Course: Molecular Biology – Part 2: Transcription and Transposition
Length: 7 weeks, 4-7 hrs/wk
School/platform: MIT/edX
Instructor: Stephen Bell, Tania Baker
Quote:
In Part 2 of this Molecular Biology course, you’ll explore transcription of DNA to RNA, a key part of the central dogma of biology and the first step of gene expression.
Take a behind-the-scenes look at modern molecular genetics, from the classic experimental events that identified the proteins and elements involved in transcription and transposition to cutting-edge assays that apply the power of genome sequencing. We’ve designed the problems in this course to build your experimental design and data analysis skills.
Yes, I’m about to rave about another MIT bio course. What can I say about this second course in the Molecular Biology trilogy that I haven’t said before about MIT’s bio-offerings: the in-class lectures are clear and engaging, they use animations and diagrams better than I’ve seen anywhere else, and the quizzes are based on interesting and occasionally amusing laboratory narratives (continuing the saga of poor confused Brian). And now that we’re all becoming experts on mRNA and DNA and PCR thanks to COVID, they’re more practical than ever.
I’d started this course back in 2017, right after I’d finished the first part on DNA replication. I could tell right away I wasn’t up to it – assays in particular were still too unfamiliar – so I dropped it almost immediately and went on to other things. I decided to re-take the first part late last year as prep, which helped. Things went a lot more smoothly this time around.
In basic biology courses, we learn that RNA is made from DNA. Here, we find out that it’s not a simple process. First, different cells make different proteins, so the same DNA has to make one set of proteins when it’s in a liver cell, and another set when it’s in a bone cell. And sometimes it has to make more utility proteins (like for digesting sugar) than other times. This is what epigenetics is for: how DNA expresses different RNAs, ultimately different proteins, depending on the circumstances. We got into nucleosomes in a big way, as well as promoters, suppressors, and activators that regulate transcription.
Then there’s transposition, which is kind of a secret you don’t hear about in basic biology. It’s a process by which pieces of DNA get pasted into genes just for the fun of it. Or to silence a gene. Or to create new mutations which may or may not be beneficial. Some downright scary statistics show up, such as: half the human genome is transposon-related sequences. But it’s ok, because most of them are ancient, more like fossils of transposons. And it could be worse: 80% of corn’s genome is transposon-related.
After all this, they snuck in an extra week on CRISPR, which was fun. That required a refresher of meiosis and crossover recombination.
And of course all of these were discovered by lab assays, and are still examined by those assays. How can you tell where the promoter is? How can you tell if a drug silences a destructive gene? How did we learn how RNA is released when transcription is done? Assays. Dozens of them. Keeping them straight is still my Achilles’ heel: which are in vivo, which are in vitro, which are quantitative, which yield sequence information, which are quick and easy, and which take months and cost a fortune?
Once again, while the post-video “test yourself” questions cover the specifics of a lecture, the graded quizzes are based on little lab scenarios: you’re trying to figure out how a particular organism regulates transcription, what assays do you need, what does this output show, what is your positive and negative control, what do you expect to see when you do this or that (and why would you really not want to do that in the first place). All this is in service of understanding exactly what’s happening in a process. As I’ve said before, you can’t fake your way through this.
The first three quizzes are included in the audit course so can be accessed for free. The final four quizzes can be unlocked for $99. This series is the first time I’ve paid for a mooc. I consider them worth it. You can decide for yourself after the first three weeks if it’s worth it to you.
There’s one more part to this molecular biology series: RNA translation into protein. I want to focus on reading for a little while, so I may take it later this summer, or I may wait until next year, but I’ll get there.
Length: 5 weeks, 1-2 hrs/wk
Yu Hua’s China in 10 Words, the only nonfiction covered in the course, served as both an entry into the class, and a wrap-up, as the course is situated within a series about understanding China. An entry survey asked us to come up with ten words we connect with China, prior to reading the works or taking the course. Given the coincidence of taking this during a pandemic that began in China, and living in a country with a leader whose racism is front and center, it was a bit disconcerting [Note: I took this course in the Spring; this post has just been sitting in my notes document since then, but I… well, I forgot about it until I saw it the other day]. I connect China with the philosophies of the Warring States period, with the poetry of the Tang (or is it Song, I get them confused) dynasty, and with bits and pieces I’ve encountered in other moocs. At the end of the course, the instructor and his grad students came up with their own list of ten words to summarize contemporary China; they of course know a lot more than I do about it.
Initially, I thought Lenin’s Kisses by Yan Lianke would be the book I’d be most likely to read on my own, just based on the description: a satiric novel about a kind of travelling circus of disabled people from a poor village who turn to entertainment for economic survival. From the excerpt included, I get the impression there are important nuances that I couldn’t follow, so I’m not sure it’s where I would start.
the excerpts in translation that were provided), so that makes it tempting as well. Red Sorghum by Mo Yan, a “native soil” novel about peasant China (their word, not mine) rounded out the field.
Length: total ~14 hours
Poets.” Kincaid confesses back: “Elementary Geology. Rocks for Jocks.” This course is essentially Physics for Poets: general concepts peeled down to their simplified forms, presented via concrete examples with minimal math. 
Each of the six weeks focuses on an object that demonstrates a related group of concepts. Skateboarding, for example, introduces force, inertia, and acceleration. I’d never considered weight as a force before (it’s usually ignored in favor of mass), but it makes a lot of sense in this context. And by spending a couple of weeks focusing on force – that is, newtons – I was much better able to grasp the idea of joules when we got to energy later on. For me, that alone was worth taking the course.
The other objects are falling balls, ramps, seesaws, wheels, and bumper cars. I can say I saw a lot of things more clearly, such as what’s a force and what isn’t, and what properties are conserved. By comparing linear velocity and momentum to angular velocity and momentum, the course helped me keep a lot more organized. I’m still a little confused about some stuff, but it’s not a total jumble. 
around, plays air hockey to simulate bumper cars, and does everything he can to demonstrate various kinds of forces and accelerations while also showing off the UVA campus. There is some math, but very little, and it’s of the a=b*c variety, very simple even for me. In fact, after I finished the course, I went back and dragged out the formulas that tended to get buried in the long runs of explanation. This also was a very worthwhile process for me. 
if relatively worthless cheating). A final exam similar (at times identical) to the Preliminary Assessment finishes things off in Week Seven. 
Course: 
I first discovered Michael Puett through Harvard’s ChinaX series when I took the first few parts of it about four years ago. I’m not sure what it is that makes him such a wonderful speaker: he’s not dynamic, or funny, or even particularly attractive (hey, we all go there sometimes), at least in ways we usually think of in terms of great speakers. But I sometimes just look for videos on youtube where he’s explaining something, even something I don’t understand (Chinese history, rather than philosophy, is his academic area, though the two aren’t all that separable). In this particular course, he has a somewhat Mr. Rogers vibe, and it’s mesmerizing. And soothing. ASMR for philosophy geeks.
Chinese thought, and as someone who’s had some prior exposure to the basics of Chinese thought, I liked it as a quick review of the high points. The lectures seemed a bit repetitive, but for someone encountering the material for the first time, I suspect that would be a plus.
philosopher under discussion. For example, the dinner table or a business meeting can become a ritual space; playing a musical instrument or a sport can, after a lot of focused practice, become spontaneous. So it, too, serves as reinforcement for the particular vocabulary.
Course: 
stuff gets in and out of the nucleus. So there’s a lot about signal sequences, about channels and pores, and about enzymes, chaperones, and all kinds of supporting players. I’m still amazed every time I get even a peek at how complicated it is to keep us alive. 
two instructors; I also felt that the videos themselves were a bit more cut-and-paste (it’s not unusual for individual videos to show edits, removing classroom issues for instance), thought that’s just an impression. We started off with lectures on experiments, and with little context, I had no idea what it was we were experimenting on. Once the more process-oriented material started I was able to catch on, but it was a tough few hours there. Then again, I have the disadvantage of having never been in a lab, so I’m always a little behind the eight ball when lab work is the topic. I’m beginning to get it, though: biochem mashes things up and assays for products; genetics creates mutations and assays for function; and cell biology often uses microscopy, including some very cool fluorescing techniques. 
Each video is followed by a set of “check” questions; these count in grading, but in most cases have unlimited attempts so are pretty much free points. Three quizzes make up the bulk of the grades, and these are, of course, more difficult and in most cases only offer one attempt. The Audit version of the course does not allow access to the third quiz; that requires paying for Verified access. But the Check questions and the first two quizzes give a pretty good idea of how well you’re understanding the material. 
This series includes several fun features. Wiltrout Questions, named for one of the off-screen professors, are open-ended “What do you think about this” questions that invite students to figure out how something might work, to “encourage active engagement in thinking about cell biology and a deepened understanding of a specific concept or approach”. After each unit, students are invited to submit Mudslips indicating “the muddiest, or least clear aspect of that class period.” Then there were the “Neat Experiments” videos, detailed and carefully animated explanations of historically important lab work in cell biology that nailed down a principle or used a new technique. These aren’t new features, of course; questions in both directions have always been part of these courses (Journal Club in another course, for example), and experiments have always been central in these courses. But it’s a nice touch to formalize them.
Another fun aspect was the naming of the proteins. One set was named Mens, Manus, and Cor; it turns out the MIT motto is the first two, “mind and hand”; the “heart” was added because, well, it’s about time (and there was a third protein that needed naming). Another set was named after Greek muses or fates or something, I don’t remember. Each of these courses has little personalizing details like this; it isn’t as though there’s strong pedagogical impact, but they’re part of what makes these courses so engaging. 
A Just Recompense 