What do you think would happen if a single V fischeri cell, which was secreting quorum sensing molecules, was placed in an extremely confined space? Explain your answer.

Watch https://www.ted.com/talks/bonnie_bassler_how_bacteria_talk?language=en

Answer the following questions in your own words!

1.According to the video, how does the number of cells in humans compare to the number of bacteria cells on a human being? How many genes make up the human genome? How many more bacterial genes are associated with the human body?

2. What special characteristic does the bacterium Vibrio fischeri have? What happens when Vibrio fischeri are at a low density? a high density?

3. Describe the symbiotic relationship between Vibrio fischeri and the Hawaiian bobtail squid.

4. What is quorum sensing?

5. True or False: the extracellular concentration of quorum sensing molecules increases in proportion to cell number.

6. What do you think would happen if a single V fischeri cell, which was secreting quorum sensing molecules, was placed in an extremely confined space? Explain your answer.

7. Define pathogenicity. How does bacterial quorum sensing play a role?

8. How are bacteria capable of intraspecies and interspecies communication?

9. Bonnie Bassler’s lab is creating anti-quorum sensing molecules in an effort to implement a “behavior modification” approach to therapeutics. What advantages does this have over the traditional use of antibiotics?

10. Describe the basic mechanism of action of these anti-quorum sensing molecules.

11. In the experiment Dr. Bassler described, what happened when experimental animals were treated with anti-quorum sensing molecules in conjunction with pathogenic bacteria ?

Which of the solutions that you just learned about seem to be most important in solving climate change? Why?

Please register for the Solve Climate by 2030: National Power Dialog & Power Dialog for the State of Alabama, REGISTER FOR THE WEBINAR (Links to an external site.) (press control and click, https://docs.google.com/forms/d/15Nn6x8PEL6DWFzI-GoqhxgAx2C-fBcckjDITVNJJJrk/viewform?edit_requested=true (Links to an external site.)) in support of the Solve Climate by 2030 (Links to an external site.) project. Write a one-page single spaced discussion paper that addresses the below questions;

-Which of the solutions that you just learned about seem to be most important in solving climate change? Why?

– Do you support moving towards these solutions?

– How could you ensure fairness and climate justice in carrying out these climate solutions?

– What do you see as your personal role, if any, in helping to advance these solutions?

What is Pseudomonas aeruginosa and why is it difficult to control and treat infections caused by this organisms?

Watch the Bonnie Bassler TED Talk on ‘How Bacteria Communicate”.

https://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate?language=en

Answer the following questions:

1. Explain how the human body could be considered 90% prokaryotic.

2. How does Vibrio fischeri control bioluminescence?

3. What is Pseudomonas aeruginosa and why is it difficult to control and treat infections caused by this organisms?

4. Define pathogenicity and virulence.

5. What are anti-quorum sensing molecules and what might they replace someday?

Bacterial Quorum Sensing: Go over the following Click and Learn HHMI Activity

https://www.hhmi.org/biointeractive/bacterial-quorum-sensing

Answer the following question

What sort of genetic mutations might affect the quorum sensing system? Explain.

Now you will perform some tests to determine whether the hypothesis is true or false and to see whether you can determine what the reactants and products might be for this reaction.

Introduction to Scientific Inquiry We could describe this reaction in words, for example: Sulfur dioxide (reactant) + water (reactant) → sulfuric acid (product) But more often, in science, these components would be described in terms of their chemical formulas: SO2 + H2O → H2SO4 The presence of the sulfuric acid in the rainwater changes its pH, making it much more acidic. Rainwater with a pH lower than 5.6 is called “acid rain.” A solution with a pH of 5.5 is ten times more acidic than a solution with a pH of 6.5. Acid rain is an important environmental problem and can have serious effects on both plant and animal life, in addition to causing deterioration of buildings. Living organisms also have many thousands of chemical reactions occurring every minute. In living organisms however, most chemical reactions require the presence of another molecule known as an enzyme. The enzyme is responsible for making the reaction happen at a rapid rate allowing life as we know it to exist. Most enzymes are proteins, and you will be studying enzymes and their effects on chemical reactions in an exercise later in the semester. Our goal in this exercise is to determine what happens during the combustion process of the candle by making some detailed observations, and by performing a few simple tests. If the combustion process involves a chemical reaction, there must be reactants and products. Something must provide fuel for the flame to burn (reactants), and one or more products must be produced as a result. Understanding this basic concept, we can develop a simple hypothesis that we can test: Hypothesis: The burning candle is composed of a material or materials (the reactants) that will be broken down into identifiable products during the combustion process. Now you will perform some tests to determine whether the hypothesis is true or false and to see whether you can determine what the reactants and products might be for this reaction. The results you collect are your data that will be analyzed later. Activity 3: Chemistry and a Burning Candle In this activity you will be trying to determine the different reactants and products that are consumed or produced while the candle burns. Although you are not doing the experiment yourself, you should read the steps below and make sure you understand what was done. The actual results for each of the steps will be found on the data sheet under activity 3 and you should write those results into your skill check worksheet 1. Be sure you are wearing your safety glasses. 2. With the candle still in the stopper, carefully relight the candle. 3. Using a pair of glassware tongs, hold the mouth of an ice cold 150 ml glass beaker above the flame for about 15-30 seconds. Remove the beaker and allow it to cool on the lab bench (Figure 2).

When a material is burned, the process is known as combustion. One question we are going to try to answer during this lab is “What is happening chemically when the candle is burned?

Can you actually see the sugar that is in the soft drink? Why or why not? Question 2-4: If you cannot see the sugar in the soft drink, how could you go about proving that it is there? Despite the fact that there is sugar in the bottle, you cannot simply see that it is there. So it is necessary to develop some type of test that will show the presence of the sugar. Some tests are qualitative and show us simply that something is there, while others are quantitative and can actually tell us how much of something is present. These tests can also help us to identify substances that we can see, but may not know what they are. In the next activity you will investigate more about what is happening during the candle burning process. When a material is burned, the process is known as combustion. One question we are going to try to answer during this lab is “What is happening chemically when the candle is burned?” Right now we are interested in finding out what is happening chemically when the candle is burning, and we will later find out how this relates to biology. Chemistry and a Burning Candle (Background for Activity 3) Chemical reactions are processes that convert one type of molecule to another. They are based on taking starting materials, known as reactants, and turning them into ending materials, known as products. The chemical reaction rearranges the chemical bonds in the reactant molecules and changes them into different molecules known as the products. Typical chemical reactions might be shown by chemical equations similar to the following sample ones: Example 1: Reactant A + Reactant B → Product Z Example 2: Reactant Q → Product H + Product J Chemical reactions occur around us all of the time in both living and non-living things. For example, the normal pH of rain in clean air is about 6.5.

How did your observations compare with those of others in the class? Do you believe that your observations are more or less valid than those of someone else in the class Why or why not?

Exercise 1: Introduction to Scientific Inquiry become a standard way for you to work whenever you perform an exercise in this class. 1. You should now spend exactly two minutes making observations about the photo of a candle on the data set sheet. These observations will likely be mostly qualitative ones, observations that are composed of descriptive words rather than numbers. These types of observations would include things like color, texture, shape and others. If you have a way of making quantitative observations you may also do so (for example, there may be a ruler available in your lab). You may also use drawings to help explain what you are observing (one picture is often worth a thousand words!). If you make any drawings, do your best to also explain what you are observing in words along with it. On the Skill Check worksheet found at the end of this exercise, write down as many observations as you can make during the two-minute period. Try to be sure that you are observing, not interpreting. Write down what you see, not what you think is happening, or why you think it is happening. 2. After you have made the observations of the candle photo, now open the link to a video of a burning candle on the data sheet. Watch the entire video and make observations of the burning candle. Be advised, that there are at least 100 different observations that are possible. Question 1-1: How did your observations compare with those of others in the class? Do you believe that your observations are more or less valid than those of someone else in the class Why or why not? (Answer these questions (and the others in this exercise) on the Skill Check worksheet). It is not unusual for two people to witness the same event, and yet to come up with different observations (i.e., think about two people that witness an accident, and come up with different versions of what happened). As a scientist, you will be trained to increase your skills in observation without interpretation. Once a scientist has made general observations about a phenomenon, these observations will generally lead to questions. It is best to keep the questions as specific as possible, as there may be a number of different and interrelated problems that underlie very broad questions. When a broad question is broken into smaller parts, each can be explored and tested, and the data later integrated to answer the original broad question. For example, • • • • Which part of the flame is the hottest? Do all candles burn the same? What is it that fuels the flame? What is happening chemically as the candle burns? Look at your observations of the burning candle. On your skill check sheet, write three questions that you would like to have answered about the burning candle. 1. 2. 3. Page 4 Exercise 1: Introduction to Scientific Inquiry Developing Hypotheses and Conducting Investigations Sometimes it is necessary to look deeper than just what we can see in order to understand how things work. Thinking back to the burning candle you observed in Activity 1, you were able to make a number of general observations about the candle and the burning process. But just because we can’t see something doesn’t mean it isn’t there or isn’t happening. For example, we see the flame of the candle, but we cannot directly see the chemical reactions that are responsible for creating the flame. These are the cases where scientists conduct investigations to learn more about a phenomenon. Activity 2: What you see is what you get…or is it? Look at the photo of the popular soft drink in the photo on the Data Sheet for Activity 2. Look at the ingredient label that is on the container. The sugar in it is sucrose (table sugar). Answer the following questions on the Skill Check worksheet Question 2-1: How much sugar is found in each serving of the soft drink? Question 2-2: What is the total amount of sugar that would be found in the entire bottle? (Hint: multiply the amount of sugar in one serving by the number of servings the bottle contains).

By day’s end, you note that all of the plants acquainted with organisms that would have of this type that you have seen have had purple flowers. been believed impossible only a few years Your hypothesis is ago.

Questions usually arise as a result of observations that have been made. We all make observations constantly, whether we realize it or not: the color of a friend’s hair, the fact that she just had a haircut, the color of your friend’s new car. The ability to make and record detailed observations is essential to scientific progress, and everything we learn in science is the result of observations that have been Page 2 Exercise 1: Introduction to Scientific Inquiry made. Observations can lead to questions that lead to more questions and so on; the two are obviously closely linked. In some cases, scientific questions can only be answered by making and recording observations, as it is not possible to manipulate the environment or system in a controlled manner. This is often described as observational or discovery science. For example, sending deep-sea submarines to What is a hypothesis? explore the ocean floor has resulted in the discovery of many unexpected life forms and A hypothesis is a possible answer or physical environments. Many attempts have tentative explanation for an observation or been made to interpret and explain all of the scientific problem observations made on these explorations, – A hypothesis must be testable and from these observations, many new – A hypothesis can be eliminated, but can never questions have been suggested for more be confirmed with 100% certainty detailed study. Entire new areas of scientific For example, after hiking through the mountains one research have sprung from these weekend, you observe a particular type of plant that has observations, and we now are intimately purple flowers. By day’s end, you note that all of the plants acquainted with organisms that would have of this type that you have seen have had purple flowers. been believed impossible only a few years Your hypothesis is ago. Much of observational science is driven “All members of the plant species known as by a goal or objective (i.e. ”Let’s find out what Plantus elegantus have purple flowers.” is down there?”); it may or may not be driven by a hypothesis. That does not make it a This hypothesis is testable; all you have to do is go out and continue to look for more of these plants and see what color less valid way to gain scientific information. Making observations is also critical to the success of experimental science. This type of science tends to be hypothesis driven and is the type of science most people think of when they think about a scientist performing an experiment in a laboratory. In this case, a question is asked, and a tentative explanation is proposed and subsequently tested by performing experiments and making observations in the process. As you will see, asking good questions and making detailed observations are not as simple to achieve as it might seem. the flowers are. You can eliminate the hypothesis (show that it is false) by simply finding one plant that has flowers of a color other than purple. But proving that the hypothesis is correct is more difficult. How many plants would you have to look at to prove that all of these plants have purple flowers? 100? 1000? A million? Showing that a hypothesis is 100% true is impossible! That is why biologists often use statistical analysis to validate a hypothesis… you can state with 99% certainty that this species of plant always has purple flowers, but never can be 100 % sure unless you have looked at every plant of this type on the Earth, a task that cannot reasonably be accomplished.

What does any of this have to do with biology or science in general?” The process of scientific inquiry is driven by the belief that natural phenomena are ruled by consistent underlying principles or rules that can be discovered and understood.

INTRODUCTION Happy Birthday to you, Happy birthday to you, Happy birthday dear student, Happy birthday to you. Mildred & Patty Hill, 1893 You have probably heard this little song many times in your life, accompanied, in most cases, by the burning of candles and the subsequent devouring of cake. But while looking at the burning candles, it’s unlikely that you’ve wondered about the physical and chemical process that is actually happening. It’s the answer to that question that will ultimately lead us to biology, with a stop off at chemistry along the way. We’ll come back to the cake later, and the combination of the burning candle and the cake will lead you to the ultimate biological goal in this exercise. At this point, you must surely be asking yourself “Am I in the twilight zone? I thought I signed up for biology class? Why are we talking about candles, cake and a birthday song? What does any of this have to do with biology or science in general?” The process of scientific inquiry is driven by the belief that natural phenomena are ruled by consistent underlying principles or rules that can be discovered and understood. Scientists conduct investigations for a number of reasons. They may, for example, wish to discover new characteristics of the natural world, explain recently observed phenomena, test the conclusions of prior investigations, or the predictions of current theories. Page 1 Exercise 1: Introduction to Scientific Inquiry The study of science has traditionally been broken up into a variety of different disciplines such as biology, chemistry, physics, astronomy and geology. Despite their differences, the methods of scientific inquiry that are used are the same, and it is often found that solving problems in one discipline requires integration of knowledge from several of the others. Knowledge of both biology and chemistry, for example, is often required to answer questions about the natural world, and it is often difficult to distinguish where one discipline ends and the other begins. Often presented as a single, linear series of steps known as the “scientific method”, true scientific inquiry is in fact much more complicated than can be described with such a simplistic approach. Scientists, in fact, perform many different activities in their attempts to understand and organize knowledge about the natural world. Conceptual principles and knowledge guide all scientific inquiries, and both current and historical knowledge influence the design and interpretation of scientific investigations. Scientists perform a variety of tasks in their pursuit of scientific knowledge. These tasks are often used numerous times, and in whatever sequence is necessary in order to understand the natural world (Figure 1)

Testing with cobalt chloride test paper turned color of paper from blue to pink Results of blowing into bromothymol blue in beaker Bromothymol blue in the beaker turned yellow after blowing into it.

Lab 1: Introduction to Scientific Inquiry Data Set You should work on these exercises on your own rather than in groups as written in the lab exercise. Your written assignment (Skill Check) that you turn in should use the data presented on this sheet, and then answers to questions should be written in your own words. Activity 1: Use the photo of the unlit candle below, and the video of the burning candle to answer the questions as you go through the Activity 1 exercise Birthday Candle unlit Candle dimensions: 70mm x 5mm Burning birthday candle video ; Use this video to make your observations of a burning candle for activity 1 https://www.youtube.com/watch?v=zkcucya5jX0 Activity 2: What you see is what you get…. Use the information below to answer the questions for Activity 2. 42 grams of sucrose Activity 3: Chemistry and A Burning Candle Results with cold beaker held over candle for 15 seconds Condensation appeared in the beaker Results with cobalt chloride test paper Cobalt chloride test paper turned from blue to pink. Results with beaker held over candle for 30 seconds Beaker is warm to the touch Results with bromothymol blue indicator in funnel Bromothymol blue turned from blue to yellow. Results with 250 ml beaker covering the candle Candle flame goes out in about 75 seconds Activity 4: The Candle-Human Connection Observations Results of plastic bag covering hand and arm. The person’s arm got sweaty, Testing with cobalt chloride test paper turned color of paper from blue to pink Results of blowing into bromothymol blue in beaker Bromothymol blue in the beaker turned yellow after blowing into it. Exercise 1: Introduction to Scientific Inquiry or In order to conduct investigations that help them learn about the natural world, scientists must have a collection of basic knowledge and skills at their disposal. This includes intellectual skills such as ways of critically thinking and approaching problem solving, a knowledge of science and mathematics, and physical and mechanical skills necessary to use the many types of analytical equipment and tools that aid in their investigations. This exercise will introduce you to the thought processes that are used to conduct scientific investigations. You will observe phenomena, ask questions, conduct simple investigations, critically analyze the information obtained, and then communicate that information to others. Along the way you should discover some basic principles of biology and chemistry that will build a foundation for future exercises in this course.

How did your observations compare with those of others in the class. Do you believe that the observations of others in the class are more or less valid than yours? Why or why not?

Skill Check Exercise 1: Introduction to Scientific Inquiry. NAME:______________Lab Section__________
Activity 1: Observing a Birthday Candle
Observations of unlighted candle (use data sheet photo to make observations
Observations of Lighted Candle (use video link on data sheet to open and watch video_
Question 1-1: How did your observations compare with those of others in the class. Do you believe that the observations of others in the class are more or less valid than yours? Why or why not?
Write three questions that you would like to have answered based on your candle observations of the burning candle.
Activity 2: What you see is what you get…or is it?
Question 2-1: How much sugar is found in each serving of the soft drink?
Question 2-2: What is the total amount of sugar that would be found in the entire bottle? (Hint: multiply the amount of sugar in one serving by the number of servings the bottle contains).
Question 2-3: Can you see the sugar that is in the soft drink while it is in the bottle?Why or why not?
Question 2-4: If you cannot see the sugar in the soft drink, how could you go about proving that it is there?

Activity 3: Chemistry and a Burning Candle

Observations (use data from the data sheet to answer these questions)

Results with cold beaker held over candle for 10 seconds

Results with cobalt chloride test paper

Results with beaker held over candle for 30 seconds

Results with bromothymol blue indicator in funnel

Results with 250 ml beaker covering the candle

For step 11 in the procedure, What happens to the candle? Why do you think this occurs? What might be present in the air that the candle would need to continue burning?

Activity 4: The Candle-Human Connection: Observations

Results of plastic bag covering hand and arm.

Results of blowing into bromothymol blue in beaker

Thinking Critically: Analysis of Data

Table 1: Analysis of Results of Activities 2, 3 & 4

Test Performed

Results of Experiment

OR

Was a
reactant consumed?

Was a

product produced?

Identity of reactant or product

Cold beaker/cobalt chloride test paper

Beaker held over candle 30 seconds

Bromothymol blue in funnel

Beaker covering candle

Plastic bag covering arm

Blowing into bromothymol blue

Preparation of Summary Statements and Chemical Equations

Summary Statement 1: The three products produced by the burning candle are ___________________, ____________________ and _____________________.

Summary Statement 2: The products produced by the human are ______________ and _______________.

Summary Statement 3: One reactant required for the candle to burn is _____________.

The equation for combustion of a candle

WAX + ____________ → _____________ + ______________ + _______________

The equation for cellular respiration in a human

FOOD + ____________ → _____________ + ______________ + Energy

Activity 5: Communicating the Conclusions

________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________