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Using Bioinformatics

August 4, 2009 in Education, Science, Technology | No comments

As bioinformatics grows up into a modern scientific discipline, the rules are being developed alongside its newest tools.  The scientific smackdown that arose from discovery of the collagen-like protein from preserved T-Rex protein only illustrates these developments.

To make matters worse, simple bioinformatics tools are already becoming outdated.  Instead of examining a few simple lines of As, T, Cs and Gs, scientists are more interested in seeing how these letters interact with each other in the diversity of cells across many living organisms.  For instance, some scientists are interested in gene regulatory networks, which can be thought of as “interlinked sets of genes that are regulated in a coordinated fashion in cells and tissues” (-PZ Myers, Pharyngula)

To understand the future and present of bioinformatics, our students must be savvy to navigate through the available (and free) tools that can augment their science education.

gene-gatewayBioinformatics Tools from the NCBI

The Gene Gateway workbook is a collection of five activities, complete with step-by-step instructions designed to introduce new users in using bioinformatics tools from the OMIM, Gene Reviews, NCBI Map Viewer, Entrez Gene, Gene Bank, Swiss-Prot, Protein Data Bank, and Protein Explorer.

Going Further: BLAST Activity with Insulin
Investigate the Insulin protein and the mutations which cause disease. This activity is an introduction to using and interpreting the Blast database. Inquiry extensions involve comparing human insulin to insulin in other species.  (From K12 Outreach – Fungal Genomics)

Using Jmol

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Periodic Mosaic

June 20, 2009 in Education | No comments

Recently, students at my school created clay tiles to make this mosaic, which is hanging in the foyer between the second and third floor hallways.

mosaic

In the upper right hand corner, I smiled to see this tile:

elementsperiodic

 

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Demo Cam

March 23, 2009 in Uncategorized | No comments

img_1773After being frustrated with my students not being able to see all of my demonstrations, I decided to make a demo cam with some of my electronic junk.

The demo cam is simply an old Sony Handicam Digital 8 camcorder mounted on an inexpensive Videosecu Universal Camera Mounting Bracket.

The camera has an adapter that splits into an RCA video/mono audio cable, which I can easily plug into my classroom television.  Switching the input on the TV is a piece of cake, and using the TV doesn’t interfere with the interactive whiteboard.

Here are some of the benefits:

1.  I can project demos onto the television above, so the entire class can see every bit of the demonstration.

2.  The zoom function is quite impressive; I can easily zoom in on discreet parts of the demonstration not easily seen – even by the person doing the demo.  This is made even easier with the use of the remote control.

img_18133.  Safety.  The demo cam allows me to show demos without the need for the students to come anywhere near it; it also is far enough away from the demo so the camera is not damaged as well.

4.  Because I have to use the record function to keep the image on screen, I can easily capture video of the demonstration.  As there is a firewire output, I can easily capture the video with a connected laptop, and share it online (below see video demonstration of adding sodium to water).


Sodium in Water from Brian Bartel on Vimeo.

5.  I can also capture slow reactions over a long period of time, import them to a computer and speed up the video to a shorter time (see video of copper in silver nitrate solution).

Some of the Drawbacks:

1.  The angle is a little ackward because of the mounting limitations.  It takes a little practice not to walk in front of it, and to make sure that the demo is in the viewing area while zooming.

2.  In order to use the TV as a monitor, I have to use the record function.  This requires me to stand on a stool, and manually rewind the tape every hour (it cannot be done with my remote).

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You Tube for our Teachers

February 18, 2009 in Education, Technology | 1 comment

My school district has finally been able to distinguish a teacher from a student, at least in terms of their online access.

We recently received an e-mail explaining that teachers would be able to access previously blocked sites (i.e. YouTube and many blogs) for educational purposes.  In order to get this access, teachers will have to sign a form explaining they understand what “Acceptable Use” and “Educational Purposes” mean.

The district is responding to staff requests for increased access privileges. At this time, the district will provide access to the previously blocked resources of YouTube and external blogging. The district will open additional resources that are identified and approved for educational purposes.

To be clear, Websense (our internet filter) will still be in place.  When teachers come upon a site that is blocked through Websense, they will be able to pass through – offering them a gentle reminder that there is reasonable cause to have the site blocked in the first place.

Under the district’s interpretation of CIPA, students will not be granted this level of access.

Finally, I feel like a professional who can make decisions about what should and shouldn’t be used in the classroom.

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Protect Student Information from Surveys

January 14, 2009 in Education | No comments

img00139At the beginning of each year, I usually receive an onslaught of survey material for my students to fill out.   These surveys are not supplied by the school or district, and usually query students about their backgrounds, interests and future plans.

While some teachers diligently have students complete them immediately, others simply use this material for ‘filler’, administering the survey when they have a few extra minutes in class.  The ones addressed to me take a two-step journey to the recycle bin.

I have always been curious about how these surveys are used, and apparently I am not alone.  In fact, the Educational Research Center of America, Inc (ERCA) recently (October 2008) agreed to change its practices for obtaining and handling personal information it collects from high school student surveys, under an agreement reached with the Attorneys General of 36 states and the District of Columbia.  See press release from Maryland.

Wisconsin is not on this list.

Nonetheless, my policy has been to avoid distributing these surveys for a variety of reasons:

  1. Administering a survey to my students is clearly a waste of my precious classroom time.  I can think of a hundred curricularly appropriate things to do with 20 minutes than cater to the wishes of a company masquerading benefits to me and to my students.*
  2. This information is a marketing tool, and is sold to interested parties.  I believe it is irresponsible to use taxpayer money to facilitate their business model.
  3. I am always weary of surveys that collect student information other than for blind research practices.  As we continually preach to students about protecting their online identities, we should model the same practice in school as well.
  4. In this day and age, students have many more options available to them in finding information about their future.  The fact that I don’t need to say the “I” word simply illustrates my point.

*There are a few entities that sell “educational products” and entice educators with freebies and other benefits in the name of education.  The bottom line is that they are businesses whose fundamental goal is to make money; beware of the wolf in sheep’s clothing.

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Extreme Phase Change

October 4, 2008 in Science | 2 comments

Usually the during the week of homecoming, my Biophysical Science class is just finishing up a basic chemistry unit on the properties of matter.  To keep the kids focused on science, I make sure to obtain a little dry ice to have my students observe a unique phase change known as sublimation.

We observe:

  1. Sublimation of dry ice
  2. Density of carbon dioxide (bubbles with hover over more dense carbon dioxide – see video)
  3. Carbon Dioxide as a liquid (under pressure) as it exists in a gas cylinder
  4. Carbon Dioxide as a liquid (by sealing off a pipette with pliers, students can safely observe carbon dioxide liquefy as the pressure increases – see phase change diagram of carbon dioxide)
  5. Rapid sublimation of carbon dioxide in water in a sealed Nalgene bottle (see videos below)


CO2 Expansion 2007 from Brian Bartel on Vimeo.

Note the rapid condensation that appears on the lab table once the pressure is equalized.


CO2 Expansion 2008 from Brian Bartel on Vimeo.

NOTE: this demonstration was done behind a Plexiglas screen when there were no kids in the room.  Below is a picture of the bottle before, after, and a piece that was lodged in the ceiling (of which I am quite proud).

Nalgene Bottle Before

Nalgene Bottle Before

Nalgene Bottle After

Nalgene Bottle After

Piece Lodged in Ceiling Tile

Piece Lodged in Ceiling Tile

I should emphasize that this rapid buildup of gas pressure can be very dangerous.  In fact, the rapid vaporization of liquid nitrogen in a sealed plastic container is exactly how I once blew up a sink (see About page).  This is why a safe alternative to a live demo is to take an extreme video for future use.

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Your Role in Education with Technology

September 2, 2008 in Education, Technology | 1 comment

As we start a new school year, I challenge all educators to do more with technology in your classroom.  I wholeheartedly encourage you to use online tools that can increase your productivity, join social networks that can link you to other educators, and generally make the most of the hardware and software that is already available to you.  But I mostly encourage you to do what you do best – teach students how to think critically and analyze, no matter what medium they are using to access information.

We need to realize that newer technologies are simply tools that only change the way we interact with how we already live our lives.  That said, technology should not inherently change what we teach, but only how we teach.

While it is easier to dismiss new technologies that threaten to nudge us out of the ruts that we are comfortable with in teaching, the classroom is much more interesting and satisfying when we discover new paths to the same destination.

We will always have distractions in life and in the classroom.  Newer technologies have only merged a wealth of useful information with every other distraction in life.  The bottom line is that we have to teach how to sift through these distractions to harvest what’s useful.  As I mentioned before, teachers are already good at this; we simply have newer tools.

David Wolman summarizes this idea nicely in his article “When Tech Attacks” (Wired Magazine, September 2008)

“It’s naive to think that the digital age will magically remedy stupidity.  We need better schools, as well as a renowned commitment to reason and scientific rigor so that people can distinguish knowledge from garbage.  The web is not an obstacle in this project.  It’s an unparalleled tool for generating, finding and sharing sound information.  What’s moronic is to assume that it hurts us more than it helps.”

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Think Before You Send

August 6, 2008 in Education, Technology | No comments

If you follow a lot of tech blogs, you’ll notice how a lot of writers talk about how they are frustrated with e-mail. You might wonder why they are so upset about something that has revolutionized how we communicate in the 21st century.

Clive Thompson from Wired Magazine blames the asymmetric nature of e-mail, in that it is “incredibly easy to send but often devilishly burdensome to receive.”

For example, in one minute I can send an email to a thousand coworkers asking them to review a document. Let’s say each recipient spends five seconds disgustedly discarding it. Boom: In just one minute, I’ve wasted 5,000 seconds — 1 hour, 23 minutes — of my organization’s time. Equally insidious is the growing plague of semi-meaningful emails — friend requests, one-word replies from your boss. Email apps weren’t designed to recognize such idiocies, which is why our inboxes become unruly messes, with important messages pushed offscreen and out of mind.

So as you are getting ready for the upcoming school year, make sure you use your e-mail account appropriately.  It’s so easy to send out a mass message to your school and district, but think aboutthe ramifications – will it be a semi-meaningful message, or will it waste others’ time?

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Education is not a Business

July 18, 2008 in Education | No comments

In the latest issue of Newsweek, Jonathan Alter discusses education reform in an article entitled “Obama’s No Brainer on Education.”

While making a few sound points (teachers should focus on student learning over job security, assessment can be effective and beneficial, etc), Alter suggests an oversimplified solution on how to fix education in the U.S. – education should be run like a business.  Furthermore, Alter suggests that Obama adopt this concept in his campaign.

Let’s not kid ourselves – education is not a business.  We cannot comfortably indoctrinate a business model onto our educational system if we believe that all children have a right to learn.  Period.

If we can suggest that education can be run like a business, then why stop there?  Why not run schools like we run the military?  Or like our health care system – oh wait, that’s a bad example.

While outcomes do matter in each scenario (schools, businesses, military, etc), the means in which they are achieved are vastly different.  In the real world, businesses fail and wars are lost.  The engine of competition that drives these entities is in opposition to the fundamental ideals upon which universal education is based.

I still believe that teaching is more than just a job.  It’s a calling.  It’s a belief that there is power in learning.  It’s a hope in our future.  In order to retain these sentiment in thousands of educators, we cannot simply treat a school as warehouse or office space.

When Obama revisits educational reform, it would help him to keep in mind the ideals of public education – and not those of the business world.  Education deserves to be evaluated and reformed in its own light.

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Creativity in Science

June 2, 2008 in Education, Science | 2 comments

Recently, our school was fortunate to have a visit from Billy Collins – former poet laureate of the U.S. He read a few entries from Poetry 180 – a collection of poems for each of the 180 days of the school year (geared at high school students). You can see all of the poems here.

Inspired by his visit, I asked my students to either select or write a poem about science – which they would post on our class discussion board. Not only did they really enjoy reading what others posted, a few did a fantastic job writing their own science poems:

We started a little competition you see
Between my bright lab partner and me
Well I made a fish that glows in the dark
So he made a cat that doesn’t meow but bark
To beat him made I a lobster with wings
So he made a crocodile that sings,
So well that I gave my dog a few extra legs
To run past his roosters laying eggs
Out of hand it then got with my alliperizebralion
Pronouncing his beast I ain’t even trying
And after I gave his firstborn the head of a moose
We both decided to call it a truce

There once was a chemist named Larry
Who wanted to be really hairy.
He brewed up a potion
That set into motion
Some hair-growing that was quite scary.

A naive young biologist, Shay,
Thought that rocks and stones had DNA.
With his rock-carving tools,
He looked like a fool,
And wasted there many a day.

As we were going over their submissions in class, one student questioned what poetry had to do with science. Of course, I took the bait and led the class into a discussion on the importance of creativity in science.

We discussed science in art, and art in science. We discussed science writing (like David Quammen and Lewis Thomas). We discussed wildlife photography, National Geographic’s CritterCam, and David Goodsell’s Molecular Art (see image right). And we also discussed one of the most important creative endeavors in science – experimental design.

Beyond the occasional creative assignment (Drawing Moles, Making Reaction Rate Videos, Einstein’s Facebook), I’ve never taught science using creativity as a common thread. And while this was readily apparent to me, I hadn’t realized how much my students had mentally segregated science from creativity.

So as I think about preparing for the next school year, I will be making sure that my students understand the influence of creative thought in science.

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