Switching it Up: Instead of Biochem, let’s try Chemical Biology MOOC

Course: Chemical Biology
Length: 6 units, total approx. 21 hours
School/platform: University of Geneva/Coursera
Instructor: Robbie Loewith, Marcus J. C. Long, et al
…[C]hemical biology straddles a nexus between chemistry, biology, and physics. Thus, chemical biology can harness rapid chemistry to observe or perturb biological processes, that are in turn reported using physical assays, all in an otherwise unperturbed living entity.
…We will discuss fluorescence as a general language used to read out biological phenomena as diverse as protein localization, membrane tension, surface phenomena, and enzyme activity. We will proceed to discuss protein labeling strategies and fusion protein design. Then we will discuss larger and larger scale chemical biology mechanism and screening efforts. Highlights include a large amount of new data, tailored in the lab videos, and a large number of skilled presenters.

I’ve often said that one of the drawbacks of moocs is that classes in a sequence can be separated by months or even years. A student enrolled in a biology program at an on-the-ground university would be taking bio and chem classes all the time, allowing for more reiteration and keeping the ideas in active brain storage; if six months elapse between bio classes, I forget what PCR is and have no idea what the RAS pathway is. And suddenly it occurred to me: I can do something about that! Wow, revelation. So instead of waiting around for the next in MIT’s cell biology series, or their continuation of general chemistry, I went looking for related classes. Though I had a couple of retakes in mind, I stumbled across this, and thought it might be interesting. Is there a difference between biochemistry and chemical biology? Turns out, yeah, but it’s a matter of emphasis: in biochem, it’s finding the result; in chembio, it’s figuring out how to get there.

I knew from the start this would be over my head, and boy, it sure was. A couple of lectures were just rivers of words floating by. But that’s one of the benefits of moocs: you can take a class that’s a little beyond your grasp, take away as much as you can, and save the rest as aspirational motivation.

I learned the difference between fluorescence and phosphorescence and all about the Jablonsky diagrams that spelled it out; I learned about membrane tension and the pathway that detects and adjusts for it; I got a good refresh on the properties of amino acids and things like the catalytic triad; and in more general terms, I dealt with assays at a level of detail that was scary. Oh, and plasmids, I’d forgotten everything I ever knew about plasmids. So it was very much worth it, though I often missed entire swaths of material. And, by the way, I passed, which should give someone pause about the utility of passing scores on moocs: I didn’t deserve to pass, yet I did. I put in the work, to be sure – I spent 51 hours on site rather than the 21 hours predicted – but a lot of my answers were the result of test-taking skills,  guessing, and perseverance rather than knowledge.

The more aspirational material, saved for a later time, was fascinating. I’m still reeling at the different ways biological molecules and processes can be examined, both in vivo and in vitro. There’s the SNIFIT which generates one ratio of fluorescent colors when closed, and another in the presence of target molecules which open it. And photocaging, which keeps a molecule inert until activated by light, allowing precise targeting of the process under study. I’m a lot hazier on TREX, GREX and barcoded libraries, but even with minimal understanding they’re fascinating. Then there were uses of my old friends from the MIT Biomoocs SDS-PAGE and Western blots, which now seem a lot simpler.

Besides video lectures by several different professors, there were also several lab segments showing fancy machines and the people who operate them (these mostly went by me), and short Readings explaining individual concepts. Several Practice Quizzes showed up during each module; these required the 80% to pass, but didn’t count in the eventual overall score. They displayed what was right and what was wrong, and could be taken over and over until the desired score was obtained (the “choose all that apply” questions were kind of tricky); I ended up getting 100% on all, not to get the score, but to make sure I had the correct information. Each module also had a Final Quiz, which partly drew on those Practice Quizzes. The Final Quizes displayed nothing except a score for the first three modules; the last three modules displayed whether a question was right or wrong. These could only be re-taken after 72 hours.  I had to retake a couple of them to get to the 80% passing score. And as I’ve said, that was mostly unearned, so I’m not putting any feathers in my cap.

For someone with a better chem baseline than I, this would probably be a great class for looking at these techniques in depth. For me, it was still a great class, just not in the way the instructors probably intended it. But some day I’m going to run across something like barcode libraries again, and I’ll be a little better prepared to understand it, now that I have some idea of where it’s going.

And now I’m going to take some additional chem and bio courses to keep me primed for the new moocs this summer; but now that I’ve had a stretch, I’m going to find something more within my level. Because stretching is great – once in a while.

Chem 1 MOOC (MIT)

Course: General Chemistry I: Atoms, Molecules, and Bonding
Length: 15 weeks, 10-12 hrs/wk
School/platform: MIT/edX
Instructor: Sylvia Ceyer, Mei Hong, Patti Christie, Alisa Krishtal
This course is designed to build core skills in chemistry, including drawing chemical structures and predicting molecular properties and reactivities, as well as to gain the necessary fundamental knowledge for advanced courses….
This chemistry course is the first in a series of two courses that together cover first-year, University-level chemistry. In this course, you will uncover the principles of chemical bonding, in the way it historically occurred: starting from the first experiments that revealed the fundamental dual wave-particle nature of energy and matter.

Short version: a great, if challenging, way to get back into chemistry.

Here’s the problem with chemistry as a subject: It sounds really cool. We all remember the baking soda volcanos from elementary school, and a lot of us would like to know just what all those ingredients in our shampoo are doing there. Not to mention fireworks and medicines and all kinds of other interesting stuff. But when you come to chemistry class, you get… math. Icky math. Equations with symbols you’ve never seen before, not to mention really complicated radicals and exponents. And sigfigs. Chemistry is obsessed with sigfigs.

But that’s what’s required. Here, the mathy stuff – about half the course – was handled very smoothly, with gradual introductions of more and more complicated elements and recitations (thank Zeus for those recitations) that went step by step through problems to make sure you’ve got it straight. It’s all about energy, speed, distances, and the *#@% Ideal Gas Law, all of which are quantitative. They deliberately avoided requiring calculus, so it’s only algebra; it’s just nasty. But that’s why God made Wolfram Alpha. It’s hard, and there are  some aspects I think I need to go over again, but it’s not out of reach. Prof. Ceyer’s simple-to-complex approach was perfect for me; as time went on, I became more and more appreciative of her, and by the end of the class, I adored her.

I had more trouble with the qualitative material — types of bonds, orbitals, periodic table trends —  much to my surprise. I think part of that was Prof. Hong’s more off-the-cuff lecture style, though I suspect more advanced students would be perfectly fine with it. However, the material is pretty standard and is easily available on Youtube, plus I’d covered most of it in earlier moocs, so it was manageable. If the instructors had been reversed – if Prof. Hong had handled the math and Prof. Ceyer the bonds – I would’ve been sunk.

A Module 0 containing basics of high school science and chemistry was provided; I spent way too much time on that, and so was behind for most of the course. In retrospect, I probably could have skipped the review entirely, but there was no way to know that in advance.  

The course page lists this as an Intermediate course. In spite of the Module 0 material, unless you were really good in high school chemistry, it’s probably not the place to start. But for that, there are other options, like the University of Kentucky chem mooc I took (twice) several years ago. Now that I think about it, I never did take the second part of that mooc; maybe I should, because MIT will be releasing a second part to this course sometime this year. I’m looking forward to it, but I’d like to be prepared. And I’m still hoping they’ll come up with an orgo course one of these years.

Cell Biology MOOC (Part 2: Signaling)

Course: Cell Biology: Signaling
Length: 5 weeks, 4-6 hrs/wk
School/platform: MIT/edX
Instructor: Iain Cheeseman, Frank Solomon
This is the second cell biology course in a four-part series…. these cell biology courses transition to a comprehensive discussion of biology at an experimental level. How do we know what we know about cells at a molecular level and how can we use that knowledge to design experiments to test hypotheses in cell biology?
….You will embark on a lively journey through cellular signaling mechanisms, regulation, and specific examples and learn how to apply key concepts and themes of this dynamic experimental science to understand the fundamental workings of cells.

Short version: Another great bio class from MIT.

I took the first part of this unfolding four-part series last summer, covering transport within the cell. I wish I’d thought to review it before starting this part, because, while it isn’t essential, there was enough overlap that some refreshing would have been helpful, particularly when it came to assays. But no matter, I’m probably going to take the entire sequence over when it’s complete. For that matter, I’m probably going to take the entire MIT Bio curriculum again, since I feel like I’d do a lot better, and get a lot more out of, the earlier courses now that I’m beginning to feel more familiar with cellular processes and lab techniques. Repetition truly is everything. In a normal university setting, I’d be in these classes all the time, but with moocs, they end up spread out months, years apart, so the accumulation process is slower.

Primarily the course covers various signaling pathways: G-proteins, which send second messengers out to start cascades;  various pathways that use dimerization and autophosphorylation to start a signal; and a few more specific paths, like insulin, epinephrine, and RTKs, and some general cell reactions like the Unfolded Protein Response. As with all MIT bio courses, the emphasis is on experimentation, both historical and contemporary, to discover how pathways work and to confirm or discard hypotheses, rather than on memorizing individual players in each pathway. Thought questions — “how might you verify that X is necessary or sufficient?” — show up frequently, since the idea is to generate the skill of thinking as a scientist. A couple of the features introduced in Part 1 were repeated here (see that course for details): “Neat Experiments” showing how certain features were initially discovered; and Mudslips (a forum for  clarifying points that seemed unclear in the lectures). The forums were active and well-covered by staff, presumably grad students.

The course is labeled as Advanced, but don’t let that intimidate you. I wouldn’t consider myself an Advanced bio student by any means, and while parts of it were difficult, it was at a good level for me. It wouldn’t be the best first bio course; if you’re not comfortable with concepts like ligands, receptors, domains, and the compartments of a cell, it might be better to pick that up first. Since there’s an emphasis on experiments, some familiarity with common procedures — blots, gels, that sort of thing — is assumed. Some review material in experimental design and processes is included, including a very helpful tutorial on Western Blot. While there’s no substitute for actual lab experience – which of course moocs can’t provide – they do a pretty good job of conveying the thought process behind various procedures.

Grading follows the usual combination of after-video questions, unit quizzes, and tests. The audit track (that is, free of charge) includes two tests, as well as after-video questions and weekly quizzes; the third test is for those on the Verified track only ($99).

Someone pointed out in the forums that it can be difficult to understand the pathways one of the professors is outlining, since his lecture style is somewhat erratic due to his enthusiasm (I suspect he’s beloved by in-person students). As compensation, online students have access to Youtube, which covers the pathways mentioned, even if not in the same terms. I found it much easier understand – and enjoy – the lectures about UPR, for instance, once I’d found a couple of Youtube videos that were more straightforward about the actual steps. By the way, this problem is not unique to this course; it comes up in most team-teaching courses, and I suspect it’s deliberate to pair instructors with different styles since some students will gravitate towards each. It’s quite possible more advanced students would prefer a more effusive style, since they’re already on board with the basics.

I’m really psyched about the next installment, coming this summer, covering the Cell Cycle. In every mitosis lecture, there are a couple of checkpoints where “the cell checks to see if everything’s ok before going on to the next step” but I’ve never seen an explanation how it knows whether everything’s ok. Now I get to find out! 

Physics for Poets MOOC

Course: How Things Work: An Introduction to Physics
Length: total ~14 hours
School/platform: UVA/Coursera
Instructor: Louis A. Bloomfield

An introduction to physics in the context of everyday objects: It’s essentially case study physics, an introduction to physics in the context of everyday objects and activities. My goal is to make physics useful, and to help you understand and manage the physical world around you.

In the 1994 Law & Order episode “Big Bang,” ADAs Ben Stone and Claire Kincaid are investigating a physics professor whose defense involves serious particle physics. In private, Stone confesses to Kincaid: “You know what I took for my science requirement? Physics for Poets.” Kincaid confesses back: “Elementary Geology. Rocks for Jocks.” This course is essentially Physics for Poets: general concepts peeled down to their simplified forms, presented via concrete examples with minimal math.

It’s one of the oldest classes on Coursera’s roster, making its debut back in 2013, and I’ve been thinking about taking it since about then. But stubbornly, I kept trying the “real’ physics courses and quitting by week 3 when I still couldn’t keep joules, newtons, and watts straight. Now that I finally cried Uncle and got here, I wish I’d done it sooner.

Each of the six weeks focuses on an object that demonstrates a related group of concepts. Skateboarding, for example, introduces force, inertia, and acceleration. I’d never considered weight as a force before (it’s usually ignored in favor of mass), but it makes a lot of sense in this context. And by spending a couple of weeks focusing on force – that is, newtons – I was much better able to grasp the idea of joules when we got to energy later on. For me, that alone was worth taking the course.

The other objects are falling balls, ramps, seesaws, wheels, and bumper cars. I can say I saw a lot of things more clearly, such as what’s a force and what isn’t, and what properties are conserved. By comparing linear velocity and momentum to angular velocity and momentum, the course helped me keep a lot more organized. I’m still a little confused about some stuff, but it’s not a total jumble.

The professor is very hands-on – and feet-on and butt-on – as he skateboards, rolls on a cart, tosses balls out of windows and across rooms, tips small levers and puts TAs on seesaws, pulls wagons around, plays air hockey to simulate bumper cars, and does everything he can to demonstrate various kinds of forces and accelerations while also showing off the UVA campus. There is some math, but very little, and it’s of the a=b*c variety, very simple even for me. In fact, after I finished the course, I went back and dragged out the formulas that tended to get buried in the long runs of explanation. This also was a very worthwhile process for me.

The course starts with a Preliminary Assessment before any teaching takes place. This is graded; for those of us who don’t sign up for the “Certificate Experience” (I guess they gave up on verification), this is the only grade you’ll see. There are ungraded (but very useful) questions embedded in the videos. Each week ends with a quiz that you can take if you’re auditing, but you can’t find out what you got right or wrong (unless you’re determined and creative, in which case you might discover students from years before have left a trail of breadcrumbs some of us might find useful. And some of us might find, for those intending to earn a grade for this, to be cheating, if relatively worthless cheating). A final exam similar (at times identical) to the Preliminary Assessment finishes things off in Week Seven.

There are some tricky concepts, but it’s basic mechanics presented in such a way as to give students more of a sense of what is actually happening than the equations they’ll see in a more typical physics course. I’m going to take another stab at a physics course, and see how much of a difference this made. I’m hopeful.

Cell Biology MOOC (Part 1: Transport)

Course: Cell Biology: Transport
Length: 4 weeks, 4-6 hrs/wk
School/platform: MIT/edX
Instructor: Rebecca Lamason, Frank Solomon

This is the first cell biology course in a four-part series. Building upon the concepts from biochemistry, genetics, and molecular biology from our 7.00x Introductory Biology and 7.05x Biochemistry MOOCs, these cell biology courses transition to a comprehensive discussion of biology at an experimental level. How do we know what we know about cells at a molecular level and how can we use that knowledge to design experiments to test hypotheses in cell biology?…You will embark on a lively journey through cellular transport mechanisms and learn how to apply key concepts and themes of this dynamic experimental science to understand the fundamental workings of cells.

I’ve said many times how much I like the way MIT does bio courses, so I was thrilled when I saw they had a new one. And this is Part 1, with three more parts to follow!

I wasn’t sure what Transport was going to cover. Turns out, it’s how proteins (mostly) get from one compartment of a cell to another: from ribosomes that form them to the endoplasmic reticulum, the Golgi, or maybe to vesicles that will transport them somewhere else; and how stuff gets in and out of the nucleus. So there’s a lot about signal sequences, about channels and pores, and about enzymes, chaperones, and all kinds of supporting players. I’m still amazed every time I get even a peek at how complicated it is to keep us alive.

These videos must have been recorded quite recently – this calendar year – because COVID-19 came up twice, once in connection with how an RNA virus moves its genome out of the nucleus (a student asked if viral infection was being covered because of the pandemic; no, it was a routine part of the course) and once in conjunction with the lab technique of using detergent to destabilize a cell’s bilayer lipid membrane to solubilize transmembrane proteins – just like washing our hands destroys the outer coating of the virus.

For me, the material was a bit easier because there was less quantitative work as there was with biochemistry: no worrying about pH or equilibrium, no MATLAB. Yet I found the lectures themselves a bit more disjointed than expected. Part of this might be that there were two instructors; I also felt that the videos themselves were a bit more cut-and-paste (it’s not unusual for individual videos to show edits, removing classroom issues for instance), thought that’s just an impression. We started off with lectures on experiments, and with little context, I had no idea what it was we were experimenting on. Once the more process-oriented material started I was able to catch on, but it was a tough few hours there. Then again, I have the disadvantage of having never been in a lab, so I’m always a little behind the eight ball when lab work is the topic. I’m beginning to get it, though: biochem mashes things up and assays for products; genetics creates mutations and assays for function; and cell biology often uses microscopy, including some very cool fluorescing techniques.

Each video is followed by a set of “check” questions; these count in grading, but in most cases have unlimited attempts so are pretty much free points. Three quizzes make up the bulk of the grades, and these are, of course, more difficult and in most cases only offer one attempt. The Audit version of the course does not allow access to the third quiz; that requires paying for Verified access. But the Check questions and the first two quizzes give a pretty good idea of how well you’re understanding the material.

I thought I was moving along pretty quickly through the course, but kept discovering the deadlines coming up fast. I have always found the time estimates to be on the skimpy side for these courses, this one included though it wasn’t as pronounced a gap since there was less quantitative material.

This series includes several fun features. Wiltrout Questions, named for one of the off-screen professors, are open-ended “What do you think about this” questions that invite students to figure out how something might work, to “encourage active engagement in thinking about cell biology and a deepened understanding of a specific concept or approach”. After each unit, students are invited to submit Mudslips indicating “the muddiest, or least clear aspect of that class period.” Then there were the “Neat Experiments” videos, detailed and carefully animated explanations of historically important lab work in cell biology that nailed down a principle or used a new technique. These aren’t new features, of course; questions in both directions have always been part of these courses (Journal Club in another course, for example), and experiments have always been central in these courses. But it’s a nice touch to formalize them.

Another fun aspect was the naming of the proteins. One set was named Mens, Manus, and Cor; it turns out the MIT motto is the first two, “mind and hand”; the “heart” was added because, well, it’s about time (and there was a third protein that needed naming). Another set was named after Greek muses or fates or something, I don’t remember. Each of these courses has little personalizing details like this; it isn’t as though there’s strong pedagogical impact, but they’re part of what makes these courses so engaging.

I have no idea what the other three parts of Cell Biology will cover – I had no idea what Transport would cover until I took it – but I’m looking forward to them!

Another Biochem mooc (MIT version)

Course: Biochemistry: Biomolecules, Methods, and Mechanisms
Length: 12? weeks, 3-6? hrs/wk
School/platform: MIT/edX
Instructor: Michael Yaffe

We developed 7.05x Biochemistry with an emphasis on:
• Developing your scientific thinking skills including articulating hypotheses, performing thought experiments, interpreting data, and designing experiments.
• Using data based on real scientific experiments and highlighting the scientific process.
• Asserting that biology is an active field that changes daily through examples of MIT (and other current) research, not static information in a textbook.
• Visualizing real molecular structures with PyMOL to better understand function and mechanism.
• Appreciating the quantitative aspects of biochemistry and practicing this quantitation with MATLAB.
• Translating topics in biochemistry to diseases and medicine.
• Conveying the authentic MIT firehose experience.
• Implementing the science of learning in the course design.

I started to take this course a couple of years ago, and ran away screaming when I saw it started with “Buffers and pH.” For some reason I felt more up to it at this point, though I haven’t done any additional work on those topics. Predictably, I did quite poorly on that unit – and a couple of other units – but it was still very worthwhile.

MIT’s biology department emphasis is always on the practical approach. That is, they go through a pathway or a process in detail, give you a couple of general questions to see if you’ve got the idea, then throw you into a story set in a lab and make you figure out the setup: what assay do you need, what product are you looking for, what reactants do you need, what would you expect to see, what does this result – graph, gel image, whatever – mean. This is, after all, what biochemists are training for, not memorizing reactions. Something I discovered late in the course: the names of the fictional lab team in the Problem Set questions are the names of biochemists. They don’t have the distinct (and amusing) personalities of those in the Molecular Bio lab scenarios, but it’s still a great approach.

The home page emphasize some prior biology is needed to succeed. As usual, I needed more (any?) organic chem in some places; they do provide a nice set of review materials on pertinent topics – orbitals, thermodynamics, functional groups – and that helped.

The material is broken down into eight modules, one released every week, but the due dates allow a week of extra time for all modules. I wish I had the chops to spend just 3 to 6 hours as predicted on the home page; for me, it was more like 10 – 12 hours, though I do a lot of extra work basically copying the whole course into a Word document for future reference. Each module consists of a set of between ten and twenty video lectures; these are each followed by a short quiz that allows unlimited attempts for each question. The module is capped off by a Problem Set, where the number of attempts are more restricted and the lab scenario is usually prominent. As you might expect, the Problem Sets count for a lot more than the Test Yourself quizzes. Some weeks have far more material than others, but it might be they seemed harder to me because they hammered my weaknesses.

Some of the Problem Sets included questions that required the use of MatLab; you can connect for free through the course (in fact I still had an account from a prior course, to my surprise). I skipped these entirely. Maybe another time. Optional PyMol assignments were also included. I used PyMol in another course, and liked it a lot, but I didn’t mess with it this time; I had too much to deal with already.

Then there’s the “final”, in the form of what they call a Competency Exam (paywalled; $150). Don’t worry if you can’t or don’t want to pay the fee; there’s plenty of testing throughout to make sure you’ve got the salient points. I’m perfectly happy with the free material available, even if I do have a score of only 26% to show for my trouble. The bright side is, the maximum could only be 30%, so if I look at it one way, I got a score of 86%. I suspect the Competency Exam is significantly harder (they call it a challenge), it’s timed (oh no…), and it would have required a review of all the material (and I was pretty much done by the time I finished the last problem set) so I’m fine with not paying $150 for the work and likely humiliation.

I’m a big fan of MIT’s approach, even though I’ll never set foot in a bio lab or work on an actual science degree. The Harvard Biochem mooc is, after the thermodynamic component, more about specific pathways, particularly the generation, metabolism, and regulation of major elements, and the testing is far more information-retrieval. I might take that again, because that’s fun, too. And I feel more up to the thermodynamics and kinetics material, thanks to this course.

Daniel Chamovitz: What a Plant Knows (Scientific American/FSG, 2012) with BONUS MOOC!

We are utterly dependent on plants. We wake up in houses made of wood from the forests of Maine, pour a cup of coffee brewed from coffee beans grown in Brazil, throw on a T-shirt made of Egyptian cotton, print out a report on paper, and drive our kids to school in cars with tires made of rubber that was grown in Africa and fueled by gasoline derived from cycads that died millions of years ago…. And plants continue to inspire and amaze us: the mighty sequoias are the largest singular, independent organisms on earth, algae are some of the smallest, and roses definitely make anyone smile.
Knowing what plants do for us, why not take a moment to find out more about what scientists have found out about them ?

I’ve lived a relatively plant-oblivious life – until about six months ago. And now I’ll talk about my plants (not even interesting ones, basic beginner stuff) like old ladies talk about their bunions.

It’s all @drunkphyto’s fault.

I was minding my own business when someone retweeted her tweet into my feed last September: “The smell of cut grass is the grass releasing a wounding compound into the air to warn other plants that they were injured. You are smelling their screams.” I immediately thought of Seth Fried’s “Animacula”, a short story in the form of a lab report about organisms with strange properties, including screaming. Oh, and Liz Ziemska’s “The Mushroom Queen” which acquainted me with the interconnectedness of fungi via mycelia.

I emailed @DrunkPhyto to tell her how excited I was about all this (yeah, I know) and, to my surprise, she gave me a friendly reply rather than a restraining order. She recommended a number of books, one of which was Chamovitz. So it ended up on my reading list. And I started eyeing the plant stand in the supermarket, until I finally brought home a tiny philodendron, then an ivy, and an oxalis, and various flowers….

I was in for another surprise. As I started reading, I realized I’d taken all these moocs on biology, physiology, biochem, anatomy, and other sciency topics, and while I’d encountered cell respiration and the Michaelis-Menten equation multiple times, I’d never learned anything specific to plant biology. I didn’t even know how photosynthesis worked! So I checked edX for any moocs on plant bio, and found little beyond agricultural ecology. Ah, but on Coursera, I found… Understanding Plants: What a Plant Knows , taught by Daniel Chamovitz! So of course I signed up. It follows the book very closely, and includes very helpful diagrams the book lacks. Double bonus: He has a second course, Understanding Plants: Fundamentals of Plant Biology , which I will take as soon as I finish up the biochem I’m struggling with.

How way leads on to way…

Plants must be aware of the dynamic visual environment around them in order to survive. They need to know the direction, amount, duration, and color of light to do so. ….Plants don’t have a nervous system that translates light signals into pictures. Instead, they translate light signals into different cues for growth. Plants don’t have eyes, just as we don’t have leaves.
But we can both detect light.

The book’s approach is to examine how plants sense their environment, through chapters like What a Plant Sees, What a Plant Feels, How a Plant Knows Where It Is, What a Plant Remembers. For each sense, the approach is to look at the human equivalent – say, sight – and break it down to its fundamental quality – sensing light – while pointing out key differences between the human version and the plant version – plants don’t have brains to interpret light signals into pictures – and presenting experimental evidence and theories for ecological significance of the sense.

There’s a fair amount of technical detail for a general readership book. The basics of electrochemical conduction, for example, and the regulation of water through ion transport to cause movement; gene expression and epigenetics; receptors and phytochromes. The experiments that revealed various processes and qualities are described in detail. I have to admit, I was surprised that Darwin was such a plant buff, proving that plants sense light in the tips of shoots. One of the most ingenious experiments was by Thomas Andrew Knight, a 19th century gentleman (rather than a scientist) who concocted a kind of water wheel to create centrifugal force to understand the role of gravity in plant growth, the International Space Shuttle being a couple of centuries in the future.

One of the most interesting chapters was What a Plant Hears, for several reasons. Caution: Spoiler ahead! First, it was a negative finding, and, as Chamovitz points out in his mooc, “one of the other problems in scientific research is that you can’t publish negative results.” This is particularly pertinent to this chapter, since a poorly-designed study in the 60s, coupled with a pop-science (in the worst sense of the phrase) book, had everyone convinced that plants like to be talked to, and they prefer classical music to rock. I’ll admit, I thought this was the case until I read this chapter; I had no idea the study was flawed and the hypotheses invalid. But because no one wants to publish negative results, failures to replicate the study weren’t anywhere near as publicized as the original work.

Even more interesting, the mooc contains a post-production video updating the hearing lecture, since later experiments have shown that plants do show responses to low frequency sounds, possibly via touch sensors (which is, fundamentally, what hearing is), and this may be related to sending roots in the direction of water. As Chamovitz says, “Science is a self-correcting system,” and new research leads to new theories.

Our dictionary’s definition of smell excludes plants from discussion. They are removed from our traditional understandings of the olfactory world because they do not have a nervous system, and olfaction for a plant is obviously a nose-less process. But let’s say we tweak this definition to “the ability to perceive odor or scent through stimuli.” Plants are indeed more than remedial smellers. What odors does a plant perceive, and how do smells influence a plant’s behavior?

The chapter on smell was also particularly interesting. Just like us, plants have receptors for volatile chemical molecules, which are the basis of smell. Anyone who has sped up the ripening of a peach or avocado by placing it in a paper bag with a ripe banana has used this sense: ethylene is given off by ripe fruits and signals other fruits to ripen. I learned this practice goes back many centuries, though it used other means: incense in China, for example.

And here’s where the book’s approach really works for me: given that this is the case, why would this happen? What’s the evolutionary advantage to having one ripe peach encourage others to ripen as well?

From an ecological perspective, this has an advantage in ensuring seed dispersal as well. Animals are attracted to ready-to-eat fruits like peaches and berries. A full display of soft fruits brought on by the ethylene-induced wave guarantees an easily identifiable market for animals, which then disperse the seeds as they go about their daily business.

So it isn’t that peach trees thought it would be a good idea if they did this; it’s that those plants that had this facility, however it was acquired (by mutation?) would have better reproductive success than those that didn’t. This is evolution in a nutshell. This is also my own musing, not a point made explicitly in the book, so if I’m off-base, tell me.

It’s this sense of smell that @DrunkPhyto was (slyly) referring to with “smelling their screams”. This exact point comes up when considering that an injured leaf will release a volatile chemical, and other leaves, on the plant and on other plants, will respond to it with self-protective measures:

While the phenomenon of plants being influenced by their neighbors through airborne chemical signals is now an accepted scientific paradigm, the question remains: are plants truly communicating with each other (in other words, purposely warning each other of approaching danger), or are the healthy ones just eavesdropping on a soliloquy by the infested plants, which do not intend to be heard?

There’s no real answer to this question, but again resorting to evolutionary advantage, plants that warn their own leaves to defend against intruders would likely survive more than plants that didn’t. How the “altruism” of warning other plants comes into it is murkier, though it’s scientifically doubted.

We don’t typically think of memory in connection with plants, but it turns out we can. Again, Chamovitz breaks down memory into its essential parts – storage, encoding, and retrieval – and shows how this works in an organism with no brain, no hippocampus. The Venus Flytrap serves as an excellent example of short-term memory: about 20 seconds. Plants that want to bloom or seed at specific times of the year keep track of the length of the day via genetic suppression or expression; this serves as a kind of medium-range memory. And the most interesting memory of all, long-term memory, spans generations via epigenetics, a topic I know far too little about:

…Not only do the stressed plants make new combinations of DNA but their offspring also make the new combinations, even though they themselves had never been directly exposed to any stress. The stress in the parents caused a stable heritable change that was passed on to all their offspring: the plants behaved as if they had been stressed.… In other words, stressed parents give rise to offspring that grew better under harsh conditions compared with regular plants.

Human experience tells a different story, since human offspring are subjected to other inputs beyond genetic inheritance. But it’s an amazing paragraph: what doesn’t kill a plant, makes the species stronger.

A look at awareness – consciousness – ends the book; it’s not as far-fetched as you might think. I myself hold two conflicting instincts about this sort of thing. I’ve always found it impossible to understand how a plant could “know” it’s time to bloom or seed, or for that matter how a red blood cell knows to pick up oxygen in the lungs and drop it off in the tissues. The biochem mooc I’m taking just did a wonderful lesson on that process, in fact, and it helped to clarify that it’s all about osmosis, competing pressures, and electrical charges repelling and attracting each other. But you could say the same thing about our brains: maybe all the art, belief, and knowledge is just a matter of manipulating matter and energy, no matter how much it feels like we control it with our will. On the other hand, I find it troubling when anyone declares some ethereal quality – like art, or religion, or emotion – is what makes people special, and when it turns out bees dance and whales communicate, the goalposts get moved to keep humans unique. I don’t try to reconcile these two ideas. Like Whitman, very well, I contradict myself; I am large, I contain multitudes.

Granted I have little to compare it to, but I don’t think I could have picked a better entrée to plant biology than this book. It combines a hint of romanticism with solid scientific evidence, and bounces off my prior learning (if unorthodox, via moocs and youtube) in biology and neuroscience to bridge the gap between human and botanical. Finding a mooc attached to it was a super-deluxe Easter egg.

For readers who’d rather not bother with the technical details, there’s still plenty to enjoy. And who knows, you might just come away with curiosity about something you always thought was way over there somewhere. Way does lead on to way, after all.

Intro to Engineering MOOC – Vaults

Course: The Art of Structural Engineering: Vaults
Length: 6 weeks, 2-3 hrs/wk
School/platform: Princeton/edX
Instructor: Maria Garlock

In this engineering course you will learn how to analyze vaults (long-span roofs) from three perspectives:
Efficiency = calculations of forces/stresses
Economy = evaluation of societal context and cost
Elegance = form/appearance based on engineering principles, not decoration
We explore iconic vaults like the Pantheon, but our main focus is on contemporary vaults built after the industrial revolution. The vaults we examine are made of different materials, such as tile, reinforced concrete, steel and glass, and were created by masterful engineers/builders like Rafael Guastavino, Anton Tedesko, Pier Luigi Nervi, Eduardo Torroja, Félix Candela, and Heinz Isler.

Let me begin with a disclaimer: This was not the right class for me to take. I was curious to learn more about the technical details of vaults, having seen some wonderful examples of structures from medieval and renaissance architecture, and this was, as advertised, a very basic introduction to the engineering of vaults. However, after a brief look at the Roman Pantheon, the course focused on concrete shells of the 20th century and more modern innovations. I lost interest quickly. Then I got sick between weeks 4 and 5, which further diminished my participation. I did end up “passing” the course, so it might be worth your while even if your particular interest is only partly covered. And I did come away with a better understanding of how vaults work, though keep in mind, I started at absolute zero.

Each week consisted of three distinct sections: a lecture series covering the historical and technical development of vault engineering, generally by focusing on one engineer who introduced a specific innovation, be it reinforced concrete or hyperparabolic shapes; a mathematical section, in PDF form, covering several equations in detail, though at a fairly simple mathematical level requiring only basic algebra; and a creative section, which invites students to post pictorial examples of some facet of the week’s material. Grading is divided fairly equally among these three sections. But don’t worry: although the material, particularly the mathematical sections (none of which go beyond basic algebra), may seem intimidating, the questions are manageable. Even though I skipped everything but the lecture sequences of weeks 5 and 6, I “passed” by a comfortable margin.

The lectures were very good, with lots of illustrative exampes, interviews with a variety of engineers and scholars, and a very step-by-step explanation of the development and construction of the technique under study.

This is part of a three-course series, with other courses covering engineering concepts of bridges and tall buildings. And again let me emphasize that although this was not the best course for my particular interests, the course was well-designed, and the series seems to be ideal for someone interested in getting a basic introduction to civil engineering.

Free Will on the Brain MOOC

Course: Libertarian Free Will: Neuroscientific and Philosophical Evidence
Length: 6 weeks, 4-6 hrs/wk
School/platform: Dartmouth/edX
Instructor: Peter Tse

In this course, we will dismantle arguments against free will, both from a philosophical and neuroscientific perspective. In supporting free will, we will tour philosophy, physics and neuroscience. We will rethink the neural code and discover that evolution has discovered a middle path between determinism and chance.

Philosophy plus neuroscience: what could be better?

But let’s get rid of one potential misconception: this course has absolutely nothing to do with the political stance known as Libertarianism. Instead, it focuses on philosophical libertarianism, which is related to non-determinism and the potential of different outcomes for different choices. The second level of this is to become a different kind of chooser, a bit more sophisticated kind of free will, in which we can decide to learn a language or a musical instrument and thus open up those choices, or follow a particular way of life and make our choices there. Sound complicated? It isn’t, really, but it helps to take the first couple of weeks of the course to see the ways this works.

The material was based largely on Dr. Tse’s book The Neural Basis of Free Will and as such had a clear point of view, yet made it clear there are other points of view as well. There were a few lecture segments that seemed a bit polemical to me, but these were clearly presented as coming from a particular point of view, rather than as fact. The instructor was engaging and clear, covering basics of both philosophy and neuroscience first then moving on to more complex topics.

The first week presented an overview of determinism vs non-determinism, and the general outline of free will within that schema. Week two continued with a philosophical approach to the classifications of free will. The remaining four weeks focused more on neuroscience, and how our brains have evolved to allow consideration of choices, as well as random fluctuations that prevent determinism.

I still have some issues with this. While the “swerve” (borrowing that phrase from Steve Greenblatt’s wonderful book on Lucretius) prevents absolute determinism and adds in an element of randomness, I still don’t see that it automatically creates free will. If we are just as beholden to the swerved paths as the originals, how is that free will? But it seems to be basis, along with quantum fluctuations (spooky-action-at-a-distance is the one I have some vague, rudimentary grasp of), of free will.

In any case it was seriously interesting all the way through. If some of the material should seem overwhelming, don’t worry; the graded questions are looking for broader concepts. A set of non-graded questions follows up each lecture, with a quiz at the end of the week drawn from those same questions. There’s reallly no excuse to miss any of those questions, in other words. They account for 75% of the course grade, with discussion counting for 25%. Since the passing grade is 70%, it’s very possible to pass the course without doing the discussion. I avoided discussion deliberately, as there was a particularly argumentative student who basically disagreed with everything, and I just didn’t want to deal with it.

Even though I’m less than convinced that the questions are answered, I greatly enjoyed the course since it hit two of my primary areas of interest.

Neuro in three acts: Fundamentals of Neuroscience MOOC series

Course: Fundamentals of Neuroscience (three course series)
Length: 5, 6, and 8 weeks, 3-5 hrs/wk
School/platform: Harvard/edX
Instructor: David Cox

Based on the introductory neurobiology courses taught at Harvard College, Fundamentals of Neuroscience is a three-part series that explores the structure and function of the entire nervous system — from the microscopic inner workings of a single nerve cell to the staggering complexity of the brain.
You’ll study the electrical properties of individual neurons, examine how neurons pass signals to one another, and how complex dynamics result from just a few neurons. You’ll explore sensation, perception, and the physiology of functional regions of the brain.
Through fun animations, documentaries, and interactive virtual labs discover what makes the brain tick and how we perceive the world around us.

I’ve been taking this three-part series for so long, I don’t even remember when it started – oh, there it is, September 4, Part 1, The Electrical Properties of the Neuron. Then, in mid-October, Part 2, Neurons and Networks started, while Part 3, the examination of the broadest system, The Brain, began on Dec. 5. It’s all self-paced; in general, I finished each segment early, since I’ve been doing introductory neuro over and over for a while now. What can I say, I like brain stuff. I still have about a week to go before I finish up Part 3, but I wanted to get my postings done before the end of the year to clear the decks for Pushcart on January 1.

IIRC, I started this course several years ago when I was still fairly new to moocs; I quickly dropped it, since it was loaded with off-site content, much of which I had a lot of trouble working (I’m not sure if it was the system, or me, that was faulty). Things went much better this time around, perhaps due to streamlined and imported bells and whistles, perhaps due to me being better prepared.

I get the sense the developers of the course were really most interested in the first segment on electrical properties of the neuron –potentials, resistance, and the effects of electrolytes – since that’s where most of the fancy stuff was found: graphics to adjust levels of electrolytes across membranes with adjustable resistance, etc. I found some of it rather difficult to follow, and the material on length constant and time constant was far too brief. It’s possible I struggled because I was less interested in this particular area. Most neuroresearch, of course, measures electrical activity, so it’s appropriate that it’s emphasized.

In this segment there was even an optional do-it-yourself lab for “Recording and stimulating a nerve.” Materials required included a spiker box, stimulation cable, computer and smartphone, and a cockroach. Yeah, I think I’ll pass on that one.

The second course in the series moved up a level to interneuron communication via neurotransmitters and modulators, synapses, and excitation/inhibition patterns. Included were several interesting “Extras”, interviews with researchers looking at such topics as optogenetics – using a light-activated channel from algae to stimulate and record neuronal activity – and connectomics, a technique to understand the informational organization of the nervous system.

Part Three was more about structure and pathways in the brain: sensory and motor pathways, as well as the connections between areas that record memories and produce emotional responses. Some of the information – the structure of the lateral geniculate nucleus along the visual pathway, for instance – was extremely detailed and very helpful, while some – the sensory pathways – seemed more of an overview.

Each week’s material consisted of a number of short video lectures with two or three graded Practice Problems following, plus a final exam at the end of each course. Multiple attempts are given for each question in both cases; most of the questions are information-retrieval, the exception being the first course where a fair amount of applying various equations is required.

A great deal of material is covered, and it can be overwhelming for those who haven’t encountered these elements before, but that’s what learning is for. Fun fact: the only neurons that seem to be able to reproduce are located in the olfactory region (smelling) and the hippocampus (memory). No one’s exactly sure what this means yet; it’s possible the memory cells, most replicated in infants, actually destroy memory by “writing over” existing patterns. But why those cells? Why not spinal cord neurons, which might allow function to be regained after devastating injury? The answer will probably be found in evolutionary function; I have no idea what it might be, but I’ll bet it’ll be fascinating.

I find it all fascinating, that what we think and feel and do all boils down to electrical impulses carried by tiny wires. In many cases, particularly in the third course, the consequences of things going awry, despite all the redundancies and plasticity, are covered briefly. Given how complicated the neural system is, it’s kind of amazing things don’t go wrong more often. Yet here we are, still. At least for now.

Beyond Medical Histories: Insight from Patient Stories mooc

Course: Beyond Medical Histories: Gaining Insight from Patient Stories
Length: 3 weeks, 2-3 hrs/wk
School/platform: Brown/edX
Instructor: Jay Baruch, MD

Physicians and healthcare providers are – fundamentally – professional story-listeners, story-shapers, and story-responders. This shouldn’t come as a surprise; people have always related to each other and the world through the telling, listening, and interpreting of stories.

Expertise with stories is a low-tech skill that’s fundamental to connection, communication, curiosity, and problem-solving. It’s a clinical ability with multiple potential benefits, ranging from making us more mindful of our thinking to improving patient engagement. Aptitude with stories can both expand our tolerance for uncertainty and reduce risk.
We’ll focus on stories – challenging stories, in particular. We’ll discuss why healthcare providers must think more creatively, even in a field that prides itself on its grounding in scientific evidence.

Any course that starts with an Amy Hempel story has real promise.

I love medical stuff, and obviously I like stories, so this sounded like a win-win: using techniques from storytelling to better understand a patiet’s presentation. It’s primarily intended for medical practitioners, particularly those in training, but everyone was explicitly welcomed.

It’s a short course, three weeks (there is a Week 0, for purposes of getting used to the edX platform, but there’s no content). There’s very little solid content; it’s mostly open response to acted-out scenarios and discussions of the issues raised. Ostensibly the weeks had different foci, but I found it all to boil down to: keep an eye on your assumptions, notice when you’re being triggered by a difficult patient, and think about what isn’t being said as well as what is being said. The instructors were mostly emergency room physicians, a setting that often requires action when there isn’t a lot of time to gather a great deal of data.

Grading is purely self-reported: did you submit an answer to a survey question? Did you post on this topic? My main struggle with the course was remembering to click the checkboxes, since I normally don’t scroll down that far.

The acted-out scenarios in W1 and 2 were dramatic as conflicts arose between patients and staff, patients and their families, families and staff. I very much liked the Week 3 exercise, in which an abstract painting was the focus: what story do you see in the painting? Look at the negative space (I had trouble with this; I didn’t see any negative space). Map one of the patient scenarios to the painting in a way that makes sense to you.

My own assumptions, and background, got in the way at times. I have a rather uncomfortable relationship with healthcare for a lot of reasons. I was hoping to find some way to become more effective at conveying my concerns, but the course focused exclusively on the other side of the picture, on receiving a story.

My main thought was: I wonder how possible any of this approach is in the current healthcare system, which focuses on efficiency and cost-effectiveness. Insurance companies and accountants have reduced primary care physicians to something like data entry clerks, and socioeconomic factors more than medical factors impact patient decisions.

I would look at this more as an in-service training unit rather than a course. Still, it was interesting, and worth the time required.

Physiology MOOC

Course: Introductory Human Physiology
Length: 10 weeks, 5-7 hrs/wk
School/platform: Duke/Coursera
Instructor: Jennifer Carbrey, Emma Jakoi

The physiologist is going to ask two questions. One is, how does the organ and the organ system work? And secondly, what’s the advantage that this organ system provides to the body? As you go through our course, what you will find is that you will learn all the terms and concepts that deal with specific organ systems. But that importantly you are going to develop a working model to allow you to understand how these organ systems coordinate to maintain life in a constantly changing environment…. You eat a bag of salty potato chips, what happens? You’ve been training for a marathon, how does your body respond? When you’re actually running the marathon, what is happening to your body? And what happens if you maintain a low salt diet?

Yes, I’ve been doing guts again. But, rather than cadaveric dissections, this time formulas and pathways were the focus: how things work, rather than where things are. The material was at the perfect level for me: while there was some review of basic anatomy, biology, and chemistry, it pretty much started where my knowledge starts to thin out, and covered quite a bit. It is intended as an intro to physiology, so there’s a lot more detail left for future explorations. The material offers it as a good review for the MCATs, so that’s probably a good estimate of the level: some background is necessary, but we’re still in undergrad territory.

I was very pleased with the content. The first week covered the fluid compartments of the body, a concept I’d brushed up against, but never really understood, in the MedChem course I took last year. These compartments turn out to be the foundation of physiology: the main job of our organ systems is to maintain homeostasis between intracellular fluid (cell cytoplasm), intravascular fluid (blood plasma), and interstitial fluid (everything else). A general overview of the endocrine system also started things off, since it’s nearly impossible to discuss anything else without the that.

The remaining nine weeks all covered different organ systems. There was a lot of overlap, but it was handled very smoothly. We started with nervous system and senses, then moved into muscles (which of course require some understanding of the nervous system), then heart (which requires some understanding of nerves and muscles)… you get the idea.

The first few weeks were very time-consuming, but those basics became the foundation for later weeks. I started the course a few weeks before the official start date, but time wasn’t a problem. As usual, I spent far more time than was strictly necessary, between entering things into Cerego and finding Youtube materials as supplements.

The lectures were a bit uneven. Some of them were great; others were hard to follow, and at some point became a flood of words. The transcripts weren’t much help in this case since they contained all the hesitations, restarts, half-thoughts abandoned in mid-word, but without the auditory clues to ignore them. However, what was very helpful was a lecture note summary outlining the lecture material. These were at a higher academic level, without a lot of preparation or metaphor to help with understanding, but combined with the lectures I found them invaluable. I wish I’d started using them before the last couple of weeks (stubbornness is my downfall again). Yet, again, I found the content to be great, which made up for any quirks of delivery. Example: I’ve been struggling with the different hormones secreted by the three layers of the adrenal cortex for years now, but one phrase – “salt, sugar, sex” – clarified everything.

I found the quiz material – some graded, some not – to be very well designed. Rather than a recitation of facts, most of the questions asked us to extrapolate from the pathways and processes covered and predict or explain the result of some action. I used Cerego for the rote stuff, but the in-video questions, the post-lecture practice quizzes, and unit exams were excellent opportunities to turn rote into reasoning. Example: “Increased delivery of Na+ to the principal cells of the renal tubule leads to increased…?” I was expecting one answer, but it wasn’t in the list; it took a bit of doing, but I realized another answer was, indeed, correct (and, in fact, turned out to be clearly stated in a lecture, though, hey, I can’t remember everything, y’know). Some units had fewer practice quizzes than others; I missed them terribly. It’s not just that I’m weird and I like taking tests (which, well, yeah, why take a course if there’s no test?), it’s that it really helped point out exactly what I needed to understand better, before getting to the end of the unit.

The forums were sporadic. Staff – including the professors – answered technical questions, but most of the answers were repetitions of the lectures. I didn’t have any questions that couldn’t be answered by searching for a relevant post from past sessions (this course has been running for a while). As far as connecting with other students over a topic of interest, well, that just doesn’t happen any more.

I’ve overall been quite pleased with Duke courses, particularly their neuro and medical options; this one was no exception. At times things could get a bit wordy, but if the goal is to understand the basics of how the body works, this fits the bill very nicely.

Anatomy, the Yale way (mooc)

Course: Anatomy of the Chest, Abdomen, and Pelvis
Length: 4 weeks, 5 – 10 hrs/wk
School/platform: Yale/Coursera
Instructor: various

This course has two main aims. The first aim is to teach you the language of medicine, and the second aim is to teach you to learn how to reason in three dimensions. Put in a more simple way, we’re asking you to learn how to see and feel what you cannot see.

Short version: These folks aren’t fooling around: if you want a detailed anatomy course without any frills, this is it. For me, it worked fine, but I think there are better options for anatomical novices.

I’d just completed the 16-week Anatomy series from Michigan when I signed up for this. I was hoping for more detail, and boy, did I get it. But there was a downside. This is not so much a mooc – that is, a cohesive course – as it is a collection of videos. Because I spend a lot of time thinking about literature, I started thinking about narrative. This is what happens when a course lacks narrative. It isn’t necessarily deal-breaker – the information is there and, drawing upon experience and using other techniques to stay oriented and motivated, it’s workable – but it certainly is a less pleasant, less engaging experience.

The course consisted of four weeks, each with one or two units: introduction/chest and lungs; mediastinum/heart; abdomen; pelvis and perineum male and female. In general, basic anatomical detail with stylized diagrams was presented first in each unit, followed by detailed cadaveric dissections, often with live clinical or testing procedures interspersed. However, there was little connective tissue, so to speak; no effort to tie anything together, or provide any kind of pathway; the result was some material felt incomplete until much later, and some felt duplicated several times. I can’t say I “enjoyed” the course, but I can say I improved my understanding of anatomy.

I suspect the time estimate for the course – 4 weeks at five to ten hours per week – would be a bit tight for anyone trying to learn the material. It would be possible to pass the course in that time frame; it’s possible to pass most Coursera courses these days without even taking the courses, because you have unlimited tries at the exams. But learning the material? Getting a good picture in your head of what’s posterior to what and how nerves and arteries branch off? Recognizing structures on dissections? I suspect, for most of us who aren’t in medical school, that takes longer. I entered a lot of material into Cerego, so that took a great deal of time, but it also helped with retention (and will continue to remind me for months to come), and I consider it time well spent.

The first unit was a review of various anatomical planes and, with the participation of a live model decorated with markings, identification of external landmarks of various organs. Since this was new to me, I spent a great deal of time on it (I started the course early so took more like six weeks than the official four, but these courses are all self-paced anyway and roll over into the next session without penalty if they aren’t completed by the end date). Several videos covered imaging techniques – x-ray, CT, MRI, and ultrasound – from a light overview of technical foundations to a guide to reading images. It’s kind of a kick to see an MRI on Grey’s Anatomy and know, “Oh, that’s with IV contrast, supine.” And it’s really fun to hear Dr. Bailey refer to the SMA or the IVC and know what that is.

Then came the actual anatomy. While I still have a lot of trouble telling a nerve from a vein from an artery from a tendon on cadaver dissections, in this case the dissection was videotaped rather than photographed, and often proceeded from skin to deepest structures. Several warnings were provided, advising us that “some people find these images disturbing” and requiring an acknowledgement to continue. The chest would be incised, the skin peeled back, the muscles examined, explained, and reflected one by one, the bones sawed through and removed, and the deeper structures pointed out. This was a lot more helpful than an isolated labeled photograph of a dissection. Material also included endoscopic videos from bronchoscopy, upper and lower GI screening endoscopies, cystoscopy, and a laparoscopic gallbladder removal. And if you stick with it to the very end, you can see a penis dissected. Longitudinally, then transversely. I may never eat kielbasa again.

“Digital practical exams” followed each section (don’t worry, it’s not a prostate exam, it’s a kind of “click on the [phrenic nerve/ureter/psoas muscle]” thing off stills from the dissection or procedure videos). I found these quite difficult. First, there’s my difficulty telling a preserved nerve from a vein from an artery from a tendon, and second, the clickable areas were sometimes oddly construed. There was a kind of logic to it once I figured out any given structure; I could relate everything else to it. These tests weren’t graded other than for completion.

Ungraded multiple choice questions ended several of the videos; these tended to show up on the graded unit exams later, along with additional questions. The questions were often difficult, as they involved putting visual concepts into words: what structure is medial to the carotid artery, what’s posterior to the hilum of the lung, how does the piriformis muscle relate to the superior gluteal nerve? This requires having a good mental image of the anatomy, in order to translate it into verbal description. In general, I’d say the testing material was effective at reinforcing learning.

It was a cold class; the only people who appeared were in the first section on physical exam and external landmarks. Everything else was voice over image. I’m not sure if that was deliberate, or just convenient. One of the post-course survey questions was on course engagement, and I gave it a 0. Anatomy engages me; the course did not. I’ve read textbooks that were more communicative. But I’m not complaining; I was here for anatomy, after all. However, I’ve taken Duke’s neuroscience course, which was every bit as detailed and intense, and they managed to maintain a high degree of engagement and even community, so it can be done; it just requires attention to narrative.


Course: Anatomy (4 course series)
Length: self-paced; 4-8 weeks per course, 2-3 hrs/wk
School/platform: University of Michigan/edX
Instructor: Kathleen Alsup, Glenn M. Fox, Kelli A. Sullivan

What You’ll Learn:
Learn the foundations of basic human anatomy for every major organ system and the relationships between systems
Understand the major functions and significance of each system, particularly from the perspective of a future healthcare worker
Learn the relevance of organ system features in wellness and pathology
Understand how to engage in the study of anatomy from a system-based approach

Short version: I love anatomy and medical stuff, so I’ll read the back of a cereal box if it has a diagram of an organ on it (which would be really weird, btw). So I jumped on this self-paced four-course series. It wasn’t my favorite medical mooc, but I finished all four sections over about six months and fleshed out (sorry!) some of the fuzzier ideas I had from previous materials by using the course as an outline and exploring materials elsewhere, rather than relying on the materials included.

I’ve taken four prior anatomy moocs – Leiden’s course on the abdomen and pelvis, Louvain’s respiration mooc, Penn’s “Out on a Limb” covering all the structures involved in the shoulder and arm, and the encyclopedic Medical Neuroscience course from Duke. This latest suite of courses from Michigan had the advantage of covering everything in four separate but related courses; it had the disadvantage of being less engaging than the other courses. As a result, I watched the videos, then went off on my own to understand the material covered, making sure I had a reliable source, and that the information was the same as given in the course. I found The Noted Anatomist and Anatomy Zone particularly useful.

It’s one of the Xseries Programs, which means that when you go to the page linked above, you’ll find a price of $179 quoted for the group of four courses. But don’t be scared (at least not yet; the time is a-comin’…). It’s true, you can pay $179 and, assuming you pass the courses, get a Certificate and whatever benefit that affords you, but you can also take the entire thing for free, as I did.

Most of the graded material was in the form of short multiple choice questions, but several units also made extensive use of labeling cadaveric dissections. I have a terrible problem “seeing” anything in cadaveric dissections. They certainly have their purpose, since diagrams make things a little too neat and orderly in the interests of clarity, and they’re essential for anyone who’s going to be doing actual dissection (medical students, future anatomists). But the images – everything desiccated and monotone yellow – are incredibly hard to decipher without a diagram, or prior knowledge, to understand what is shown. Add to that the shrinking of the images necessary for packaging in the video, and I found them pretty useless. Other options, however, are limited. “Live dissections”, filmed during surgical procedures, are very rare at this level (there were a few in the Leiden course). Anatomical artist Frank Netter has made some extraordinary diagrams that bridge that gap, but those are protected by copyright and thus might be expensive (or impossible) to include in a mooc (the Penn course managed, but that’s Penn). Fortunately, there’s a wealth of material out there, and sometimes a casual hand-drawn diagram – or a video using 3D software to recreate structures – was just what I needed to understand how things worked together.

I found the Neuro course to be my favorite of the four, probably because I really like brain stuff. I finally feel like I have some understanding of the internal capsule, and subcortical white and gray matter in general. I learned a few more acronyms (“Two zebras bit my cupcake” for the branches of the facial nerve), and did a lot of detailed work on the cranial nerves. The cranial nerve nuclei were not part of this course, but I reviewed them anyway. I still don’t quite get the hippocampus, since drawings showing the separate layers seem to be completely different from the diagram of the external structure and I don’t understand how they relate, but that’s ok, next time.

And of course, Cerego played a central role in this course, since definitions and diagrams are right in their wheelhouse. I’m going to be editing these sets for a while, since sometimes I would capture something that turned out to be less than useful later. I need to re-do the branches of the thoracic aorta, for instance; I need to approach it more systematically, starting with the main branches and adding layers, rather than just using a huge diagram containing everything but the kitchen sink. I took the more top-down approach with the abdominal aorta, and it worked out quite well. Oh, and thanks to the GI system course, I think I finally understand the portal system. For some reason, I didn’t have it together for the bone course, so I’ll have to put bones in Cerego at some future time.

I always feel bad when I’m less than enthusiastic about a mooc, because, of course, opinions are subjective; I’m sure a lot of people find this series to be exactly what they need and are thrilled with it. Smart and talented people put a lot of work into these things and I’m grateful they’re out there; I need the course structure that even the best Youtube channel doesn’t provide. I did find it a valuable outline for learning. But there must be a better way to teach anatomy – or maybe, providing an outline, and letting students create their own learning (a term I hear over and over again in the context of math classes) is the best approach. As a preparation for further anatomical study, it’s probably as good an option as anything online. And for anatomy geeks, it beats cereal boxes with pictures of organs on them by a mile.

Viral MOOC

Course: Viruses & How to Beat Them: Cells, Immunity, Vaccines
Length: 8 weeks, 2-3 hrs/wk
School/platform: IsraelX/edX
Instructor: Jonathan Gershoni

Have you ever wondered what viruses actually are?
Have you been curious about the ways they invade our bodies, attack our cells and make us sick? Come and learn what viruses are made of and understand the mechanisms of how they hijack and take over our cells.
There is no need for a background in science – just bring your curious mind!

Short version: Well-done introductory course beginning with a broad overview of biology basics, then focusing on pathogens and the immune system, particularly as it interacts with viruses. Great visuals, interesting but plain-language interviews with some serious heavy-hitters (like Nobel laureates David Baltimore and Bruce Beutler, and Robert Gallo, co-discoverer of the HIV virus), and a friendly style make this particularly accessible and, yes, fun.

This is another of those courses that just popped into my inbox out of the blue a few days before it opened. I was debating whether I wanted to re-start MIT’s 728 series on DNA, so I thought this might help make up my mind (it did: I just don’t want to work as hard as 728 demands, right now). It served as a nice refresher of the basics, from chemistry to cell bio to DNA to immunology, ending with a rational look at vaccines (spoiler alert: scientists are for them). It wasn’t quite as virus-specific as I’d expected, but, first, as an introductory course, some preliminary material was necessary, and second, seating the virology in a network of other concepts makes sense.

Each week included lecture videos with ungraded “test yourself” questions, and a lab demonstration or interview on a pertinent topic. A summary lecture, complete with concept map (which I greatly appreciated) finished off the week’s material. A live Q&A session, inviting student questions through the forum and participation through a software portal, took place around week 4. Since participation required downloading something, I didn’t attend, and no video has yet been released for us slowpokes so I have no idea how it was, but the question thread was booming so I’m hopeful.

Graded material included weekly quizzes, a midterm, and a final, with the final heavily weighted. At first I thought of the questions as standard information retrieval, but there are definite shades of meaning in there that require some interpretation and extrapolation. Every once in a while, a congratulatory GIF would pop up when a question was answered correctly; this generally scared the bejesus out of me, showing once again that I really need to calm down.

This is the 3rd of 4 courses I’ve taken in the past couple of months from IsraelX, a group of several schools; that’s kind of a brilliant idea, I’m surprised other countries haven’t done this. I’ve enjoyed each of the courses I’ve taken, and found them very helpful to understanding the various fields (which range from design theory to bio to religion to history). Although most of the rest of their 11 courses on the schedule are outside my areas of interest, I’m hopeful I’ll be learning more from them soon.

Biochem MOOC (Harvard version)

Course: Principles of Biochemistry
Length: 15 weeks, 4-6 hrs/wk
School/platform: Harvard/edX
Instructor: Alain Viel, Rachelle Gaudet

Principles of Biochemistry integrates an introduction to the structure of macromolecules and a biochemical approach to cellular function. Topics addressing protein function will include enzyme kinetics, the characterization of major metabolic pathways and their interconnection into tightly regulated networks, and the manipulation of enzymes and pathways with mutations or drugs. An exploration of simple cells (red blood cells) to more complex tissues (muscle and liver) will be used as a framework to discuss the progression in metabolic complexity. Learners will also develop problem solving and analytical skills that are more generally applicable to the life sciences.

If I seem to have been quiet lately, it’s partly because I’ve been taking this course. It’s massive. Not just the amount of content, but the detail involved. While it wasn’t particularly creative or engaging (with a couple of notable exceptions), it was exactly the material I wanted (and needed) to cover, so I’m delighted I enrolled.

It’s listed as an intermediate course, and recommends college-level biology and chemistry, including organic chemistry. So here I go setting the record for courses taken requiring orgo without ever having taken it other than what’s on YouTube (and let me say again, Leah4Sci and The Organic Chemistry Tutor have some great vids that have been very helpful in filling in some gaps; but would someone please do a full-on OC mooc?). But while there wasn’t anything I’d never heard of before, I suspect someone with a stronger chemistry background might have an easier time of it. After all, I still have to stop and think every time someone says “carboxyl group.” And don’t even talk to me about nitrogen.

Much of the content is in the form of metabolic pathways: glycolysis, for example, or the synthesis of fatty acid chains, along with regulatory mechanism and interrelations. It’s like one giant Butterfly Effect: one thing gets a little out of whack, and all kinds of things happen as the body tries to maintain homeostasis. Molecular energetics, protein structure, enzymatic mechanisms, it’s a broad spectrum of topics alongside the metabolic pathways. Clinical applications look at diabetes, gout, and a few other metabolic diseases, as well as a unit on the use of PET scans in tracking in vivo pathways.

It was a pretty grueling course, partly because so much of it went like this:

One of the subunit of the activated small G protein will in turn activate a membrane-bound enzyme called an adenylyl cyclase, which catalyzes the conversion of ATP into cyclic AMP. The concentration of cyclic AMP rises and cyclic AMP interact with the protein Kinase called protein Kinase-A, or PKA. This Kinase will become activated and then will phosphorylate PFK-2 on the Kinase domain.
The phosphorylation of PFK-2 will result in the inhibition of the Kinase domain and the activation of the Phosphatase domain. Therefore, PFK-2 will catalyze the conversion of Fructose 2,6-bisphosphate back into Fructose-6-phosphate. The concentration of Fructose 2,6-bisphosphate in the cell decreases, and PFK-1 activity will decrease as well.

While all that actually makes sense when you break it down (if you can remember what PFK and AMP are, since you’ve encountered a dozen new enzymes in two days), it’s kind of insane on the first six or twelve takes.

The lectures tend to have a question-and-answer structure, although the answers are so extensive, it’s often hard to remember there was a question, let alone what it was. “Why does HSP70 production increase with heat stress?” “How does the potential cell membrane bend to form a sphere?” Sometimes these questions are asked by the lecturer, sometimes by an off-camera TA. One of those TAs did a very kinetic presentation on glycolysis, sliding bits of paper around to describe the various steps. A couple of brief video clips from other providers added to the presentation on diabetes. And the PET scan section was presented by a different professor entirely. So there was some variety in the presentation.

The course wasn’t all multisyllabic strings of chemicals. For instance, fun fact: in the 40s when biochemists were first trying to figure out protein folding, one of the proteins they used was RNAse A, also known as bovine pancreatic ribonuclease. The Armour meat packing company – maker of Hot Dogs, Armour Hot Dogs, What Kind of Kids Love Armour Hot Dogs – just happened to have purified a kilogram of this stuff, so gave it out to scientists to study, which helped a great deal. Don’t think to hard about why a hot dog company was purifying bovine enzymes in the 40s. You don’t want to go there.

Graded material included a few questions after each video, plus a unit quiz at the end of one to three sections. Most of the questions were information-retrieval multiple choice, with two or three chances at each, meaning my grade far exceeds my grasp. But that’s ok, I’m not relying on this as a true measure of understanding. That’s why I’m going through it all again, just to get it to sink in a little better.

One of the great ancillary benefits that had nothing to do with the course itself was my dive into Cerego. I’ve been a fan of the spaced-repetition flashcard site (for lack of a better term) for a while now, finding all kinds of interesting things in their Public Library, both pertaining to moocs I’m taking, and just other stuff like countries and capitals and brain anatomy. But they suddenly discontinued access to the Public Library; if I wanted to use a memory set for glycolysis, was going to have to make one myself. I’ve tried to do this before, but was never happy with the results and was fine with what someone else had to say about chemical groups or DNA replication. But now I have my own set for biochemistry! I’m like a kindergartener who just brought home her first finger painting.

Optional ungraded assignments using PyMol were also included. Because this required downloading software, and I’d just replaced my old computer (it kept threatening to set itself on fire), I didn’t want to fool around with extra stuff. The assignments look interesting; now that I feel more relaxed about both my computer, and my time, I think I’ll take a crack at it as I go through the material again (adding more Cerego modules every day…).

I was very pleased with this course. I suspect its value depends on the background and motivations of the student: it might not be the best place to start for someone with only mild curiosity about biochemistry and metabolism (another Harvard mooc, “Cell Biology: Mitochondria” is a lot gentler, and far more visually appealing), but even those with a weaker background, like me, can find this beneficial if enough effort and outside remedial work is mixed in. And, if you’re wondering why the title specifies “Harvard Version,” it’s because MIT also has a biochem mooc; it’s got a different focus (much more lab-oriented), but it’s also a) difficult and b) very much worth it.

Molecular Bio MOOC, part I: DNA copied while you wait (or while you don’t)

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 mooc, 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 Leah4Sci.com, 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 overall 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 was often slightly 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.