Writing to think

After being merged with GSU, GPC (now PC) faculty got an email offering us $2,000 to convert one of our courses to a “writing intensive course”, part of Georgia State’s Writing Across the Curriculum program.  Willing to do anything ethical for cash, emboldened by the lowering of entropy in my life over the past year and eager to take advantage of a benefit of aforementioned merger, I accepted. Well, I applied and they accepted me.

In the past I have included plenty of writing in my courses, with the firm belief that what they know doesn’t matter if they can’t communicate it in a complete sentence that is appropriate for their audience.  Not that I thought it wouldn’t be any work, but this didn’t look to be all that different from what I have already done.

Then I read the required reading (uh oh) for the mandatory conference this week, and uh, it turns out that I don’t teach students how to think by writing at. all.   I have focused on the finished product for so long that I lost sight of the fact that I myself use writing to develop thoughts.  Ugh, such a boring post, but kind of an important development in my head: figure out how to show my students to use writing to think critically.

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Interesting ignorance – Stentor

In majors Biology lab last week we (un)covered the protists.  One of the many living critters we looked at was Stentor. How is it that I have managed to know so little about such an amazing Genus?  I should have had students take videos, but the actual oohs and ahhs from students seemed enough at the time.  Here is one off youtube:

If you aren’t impressed: these are giant one-celled creatures that can be up to 1mm long.  In fact, they are clearly bigger than the rotifers we also saw in these cultures, and those are (admittedly small) ANIMALS.  Single celled organism that is bigger than a multicellular animal with a mouth, intestines, anus, nerves, eyespots & other ORGANS.  No?

Let’s try this: when they aren’t hunting around for food (in ponds, Stentor are normally found in freshwater ponds) they hold on to something and extend out to look like a trumpet:

Not impressed?  They have fibers inside them that run the length of the cell that allow them to contract very quickly (they can contract themselves much faster than your muscle cell). It looks like they aren’t made of the fiber systems we know about in all other cells (microtubules or actin).  Stentor has both microtubules and actin, its just that these don’t appear to be made of them.


See those purple-ish spots?  Those are its nucleus (it has several actual), which is pinched off into little balls. If you cut this cell into pieces, each piece will regenerate a whole cell identical to the original.   Scientists in 1896 discovered that, as long as the fragments were bigger than 70-80 microns in diameter, they could regenerate the whole cell. Your cells don’t do that.  There is a lot of “How in the HELL does it pull THAT off?”.  For instance: how is it that the cytoplasm doesn’t leak out all over the place?


A piece of Figure 33 (in the subsection “Minced Stentors”) of The Biology of Stentor, Vance Tartar (1961)

Its both sad and wonderful that Stentor is understudied.  Sad because there is so much to be learned by looking at organisms distantly related to us, but because these don’t cause disease in humans or food crops there is very little grant money to study them.  Wonderful because science requires ignorance.  Finding interesting ignorance that is accessible to students can be difficult sometimes, but in this case its right out there in a scoop-full of pond water.


The Biology of Stentor, Vance (1961)

Marshall Lab website (UCSF)

Stentor coeruleus. Slabodnick et al Current Biology 2014


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Would I know a misperception if I saw it?

Thinking a lot about student misperceptions recently while actively measuring their prevalence in all my classes this semester.  Writing these thoughts up on this blog helps me to connect the thoughts I have in the fragmented time that I actually can focus on this sort of thing.  I am trying to read all of the references given by AAAS’s Project 2061 misperception database. (here)

From: “The effects of instruction on college nonmajors’ conceptions of respiration and photosynthesis”  Journal of Research in Science Teaching Volume 27, Issue 8, pages 761–776, November 1990


I would say that assuming that students who select these two options are completely naïve ignores the possibility that students are including “minerals” in their definition of food and that they have a typical lack of commitment to consistency in their answers that many novices have. By analogy, imagine a parent gets a survey from their child’s school district. They are not experts on early childhood education, and most likely do not perceive all or any of the value of the survey questions, much the same as students who can not perceive all or any value to the questions they get in class beyond it’s contribution to their grade. If that survey asks how much time your kids spend studying in front of the TV and you select “not at all” but then in another question it asks how much information  your child gets from watching tv shows and you select “sometimes”, those two are at odds to the person asking the question but might not be to the parent. It is possible that the parent has their own idiosyncratic interpretation of the question (“what exactly is meant by studying?”, for instance) that allows the “not at all” and the “sometimes” answers to be consistent with each other. It is also probable that, much like many non-majors students, the parents are not truly interested in the question to the point where they are going to carefully make sure that their answers are 100% consistent with each other. Like many students, parents are answering the questions because they know or feel they have to, and that motivation is going to affect whether they are completely committed to showing what they do and don’t know or believe.

Interesting to me how this resembles strands in a wonderful book I am reading on the importance of ignorance in scientific research, a book that if you have read this post down to here, you really should read. (link)  If one is trying to approach teaching and student learning in a scientific way, to what extent are we permanently ignorant of what a student is truly thinking and how committed to their answers they are?

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Is cerebral palsy genetic?

I honestly knew very very little about CP.  After a couple hours of reading this morning, I would shave a micron off the “v” in one of those verys.

The causes are numerous, from prenatal infections to exposure to methyl mercury to preterm birth.  I was a little  surprised to learn that it isn’t rare, occurring in just over in 1 in 500 births. The causes look mostly non-genetic to me, but of courses genetics affects everything.

Several research papers, some free like this one show that having a specific variant of the APOE gene correlates with increased severity of CP.  Interestingly, that same variant increases your chance for Alzheimer’s disease very dramatically (see here).  This gene variant doesn’t appear to cause CP, only to make it’s pathology more severe.  The ApoE protein is involved in moving fat-soluble vitamins, cholesterol and lipo-proteins around in the body, activities that are important for keeping neurons alive and happy.  The ApoE4 version of the protein doesn’t do a great job at this ( it appears to bind these things too tightly (here) but this is one paper and I don’t know jack about this area).

Several genetic diseases of metabolism might masquerade as CP.  This paper describes over 54 genetic diseases with CP-like symptoms, most of which were treatable to some degree.  Some of these had to be treated since birth, others get better with treatment even later in life.  These genetic diseases are rare, some based on the report of one patient.

Using Google to look up genetic diseases in that paper I found this incredible site which just happens to be put out by the authors of that paper.  The site is focused on treatable genetic diseases that cause intellectual disability.  Yet more evidence against  intelligent design.


Leach EL, Shevell M, Bowden K, Stockler-Ipsiroglu S, van Karnebeek CD. Treatable inborn errors of metabolism presenting as cerebral palsy mimics: systematic literature review. Orphanet Journal of Rare Diseases. 2014;9:197. doi:10.1186/s13023-014-0197-2.
LIEN E, ANDERSEN GL, BAO Y, et al. Apolipoprotein E polymorphisms and severity of cerebral palsy: a cross-sectional study in 255 children in Norway. Developmental medicine and child neurology. 2013;55(4):372-377. doi:10.1111/dmcn.12086.
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Cubes versus naked women (books please)

What is YOUR choice?

What is YOUR choice?

In Sanjoy Mahajan’s 2009 course on teaching he states that

You know if you know anyone who’s a symphony orchestra player, they say, oh yeah, the best way to start hating music is to be a professional musician. They love music, and then they had to do it for pay, in all of a sudden they don’t like as much anymore, not all of a sudden, but slowly. So there are many, many studies about that– motivation.

So what you want to do really is to find intrinsic motivation. And so the difference between extrinsic and intrinsic motivation is fundamental. And what you want to try to do is create the environment always where the motivation is intrinsic, so that the questions are interesting.

So what that means is you don’t want to use bad questions that people don’t have an interest in, and then force them to be interested because you give them extrinsic motivation.That’s a fundamental bad choice, and then it’s being solved with the fundamental wrong approach.

Not being someone who can hear something like that and not want to see those “many many studies” for myself, I did some searching and found what looks to be the first publication in these “many many” (here). The experimental setup is pretty simple.  Research subjects, all students in an undergradaute psychology course  (who had to be the most well understood group of humans during the 1960s).  Importantly, Deci is honest in saying that the students were required to participate as a part of their introductory course, which right away sends up little red flags about their motivations, but moving on….

The subjects came to 3 sessions where they sat in a room “at a table with the puzzle pieces in front of them, three drawings of configurations to the right of them, the latest issues of New Yorker, Time, and Playboy to their left, and the experimenter on the opposite side of the table. ”  The puzzle was Parker Brothers Soma.  At each session they tried to make various designs with the cubes.  One group was paid $1 during the second session, the control group was not.  In the middle of each session, the experimenter leaves the room.  There is a mirror in the room.  Red flag #2: unless you are part of an pre-contact native tribe from South America, aren’t you always aware that mirrors in these situations are ALWAYS 2 way, and that you are being observed, and that you should do the OPPOSITE of whatever you would normally do by yourself.  But moving on….

For 8 minutes they are observed and the number of minutes they play with the puzzle cubes during this free period was counted.  Interestingly, the group that was paid DOES spend less time messing around with the cubes.  They repeat the experiment in different ways (verbal rewards don’t substitute for money, but the group that is verbally encouraged plays with the cubes more) and get similar results.  Its a small N, but interesting.

I am sure there is a lot of literature that follows this study.  And there are all kinds of reasons for me to suspect my own, untrained conclusions when I am so far out of my field.  But it seems to me that all they could conclude is whether the subjects did or did not play with the cubes, not whether they enjoy playing with the cubes. Being behind an obvious (I am assuming) two way mirror isn’t exactly a free-choice situation.  It certainly isn’t a situation in which I would pick up a Playboy magazine, that’s for sure.  Wouldn’t play with the cubes either.  Hopefully I would have brought my own book in with me.

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Several years ago I watched Sanjoy Mahajan’s MIT 2009 course on Teaching College Level Science & Engineering (here) and among the many things I learned was that extrinsic motivations actually decrease performance in a variety of ways.  Ever since then I have wondered how that plays out in my classes… I can’t just give away points, but if I did, would students perform better?  I don’t think its as simple as that, but the possibility that intrinsic motivators could help students is definitely an exciting one to me.  I don’t think (or I don’t remember, it was a little hazy back then) that I went back and looked at any primary research studies on this then and that is what I have been doing this morning.

In Dan Pink’s TED talk (not a fan of them but apparently that doesn’t stop me from watching them) was this study from the Boston Fed (here) showing pretty dramatic decreases in game performance as the monetary rewards increased.  I’m not even remotely qualified in this field, and this apparently isn’t a published study, so who knows what that means, but it seems to fit with a lot of other abstracts I read on the subject.  There is even a study published in PNAS looking at the “neural basis of the undermining effect of monetary reward on intrinsic motivation” (here).

Are points in a classroom having the same effect as money?  I am sure (or I sure hope) there are published studies looking into this, but I am out of time this morning and need to get some classwork done before the raccoons wake up and demand their pancakes.  Its amazing what some free time, a space of your own and a completed tenure application (>300 pages) will do for your ability to think straight.

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Endosybionts in a tent.

I spent last night camping in the backyard with the kids.  As the slept next to me in the tent, with the rush of the freeway almost perfectly simulating a rushing river (except for the occasional motorcycle… giant Jurassic dragonflies??) the Chlorella Virus project became mentally 3 dimensional ….

I can’t rush in and assume that the virus selectivity for Chlorella hosts isn’t going to be a problem (see Van Etten’s reviews (such as here) or table 2 here). That could be a lot of wasted effort.

Perhaps better to work on isolating an endosymbiotic Chlorella from our pond directly, growing that in isolation and using it to screen for virus.  Most studies focus on isolating an algal-free host (old age or paraquat works too).. more practical: sonication method for isolation from Paramecium (here).

If you ever have access to a flow cytometer, studying the isolated Chlorella could be interesting (like here), but I can’t find anyone sucking Paramecia into the cytometer (seems like that would be an extremely interesting way to look at the endosymbiosis).

Apparently Paramecia will gobble up Carmine and that makes fro good light microscopy movies, although the vibration problem in room 3280 would need to be addressed.

Finally… here is a crazy idea: make walnut extract and culture Paramecia in it… do they eject their Chlorella?  Is jugalone-containing run off relevant in the pond?  Potential student ecology type project.

Next step: isolate Paramecium from the pond, get it growing as pure as you can, sonicate it.

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