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2011 January 31

New A.P. Biology Is Ready

Filed under: Uncategorized — gasstationwithoutpumps @ 08:57

The New York Times has just published an article announcing the release of the new AP Bio curriculum: New A.P. Biology Is Ready, but U.S. History Isn’t. This is the curriculum I blogged about in  Timeline of changes to AP Biology and Advanced Placement Bio changes announced.

The Assemblathon

Filed under: Uncategorized — gasstationwithoutpumps @ 03:35
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There is a new bioinformatics contest: The Assemblathon.  The idea is to provide a CASP-like competition for judging the quality of genome assembly methods from next-generation sequence data.

Actually there are two contests, the Assemblathon and the de Novo Genome Assessment Project (dnGASP), which is based in Europe.

I’ve been thinking that I ought to be entering the Assemblathon, since genome assembly is one of the fields I’m planning to investigate for my sabbatical, but I have no software for assembling Illumina reads (or simulations of them, which is what the Assemblathon is using).  The deadline for submitting assemblies is Feb 6, so there is certainly no time for developing new software (even if I had time for research with my teaching load this year). My main interest is in small genomes (prokaryotes), but the Assemblathon is focused on diploid genomes about the size of a human chromosome.

Of course, the results of the Assemblathon will be coming out just in time for the Banana Slug Genomics class this spring, and we’ll certainly be looking at the results very carefully and trying to get our hands on the software that performs best, because the banana slug genome is probably at least as difficult as the Assemblathon pseudo-genome.  (It may be polyploid and it is almost certainly bigger than one human chromosome.)


The History of Science Fairs

Filed under: Science fair — gasstationwithoutpumps @ 00:34
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Science Fair season is in full swing again, as I’m reminded by a nice post titled The History of Science Fairs from eGFI – For Teachers .  (They have a less-good post What is a Science Fair?, which appears to have borrowed liberally from Wikipedia—I recognize some of the phrases.)

This week I’ll be judging one elementary-school science fair, and next week a middle-school science fair.  All the school fairs have to be done soon, as the students who win at those fairs have to register for the Santa Cruz County Science Fair by Feb 16.  (High-schoolers, who don’t have school-level fairs in this county, can register directly for the county science fair.)

I’ll also be judging at the County Science Fair on Saturday 12 March 2011. I encourage scientists and engineers (including grad students and postdocs) to volunteer to judge at school, regional, and state science fairs  [Judges’ page for Santa Cruz County]. There is nearly always a shortage of qualified judges (particularly in the behavioral and biological sciences).

I don’t know whether I’ll be judging at the state science fair this year.  If I have to go to LA to accompany my son, I’ll volunteer, but he’s not sure that his project will be ready for the Feb 16 deadline and it’s his decision whether he submits it or not.  Even if he does finish it soon enough, there is no guarantee that it will be good enough to get him entry to the state science fair (though, as a proud parent, I think it is good enough).  He’s been to the state science fair for the past three years in a row, so it isn’t a big deal for him.  He’d like to win state some year, but neither of us think that this year’s project is that good.

2011 January 30

Biology teachers teaching creationism

Filed under: Uncategorized — gasstationwithoutpumps @ 10:53
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In the most recent issue of Science magazine, there is an article (not free, unfortunately) by Michael B. Berkman and Eric Plutzer, “Defeating Creationism in the Courtroom, But Not in the Classroom (Science 28 January 2011: Vol. 331 no. 6016 pp. 404-405 doi:10.1126/science.1198902), which seems to be a followup on their earlier (free) article in PLoS BiologyEvolution and Creationism in America’s Classrooms: A National Portrait (PLoS Biol 6(5): e124. doi:10.1371/journal.pbio.0060124).

Despite the repeated court decisions that creationism is religion and should not be taught in public schools, they found that “13% of the teachers surveyed explicitly advocate creationism or intelligent design by spending at least 1 hour of class time presenting it in a positive light (an additional 5% of teachers report that they endorse creationism in passing or when answering student questions).”  This survey was a “National Survey of High School Biology teachers, based on a nationally representative probability sample of 926 public high school biology instructors.”

So 15–18% of high-school biology teachers are teaching religion instead of science, only “28% of all biology teachers consistently implement the major recommendations and conclusions of the National Research Council.” The majority of high school biology teachers seem to be avoiding the issue, and thus not teaching the most central concept in biology—the model that makes sense out of the data. The authors go on to suggest that these authors do as much harm to science education as the explicit creationists, as they give the message that scientific theories, like religion, are matters of belief rather than of evidence and predictive power.

Their suggestion for improvement seems to me to likely be ineffective: better pre-service training of teachers in biology, with explicit training in evolution. “Better understanding of the field should provide them with more confidence to teach evolution forthrightly, even in communities where public opinion is sympathetic to creationism.”

Maybe this is so, but I somehow doubt that the problem is ignorance of evolution on the part of biology teachers.  I suspect rather that it is the selection process for teachers which discourages those who favor scientific thought processes over religious beliefs from entering the field of secondary education. Education classes are taught fairly dogmatically, with memes repeated for decades even in the face of contradicting research evidence.  Such an education is bound to appeal more to those who accept authority as the basis for an argument than those who look for evidence from experiments that have falsifiable hypotheses.

In any case, it is deeply disturbing that for many high school students the only “science” class they take will be a religion class instead.

Two memes colliding

Filed under: Uncategorized — gasstationwithoutpumps @ 08:15
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I have seen some bad pedagogic decisions made as a result of combining the following two ideas, each of which makes good sense by itself:

  • Teach the students you have, not the students you wish you had.
  • Don’t track students, but allow them to choose to challenge themselves.

The first meme, “teach the students you have,” makes good sense from the standpoint of educational effectiveness and efficiency.  If you pitch your classes outside the “zone of proximal development” of your students, they won’t learn much.  To get maximal learning from the class you need to adjust the pace and level of instruction of the course so that as many students as possible are stretched, but not left behind.

The second meme, “don’t track students,” makes good sense from the standpoint of social justice and not holding students back because of preconceived ideas about what they can do. Self-selection is often better than selection by teachers or counselors. Certainly I took some advantage in college of my ability to skip tedious prerequisites and get directly to material that interested me.

The problem comes when these two memes are clumsily combined, as happens too frequently.  Students may be encouraged to take advanced or AP classes, even if they lack the foundations needed to understand the contents of the course.  Having a few students flounder in a course over their heads is not a disaster, and some of them may, in fact, rise to the challenge and do well.  But if many students are encouraged to “challenge themselves” beyond the level of their preparation, the “teach-the-students-you-have” meme kicks in and the course gets watered down.  The students (now perhaps in the minority) who would have benefited from a challenging course do not get it, and may not even realize that they have been short-changed.

I’ve seen this pattern repeatedly at the university: entry-level courses getting gradually watered down until the students coming out of the course no longer are prepared for subsequent courses.  Sometimes a new course gets added after the intro course, essentially re-creating the originally designed intro course.  Unfortunately, there is only so much room in the curriculum for courses, so courses at the top end (where enrollments are smaller) often get cut in the process.  The result is a gradual downward slide of the level of education.

I don’t know if there is a simple solution to the problem, since both memes are strongly held in the education community.  Engineering faculty have sometimes held the line on “teach the students you’ve got” by insisting on the teaching the subject as specified in the curriculum and accepting high failure rates in initial classes.  Other disciplines have tried complicated placement and advising schemes to try to direct students to the appropriate level and pace of course, without notable success, as the placement tools are not very good predictors of student success.  Math has been doing this for decades and has still seen some slippage in the calculus classes.  Chemistry has tried it more recently, stretching out their 2-semester intro general chem course into three semesters, then adding another course before that.  They have a placement test for skipping the first course, but it turned out not to be very predictive of performance in the courses.

Elementary schools have embraced both memes, and insisted so strongly on the value of heterogeneous classrooms that they have closed their eyes to the inexorable slide in standards. High schools are intermediate, with some classes more advanced than others, and some prerequisites, but often little difference in the different levels of a course.  College-bound students are strongly rewarded for taking “honors” or AP classes by getting an extra point on their grades, even if the resulting mix of students pulls the class level down to an average-student level, rather than the more advanced course that the extra point on the GPA is supposed to signify.

Personally, I think that there should be some sorting of students so that most students are in classes with other students who are ready to learn about the same material at about the same pace.  Grouping students by readiness to learn specific material makes “teach the students you’ve got” work well.  If the grouping is subject-specific and frequently adjusted to match the achievement of the individual students, rather than based on some arbitrary criterion in 3rd grade (the way many “GATE” programs are set up), it does not have the negative social consequences of classical “tracking”.

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