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Bora had an enjoyable post yesterday on obsolete lab skills. I can empathize because I have a pretty good collection of obsolete lab skills myself. These days I’m rarely (okay, never) called upon to do rocket immunoelectrophoresis, take blood from a rat’s tail, culture tumor cells in the anterior eye chamber of a frog, locate obscure parasites in solutions of liquid nitrogen, or inoculate Kalanchoe leaves with pathogenic bacteria.

(Wow! It sounds like I worked for the three witches in MacBeth! Fire burn and cauldron bubble!)


I don’t entirely think that my lab skills are “obsolete.” I prefer to describe them as “specialized.” Some of the things that I learned doing lab work have even transferred to the outside world. I make stock solutions of chicken broth. I never leave food containers uncovered (dirt falls down!). And if I had to draw blood, or pick up a mouse without getting bit, I could still do it.

But, the comments on Bora’s post made me think deeper. There’s always a big lag between the kinds of techniques that we use in practice and the kinds of techniques that we teach in the classroom. Maybe now is the time to start dealing with this gap and it’s manifestation in biology.

Sure, my perspective may be a bit skewed because of where I work, but I have seen the field of biology experience a big shift in how people work and how they spend their time.

One of my coworkers describes the change this way. He says, that when we were graduate students, most of our time was spent at the bench constructing the right plasmid to test something or doing assays that could be interpreted from running the right gel or doing the perfect Southern, Northern, or Western blot. We lived for beautiful gels.

Now, (at least for some of us), we spend very little time at the bench. We either get our data from an on-line database, or we outsource the wet lab experiments and send samples off to service labs. The service labs perform the high throughput DNA sequencing or mass spectrometry assays, leaving us to spend our time working with the data.

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The problem is that the schools haven’t adjusted. Science teachers rarely use computers as a tool for science beyond literature research and writing reports. Lately, some of my collaborations with the laboratory education world, have convinced me that the gap between those of us who work with data and those of us who do not is getting wider.

Maybe it’s time for schools to start looking at the techniques and tools we’re using now, and spend a little less time on the techniques we used then. Or we can go the wiki for obsolete lab techniques and add more items to the list.

Comments

  1. #1 Kamel
    February 25, 2008

    I’m all for more bio-informatics type labs, but I don’t know that I agree that schools *need* to adjust. To a certain degree, obviously they do as novel techniques emerge, but part of teaching these ‘obsolete’ techniques is teaching the underlying biochemistry not just ‘how to get things done in the lab’. Now we have kits for everything, pre-cast gels, etc. and the chemistry-set approach has produced people who *don’t* understand the techniques they’re using. I recently had a discussion with a colleague – who has an M.Sc in biochem – and it became clear that they didn’t understand the underlying principles of a western blot. All that mattered was THAT it worked, not understanding HOW it worked. Maybe I’m crusty and old-fashioned, but I see view it like teaching kids how to do math before handing them a calculator.

    I think the same idea can be applied to these outsourcing services. Surely knowing how mass-spec/flow cytometry/etc. works helps analyze the data properly, no?

  2. #2 Sandra Porter
    February 25, 2008

    Kamel,

    I agree that we need to teach the principles and the math. I remember how shocked I was 20 years ago to find out that a MD PhD candidate in our lab didn’t understand the concept of a % solution (i.e. x grams/100 mls). (He thought you measured out 100 mls and then added the solid stuff).

    But times change and the line is shifting. We no longer mouth pipette.

    I support the science kits because they allow students to do interesting experiments. It’s unfortunate, but most teachers lack the technical abilities, time, and facilities to prepare the materials for the kinds of experiments that you can do with the kits.

    What I see is that, out in the world we spend 90-95% of our time doing activities that I never see my kids get taught in school. If students could spend even 5% of their time learning how to graph with Excel or do calculations and modeling with spread sheets, I’d be happy.

    It’s as if we’re doing biochemistry and students are learning how to blow glassware.

  3. #3 Epicanis
    February 25, 2008

    It’s as if we’re doing biochemistry and students are learning how to blow glassware.
    Oddly enough, the one “obsolete” science-related skill I am especially interested in learning myself is glass-blowing. Unfortunately, I get the impression that even suggesting that colleges offer an elective class in the subject is like asking the pre-med program to offer a class on cupping and scourging.

    Personally, I think science education has gotten way too lazy already about turning labs into canned “wind-up-toy” exercises and vocational training for specific brand-name products, much as the classroom instruction seems to often turn into memorization exercises (thanks, “Standardized Testing”…).

    I tend to agree that the recognition of a computer as a normal tool for laboratory work is underappreciated, but am quite cynical about what will happen as this is added to the curriculum. (I strongly suspect a lot of vocational training “here is what buttons to push in Microsoft® Excel®” and whatever other specific products whose manufacturer cuts deals with the administration, rather than education concerning precisely why the analysis works and what it’s accomplishing.

    I’m starting to hit the “cranky old person” stage very prematurely, aren’t I? I’ll be screaming “you dang kids get off my lawn!” any day now at this rate…

  4. #4 Sandra Porter
    February 25, 2008

    The funny thing is, I remember, as a graduate student, when one of the instructors in our department UW (microbiology) started including molecular biology activities in her microbiology lab course. She had students doing really cool things with cloning Tn5 and mapping transposon insertions.

    Boy was there a stink from some of the faculty! They were outraged that one of our courses would cover what they called “vocational education” – i.e. agarose gels, Western blots, etc.

  5. #5 Jim Thomerson
    February 25, 2008

    I watched one of our grad students average a set of 30 values ranging from six to eight on the calculator and happily write down 9.2 for the average. I pointed out that this was unlikely to be correct, and explained how you do such calculations in your head. My observations of thinking people vs cookbook readers suggests to me that folks who understand the why can master the how better than the cookbook people. (Yes, crusty old person here!)

  6. #6 Sandra Porter
    February 25, 2008

    Oh my! I don’t think doing quick math in your head should ever become obsolete! Part of my argument, really, is that we need more work with math and data analysis, not less.

  7. #7 Sarcastic biologist
    February 25, 2008

    Maybe it’s time for schools to start looking at the techniques and tools we’re using now, and spend a little less time on the techniques we used then.

    “We,” Kemosabe?
    Did you know there was a whole big wide world of Biology–yes! even still today!–that is actually concerned with objects above the level of the molecule? It’s true! Some of us are actually dinosaurian enough to still be studying organisms!

  8. #8 Sandra Porter
    February 25, 2008

    Sarcastic biologist,

    Sure, I speak from my limited perspective.

    Are there many biologists who study organisms without using computers?

  9. #9 Sandra Porter
    February 25, 2008

    Sarcastic biologist:

    Okay, maybe I’m just really dense, but I just don’t understand why you would choose study organisms without any aid from a computer.

    Why give up the ability to work with digital images, videos, or sound?

    Why not use a computer to graph data or to model how things might behave?

    Why not use a computer to look at maps and do things like overlay maps of species distributions over time?

    Why not use databases that describe different organisms and where they live?

    To me, saying that you can’t find value in using a computer to do science is like saying you don’t need libraries.

  10. #10 Jim Thomerson
    February 25, 2008

    A cautionary tale. When I first got into using computers, I used a spreadsheet to compute a number of body proportion ratios. I made a mistake and divided through by the wrong column, and all the ratios are off by about 10%. I did not see the mistake, nor did my coauthors, the reviewers, or the editor. It was discovered a couple of years later by a French worker reviewing the genus. If I had done that work with pencil and paper, with or without a calculator, I would not have made the mistake. I should say that I have used spreadsheets a number of times since; have exercized a little more care and no mistakes.

  11. #11 kezdro
    February 25, 2008

    Ah – please don’t use Excel for calculations beyond a basic level.. It’s had, and has, numerous problems with it’s ability to handle even that, has quirks that can seriously throw off calculations, and it’s statistics routines are not sound. See here for some elaboration on the subject:
    http://www.burns-stat.com/pages/Tutor/spreadsheet_addiction.html#excel
    You might want to, if you do use statistics, look into R – Greg Laden has some experience with it too, I understand.

    As for me, I’m an undergrad in Molec Bio, and I’m still doing Western Blots, running gels, and such – in one of the working labs on campus. And we’re not underfunded/supplied either..
    I do wonder what I’m learning that I might not need in the future, though…

  12. #12 Sandra Porter
    February 25, 2008

    Thanks Jim and Kezdro,

    That is exactly why we should be using these tools. We need to demystify them so that we don’t have all kinds of biologists blindly believing that the computer is always right.

    I always check a few of the calculations by hand just to be safe.

  13. #13 Epicanis
    February 25, 2008

    In fairness to “Sarcastic Biologist”, I don’t think the point really had anything to do with using computers, but the fact that there does sometimes seem to be an abandonment of biological study above the level of molecular techniques.

    Sort of a tangential example – I’ve been trying to find out how researchers originally distinguished haploid yeast cells of the a and α “genders”. I’m under the impression this information was discovered some time ago, and the way it was discovered strikes me as useful background information.

    However, all I can seem to find out about are specific details of the molecular genetics involved in the specific genes, the sequences and structure of the mating-type peptides, and so forth. It’s like the original basic knowledge is virtually forgotten, or at least inaccessible.

    Admittedly, trying to fit both basic knowledge and the rapidly-growing more modern “relevant” stuff into the same 4-year curriculum gets more difficult all the time. And I WAS the guy in the Pathogenic Microbiology lab complaining about having to use the tedious specialized-media/carbon assimilation/etc. tests to identify things instead of PCR. Still, I think it’s a valid observation.

  14. #14 Sandra Porter
    February 26, 2008

    Epicanis: I’m not sure if there’s so much of an abandonment as there are many types of interesting things that all compete for our attention. There’s a certain appeal to getting all the information about the proteins in one cell at a time vs. knowing all kinds of things about one protein. I like getting to know molecules on an individual basis, too, so I can appreciate all different kinds of approaches.

    As far as the yeast question, I might be able to find that. We used to have students do experiments with yeast and mating types when I was a TA in grad school. I’ll see if I can find out. Those shmoos are kind of cute.

  15. #15 Epicanis
    February 26, 2008

    I’d be really interested if you managed to find an answer. At some point I’d like to figure out how to reconcile the common assertion that yeast are normally haploid with a comment in a review paper on yeast virology that stated that yeast “in the wild” spend most of their time in a diploid state, too…

  16. #16 Coturnix
    February 26, 2008

    I also think that the point Sarcastic Biologist was making that the BIO101 labs have gone far too molecular. With the creeping dictatorship of IACUCs, it is almost impossible to use vertebrates in teaching labs. But in my experience, nothing gets students as excited as exercises with animals. Forget glassware and computers – let them do physiological experiments on crayfish and cockroaches and earthworms, let them dissect crickets and frogs and cats and sharks and fetal pigs. Let them cross-pollinate flowers. Identify insects. Suddenly they light up and get engaged and actually tend to understand what you are doing and why, how does a technique provide answers to a question, etc. It is the disconnect from nature that is off-putting in modern biology labs – biology is supposed to be about Life, yet there is none of it in the labs these days.

  17. #17 Sandra Porter
    February 26, 2008

    I never taught Bio101 but I walked through that lab often because of the room location. Like your school, our students didn’t work with living vertebrate animals, but that was more a matter of cost. We didn’t have an IACUC. Our students did dissect fetal pigs and/or cats and they all worked with plants and insects and dissected a wide variety of sea creatures. I don’t think Bio101 was very molecular at all – at least not at our college.

    I taught the biotech labs and microbiology, so we mainly worked with bacteria, yeast, cultured cells, and phage. Bacteria and yeast are small, but they’re still alive.

  18. #18 Coturnix
    February 26, 2008

    Bacteria are cool. Protists are even cooler. Fungi rock.

  19. #19 Jim Thomerson
    February 26, 2008

    Can you really trust a graph drawn by someone who does not know how to use a slide rule? Kidding aside, I think it is important not just to know what we know, but to know how we came to know it and why we felt it important to do so.

    We accepted a student from a major research university into our MS program. She was assisting me in setting up introductory biology labs. We were doing something which required a molar concentration of sucrose. On the shelf was a percentage solution of sucrose. I started converting, talking to myself. She stopped me and asked what I was doing. I explained. Then she told me she had never been in a lab before, and that I would have to explain things to her. We gave her a good bit of lab experience and she turned out OK.

    The situation at that research university has changed since. But at the time, labs were optional and not required. In fact not offered with most courses. So they graduated BS people with no lab experience. I would say that obsolete lab experience is better than no experience at all.

  20. #20 bsci
    February 26, 2008

    While I think undergrad labs are a good place to do some basic (obselete) work that helps understand the fundamentals of certain concepts, I’m not sure lab courses can cover data analysis in the same way. The real issue with data analysis is it requires most biologists to get significantly more training in programming, math, statistics, and signal processing.

    Some of the above examples comment on students who can’t average, but in what area of biology is it ok for someone to not be aware of Fourier transforms and various data mining algorithms? This involves a larger rethinking of the entire curriculum.

  21. #21 Sandra Porter
    February 26, 2008

    Jim: I completely agree. About a third of the students in our community college biotech program had B.Sc. degrees from Universities, but they hadn’t made their own solutions or media or poured their own gels.

    They spent 10-15 hours per week in the lab, in our program, and they did very well finding work when they were done.

    They also did some bioinformatics, used spreadsheets, and graphed all kinds of data. Including some computer work doesn’t mean that you have to get rid of everything else.

  22. #22 Epicanis
    February 26, 2008

    The descriptions of people getting bachelor’s degrees in science without any lab experience are mind-boggling to me.

    Modern science is not something one “knows”, it’s something one “does“. The idea of walking away with a science degree without any lab experience to me is like walking away with a degree in English while being illiterate (or only able to speak or read in non-English languages. Substitute any other language name for “English” if you feel the need…)

    This relates to my complaint about the “wind-up-toy” labs. One isn’t really “doing” science when one mixes canned reagents in pre-determined amounts according to a canned procedure with a known, pre-determined outcome. In these cases, all you have is a mere lab demonstration that the instructor isn’t performing themselves – sometimes with three or four people in a group all jockeying for position to take turns doing bits of the procedure so that nobody even gets to experience the whole rote procedure.

    On the opposite end of the scale, I have had what I think of as really good lab classes. I was particularly impressed with our Microbial Diversity class, when we all went out to the same field site and took a soil sample, spending the rest of the semester isolating a collection of individual bacterial cultures and attempting to identify them by PCR. I felt like I learned quite a lot in that class.

    (Oh, for the record, a couple of posts back, the “genders” of yeast were supposed to read “a” and “α” – scienceblogs.com seems to mangle special characters if you preview first…)

  23. #23 Sandra Porter
    February 26, 2008

    Epicanis: I knew what you meant about the yeast mating types and I found a review paper that has the answer – or part of it anyway. The paper is Mating Types and Sexual Development in Filamentous Ascomycetes. EVELYNE COPPIN,* ROBERT DEBUCHY, SYLVIE, MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, Dec. 1997, p. 411–428

    It was kind of amazing to me to find that yeast mating types were known in 1904.

    As far as lab skills, I was surprised about the lack of lab skills in undergraduates, too. I guess it makes a good argument for encouraging undergraduate research.

    As far as kits, I will have to write more about those later on.

  24. #24 Joseph Cook
    February 26, 2008

    I agree that all the “obsolete” skills we learn as undergraduates are important for understanding the underlying priciples. However, if you have ever looked at the job postings today, you will see many jobs requiring a large list of complicated skills that most graduates don’t have. I think more effort needs to be placed in educating young (and old crusty) scientists in these current skill sets. Perhaps public Institutes could provide training ground for people needing these skills (Internships, temporary posts, etc.). Maybe in conjuction with Universities. Such institutions could provide cheap outsource services to scientists while at the same time providing valuable training for all scientists. It beats outsourcing these jobs to India.
    Hmmm! Any venture capitalist reading this?

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