The introductory biology course that I teach focuses on cellular biology. I start with an overview of the basic types of biological molecules (carbohydrates, lipids, proteins, and nucleic acids) and the different structures found inside of cells. I then spend several weeks covering energy acquisition (photosynthesis through glycolysis and respiration). A significant portion of the course is then spent discussing inheritance and how genetic information is stored in our DNA. We then end the course with a unit on evolution.

I love teaching cell biology, but one of the challenges with teaching this material is that it can be hard for students to grasp the concepts because they can’t visualize them. I try to use lots of great graphics and we use the microscope in the lab to actually look at cells. Our publisher has produced a wide array of great videos and YouTube is a great resource. These things work well for the visual learner. To meet the needs of my kinesthetic learners, I bring in molecular models and sometimes we act out complicated pathways (electron transport in photosynthesis for example). One thing that worked well during my summer class was to use candy to build models of DNA. For this activity I used bite sized Twizzlers, cherry sours and jelly beans. Toothpicks were used to link together each “molecule”. I have seen similar versions of this activity that used whole Twizzlers to form the backbone of DNA, but I wanted to cover some more of the important details of DNA structure.

Understanding the structure of DNA is essential for understanding the concepts of replication and transcription. Students need to understand that DNA is composed of subunits called nucleotides. Each nucleotide has three components, a phosphate group, a sugar (deoxyribose), and a nitrogen containing base. Cherry sours represented the phosphate group, the Twizzlers represented the sugar, and different colored jelly beans were used to represent each base (Guanine= green, Cytosine=pink, Adenine= yellow, Thymine = orange).

We made a handful nucleotides, making sure that there were equal numbers of complementary bases (Guanine is complementary to Cytosine; Adenine is complementary to Thymine)

The nucleotides were then joined together to form a single stranded nucleic acid. You can point out the repetitive structure of the sugar-phosphate backbone. You can show the students that the chain has directionality, one end has a free phosphate group (5′ end) and one has a free sugar (3′ end). You can also talk about how it is the sequence of the bases that holds the information stored in DNA.

Using the first strand as a template, students can then build a complementary strand of DNA. It is important here that the new strand is oriented in the opposite direction that the template, with the phosphate group at the bottom and the free sugar at the top.

Once the two strands are complete, they can be connected by forming “hydrogen bonds” between the bases. The final result can be seen below. There are two antiparallel strands of DNA held together by the interactions between the bases. This can serve as a great jumping off point to talk about DNA replication, followed by the topics transcription and translation.

Mario Drawn Using HTML and JavaScript

A number of people in our community have started asking the “how do I get started as a games programmer?”  I believe we live in an exciting time to learn the craft of computer programming.   All the tools you need to start a simple game, exist in your web browser today.

In this post, I will introduce a very simple programmable browser feature that enables you to start learning computer graphics.   Using the Canvas tag,  browser based users can view games and visualizations that you create without installing additional software like Silverlight or Flash.   Since the technology is just part of a HTML web page, you can publish and share your work with the world!

Check out some awesome visualizations and gameful experiences using HTML and JavaScript.

• http://d3js.org/
• http://limejs.com
• http://browserquest.mozilla.org/

The “canvas” tag gives programmers a rectangular 2D “drawing pad” that can be placed in your browser.   In this tutorial, I want to introduce you to drawing simple animations using the Canvas tag.     If you are new to browser based programming, I would highly recommend that you check out the following free websites and tutorials.

• Code Academy – I would focus your attention on learning JavaScript and HTML.
• Khan Academy for Computer Science – https://www.khanacademy.org/cs –  They have created an amazing collection of learning tutorials.
• http://eloquentjavascript.net/ – This is a great FREE book helping to introduce JavaScript.   While it does not cover any “canvas” concepts, it provides a good reference for the basic and advanced features of the language.

As I work with the canvas tag, I appreciate that the coding experience feels rapid.   I can make small code changes and refresh the browser to see the impact quickly.    It’s fun working with a programming technology that does not require compiling.    Thanks to Google, Apple, Microsoft, and Firefox, the browsers are getting faster and more capable.    I think programming using the Canvas tag can be a great technology option for students and teachers who have Chromebooks.

To demonstrate this pattern for simple animation, let’s create a small clock using the Canvas tag. I have included all the code below. You can see the clock below.

[cc lang=”html”]

Your browser does not support the HTML5 canvas tag.

[/cc]

When you start coding with the canvas tag, you need to include the tag in the
body of the document. In the example below, the canvas tag is 400 x 400
pixels. We have assigned a name of “myCanvas” to the element.
The name of the canvas is important so that we can reference this element
in JavaScript later.

[cc lang=”html”]

Your browser does not support the HTML5 canvas tag.

[/cc]

On the body tag, we are using the “onload” event to trigger a function
we created called “bodyOnLoad.” This function is responsible for
starting our clock and drawing it.

[cc lang=”html”]
function bodyOnLoad(){
drawClock();
}
[/cc]

In the following code sample, focus your attention on the 4 elements
required to perform simple animation. You need to get access to the drawing
context of the canvas. (i.e variable g ) . You need to clear to the screen.
In the final code sample, you can see that I used a rectangle. After clearing
the screen, you are free to draw anything else that you like. The final line
of code in “drawClock” schedules the function to be called again in one second.

[cc lang=”js”]
function drawClock()
{
// Access the drawing context for the canvas tag.
var c=document.getElementById(“myCanvas”);
var g=c.getContext(“2d”);

// Clear the screen

// Draw stuff

// Do this process again in 1 second
setTimeout(drawClock, 1000);
}
[/cc]

The following code draws a black rectangle over the canvas.
The rectangle is positioned on the upper left corner of the canvas.
(i.e. Point 0,0) In the canvas tag, the X-axis increases from left to right.
The Y-axis increases from top to bottom. This is backwards from standard
cartesian coordinate systems. 🙂

[cc lang=”js”]
g.fillStyle=”#000000″;
g.fillRect(0,0,clockWidth,clockWidth);
[/cc]

Code to draw the circle of the clock using the “arc” function. We had to
specify the center of the circle, radius, a start angle in radians, and
end angle in radians.

[cc lang=”js”]
g.beginPath();
g.strokeStyle = ‘yellow’;
g.arc(clockCenterX,clockCenterY,clockWidth/2 * 0.9, 0, 2*Math.PI);
g.stroke();
[/cc]

The following shows how we draw one hand of the clock. The line is colored
red. We move to the center of the clock. We draw a line outward to point
(hourX, hourY) To learn more about the polar coordinate math,
please check out the following link.

[cc lang=”js”]
g.beginPath();
g.strokeStyle = ‘#ff0000’;
g.moveTo(clockCenterX, clockCenterY);
g.lineTo(hourX, hourY);
g.stroke();
[/cc]

To learn more about the canvas tag and discover more tutorials on this
browser feature, check out the following resource from W3Schools.com

Photo by Randi Boice.

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One of the challenges of teaching biology is that many of the topics that we cover occur at the molecular level and are difficult for students to visualize. YouTube has made teaching these topics so much easier. I frequently include videos into my lectures so that my students can see biology in action. My motto for teaching is “Life is Beautiful” (see this post). I can use videos to help inspire my students to see that for themselves. Here are a few videos that I have found useful for teaching cell biology:

Phagocytosis

I love the dramatic soundtrack on this video as an amoeba engulfs a paramecium. You can use this video to explain the process of phagocytosis. You can point out the formation of psuedopodia and talk about how the cytoskeleton is used to help the amoeba ooze across the screen. You can compare and contrast the movement of the paramecium which uses cilia instead.

Osmosis/Contractile Vacuole

When talking about osmosis it is always good to give lots of visual aids. This topic is really hard for students to grasp. This video demonstrates osmosis in  action in paramecium cells. Because they live in a hypotonic enviroment, osmosis drives water into the cytoplasm. They collect the excess water in a specialized organelle called a contractile vacuole. Once full, it contracts, expelling water from the cell. It is really neat to watch. I like to show the video and then view the process live in the lab under the microscope

Cellular Reproduction

We recently began the unit on cellular reproduction in my summer course. I like to begin the unit with this video animation of the development of a baby from fertilization to birth. I use it to lead into a discussion of mitosis and meiosis and how the different processes play a role in human reproduction. I love how this video shows the union of gametes and then follows the sequence of cellular divisions that ultimately lead to the formation of a human child. It doesn’t have any captions or narration so you can add commentary as you wish. The only drawback is that the video quality isn’t great when you view it in full screen mode.

If a picture speaks a thousand words, how many more can a good video convey? What good biology related videos have you found? Do you have any favorites? Feel free to add them to the list in the comments section. These are just a few of the ones that I have come across. I will share more as I find them.

There is a difference between a job and a vocation. A job is simply something you do to earn money. A vocation is something deeper. It is a calling. It is part of your identity and your sense of purpose.  The journey to discovering your vocation can be a long winding road. Mine has taken many twists and turns, but I feel like I am truly living out my vocation as a biology professor.  Each day I get to share  my passion for science with my students. I get to help them (well, most of them anyway) to reach their educational goals and to find their own career paths.

Teaching gives me the opportunity to connect with people from all walks of life and to impact their lives in a tangible way. In my last post I talked about how I love to teach non-traditional students. My mom was a nontraditional student, so it gives me great joy to help someone out in a similar situation. Teaching also gives me an opportunity to exercise my mind. There are always new things to learn and there are always new challenges to confront.  Is it all puppies and kittens? No, but knowing that I am doing something that I truly love helps me to get past the things I don’t like, like the mundane paperwork and “challenging” students.

I have some colleagues who don’t share my passion and sense of purpose. They didn’t really intend to teach, but kind of ended up in the position by default. Some are actually great teachers, but they are unhappy. It wears on them. The little things that I find mildly annoying, drive them crazy. Others are miserable, they do the bare minimum, and they take it out on their students.

What is your passion? What do you love to do? Are you living out your vocation or are you simply working for a paycheck?

5 signs that you love your career:

– You wake up each day excited for the work ahead

– You finish the day feeling like you have made a difference in the world

– You don’t care if you get paid well below the national average for your chosen career field

– You find yourself trying to get other people to consider it as a career

– You feel like there is a world of opportunity ahead of you

5 signs that you are on the wrong career path

– You dread going to work

– You are completely drained by the end of the day

– You are deeply offended by the small amount of money that you get in turn for your sacrifice

– You spend a lot of time warning others of the pitfalls of your career path

– You feel trapped

What can you do if you feel like you are in the wrong place? Take time to reflect on how you got there. Read some good books on career planning and finding your passions (Quitter by Jon Acuff is a good one). Know that life is constantly moving and changing, and you have to power to make choices that take you down a different path.

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