Thursday, December 12, 2013

Some resources on learning #howtocode

An ongoing list of resources for learning how to program:

Jennifer Campbell and Paul Gries
Learn to Program (Part I): The Fundamentals (Python)
Learn to Program (Part II): Crafting Quality Code (Python)

David Evans
Introduction to Computer Science (Python)

MIT OpenCourseWare
John Guttag
Introduction to Computer Science and Programming (Python)

Codecademy - Python

UC Davis Genome Center
Keith Bradnam & Ian Korf
Unix & Perl Primer for Biologists

Wednesday, November 20, 2013

Hyperlapse videos

During the biotechnology lab a few of us watched an amazing hyperlapse video of UC Davis by Joseph Na:

UC Davis from Joseph Na on Vimeo.

Here are some others from Paris and Berlin:

Paris 2013 TimeLapse in Motion (Hyperlapse by Kirill Neiezhmakov) from Kirill Neiezhmakov on Vimeo.

berlin hyper-lapse from b-zOOmi on Vimeo.

And there is a hyperlapse video that uses Google Street View to weave the ultimate virtual road trip:

Google Street View Hyperlapse from Teehan+Lax Labs on Vimeo.

The Javascript source code is available on GitHub.

Saturday, November 9, 2013

Club Friday: A field trip to Sacramento's Hacker Lab

The American River College Research Club organized a pretty cool trip to the Sacramento HackerLab.
We love the HackerLab 3D-printers

Source: ARC Research Club

Source: ARC Research Club

A mega-digital printer (Epson 9900)

Some digital printer products
Source: ARC Research Club

The MakerSpace at HackerLab
 Source: ARC Research Club

MakerSpace rules
What to do with empty CD holders

Thanks to the Sacramento HackerLab for hosting our field trip!

Tuesday, October 29, 2013

Is there a STEM workforce shortage? New Bayer survey says YES (a continuing story)

Updated 30-Oct-2013

There's been much debate about whether the U.S. has a workforce shortage in STEM jobs. Bayer Corporation recently added to the discussion with their Facts of Science Education survey, which indicates a substantial need for STEM graduates, especially at the four-year or two-year degree level.

Bayer survey documents are also available here.

Jerry MacCleary, President, Bayer MaterialScience LLC, comments on the survey:
While much of the debate today centers on the country’s pool of STEM Ph.D.s., this survey focuses on the lion’s share of our STEM workforce -- those with four-year STEM degrees or less. For this particular debate, we believe the jury is no longer out.  As professionals responsible for scouting and hiring talent, the recruiters’ firsthand knowledge is an excellent barometer of the STEM workforce realities that companies in a range of industries are facing today. 

It will be important to know how Bayer defines the STEM workforce. For example, does the survey highlight science graduates, which tends to get maligned in the STEM debate?
And how will STEM skeptics respond to Bayer report? IEEE Spectrum had an ongoing discussion in September 2013 on whether the STEM workforce shortage is a myth, fueled by IEEE Spectrum Contributing Editor Robert Charette's feature story.

The discussion continues...

Monday, October 28, 2013

Honors Reads: Steinbeck's 'Sea of Cortez' with Prof. Christian Kiefer

The American River College Honors Reads continues, in which the Honors students and faculty explore one book in depth. This semester's selection is John Steinbeck's The Log from the Sea of Cortez.

Prof. Christian Kiefer (English) introduced the latest Honors Reads talk, framing the Sea of Cortez in the context of travel narratives.

The writer John Steinbeck and marine biologist Ed Ricketts journeyed the coast of the Gulf of California on the boat Western Flyer.

The Western Flyer in the Sea of Cortez. Source: Flickr/Hollywood History Tours

The route of the Sea of Cortez in the Gulf of California Source: Wikimedia

After Prof. Kiefer's introduction, his students did readings from their essays on the Sea of Cortez:
  • Rebekah Nand, "The Social Construction of Reality and Non-Teleological Thinking"
  • Christian Rice, "Science, Steinbeck, and Subjectivity"
  • Katie Rosander, "Steinbeck, Humanity, and the Question of Existence"
  • Martin Monson, "A Glimpse of Perfection: Truth and Perfection in The Log from the Sea of Cortez"

Prof. Kiefer and his students did a Q&A with the audience.

During the readings and discussion, the Honors students exchanged several thought-provoking ideas from the Sea of Cortez. A few points: 

Teleological (purpose existing in Nature) vs. non-teleological thinking (order in Nature is an illusion)

From the Sea of Cortez (Chapter 14)
“Teleological thinking"... is most frequently associated with the evaluating of causes and effects, the purposiveness of events.
In contrast,
Non-teleological thinking concerns itself primarily not with what should be, or could be, or might be, but rather with what actually “is”— attempting at most to answer the already sufficiently difficult questions what or how, instead of why.
Does Nature have a purpose? Astrophysicist Neil deGrasse Tyson weighs in on Minute Physics.

The teleological vs. non-teleological question blends into the purpose of the Sea of Cortez journey itself. According to the Honors Reads group, the Sea of Cortez expedition looks more like a "joy ride" than a tightly-scripted scientific mission (Chapter 21):
The lies we tell about our duty and our purposes, the meaningless words of science and philosophy, are walls that topple before a bewildered little “why.” Finally, we learned to know why we did these things. The animals were very beautiful. Here was life from which we borrowed life and excitement.
Philosophy professor Jesse Prinz (City University of New York), writes that experiencing wonder is a human endeavor, even in science. 

The concept of umwelt

Umwelt = any organism or species overall perception of their current surroundings and previous experiences, which will be unique to each organism.
Source: Biology-Online

Umwelt appears in the Sea of Cortez. For example (Chapter 11):

It is difficult, when watching the little beasts, not to trace human parallels. The greatest danger to a speculative biologist is analogy. It is a pitfall to be avoided— the industry of the bee, the economics of the ant, the villainy of the snake, all in human terms have given us profound misconceptions of the animals.
Source: xkcd

Neuroscientist David Eagleman offers a good explainer on umwelt:
In 1909, the biologist Jakob von Uexküll introduced the concept of the umwelt. He wanted a word to express a simple (but often overlooked) observation: different animals in the same ecosystem pick up on different environmental signals. In the blind and deaf world of the tick, the important signals are temperature and the odor of butyric acid. For the black ghost knifefish, it's electrical fields. For the echolocating bat, it's air-compression waves. The small subset of the world that an animal is able to detect is its umwelt. The bigger reality, whatever that might mean, is called the umgebung.
The interesting part is that each organism presumably assumes its umwelt to be the entire objective reality "out there." Why would any of us stop to think that there is more beyond what we can sense? In the movie The Truman Show, the eponymous Truman lives in a world completely constructed around him by an intrepid television producer. At one point an interviewer asks the producer, "Why do you think Truman has never come close to discovering the true nature of his world?" The producer replies, "We accept the reality of the world with which we're presented." We accept our umwelt and stop there.
In addition, Eagleman adds a social application from appreciating umwelt.
I think it would be useful if the concept of the umwelt were embedded in the public lexicon. It neatly captures the idea of limited knowledge, of unobtainable information, and of unimagined possibilities. Consider the criticisms of policy, the assertions of dogma, the declarations of fact that you hear every day — and just imagine if all of these could be infused with the proper intellectual humility that comes from appreciating the amount unseen.

The next Honors Reads talk is by Prof. Edward Hashima (History) on November 13, 4:30 pm - 6:00 pm, in Room D107.

Source: Wikimedia

Tuesday, October 22, 2013

Attracted by Gravity: From the ARC Physics/Astronomy Lunch Lectures

Nowadays the mention of "Gravity" reminds many people of this:

However, for the ARC Physics/Astronomy lecture series, Gravity has a more attractive meaning...

I. The Cavendish Balance

Sir Isaac Newton reasoned that any two objects have a gravitational attraction on each other, and he expressed the gravitational force as:

But what is the value of G, the gravitational constant?

During one Physics/Astronomy lunch lecture,  Prof. Chuck Hunt (Physics, ARC) described Henry Cavendish's ingenious device to measure the gravitational constant G.

Some background information from PASCO
The gravitational attraction of all objects toward the Earth is
obvious. The gravitational attraction of every object to every
other object, however, is anything but obvious. Despite the lack
of direct evidence for any such attraction between everyday
objects, Isaac Newton was able to deduce his law of universal
However, in Newton's time, every measurable example of this
gravitational force included the Earth as one of the masses. It was
therefore impossible to measure the constant, G, without first
knowing the mass of the Earth (or vice versa).
The answer to this problem came from Henry Cavendish in 1798,
when he performed experiments with a torsion balance,
measuring the gravitational attraction between relatively small
objects in the laboratory. The value he determined for G allowed
the mass and density of the Earth to be determined. Cavendish's
experiment was so well constructed that it was a hundred years
before more accurate measurements were made.
A video explainer of the Cavendish experiment

Prof. Hunt presented a classroom version of Cavendish's balance from the science education company PASCO that can be used to accurately determine G

PASCO's Gravitational Torsion Balance (based on Cavendish's classic design)

The Cavendish balance measures the gravitational attraction between the large and small masses in the device, and the attraction can be monitored by the movement of a light beam from the balance.

Prof. Hunt showed an example of the light beam measurements he used with the PASCO balance.

And the graph from the data plot.

And the math to determine G. You can find more details in the PASCO instruction manual.

II. Gravitationally Bound Systems

In a previous lunch lecture, Prof. Victor Zarate (Physics, ARC) talked about another aspect of gravity: Gravitationally Bound Systems.

What is a gravitationally bound system?

A good example of a gravitationally bound system is the International Space Station (ISS) in orbit around Earth.

Source: NASA

Khan Academy has an explainer on calculating the speed of the International Space Station (ISS) to stay in orbit.

Prof. Zarate kindly provided a copy of his presentation slides so that you can learn more about the math underlying gravitationally bound systems, as well as other examples.

Here's another example of some gravitationally bound systems...
But there are less desirable systems. For example, you probably don't want to be one of these gravitationally bound objects.

Friday, October 18, 2013

Metabolism LIVE with Prof. Rick Topinka

I saw Prof. Rick Topinka doing some interesting science with his non-majors biology students.
Metabolism, such as cellular respiration, is a favorite, but confounding, biology topic. OpenStax College has an #openaccess series of textbook modules to learn about cellular metabolism.

But Prof. Topinka has an interesting way to help biology students learn cellular respiration. With theatrical flourish, the students become molecular actors in metabolic play, dancing through the complexities of the respiration reactions.

Last spring I watched another student live-action play of cellular respiration in Prof. Topinka's classroom.

I was able to catch some of the student-enacted cellular respiration on video.

Thanks, Rick, for a peek into your class!

Sunday, October 13, 2013

Biotechnology at Sac State's Expanding Your Horizons

I participated with the North Valley Biotechnology Center in the Expanding Your Horizons conference at Sacramento State University. This conference featured hands-on workshops and exhibits to encourage more 6th to 8th grade girls into STEM careers.

Sac State published a preview article for the event: Expanding Your Horizons Connects Girls to Science.

Yay! The article mentions our workshop “Eat Your Way to DNA” – Using a strawberry and common household products to extract a real DNA sample to take home.

There was one DNA activity that required some review practice...

Scenes from my day at Expanding Your Horizons

First workshop activity - DNA origami

Next - Strawberry DNA
Students crush strawberries before adding detergent.

Filtering strawberry detergent solution

Origami DNA and Strawberry DNA isolation

Success! Spooling strawberry DNA from alcohol solution.

After the morning workshop, we're at the exhibition room:

The North Valley Biotechnology Center table

Playing with salmon DNA

Some more exhibits at Expanding Your Horizons

Sac State posted more photos from Expanding Your Horizons!