Category Archives: Molecular Science

New breakthroughs in molecular science, and new descriptions of old concepts in molecular science.

Welcome to Immune Defense

Our new game is a two dimensional strategy game called Immune Defense.  Seven kinds of white bloods cells can be bought and deployed in the never-ending, always-escalating war against 15 viral and bacterial pathogens.

Part 1 of Immune Defense to be released February 1, 2013.  Part 2 will be ready for beta testing In June, 2013.

Description for scientists:

Players must use the right combination of phagocytes, T-Cells and B-Cells for each combination of bacteria, viruses and parasites.  Players also regulate the type of proteins that appear on each cell’s surface and spend points to buy cells, to move drag cytokines and to activate white blood cells.  Surface proteins are required to recognize pathogens and receive signals.  Some signals cause cells to move, other cause activation, other tether cells to a location.  Activation is required for the most effective killing of pathogens… but it comes at a cost: more activated white blood cells raises your inflammation rate.  The game is over if your inflammation gets too high.  (Should have saved some points to buy a T-Reg!)

Description for Teachers:

Immune Defense is a simple, free game that anyone over 10 can play.  It is Macintosh compatible, can be played in a browser window if you have an internet connection and it can be downloaded and installed if you do not.  Low end computers can play this game.  A 30-minute period is sufficient, and a 60 minute period is not too long.  The game teaches many science standards that are appropriate for 5th through 12th grades; see below for Learning Objectives.  The game style and game play has been optimized for 9th and 10th grade students.  But we know that younger and older students enjoy the game.

Please contact me mstegman at FAS.org is you have any questions at all!  Or please add your comment below.

Evaluation of Immune Defense in Classrooms.

We are testing Immune Defense in classrooms this coming school year, and we need your help!   If you teach any subject to 9th or 10th grade and think our learning objectives, video game art, technology development, cells/proteins or nanotechnology, etc. fits into your curriculum and can give us three 45-minute periods, please see our evaluation collaborator’s website for more information on how you can join us!  Maine International Center for Digital Learning MICDL.org. 

These are the general Learning Objectives:

—Randomness of molecular diffusion
—Specificity of interactions between protein signals and protein receptors
—Low and high affinity interactions are different
—Cells have specific functions because of their unique complement of proteins
—Cells can signal to each other
—Cells respond to their environment if they have the correct receptors
—Regulating which proteins you have on hand is important for cell function
—Altering the proteins you have on hand is called cell differentiation
—Pathogens have evolved to thwart our immune system
—Viruses, bacteria and parasites have different ways of attacking and
—White blood cells, antibodies and complement factors all play different roles to combat different pathogens
—Structure and function of biologically relevant molecules and proteins
—The role of Oxidation and free radical chemistry in defense against pathogens
—Introduction to technology and nanotechnology
—Introduction to web based databases and resources
—Introduction to research methods and data presentation
—The player will see real data images of the cells and molecules presented in the game. The player will also be given their own online handbook of links to sites like Leica Microscope’s education page. Curious students can thus satisfy their quest for further information. Because links are presented in context of the game, this advanced information is meaningful to players.

 

Description for players:

Immune Defense takes place in the Immune Attack universe, chronologically, after the action in Immune Attack.  (Download our PC only, 3D game free on our site, ImmuneAttack.org!)  What we did not see in Immune Attack is that you, the new pilot who has no previous training in cell biology or immunology, accidentally and against the repeated advice of the artificial intelligence of the Microbot, gave a white blood cells a fly by.  Zooming down super close to the surface of an activated Macrophage, your Microbot was caught in an phagocytosis event.  Bitterly angry with you, the tiny, artificially intelligent Bot literally stewed for an hour in the acid and free radical oxidizing agents used by Macrophages to kill pathogens.

By the time the Bot was rescued, the acid and oxidation had done a lot of damage…  damage to your friendship with the little Bot!  However, artificial intelligence is more creative than you’d expect, and creative solutions are so much better than holding a grudge.  Every intelligent being knows that.

So the Microbot created a video game for you.  If you can master this game, Bot says, then it allow you to pilot it.  Until you master this 2D simulation of the Immune System, however, the Bot is refusing to heed your instructions.  So you’d better get busy and win this game, because your orders are to use this Microbot to heal patients… and explaining that you are having a personal disagreement with a Bot will be hard to explain to your superior.

Game Development notes:

Originally conceived as a tower defense styled game, Immune Defense originally had a Tower Defense style menu.  We found that the tower defense menu really did not help players figure out what to do.  When we thought about it, we decided our game had morphed into a real time strategy kind of game… so we spent some time working out what kind of game user interface (GUI).  We have a rough version you can play at our Testing Site.  This version still includes our tower defense styled GUI.  Soon, we’ll have a version of the game with a new GUI that matches its real time strategy mechanisms better.  You will be able to compare the two GUI’s and see for yourself what a difference they make.

Credits:

Immune Defense is a work in progress, but here are the credits so far.
Federation of American Scientists
………..Melanie Stegman, lead scientist, writer, designer, producer
………..—Jerold Council, intern and immunology text book interpreter
Cosmocyte, game development:
………..—Cameron Slayden, CMI
………..—Alec Slayden, Technical Lead
Scientific Advisory Group most helpful volunteer:
………..Howard Young, Ph.D.
Freelance programmer:
………..Ohad Frenkel

Here is the view from your Microbot cockpit.

Here is the view from your Microbot cockpit.

Association of Medical Illustrators presentation

What follows is my personal history with Medical Illustration.  I was very proud to present my work on Immune Attack and Immune Defense at the 2012 conference of the Association of Medical Illustrators.

Click here for my slides: Association of Medical Illustrators presentation, July 28, 2012

I am proud to carry on the tradition of communicating biology to a wide audience with my game Immune Defense.  So.  Science Video Games.  Where in the world did they come from?  Well, let’s look a little bit into the past.  Have you heard of Medical Illustration?  Have you ever wondered maybe bout how medical students learn about body parts, without the body?  Or perhaps you’ve wondered how a surgeon gets an idea of how a surgery should proceed, without actually doing the surgery?  Medical Illustration is the assembly of facts and information about procedures and about body parts into an image, a video or an interactive software that explains the parts, their relationship and the purpose of the procedure to the viewer.  A medical illustrator is part scientist, part artist.  Presenting science requires understanding which aspects of it are key to the understanding of it, that is which are the core concepts?  In a drawing of a surgery the question is what is the key moment, what does it look like when the procedure is halfway finished in the correct manner?

Medical Illustration is a long tradition that has changed a lot as new science and new technology have become available.  Check out the information and drawings at the Association of Medical Illustrators website, www.AMI.org, presentation and techniques. These days, medical illustration often involves gathering information about proteins and cells and presenting this gathered information in an image/video/interactive software.  The information that needs to be gathered comes from many sources.  Biochemists spend a lot of time studying one protein, and publish their results generally on their one protein.    Cell Biologists spend a lot of time looking at one kind of cell.  But there is a vast amount of knowledge to be gained from looking at how many proteins interact, how many cell types interact, how one protein moves, how many proteins associate with each other on a vesicle…  Who has the skills to put all this data into a comprehensive format?  Yep, Medical Illustrators.

Sounds like I am fond of medical illustrators, doesn’t it?  I am.  As a biochemist, I spent 7 years studying one protein, a motor protein–or at least a protein that has a similar amino acid sequence to other proteins that had motor activity.  My protein did not have any activity.  It just sat there in my test tube, silent.  I had read the papers, I knew all the assays that were supposed to reveal the activity of my motor-like protein.  I knew there was ATP that was broken, a microtubule to be released, a new microtubule to be grabbed, a new ATP to be grabbed  …  I knew lots of words about my protein, my brain was filled with data and numbers and methods.

However, Ron Vale the motor protein biochemist asked Graham Johnson the medical illustrator to make a movie of Ron’s protein Kinesin walking along a microtubule.  Using the data from many biochemical experiments in test tubes, Graham created a movie of what Kinesin must look like.

Now I had a story, a comprehensive idea, a foundation of thought about my possible motor protein that I could build on.  All those biochemical experiments had been summed up into a video.  A story is a compact way for our brain to store a lot of information!  Space in my brain was now available for building up some new words about my protein.  I imagined a new role for my possible motor protein, building on the story of the original motor protein.  I did a whole bunch more biochemical assays, and well, no one has made a movie of my data yet, but you could read the papers if you wanted to

Another video, requested by Harvard’s Biovisions group, showed Kinesin (at 1:16) walking gloriously along a microtubule, carrying its huge vesicle …  it was a very clear image and showed both aspects of Kinesin’s activities:  Kinesin walks on microtubules but only does so when its other end is bound to a vesicle.  This video, and still images from it, made it possible for me to quickly and completely explain to my colleagues what my thoughts about my own protein were.

Communication of ideas is very important to a scientist.  Mostly, it is important to explain what you are thinking so that your colleagues can attack your idea.  Without attack you will never advance your ideas and if no one understands your idea they can’t attack it properly!

So, there is my personal history with Medical Illustration.  I am proud to carry on the tradition of communicating biology to a wide audience with my game Immune Defense.  I was very proud to present my work on Immune Attack and Immune Defense at the 2012 conference of the Association of Medical Illustrators.

Click here for my slides: Association of Medical Illustrators presentation, July 28, 2012

Teachers role in a high tech classroom

Everyone seems to have an opinion about teacher’s role in the classroom of the future.  Some claim that teachers should get out of the way and let kids simply have unfettered access to the internet.  Others imagine a classroom in which teachers curate the vast world of information that is available and facilitate students’ understanding.  Certainly, there is more to learn in any subject than any one person could be an expert in.  How can we take the best advantage of technology in the classroom?

Please share your comments below!  I am preparing a blog post addressing the role of teachers in the future, and I would appreciate your thoughts and any resources!

 

March Learning Tech Newsletter. Educational Molecules for Fun

We need you
Are you a teacher with access to PC computers?  Test IA in your classroom!  We spent 2010 developing an excellent test of learning and attitudes toward molecular biology.  Now we need students in 7th – 12th grades to play IA1.0 for 2 class periods and and then take our survey.  Please register here and we will send you more information.

 

Serious talks!  Melanie Stegman, speaking in DC and NYC

Melanie Stegman, Director of the Learning Technologies Program at FAS, speaks March 30 in Washington, DC in a forum on Technologies in Education.  The forum is held by the Atlantic Monthly.  Here is a link to upcoming events held by the Atlantic Monthly.

Melanie Stegman speaks April 7 in New York City at the second NYC Health Games event. This event is organized by Kognito Interactive with the support and input of Games for Health, Games for Change, and the NYU ECT program.

 

Moleclues and the Year of Chemistry

http://www.moleclues.org/ is a website where you can learn about the things molecules do… like make us fall in love, for instance.

Moleclues wants you to know that 2011 is the YEAR OF CHEMISTRY!  Watch their videos about chemistry, there will be a new one every month of 2011.  http://www.moleclues.org/chemistry-calendar Teachers can also get some teachers guides for each month… topics range from fashion, to weather, to love…

 

Immunology Is…  FUN!

Making IA2.0 requires finding the fun in Immunology

Many thousands of people spend their lives in windowless laboratories, standing day in and day out, barely speaking to their silent lab mates, often working in a 4°C room, or holding their arms up for hours while they conduct their experiments inside the awkward, but sterile cell culture hood.

Why are they doing this?

…continued in Melanie’s blog post on finding the fun in immunology.

Friend us…   You can support the cause of technology for education by playing IA1.0, sharing and commenting on our blog posts, following us on facebook, and/or joining FAS.

 

2011 is the Year of Chemistry

www.moleclues.org is a website where you can learn about the things molecules do… like make us fall in love, for instance.

The people behind Moleclues and the Year of Chemistry are The Molecular Frontiers Foundation.

Moleclues wants you to know that 2011 is the international YEAR OF CHEMISTRY!  Watch their videos about chemistry, there will be a new one every month of 2011.  http://www.moleclues.org/chemistry-calendar Teachers can also get some teachers guides for each month… topics range from fashion, to weather, to love…

Molecular Frontiers is collaborating with Chalmers University of Technology, University of Gothenburg, Universeum and the film company Untamed Science to produce 12 videos during the International Year of Chemistry 2011. The topic of the monthly videos follows the themes set up by Swedish Chemical Society.

 

STEM Video Game Challenge!

STEM Challenge!

 

 

 

This fall the first  National STEM Video Game Challenge invited professional, collegiate, and youth developers to submit prototypes of games to inspire STEM learning for kids pre-k to 4th grade.  The winners will be announced soon.  You can get your students or yourself involved next year!

Read about the contest at the http://www.cooneycenterprizes.org

I served as a judge for this year’s contest.  I played every game submitted in the STEM game category.  I can tell you that we have many smart, and free thinking young minds out there.  Encourage the minds you know to compete next year!  I will be discussing software that middle school and High School students can use to design and create games.

You can read what another STEM Challenge game judge wrote Here.

Find the fun in immunology

To build appreciation for the science of immunology, we need to find the fun in it.

Many thousands of people spend their lives in windowless laboratories, standing day in and day out, barely speaking to their silent lab mates, often working in a 4°C room, or holding their arms up for hours while they conduct their experiments inside the awkward, but sterile cell culture hood.

Why are they doing this?

They are immunologists. Immunologists address the problems of the immune system that their fellow humans have to live with, like Leukemia, AIDS, allergies and autoimmune disorders. Immunologists use biochemistry, cell biology, molecular biology and genetics to look for ways to help patients and prevent disease.

So, we could simply say that these immunologists are serving their fellow man. But their motivation is not simply to help mankind. Something else drives them to spend those days in a tissue culture hood counting thousands of white blood cells.

Why did these immunologists take the lab path? Why didn’t they become social workers, firemen or even medical doctors? Well, I’ll tell you. Immunology is fun. Immunology involves watching cells identify and destroy other cells. These cells appear to be very similar to every other cell in the universe. These cells have outer membranes, nuclei, DNA and proteins that are almost indistinguishable from every other cell.

The questions are why this particular cell kills bacteria. Why doesn’t this cell kill all types of bacteria? Why does this cell in some people, not kill bacteria? The answers involve making endless comparisons between healthy and sick patients, between pathogenic and non-pathogenic bacteria, between humans and mice and between mice and flies.

So, Immunology is a puzzle. How does the puzzle work? We collect up as many clues as we can, we make a guess, we do an experiment and we try to figure out whether our idea was correct. We compare what we thought would happen to what did happen.

We have tools we can use. And we have rules for addressing these puzzles. We have several paths that others have taken before us that guide our way: We have biochemistry, cell biology, genetics, chemistry and physics. Each of these paths have their own rules and their own tools.

If you could jump in and try out these tools, and attempt a few of the puzzles yourself, then you would understand how immunology works. You would experience the fun! This is what we are doing with Immune Attack 2.0: we are letting you play Immunology… without the hours of standing in a windowless lab.

Students at Shadow Mountain High School, Phoenix, AZ Recommend Immune Attack

Wonder whether your students will like Immune Attack? Wonder whether it is game enough to hold their attention? Well watch this video.

And oh, if you work for a AAA video game company you can reach me by email!

Thank you to Debbie Kovesdy, her students and the biology teachers who participated in our evaluation. If YOU would like your students to participate in our evaluation, please let me know! We need more students to strengthen our data… We have significant gains in LEARNING and CONFIDENCE. Be a part of a revolution in learning and in gaming!

Register here!!!!

USA Science and Engineering Festival!

At the USA Science and Engineering Expo, we had a great time introducing our “free Video Game” to 4000 people. While kids of all ages ran into our booth to see for themselves whether Immune Attack was any good or not, parents were happy to hear that our video game is about white blood cells fighting bacteria. The main character isn’t a military character, it’s a Microbot. It’s main weapon is a ray gun that activates proteins.

The crowd at the USA Science and Engineering expo was curious and eager to hear about real science! Some high school kids wanted to talk about careers in science. FAS is a science policy think tank, so we had plenty to talk about! Additionally, video game production requires many different types of scientific, mathematical and engineering related skills. Someone needs to design the game and designing means testing to find out whether the game is fun. Testing means experimental design! Which audience finds your game fun? And what is your control game? Then someone will program the game. Someone else is an expert at drawing three-dimensional objects using software like Maya, Studio Max, or Cinema4D. Then still another artist uses other software to create all of the backgrounds. Then another artist uses more technology to create the characters. And if you are making a realistic video game, then someone serves as a subject matter expert and makes sure the historical context is correct, or that the science in the Microbot is accurate… I could go on and on. See below for links to art and biological science in particular:

I enjoyed meeting all of you. Please support technology in our schools! Why? Because you can’t see viruses, you can’t see bacteria. You can’t see proteins. But you can see them in a video game! Imagine learning soccer, but never being shown the field. Previously, we did not have ways to see bacteria and proteins, but now we do! And the new data is being used by many people in the Medical Illustration Field to create videos and diagrams that explain the molecular science that affects our everyday lives.

Here are some examples of great medical illustration resources:

The Association of Medical Illustrators

The book: The Machinery of Life

The Biomedical Communications department at the University of Texas Southwestern.