Agarose Gel Electrophoresis of different dye mixtures illustrate how things of different electrical charge and size can be separated when applying an electric field and utilizing a molecular sieve (agarose).
A laboratory report contains a section devoted to Materials and Methods. This is important because it indicates how to repeat the experiment or exercise as closely as it was performed initially. It reads out a little like a recipe. In a recipe, we know what the input materials are. We often refer to the ingredients as reagents since we often expect some sort of reaction to occur in our scientific inquiry. But ingredients alone do not adequately aid in the reproduction of an experiment. The methodology is equally important. Therefore, the language of the methodology must be clear and precise. We must respect the order in which procedures occur otherwise the outcomes will be different. Below is a food recipe as an example of how culinary experiments are performed. With the provided recipe — a series of materials and methods– we can try to reproduce the dish. We can also identify areas that can be varied with respect to materials and the methodology that would alter or enhance the outcome. In science, sometimes the methodology is fundamentally flawed and must be altered. The transparency of the process is important because it permits a review by peers to review and judge the validity of subsequent results.
How to make Cambodian style fish with spicy tomato sauce
Heat 2 tablespoon of oil and fry fish, when it’s golden brown remove from wok.
Clean wok, heat 1 tablespoon of oil and fry garlic and onion about 1 minute, add celery, dried chili and tomato, stir and fry 4 minutes.
Add fish sauce, soy sauce, sugar and black pepper.
Pour tomato sauce over fish and garnish with spring onion, basil.
What’s different with these Materials/Methods?
Remember that we use metric units in science. Fortunately, volumetric measurements like tablespoon and teaspoon are standardly converted to milliliters. We’re not so lucky with other types of volumetric measurements, such as the Pint. One needs to be careful when speaking of pints since the imperial pint and the U.S. pint are different measurements. The dry pint obfuscates things further. Regardless of understanding these differences in measure, it is always preferable to speak in a standard term with scientific measurements reported in metric units. Let’s not even begin trying to fathom a conversion for a dash. Methods, in science, are not written out so plainly in a pointed form. The language is more descriptive. As we can see, there are many variations in outcomes for the included recipe. The methodology is a bit vague (lacking temperatures and standardization in cooking vessels). We have to remember that methodology in science should be much more repeatable.
I’ve split the class into 3 groups. Everyone in the group is required to take part. The assigned secretaries will post the results of the findings here on Openlab as a new post. We’ve seen that the City has passed a cap to large beverage sizes in an effort to curb the obesity epidemic. This project is geared towards putting the beverage cap into perspective by quantifying the caloric impact on our diet and thinking a little about the economics.
Group 1:
Identify the sizes of drinks containers currently available at 2 fast food venues and at 1 movie theater.
Identify the price of each type of beverage at each size for each location.
Convert the sizes from fluid ounces to milliliters.
Indicate the price per volume of each size.
Calculate the cost of drinking 1 of the largest size versus 1 of the smallest size every third day for 30 days at the least expensive venue.
Assume that the cost difference to the vendor between dispensing the largest and the smallest beverage size (before the cap) is 2%. Based on the sales price, how much money does the vendor lose when a customer purchases the smallest size instead?
Group 2:
Find the amount of calories that a male of 175 cm and 82 kg should be consuming on a daily basis.
Indicate the amount of calories consumed per meal considering there are 3 meals in a day.
If a 591 ml bottle of Coke is consumed at each meal, indicate the amount of calories left over for the meal.
If a 100 ml can of Red Bull is consumed at each meal, indicate the amount of calories left over for the meal.
If a 695 ml can of Four Loko is consumed in a day (not at each meal), indicate the amount of calories left over for the day.
Consider the individual drinks 1 bottle of Coke a day while consuming the regular amount of calories.
How much walking must he do to burn those extra calories in a day?
How much running in a week must he do to burn off those extra calories each month (30 days)?
Group 3:
Identify the sizes of drinks containers currently available at 2 fast food venues and at 1 movie theater.
Mayor Bloomberg’s “Soda Ban” has become a reality. The ban was proposed to help curb the epidemic of obesity in the city. But is it a ban? Not really. It’s a cap placed on the size of beverages. You can still buy 2 or more beverages if you like.
Previously, the Mayor had championed a general smoking ban in public spaces that included parks and plazas. This was largely based on the idea that it was in the interest of public health and other municipalities have seen positive outcomes. One example of such improvement over public health after a smoking ban comes from Pueblo, Colorado where a 27% decrease in heart attack cases resulted from a ban while surrounding municipalities had unchanged rates.
The large beverage cap was a discussion on a recent Science Friday. Do you think we will see public health benefits from a beverage cap? Check out the discussion on Science Friday and figure out where you fit in on the debate. Do you see this figuring in to ameliorating the obesity issue? Will the public truly benefit from this? What do you think about the marketing campaign and the formation of artificial grassroots movements that are sponsored by the American Beverage Association who benefit from the increased sales of their product?
This year marks the 50th anniversary of the publication of Silent Spring. In this book, Rachel Carson, described the bleak future that could possibly exist based on the changes to the environment that human activity was causing. Specifically, she warned about the dangers of pest control in the chemical called DDT. She urged the public to consider the consequences of using chemicals like this that were taking a toll on predatory birds, often apex predators in their ecosystems. While DDT is a neurological toxin specific to arthropods (intended to control mosquito populations), the chemical accumulated within the environment and would biomagnify in predatory birds where it was deleterious to various systems and resulted in a thinning of egg shells that caused the destruction of eggs. Apex predators often serve as sentinels for the health of the environment. As peregrine falcon populations became extirpated, the reality of a silent Spring was becoming apparent to the public. 10 years after the publication of her book, the United States government banned the use of DDT.
Banding of Peregrine Falcons in New York State. Hardly any falcons were banded in the 1960’s and 1970’s. After the ban of DDT usage in 1972, successful hatching of Peregrine Falcons and reintroduced Falcons increased the censused population of birds as evidenced by the number of issued bands on an annual basis.
The Christmas Bird Count observations in New York State indicate that there has been an increased rate of spotting wild Peregrine Falcons a decade after the ban of DDT usage in 1972. The increased amount of spotting during the CBC illustrates the enhanced health of the environment through the sentinel species.
The population of Peregrine Falcons has rebounded and they are no longer on the endangered species list. Many often adapt to city dwelling. Below is a picture of nestling falcons readying to fledge at Riverside Church.
Criticizing Silent Spring
Despite the success of the DDT ban and the improved healthiness of local environments, the book often found criticisms. Below is a review of the book from Amazon.com by a user called “Jane Orient”:
DDT was actually good for birds. There is a vast amount of material to refute assertions to the contrary. Bird counts in 1960 (after DDT) vs. 1941 (before DDT) showed 12 times more robins, 21 times more cowbirds, 38 times more blackbirds, 131 times more grackles, etc. Possible protective effects include: increasing plant yields; increasing protective cover; eliminating mosquito-borne bird diseases; and inducing liver enzymes that break down naturally occurring environmental toxins and carcinogens.
Sometimes we see claims that are true in nature that are actually “truthy“. The claim indicates that DDT usage was good for birds and cites some real facts regarding the increased number of birds. While these facts may be real, anyone with a shred of intelligence would point out that they are all prey species and that the decimation of predator species like the Peregrine Falcon resulted in a population explosion. Misleading people with true statements followed by unverifiable statements can often confuse and sway lay people who are not familiar with the argument. By beginning with true facts, the reviewer has augmented the subsequent baseless claims about toxicity. The greatest argument against Silent Spring follows from the same reviewer:
This is one of the most influential books of our time. Even now, it contributes to the death of one child every 12 seconds, mostly in the Third World, because it helped to bring about the ban of DDT with a resulting resurgence of malaria and other insect-borne diseases.
Rachel Carson herself stated:
It is not my contention that chemical insecticides must never be used. I do contend that we have put poisonous and biologically potent chemicals indiscriminately into the hands of persons largely or wholly ignorant of their potentials for harm. We have subjected enormous numbers of people to contact with these poisons, without their consent and often without their knowledge.
Additionally, the DDT ban in 1972 was for the United States. DDT was still manufactured in the U.S. and utilized elsewhere. DDT simply fell out of favor since it was becoming less effective.
Revisiting Silent Spring
As humans, we often have huge impacts on our local environments. The city is a densely populated space and we have created a waste issue. This waste has resulted in the explosion of invasive rodent species. As a consequence, public and private spaces have taken to using anti-coagulant baits instead of addressing waste and sanitation issues. The consequences can be seen below:
Necropsy photos from the New York Department of Environmental Conservation (NYS-DEC) of Lima (red-tailed hawk mate of Pale Male). Within a month of Lima’s death, 4 other hawks in Manhattan were found dead attributable to anti-coagulant rodenticides. One was a motor vehicle accident that probably occurred due to poisoning. This image is taken from a public document by the NY DEC.
The report that accompanied this photo and related hawk deaths in the month of March 2012 indicate that multiple types of anticoagulant rodenticides resulted in spontaneous hemorrhaging or bleeding caused by stress of egg-laying.
Above is a picture of a female red-tailed hawk nesting in Riverside Park. Below is a picture of her from the necropsy report. She died from hemorrhaging following laying an egg.
Necropsy report photo of female red-tailed hawk who died from hemorrhaging after laying an egg. The report indicates that her body contained multiple anti-coagulant rodenticides. The image is taken from a public document issued by the New York State Department of Environmental Conservation.
The Results section of a Lab Report is descriptive. It tells what is observed without analysis of the content. Graphical aids can help summarize the data. We often see the summaries as tables and graphs. Below is a common tabular summary of data that we come across on a daily basis.
The nutritional informational table from this box of Mac & Cheese provides a quick comparison of the contents in a serving and the recommended daily values. While a paragraph stating these values would be descriptive, the tabular form is much more effective at summarizing the information that is pertinent. As always, all figures (pictures, graphs and titles) should have proper labeling. Legends are also important to indicate abbreviations and symbols that pertain tot he data. The titles should be descriptive and all figures should be numbered in numerical sequence so the accompanying text can readily refer to the specific figure of interest. Titles and legends of graphical or tabular data should be informative so that they could be parsed readily without needing to search through the text of the Results section.
Results are written in the third person. They explain what was observed and should be stated in a fashion such as: “This happened…. The color changed to this…. Something happened in response to that…” Methodology does not play a role unless it is a result of the method. Simply re-iterating the methods is not appropriate.
That’s Empirical
Remember that observations are empirical. The scientific method is based on an existing corpus of knowledge. When we test our hypotheses formulated on a series of observations, we utilize experimentation to identify new observations. The use of our senses and experimentation yields data in the form of our observations. The Results section is about empiricism. It doesn’t take into account the analysis. If a tree fell in the woods, it is reported that a tree has fallen. How it might have fallen or why is irrelevant unless that was directly observed as well or a part of the experimental paradigm. Deciphering if it made a sound as it fell when no one was around to hear it would be a conclusion left for analysis and is not an observable report.
We can call any compound that adds H+ ions (a free proton) into solution an acid. Along with this, we would expect that any compound that would decrease the concentration of free H+ of a solution as a base. pH is the power of H+ of a solution. We define this power as a molar concentration of H+ in solution. This concentration invariably ends up being a relatively small number (though great in absolute numbers) and is expressed as a decimal number. Because the range of the concentrations is so great, we express these numbers as logarithmic numbers to avoid writing many 0’s after the decimal and to facilitate communicating the concentration. Since these numbers are so (relatively) small, we use the negative logarithm to describe this concentration.
Mathematically defined, pH = -Log10[H+]
The pH scale ranges so that anything below pH 7 is acidic and anything above pH 7 is alkaline. So a smaller number is more acidic. But didn’t we just state that something acidic contains more H+ ions? Remember, because we are dealing with a negative Logarithm, this means the concentration is higher.
Now you’re just talking crazy!
If we have a quantity that is 102, we know that translates into 100. Just as if we have a quantity of 104, we know that translates into 10000. Just as it becomes inconvenient to keep writing all those 0’s, it’s really impractical to write many many 0’s after a decimal. It’s really hard to talk about too! So we likewise will express numbers like 0.0001 as 10-4. A logarithm is the reverse function of an exponent. More precisely, the logarithm of a number is the exponent by which the base has to be raised to produce that number. Therefore:
Log10(0.0001) = -4
Log1010-4 = -4
So how do we define a solution that is pH 2? Well, we already decided that this solution is below pH 7 — making it an acid. But what does this mean in terms of H+ ion concentration?
Let’s work this out algebraically:
pH = -Log10[H+] Let’s bring the (-) over to the other side by multiplying both sides by -1
-(pH) = Log10[H+] Now let’s reverse the Log → base 10 remembering that logarithms are opposite functions of exponents
10-(pH) = [H+] Plug in the pH → molar concentration of [H+]
As we can now see, a solution of pH 2 is acidic because the molar concentration of [H+] is 10-2mole/L or 0.01M
You’re still talking crazy! That number is small!
It’s not a small number. Remember that a mole is 6.022 X 1023. That’s a very large number! Think about it! A solution of pH 4 is acidic, but if we plug in the formula, we realize that this is equal to 0.0001M H+ – less than pH 2 at 0.01M!
But let’s compare it to the [H+] content of H2O. Now I’m going to sound crazier! Water can be thought of as being in an equilibrium where some of the molecules are ionizing and deionizing. We can express this in 2 ways:
H2O ⇋ H+ + OH–
2H2O ⇋ H3O+ + OH–
So at any given point, a liter of H2O at neutral pH (7) has 10-7 moles of H+ ions. Incidentally, it also has 10-7 moles of OH– in solution. The second expression indicates the formation of a hydronium ion (H3O+) instead of a free proton in solution. So something that is pH 2 is a stronger acid than pH 4, right? Nope. That just indicates the amount of free protons in solution. It is more acidic but acid strength means something else. When we talk about strong acids, it means that it is more likely to donate a proton to the solution because it is more likely to ionize. Let’s look at the following:
HA ⇋ H+(aq) + A–(aq) Where HA is an acid dissociating in solution
If this dissociation is very high, then we say that it is a strong acid. Similarly, a compound like NaOH readily dissociates completely in solution and provides OH– ions that can readily remove H+ from solution –a strong base! We speak of dissociation in terms of rates and we express this as the acid dissociation constant, Ka. This is calculated using the concentrations of [H+] (proton), [A–] (conjugate base) and [HA] (non-dissociated) at equilibrium:
Ka = ([H+][A–])/[HA]
Just like the orders of magnitude we have when discussing pH, the rates of dissociation are more conveniently communicated on a logarithmic scale.
pKa = -Log10Ka
Think about it this way, if the concentration of the dissociated ions is very high, the numerator in the rate is very high → Ka is great. In other words, at equilibrium, the dissociation reaction looks more unidirectional than bi-directional as the compound is readily ionized:
HA → H+(aq) + A–(aq)
On this scale, we refer to anything with a pKa < -2 as a strong acid since it will readily dissociate in solution. This form of the dissociation constant is extremely useful in estimating the pH of buffer solutions and for finding the equilibrium pH of the acid-base reaction (between the proton and the conjugate base). We can estimate the pH by utilizing the Henderson-Hasselbalch Equation:
pH = pKa + Log10([A–]/[HA])
Titration of a Weak acid by a strong Base
So what happened in lab when we titrated our Acetic acid (a weak acid)? Check out this video from the Khan Academy that explains the change in dissociation of the weak acid as the protons are continuously removed from solution by the NaOH
On the first day of class, I engaged you in a discussion about science and why we were studying the topic. Some chose the “appeasement of the instructor” route by indicating that we “need to learn more about ourselves each day.” We eventually came to the conclusion that we are studying science because it is a required course. But this raised a new question, “Why is it a requirement?”
The polls
In order to come to an understanding of “why”, I conducted the following polls without revealing the results until both sets were performed. The first poll asked if you agreed with a quoted statement (without attribution). The second poll inquired about the appropriateness of any portion of the previous poll. The responses are below:
If it’s a legitimate rape, the female body has ways to try to shut the whole thing down. -W. Todd Akin
Akin Quote Follow-up. Those who chose “D” indicated that they did not find the question nor the statement offensive, but did not agree with the statement and therefore defaulted the last option. They also indicated that it was relevant to the course. The answer “C” is inconsistent with the results of the first poll.
After revealing the results, a few students came forward to indicate why they answered the way they did. There was the further clarification in the second poll that “D” was a default choice since none of the other options were viable. The minority who indicated the statement was TRUE did not come forth and defend it, while some who indicated FALSE stated that “It didn’t seem possible“. When finally attributing the source of the statement and it’s context, someone stated “I really think it’s FALSE now.”
I intentionally conducted both polls together without revealing the results in order to remove biases. For those who do not recall the context of the statement and the discussion, you can find it here or here and even here (as well as many other places). Option “C” in the second poll was also inserted as a consistency check. The responses were indeed inconsistent. Perhaps we did not understand the point of the exercise or the questions? In any case, the class discussion was fruitful. We also concluded, that the statement was actually 100% inaccurate with reality.
The “Why”
From this exercise, we learned that the class was not aware of any controversy. What seemed superficially political was in fact an issue of Science and deliberately illustrated our place in the political process. When we review the question “Why do we study Science?” we have to remember that Science is an integrated part of lives even if we don’t consciously think about it. Science and Biology is all around us. Laboratory science is a general education requirement. We learn science even if we have no interest in it because it is the basis for all that is around us. Most importantly, science changes the way we think. It challenges us to become more analytical and understand mechanisms.
In a New York Times exercise, Neil deGrasse Tyson provided an eloquent response to what he would do differently as President of the country that actually explains why we learn science.
When you’re scientifically literate, the world looks different. Science provides a particular way of questioning what you see and hear. When empowered by this state of mind, objective realities matter. These are the truths on which good governance should be based and which exist outside of particular belief systems.
Our government doesn’t work — not because we have dysfunctional politicians, but because we have dysfunctional voters. As a scientist and educator, my goal, wouldn’t be to lead a dysfunctional electorate, but to bring an objective reality to the electorate so it could choose the right leaders in the first place.
In short, we learn science to become conscientious members of society. This course is not about civic engagement, but I hope I’ve illustrated why we need to be aware of various concepts that are intertwined with our lives and our place in society.
Clarification
Any act of coercive sex is rape. There are no semantics that change this definition. Any use of modifier words like “legitimate” is not in line with an objective reality and is simply ignorantstupid.
This is the Openlab page for Dr. Seto’s General Biology I (Fall 2012) section that is part of a Learning Community. The theme of the Learning Community focuses on social responsibility. We will be learning about scientific inquiry and the methods in which we utilize concepts of science in our daily lives.
