexan phylogeny to the ground, and in Figure 1 it is just ... hideously complex. Plasmodium is at the top.
This clade has evolved parasitism multiple times; lost plastids multiple times; kept plastids in weird ways and just generally is way out there. Plus - it harbours one of humanities biggest killers (plasmodium).
All credit to Jan - just reading about this makes my eyes / brain smart as the original taxonomy is created before the molecular phylogenetic tree so ones just has a host of terms of define/redefine/junk whatever.
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Ewan Birney
@ewanbirney
Metrics on science (people, institutes) are crude tools and should be used with extreme care - my basic rules:
1. Never be lazy and use metrics when you can just read the science (even the goddamn abstracts is better!). We've all been there - don't do it. I have to book in time to read the papers / assessment, but this is potentially travel time
(its also fun reading science - that's why we love our science right - and broadens your own knowledge, so there are positives about being 'forced' to read papers)
Read 10 tweets
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Ewan Birney
@ewanbirney
Great meeting with Dr Morishita and Professor Takeda at the University of Tokyo (other campus though - testing my Tokyo metro skills) on Medaka fish genome and annotation. They have some great HiC data during Medaka development in the works - look out for the publication
Worth stressing again that there are classes of questions we can't answer in human - we can make statistical models, and fit those models, but we can (rarely) challenge or explore the underlying model in human - eg, how many GxE loci are there and do they overlap with GxG?
There is a surprisingly large amount of "this is the simplest model we can think of to describe the data so let's use it" in human genetics, and some real handwaving moments - how much "variance" is due to structured environment and how much due to individual chance events?
Read 11 tweets
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Ewan Birney
@ewanbirney
I found this piece on the #1619Project very moving; excellent long read writing on the African American arc of history and it’s role in American history. nytimes.com/interactive/20…
When I worked in the Mayor’s office in Baltimore, just before I started my PhD it was the start of a still on going education into African American history and culture.
It’s hard not to cry or rage as one understands the African American story; probably the most heart rending moment was when I spent two days with the adult literacy project in Baltimore. Exceptionally dedicated and patient teachers helping grown men and women learn how to read
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