In celebration of Mystery in Science

As many teachers do during the summer, I brainstormed some ideas and themes I wanted to discuss in the upcoming school year. To do this, I started comparing my experience teaching science with that of my life as  a researcher in R&D. I concluded that there was an element of mystery that drove my bench research that was decidedly missing in many science classrooms. For bench scientists, much of their time conducting research is spent controlling variables and perfecting models that seek to reduce as much mystery as possible but undoubtedly, some still remains. For students, that is a good thing. When mystery is properly integrated, it facilitates curiosity, a necessary skill for all students to have regardless of the subject matter.

Most labs in science classrooms are designed to reduce frustration associated with the mystery of lab work. The steps are clear or can be fairly easily elucidated, and the results are usually prescribed given that post lab questions are often tied to the achievements of a certain result. This predictability can  be easier for the student, especially those who aren’t comfortable with the idea of “not getting the right result.” This summer, I have been thinking about ways to resolve the differences between the true nature of mystery in science with the student’s desire for scientific predictability. This blog entry will not provide a decisive answer but rather highlight some of the places I am going to add elements of mystery to my lab curricula this year.

I am calling the first type “Mystery in Method.” The students start with the same set of ingredients and devise a way to get to a set end point. Example experiments could include giving each student a plant in water (elodea or chara) and creating a methodology to increase and/or decrease photosynthetic rate by altering the water environment. Obviously, the mystery is creating a testable protocol to follow to reach a conclusion which, in this case, would be some readout of photosynthetic efficacy, perhaps CO2 consumption or O2 production. I’ve already integrated Mystery in Method many times in public schools and noted that while there was initial hesitation and lots of frustration, with guidance and time, the students adapted to it and found a greater sense of engagement in lab by year’s end.

The second type is called “Mystery in Results”, and obviously the mystery appears at the end. This can usually be accomplished by giving the students a specific set of instructions to follow to look at some experimental read out of their experiment. One example would involve students growing bacteria from different sources and isolating their DNA. Then, the students could perform a restriction enzyme digest on their own samples to see how the sequences of the DNA differed by running the purified DNA samples on an agarose gel to examine the different lengths that result. Both the digest and the gel have their own specific instructions that must be followed, but the starting and ending points of the experiment allow for an element of mystery. Another example would be doing a simple chemiluminescence experiment with luminol, ammonium ferracyanide, hydrochloric acid, and sodium hydroxide to get a glowing beaker. Here the students don’t know what the end looks like but will get a truly cool looking result if they follow the steps accurately.

The final type of experiment is what I refer to as the “Cave of Mystery” and combines the creation of a protocol with the gathering of mysterious results. This experiment is the ultimate replicator of mystery as experienced by biotechnological researchers. It begins with an idea and not much else. It’s then up to the student to determine how to research the idea, devise a strategy to test it, determine what data to collect, and how to use what is collected to guide further experiments. This sort of experiment is challenging, time-consuming, often repetitive and ultimately, the best way to understand true scientific inquiry. I’ll write a longer post about navigating the “Cave of Mystery” as a means of science fair project creation during the winter, but for now these sorts of experiments are great long term projects.

By re-introducing science students to the power of mystery, it creates ownership of the experiments and really gives the students a chance to experience the ectasy and agony of being a scientist. So here’s to a wonderful 2015-2016 school year, and may you all embrace the mystery of discovery!


Do Spices inhibit bacterial growth?

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 survive by getting resources, reproducing, and warding off prey. They also respond to stimuli, have a penchant for certain foods, and in our own bodies, outnumber our cells. Some are 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 information. This included everything about reproduction to hand sanitizers 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 andspices. As a whole, they were all curious as to whether or not bacteria would grow and what it would 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 make assumptions 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 particularly dangerous example ( For this, I wanted them to take bacteria from their spice plates and replate it with various substances added that might confer resistance, such as ethanol.

We’ve discussed ethanol in various capacities regarding its antiseptic abilities. They all know that it and isopropanol are used in products like Purell 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 propagate 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 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 counterintuitive 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 observed by the naked eye so that we may truly see life on the smallest scales up close.

Acids and Bases for All Ages

When I taught high school biology and chemistry, I noticed that when the subject of the pH scale was broached, there were generally two responses: one group of students knew that it simply existed and the other group had a slight knowledge of it that stopped at “acids at one end and bases on the other.” I also observed that many college prep biology and chemistry courses omitted it, leaving it to be covered in AP chemistry.

There are some pretty good reasons for this. First of all, the relationship between pH and concentrations of acids and bases requires the use of logarithms and knowledge of molarity. In addition, the act of making solutions of a certain pH can be a very frustrating experience. It is also very confusing to think of atomic rearrangements in solution and for those of you who have never had the joy of adding acid or base to achieve an optimal pH, it takes a very careful hand and incredible patience; in other words, skills that many students struggle with, which is all the more reason for them to try it!

The first step to effectively teaching acid and base chemistry is to temporarily put math in the backseat and discuss gross observations regarding pH. In a well protected and ventilated environment students added sodium hydroxide (NaOH) caplets to a hydrochloric acid solution (HCl). The caplets bubbled and the test tube heated up dramatically which the students all immediately responded to with a sense of wonder. Eventually, they noticed that a white solid that didn’t look like sodium hydroxide appeared on the bottom of the test tube. It was more crystallized, and some students even observed that it looked like salt. Without teaching any theory, the students learned that some pretty interesting stuff had happened so at this point, we took a break to explain the reasons for the reaction they had just seen.

For those unfamiliar with chemistry, the reaction between NaOH and HCl produces water (H2O) and table salt (NaCl). When I told the students this, it was met with a series of baffled looks and confusion, and many asked if they could drink the resulting solution. They can’t, BUT the reaction did take two chemicals that were foreign or scary sounding and produced two completely innocuous materials that they were all familiar with. From there, we discussed what happened to the actual reactants and how they came apart in water, the breaking of those bonds being the thing that produced the heat. I compared the breaking of a chemical bond to the breaking of a pencil, and that whenever anything is broken a small amount of energy in the form of heat is generated, though this didn’t answer the question of how water and salt ended up in the solution.

I next wrote on the board that if the NaOH and the HCl come apart, it forms Na, O, H, H, and Cl (we initially ignored the charges and the O and H existing as a hydroxide ion). I then asked the students what combinations they could make with those elements,  and they quickly saw NaCl and H2O as two possibilities. From there, we discussed what chemically determines what an acid or base is. To do that, I brought out sulfuric, phosphoric, and acetic acid and showed them the chemical formulas. The students noticed that they all started with a hydrogen, and that the bases (lithium hydroxide, calcium hydroxide, potassium hydroxide) all ended with OH so that the H and OH form water, and whatever is left will combine to form salts. This ended our gross discussion of acid and base theory. We could now perform titrations to investigate the properties of the pH scale.

Titrations are used to determine the concentration of an unknown acid or base. It is performed with a long and expensive piece of equipment called a biuret that holds about 100 mL of an acid or base of a known concentration. An Erlenmeyer flask that contains a known volume of acid or base (if the biuret contains the base, the flask contains the acid and vice versa) is placed underneath the biuret. The flask also contains a few drops of a chemical indicator called phenopthalein which turns pink when exposed to an acid and cloudy for a base. As the students add liquid from the biuret into the flask, the indicator changes the color of the solution allowing them to see the pH changes in action.

The goal for this lab was for students to reach the equivalence point where the solution in the beaker below was neutral and could be confirmed with color as well as a pH meter or strips. At the equivalence point, it is possible to use a special formula that relates the concentration and volume of the base with that of the acid: Cbase x Vbase = Cacid x Vacid where Cbase is the concentration of the base (for us, 1 to 2 M), Vbase is the amount of base added from the biuret, Vacid is the volume of the acid (50 mL in our acid) and Cacid is the unknown. However, reaching the equivalence point is not an easy task. Given the logarithmic nature of the pH scale, the pH increases in a non linear fashion as the base is added. Initially, the biuret can be left open for seconds at a time with only a slight change in ph  but must be added drop by drop as the solution reaches neutrality. I had plenty of acid and base on hand, as the students needed many attempts to reach the equivalence point. They were frustrated, but their timing and aim improved over time. Eventually, all of them ended the experiment feeling elated with their accomplishment of reaching the equivalence point. In addition to teaching them a valuable lesson about pH and titrations, turning the stopcock of the biuret in time improves fine motor skills.As an extension of our original experiment, we also titrated a weak acid solution with a strong base and discussed the nature of a strong vs. weak acid.

After a few short sessions, students from ages 8-14 now have a working knowledge of the pH scale and the chemical make -up of acids and bases. They even learned a little bit about a log scale and titrations, and they had a great time doing it!

(Will add images soon)

A Guided Introduction to Experimental Design and Optimization

For students not used to creating their own protocols, the process of guiding them to do so can be arduous. Many students are used to being given a list of steps to follow, and the slightest deviations from the classroom norms are met with tremendous amounts of hesitation. After all, the act of composing a list of steps does not come naturally to many students but can be gradually introduced. At Acera, we frown on those “cookbook” style labs and seek to introduce the skills of invention and scientific inquiry into our lab projects. The introduction of those tactics to some students, however, is incredibly challenging, so the goal of our November experiment was to teach the basics of experimental design by having students alter the ratio of 2 chemicals to see how it changed the overall chemical reaction.


Potassium Nitrate, or “salt peter”, is a well known oxidizer or donor of electrons. When it encounters a reducer, such as dextrose or sucrose, and a flame, it produces lots of non-toxic smoke. Increasing the sugar slows the reaction to the point at which only a trickle of smoke that lasts up to an hour emerges. On the contrary, changing the nitrate concentration increases the rate of reaction and the smoke output. I asked students to design an experiment to test which ratio of potassium nitrate and dextrose produces the most smoke. The experimental process is simple: Combine a 5 part ratio of nitrate:dextrose with 1% sodium bicarbonate in a 600 mL tempered glass beaker and heat while stirring with a strong wooden stick at 250-300C for 15-30 minutes until the sugar is melted, dark brown, and paste-like in consistency. The resulting mixture is then scraped onto aluminum foil and allowed to cool. Finally, it is brought outside and the teacher can safely light the dried paste on a metal baking sheet while the students watch from a minimum of 5 meters back.


It is important to note that this is a very strong reaction, and there are many safety considerations. We mandate that students wear lab coats, a face shield or goggles, and two pairs of gloves during the heating. Also, when the time comes, the students must not light the reactions. The ignition and resulting smoke can emerge very quickly. It is also recommended that the teacher practice and demo this lab extensively in advance to gain familiarity with the overall process.


So, the question is, why perform such an extreme reaction when more mild ones can be substituted? After all, there are pretty easy ways for students to work with chemical ratios, including baking soda and vinegar. Simply put, the students want to work with something that is a little bit more reactive and will naturally pay closer attention when they are working with something that they perceive is “dangerous.”


Obviously, safety is a top priority, and our students have undergone extensive safety training that was detailed in a prior blog entry. The training was to prepare students for adverse events that may happen when working with chemicals that are beyond the norms of traditional school science. Having this lab tech training means that they can do things that are a little bit out of the realm of normal. A more dramatic reaction will really help them to understand the nature of the chemicals, the energy transfers involved, redox reactions, and the importance of experimental ratios in guiding research. Finally, the students will think it’s cool!


This is an important point, and once they start seeing the different reactions, they will attempt to optimize their ratios and experimental design to create even more smoke producing reactions. The streamlining of protocols is a very important skill for scientists to have and can be used for all future experiments. For the teacher, it is also crucial to remind students to keep a running log of their results and adaptions to their protocols. After all, the purpose of this lab is to optimize an experimental ratio and work on lab report writing skills.


Another facet of this experiment is allowing students to collect their own lab results. They know that they need to find the reaction that produces the most smoke, but the students are able to come up with different means of getting that information. Some measured duration, others took pictures and isolated the smoke hue, while still others measured the meters away from the reaction in which the smoke plume was visible. No matter what method the students used, they all collected a set of data points that they could use to compare the different ratios.

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Once the students had completed the ratios or exhausted their lab time, the conclusion was completed and a number of different topics were addressed. I started the post lab by asking the students what things the conclusion should contain. They mentioned discussing which reaction was the strongest and why, on a chemical basis, the reaction behaved the way it did. The student reactions were varied. They responded with a variety of tie ins to chemistry including energy generation, the science of redox reactions, and predicting reaction products between the nitrate, dextrose, and sodium bicarbonate.


From here, there are a number of jumping off points for future discussions including redox reactions, energy, and even the environmental effects of CO2/CO. As for the lessons taught in this lab, experimental design is something that can be worked on and perfected throughout the year. The more the students get exposure to true inquiry, the easier it will get. Like all skills, it needs to be reinforced and practiced to become second nature.

Teaching Energy as a Concept

Throughout this year, the underlying theme for all our experiments was chemical reactions and the importance of energy. Generally, in a traditional chemistry classroom, there are five basic types of reactions that are discussed and tangentially performed: single replacement, double replacement, combustion, synthesis and decomposition. In most curricula, the importance is placed on the names and details regarding the reactions without emphasis on the underlying reasons for why the reactions proceed. In essence, chemistry is the study of transformations and energy is a tremendous guiding force in ensuring reactions occur spontaneously yet energy is usually not discussed in this unit.

A simplistic view of a calorimeter

Calorimetry studies the energy generated in chemical reactions but is usually only reserved for AP Chemistry classes yet the general ideas behind this concept can be taught to virtually any age. In short, it is the study of energy in the form of heat. The process for conducting a calorimetry experiment is very simple: when a known amount of chemical is added to a known amount of water, the chemical may ionize (“come apart”) depending on its bonding and release energy into the water changing the heat of the solution. This change in temperature is directly proportional to the heat produced by the reaction of the added chemicals with water. To measure the energy produced, students can build a simple apparatus called a calorimeter using a beaker, test tube, or even a styrofoam cup, a lid or cap, and a lab thermometer though far more complex designs are possible. For an added math element, the students can actually calculate the heat in Joules produced by multiplying the change in temperature of the water (in Celsius), the mass of the water plus added chemical, and the specific heat capacity, which is a constant. For an added lesson in metric system skills, the students can convert the heat in joules to kilojoules (kJ), a more common unit in the reporting of energy or to kilocalories for a real world link to foods and energy. In addition, as either an introduction or extension activity, students can actually experimentally determine the specific heat capacity of water which is 4.18 Joules / (grams * Celsius).

The formula for the calculation of heat generated in reaction

In the Acera lab, we spent several weeks on this project. First, the students were given a class period of two hours to design and troubleshoot a calorimeter with common items they found in the lab or school. Some of the problems that the students faced in their calorimeter design was water leakage, how to add the chemical in an effective manner, and the biggest problem of how to avoid heat loss to the surrounding environment. Finally, given the tremendous amount of choice regarding size of hardware and limitation of reaction materials, the students need to be cognizant of choosing the best equipment for the job and for the reaction materials required. In order to begin, the students needed a cogent design but adapted the design if a problem arose as troubleshooting is a routine part of every experiment.

Several examples of calorimeters

Several examples of calorimeters

Once they feel they have a final optimized design, I gave them a variety of chemicals in which to experiment. This included ammonium nitrate, which endothermically reacts with water and lowers the temperature of the liquid. I also gave them dextrose, which does not ionize in water due to its bonding and thus, does not modulate the temperature. I also included the exothermically reacting chemicals lithium chloride, sodium chloride, hydrochloric acid, and sodium hydroxide. Finally, with my assistance, the students also reacted very small amounts (0.1 – 0.3 grams) of elemental sodium and lithium under a chemical extraction arm (or hood) to collect the gases.

Students performing calorimetry experiments

Students performing calorimetry experiments

Safety note: It is advised not to let the students react the elemental sodium and lithium unsupervised as they react with water very strongly. In addition, the sodium must be sliced very thin as spherical pieces can result in flash of light and a loud popping noise. While harmless, the reaction can be very startling. You could leave these out entirely but the very rapid reaction of these reactions can provide a lot of insight into the nature of the first column of the period table.

Lab notebook schematic of a calorimeter

Lab notebook schematic of a calorimeter

Once the the students have gathered all their data from the various experiments, the real scientific learning begun as they researched the chemicals to determine why they behaved the way they did. In our class, the concepts that this analysis touched upon was reaction types, ionic vs. covalent chemical bonding, energy creation from broken chemical bonds, and of course the nature of chemical reactions. By performing these experiments, they understood the ideas behind ionization and rearrangement of the atoms in the compound which included different reaction types. It is true that the upfront vocabulary behind the experiments was minimized but the #1 most common complaint I received as a teacher is that science education has too much complicated vocabulary. In this experiment, the students organically came by the various vocabulary with research which is similar to real life lab environments.

Lab notebook results page

Lab notebook results page

The only rules I have regarding the experimental analysis is that the students are done writing when they are no longer able to write original thoughts that they understand. This means that the students cannot repeat themselves and they also cannot copy down words or concepts that they can’t explain in their own words. Whenever students aren’t given some guidelines, there is the danger that they will begin copying down passages from textbooks that they don’t understand which is not productive by any means.

Cumulative results on the whiteboard

Cumulative results on the whiteboard

The more advanced students delved into the electron configurations of ionic vs. covalent bonds while some examined the physical chemistry of reactions and the students scientific mastery simply discussed the basics of endothermic and exothermic reactions and the links to the chemicals they worked with. As the students were writing their conclusions, I offered feedback and helped guide them away from quagmires. All students should however, discuss and suggest the reasons for the differences in energy and namely, why the addition of a chlorine ion to sodium and lithium lowers the heat generated in solution. Finally, when we performed this lab, I asked the students to write their results on the whiteboard so that they can compare their results to that of other students and to potentially discuss it in their lab notebooks.

Lab notebook results page

Lab notebook results page

In conclusion, this unit provided a view on the nature of energy and chemical reactions. From here, we moved into the optimization of chemical ratios in producing a more energetic reaction which I will discuss in my next blog. However, additional jumping off points can be an analysis of the individual reactions, food calorimetry, or even enzymes and energy in organic materials.

Reimagining Lab Safety

The beginning of every year in a school lab traditionally consists of a didactic read aloud from a handout on lab safety. Sure, the teacher can pepper the language with a bit of levity but in the end, it’s still a set of rules that students will memorize long enough to pass the requisite safety quiz to get into the lab. The teachers and students know of the importance but this doesn’t stop the fact that it is viewed as an impetus in getting to the lab and doing experiments. At Acera, we removed the teacher led aspects of the safety aspect to give the students more ownership of the rules of the lab. After all, they will be the ones using it and they are the ones that are the most unfamiliar with the ways of laboratory research. This made the process significantly more interesting, entertaining, and useful in giving students a groundwork in lab safety.

Our first day of training consisted of the development of a set of lab norms. To do this, the teacher simply asked what rules should be followed while in lab that are not standard for the classroom. Sample dialogue included:

Teacher: What is a good rule to have in lab?
Student: Don’t eat lab chemicals!
Teacher: Why is that a good one?
Student: Because they could be dangerous.

Given that most every student will ask about putting lab chemicals in their mouth, the students must obviously know why they can’t eat potentially hazardous chemicals. It is also important to ask the students why a certain rule is in place so that the consequences are clear.

After the rules discussion, we performed an interactive safety demonstration. With guidance from the teacher, the students acted out what to do in case of chemical fires, fire blanket, chemical burns on skin, eye wash and emergency shower use (which included activating both of those), spills, glove removal, the NFPA diamond and proper chemical handling, and appropriate personal protective equipment (PPE). By bringing in the student to demonstrate, they get to touch and use the equipment but in a non-emergency manner. This helps them to use their bodies to perform the actions and gain familiarity with the motions required to use the equipment.

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Given that ours is a K-8 school, we have a school set of safety levels for experiments that go from 1 (least hazardous) to 5 (most hazardous). Experiments at each stage have different safety considerations and students should show respect and maintain safety for everything we do even if it simply involves kitchen chemicals. After establishing the lab norms and all the safety practices, the students were then tasked with making a creative project on the safety levels and the considerations of each level. Some students made posters, puppet shows, and skits, both filmed and animated. This helped to create a more organic feel to the training and enabled them to be creative and to capture these “rules” and adhere them to their own personalities in a simulated lab situation. In addition, since many of these activities demonstrated what not to do, they experienced firsthand through fictional demos the results of veering away from the lab norms.

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Finally, the students took a safety assessment that they all must have scored a 100% on to take part in lab activities. The students will of course allowed retakes until they reach that goal. After achieving the perfect score, the students were then given a duplicate safety contract for both student and guardian to sign.

Feedback from the process has been very positive from the students and despite it being “safety training,” they learned and had fun doing it. They were able to gain a working knowledge of the lab and will be prepared for unexpected events. Ensuring that the students are comfortable and prepared is the first step in enabling some fascinating science in all of unpredictability and move away from the cookbook labs that are standard in K-12 science education.