Friday, October 05, 2012

Online Training of Competent, Employable, Bioinformatics Professionals

I think that undergraduate education at most universities is done very badly. There are far too many courses that consist of professors giving standard lectures to large classes with evaluations focused on "memorize and regurgitate" exams. Most courses pay no heed to student-centered learning even though there has been sound pedagogical research showing that student participation leads to better learning. Most courses and programs provide no "value-added" component that takes advantage of being physically located in an enriched scholarly environment. Most courses do not teach critical thinking.

Given the horrible status of most university courses, it's not surprising that they can be replaced by online courses where the student never needs to set foot on a university campus to get the same quality of education. This is not an endorsement of online courses, it's a comment on the poor quality of campus-based courses.

David B. Searls is an "independent consultant" who published an article in PLOS Computational Biology: An Online Bioinformatics Curriculum.

Searls claims that ...
Moreover, there is every indication that the instruction can be effective; the U.S. Department of Education, in an exhaustive meta-analysis of 51 published head-to-head trials, found that “on average, students in online learning conditions performed better than those receiving face-to-face instruction” [2].
The reference is Evaluation of Evidence-Based Practices in Online Learning: A Meta-Analysis and Review of Online Learning Studies and it evaluates the effectiveness of online courses in K12 education in the United States. Here's the abstract ...
A systematic search of the research literature from 1996 through July 2008 identified more than a thousand empirical studies of online learning. Analysts screened these studies to find those that (a) contrasted an online to a face-to-face condition, (b) measured student learning outcomes, (c) used a rigorous research design, and (d) provided adequate information to calculate an effect size. As a result of this screening, 50 independent effects were identified that could be subjected to meta-analysis. The meta-analysis found that, on average, students in online learning conditions performed modestly better than those receiving face-to-face instruction. The difference between student outcomes for online and face-to-face classes—measured as the difference between treatment and control means, divided by the pooled standard deviation—was larger in those studies contrasting conditions that blended elements of online and face-to-face instruction with conditions taught entirely face-to-face. Analysts noted that these blended conditions often included additional learning time and instructional elements not received by students in control conditions. This finding suggests that the positive effects associated with blended learning should not be attributed to the media, per se. An unexpected finding was the small number of rigorous published studies contrasting online and face-to-face learning conditions for K–12 students. In light of this small corpus, caution is required in generalizing to the K–12 population because the results are derived for the most part from studies in other settings (e.g., medical training, higher education).
That's hardly a ringing endorsement of online education. Nevertheless, David Searles concludes ...
Clearly a revolution in open online learning is at hand. This is a welcome addition to a movement that also encompasses open online scientific publication, of which this journal is an example. As such, this is an appropriate forum to assess the current potential for a freely accessible online bioinformatics education.

Both the completeness and the quality of such an unconventional education should be evaluated. Such judgments cannot be entirely objective, and even curricula in conventional university settings vary widely. Thus, this must ultimately be considered an “opinion piece.” Even its purely factual content has to be viewed as evanescent, given the rate of change in online education, and the fact that newly announced initiatives may increase the selection and quality of courses available to a considerable extent even within the year.

Even so, the first opinion offered here is that it is probably already possible for a motivated student to become a competent, employable bioinformatics professional in the comfort of his or her own home—with certain important caveats to be elaborated in the discussion at the end. By way of evidence, a suggested curriculum will be laid out that is supported by existing online resources.
One of the recommended courses is a biology course from the MIT OpenCourseWare site. I've looked at the biochemistry, molecular biology, and evolution courses on this site and I judge them to be far below the standard that I think is suitable for university students. Here's part of the recommended course: Biochemical Reactions, Enzymes, and ATP.

Everything in this 43 minute lecture can be read in a biochemistry textbook. The instructor adds nothing. Most of the topics covered in this lecture should have been covered in an introductory chemistry course. Indeed, most of it should have been covered in high school. Some of the material is wrong, or at best, misleading.

If it's possible to train a "competent, employable, bioinformatics professional" using courses like this then what that proves is that university bioinformatics programs are in terrible shape. It's easy to imagine why if the focus is on "training" potential employees rather than critical thinking and understanding.


[Hat Tip: Nick Block who sent me the links in an email message.]

17 comments :

  1. I really enjoy your perspective on this. Do you think it's impossible to teach critical thinking and understanding online?

    After have a rather mediocre university experience myself I felt true envy when reading about the tutoring system at Oxford and Cambridge. I don't understand why this isn't adopted at all universities. It's cheap, effective, and once it get's going self maintaining.


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    1. As a grad student at Cambridge, I did some tutoring for two years (I was not an undergrad there, so never _received_ tutoring - so my comments are only from one side). On the whole I agree that it is a good system which works well at Oxford and Cambridge, and which could work well at some (perhaps many) other universities.

      That said: it's _not_ cheap. It involves paying tutors to see students in groups of 2-4 for one hour every two weeks for each module (of which they take around six in the program for which I was tutoring). That's more tutoring than can be done by the university faculty, so they have to use grad students for much of it. The grad students are typically from all over the world, so have not studied the courses they are tutoring (one hopes that most of them have equivalent knowledge). The system works best for strong students who complete their assignments before the supervisions (this is what they're _expected_ to do), so that the supervision time is used to give them feedback on their efforts. But of course such students are few and far between; in my experience students tended to come to supervisions with "show me how to get started" questions (having put in almost no time attempting the assignments themselves), so they never actually got feedback on their thinking.

      So I see three obstacles to employing this system more widely: 1) high cost; 2) need high quality grad students to give quality tutoring; 3) need high quality undergrads to make good use of tutoring.

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    2. Effective but not cheap.

      CJ

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  2. I grew up with the Oxbridge tutorial system, and with the "Socratic" system of learning. Now teaching larger courses in the US, I do my best to retain the same principles.

    I have just spent most of this week grading student essays (giving intense feedback to each, with the opportunity to rewrite for a better grade), and grading exams that are open book with problem-based questions.

    I have taught like this for the past 30 years. However, there are now few places in the US where someone could put this much time into teaching and hope to get tenure. And therein lies a problem.

    Christine Janis (have to post as anonymous due to my University interfering with the system).

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  3. I didn't watch the video but I did look at the three practice questions. Most of my students (Grade 12 Biology) would be able to answer them all. So if those questions are representative of the level of information in the video...yep, high school level.

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    1. May I welcome you to the world where a significant proportion of graduate students in biomedical sciences does not know how to solve quadratic equation?

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  4. I didn't watch the video but I did look at the three practice questions. Most of my students (Grade 12 Biology) would be able to answer them all. So if those questions are representative of the level of information in the video...yep, high school level.

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  5. Oh oh, in the very first question there is a glaring logic error:

    If the ΔG of a reaction is negative, which of the following is a true statement?
    A.All of these options.
    B.Energy is released in this reaction.
    C.The reaction is exergonic.
    D.None of these options.
    E.The reaction is spontaneous.


    but answer A cannot possibly be the correct answer on account of the inclusion of answer D.

    This observation may be beside the point I know, but when I see something like this I immediately wonder how much time and care went into development of the exercise.

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    1. Yeah, pretty careless of them. But then designing decent multiple guess questions takes a bit of thought....

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    2. Yeah, pretty careless of them. But then designing decent multiple guess questions takes a bit of thought....

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  6. ha ha, you're right! It might seem a little nitpicky, but at the same time it damages the overall credibility.

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    1. Yes. And although the intent of the question is obvious, were I to craft such a question for my students, I would expect several comments pointing out the error and they would be absolutely correct to do so. Hmmm, maybe I should do so on purpose next exam, as an experiment to see how many students notice the problem. I will need to include an option F: this question cannot be answered correctly.

      Could this be one small step toward instilling critical thinking skills as opposed to rote memorization? ;)

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    2. That looks like more of a test of their ability to read all of the options. You need to cast that net over a wider pool so that they only know it is an option to say that a question cannot be answered correctly, but don't really expect they'll have to use it.

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  7. Here's part of the recommended course: Biochemical Reactions, Enzymes, and ATP.

    Everything in this 43 minute lecture can be read in a biochemistry textbook. The instructor adds nothing. Most of the topics covered in this lecture should have been covered in an introductory chemistry course. Indeed, most of it should have been covered in high school. Some of the material is wrong, or at best, misleading.


    Just to point out - this is from a 7.01x course, which is the general requirement biology course that all students have to take. A lot of which are math, physics, CS and engineering students who have indeed not had high school biology on that level and this material is completely new to them (and this is the one course in the general requirements that students struggle the most with).

    This is not 7.05, the actual biochemistry course, nor the 7.08 Biological Chemistry or 7.35 Metabolic Biochemistry course. That said, I was not at all happy with 7.05 when I was taking it as it compresses (or simply omits) too much material in just a single term, with the predictable result that it is impossible to actually learn much biochemistry from it if that's your first serious exposure to the subject. But it is still a biochemistry course, not an intro biology one that overlaps a lot with high school material

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  8. Shawn, it gets much worse. The third question asks:

    Which of the following statements is true with respect to ATP?
    a.ATP is commonly used in coupled reactions
    b.The hydrolysis of ATP is an endergonic reaction
    c.The hydrolysis of ATP produces inorganic phosphate and ATP.
    d.ATP is used as an energy source and a building block in RNA.
    e.ATP can donate a phosphate group that becomes covalently linked to a protein.

    The site claims that a, c, d, & e are all true. That's right, hydrolysis of ATP produces inorganic phosphate and fresh ATP! MIT OpenCourseWare has discovered a source of unlimited energy!

    Pretty sad.

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    1. Ha. So much for the adage that there is no such thing as a free lunch.

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  9. Honestly, I felt like most of what I did in my biology degree (from a top UK university, but heavily biased towards lectures, with little face-to-face time in smaller groups) we had already done in school. And what little was added on could easily be read in a text book. Looking at the biology part of the courses Searls recommends, they look pretty much equivalent to the content of my degree, which I agree was terrible.

    I am a post-doc in bioinformatics from a biology background. I have to teach myself the maths and computing skills needed and I'm finding a lot of the online courses invaluable for that. Especially the MIT ones which offer you the choice of watching a full lecture or just clips covering the important concepts, backed up by reading. I suppose for many it helps to be given some structure to follow. For example, I've done some programming and doing the MIT basic programming course has filled in a lot of the gaps in my knowledge and made me a much better programmer - the bioinformatics training I had simply taught us the syntax of Perl, without the conceptual knowledge or practice needed for real learning.

    That said, like any degree, the content of the programme of study recommended by Searls is bound to be subjective and I would hope any prospective student would be able to recognise that. I also assumed that he did not recommend this as a replacement for more formal training and that it was intended to fill in the gaps most bioinformaticians have from coming from either a pure computing or a biology background.

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