It’s not uncommon in statistical analysis of sequence data to think in terms of presence-absence instead of quantity. In this quick little post, I walk through how to convert a pandas DataFrame of numerical values to one containing 1s and 0s representing presence/absence. I also show how to do this in R, for all you R people.
I'm a geobiology grad student at MIT who sometimes writes about geobiology, grad school, and other things you might expect. More often, I write nonsense for my language blog. Thanks for visiting!
The public origin of life debate sometimes feels like a parallel universe to the scientific one. And in many ways, it really is a parallel debate.—the big questions have almost nothing to do with one antoher and, more fundamentally, the battle raging beyond the ivory tower has more to do with faith than research. According to a 2019 Gallup poll, 40% of Americans believe that God created humans in their current form no more than about 10,000 years ago. And if that’s your view, it doesn’t much matter whether the person you’re debating thinks that life got started at a hydrothermal vent on the bottom of the ocean or in a warm little pond of primordial soup. That’s just not the point.
Oxygen is one of those things that nobody thinks about unless they either don’t have it or they’re a scientist. Either way, once you do start to think about oxygen, its usually not long until you start thinking there’s nothing more important in the universe.
I’ve kept working on my Anki card format and now have a much better template than the one I use in this deck.
My new template automatically generates cloze deletions based on example sentences (no need to make separate notes for clozes or make “fake” clozes on basic cards by hand) and color-codes nouns by gender using conditional formatting.
Check out the template, or read my post about conditional formatting in Anki based on field contents.
You can find those posts on my language blog, Monoglot Anxiety. I decided it was best to separate my language hobby from my personal homepage, so all future German/Anki posts will be there.
After finishing Duolingo German, I started making digital flashcards so that I’d have something to keep my iThumbs occupied through corona lockdown better than scrolling through the reams of international and domestic horrors served up by my newsfeed. I ended up spending months of experimenting with Anki and looking into popular German vocabulary sets online, and this 1000-word flashcard deck of core German vocabulary is the result.
Something I’ve thoroughly enjoyed in the first few weeks of taking a phylogenomics course is getting to think about non-microbial life for a change. The class will reorient its focus in a microbial direction here in the upcoming weeks, but thinking about familiar groups of macroscopic organisms to start makes it a lot easier to get a grip on fundamental concepts in phylogenomics and evolution.
Coming to Boston was definitely easier than going to Denmark this summer—at least there wasn’t a risk of being turned away at the border—but it also wasn’t exactly easy. Cancelled flights, state travel rules, booked-up COVID-19 test centers, and layer upon layer of MIT pandemic policy made it all a bit more complicated than I anticipated.
And on top of all that, my mattress won’t be here for another week! They said 3-5 days 14 days ago!