Tag Archives: biology

Computational Thinking in Biology: What is an InSPECT Dataflow Diagram?

Integrating computational thinking into core science content and practices is a major goal of our InSPECT project, which is developing hands-on high school biology investigations using simple electronic sensors with Internet of Things (IoT) connectivity—a far cry from the simple germination experiments students usually encounter.

An article in the Fall 2017 Concord Consortium newsletter (“Science Thinking for Tomorrow Today”) describes the overall InSPECT project. Let’s take a closer look at a unique and powerful component of the project: virtual programming using a dataflow diagram.

The Dataflow interface enables students to do virtual programming within the browser-based interface. 

Dataflow diagrams have been around since the 1970s. They’re a visual model of the “flow” of data through a system. InSPECT has created a diagramming environment called Dataflow, the first version of which was developed in partnership with Peter Sand at Manylabs, that is much more than boxes and arrows on a page; components come alive when wirelessly synced to sensors, whose numerical data are displayed on the screen in real time as it’s recorded.

An eco-column activity includes sensors plugged into a Raspberry Pi computer. Dataflow automates data collection and initiates actions, such as raising or lowering temperature.

InSPECT is piloting an eco-column activity that includes electronic sensors plugged into a low-cost Raspberry Pi computer the size of a credit card. The sensors collect data about conditions inside the eco-column chambers, such as humidity and oxygen levels, sending it wirelessly over the Internet to Dataflow, which can automate data collection 24 hours a day, uninterrupted and unattended.

With the addition of actuators, Dataflow also can be programmed to create actions based on the sensor data. Students control the real-world actuators by defining variables and setting up conditionals that are entered directly into Dataflow’s simple, visual interface, which can run in any browser on a Mac or PC platform. For example, students can program a Dataflow diagram to adjust the current to a Peltier cooler in order to tweak the temperature of an eco-chamber when the sensor reading becomes too low or too high.

Finally, students can visualize, analyze, and interpret their data by exporting it to one of Concord Consortium’s most popular tools, CODAP (Common Online Data Analysis Platform), a free web-based environment for data analysis. Dataflow can be embedded directly into CODAP.

The use of sensor technology is still new to many biology classes, but our early research is based on the idea that when students collect data in real time, they make a powerful connection to the concepts they are studying. Using Dataflow, students not only learn to design the experiment and control the variables, they come to understand dynamic ecological systems.

The InSPECT project is currently recruiting biology teachers for our fall 2018 and spring 2019 studies. Our goal is to explore how to support integrated science practices and computational thinking in biology. We have several labs to select from involving photosynthesis, respiration, seed germination, and/or plant growth in chambers that can be from three classes to four weeks long. If you’re interested, contact us at inspect@concord.org.

Designer dragons? Talking to students about the ethical implications of editing DNA

University of Michigan School for Environment and Sustainability, Flickr (CC-BY-2.0)

A breakthrough in medical research has allowed a team of scientists to edit the DNA of human embryos to repair a version of a gene that causes cardiomyopathy, a genetic disease resulting in heart failure. While some see this genome editing technology—known as CRISPR—as a remarkable tour de force, others find the practice extremely alarming.

Meanwhile, some middle school students are already practicing genetic engineering in the classroom with inexpensive kits. Geniventure, our dragon genetics game for middle and high school students, also allows students to manipulate genomes, but the DNA in Geniventure is virtual and the species is a mythical creature called a “drake,” the model species for dragons.

Working with drakes and dragons allows us to combine various real-world genes without having to be restricted to the genome of a specific species, a problem that scientists in many countries often run into. We’ve combined real genes from mice, fruit flies, lizards, and other model organisms into the genome of our fantastical creatures. Students thus experience many of the same real genes that scientists around the world are also studying. Importantly, using dragons also allows teachers to talk about ethical issues, including the implications associated with modifying DNA.

CRISPR incites fears of designer babiesthe idea that parents will someday want to choose particular traits for their unborn children. In Geniventure, students do “design” drakes in challenges that require them to change alleles to match a target. Teachers guiding students through these challenges have an opportunity to discuss the notion of modifying an organism’s genes for a particular purpose. They can pose questions to get students thinking about the ethical implications of gene editing: Are there circumstances where you wouldn’t want to edit a drake’s genes? What might happen if you changed the wrong gene and you couldn’t change it back? What effect would that have on the drake’s future offspring?

“Designing” drakes. Geniventure tasks students with manipulating drake genes by selecting alleles from pull-down menus in order to match a target drake.

It’s easier to discuss these issues when we are talking about drakes and dragons because humans aren’t anything like these fictitious creatures. But since the genes are modeled after real genes (e.g., the the albino gene is modeled after skin color in humans), we can translate conversations about dragons to similar debates by scientists and regulatory officials about human gene editing. In Geniventure, students change an albino drake’s genes from producing a broken enzyme so that it can create a functional protein and generate a drake with color distributed throughout its scales. Albinism is also an inherited genetic condition in humans, so there is a significant parallel that could bridge the conversation.

Scientists are using CRISPR to investigate the prevention of inherited diseases like Huntington’s disease, cystic fibrosis, and even some cancers, though there is opposition and concern over this technology. One major fear is the safety to a developing embryo. DNA that’s been modified in an embryo would be passed down for generations, which raises concerns that any mutations as a result of the gene editing could cause new diseases and become a permanent part of that family’s genetic blueprint. Geniventure enables students and teachers to start discussions about these important topics.

Digital gaming will connect afterschool students with biotech mentors

Our nation’s future competitiveness and our citizens’ overall STEM literacy rely on our efforts to forge connections between the future workforce and the world of emerging STEM careers. Biotechnology, and genetics in particular, are rapidly advancing areas that will offer new jobs across the spectrum from technicians to scientists. A new $1.2 million National Science Foundation-funded project at the Concord Consortium will use Geniverse, an immersive digital game where students put genetics knowledge into action as they breed dragons, to help connect underserved students with local biotechnology professionals to strengthen student awareness of STEM careers.

East End House Students

Students from East End House enjoy collaborating on computer-based science activities.

Geniverse is our free, web-based software designed for high school biology that engages students in exploring heredity and genetics by breeding and studying virtual dragons. This game-like software allows students to undertake genetics experimentation with results that closely mimic real-world genetics. The new GeniConnect project will extend the gaming aspects of Geniverse and revise the content to more fully target middle school biology, introducing Geniverse to the afterschool environment.

The three-year GeniConnect project will develop and research a coherent series of student experiences in biotechnology and genetics involving game-based learning, industry mentoring, and hands-on laboratory work. Industry professionals from Biogen, Monsanto, and other firms will mentor afterschool students at East End House, a community center in East Cambridge, Massachusetts.

With researchers from Purdue University, we’ll explore how an immersive game and a connection to a real scientist can increase STEM knowledge, motivation, and career awareness of underserved youth. We will also develop and research a scalable model for STEM industry/afterschool partnerships, and produce a STEM Partnership Toolkit for the development of robust, educationally sound partnerships among industry professionals and afterschool programs. The Toolkit will be distributed to approximately 500 community-based organizations and afterschool programs nationally that are member organizations of the Alliance for Strong Families and Communities.

Geniverse Narrative

Beautiful graphics designed by FableVision Studios engage students in a compelling narrative. Students follow the arduous journey of their heroic character and suffering dragon to the Drake Breeder’s Guild.

Geniverse Lab

Students are welcomed into the Drake Breeder’s Guild where they will learn the tricks of the genetic trade. (Drakes are a model species that can help solve genetic mysteries in dragons, in much the same way as the mouse is a model species for human genetic disease.) Students are engaging in an authentic, experiment-driven approach to biology—in a fantastical world.

The National Science Foundation funds grant to pair intelligent tutoring system and Geniverse

Games, modeling, and simulation technologies hold great potential for helping students learn science concepts and engage with the practices of science, and these environments often capture meaningful data about student interactions. At the same time, intelligent tutoring systems (ITS) have undergone important advancements in providing support for individual student learning. Their complex statistical user models can identify student difficulties effectively and apply real-time probabilistic approaches to select options for assistance.

The Concord Consortium is proud to announce a four-year $1.5 million grant from the National Science Foundation that will pair Geniverse with robust intelligent tutoring systems to provide real-time classroom support. The new GeniGUIDE—Guiding Understanding via Information from Digital Environments—project will combine a deeply digital environment with an ITS core.

Geniverse is our free, web-based software for high school biology that engages students in exploring heredity and genetics by breeding and studying virtual dragons. Interactive models, powered by real genes, enable students to do simulated experiments that generate realistic and meaningful genetic data, all within an engaging, game-like context.

Geniverse Breeding

Students are introduced to drake traits and inheritance patterns, do experiments, look at data, draw tentative conclusions, and then test these conclusions with more experimentation. (Drakes are a model species that can help solve genetic mysteries in dragons, in much the same way as the mouse is a model species for human genetic disease.)

The GeniGUIDE project will improve student learning of genetics content by using student data from Geniverse. The software will continually monitor individual student actions, taking advantage of ITS capabilities to sense and guide students automatically through problems that have common, easily rectified issues. At the classroom level, it will make use of this same capability to help learners by connecting them to each other. When it identifies a student in need of assistance that transcends basic feedback, the system will connect the student with other peers in the classroom who have recently completed similar challenges, thus cultivating a supportive environment.

At the highest level, the software will leverage the rich data being collected about student actions and the system’s evolving models of student learning to form a valuable real-time resource for teachers. GeniGUIDE will identify students most in need of help at any given time and provide alerts to the teacher. The alerts will include contextual guidance about students’ past difficulties and most recent attempts as well as suggestions for pedagogical strategies most likely to aid individual students as they move forward.

The Concord Consortium and North Carolina State University will research this layered learner guidance system that aids students and informs interactions between student peers and between students and teachers. The project’s theoretical and practical advances promise to offer a deeper understanding of how diagnostic formative data can be used in technology-rich K-12 classrooms. As adaptive student learning environments find broad application in education, GeniGUIDE technologies will serve as an important foundation for the next generation of teacher support systems.

Strange thermal conductivity of leaves?

One way to tell if a plant is a plastic fake or not is to touch a leaf. If it feels cool, the plant is a real one. Have you ever wondered why a leaf feels cool? (A leaf of an indoor plant always rests at about the room temperature, plastic or real. It is not really cooler before you touch it. You can confirm this by measuring its temperature using a sensitive temperature sensor.)

We know metals feel cold because they conduct heat fast. Within a given amount of time, our fingers lose more thermal energy to a piece of metal than to a piece of wood.

Do leaves also conduct heat fast? On the contrary.

Let's put a fresh leaf on top of a piece of dry paper. The first set of IR images in this post shows what happened after I used two fingers to touch the leaf (on the left) and the paper to warm them up. The result tells that the leaf actually conducted heat more slowly than the paper, which has much lower thermal conductivity than metals.

Source: Wikipedia.
Now, we have a problem. We know leaves feel cooler than paper. But leaves conduct heat more slowly than paper! Our sense of touch honestly tells us that our fingers lose more thermal energy to leaves than to paper. So where does the thermal energy go on a leaf, if it doesn't diffuse to other parts?

My theory is that the thermal energy goes to heat up the water in the spongy layer of the leaf. The spongy layer lies beneath the palisade layer--the waxy surface layer of the leaf. Its cells are irregular in shape and loosely packed--hence the name "the spongy layer." During transpiration, the spongy layer is full of water in the spaces before they exit stoma. The specific heat of water is considerably high--4.18 J/(g*K) and the spongy layer is filled with water.

My theory is backed by the fact that a dry leaf conducts heat as fast as paper (IR images not shown here). This should not surprise you as paper is made of dehydrated wood fibers.

Now, the question is why the water in the spongy layer doesn't dissipate thermal energy quickly as water in a cup does (I confirmed the energy dissipation in water by IR imaging, which is not shown here). The thermal conductivity of liquid water is about 0.58 W/(m*K), compared with 0.024 W/(m*K) for air, 0.016 W/(m*K) for water vapor, and 0.05 W/(m*K) for paper. Somehow, the water trapped in the spongy layer cannot conduct heat like free water does.

Let's get get a wet (20% of full water absorption capacity) sponge (left) and a dry one (right) and look at their thermal conductivities under an IR camera. Again, I used my fingers to leave a heat mark on each. The second set of IR images shows a surprising result: the wet sponge appeared to conduct heat more slowly than the dry one!

Does this thermal conductivity protect plants' leaves? Have you wondered why some plants are anti-freezing and some are not? Leaves may have very complicated thermal regulation that we don't quite understand.

The thermogenesis of a moth

Is a moth warm-blooded or cold-blooded? If you google this, some would tell you it is cold-blooded. They are not completely right. This infrared study shows how a moth warms up before it flies. So at least a moth is warm-blooded when it moves.

Click to view a larger image

The moth (see the close-up photo above--what species is it?) was kept in a jar. The first IR image shows that when it was idle (sleeping?), its body temperature agreed with the ambient temperature. This means that it does not lose heat to the environment--a clever way for saving energy.
However, before making a move, it needs to heat up its flight muscles (near its head where the wings are attached) to above 30 degrees Celsius. In this observation, the warming process took 1-2 minutes for the moth in our experiment, as is shown by the sequence of the IR images. (Note: You may only observe this effect when the moth is energetic. A moth on the verge of death does not have enough energy to warm up.)

Note that we used the automatic color remapping, i.e., the heat map is rescaled based on the lowest and highest temperatures detected in the view. As a result, while the moth warmed up and appeared redder in the IR view, the background--in contrast--became bluer in the IR view. This, however, does not mean that the temperature of the background has decreased. The automatic remapping could create some confusion, but it is necessary in many cases, especially when you don't know what to expect. It maximizes the difference by increasing the contrast and, therefore, allows the observer to pick up small changes.

The last image shows that the temperature was ready and the moth started to move. In this particular experiment, the moth responded slowly because it could have been exhausted as it had struggled quite a bit before it was imaged.

What interests me in this experiment is thermogenesis: the process of heat production in organisms. What biochemical reactions are responsible for the thermogenesis in moths and bees? Can we learn from them to find a green way to heat our homes?

An infrared view of bees


A bumble bee.
I have been wanting to see what I can do with IR imaging in my backyard. Folks at the Discovery and Animal Planet channels use IR imaging regularly to show thermal patterns of animals and plants. So I guess I could do something with it. I cannot afford a high-definition IR camera. But I think my low-grade IR camera should be able to catch something. Here is an interesting story about bees.

Bees are warm-blooded insects. In order to fly, bees must heat up their flight muscles to above 30oC. So let's check this using an IR camera.

Indeed, a bee looks warm through the IR camera. To be more specific, the thorax of a bee appears to be warmer than the rest of its body (see the IR image to the right). I observed both a honey bee and a bumble bee. Both types have a warmer thorax, where the flight muscles are located. Exactly why the muscles can operate only at a warm temperature is an interesting question.

Bees are known to form societies that depend on successful division of work. Researchers have been using high-definition IR imaging to study bee behavior. With the assistance of IR imaging, German researchers led by Prof. Dr. Jürgen Tautz at Würzburg University found a new type of role known as the heater bees. The heater bees are responsible for maintaining the temperature in the hive where young bees (pupae) grow in sealed wax cells. The bees purposely leave some empty cells among those pupa cells so that the heater bees can crawl into them to warm up the pupae. By varying the temperature of each pupa they can determine what kind of bee it will become. As a result, the heater bees are vital in determining what job a young bee will perform once it matures. In the IR video, heater bees' thoraxes also appeared to be warmer, agreeing with what I observed using my IR camera for a worker bee.

Another article published in Optics Express discussed using IR imaging to evaluate beehive population. The idea is based on the assumption that the more bees in a hive, the warmer it would be. An unhealthy colony that has lost population would appear colder in the IR view, as the number of heater bees might have died down because of the lack of worker bees and hence the food they bring back. And if there are not enough heater bees, the pupae would not grow up normally, worsening the situation.

If you don't want to disturb bees and get stung by them, the non-touch, non-invasive IR imaging is probably the best way to go. :-)

PS on 8/3/2011:

Other flying insects like flies, dragonflies, cicadas, and wasps have a similar thermogram (i.e., warm thorax while active). See these two additional images. Or see this blog post about a moth.

I didn't observe warming in ants. They probably don't produce heat. Or they could be just too small to emit any appreciable IR radiation.