Molecular Bio MOOC, part I: DNA copied while you wait

Course: Molecular Biology – Part 1: DNA Replication and Repair
Length: 8 weeks 4-6 hrs/wk
School/platform: MIT/edX
Instructors: Stephen Bell, Tania Baker

Do you feel like studying biology is just memorizing hundreds of protein names and functions? Wake up, and take a different approach with MIT Biology’s 7.28x. You’ll experience an approach to learning infused in experimental research with animations that make complex details come to life….
What you’ll learn:
• How to compare and contrast the mechanisms of DNA replication in prokaryotes and eukaryotes
• How to describe several enzymatic mechanisms that the cell uses to repair or tolerate DNA damage
• How to analyze protein structures to infer functional information
• How to design methods for the best experiment to test a hypothesis related to DNA replication or repair proteins
• How to interpret data from DNA replication and repair experiments

I have to smile when I see, on the sign-up page for this course, the estimation that it will take 4 to 6 hours per week. This is repeated in the introductory material: about two hours of video lecture, another hour of ungraded comprehension questions, and one to three hours for the weekly graded quiz. That might work for some people, particularly those familiar with the design and interpretation of lab assays. I probably spent more like 10 to 12 hours a week.

And every minute was worth it.

This is the first third of the MIT microbiology series, focusing, as the title says,on DNA replication and repair. Part 2 will cover transcription (starts in a couple of weeks), and part 3 will get into RNA translation. They all build on the 7.00x “Biology: Secret of Life” course I took earlier, and list it as a recommended prerequisite.

Most moocs include some kind of “goals and objectives” for each week; most are pretty abstract and not terribly useful. But the ones for these courses are different: they’re extremely helpful. The objectives serve as a blueprint for the quizzes. If it says “Predict the effect a disruption of telomerase function would have”, you can bet you’ll have to pick an assay result that shows the effect in a given situation. If an objective is “Analyze protein structure to infer functional information”, chances are good you’ll have to find a binding site that’ll work with a particular molecule. That objectives list is the study guide to the course. If you can handle that list, you’ve learned the material.

The lecture videos, diagrams, and short animations all serve to lay out a clear picture of exactly what happens at each stage of DNA replication and repair – including proteins involved, energy requirements, and what happens in the event of failure – but that’s only the beginning. What these courses do incredibly well is simulate lab conditions that illustrate these processes, which, by the way, are the means by which the picture of what’s happening is discovered and confirmed in the first place. This isn’t makework, it’s what biologists do. Obviously, mooc students aren’t going to be able to culture e. coli or obtain fluorescently labeled dNTPs or run gel electrophoresis, and to their credit they don’t try to substitute videos of people doing those things and call it a virtual lab. Instead, they write up a little multi-act play in the form of the weekly quiz:

You study Okazaki fragment DNA maturation and nucleosome assembly. Your advisor wants to understand how the lagging strand DNA polymerase decides to stop extending an Okazaki fragment. He asks you to test the hypothesis that Okazaki fragment length relates to nucleosome positioning in the budding yeast, S. cerevisiae. Your advisor’s hypotheses mainly focus on the lagging strand DNA polymerase.

The questions then go through a series of steps: your labmate Zoe asks a question about why you’re doing something one way and not another, and you have to pick the right rationale; you run this assay and get this result, what do you conclude; you decide to try a different angle, what assay do you want, what reagents do you need, and what result do you expect? When your labmate Brian (oh, dear Brian, poor never-quite-right Brian, beloved by all but trusted by none) runs the assay and gets a weird result, what’s the most likely thing he did wrong? When you get stuck, the more experienced Alice will be able to glance at your results and suggest a course of action, at which point you need to figure out what she’s correcting. It’s pretty ingenious to design a quiz like this, and even more so to design it so that no subsequent questions give away the answers to prior questions (trust me, I looked).

You can’t fake this course. Too many moocs are eminently fakeable; some day I’m going to see if I can get a good grade in a course without ever watching a lecture or reading anything, just by searching for answers in lecture transcripts or other online sources. But not here: you either know what you’re doing, and can put six different threads of information together into a picture of what’s going on in that particular DNA, or you can’t. Sometimes you can narrow it down a little, but that’s about it. What really freaked me out regularly is that, buried among seriously complex scenarios are some laughably simple questions. I kept thinking, This one must be a trick. No tricks, though. Just damn good test design. I don’t always feel like I’ve earned my grade in a mooc, but I sure did here.

For those who are more advanced, the course includes a “journal club” featuring current articles relating to the topics of each week. I wasn’t in any shape to participate, but it’s a great way to design in multiple levels. Maybe next time, I’ll be able to make use of it. Forums were active and helpful; I wish I’d been able to offer as much as I asked, but, again, maybe next time.

Every time I take a biology or anatomy course, I come away with a sense of awe. Awe, in the classic sense, is wonder mixed with dread or fear, a sense of being dwarfed by something so immense as to be nearly incomprehensible. It’s often applied to the beauties of nature: the Grand Canyon, the recent images of Jupiter brought to us by an exploratory vehicle launched six years ago. As amazing as those things are, they’re nothing compared to the billions – I don’t know, billions, trillions? – of separate, interrelated events happening in our bodies every second, events that we really have no control over, but that must take place in order for us to be here. The molecules keeping us alive make the Grand Canyon seem kinda small, if you ask me.

Jupiter’s still really cool, though. Maybe transcription or translation will dwarf that, too.

MedChem MOOC

Course: Medicinal Chemistry: The Molecular Basis of Drug Discovery
Length: 7 weeks
School/platform: Davidson/edX
Instructors: Erland Stevens

This medicinal chemistry course explores how chemists modify a molecule’s structure to design a safe and effective drug.
This course opens with a brief history of drug discovery and introduces the modern drug approval process. Then, we will transition to learning about receptors and enzymes, the body’s molecules most often targeted by drugs. We will also discuss the topics of pharmacokinetics (drug adsorption, elimination, and half-life) and metabolism. The course closes with units on how potential drug molecules are identified and subsequently optimized into safe and effective drugs.

Short version: nicely-done course, with lots of small, well-conceived extras.

I’ve realized for some time that a better understanding of chemistry, particularly organic chemistry, would help a lot with the biology courses I’ve been taking. Alas, I haven’t found an intro-level organic chemistry mooc, but I thought I might get some helpful exposure though this course, even though I’m more interested in how drugs affect biology than in optimizing drugs via lab analysis of their properties. I saw “some experience” with organic chem was recommended, so I spent a week trying to get a sense of the basics on Youtube (Leah Fisch’s vids, aka, were particularly helpful). I also found a Cerego set on functional groups (Cerego’s great for pure memorization and for keeping ideas from getting all dusty between moocs), but wasn’t optimistic about my chances of completing the course. Turns out I did fine, though I suspect my final score greatly exaggerates my overall comprehension. I did get some good exposure to heretofore unknown aspects of chemistry, which was the point. And it was interesting to see the process of drug development.

Each week included six or eight subtopics, each with a combination of video lectures, readings, and a few graded exercises, as well as an ungraded “virtual lab” offering practice in the concepts via computer modelling. Expert interviews closed the week: everything from a patent attorney (Fun Things to Do With a Chemistry Degree if you Don’t Want to Work in a Lab) and drug company CEO – both Davidson alumni – to research scientists specializing in the technical areas featured during the week . Three exams were spaced throughout the course, covering material from two or three weeks each.

I had some concerns early on that, because the course was created “in partnership” with a pharmaceutical company, that there would be some emphasis on the business side of drug development: defending pricing, cutting regulation, that sort of thing. No need to worry: although there was some mention of those factors in Week 1 in the overview of the drug development process, I never felt like an agenda was being pushed (and I’m pretty sensitive, to the point of paranoia, to agendas, especially now).

The second and third weeks were math-heavy, with Excel playing a central role. I’ve always avoided Excel as much as possible, but it was time to bite the bullet. Fortunately, there was plenty of explanation and great forum support. I had a very bad moment when I saw the phrase “area under the curve” – oh god, please don’t make me integrate – but it turned out to be simplified by another formula. Derivation of the formula was part of the material, but I was not in a position to really incorporate it. And that’s part of the reason I feel my comprehension wasn’t equal to my final grade. But I survived, if less nobly than was possible, and lived to fight another day in the sections on chemical bonds and reactions.

Discussion forums were active and helpful, with very prompt responses by Dr. Stevens himself. I’ve become very fond of many of the TAs and grad students who’ve handled discussion boards in various courses over the years, but there’s still something special, maybe because it’s becoming very rare, about the instructor covering the boards. I felt welcomed and supported in spite of my lack of technical background.

Another small extra with great impact: each lecture included a summary; not a transcript, which is available too, but a brief recap complete with clear diagrams. While hand-drawn diagrams are great during a lecture so you can see exactly what goes with what description, when it comes to putting something in my notes, a laser-printed typeset diagram beats a screen clip of a blackboard sketch every time. So the best of both worlds was provided.

Another greatly appreciated timesaver was the FAQ appended to each section. This was a combination of minor corrections to videos, more detailed instructions on various processes, and an accumulated knowledge contributed by forum discussion in previous sessions. I found the answer to many questions here, not to mention interesting extensions or applications of concepts introduced. I’ve never seen this before. If there’s a Best Practices for Moocs handbooks around, someone should add this one; it creates something like a culture for the course, across time.

Each of the brief introductory videos to each week was shot at a different location on the Davidson campus, with some link to the topic of the week: the dining hall kitchen for metabolism, a sports arena for competition. The PR for Davidson College probably doesn’t hurt, either. This is my second Davidson mooc, by the way (the first was in Digital Humanities, way on the other side of the aisle), and both have been very good.

Various databases and software packages, most online (the one that was download-only was in an optional Virtual Lab), came into play, including The Drug Bank, Molinspiration, and the Protein Data Bank. I’ve used similar packages, maybe the same ones through an interface, in my biology courses. Molinspiration particularly amused me: if you draw too many bonds on a given atom, it eventually asks: “Are you trying to draw a hedgehog?”

I picked up a great new vocabulary term. In addition to in vivo and in vitro (“in the organism” and “in the lab”), we now have in silico, “in computer simulation”. I don’t know why this strikes me so hilariously, but it does. It’s perfect!

A pre-test and post-test bracketed the course. Neither were graded beyond a single “extra credit” point for completion. The pre-test instructions emphasized that we weren’t expected to get the questions right; it wasn’t a prerequisite test, but merely a way to establish a starting benchmark. Good thing, since I had no idea what any of the questions were asking. The post-test came after a long, hard seven weeks, and while I was feeling overwhelmed by other courses besides. I made a half-hearted attempt at the first 10 of 15 before I decided I didn’t need the extra point that badly; I was feeling pretty discouraged about my retention of the material at that point.

I commented to that effect on the forums. Dr. Stevens replied with an explanation of how he used those scores, what he looked for in terms of a class “growth” average, and the formula used to calculate it. I was then more motivated to put some work into the last five questions. I regretted my slapdash approach to the first ten, in fact (see what a little pep talk can do? Yes, I’m an attention whore, but seriously, a little nudge works wonders), so I gave the final five a more serious shot. Given the equation, I figured if I got ¼ of the pretest correct merely by probability of multiple choice selection, all I needed to do was get seven of the post test correct to meet his hoped-for growth level. I’ll never know, since the scores aren’t revealed. I hope, at the very least, I didn’t drag down the group average too much. The course deserved better than that.

This was a great experience, even though my primary interest was more around the edges of the course focus. For those specifically interested in the drug development process, I’m thinking it’d be a great place to start.


Course: Dinosaur Ecosystems

Length: 6 weeks
School/platform: Hong Kong University/edX
Instructors: Dr. Michael Pittman, Prof. Xu Xing

Using the Late Cretaceous fossil site of Erlian, China as an example, we bring you to the Gobi desert, as well as leading international museums and institutions to find out how we reconstruct dinosaur ecosystems.
This biology and life science course will focus on the knowledge we can gain from studying animals and plants. You will learn about a dinosaur’s biology including their appearance, classification and diet. We will take a close look at the mostly meat eating theropod dinosaurs, as well as the main plant eating dinosaurs, the sauropodomorphs and ornithischians. At the end of the course, you will learn how palaeontologists use fossil and modern evidence to reconstruct dinosaurs and their ecosystems.

I love the folks at HKU. I’m still studying ancient Chinese philosophy, and China in general, because of their Humanity and Nature in Chinese Thought mooc; their Twitter account ranges from interesting to seriously amusing; and they really put a lot of work into their moocs. I mean, just the course logo required several revisions to make sure the dinosaur neck would “align with archaeological findings”. Staff did a great job covering the discussion forums, offering information and resources along the way.

Problem is… I just don’t care at all about dinosaurs.

I thought I’d give this course a try anyway. Given the teasers they were sending out, and my general affection for them, I thought maybe I’d change my mind. I didn’t, but that’s not their fault. The lectures were clear, beautifully illustrated (many of the drawings were by award-winning paleoartist Julius Csotonyi), and varied: some involved sifting through sands at the Gobi Desert, others hunting through back-room storage facilities of the American Museum of Natural History in New York, and they even took a trip to Glen Rose, Texas to check out fossilized dinosaur tracks.

The instructors were impressive. While the course was running, instructor Prof. Pittman made some news himself for his research into laser-stimulated fluorescence on fossils to reveal more detailed information than ever available about soft-tissue distribution – news Chelsea Clinton noticed, by the way. And Prof. Xu had previously discovered a new species, Gigantoraptor, among collected fossils from Erlian. They were joined by several other scientists during the course, some in the field, others in classrooms, museums, and labs.

The first four weeks reminded me of the catalogs found in Whitman’s poetry. I love Whitman, but by the time he lists every resident or occupation or flower the mood is lost. Much of the time, the lectures felt like a list of features of various critters, and I didn’t have the background to understand how anything related to anything else. So while it’s great to know that ornithominids and Alectrosaurus have arctometatarsalian feet that help them run faster, I’m not sure how those guys relate to therapods or ornithischians.

In other words, I really needed to create an overal taxonomy, but when I went looking for one, I found lots of conflicting information so I never got there. (addendum: during the last days of the course, I noticed a poster with a taxonomic layout was stored in a section of the course I hadn’t visited; I don’t know if it was there all along, but it’s exactly what I was looking for). I also should have made a chart for all the critters, with information about size, earliest and latest fossils, eating habits, etc. etc., but I didn’t do that either. I didn’t put enough effort into making the course meaningful to me, and that’s my fault. I feel like I let down the graphic designers who put so much work into a scientifically accurate logo.

The weekly graded quizzes relied on information-retrieval questions, so even with my cursory effort and primitive understanding I managed to do quite well grade-wise. I would think creative questions would be a natural for a course like this, more along the lines of “It’s 180 million years ago, the treetops are shredded, who am I?” But that might be a lot to ask for an introductory-level course offered to people from all educational backgrounds.

As I write this post, I’m beginning to see that I did pick up more than I’d realized from the course, and greatly enjoyed many aspects of it (which is one reason I write these posts). HKU has a great overview of the course that’s more reliable than my mumblings. Those who really like dinosaurs and have some idea of who’s what would probably find it packed with detailed information that helps determine what life was like for these guys; the forums were full of praise at the end of the course. Oddly, my favorite lecture was about foraminifera, teeny tiny marine animals unrelated to dinosaurs. Go figure. I also greatly enjoyed the sections on bone histology in the last week. I’d have to say the last two weeks were my favorite part of the course, in fact; they were less of a catalog of this-dinosaur-has-this-kind-of-teeth-and-that-dinosaur-has-a-beak.

Of course, the idea of dinosaur beaks is pretty cool in itself. Fun fact: Tyrannosaurus Rex had feathers. Or, at least, feather-like structures covering its skin. Want to amaze your friends? Tell them birds are dinosaurs. Which, by the way, they are, but only a scientist will believe you. A friend of mine (Hi, Lisa) just made a joke about the dinosaur-noodle soup she had the other night, and one of the clever tweets the course made, sent during Chinese New Year festivities, was a video about the Year of the Dinosaur (which most people are calling the Year of the Rooster).

About once a decade, I check to see if I still can’t play the guitar (I could when I was 16, but I seem to have lost it shortly thereafter), and more often I try to do some kind of visual art to see if I’ve suddenly developed some artistic sense (I haven’t). It was worth a try to see if I could get interested in dinosaurs, and if anyone could lure me in, it would’ve been these guys. I guess it’s just not to be. Foraminifera, maybe…

Questioning Reality MOOC

Course: Question Reality! Science, philosophy, and the search for meaning
Length: 6 weeks, 2-4 hrs/wk
School/platform: Dartmouth/edX
Instructors: Marcelo Gleiser

How much can we know of the physical world? Can we know everything? Or are there fundamental limits to how much we can explain? If there are limits, to what extent can we explain the nature of physical reality? RealityX investigates the limits of knowledge and what we can and cannot know of the world and ourselves.
We will trace the evolution of ideas about the nature of reality in philosophy and the natural sciences through the ages. Starting with the philosophers of Ancient Greece and ending with cutting edge theories about the universe, quantum physics, and the nature of consciousness.

Current events have a lot of us questioning reality these days. Different type of questions, though. The main questions in this course are outlined above: how do we know things, and how much is it possible for us to ever know? The course combines philosophical and scientific explorations, and proceeds chronologically from the pre-Socratics to the Renaissance to Einstein to the present day. Prof. Gleiser is a theoretical physicist specializing in particle cosmology, and the course roughly follows his book The Island of Knowledge, written for the general science reader.

I’ve taken three or four of these science/philosophy courses, and each time I get a little more comfortable. This one is pretty introductory, and it hits all the “ooooh, cool” spots (How would we know if we’re brains in vats? Why should we care about Schrodinger’s cats?) without requiring reading anything beyond Gleisner’s NPR blog articles. I have to say I found his explanation of electron orbits to be the most helpful one I’ve encountered, though it’s possible I’m just now at the point where I’m ready to start understanding things like what standing waves have to do with quantum theory.

Each week started with a great feature: an ungraded What Do You Know pretest, full of questions that range from factual (T/F: Violet light has more energy than red light) to conceptual opinion (Agree/disagree: Mathematics is something we invent; Reality only exists in our minds). These questions are repeated at the end of the week, offering concrete evidence that something was, indeed, learned, even if only a better definition of “reality”. Material also included a video lecture and several interviews with other philosophers and scientists on the topics covered. A few graded multiple-choice questions were scattered through the material, along with several short written assignments in the form of posts, journal entries, and short self-graded essays. A Reddit AMA with Prof. Gleiser finished off the week.

The discussion forums were active and I got into some excellent discussions along the way. I also enjoyed a project from the first week: understanding a pendulum’s motion. Now, I took the easy route and used the available online pendulum simulator, because I’m a klutz, but it was an interesting way to play around with the topic of observation and experiment.

I found myself often confused by the logistics of the course, so I just plugged away at whatever looked interesting, be it posting on a discussion or self-grading an essay or answering questions (though I never did find the Learning Journal). I say that a lot, don’t I. In this case, the multiple evaluation options were complicated by a bilingual approach: the course was offered in Portuguese as well as English, with all written material in both languages so everything appeared twice. I wholeheartedly support broadening the appeal to include more people worldwide, and I would rather deal with my befuddlement than restrict the audience. It’s a tough problem, and I applaud them for taking it on. I got used to the double-entries after just a few weeks; if more courses took this approach, we’d all get used to it, and it’s a small price to pay for inclusion of those who would otherwise be unable to participate.

One of the great discoveries for me in the course was another book, mentioned in Week 3: Steven Greenblatt’s The Swerve: How the World Became Modern . I’ve only gone through 80 pages, but it’s wonderful: Poggio, Medieval Book-Raider, goes among the monks to rediscover Lucretius and atomism as Europe turned towards renaissance. Manuscripts, history, philosophy, science, the classics, all packaged in a wonderfully told story: who could ask for more.

Science & Cooking MOOC: What a difference 3 years and 80+ moocs make

Course: Science & Cooking: From Haute Cuisine to Soft Matter Science (part 1)
Length: 6 weeks, 5-7 hrs/wk
School/platform: Harvard/edX
Instructors: Michael Brenner, Pia Sörensen

This course was originally developed as a way to teach science to non-science majors at Harvard University…. As a way to do this we’re now going to use food as a way to explain the underlying scientific principles that are all around us when we interact with food, or we eat, or go to a restaurant and so on.
We’re going to do this not only in the context of recipes that you cook in your very own kitchen, you’re also going to be watching amazing dishes being created by world-famous chefs, and you’re going to learn to understand the underlying scientific principles. And sometimes they work, but not always, but we’ll understand both when they work, and when they don’t work, from the scientific principles behind them. And as a way to cap all of this off we will then send you into your kitchen where you will do your own experiments; you’ll take measurements and make observations, and you will then get to eat your lab.

Three years ago, this course was impossible for me. The math scared me, the science was bewildering, and I had no idea what I was doing, mooc-wise. My specific goal for taking it again was to see if I’d made any progress at all. I’m relieved to report: I have! It was a lot easier this time around. Whew!

I should say that I suspect the course has been pared down from the version I took back then. I don’t remember it as being two parts, I remember it as being longer, and I remember it as having a lot more complicated material, so it’s possible the part that was so difficult just wasn’t included in this run. In that case, I’ll have to see what happens when Part 2 rolls around.

Grading is based on three components: weekly homework (they’re quizzes, no matter what they’re called), weekly labs, and a final project. I only did the homework. This was partly because that’s all I was interested in for my comparison, and partly because I didn’t want to make extra purchases. Nothing serious, mostly routine things most people have in their homes, like sugar and eggs, but there were a few things I don’t have, like a kitchen scale and a reliable thermometer. I did some of the labs the first time around, and they’re quite useful for anyone practicing for future lab science courses, as they require record keeping and hypothesizing. And they’re fun, or what most people would see as more fun than calculating moles and temperature diffusion. Because of the grade structuring, it’s possible to completely skip the traditional problem-solving homework and just do the practical aspects, and still pass the course.

I found the first week – moles, pH, a touch of stoichiometry – to be the most difficult. The equations for heat diffusion and transfer were extremely simplified, so were pretty much plug-ins. Phase transitions, which gave me so much trouble last time, turned out to be quite easy, mostly because of the work I’d done in Mike Brown’s Solar System mooc. Each unit had conceptual questions, usually as ungraded “practice” problems; these were understandable either from cooking experience, or from a bit of reason based on the lectures.

Ungraded review materials offer extra practice in math and the very basic levels of science: density, concentrations and so on. Last time, I found these oppressive and this time they were a snap (though they are still very casual about rounding and significant figures). Personally, I’d rather use my own stash of materials collected from Youtubers over the past several years, and Khan Academy is great for isolated subjects, but it’s all there for anyone who wants it. There’s also a section of advanced materials more in line with traditional science courses – mostly readings, with ungraded problems –for those who want to better understand the equations (and it’s possible some of the earlier material has been moved there), so there’s a broad range of appeal for students from various mathematical and scientific comfort levels.

And of course there’s the fun stuff: watching serious professional chefs do their thing. Ferran Adria talks spherification. Joan Roca evaporates lemon peel into a cloud; Dave Arnold demonstrates how a degree or two can change the texture of an egg; Joann Chang spins sugar for croquembouche; Enri Rovira makes his famous chocolate eggs. Most of this material is available on Youtube in one form or another; every once in a while I pull up a tape and watch something amazing (and I see Top Chef‘s Voltaggio brothers are now in the mix).

Add to that two of the most likeable professors I’ve encountered on mooc videos (be aware they have nothing to do with the course at this point; after so many iterations, it’s run by TAs). There’s a reason this has been running over and over as long as it has: it’s fun!

The Immune System Gone Wild MOOC

Course: Fundamentals of Immunology: Death by Friendly Fire
Length: 5 weeks
School/platform: Rice/edX
Instructors: Alma Moon Novotny
In this biology and life sciences course, we’ll flip the basic question of, “How does the immune system protect you?” to, “How can your immune system endanger you?”
First, we will look at basic mechanisms that determine whether the immune system is roused to action or instructed to stand down, including the roles of inflammasomes and T regulatory cells and the results of mutation to genes and their importance in producing regulatory proteins. Then, we will apply these insights to explain the etiology and treatment of autoimmune diseases and look at a variety of misdirected immune attacks, including allergies, attacks on red blood cells and cellular responses that can produce damage ranging from rashes to autoimmune cellular destruction. Finally we will discuss the protection of transplants from an immune system that views them as foreign invaders instead of necessary replacements.

Short version: Good course, covering a lot of ground (with some unique flair) in a very short time.

It’s the third in an Immunology series from Rice. I’d missed the first two, so I spent a couple of weeks getting up to speed on the basics. I had most of the essential vocabulary and some understanding of what was going on – innate vs. acquired, MHCs, opsonisation, even some understanding of the complement cascade leading to MAC attack though I didn’t get to the point of memorizing the pathways – but still ended up scrambling for a lot of detail I seem to have overlooked. On the plus side, I’ve done enough medical reading to be perfectly comfortable with the overall physiological mechanisms of myasthenia gravis and lupus etc., so until we got to which cytokines or antibodies or receptors were involved, I could relax for a while. I passed with room to spare, but I wouldn’t say I’m secure in the subject. It’s more like I understand the general outline of what’s involved, and I now have the background to nail down the details more firmly. But for a free 4-week course, that’s plenty.

The four content weeks covered tolerance (how our immune systems learn to tell the difference between what’s dangerous and what’s not), autoimmune disease, hypersensitivities, and transplant issues. Each week included practice questions and a weekly exam, and some weeks had review exams of prior material (a terrific idea; I wish more courses did this). Week 5 was for self-review and the final exam.

The lectures included clever drawings of various immune system cells coded with their distinguishing characteristics: what receptors they carry, what they upregulate, downregulate, or bind to, what features they’re armed with. Other illustrations provided good support to the lectures as well, though I went hunting for some of my own personal favorites on antibody structure and MHC genetics. We all have our favorite diagrams. If I’d taken the first two courses before this one (like you’re supposed to), I might’ve not needed the extra visuals.

All exams were multiple choice; the weekly exams allowed three chances to answer. I’m usually pretty dismissive of that kind of thing, but the questions were very well-designed: some information retrieval things (they called them “factoids”) but lots of “thinking” questions that required analysis or synthesis of information in light of the concepts presented. Sometimes the question structure itself was a little weird, but it’s all about being able to manipulate the material. The final exam was also multiple choice, but allowed only one try, and counted for 50% of the grade, so guessing doesn’t work as an overall strategy (not that I’ve ever understood why anyone would bother to fake his way through a mooc, but it happens). I loved that the 40-question final was broken down in to 8 parts of 5 questions each. Not only is it less likely to trigger panic (oh my god, look at all these questions, how will I ever do them all?!?), but it forces kind of mini-reviews along the way.

The forums were active and staff, including Prof. Novotny, were available to answer questions that went a bit beyond the material (like, Hey, do animals also have a sex differential in autoimmune disease frequency? Yes, yes they do, in fact. That seems significant to me for some reason). There were a few minor first-run glitches: edX opened more of the system than they were supposed to in the Week 0 period, intended only for review of the outlines from the previous two courses (which, as someone who didn’t take the earlier courses, I found helpful, but nowhere near sufficient as preparation for this segment, by the way). They did an admirable job keeping up with unexpected but eager hordes of students flooding the forums before staff was in place. A few answer-coding problems cropped up throughout the course in ungraded sections. But overall, the execution was great. They really put a lot of thought into the images used, and I found it helpful in remembering what roles individual cells played in the immune process.

I was quite pleased with this course. It’s a nice balance of detailed molecular interactions and general clinical features, done with creativity and humor. I also have become a big fan of im-profthe immune system. I’ve had these vague notions of B cells and T cells, but I’m always amazed, whenever I take a biology course, that anything ever works – do you know how many millions of things have to happen for you to just go on living? – and the interactions of all the moving parts are fascinating. I’m eager to take the first two courses when they roll around again (and possibly retake this one, since I’ll be much better prepared). I understand there’s also a fourth part coming, The Immune System Fights Back. That sounds like fun.


Course: Introduction to Biology – The Secret of Life
Length: 9 weeks (self-paced)
School/platform: MIT/edX
Instructors: Eric Lander

Explore the secret of life through the basics of biochemistry, genetics, molecular biology, recombinant DNA, genomics and rational medicine.

Short version: Fantastic course. Excellent material, engaging and varied presentation style, homework and exams that test conceptual understanding and synthesis, humor. Not much forum activity, however. Not an easy course, but do-able with effort.

It’s something of an odd administrative setup. The course is intended as preparation for a Competency Exam, available only to those who sign up for the Verified track (which costs money). I’m not sure of the details, like the exact fees or the conditions of the Exam, or the significance of it: is it recognized by MIT? beyond moocdom? In any case, that was irrelevant to my purpose, which was to understand biology.

In that, it was a great success: Dr. Lander, in addition to being one of the leading geneticists in the world, and by the way one of the founders of the Innocence Project, is an outstanding teacher. All of his lectures take place in an in-session MIT classroom, and he has a great time telling stories about yeast juice, Linus Pauling in bed with a head cold inventing protein folding (but totally missing it on DNA structure), and asking a lot of “how do you think you’d do that?” questions once we started looking at gene cloning procedures. There are several “fun” videos thrown in as well, including MIT’s own version of “Gangnam Style” (remember that?) in which Dr. Lander appears (as well as Noam Chomsky, for pete’s sake) and a much older Stanford version of protein synthesis on the football field.

In addition to the lectures, a variety of Deep Dives and Lab videos offered by a variety of MIT students and staff explained important concepts and procedures in great detail. A problem set, intended as formative assessment (meaning the purpose is more about learning to apply concepts, not judging progress) finished off each week, with an additional Exam (generally the same types of questions as on the Problem Sets) every three or four weeks. Right/wrong answers are indicated, and you can keep track of your scores to see how you’re doing, but the only “grade” is for the Competency Exam, if that option is selected, at the conclusion of the course.

The content of the course revolves around a “coat of arms” joining biochemistry, genetics, and proteins, with genomics taking the long view. The material is something of a narrative roughly following the chronological history of biology. As a result, there’s always a sense of “you won’t believe what happened next.”

Weeks 1 through 4 started with basic biochemistry (there’s very little cell biology, however, which was a bit disappointing), then moved on to the discovery of enzymes, proteins, and amino acids, basic genetics and heredity. I did this section about a year ago but it was worth doing it again. Very little prior knowledge is assumed; some chemistry is probably helpful, but my chem is very low-level and it wasn’t a problem for me. The problem sets were terrific: maneuverable protein images, protein design apps, questions on biochemical pathways that really tested my ability to read and understand the chart.

Weeks 5, 6, and 7 moved into a detailed look at DNA: replication, transcription, translation, mutations, and the process of cloning DNA (which is nothing like cloning sheep or people). I loved this unit. The exercises were particularly helpful: “edit a gene” software, “make a plasmid” questions, very practically-oriented problems requiring application of concepts, with virtually no information-retrieval questions.

I bailed out in week 8 because I had other courses starting, and since I wasn’t going to take the Competency Exam, it didn’t matter. That’s something of a cop-out; mostly I’m just not that interested in genomic research, which is kind of sad since 1) it’s really what biology is about these days, and 2) it’s Dr. Lander’s specialty. But I got more than enough out of the course to have made it very worthwhile, and I can always go back and pick up the final portion when I’ve got less on my plate.

On the down side, there was very little interaction or support on the forums. Early on, some technical issues were addressed, but questions about content often went unanswered. I’m not sure if that’s because they’re focusing on the verified track (which, in their Philosophy moocs at least, MIT has segregated from audit track posts – two-tier education, coming to a mooc near you) or if it was just a quiet bunch.

I can’t speak to the Competency Exam track, but if your goal is to better understand the areas of biology mentioned above, this is a great course for it (you’ll need to go elsewhere for cell biology; Harvard’s mitochondria course might be a good place to start). I’d say in terms of learning, it’s one of the best courses I’ve taken. It also happens to be fun. What more could you ask for?

Belgian Breathing MOOC

Course: Respiration in the Human Body
Length: 7 weeks (self-paced)
School/platform: Université catholique de Louvain (Belgium)/edX

How do we breathe? What is the purpose of our lungs? What is the link between oxygen and life ? These questions open a vast field of discovery to help us understand respiration. This course is for anyone who wants to understand human respiratory physiology, the operation of respiration and the lungs.
…During the course experts will discuss specific and practical topics such as how to comprehend oxygenation of a patient, why and when to administer oxygen, and what hyperventilation means.
This course will also discuss in depth human anatomy, physical volumes and pressures of gasses, blood, oxygen, CO₂, lungs, tissues, smoking and chronic bronchitis.

No, the Belgians don’t breathe any differently than the rest of the world. But they sometimes do make MOOCs partly in French, like this one.

There is an all-French version of this course. I’m not sure why they decided to rework it for speakers of English – the videos are in French, but the captions, transcripts, and all text materials (including very helpful formatted handouts with embedded images) are in English – but I’m very glad they did, since I just love medical stuff. There were a few weird translation moments, and it did take a slight extra effort to coordinate words and images, but it worked fine.

Respiration is, alas, about half math and physics. It was kept very simple in this class, with basic explanations of pressure, diffusion, and maybe four basic formulas, none of which involved anything more complicated than multiplication and addition. Things still got kind of complicated, because there’s a difference between the pressure of oxygen in the blood, and the content, and then there’s always figuring out which of several values is altered when altitude is increased, when submersion is involved, or when simultaneous conditions, like asthma or anemia, are present. Then there’s some extra challenge when occasional European conventions, like using commas instead of decimal points, show up.

The course is self-paced, so all five modules were released at the start. The first two cover the basics of plain vanilla respiration, while later modules add in things like altitude shifts, effects of pulmonary diseases, pregnancy and fetal respiration, and pollution. Each section of a module (usually four sections) include a single video, which is mostly lecture with a few health-worker interviews sprinkled in. The lectures were clear and very well-presented; the interviews, not so much. Several of us took exception with the first lecture which proclaims life is not possible without oxygen; there is a sense in which that’s true (human life as we know it, say), but there’s also a sense in which it’s nonsense, since life existed on earth before there was oxygen. In fact, life created oxygen. But that’s a quibble.

Each section also contains several graded “homework” questions. Most are multiple choice, but there’s usually at least one “post your answer” question per section: pick a location at altitude and show what it does to arterial oxygen content, or describe some pollutant and its effects on the body. These are honor-graded, as in, did you do it, check yes or no. The midterm and final, each worth 20% of the final “grade”, are peer-assessed and in similar vein (oops, Freudian pun) to the “post your answer” questions. Passing is set at 50%, “excellent” at 70%. I’m not sure why they have such low expectations. My final hasn’t been assessed yet (I’m not optimistic, since I misunderstood a couple of the questions) but I’m already over the “excellent” mark.

Staff coverage of the discussion boards was very limited. In the first week, a technical issue was quickly resolved, but content questions were largely unanswered or involved long delays (two weeks). This may be due to summer vacations, or to the general trend of moocs as standalone and unsupported (a trend that dismays me greatly). It felt to me that there was generally less student participation than I’ve seen in other medically-oriented courses. Typically, a couple of students will have advanced training in technical areas and will be able to offer help, but that didn’t seem to happen here. It could be the time of year, or it could be the language issue. It could be the constant stream of forced posting that always dilutes actual communication, though someone in moocland thinks it’s a great component.

I wouldn’t say it’s an easy course, particularly for those of us who are permanently mathematically confused. But it’s very do-able. It’s also not the slickest mooc on the block, but I’ve seen some very slick moocs that were crap. It works; with a little bit of accommodation it gets the job done. While it might be too much trouble for someone with casual interest in respiration, I’d recommend it for someone who wants a basic understanding of what actually happens when we breathe.

Mitochondriacal MOOC

Course: Cell Biology: Mitochondria
School/platform: Harvard/edX
Instructors: Robert A. Lue

We will focus, in particular, on the mitochondrion, the organelle that powers the cell. In this context, we will look at the processes of cell metabolism. Finally, we will examine the F1F0 ATP synthase, the molecular machine that is responsible for the synthesis of most of the ATP that your cells require to do work. To underscore the importance of cell biology to our lives, we will address questions of development and disease and implications of science in society.

How much you get from this course probably depends on where you’re starting from, but for me, with one basic bio course and a couple of introductory chems, it was at just the right level. And beautiful: take a look at the teaser video for the course. The animations are terrific, and while it’s possible to learn the material from simple pencil drawings, I always appreciate creativity and style. But it goes beyond aesthetics; it’s memorable, which makes it understandable beyond memorizing words. I can recall NADH reducing Complex II which is then oxidized by Coenzyme Q, while using the energy from the internal redox reactions to pump protons against the concentration gradient, because I can “see” the process happening in my head. Beyond the visual component, the lectures were clear; the quiz and exam questions required thought and combinations of concepts and thus tested understanding rather than the ability to look up factual information. As the icing on the cake, the forum was active with both students and staff providing helpful clarifications.

The first couple of weeks were for me mostly review material on overall cellular biology topics I’d seen in the archived (inactive) MIT Intro to Biology course (the chem courses I’ve taken were helpful as well in understanding bonds and redox reactions). But since I’m still very new to all of this, I like going through it from a slightly different angle which emphasizes different points. Material on endosymbiosis included a wonderful video by paper-cut artist Andrew Benincasa (it’s available at his website if you’re curious why I’m so impressed; his other vids are well worth watching too). There was a fair amount of material on mitochondrial disease, something I’d never heard of before (three-way IVF? Who knew?). In addition to the biology, the human element was part of the presentation through one woman’s very personal story.

In weeks 3 and 4, mitochondria got real. We went into glycolysis, the citric acid cycle, ECT, and the grand finale, ATP synthesis, in significant detail. The idea was not to delve into the atomic level of chemical reactions, but to understand how interrupting the process at any given stage would affect various parameters like oxygen consumption or ATP production, and how those parameters might be measured. It was complicated, with a need to see not just the step-by-step but the overall process. I can’t say I’m an expert, but I could reason my way through the final so the educational methodology worked and I have enough of a foundation to keep going.

I hope I do get to keep going. I hope this is the first in a series of cell biology courses. In addition to being a molecular/cellular biologist and a very good teacher, Prof. Lue is director of HarvardX, which includes the mooc division, so I’m hoping he has more up his sleeve.

Gutsy MOOC

Course: Anatomy of the Abdomen and Pelvis
School/platform: Leiden University (Netherlands)/Coursera
You will explore the 3D anatomy of the organs from a basic level, providing thorough anatomical understanding, to its advanced application in surgical procedures. This course will challenge you to discover and help you to understand the anatomy of the abdomen and pelvis in all its aspects, ranging from its embryological underpinnings, via digital microscopy to gross topography and its clinical applications.

One of the particular benefits of MOOCs is the ability to take courses from universities all over the world. I’ve taken courses at two Netherlands universities now, and I have to say, Dutch professors are awesome. That, and my enthusiasm for the subject material, might’ve had something to do with how much I enjoyed this course. It wasn’t the slickest MOOC I’ve taken, in terms of production values, but I’ll trade slick for heart and content any time, and this was loaded with both. And with guts.

I was a little uncertain at first, since we started at the “first comes the esophagus then the stomach” level. I shouldn’t have worried. The material often was presented in what I’ve come to think of as a spiral manner: the first pass includes the most general information, then successive passes go into more and more detail, meaning repetition and connection that helps everything stick. So while the abdominal muscles were mentioned in the first week, it wasn’t until Week 5 that we really dove into the details of origin, insertion, and action. Every week mentioned aspects of embryological development, tissue histology, and clinical practice, so that by the final, I was able to distinguish between a stained slide of the duodenum vs ileum, determine which embryonic features turned into which adult structures and which just melted away with growth, and could consider the path of referred pain to various sites.

The course was set up in six weeks (there is a seventh week, but it’s only to include a final exam) and, because of the new structure of the Coursera platform (sigh), all the material is released at once. The only requirement to pass the course was to score at least 80% on each weekly unit exam, and on the final. But there was a lot more than that available.

The material for each weekly unit included numerous videos: some were lectures, some cadaver and live dissections (these came with trigger warnings for the squeamish, who probably aren’t going to be taking abdominal anatomy anyway), a few were animations, stained slide presentations, and laparoscopic videos. Readings were also featured, sometimes reiterating the lecture material, sometimes supplementing it. There were numerous ungraded practice quizzes as well as “e-tivity” (extra points for that term, though I can’t decide if I love it or hate it) posting prompts such as: Find a couple of sources with information about (the allantois/tubal pregnancy/aortic aneurysms) and write a paragraph or two addressing specific questions. Though these weren’t graded, looking for information through reputable sources (NIH, peer-reviewed publications) and just looking through the answers of other students was extremely helpful; we all seemed to focus on different aspects. Because so many students seemed more well-prepared than I, after a while I got intimidated and stopped submitting my clumsy answers, but the rest of the process was still quite valuable.

Some weeks used a subset the University’s CASK system (online Clinical Anatomical Skills). This included a lot of elements, some of which I found more helpful than others. I was completely unable to figure out the “view a cross-section of the body by any two planes” feature, similar to the Sylvius 4 system from Duke’s Neuroscience. I think more detailed instructions – perhaps a mini-tutorial – might have helped, but no one else complained, so I’ll take the hit for technical mediocrity and impatience. I also found the histology section to be confusing, but I wasn’t sure what I was looking for; again, a more structured approach might have been beneficial, though I might have just flubbed through that as well. I did find the Q-and-A for some sections, like embryology, to be extremely helpful, though inguinal anatomy remained a mystery to me until I found some videos on Youtube. Which, by the way, was encouraged all along; several collections were recommended. There’s a great deal of basic medical education on Youtube, and I mean the real thing, not somebody’s high school biology project.

One of the standout moments of the course came in Week 4. Let me tell you, peritoneal development is complicated business. From about 6 to 11 weeks, an embryo’s intestines are kicked out of the body because there just isn’t enough room, and they twist and rotate in an astonishing peritoneal ballet to fit back in and get everything in the right place, all the while other things are moving around. Every time I take one of these courses, I say again I can’t believe everything works, since it requires so many things to happen just so. But the thing here was the demonstration: a few years ago Dr. Gobée (one of many instructors involved in the course) constructed a giant working model of all this for his medical students, with the stomach and liver that rotate the way they do, and an aorta and vena cava and pancreas and, especially, intestines that extend and twist and retract the way they do, and everything with a plastic peritoneum draped over it, just so we could see exactly what happens and why the peritoneum ends up where it does. It was a great model, and highly instructive. Here we are with dozens of animations of gut rotation on Youtube, and sophisticated imaging technology via CASK, but this model drew more positive comments on the discussion forums than anything else in the course. If you build it, they will come – even if it isn’t the slickest technology.

My personal funny bone was tickled by the head on the anatomical diagram shown here. Most of these diagrams were headless, since we’re more interested in the muscles and organs than the face (or the unflayed exposed parts, which I’ve censored so this blog won’t get flagged for x-rated pictures; I have enough trouble with some of the passages I quote in my literary posts), but in this case it was kind of hilarious to have some Zoolander looking back, as if to say, “Well, whaddya think?” I still don’t know if that diagram was photoshopped or if some print material includes it. Some of the module titles also made me smile. “Knowing your peritoneal relationships” isn’t networking advice, and “The Gems of the Pelvis” turned out to be the female reproductive organs.

This was the first time I’d encountered the kind of pre-testing I’ve encountered in math classes: questions on material that hasn’t been taught yet. I’m still not sure if the motivation was to encourage us to find information on our own – construct our own learning, as the phrase goes in math ed – or to prime us so that when we encountered the material, it was something we’d already thought about, as was used to very good effect in a recent calculus course (which I still haven’t talked about, I’ll get there, I promise, I’m still recovering). I was caught off guard at first, but once I realized I could look things up, I started having a lot of fun. And constructing my own learning. See, it works. However, I do think the course relied a little too much on the “go out and find some material on this” approach.

The graded exams – one per week, plus the final – were challenging in that, unlike the practice exams where the incorrect questions were marked as wrong with perhaps a hint as to the error, no feedback at all was given, only a score. Unlimited attempts were permitted, but only after 30 minutes had elapsed since the last attempt. With no indication of which question I’d gotten wrong, I only had so much patience for fumbling around trying to find it after I hit the pass mark. I should say, however, that the questions were great: a few of them were straightforward information retrieval questions, but most of them required putting together multiple kinds of information, like knowing not only what nerve system runs close to the aorta, but what the effects of damage would be. Then there was the one that required knowing 1) how the stomach absorbs medications and into what vessel; 2) where that vessel goes, and 3) picking it out on a CT slice. I wish I knew if I’d answered that one correctly, because it was Gem of Put-it-all-together Questions.

Of course, you have to really want to know this stuff, either because you need to know it for future coursework or career, or because you just like medical stuff, which is my thing. And you have to be a little patient with a course that doesn’t fit into the cookie-cutter mold. But I’m happy to see oddball MOOCs, I’m thrilled to see teachers who put some thought into how to teach, and I greatly enjoyed this course.

Einsteinian MOOC

Course: The Einstein Revolution
School/platform: Harvard/edX
Instructors: Peter Galison, Ion Mihailescu

Participants in the course will follow seventeen lessons, each of which will present a mix of science (no prerequisites!) and the broader, relevant cultural surround. Some weeks will examine the physics concepts, while others will see excerpts of films or discuss modernist poetry that took off from relativity. Or we might be looking at the philosophical roots and philosophical consequences of Einstein’s works. At other times we will be fully engaged with historical and political questions: the building, dropping, and proliferation of nuclear weapons, for example.

Philosophy +history+ low-level science + art + biography = what could be better? I haven’t been this happy since I found that vid about Dante’s model of Paradise using four-dimensional geometry.

Galison is a Professor of History of Science and Physics (and the recipient of a MacArthur “genius” grant in 1997). The course is largely based on his book, Einstein’s Clocks and Poincare’s Maps, which just happen to be topics of the first few weeks.

But while there’s a lot of science, it doesn’t stop there. Yes, there’s Brownian motion and the photoelectric effect, but there’s also realism vs positivism and the Vienna Circle. The equivalence principle and Minkowski’s geometric interpretation of relativity take up considerable time, but so does the art of Hannah Hoch, along with Prof. Hillary Chute’s heartbreaking interview about Japanese manga relating to Hiroshima. You’ll meet Boltzmann, Mach, Bohr, Schrodinger and Heisenberg, but also Blau and Meitner, and you’ll find out why those last two names are not familiar – and why they should be.

I have to admit to being less than happy early on. In fact, the first couple of weeks were pretty brutal, math and science-wise. It’s not that anything was that complex; certainly no calculus or serious computation. I just found it draining, and there were details that made no sense to me (and still don’t). But then there was a stretch of history and philosophy, and some art, and I felt a lot better. The longer the course went on, the happier I was to have pushed through the rough start. Another drawback: there was no staff. Sadly, that’s not unusual, particularly since this was the second run of the course. Automoocs: push a button and they start. The cohort was quite lively nevertheless, and we managed.

Grading was structured so that it was possible to “pass” even if an area was mostly ignored. Between physics assignments, peer-assessed essays, and forum posts, there was plenty of opportunity to collect enough points even if, say, you wanted to skip a couple of essays (as the lowest two would be dropped anyway) or did poorly on some science (where the lowest two scores were dropped as well).

Scores, however, aren’t really the purpose in a course like this, at least not for me. From my point of view, it’s just a great way to see how art, philosophy, and science can interact, and to watch a fascinating era in human history develop over a half-century. It’s more of an exploration, meant perhaps to broaden rather than deepen one’s view. I found the approach to be unique and quite enjoyable, an inviting hook into further study.

Neuroscience MOOC

Image by Kevin Reginald Parks, MOOC participant, alternative medicine specialist... and artist

Image by Kevin Reginald Parks, MOOC participant, alternative medicine specialist… and artist

Course: Medical Neuroscience
School/platform: Duke/Coursera
Instructors: Leonard White, PhD

The course provides students an understanding of the essential principles of neurological function, from cellular and molecular mechanisms of neural signaling and plasticity to the organization and function of sensory and motor systems. This course emphasizes the neural and vascular anatomy of the human brain and spinal cord, providing an anatomical framework for localizing lesions within the central nervous system. It also emphasizes the neurobiological foundation for understanding cognition, mental illness and disorders of human behavior.
The overall goal is to equip students in the health professions for interpreting impairments of sensation, action and cognition that accompany neurological injury, disease or dysfunction.

[addendum: Coursera has converted this course to their new platform; content may have changed, and the experience may be very different]

This was another of the three “killer moocs” I took concurrently – but I’m very glad I took the chance, in spite of the workload, and the warnings that this was intended for graduate medical professionals with solid grounding in biology, chemistry, and anatomy. I loved this course, and I highly recommend it to anyone who’s willing devote serious time and effort to covering a huge array of information about the nervous system. The materials were well-organized and clear, and included a variety of styles: text, video, animations, diagrams, anatomical photographs and specimens. Staff, both Duke staff and volunteer CTAs, were extremely involved and generous with their time and talents: one CTA created a fantastic website of study materials, and Dr. White held three live hang-outs during the twelve week session. And, by the way, fellow students (who range from practicing health science professionals to medical students to the curious, like me) were helpful, encouraging, and all-around delightful.

The course will migrate to the new Coursera platform in April or May, where it will be offered again on a more “on demand” schedule. I am (somewhat famously) not a fan of the new platform, so although staff has assured us changes will be minimal, I’m glad I got to take the last “session-based” run of the course. And yet, because it is such a great course, and because it involves a massive amount of fascinating material, I might just show up in that new session, just for fun.

What’s involved? Twelve intense weeks of detailed neurological anatomy, physiology, and biochemistry. Material was divided into six two-week units, each with its own quiz. There was also a series of short “functional anatomy” quizzes (identify locations on a cross-section with either a named structure, or a function), plus a comprehensive final. All of these exams were timed, but generously so; multiple attempts were allowed, but not only would you not know which questions you got wrong, you also got mostly different questions each time. Two peer-assessed assignments were also included, though they together only counted for 10% of the total grade. They were, however, extremely helpful in developing an understanding of the material covered.

Although no book was required, the course followed the extraordinary and comprehensive textbook used for the in-person course, available through Sinauer Publishers, whose site includes a variety of free animations and other materials. The text was edited by, among others, Dr. White and Dr. Purves, whose “Visual Perception” mooc I took a year ago. Many illustrations from this book neuro brain views jpegwere included in the videos, and I found them both aesthetically pleasing (come on, you know how many books have boring or just plain ugly illustrations) and very intuitive. Also in the videos were screen shots from the “interactive atlas” of neuroanatomy known as Sylvius 4, allowing us to see internal structures via stained cross-sections, arranged anatomically.

Anatomy was the first unit covered, and included both illustrative diagrams and detailed lab examinations of the surface and various cut views of a human brain. What are the different kinds of cells in the nervous system? What are the boundaries of the lobes? What are the important areas? What’s inside? Where are the cranial nerves? What about the spinal cord? What’s the blood supply to the brain? And what about the ventricles, the cerebrospinal fluid, how does that work? And by the way: depending on how it’s sliced (or isn’t), sometimes the nervous system looks like a butterfly, sometimes like an angry falcon, sometimes like a grinning skull, and sometimes like a prehistoric fertility icon. And that’s just for starters.

The first peer assessed assignment was connected with this unit: draw a picture of the brain, showing a specific level of detail. We were encouraged to be creative and use what was at hand – “draw in the dirt at your feet with a stick, if you wish” – and the assignment generated some of the most creative work I’ve seen in a mooc: not only beautifully drawn standard diagrams, but brains made from pills, from crumpled up trash bags, from flower petals, from pushpins on a bulletin board, from vegetables, brains drawn on the beach, on snow, and, my favorite, cats-on-the-brain, shown here (submitted by Romanian veterinary student – and talented artist – Iulia Cimpoieș).

The second two-week unit was all about neural signaling. This was the hardest part for me, since I have only the most elementary grasp of chemistry. I’m completely fascinated, when looking at the multitudinous and complicated steps involved in passing a signal along an axon, and then passing it across a synapse to another cell – which neurotransmitter, which receptor, which ion – that we’re able to do anything at all, let alone study how those things happen. Life really is a miracle. I’d like to be able to understand these processes better. Fortunately for me, a general understanding of the major classes of neurotransmitters and types of receptors was sufficient to cover the subsequent material.

The next two units were central: sensory and motor pathways, and recognizing how an interruption in the flow of information would affect various kinds of perception or function. This is what’s crucial to the medical professionals, the physical therapists, the physiatrists, the nurses, and to the primary care practitioners. What does it mean if someone has a slowly-reacting pupil on one side? If someone has weakness in one leg, but can’t feel touch on the other, where is the most likely site of the problem? What does it mean if they can feel touch but not pain? if they can’t tap their fingers to their thumb in succession? and one of the most interesting tidbits: the difference between the emotional smile, and the forced smile. Different pathways are involved. We also learned more than you’d ever want to know about urination. Again, I’m amazed anyone can pee, given all that has to happen. And by the way, maybe I’m highly suggestible, but there’s something about listening to someone talk about peeing, even when phrased as muscle contractions, nerve inputs, and signals to sphincters, that made me want to pee over and over. These pathways were the focus of the second peer-assessed assignment, also a drawing task. I found this to be extremely helpful. I probably should’ve done more drawing, until I could keep all the pathways straight.

Then we looked at the development of the nervous system over the lifespan, including embryonic development, recovery from damage, and the aging process. Here’s where I discovered a neurotransmitter called Sonic Hedgehog and its two protein helper pals, Patched and Smoothened. It’s also where I discovered the “pinwheel” organization of visual cortex neurons favoring various orientations, and how those pinwheels, as yet inexplicably, seem to have a density of π across species. Makes the hair stand up on the back of your neck, doesn’t it?

The final unit covered aspects of cognition, memory, and sleep. I discovered that, just like there’s nothing like a lecture on peeing that makes you need to pee, there’s also nothing like someone talking about different kinds of sleep, different wavelengths involved, different purposes and effects, that makes me want to take a nap.

The “killer” aspect wasn’t in the difficulty of the material; nothing was that confusing. Everything was very well explained in multiple forms, there were plenty of materials available, and the assignments were beautifully designed to aid in learning what was most important. What made it difficult was simply the volume of material: nearly a dozen different neural pathways, scores of anatomical locations with varied functions, and a vocabulary full of words like “dorsomedial” as opposed to “anterolateral”, all of which are crucial to identifying what’s happening. I was lucky I had a good deal of the vocabulary going in, but I still didn’t have fluency in many instances, so I had to keep thinking, Where is dorsolateral? before I could move on. It’s just a lot to keep straight.

But it’s doable. I know, because I did it. I wouldn’t say I’m an expert on the nervous system, and I had to check my notes frequently on all the tests, but I think I passed (the grading system is complex – 40% for quizzes, 25% for the final, etc – so I won’t be sure until grades are released). What I’d like to do is be able to pass without notes. Then again, I’m not a medical student or a health practitioner; this is all just out of curiousity – for fun. And it was. But hard work, definitely. I put a lot of time into this – and loved every minute.

I’ve been reading general-readership medical nonfiction all my life. It started in the 60s when I was a fifth grader devouring anything readable, including my family’s issue of Reader’s Digest: William Nolen’s description of his surgical training, the “I am Joe’s [organ of the month – they started with the famous ones like heart and stomach then moved on to lungs and kidneys, eventually arriving at the pancreas, IIRC], jeremiads about what were then called venereal diseases, phrased in such oblique terms that it years before I realized syphilis had anything to do with sex. I have shelves of these books: tours through medical school and residency, as well as patient accounts of struggles with cancer and heart disease. Some are fictionalized. Some are hilarious (House of God and Calling Dr. Horowitz. Some made me angry. All were fascinating. Of course, the writings of neurologist Oliver Sacks stand at the pinnacle.

But they aren’t textbooks. Sure, I learned a few of the obscene mnemonics, but I never learned the bones or nerves that went with them. I know them now. I learned the bones of the wrist corresponding to “Scared lovers try positions that they can’t handle” in the Upper Limb course last year, and now, thanks to Neuroscience, I know all about the cranial nerves memorialized in “Oh oh oh to touch and feel a girl’s vagina, ah, heaven”. The mnemonics have been cleaned up (in the case of the cranial nerves, necessarily so, since the acoustic nerve is really the vestibulochochlear nerve, and the accessory nerve is better referred to as the spinal accessory nerve.

Of course, now that the internet is here, anatomy and medicine isn’t the mystery it was in the 60s. Anyone with a cell phone can find materials for pretty much any medical topic, from simplest explanations to actual course materials. But I still do far better in a course, where material is structured and presented, rather than just groping my way through Youtube and pdfs. I’m incredibly grateful that this course is available to anyone who wants to take it – even me.

Anatomical MOOC: The shoulder bone’s connected to what again?

Course: Going Out on a Limb: Anatomy of the Upper Limb
School: Penn via edX
Instructors: Dr. James S. White
Anatomy lab isn’t just for first year medical students anymore. With this online anatomy course, anyone can learn about the upper limb, without the cadaver.
…We’ll start with basic human anatomical terminology and apply that knowledge to examining the bones of the upper limb and how they articulate at joints. You will also learn about the muscles that produce movement at those joints in addition to the innervation and blood supply of the upper limb.

You’d think anatomy would be incredibly boring: “The finger bone’s connected to the hand bone, The hand bone’s connected to the arm bone…” (which, by the way, is anatomically wrong) without the music. Sure, there was a lot of that, but I found it fascinating anyway. Then again, I’m weird. And I really, really like medical stuff. Which, of course, is why I took it, since I have absolutely no reason to learn anatomy. Most of the students were in, or aspiring to, health care or fitness fields (and boy, did they know their stuff; lots of information on the discussion boards), and that’s at whom the course was aimed. In fact, Dr. White indicated it’s pretty much one section of first-year medical school anatomy (minus the cadavers).

Medical school students are, of course, expected to have all of this memorized. That’s why medical students are in their 20s, not their 60s; it’d take me a year to memorize all this, and then I’d lose it since it’s not information I would use on a regular basis (or ever again, really). But while there were plenty of charts of muscles, actions, origins and attachments, and innervations, and hundreds of diagrams from the anatomical planes and position to the detailed routes of nerves and tendons, there were also some interesting tidbits that were more retainable for even the likes of me.

Like for instance, the brachial plexus mixes up all the nerves from the cervical vertebrae so that every arm muscle is innervated by more than one spinal cord segment, which allows function to continue in spite of severe injury to a particular nerve. And that’s also why, when my cervical disks started collapsing one after the other, my arms often hurt in the same place.

Remember how we all learned in junior high that the shoulder’s a ball and socket joint? Well, that’s true, except the socket is extremely shallow, so the whole shoulder is held together by tendons and muscles, which is why some people (like my ex-husband) dislocate a shoulder if they sneeze too hard. And a wristwatch is really a forearm watch, because the wrist bones are in what most people consider the hand. Rotator cuff injuries, carpal tunnel syndrome, all sorts of fun things were all splayed out for us on multicolor slides.

While the quizzes did have a lot of “what is this structure” questions, there were also some items that required putting together the anatomy and working with it. Such as: Why is a fall on an outstretched hand more likely to injure the scaphoid or lunate bones than to the triquetrum? It has nothing to do with the wrist bones; it’s the cartilage on the end of the ulna that absorbs some of the shock to the triquetrum. And, by the way, I love the word triquetrum, it’s my favorite bone. Here’s another one: A woman has upper limb weakness after surgery, and is unable to protract her scapula. What muscle has most likely been affected? And my favorite question(s) of the entire course:

To bring the palm of the hand from anatomic position to facing posteriorly using the shoulder joint, one would have to do which of the following actions?
– Medial rotation – correct
– Lateral rotation
– Pronation
– Supination
To bring the palm of the hand from anatomic position to facing posteriorly using the elbow and wrist radioulnar joints, one would have to do which of the following actions?
– Medial rotation
– Lateral rotation
– Pronation – correct
– Supination

See, you can turn your palm backwards either by moving your whole arm at the shoulder, or by flipping your radius over the stationary ulna, and those are completely different actions using completely different muscles. Cool! No? Well, I had fun. And the best part is: Thoracic anatomy is in the works. I’m really looking forward to that.

Like I said, I’m weird.


Course: Introduction to Forensic Science (8 weeks)
School: Nanyang Technological University, Singapore via Coursera (free)
Instructors: Roderick Bates, Associate Professor of Chemistry

This course aims to help everyone understand more on how basic scientific principles underpin Forensic Science and can contribute to solving criminal cases.
Some questions which we will attempt to address include:
• How did forensics come about? What is the role of forensics in police work? Can these methods be used in non-criminal areas?
• Blood. What is it? How can traces of blood be found and used in evidence?
• Is DNA chemistry really so powerful?
• What happens (biologically and chemically) if someone tries to poison me? What happens if I try to poison myself?
• How can we tell how long someone has been dead? What if they have been dead for a really long time?
• Can a little piece of a carpet fluff, or a single hair, convict someone?
• Was Emperor Napoleon murdered by the perfidious British, or killed by his wallpaper?

[addendum: Coursera has converted this course to their new platform; content may have changed, and the experience may be very different]

Have you read the collected works of Kathy Reichs and Patricia Cornwell? Know every episode of CSI, L&O, and Quincy by heart? (Ok, I’m really dating myself with that last one) Do you have Halpern’s 1979 primer on the New York City OCME, or a complete set of Baden’s publishings? If so, you might find yourself overprepared for most of this class, but the analytical chemistry in the second week might make it worth your while anyway.

A look at the topics might give you some idea of just how superficially they were covered: fingerprinting, fibers, and firearms appeared in a single week (a little more than an hour in lectures, plus some short case overviews), as did time of death calculations and everything you wanted to know about blood, from typing to spatter patterns. It is of course an introductory course of only eight weeks duration, so only so much depth and detail can be expected.

Lectures on weekly topics were punctuated with several abbreviated descriptions of actual cases of forensic science at work: the unearthing of King Richard III, the murder of JonBenét Ramsey, Wayne Williams’ capture, and Alexander Litvinenko’s bizarre assassination, as well as a host of lesser-known victims and assailants. Again, I found these quite superficial, but I’m weird.

Assignments that counted towards the final grade had a varied format. Most weeks included a one-question “opinion poll” intended to be completed before viewing the lectures, as a way of priming the material. Three multiple-choice quizzes appeared at intervals, about 20 questions in length with two tries allowed. And then there was the dreaded Peer Assessment: two case analyses. I was impressed that the first of these was more of a practice run, as it counted very little towards the final grade but gave us a chance to see what was expected. A weightier case analysis served as a sort of final exam, though some technical issues raised concerns (as usual, I’m writing this before I have any idea what my grade is; I expect to “pass” but who knows with peer assessment).

Considering the drama of the video graphics – imagine that bloody handprint punctuated by pounding bass and drums – it was a remarkably bland class. There were some attempts at humor, but most of them fell rather flat. As always, I criticize reluctantly, since it’s a course offered for free, and I’m sure there are students for whom it’s the perfect class. I just can’t work up a lot of enthusiasm. Yet, I completed the course, and considering I drop courses pretty easily these days, that says something.

BrainSpace MOOC

Course: The Brain and Space
School: Duke via Coursera (free)
Instructors: Dr. Jennifer M. Groh

Knowing where things are is effortless. But “under the hood,” your brain must figure out even the simplest of details about the world around you and your position in it. Recognizing your mother, finding your phone, going to the grocery store, playing the banjo – these require careful sleuthing and coordination across different sensory and motor domains. This course traces the brain’s detective work to create this sense of space and argues that the brain’s spatial focus permeates our cognitive abilities, affecting the way we think and remember.

[Addendum: This course has been converted to the new Coursera platform; content may have changed, and the experience is likely to be different]

How do we know where we are? How do we know where to look when we hear a sound? How do we scratch the right place when we have an itch? I took this course to find out; I had no idea it was so complicated. In fact, the more I learn about how the brain works, the more surprised I am that we’re able to feed ourselves without stabbing our eyes out.

There’s a great deal of material here: everything from neuron potentials to how we determine where sounds come from, memory, and navigation. I found several lectures to be of special interest to me: the historical development of our understanding of sight, for instance, though that was more introduction material. Leave it to me to fixate on the most humanities-oriented part of a science class. Likewise, I was fascinated to find out that reading a word like “cat” might cause neurons to fire that indicate we connect the word with petting a cat, hearing the cat purr, or seeing a cat. As a (former) cat person, I know I can almost feel myself petting one of my departed girls when talk turns to cats; I had no idea it was a real neurological thing. I thought I was just… weird. I also found the lectures on meters vs maps to be of special interest, as it gets into how we have to translate one kind of system to another. The more I learn about how the brain works, the more surprised I am that we manage to get anything done at all.

Lots of examples and demonstration of concepts were included: a bean-bag toss showed how we learn our physical relationship to space (“limb by limb”), and we listened to a cat’s neuron – a single neuron – fire as various visual stimuli were placed in its visual field (and, no, I don’t want to think about how that was done… shame on me, my dear departed kitties are probably very disappointed in me right now). As a nice little bow on this package, as I was finishing up the last week, Numberphile released a video about the various paths we use to store the words for numbers in our brains. Given my difficulty with math, I keep hoping I’ll find a way to leapfrog over whatever my problem is; I don’t see that happening anytime soon, but it’s an interesting notion anyway, and tied in nicely with this course.

The material was all released at once, in another of those scheduled/self-paced hybrids (it’s still running as I type this, in fact). I completed the six weeks of lectures in less than a month, though I wasn’t in any particular hurry; I just kept coming back to it. In standard MOOC fashion, each week’s lectures were followed by a multiple choice quiz with two attempts.

I didn’t have high expectations for this course – I’d found the first one less than enthralling – but it snuck up on me, and I quite enjoyed it. In addition to interesting material, I kept running into little touches I truly enjoyed. Silly things, not that relevant to the subject matter – like the “eye movement hat”, a sort of jester’s cap with eyeballs instead of bells, that was not only worn during discussions of eye movements, but kept showing up on different walls in the office. Music that was part of the acoustic processing material, and it turns out Dr. Groh plays the banjo, which might account for the instrumentals closing out some of the videos. But on one memorable occasion, a video ended with Dan Reeder (a rather crazy singer/songwriter who comes up with some… pretty odd lyrics sometimes) singing “The Brain is Not The Mind.” Three day earworm, that. Uh oh, there it goes again. Come to think of it, that would be a fun unit for a brain MOOC: the mechanism of earworms.

This is one of three courses, plus a capstone project, that are part of the specialization program called Neuroscience: Perception, Action, and The Brain. I’d already taken one of the courses (Visual Perception and the Brain). I have no interest in specialization programs – they cost money, for one thing, and I have no need of credentials in any case – but I’m generally interested in the brain, and I’d already taken one of the other courses, so I thought I’d take a look. Turned out to be a good thing.

The-One-Where-I-Take-A-Caltech-Astronomy-Course-From-@plutokiller MOOC


Course: The Science of the Solar System
School: Caltech (Coursera)
Instructors: Mike Brown

This course is a scientific exploration of our solar system. You will learn both what we know about the solar system around us but also how we have been using the tools of science to learn the things that we know. You will get to use some of the tools yourself.… we will focus our examination of the solar system on four main topics: (1) Where is there water on Mars? (2) What is inside of a giant planet? (3) How can we use the smallest bodies in the solar system to answer the biggest questions? (4) Where might we look for life?
To answer these questions we will learn about details of atmospheric chemistry and dynamics, planetary interiors and magnetism, the geological history of planets, spacecraft exploration, telescopic observations of planets around other stars, spectroscopic determinations of composition, biochemistry of water- and non-water based life, and many more. In short, we’ll learn about the whole solar system and about planets in other systems besides ours.

[Addendum: This course has been converted to the new Coursera platform; some content may have changed, and the experience may be very different from that described here]

Some courses, I just take. Some courses, I love. Like this one.

Mike Brown killed Pluto, and he’s proud of it, and he explains why towards the end of this course, just before he explains how to look for signs of life in the universe.

But we started out a lot closer – right next door, with Mars. And we heard stories, going back to Galileo and Percival Lowell and how our view of Mars has changed from the time of ancient Greece, and with plenty of droll, understated humor (like – and this is a direct quote from world-class astronomer with the chops to get Pluto kicked out of the planet club: “And as far as I can tell, they were looking at the region with the sea monster and the porpoise, oh, and the stingray. And yet, we think Mars has no oceans”). So by the time the math and physics came in, I was already hooked. Then we went to Mars, and it was too late to turn back.

You see, this ran concurrently with the real-life CalTech course, and while those kids, and some of the MOOC students, didn’t need any coddling, the rest of us needed all we could get. Because, of course, this is a science class. One of my favorite moments came in the middle of Week 1, when Mike said those immortal words: “As you might remember from orbital mechanics….” Other favorite lines:

What does it take for something to be really old? Nothing. Nothing can have happened in something like 4 billion years.
Usually when we think about quantum mechanical states – if you ever think about quantum mechanical states – …
This is a differential equation, but its about the simplest differential equation in the world.
It’s a very strange thing. Why you might ask? Why: because quantum mechanics.

It’s tough to design a MOOC that will appeal to both scientists (and there were lots of past, present, and future scientists in the course) and the rest of us, but this managed with a multi-leveled approach. The MOOC quizzes were more conceptual than quantitative (hey, you’d be surprised how hard conceptual can be), but if you felt that was not rigorous enough, the CalTech homework was available (right over there, see?), complete with designated discussion forums (which, I see, when unused after W2… I mean, CalTech kids took orbital mechanics and differential equations in kindergarten, they aren’t fooling around). Also available was the CalTech students’ public blog. I took a look at these things early on, but then I went back to my “explain it to me like I’m six” questions. Still, it’s great the more detailed material is available for those who dare.

One of the best features was this mix of Those Who Understand and Those Who Go “Huh?” There were lots of people able to help the rest of us who were welcomed to ask basic questions. When there’s a balance of people with questions and people with answers, it’s a synergystic thing that really cooks, and it’s one of the magical things that MOOCs can do. It’s a tough balance to draw: you have to attract people who have answers (marquee-value names like Mike Brown and CalTech help with that) without scaring away those who not only don’t remember orbital mechanics, they aren’t really sure what it is. The teaser video (oops, gone) might help with that, though I think he’d be better off to run Lecture 3:10: “I love holding this little piece of iron meteorite in my hand, and showing it to people, and explaining to them that this, this is the core of a tiny mini planet that was forming back at the very beginning of the solar system, that sadly had an impact which catastrophically shattered it into pieces, but then let parts of it fall onto the earth.” How could anyone resist?

I can’t say I did well; I started out pretty strong, but there was just too much stuff for me to keep straight. But I did come away with a basic understanding of about half of it, and glimpses of the rest. And some wonderful extras that weren’t in the syllabus, but were wonderful nonetheless:

Google Mars. As much as I hate Google Earth, that’s how much I love Google Mars. Except, ok, I don’t love Google Mars so much as I love the idea of Google Mars. We used jmars a lot more during the course, because it offers different types of maps, but it’s still cool that there is such a thing as Google Mars.

Blackbody radiation and emission spectroscopy sort of makes sense to me now. It’s probably the most useful thing for me to understand at my (very low) level, since it comes up over and over again, and I’ve always found it confusing. Ok, this was in the syllabus.

Have you ever looked up the etymology of “adiabat” (coined in 1838 by Scottish engineer/physicist John Rankine from Greek adiabatos “not to be passed through,” from “α-” “not” + διὰ [“through”] + βαῖνειν [“passable”] = not +passable + through)? If I can’t handle the physics, at least I can play with words. I can’t say I’m able to connect my feeble understanding of the adiabat as it applies to what’s going on inside Jupiter, and the more frequently given example of clouds smacking into mountains and raining on one side, but maybe another MOOC.

And speaking of Jupiter’s interior: degenerate matter. Cool.

The Cavendish experiment was first performed in 1797, and here I am just finding out about it now. But it’s awesome; I still can’t believe gravity works in a way you can see, with stuff you put together in your basement. It seems to be one of those things every high school student does for extra credit, so there are lots of examples on Youtube.

5678. That is: 56 = 7 * 8. WHY DID NO ONE EVER TELL ME THIS BEFORE??!?!

Hematitic Concretions would be a great band name.

One of the nice touches was guest lecturers, including Mike’s fellow CalTech professors Bethany Ehlmann, John Grotzinger (who talked about these pictures of Mars sent back by Curiosity Rover), and Heather Knutson, rising-star (pun intended) gradTAs Danielle Piskorz and Mike Wong, and JPL Deputy Chief Scientist Kevin Hand. We took a virtual trip to Hawaii to check out the Subaru telescope. While that was taped a while ago, by chance Mike was scheduled for time on the Keck telescope on the same Hawaiian mountain during the course’s run, so he answered on-the-spot questions, even as he recovered from a bout of food poisoning.

If you have the slightest interest in solar system astronomy, or any science really, I highly recommend this. I found it to be difficult, but not impossible; I think I even “passed”, much to my surprise. Lots of work, and I put in a great deal of time, far more than the 4-6 hours/week estimated in the introductory blurb. I was lucky I’d just taken two chem courses and three earth science courses, so the only piece I was really missing was physics. If you don’t have any science background, try it anyway – MOOCs don’t have to be about grades, you know. The lectures are great, you’ll probably pick up more than you expect, and you might find yourself wanting to know more. That’s how they rope us in, you see, the scientists, dangling these bright shiny things in front of us…

In fact, that’s become for me the sign of a great course: does it leave me wanting more? This one does. I really, really need to take some very basic physics. Unfortunately, that involves calculus, which I’ve been thwacking away at for a couple of years now, but maybe a more concrete approach would help. I’d love to do this course again, when I have more of the background, and pick up all the things I missed. And enjoy the lectures again. Just for the fun of it.

A Tale of Two Chem MOOCs

Course: Chemistry
School: University of Kentucky via Coursera (free)
Instructors: Dr. Allison Soult, Dr. Kim Woodrum
Allison Soult and Kim Woodrum bring their experience to the course covering atomic structure, periodic trends, compounds, reactions, stoichiometry, and thermochemistry. Instruction consists of concepts, calculations, and video demonstrations of the principles being discussed. Practice problems and end of unit assessments will help students gauge their understanding of the material.
Course: Introduction to Chemistry: Reactions and Ratios
School: Duke University via Coursera (free)
Instructor: Prof. Dorian A. Canelas
Topics include introductions to atoms, molecules, ions, the periodic table, stoichiometry, and chemical reactions. The pattern of the use of ratios in chemical problem solving will be emphasized….Each week the course will contain a series of short video lectures with interactive questions embedded in the lectures. Students will have opportunities to practice each week via exercises at two levels of depth: one set of foundational problems directly related to lecture videos and another set of problems requiring more synthesis of ideas and application of pre-existing algebra skills.

[Addendum: These courses have been converted to the new Coursera platform; content may have changed, and the experience is likely to be different]

Why did I take two chemistry courses more or less consecutively? I really, really wanted to learn some chemistry.

Actually, it was a fluke of scheduling. And, by the way, I was scared to death of both of them, thanks to being traumatized by chemistry in high school. My recollection was that chemistry is a lot of algebra, and no matter how much math I’ve been doing, it’s still a struggle. I’d heard Duke’s course was hard, but really good, and very conceptual, so I hoped the Kentucky course, which ran first, would give me enough of an introduction to at least make a dent in the “real” course.

Thing didn’t quite turn out that way.

The Kentucky course relied heavily on calculations and extensive practice. Each week included a set of ungraded homework, with answers immediately available. The weekly tests were more or less standard “take it over and over until you get them all right” but doing the work was a sure way to get the material down. The first unit was particularly brutal for algebraphobes, covering everything from quantum energy states to orbitals and electron configurations. I finally got over my fear of scientific notation by just buckling down and figuring a way to understand it (if the coefficient gets larger, the exponent has to get smaller) instead of trying to remember left and right and when to count zeroes and when to count places. Yes, I really am that stupid about math. Chemistry? I shouldn’t have been allowed out of sixth grade.

I found the initial materials were well-presented and explained clearly; the middle section seemed a lot less clear, but that could’ve been merely my reaction. The lectures were fairly dry; a couple of demonstrations were included, for “interest” I suppose, but I didn’t find them particularly illuminating. I do wish more of a conceptual overview had been included, but in terms of learning specific calculations, it worked well, and I probably needed that more than anything else.

There were, of course, drawbacks to the skill-drill approach. First, the practice problems, while great for learning the material, had a significant number of errors throughout the course, particularly towards the middle and end. A couple of more advanced students helped verify the correct answers, but, Second, there was no staff, and, even worse, no CTAs to help out (as it happens, one of those helpful advanced students turned up as a CTA in the Duke course, but he had no official status here). I find the number of errors kind of inexcusable, since this is not the first run of the course; lack of response showed a distinct lack of interest on the part of the university – and on the part of Coursera, for that matter. But I suppose they figure, it’s better than nothing, and since I did learn quite a few calculative procedures and techniques, I suppose it is. It’s just that I’m very protective of MOOCs, and when a course opens itself up to criticism by this kind of carelessness (literally, care-lessness), it’s hard to advocate for their value against legitimate criticism.

The material was released all at once, with a suggested schedule. Because I wanted to finish before the Duke course started, I sped it up a little; I didn’t really complete the last unit, and I didn’t take the final exam. Because of the way the course was graded, it’s possible I “passed” anyway, which seems rather silly to me.

The Duke course was a lot more, well, I don’t know what it was. A lot of my classmates kept writing posts about what a wonderful course it was, but I found it garbled, disorganized, and unpleasant. If I hadn’t already taken the Kentucky course, I would’ve had no idea what was going on; in fact, during the week we covered material new to me, I was lost, combing YouTube looking for explanations, since the ones given in the lectures made little sense to me. On the plus side, I conquered my fear of significant digits, thanks to a couple of very patient and helpful CTAs.

The course followed the exact same framework as Duke’s Genetics & Evolution, which I adored; that goes to show you, it isn’t the template, it’s how you embody it. No one else seemed to have any problems, however, so maybe it’s me. I did see significant effort go into providing more of a context for the material covered, but I didn’t get a lot out of that; it seemed random and not particularly interesting. Then again, I’m not trying to be a chemist. But I wasn’t trying to be a geneticist, either, and that course had me glued to my seat.

A weekly test and final exam made up most of the basic evaluation materials, with an option to take “advanced problem sets” and write a peer-assessed paper. The advanced problem sets followed a pattern I recognize from looking over the shoulder of a lot of creative math teachers: questions about the problem. Do you understand the words? What values and equations do you need? Sketch your approach to the problem in words. Can you change the values to create a problem that uses different values? Is the new problem easier or harder? This sort of thing no doubt works wonderfully in a classroom, but here, I’m pretty sure any answer was accepted, and obviously there could be no feedback in a machine-graded system; because these were graded, we couldn’t discuss them. So while I can appreciate the concept behind that kind of question structure, I wonder if there’s a better way to implement this kind of feature – such as in homework which can be discussed.

The peer-assessed paper seemed to me a total waste of time, since I didn’t know enough chemistry to write about a chemical problem, but it didn’t seem to matter, since a grade was not part of the peer assessment; mere submission gave full credit. The most educational part of the process would’ve been reading the best papers (which were posted on the discussion boards as they were assessed). I confess, I didn’t bother, and that’s on me.

All in all, I far preferred the Kentucky course, though I found the lack of concern over errors, and the lack of CTA support, to be something of a problem. Of course, with Coursera moving inexorably to self-paced courses, this is the way of the future. At least I feel like I came away with some skills. I’m not sure what I came away from the Duke course with. I might even take the Kentucky course again; no way I’m taking the second of the Duke courses.

I’ve frequently said that no MOOC works for everyone, and that every course I’ve loved, someone else has hated, and vice versa. Some combination of the best parts of these – the increased detail, clarity, practice of Kentucky with the context and CTAs of Duke – would, of course, be ideal. But unlikely. In the meantime, it’s a matter of personal preference.

I’m-Running-Out-Of-Titles-For-Earth-Science MOOC

Course: Planet Earth… And You!
School: University of Illinois at Urbana-Champaign via Coursera (free)
Instructors: Dr. Stephen Marshak, Dr. Eileen Herrstrom
Earthquakes, volcanoes, mountain building, ice ages, landslides, floods, life evolution, plate motions—all of these phenomena have interacted over the vast expanses of deep time to sculpt the dynamic planet that we live on today. Planet Earth presents an overview of several aspects of our home, from a geological perspective. We begin with earthquakes—what they are, what causes them, what effects they have, and what we can do about them. We will emphasize that plate tectonics—the grand unifying theory of geology—explains how the map of our planet’s surface has changed radically over geologic time, and why present-day geologic activity—including a variety of devastating natural disasters such as earthquakes—occur where they do. We consider volcanoes, types of eruptions, and typical rocks found there. Finally, we will delve into the processes that produce the energy and mineral resources that modern society depends on, to help understand the context of the environment and sustainability challenges that we will face in the future.

[Addendum: This course has been converted to the new Coursera platform; content may have changed, and the experience is likely to be different]

It was the best of MOOCs, it was the worst of MOOCs…

First, the good news: the lectures were superb. Information was well-organized and presented clearly, with plenty of visuals in a variety of formats: hand-drawn sketches, photographs, professionally printed diagrams. Not to mention visual aids: I finally understand the many kinds of earthquake waves, thanks to … a slinky! Other pictorials were included, but it was the slinky that showed me how a wave could travel both parallel to, and perpendicular to, a slip.

Dr. Marshak’s lecture style was a pleasant surprise; I found it extremely effective. He speaks very calmly and quietly, like he’s talking to one person instead of a class or even a camera. I don’t put a lot of importance on style, since substance is so much more important, but considering how many times I rewind and replay videos, it’s always nice when listening is a pleasure. Another interesting touch was his inclusion of emotionally intense information at the end of the earthquake and volcano lectures. In the case of the former, I was nearly in tears as he described the extent of the damage done by the Japanese earthquake of 2011; likewise, I was deeply moved by his explanation of the casts of Pompeii. These segments weren’t just about earth science; they were about people affected by the scientific processes we’d been learning about, connecting us in a more human way to what we’d studied. It was a great way to finish off the material for those weeks.

Likewise, Dr. Herrstrom’s explanation of the science needed for the first two labs was clear and complete. She made a nice summary of the more expansive lectures, focusing on the information necessary to execute tasks.

I also applaud the effort to create a multi-modal learning experience. The lectures and the weekly quizzes were only the beginning of the coursework: each week we had a lab, an assignment, and a discussion topic, with two peer reviews of those discussion topics during the five-week span. People learn in different ways, and this course tried to provide multiple avenues. The execution left a lot to be desired, but the theory was excellent.

The CTAs (students chosen for their ability to deal with other students patiently and helpfully, who usually have some background in the subject) were wonderful. When things went south (and they did), they – all volunteers, not paid staff – were caught in the middle, yet they maintained a superhuman level of grace under pressure. At one point I said they deserved combat pay. At the very least, they deserve medals.

And it’s a good thing they were there, because actual staff – people employed by the University, people connected with producing the course, presumably people who had some interest in how the course was received – were few and far between. In fact, other than one staff person identified only as Univ. of Illinois Support #6 who showed up quoting legalese (a whole other kettle of fish, I’m not gonna go there), the course was without staff. This is the vision for the future, I realize, and there are courses where this works, particularly when good CTAs are involved. But here, where so many problems cropped up, it was as if this were an orphan class, and whomever was responsible for it – someone at the University of Illinois at Urbana/Champaign, presumably – just didn’t give a damn.

The main problem was in the labs.

The first lab – using seismographs to locate an earthquake – was pretty good, if slightly miscalibrated. The visuals of the seismographs and graphs were much too small to allow detailed measurements necessary to obtain the kind of precision the answers required. I spent a lot of time on the lectures, so I didn’t get to the labs until fairly late in the week by which time the autograder had been “adjusted”. How adjusted, I don’t know – and I still don’t know if I really did the measurements correctly, or if anything was accepted as a valid answer at that point.

The labs went downhill from there. If the point was for us to learn to use Google Earth, well, I still don’t really know how, I just know how to click on this folder and watch the world go by. I’ll admit, I have an attitude towards Google Earth. But, unlike the first lab, where the purpose seemed clear and I understood the connection to the lecture, the rest of them seemed like busywork culminating in looking at things I wasn’t able to interpret or understand. How many valleys are in this view? I don’t know – which of that stuff is a valley? Are there several towns, or many nearby towns, in the ashfall zone of Vesuvius? Tell me what “nearby” means, and the cutoff between “several” and “many”, and I’ll tell you. In the plate tectonics lab – a topic in which I’m very interested, by the way – I gave up on Google Earth and just looked for map images of the pertinent plate boundaries.

In one case, a student documented 14 problems with a single lab, including one question that seemed to include all wrong multiple-choice answers. Either that, or I was measuring the wrong thing, or measuring the wrong way, since the answer I selected was marked as correct. I’m not sure what I was supposed to learn from that.

I had it better than some, however; there were lots of people who couldn’t get Google Earth to load at all. A couple of us posted still shots to fill the void in Week 4, but I think most people just gave up.

The “assignments” seemed to be low-level quizzes in disguise; I’m not sure why they were separated out. I don’t even remember them, in fact, other than I had to enter my hometown latitude and longitude every week. I suppose I should take the 20 points and be merrily on my way, but I wonder if these were supposed to be something else, and it just never happened.

The one assignment I loved – an extra credit assignment – was mineral identification. That module was off-site, part of Black Hawk College’s website rather than Illinois or Coursera. But it was fun. I like rocks.

The discussion assignments weren’t my particular cup of tea, but there’s plenty of room for disagreement on that; some students seemed to like them. We’d have to write a letter advocating for or against a town’s earthquake preparedness expenditures, a mine, or convince residents to evacuate before a potential volcanic eruption. A great deal of information could get packed into things like that – but we were limited to 150 – 200 words. Later, staff backpedaled and claimed that was a “suggestion” but since that “suggestion” was on the grading rubric, it felt more like a requirement. Again, there was some kind of disconnect between what was intended and the material itself. Follow that with a “grading rubric” 20 options for one type of post and 12 for another… and it was overcomplicated to the point of absurdity. Again, a good concept, run into the ground by poor execution.

But sometimes, adversity creates opportunity. I again fell in with this loose consort of ironic MOOCers who made the five weeks delightful with the creation of a “Whine Corner.” As in Origins, it wasn’t so much about complaining as it was about camaraderie and horseplay. It’s a flexible little sub-community, already moved on in ever-changing form to other courses, where new students add their humor.

I can’t help but wonder what went wrong with this course, leaving it like cloven into good and bad like Calvino’s Viscount. It’s a shame, because this could’ve been terrific; if they fix the problems, it still can be. And I do finally understand earthquake waves.

Genetic MOOC

Course: Introduction to Genetics and Evolution
School: Duke via Coursera (free)
Instructor: Mohamed Noor
Introduction to Genetics and Evolution is a college-level class being offered simultaneously to new students at Duke University. The course gives interested people a very basic overview of some principles behind these very fundamental areas of biology. We often hear about new “genome sequences,” commercial kits that can tell you about your ancestry (including pre-human) from your DNA or disease predispositions, debates about the truth of evolution, why animals behave the way they do, and how people found “genetic evidence for natural selection.” This course provides the basic biology you need to understand all of these issues better, tries to clarify some misconceptions, and tries to prepare students for future, more advanced coursework in Biology.
…The genetics lectures are limited to basic transmission genetics, recombination, genetic mapping, and basic quantitative genetics….The evolution topics covered in the present course are largely confined to “microevolution”…

[addendum: This course has been modified to fit the new Coursera platform. The experience may be very different]

How good is this course, you wanna know? It’s so good, that although I had no particular interest in genetics or evolution, although I only signed up because some friends of mine from another course were enthusiastic about it, and I happened to have no classes running during the week it started, although I planned to drop it in W2 or W3 when other courses, courses I was definitely interested in, started – in spite of all that, it became the centerpiece of my MOOCing for the past eleven weeks, and by far my favorite course of the Winter session.

That’s what a great MOOC can do.

It starts with a great professor, in this case, Mohamed Noor. He’s the kind of guy who can use “bee-bop around” and “stochastic forces” in the same sentence and it sounds perfectly natural. He’s the kind of guy who seems so relaxed and personable, it’s hard to believe he’s a science professor at a prestigious university, while at the same time he evinces such command over a wide swathe of complex theory and practice, including the current state of research, that it’s hard to believe he’s bothering to talk to mere students. He’s the kind of guy who uses the three major releases of “I Love Rock ‘n’ Roll” as an analogy for relative reproductive fitness, and pulls it off. He’s the kind of guy who lectures in t-shirts with a bobble-head Darwin and a painting of a drosophila (fruit fly, the geneticist’s go-to critter) on the whiteboard behind him, without giving the sense that he’s trying too hard (his faculty profile shows him in a suit and tie, and that’s the shot that looks forced to me). For a sample, here’s a pastiche of “catch phrases” from the course, brilliantly cobbled together by a student from the 2013 run of the course.

While the course was fun, it wasn’t easy. In the live Hangout just before the final exam, a student told Dr. Noor, “You really made us work, man.” Yep: the official estimate is 5 -6 hours, but it took me more like 10 – 12 hours (I’m slow). And I loved every minute. If you’re not up to investing that kind of work, there is another option: some of the lecture videos are labeled as “General”; they give an overview of the topics, but don’t go into details of calculation or the many variations possible. GenEv Light, as it were. OF course, there’s always the risk you’ll get sucked in…

Each week started with a set of lecture videos, but that was only the beginning. I’d take careful notes, felt like I understood everything, and then… a series of practice problems left me going, “Huh?” Working through the problems gave me a much better sense of what population genetics could show, or how epistasis works, beyond the definition. A variety of other supplementary materials (software, definitions, articles, etc.) was included, and collaboration was not only welcomed, it was planned for on the message boards with weekly “Most Confusing?” and “Practice Problems” threads organized by the CTAs.

Student discussion of graded problem sets was also encouraged in an entire subforum organized by the Staff TA. This may seem like it would make the problems a piece of cake, but most of them required interpretation and analysis of the material, not just regurgitation of facts or calculation via formulas, meaning often there was a kind of debate between Team Answer A and team Answer C with Team Answer E raising a few good points as well. These boards were closely monitored, not for “cheating” but for excessive confusion; though the need was rare, on occasion a question would be clarified – ju- u- u – ust a little tiny bit – and in a way that wouldn’t help unless you understood the issue thoroughly in the first place.

By the way – it’s not easy to design questions like that. It’s a lot simpler to pick a key sentence from the lecture, rephrase it, and frame it as sentence completion, but asking something like, “What type of selection might you imagine operates on running speed in cheetahs?” or “Earlier in the semester, we discussed overdominance and the example of sickle-cell anemia. If you were to look at such a case, what might you expect in terms of the McDonald-Kreitman test’s predictions?” (both actual practice questions) takes more effort. Answering them requires a lot more than a complete set of notes.

Another nice detail was the structure and pacing of the course. An optional introductory set of lectures dealt with the evolution vs religion question pretty thoroughly. The midterm was scheduled for a week when no new material was released, meaning time could be spent on review and preparation. But it showed in subtler ways as well: I found weeks 2 and 7 to be particularly difficult, and weeks 3 and 8 were particularly “fun”; week 8, by the way, included sexual selection, including some amusing behaviors of various species. Though we were cautioned against anthropomorphizing any of that, it was easy to draw a parallel between the “song” of the water mite and the kind of conversational cues that might facilitate or discourage a human couple’s romantic connection. With my penchant for similarities in opposites, I drew a connection between what Peter Struck called the “cute puppy syndrome” used by Virgil in The Aeneid to make Dido more naturally attracted to Aeneas, and the egg-carrying behavior of the male waterbug that tends to increase its mating possibilities. A fun week, after having torn my hair out over the molecular clock.

The discussion forums were as rich and valuable as the rest of the material. The CTAs were terrific (I knew some of them from other courses, primarily Origins), both in directing discussions of the material (“check the last two minutes of lecture 3; do you see how that relates to your question?”) and in offering auxiliary discussions (“DNA in the News” was a popular thread, as was “Humor,” of course). The course TA mostly operated behind the scenes, except for the Hangouts, but a course like this doesn’t just happen; the day-to-day technical running, the release of materials, link posting, etc., all takes attention and work, and he did a great job. Fellow students were helpful and encouraging as well. And, as in any course dealing with this material, occasionally discussions got heated; this was kept under control by CTAs and staff refocusing on the course material and forbidding anything approaching disrespect. Again, that takes a lot of work, both to monitor, and to ameliorate without getting heavy-handed.

Most of the “grade” for the course depended on a timed midterm and a timed final; discussion of these was firmly forbidden, so even if you could bluff your way through the problem sets, you were on your own for these – which used similar question structures as the problem sets, but tweaked the situations just a little.

Timed tests can be problematic for some, for technical reasons; this is the first time I’ve encountered the brilliant idea to break the timed tests up into two separate sessions. Students, particularly those from countries with less-than-dependable internet connectivity or, for that matter, electricity, sometimes find they end up with scores of 0 due to technical issues (or, simply from not following instructions and going over the time limit); this two-tests process assures that at least half the score can be salvaged. Problems still happen – but it’s a simple way to make them less likely, and to make non-academic technical issues, or simple user errors (clicking “Submit” by accident seems popular) less costly.

I was very worried about these timed exams. I tend to work very slowly; and, I get confused after relatively short periods and need a break. These were fair exams, though, modeled on the problem sets, but not copying them. I did a lot of review for both exams – re-watched the videos (at 1.5 speed, it was pretty funny), re-did the problem sets. To my surprise, I aced the midterm (I don’t know my “grade” on the final yet, though I doubt I did that well; I’ll admit, I didn’t put as much effort into it, so I didn’t deserve to do as well). I don’t usually brag about scores in these posts, since they don’t usually mean much, but this score meant something. That 100% required some degree of understanding. I earned it. The test was designed to make me earn it – and the course was designed to make me want to earn it.

That’s what a MOOC can be. That’s what a teacher can do.

Illusory MOOC

Course: Visual Perception and the Brain
School: Duke via Coursera (free)
Instructor: Dale Purves
The purpose of the course is to consider how what we see is generated by the visual system.

Thus the objectives of the course are:
– To introduce you to some fascinating perceptual phenomenology
– To make you think about how this phenomenology can be explained
– To make you consider what possible explanations imply about brain function.

[Addendum: This course has been converted to the new Coursera platform; content may have changed, and the experience is likely to be different]

A course about the science behind optical illusions? What could be more fun?

By coincidence, we were in the Color unit on the day #TheDress went Twittercrazy (The Guardian‘s article used the same illustration chosen as the header of the course). Except… since this is one of those “release all the material on day 1 and take as you will” courses, I’d long completed that unit. Nevertheless, I joined in, commenting on the discussion board that Coursera was missing out on a marketing opportunity by not tweeting about the course while the hashtag was trending; they did, a bit later, but forgot the hashtag, and, unforgivably, misspelled the professor’s name. As I understand it, the whole issue was nonsense anyway: several different copies of the photo were circulating, and a lot of it had to do with color balancing in processing as well as lighting during the photography itself. But it was fun anyway.

Prof. Purves was emphatic during the first week of class, however: what we call optical illusions are not “illusions.” They are, in fact, the way our visual system has evolved to give us a perception of reality that is survival-based. We see optical illusions, the dress, and everything else, that way – even when we don’t realize it – because our visual pathways can’t handle anything beyond a photon stimulating a cell in the fovea, so at least three factors – illumination, reflectance, transmittance – are conflated and lost forever to our perception. It’s the genius of evolution that we’ve been able to “see” well enough to survive this long, so that we’re here to fight about whether the dress is white and gold or blue and black .

The things you come across in MOOCs. By the way, you can take a look at the prof’s website to see many of the concepts covered in this course – and then some. I, for instance, still don’t believe these two tables have the same dimensions, merely rotated 90°. A quick screen clip, some playing around with Word shapes, and… yeah, they really are.

The first week introduced the foundational concept of the course, the “inverse problem” – the difficulty of recreating reality from that conflation that gets transmitted as a single stimulus – then, after a couple of weeks on the structure of the primary visual system and various ways of conceptualizing our ability to see, repeatedly went back to that inverse problem as we looked at our perception of lightness and brightness, color, depth, geometry, and motion. They all came back to that inverse problem, and a similar way of getting around it as an adaptive trait. It’s an idea I came to wonder a great deal about – can we perceive anything the way it is?

A fascinating idea – lots of the ideas in this course were thought-provoking – yetI found it to be one of the drier courses I’ve taken, complicated by twisted syntax and some of the most “academic” discourse I’ve encountered in any MOOC. Take this description of the Bayes Theorem: “And it’s a statement of conditional probabilities, the left hand side of this equation being equivalent to the right and the left hand side of the equation expresses the probability of A given B, where A is in vision, an image or a stimulus, and B, would be the underlying state of the world. This is called the posterior probability, this left hand side of the equation. And it is given by the probability of B given A, that is what’s the probability of the state of the world given the image, were multiplied by the probability of, of the image in the first place, and that’s generally normalized by the probability of underlying states of the world.” I’m glad I’d run into this before in a more comprehensible form, or I would’ve wept.

Staff presence was limited to operational issues. In fact, a “warning” greeted us at the start of class – it wasn’t called a warning, but I’m not sure what else it could be called: “The TAs will also attempt to directly respond to some posts in order to facilitate discussion or address certain problems. Please be aware that the TAs are neither professional experts in computer science, biology or life science.” I suppose it’s just as well they didn’t actually attempt to facilitate discussion, although logistical issues were addressed – questions on written assignment requirements, problems with exam submissions, etc.

Some of us (including classmates from the concurrent Plato course – more good timing) used the message boards to bandy about more philosophical approaches to the material, dipping into epistemology. At one point, that disintegrated into a pissing match so I backed off. That happens sometimes. It happens more often when a course isn’t well-monitored. As I keep saying, every MOOC is different. Some MOOCs show ownership; others, don’t. It’s kind of a shame, because Dr. Purves obviously had great depth of knowledge about, and passion for, his field. Some of that came across, but it could’ve been a knock-your-socks off experience, and it wasn’t.

Grading was based on quizzes – they were timed, but generously so, and multiple attempts were permitted – and a final peer assessed paper that could be viewed as optional, depending on one’s goals; some students are quite fond of Certificates of Achievement, with or without Distinction, and as there was no Distinction here, and a Certificate could be earned by acing the quizzes, it was possible to skip the paper. However, I found it beneficial; I could pull my thoughts together in an organized way and put the Inverse Problem and the concept of survival-based perception into my own words and tell a story. I’ll also get to see other papers, which is a huge benefit of doing any Peer Assessment (only a tiny fraction of students show up on the message boards, and it’s always fun to see what others are thinking).

I signed up for this course because of the Philosophy and the Sciences course I took last Fall; it was a natural continuation of the science portion. It’s material worth learning, and I find the point of view fascinating (I’ve used it in other courses already), even if the packaging was a little disappointing.