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2011 June 20

Rethinking Science Fairs (7 mostly bad ideas from John Spencer)

Filed under: Science fair — gasstationwithoutpumps @ 11:50
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John Spencer wrote an article (in his own blog and in the TeachPaperless blog): Rethinking Science Fairs (7 Ideas). He comes from a decidedly English-teacher view of the world, and seems to have missed the point of science fairs entirely, so his suggestions make almost no sense.  For my views on science fair, see some of my previous posts, or all the posts I’ve tagged with “science fair”.

Let’s look at his ideas one by one:

1. Quit giving awards: Instead of simply celebrating the individual achievements, highlight the collective research that the entire group accomplished.

John may really believe that individual effort should not be recognized and that only the group ever matters. Perhaps John also believes that all single-author writing should be abolished, and only committee reports allowed to be published.

I have seen teachers seriously propose that all awards (academic, athletic, citizenship, artistic, … ) be abolished from schools, and that no student ever get recognized for doing anything good.  I’ve never been clear how this helps students learn that there is value in doing things well.  Indeed, the main goal of such teachers seems to be to hammer down anyone who sticks out, and make sure that all students end up uniformly mediocre.

Given how little celebration there is of individual academic effort in most places in the US, though, I can’t see how this will help promote science learning and effort from students.  In collective research at the school level, either one person does all the work (and doesn’t get recognized for it) or very little actually gets done.  What is the incentive to spend much time working on a project that 29 other kids are also doing?  Large group science projects would make more sense if there were projects in which 30 kids could all meaningfully contribute (like a theater production), but I can’t think of any middle-school science projects big enough for that to work.

2. Broaden the definition of science:  My project was fictitious.  I get it.  However, I had a love of social science and sociology that a teacher could have tapped into for a more alternative, human-oriented project.

Behavioral science is usually the biggest category at science fairs, so I’m not sure what change he is asking for here—that only behavioral science be allowed?  That social activity without a science component at all be allowed?

3. Allow fiction: I’m not suggesting that we abandon scientific inquiry.  Yet, I can see a place for students proposing theories through allegorical science fiction.  Let a kid write a scientific dystopia where he or she examines some of the values inherent in science.

Spoken like an English teacher, who sees fiction as a suitable replacement for science.  I have no problem with English teachers having author fairs and celebrating writing, why do they object to celebrating science? Allegorical science fiction is a fine thing (I’ve read plenty of it), but it is no substitute for doing science.  Science fair is not the place for proposing “theories” (which have a very different meaning in science than what John is using the word for), but for doing experiments to test the predictions of a specific model.

4. Encourage collaboration: Rather than sharing experiments after the fact, let students collaborate in multiple projects throughout the process.  A student who becomes an expert in data analysis, for example, could lend his or her expertise in other projects.  Similarly, students could modify experiments based upon the observations of others.

Most science fairs (all the ones I’ve ever judged for) allow students to work either as individuals or as small groups. Collaboration is indeed encouraged by many teachers, though only in small groups—large group projects run into serious logistic difficulties, accomplishing less and less as the group gets bigger. I’ve talked about group projects before—group sizes that are optimal for science-fair-sized projects are from one to three students, depending on the project.

John’s proposal that students specialize (doing just data analysis , for example) seems more appropriate for college students than for middle-school students, and more appropriate for projects too large for middle-school science fairs.

5. Modify the presentation component: instead of simply boards or papers, allow for podcasts, websites, blogs, videos and social media reflection.  Create discussion groups where they share their data verbally in a group.

This makes some sense, as the poster presentation is a bit of a limitation on science fairs.  Most of the posters produced bear little resemblance to the posters used at real scientific conferences (except at the high school level, where many students are working with college professors on real science).

Google science fair has experimented with other media—entries had to be done by creating a Google web site, with either a 2-minute video or 20 slides in a Google Docs presentation (not both).  The constraints of these media were even more restrictive than the standard poster, and I know kids who looked at the Google contest as an advertising contest rather than a science contest (and so decided not to participate).

Podcasts and social media reflection are really poor ways to convey the content of a several-month scientific investigation, which is what a good science project is.  A blog recording the daily progress of a project would be an interesting accompaniment to a science fair project, but what is really needed is a solid written report.  It is indeed unfortunate that most science fairs do not judge the reports—indeed in many cases the judges do not get copies of the reports nor time to read them.

I don’t know why John thinks that “sharing data verbally in a group” is a good idea—chatting about data is such a tiny part of a science project (in the real world as well as science fair) that it has almost no point.  When scientists get together to talk, discussions of data only come up when the data are surprising—much more often they talk about methods for gathering data, models that arise from the data, and new experiments that can test those models.

6. Make it a real fair: In other words, instead of simply walking around and checking the grades of each project, create a festival.  Make it a carnival of inquiry.  Bust out the pond water.  Take out the magnifying glasses.  Let children experience the joy of scientific discovery.

John is talking about a different sort of event—one that is also quite common.  I organized a few of these as “Family Science Night”.  They are fun and get kids interested in science—great events and excellent edutainment. They are the advertising, while science fair projects are the work.  Perhaps John believes that science education should be only the entertainment part, and not the work of actually doing large projects.

7. Go global:  Let students compare similar experiments across the world.  Have students develop a shared experiment using Skype, social media, blogging, shared documents and video and then encourage hard dialogue about the cultural conflicts they experience.  Science can become the common ground for crossing the boundaries of presuppositions.

Why should “cultural conflicts” be what students talk about rather than the science itself?  This sounds like John only regards social interactions as interesting, and believes that the only point of science is to give people an excuse for socializing.  There are many easier ways to get at cultural conflicts, if that were the goal.

Running collaborations remotely adds a huge communication overhead to a project.  The science component of science fair projects would have to be scaled way back in order to accommodate this overhead.  If playing with social media is the goal, perhaps some other project could be devised—one that would actually benefit from geographic separation.  Sacrificing science on the altar of social media seems the wrong way to go.

All of John’s suggestions seem to be to take the “science” out of “science fair”.  O, I get that he doesn’t like science, but why take it out of one of the few places it is left in public education?

Human mutation rates

Filed under: Uncategorized — gasstationwithoutpumps @ 10:02
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I just finished reading an article on human mutation rates:

Variation in genome-wide mutation rates within and between human families by Donald F Conrad, Jonathan E M Keebler, Mark A DePristo, Sarah J Lindsay, Yujun Zhang, Ferran Casals, Youssef Idaghdour, Chris L Hartl, Carlos Torroja, Kiran V Garimella, Martine Zilversmit, Reed Cartwright, Guy A RouleauMark Daly, Eric A Stone, Matthew E Hurles,& Philip Awadalla for the 1000 Genomes Project
Nature Genetics
(2011) Published online 12 June 2011

The article computes mutation rates for two triples (father, mother, and child) who have been thoroughly re-sequenced as part of the 1000 genomes project.  For each triple, they identify possible sites of de novo mutations (appearing in the child but not inherited from either parent) using different methods, then re-examine each of the possible candidates with further sequencing, to try to separate out germ-line (inheritable) mutations from somatic (in the body) or cell-culture mutations.

They found that few of the observed de novo mutations in the sequencing were actually germ-line mutations (only about one in 20).  The final mutation rates they get were about 1e-8 (one change in 108 bases).  This rate is comparable with sex-averaged rates from other more population-based estimates, but at the low end.  They point out that mutation rates may vary between individuals (based on age and environmental conditions), and that a few high-mutation-rate individuals may  make the mean rate over many generations higher than the most frequently observed rate at the current time, so both the 1e-8 rate and the highest estimates (4e-8 for paternal mutations estimated from species-divergence from chimps) may still be consistent.  Other possible explanations for the wide spread are given—for example, that the divergence from chimp may be further back in time than the current best estimates.

If we take the 1e-8 error rate as typical, we would expect to see about 60 de novo mutations in each individual (remember that the 3Gbase human genome size is the haploid size, but humans are diploid, so we inherit about 6Gbases from our parents).  The variation from person to person could be quite wide though, even if there were no environmental factors affecting the mutation rate—a Poisson process has a standard deviation of the square root of the mean, so  mean 60 implies a standard deviation of about 8.

One surprising result they got was that for one of the triples, the paternal mutation rate was lower than the maternal one (most estimates have the paternal mutation rate around 4 times the maternal rate, attributed to higher numbers of replications of DNA in the male germ line).  The ages of the parents at conception was not recorded for either triple, but age almost certainly plays a major role in mutation rate. The 4 estimates of mutation rate they got (2 maternal and 2 paternal) had about an 8-to-1 range (much wider than the error bars on the individual estimates), so clearly many more triples need to be examined to get a broader picture of maternal and paternal mutation rates in the population as a whole.  It would be good to have triples in which the ages of the parents are recorded, and to have further generations sequenced to make germline/non-germline mutations easier to separate.

Estimated mutation rates, with previously published estimates above the green line, and new ones below it. Figure copied from the article.

2011 June 17

Giant viruses

Filed under: Uncategorized — gasstationwithoutpumps @ 07:45
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American Scientist has a nice overview article on Giant Viruses, viruses as big as bacterial cells, with as many genes.  Mimivirus, for example, has a 1.2 megabase genome, with 1018 genes, and has a diameter of 750 nm. OK, that’s an extreme example—the biggest known—but there are several giant viruses, defined as having a diameter of 200 nm or more and a genome of 300 kbase or more.  Mimivirus is big not just because of its large genome.  The capsid proper is only about 500n, across (still huge), but it is also covered with a layer of closely packed fibers that may be related to collagen.  So far, mimivirus is the only known giant virus to have this fiber coat.

The usual technique for separating viruses from cells is filtration with a 200nm filter, so giant viruses are pretty much defined as those that get missed by the usual separation technique (like artificial intelligence is facetiously defined as those things we’d like to do on a computer, but don’t know how to).  There is a project I’ve been loosely associated with to extract viral genes from salt ponds, and I’m now wondering whether there are any giant viruses among the halophiles—they won’t have been evident in the viral fraction that was sequenced.

There is some hope for finding evidence of giant viruses, though, even in the current metagenomic data.  It turns out that giant viruses have viruses that infect them (called virophages).  Although viral satellites have been known for a while (small bits of nucleic acid that hitchhike in the viral capsids and rely on them for replication), a giant virus found in 2008 (called mamavirus) has a satellite (called Sputnik) that interferes with the infectivity of mamavirus.  Other vibrophages have been found since.

There is a sidebar to the article on giant viruses (hidden behind a tree of DNA replication genes) that discusses the current controversy over whether viruses are alive. Personally, I favor Jean-Michel Claverie’s statement, “I believe that the virus factory should be considered the actual virus organism when referring to a virus. Incidentally, in this interpretation, the living nature of viruses is undisputable, on the same footing as intracellular bacterial parasites.” If you view the reproductive machinery as the organism, and the virion as an intermediate form (like bacterial cysts or fungal spores), then viruses fit fairly comfortably in the spectrum of living things, at the extreme end of parasites that can’t live without hosts.  This seems to me a much more reasonable position than one that insists that living things must fit on the mystical “tree of life”.



2011 June 15

Hold the presses! Can’t distribute software!

Filed under: Digital music,Software — gasstationwithoutpumps @ 03:15

This post was going to be a release of a .c file and a .h file for making WAV files from C programs. Unfortunately, the blog site provides no convenient way for distributing software files. The file extensions they allow are limited to jpg, jpeg, png, gif, pdf, doc, ppt, odt, pptx, docx, pps, ppsx, xls, xlsx for “security reasons”. Allowing docx and prohibiting plain text files clear has nothing to do with security, but trying to support the Microsoft monopoly. I may need to seriously rethink whether I want to run this blog on, as I’ll be wanting to include file types that they do not support (program source code, perhaps schematics or PC board layouts).

Maybe it is time to abandon and find a friendlier blogging site that allows reasonable other file formats.

UPDATE: 8 October 2011 does have a perfectly fine way to show code snippets, explained on Posting Source Code.  I don’t think that documentation existed when I first posted this message—at least I couldn’t find it then.  The method is actually fairly simple: just put [sourcecode language=”python”] and [/sourcecode] around the code (with any of 28 different formatting sytles, including “cpp” for c++ and “text” for generic formatting).  So I can do snippets fairly easily, though multi-file programs may be a pain to distribute.  Downloading the snippets to the clipboard is easy, but downloading to files is not supported.  Still, that is probably good enough for this blog.

Digital-to-analog converter

Filed under: Digital music,Digital-to-analog conversion — gasstationwithoutpumps @ 01:30

One of the first concerns for producing musical sounds from a computer is converting the stream of numbers computed by the algorithm into a stream of voltages uniformly spaced in time. The uniform timing is the responsibility of the computer (in my case, an Arduino board), and I’ll cover that in a later post, but the conversion to voltages is best done with a digital-to-analog converter (DAC). (One can also try using the pulse-width modulation of the Arduino’s digital pins—I’ll cover that in a later post also.)

When I first built hardware for digital sound, DACs were expensive parts. My first board used a DAC0801LCN, an 8-bit DAC that is (amazingly) still available. It came in a 16-pin DIP and needed a fairly large power-supply voltage (±4.5v to ±18v).  It also uses up a lot of output pins on the Arduino (each of the 8-bits is a separate pin).

Old DAC circuitry on a vector board.

The DIP packaging was pretty nice, though, as I could use wirewrap sockets and wire the board without much trouble. (I can’t find my old hobbywrap wirewrap tool, and wire wrapping seems to have gone out of style with hobbyists—too bad as it was a very cheap, low-tech way to connect circuits, with less trouble than soldering and more robustness than breadboards.)

Here is the back of my old DAC board, showing some wire-wrapped and some soldered connections.

For my Arduino, I wanted a DAC that I could plug into the Arduino board directly, without ribbon cables or other complications, and that would not use up many of the I/O pins on the Arduino.
Modern DACs are mostly serial-interface devices, to cut down on pin count, so the resolution of the DAC is no longer tied to the number of pins used to interface to it. Since DACs have gotten dirt cheap in the past 30 years, I figured I’d go with a 12-bit DAC instead of an 8-bit one. This may have been a foolish choice, as a 16-bit DAC would not have cost much more and might have simplified the interface software (12 bits are not aligned to 8-bit words).

I ended up choosing a Texas Instruments part (TLV5618A) which has 2 12-bit DACs in an 8-pin DIP. Three pins are used for the serial digital interface, two for the analog outputs, two for power, and one for an analog reference input.  TI recommends a 2.048 voltage reference when using a 5v power supply, probably to make the voltage steps be a uniform 1mV.

The pinout for the TLV5618 DAC. Pins 4 and 7 are the outputs, Pins 5 and 8 are the power supply, Pin 6 is a reference voltage input, and pins 1,2, and 3 are the digital inputs.

If I’d been thinking clearly, I would have simply hooked the reference pin up to the 3.3v power supply on the Arduino (the data sheet says that the reference could be as high as Vdd-1.5v, which would be 3.5v), but instead I used a pair of resistors (a 22kΩ and a 15kΩ) to make a voltage divider that produces about 2.03 volts. I also put a capacitor between the reference pin and ground, so that it wouldn’t be too sensitive to noise on the power supply. Someone who cared more than me would probably use a zener diode to set the reference voltage more precisely with less noise, but I had resistors and capacitors on hand and would have had to wait several days to buy a zener diode. (It would also irk me to pay more for shipping than for the 40¢ part.)

Here is the schematic from my lab notebook. I realize that the capacitor does not have a size in the schematic—in fact I don't know much about the capacitor I used. I got a whole bunch of them in a grab bag at some point, and the labeling on them doesn't tell me much. They are labeled 564J100, which probably means 560nF ±5% and a 100volt rating (see the Wikipedia article on capacitor marking). I suppose I should try measuring the capacitance to confirm that assumption. I should also learn to use a free schematic capture program, so that people won't have to see the mess from my lab notebook.

The outputs are connected (via 2.2kΩ series resistors) to a headphone jack.  The DACs are capable of powering a small headphone (like an earbud), or you can use powered computer speakers or a headphone amplifier.  The series resistors are to keep from accidentally shorting out the DACs.

I built my digital-to-analog converter on the prototyping shield sold by ladyada.

I soldered up the board (including a socket for the DAC). One of the things I don’t like about the Ladyada prototyping shield is that the only access to the Arduino pins is through a set of female headers. I’m thinking of removing the both those headers and the male ones that connect to the Arduino on the bottom, and using long-tail female headers to both connect to the Arduino board and provide the ability to stack on top of the protoboard.  That would free up the holes where the female connectors are now to solder wires to. Ladyada sells the connectors as shield stacking connectors for Arduino, so I’m a little annoyed that they didn’t design them into the prototyping shield in the first place.  It would be a trivial change to their design, not even requiring a new PC board—just different header pieces and new instructions.

Prototyping board with a digital to analog converter

Finished prototyping board with a digital to analog converter

In a later post I’ll talk about how to communicate with the DAC over the serial link.

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