Lab Science and Executive Functioning

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When I first learned about executive functioning (EF), I was skeptical as at first glance, it sounded like another ephemeral educational buzzword that lives and dies in PD sessions. Thankfully, I was quickly turned and realize that EF is a crucial skill that all students need practice with and that hands on science can serve as a wonderful subject in which to learn and practice EF.

Understood.org has this to say:

Executive function is like the CEO of the brain. It’s in charge of making sure things get done from the planning stages of the job to the final deadline. When kids have issues with executive functioning, any task that requires planning, organization, memory, time management and flexible thinking becomes a challenge.

The way it was introduced to me was as such:

“What are you going to have for dinner?” – Immediately, your brain starts thinking ahead about what you have at your house, what you need to buy, and the times you need to procure, cook, and eat. So, a simple question caused a rush of neurological infrastructure to start thinking ahead to what you would need to solve a problem. We largely do this because as adults, we-hopefully-think and plan ahead but in kids with EF difficulties, this area of the brain hasn’t developed those skill sets. I always wondered why students forget to bring something to write with to class and are surprised they needed to bring one in the first place but as it turns out, a lack of EF skills could be the culprit. So, how can science help this? Easy! Being a scientist requires incredible amounts of thinking ahead, planning, and organization in order to plan, conduct, and analyze experiments.

Here is a link to a simple doc I made for a Vitamin C chemistry clock reaction for 4th and 5th graders with a few EF tags in it. Now this is by no means a complete EF work-up and I’ll expand on some ideas in this entry in subsequent entries but this doc does highlight one of my favorite EF lab tactics for lab procedures and that is thinking about the right tool for the job. Traditionally, teachers tend to put out beakers and equipment for this lab or give each group a set of tools. While this does save time, it does take away some of the inquiry of finding the right tools.

In the beginning of the year, in addition to normal lab safety, we workshopped the following ideas:

In the pictures you can see examples of the students worked stations which they designed into quadrants and boxes to organize their materials and keep them separate.

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Step 1: Make a vitamin C solution by crushing a 1000 mg vitamin C tablet and dissolving it in 60 mL of distilled water. Label as “vitamin C stock solution”.

I asked the students how they are going to crush the tablets. They suggested smashing it hammers, bricks, the bottoms of beakers and I asked them how they were ensure they recovered all of the powder. Then, one of them suggested a mortar and pestle and demo-ed why that will be useful for recovery. So we had that tool established and that wrote that in the materials box next to the step.

Next, we turned our attention to the 60 mL distilled water. Someone suggested a beaker but noticed that there was no 60 mL line and that getting exactly that amount was going to be logistically impossible. Another student said that graduated cylinders have that marking and it was determined that we should use those to measure out liquids to be precise. I also told them at the markers on beakers are only 95% accurate which convinced them further.

Then, we decided to look at various size graduated cylinders we have: 10 mL, 25 mL, 50 mL, 100 mL, 250 mL, and 500 mL. As a student suggested a size, myself or a student modeled it and we made some determinations about the various sizes:

250 mL and 500 mL: too big as it was hard to see where the 60 mL line

10 mL and 25 mL: too small as we would have to fill it multiple times. Since there is only one distilled water sink, it would take a long time for all the groups to cycle through.

50 mL: same problem but the students said they could use a 50 mL and a 10 mL GC and since we are only measuring water, we wouldn’t need to do any cleaning to get the proper amount so that was an option.

100 mL: Also, an option but the students said there could be a line as students fill and empty the GC to get the proper amount of water. Then, a student suggested filling the 100 mL GC to slightly above 60 and using a dropper back at the bench to get the specific amount. This was the option that a majority of the students went with but some opted for the 50 mL and 10 mL combination but also used a transfer pipette.

This seems like a lot of work for 1 step but after a couple experiments, it becomes part of the routine. Most importantly, it allows students to think ahead and place themselves in the experiment going through the steps in their own minds before rushing into the lab. EF skills are important in ensuring that students “mind map” a task and think ahead to the logistics of a project.

As we were creating a dialogue around equipment, I told them that at the beginning of my science tenure, I was frequently reprimanded by my bosses for what I realize now was poor EF skills. Then, one of my students raised their hand and asked why I just didn’t just create these dialogue boxes next to steps and think about data collection before the experiment like we are doing. That was a good question and I didn’t have a real answer aside from that doing so would have alleviated some headaches.

A lab environment is overwhelming for the student with EF difficulties and next time, I will talk about how to set up a work station on a benchpad that keeps equipment, chemicals, and notes separate and organize and how to utilize downtime in between steps to set up subsequent experiments

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An Inquiry Driven Visualizing DNA Using Fruit

My goal for this year is to pop the hood on my teaching pedagogy and write about how to practically teach molecular biology. Over the next few months, I am going to be posting information about teaching common biological activities but in a more intuitive that makes the procedure less cookbook and more of an exploration. The first entry is about the very common practice of purifying DNA from fruit using simply household chemicals, a great starting point for the practice of molecular bio. Many students have done this but there are many different adaptions and add-ons one can do to the procedure in order to add elements of experimentation and mystery all while exploring the chemical properties of the DNA molecule.

Students tend to vary greatly in their overall knowledge of DNA and so it is important to ensure students understand what it is and provide a number of fast facts that will hook the student’s attention.

Talking Points to Build Interest Around DNA Prior to Purifying It

  • Each one of your cells has about 6 feet of DNA packaged inside. DNA is coiled around a complex of proteins called histones which tightly bond to the DNA and keep it condensed. Since this is an abstract concept to envision, envision a long of yarn wrapped into a tight ball. Unwrapped, it would stretch on for a hundred foot but when wrapped, it is easy to handle and takes up a lot less space
  • If one were to remove the DNA in each of their cells and line up the strands from end to end, it would stretch to somewhere between Jupiter and Saturn! Imagine spending months upon months in a space ship viewing the same person’s DNA the whole time. Wow!
  • Most of the attention DNA gets is from genes, the blueprints for proteins that students and scientists alike spend lots of time studying but that only accounts for a small percentage of the overall genome! The other sequences, called introns, have a fascinating story to tell as well.
    • Transposons are remnants of viruses that have implanted themselves in our DNA and are present in our evolutionary ancestors. During times of extreme cellular stress, some have the availability to catalyze their own removal and move to different places in the genome.
    • There are also psuedogenes, inactive copies of nearby genes that collect mutations at a higher rate than their functioning neighbors.
    • There are sequences that allow for intramolecular bonding that can be sometimes be millions of bases apart but loop together to find each other to allow for tighter packing. After all, 6 feet of DNA have to fit into a space far smaller than the head of a pin

Materials

Quart freezer bags
Fruit (strawberry works best but bananas and blueberries also work)
Shampoo
Salt
Meat Tenderizer
Soap
Plastic cups or beakers
wood or glass stir rod
Cold 99% Isopropyl Alcohol or Ethanol

Note: The most important piece of pre-experimental planning is to place the alcohol required for the last step of the process in a freezer. The DNA solubilizes in alcohol and chilling the alcohol enables the DNA to clump together faster as well as rise to the top.

Below is a common procedure for purifying DNA from fruit. Connections to other areas or experimental variations are in bold below the steps. 

  1. Remove the stem and place the strawberry in the bag and seal, ensuring that all the air has been removed from the bag

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  • Mathematics connection: Have the students weigh the strawberry and hypothesize what percentage of the total weight of it is represented by DNA.

2. Gently mush the strawberry ensuring that all chunks are broken into small pieces. No single piece of strawberry is larger than a couple of millimeters

  • Math/Physics connection: Why is it important to get the pieces as small as possible? Take a rough volume of the pieces and consider the importance of surface area in allowing reagents to reach their target. 

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3. Place 1 squirt of soap/shampoo along with 1/2 tsp salt or meat tenderizer into the bag and 25-50 mL of water into the bag and gently slosh around the slurry allowing the surfactants and

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  • Experimental design challenge: What effect would changing the amounts of  reagents have on the amount of DNA recovery? Students can change one variable at a time and see how that changes the overall DNA yield
  • Chemistry connection: Soap is required to break down the cell membrane, which is largely composed of lipids. Why is soap such a powerful degreasing agent? And why don’t our cells pop open when we use soap?
  • Biochemistry connection: Why is meat tenderizer used? Read the ingredient label and hypothesize which components of the tenderizer make the most different. 

    4. Allow the bag to rest for 10-15 minutes to allow the chemical reactions to proceed

5. Pour the contents of the bag into a coffee filter place on top of a beaker and allow the liquid containing the DNA to filter down into the beaker below. 

6. With the DNA solution in the beaker below, about 2-3 volumes of  COLD alcohol can be poured in. The results work best if the students are stirring their solutions as the alcohol is poured.

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The DNA should be stuck to the stir rod and the students can squeeze out as much of the water and alcohol as possible. If the students weighed the strawberry in the first step, they can weigh the DNA, on the stir rod and calculate what percentage of the total weight of the strawberry is taken up by the genetic material. 

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This process can be repeated with different fruits though their DNA is not as sticky as strawberries. This can make quantitative comparisons of fruit DNA more difficult but a qualitative observation is still possible.

 

History Connections to DNA in general

  • The discovery of DNA as the genetic material of the cell and its structure was filled with colorful scientists and characters. The research of Griffith, Avery, McCleod, Watson, Crick, and Franklin helped to prove the properties and structure of DNA. Their research and lives also demonstrated what science in the 1940’s and 1950’s ws like. The discovery of the double helix was a race between competing labs and while Watson and Crick published first, there were others. What were some of the other researchers studying DNA and what contributions to science did they provide?
  • While Watson and Crick get most of the credit for the discovery of the DNA double helix, Franklin’s work on elucidating its X-ray structure was paramount. For decades, her work was marginalized. What were the social circumstances around the role of women in science during that era and how has it changed?

Microbiology for the Masses

One of the biggest problems with biology is that it requires a lab. Culturing bacteria, something that grows everywhere and over every surface on this planet, requires a great deal of complex incubation steps and manipulating it requires a shaker, 2 temperature specific water baths set to hot and cold, expensive pipettes and reagents, and various autoclaved sterile equipment. In order words, if you wanted to do this at home, you are looking at an investment of thousands of dollars and the loss of an entire room of your house.

That is now looking to change as there is a growing market of synthetic biology platforms- dubbed “garage biology”- that can enable people to do sophisticated biological research in their own home without the need for the expensive and space consuming equipment. Last month, I travelled up to Montreal to try one such platform and  felt that I held the future of science in my hands.

 

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In a robotics makerspace in the hip area of Saint Viateur, I experienced the Amino, an all in one platform for the growth, transformation and genetic manipulation, and propagation of bacteria that combines the rigor and specificity of a full scale lab with the convenience of a device that takes up little more space than a personal computer. As I was doing a bacterial transformation (the implantation of DNA into a bacterial target), I felt as if I knew how the mindset of those who tested the first PCs. After all, before the first PC, navigating a computer required a morass of complex and/or convoluted systems of commands. The PC simplified all that by taking away the levels of complexity and creating a user-friendly interface that all could enjoy. In other words, these are the same theoretical gains a budding scientist would experience by using the Amino platform.

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Performing a bacterial transfection sounds daunting but in theory, is a very simple concept. One simply starts by growing bacteria-usually a strain of Ecoli that is harmless to humans-in a small 37C dome located on the top of the amino. 37C translates to roughly 98.6F, or human body temperature. The process really commences when the bacteria is transferred via a simple plastic inoculating loop to a nutrient broth that is then placed in a tube well that has been pre-cooled to 19C. This puts an environmental stress on the bacteria causing it to release a set of proteins that allow it to adapt to the new temperature. Just when it equilibrates to the changes, the bacterial tube is transferred to a second well that has been heated to 42C at which point foreign DNA can be added. This part of the transformation is called heat shock and this sudden change of temperature causes the bacterial to open its cell walls allowing to take in material from the surrounding environment. After this, the transformed bacteria is injected in a growth tube by something as simple as a plastic transfer pipette.

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The heart of this whole experiment is the DNA that is added to this bacterial mixture. With the right DNA, it is possible to have a tube of microbes begin to produce a variety of things from flavor extracts to paint to simply growing more of a certain sequence for use in other experiments. There are a few additional steps to get it to this form but the removal of the bacteria and purification of the product is mostly built into the Amino. Adding in some basic PCR and molecular biology equipment can enable users to generate their own sequences to insert and really do sophisticated biology in their own home. Even further, these “cDNA” libraries can be shared with others to allow an open source biology platform across all Amino users.

The software for the Amino is based on Arduino which allows a number of external apps to interface and allow all manners of experimental readouts, many of which have not quite been explored yet but the potential is virtually limitless. The base unit does have it’s own very useful readout features and all of them can be viewed its own website where users can monitor the colony number, pH, and temperature of the reacting mixture. As the bacteria grows, there will be changes in all of these that denote colony health and there are countless experiments that can be designed to simply test how certain things affect microbial growth so adding cDNA isn’t even necessary to begin to exploring the magical tiny world of bacterial cells.

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Science teachers are often seen as gatekeepers of content but that is changing. Tools like the Amino will allow curious users to begin their own deep dives into microbiology and similar platforms are being developed that will allow individuals to explore concepts in biochemistry, organic chemistry, and even particle physics all using the garage technology platform! Until then, my students will be working to beta test the Amino and do their own investigations. They will have their own ideas, projects, and experiments to test and most certainly will have a multitude of questions regarding controls, methodologies, interpretations, and troubleshooting. So my role is less as a science “teacher” and more a “principle investigator.” Rather than opening the doors for students to learn, I remove the blockades that will help students learn and gain valuable experience so that in a few years, they can solve their own problems and help others with theirs.

Much ink has been spilled over the importance of student driven inquiry based models of learning and innovations like the Amino will help drive the science end of this. The creators of the Amino have had requests for the machine from all over the world. North America, China, France, and even schools in the Amazon Basin want it and from personal experience, I can see why!  As a research scientist, the idea that an elementary student can study biology the same way I did when I was in the tech realm is thrilling. After all, personal commuting got really exciting when it hit the garage so perhaps the same can be said for biology.

For more information on the Amino and how to contact them check out http://www.amino.bio!

Teaching The Chemistry of Electricity

As a fan of the Walking Dead, I often wonder what would happen if something catastrophic happened, and suddenly our power grids became non-functional. Would anyone happen to know how to generate power from chemicals using engineering or chemistry? For this reason and many more that are tied to teaching chemistry, I decided to explore electrochemistry and how the principles therein spawned batteries.

There is a lot there to explore – from electron behavior and their organization, all the way to redox reactions –  so we started the lab by talking about ions in general. A classic intro to electrochemistry experiments is to connect graphite plates to a battery and place them in various solutions to hydrolyze water. We talked about how the battery sends energy onto the graphite plates allowing water to be split into its individual elements, namely hydrogen and oxygen gas, which can be spotted by the bubbles produced. The students then compared the bubbling in a number of different solutions, both ionic and covalent. It was pretty easy to see that only the ionic salts were able to produce any significant amount of bubbling and thus had some kind of impact on the water. This led into a discussion of charge and the “ionization” of molecules in solution and of course, ionic bonds.

 

The last step I had them do was to connect their Daniell cells to a voltmeter so they could measure the voltage moving across the plates. I also asked them to switch the electrodes to see how the voltage changed so they could think about positive and negative voltages and its ties to whether or not a voltage can be generated spontaneously vs. non-spontaneously.

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Lots of good opportunities for practicing observational skills

The question of reaction spontaneity had been bandied about in a few other experiments, and this one was a part of an overall narrative on what makes a chemical reaction go. This is a question that the students ask me all the time. Normally this takes the form of feverish, excited questions about which combinations of chemicals would create the largest explosion, e.g “WHAT WOULD HAPPEN IF YOU COMBINE SULFURIC ACID AND HYDROCHLORIC ACID!?!?” (Answer: Not much…unless you add water or a base). We did a separate set of experiments that looked at various ionic solutions and their reactions with solid zinc in order to further demonstrate the nature of reaction spontaneity. This also led into a discussion of the activity series, a subject that was also broached in our Daniell cell experiments.

This set of experiments in electrochemistry represented over 2 months and well over 30 classroom hours. It got students thinking about a number of different chemical phenomenon, and all of them came out of these experiments with a general understanding of some or all of the following concepts: electrons, their orbitals, metals, reduction potentials, electricity, redox reactions, reaction spontaneity, and the activity series, all to varying degrees. In general, this provided a great introduction to many concepts that the students will explore more in high school. As an added bonus, if a zombie attack wipes out our power grids, they will have a basic knowledge of how to generate voltages using common materials!

A Deep Dive into Bacteria

There are so many ways in which studying bacteria is useful from an educational standpoint. It enables students to envision the lives and activities of the smallest and most ubiquitous forms of life on Earth and relate their activities to their own. All bacteria need to survive by getting resources, reproduce, and ward off prey. They also respond to stimuli, have a penchant for certain foods, and in our own bodies, outnumber our cells. Some after dangerous, some are innocuous, and all are mysterious given their microscopic size.

We started our adventure learning about bacteria by doing a quick web search to return general facts about them. I gave the students 20 minutes to uncover as many things as possible about them and then created a master list of bacterial informational. This included everything about reproduction to hand santizers to their ability to survive in space under the right conditions. After that, we began our first experiment by thinking about spices and the original purpose of spices in preserving food. I purchased 4 spices: cayenne, cumin, paprika, and black pepper. I gave the students a simple experimental goal and asked them to design an experiment to determine if spices inhibit bacterial growth.

I gave them petri dishes, glassware, agar, spices, and nothing else as the students looked up how to prepare the plates for the bacteria to grow. It was interesting for me to watch them struggle with things that as a scientist seemed second nature like how to dissolve the agar, how much of it to use, and when to apply the spices (in the agar directly vs. sprinkled on top). What resulted was a wide range of plates with different combinations of agar and spices. As a whole, they were all curious as to whether or not bacteria will grow and what it will look like. Several days later when they returned to lab, they saw that bacteria was growing on practically all the plates which disagreed with most of their ideas regarding how spices should inhibit bacterial growth. Some even saw growth on cayenne and cumin that looked like mold. As I told them, scientists can’t just assume that and that more analysis needs to be done so we saved those plants with the hope of purifying DNA and sending it out for sequencing.

For their follow up experiment, I wanted to them to mutate their bacteria. There are a great many ties to some very socially relevant problems regarding bacteria and drug resistance. I shared with them the case study of tuberculosis in Russia as a particular dangerous example (http://www.nature.com/news/russia-s-drug-resistant-tb-spreading-more-easily-1.14589). For this, I wanted them to take bacteria from their spice plates and replate it with various substances added that may confer resistance such as ethanol.

We’ve discussed ethanol in various capacities regarding their antiseptic abilities. They all know that it and isopropanol are used in products like Purrell that boast of killing 99.99% of bacteria. We discussed what that actually means and that if a trillion bacteria exist (a likely scenario for most surfaces), there are still millions that survive possibly with something genetic that will enable them to propogate back to their original numbers within a matter of days or even hours. Indeed the students saw that ethanol didn’t seem to inhibit growth when growth was stretched out for a long period of time and in a couple cases, encouraged growth. This was a truly fascinating thing to witness and taught them a valuable lesson regarding the life cycle and adaptability of bacteria.

Our final experiment consisted of our first steps in classifying bacteria with a simple gram stain. This tests for the presence of a carbohydrate called lipopolysaccharide, a molecule that helps bacteria to resist antibiotics. Some strains have it and others do not and through a series of dyes, the LPS containing bacteria are revealed colorimetrically. For the first time in this series of tests, I gave them an exact protocol. At first glance, following protocols seems counterinuitive to creativity but the ability to follow steps and get a result is extremely important to life. After all, when one is putting together furniture, it’s probably not a good idea to skip or veer from the steps. In addition, getting a result is not the same as getting a prescribed one and most students saw mostly gram positive but also several colonies of gram negative. This showed students that different types of bacteria were growing in their cultures. Ideally, we would have loved to sequence all the bacteria but unfortunately, DNA sequencing is still an expensive endeavor when done with many samples.

This series of experiments provided a valuable introduction to bacteria, their life cycles, and ability to survive and thrive in a variety of conditions. By doing this, we took the microscopic and brought it out to be seen by the naked eye so that we may truly see life on the smallest scales up close.