Tag Archives: Chemistry

Thinking about thinking.

I’ve often taught Science as a way of thinking critically. That is, science education has (at least) two aspects. First, is the content knowledge. This is necessary because it’s not always necessary to reinvent the wheel. If every person had to start with their own tabula rasa and fill it themselves, without the help of those who came before, progress would be non-existent. Further- and this leads into the second aspect, prior knowledge provides a proving ground for developing critical thinking.

For example, every introductory biology class spends a decent amount of time talking about photosynthesis and cell respiration. Just memorizing the pathways is not enough to actually learn anything. In fact, it’s probably the quickest way to ensure that you don’t learn. Instead, it’s useful to talk about how this pathway was discovered.


von Helmont

Instead, it’s useful to talk about how this pathway was discovered. What was the question that people sought to answer? What was known /thought / assumed initially? What were the first (apparently unsuccessful) experiments done to address the question?


Jan Baptist von Helmont did one of the first good experiments to ask the question: Where does a tree’s mass come from?

He used a willow tree for his experiment and monitored the mass of the tree, the mass of the soil, and the mass of the water he gave it. Because the mass of the soil changed very little, while the mass of the tree grew enormously, he concluded that the tree’s substance came from the water he provided. In his own words, “But I have learned by this handicraft-operation that all Vegetables do immediately, and materially proceed out of the Element of water onely. ”

(It is notable that von Helmont recognized, in other experiments, that carbon dioxide was released from burned wood. He called this ‘gas sylvestre,’ referring to the Latin term for wood / forest, silva. This is important because the majority of a tree’s mass comes from the carbon dioxide in the air. von Helmont didn’t do just one experiment in his lifetime, after all.)

The importance of these historical experiments is that it allows the student to consider, ‘if I were in this person’s position, knowing what he or she did, how would I go about asking such a question?’

It was with this in mind that I came across this video on critical thinking, which I would say is the true value of science.


The topics we ask questions about depends on our interests. Perhaps today we are interested in where the mass of a tree comes from and we’ll be biologists. Perhaps most of the time we have a driving interest in the way that molecules interact, so we are primarily chemists. Regardless of the topic, we use the same critical thinking and experimental procedures to answer our questions, so we are really all scientists.




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Posted by on September 9, 2016 in Uncategorized


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Phlogiston, bloodletting, and the four humors

Phlogiston – You know, the stuff that’s in stuff. The burny stuff that’s released by fire?Screen Shot 2016-06-09 at 5.20.34 PM.png

Not familiar? Well, that’s because it’s isn’t a thing at all – anymore.

Screen Shot 2016-06-14 at 10.04.59 PMGeorg Ernst Stahl (1659–1734) lived in a complicated time for science. It was just being brought out of the dark ages in many ways and much of what he studied sounds completely foreign and backward to modern ears.

Primarily, Stahl studied the distinction between living and dead material. This vital force was supposedly the anima, or spirit, of a living thing, that gives it ‘agency.’ This was the same force, known as vitalism, that even Louis Pasteur believed was necessary for enzymatic reactions to proceed. Pasteur wasn’t wrong about much, but this one time he fell victim to the prevailing zeitgeist.

Stahl also proposed, in his De motu tonico vitali, that there was a ‘tonic motion’ in things that needed to be permitted for proper circulation of blood. When inflammation or other obstructions occurred, the problem was that this tonic motion was being blocked. One cure for these obstructions was the practice of bloodletting, which addressed the most easily managed of the four humors and was used to treat just about everything.

Although this may sound like a criticism of  Stahl, he was highly regarded as a professor and physician in his time and his work was critical in that it added an experimental element to scientific work. As a testimony to his reputation, he served as physician to both Duke Johann Ernst of Sachsen-Weimar and King Freiderich Wilhelm I of Prussia.

To get to the point here, he proposed the existance of a substance, Phlogiston, that was a component of many things that was released when that thing was burnt. Phlogiston was colorless, odorless, and weightless and it spoke to the question why something, once burnt, could not be burnt again. Ash, for example, was completely deflogistated matter. It contained no more phlogiston and was therefore impervious to further burning.

Additionally, air could fill with phlogiston, becoming saturated. When this happened, the principle of diffusion Screen Shot 2016-06-10 at 4.26.42 PMwould kick in to prevent further diffusion of phlogiston out of a substance. Recall that the basic principle of diffusion is that substances go from regions of high concentration to regions of low concentration (Actually, the random movement of particles will continue unendingly. The apparent result of this movement is that a non-random, concentrated source of particles becomes a random distribution that is effectively uniform. Actually, the particles are still moving, but the random distribution appears stable).

It sets up a simple equation for combustion of any (flamable) thing like this:

Phlogiston(s) + heat + something else –> Phlogiston(g) + ash + energy

Actually, it’s a great hypothesis. It does a servicable job in predicting the behavior of a combustible material in a simple system.  Imagine that phlogiston = carbon. This phlogiston / carbon exists in different forms around us: a waxy hydrocarbon chain in the candle, CO2 in the air, and as the backbone of sugars. However, it fails to recognize a couple of important things too: Mass doesn’t just disappear, the CO2 does have mass, of course, but it’s harder to appreciate. Also, flames don’t necessarily go out because of too much CO2 in the surrounding air, but because of a lack of something else, Oxygen.

However, it does fail to recognize a couple of important aspects. First, mass doesn’t just disappear during combustion. What remains as ash is lighter than the starting material.  CO2 is released and despit that fact that it is harder to appreciate, it does have mass. Second, flames don’t necessarily go out because of too much CO2 in the surrounding air, but because of a lack of something else.

preistly making o2It was by following in Stahl’s footsteps that Joseph Priestley discovered oxygen. Priestley had a knack for studying gasses. He was good at capturing and manipulating them in a controlled way. The figure to the left is an apparatus  of a type common to Priestly’s work, where a substance is heated (e.g., KClO3) to boil off a gas (e.g. O2) in a way that the gas displaces water in an inverted flask so that it may be captured in pure form.

Priestley found that oxygen purified in this way could refresh deflogistated (-perhaps, phlogistated?)26844_lg air allowing it to support combustion once more. It could also rescue an animal from suffocating in a bell jar (something that Preistley did enough that is sounds almost like a hobby of his.) The idea that air was composed of numerous components was a new one, and already Preistley was purifying these substances and demonstrating their requirement for life and for chemical reactions.

So, how does this change the way we needed to think about phlogiston?

It explains that mass doesn’t just disappear when burnt. It goes somewhere, it becomes something else (CO2). It changes the requirement for combustion from one considering the diffusion of matter out of one thing and into the air into a chemical conversion of something into something else.

Instead of the Phlogiston equation, we have the combustion reaction (either proceeding until completion or not):

Screen Shot 2016-06-12 at 8.51.00 PM

Phlogiston might still fit in as carbon if we are insistant, but now we see that something else is required as well: Oxygen.

Flames don’t necessarily go out because of too much Phlogiston (CO2) in the surrounding air, but because of a lack of something else, Oxygen.

The importance of Stahl’s work was not that he was right or wrong, but that Stahl was attempting to bring rigor and experimentation into science. In medicine and chemistry, Stahl believed in taking an empirical approach to his work. Ultimately, this was a stepping stone from the pseudoscience of alchemy to the real science of chemistry.


:istr makes a nucleophilic attack on chemy, resulting in the leaving group (Al) to leave and precipitate out.




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Posted by on June 14, 2016 in Uncategorized


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It crawls… It creeps… It eats you alive!

Compounded Interest

How money or value or perhaps even The Blob grows. In the simplest of all settings, interest can be as straight forward as, I’ll loan you $10 for a hamburger today, and you pay me back $11 on Tuesday. In this case, Wimpy is taking out a loan of $10 at 10% simple interest.

That’s great for a cartoon, but it’s not the case in most real-life examples of interest. In real life, a loan you take today might accrue interest every year, month, day, or even continuously. Although the last case is one of the most interesting ones as it deals with a special number ‘e’, I just want to address the more intuitive cases.


Clean Shaven Man

Let’s say Wimpy is keen on that hamburger today, but he won’t have any cash until Tuesday again. This time, his usual rubes are all cash strapped as well, so poor Wimpy has to go to a formal lender. This lender is OK with the loan, but as insurance against Wimpy’s ability to pay back the loan on time, he insists on compounding interest every week.

“Let’s be clear about this Wimpy,” his loan officer says, as he walks him through the conditions. “You can have your $10 today at 10% interest. The loan is due on Tuesday, and that will come to a total of $11. If you can pay it off then, great. But if you need more time, we will be compounding the interest – that means that you will essentially be getting a new loan of $11, at the same 10% rate.”

“OK,” says wimpy and leaves his mark on the loan document.


This is exactly the right way to think about it.

  1. initial loan is made: $10 at 10%, due in one week.
  2. If the loan continues, another 10% is charged on the new total.
  3. Week after week, this goes on until Wimpy can pay up or he’s referred to collections and they repossess his barbershop.


Mathematically, this takes the Principal (loan amount ) and multiplies it by 10% every week.

  1. week 0: $10
  2. week 1:$10 + 10% = Principal x 1.1                                                          -> $11.00
  3. week 2: ($10 + 10%) x 110% = (Principal x 1.1)2                                              -> $12.10
  4. week 3: (($10 + 10%) x 110%) x 110% = (Principal x 1.1)3       -> $13.31


This can be generalized by the formula:

Amount owed at time      t = P (1 + R)t

Where P = principal

R = rate (expressed as a decimal)

T = the number of times interest is compounded

(whether its days, years, months, whatever)

(10)(1+.1)3               -> $13.31


This goes for any compounded growth.


oooo – Air Conditioning!

The Blob arrived in Downingtown, PA in 1958. At first it was just something riding into town on a meteorite. But soon after, an old man touched it and got it stuck to himself. Steve McQueen comes to the rescue and gets the old fellow into town to see a doctor. Meanwhile, it becomes evident that the blob is not letting go, and is hurting terribly. Dr. Hallen decides to amputate, but before he can, the blob grows large enough to eat the old man, then a nurse, and then the doctor.

From then on, the thing just keeps growing. Let’s say it grows at a rate of about 50% an hour and use the same formula…


  1. hour 0: 100g
  2. hour 1:100g + 50% = Principal x 1.5                                             -> 150g
  3. hour 2: (100 + 50%) x 150% = (Principal x 1.5)2                                               -> 225g
  4. hour 3: ((100 + 50%) x 150%) x 150% = (Principal x 1.5)3        -> 338g
  5. hour 24:         ——-à                                                                       ->1,683,411g


You can really see how this thing gets huge fast (or at least massive, we never talked about the density of this thing).

Graphically, the blob’s growth looks like this:


One troubling thing is that this could also represent the balance on a credit card that isn’t attended to.

“It crawls… It creeps… It eats you alive!”

-Tagline, The Blob 1958


For a good explanation of interest, compound interest, and ‘e’ – check out Khan Academy’s lectures on this or this site that does a great job illustrating the difference between several types of interest.



Posted by on June 13, 2014 in Uncategorized


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strutting and fretting

ImageI just signed up to take the Praxis exams on Biology and Chemistry. These are content knowledge exams for those who are interested in teaching these subjects at the High School level. I’ve been teaching biology for several years and have been immersed in it for about fifteen years before that, so I’m not terribly worried about that one (although I may need to read up on some botany, as I largely ignore it in my classes – my apologies to any botanists out there.) Despite some low-level understanding of chemistry and familiarity with organic chemistry, it does worry me. There’s a lot of potential information to cover and I have about three weeks to get re-acquainted with the subject.

Why am I doing this? A good question. Because adjunct teaching is neither fulfilling (you never feel a part of something, but merely an add-on), nor rewarding (financially).

-Whoa! Wait a minute, doc. You’re not seriously thinking of teaching in a High School as a way to get paid well, are you?

No. Just paid.


Kansas has what it calls an ‘alternative pathway’  to a ‘restricted’ teaching certification. It’s designed for professionals with strong backgrounds in math and science, and are interested in a career change to teaching.

It’s heavily advertised on the radio here (at least on NPR, the non-profit, public radio station). However, most school administrators I’ve spoken with are unaware of the program.

Further, I’ve also heard that taking on educators with restricted licenses means that these teachers cannot qualify as

In order to get into the program (in addition to the classes you’ve taken in the subject’s content), you have to:

  • pass these Praxis exams to prove you actually do know the content and not just a dusty piece of paper from University.
  • Find a school that needs you
  • Get that school to provisionally hire you
  • Enroll in a program to earn your certification while you teach.

So far, I’ve signed up to take the exams and found a school that is willing to entertain the idea of taking me on so long as I can teach both biology and chemistry.


What is not entirely clear to me is whether these restricted licenses are considered ‘full’ licensure. The ‘No Child Left Behind’ Law requires all teachers to be ‘Highly Qualified’ and then defines that as:

Highly Qualified Teachers: To be deemed highly qualified, teachers must have: 1) a bachelor’s degree, 2) full state certification or licensure, and 3) prove that they know each subject they teach.

ImageCurrently, I am proceeding under the understanding that these programs do talk to one another and that the restricted licensure will not leave someone unable to meet federal demands.

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Posted by on June 1, 2014 in Uncategorized


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Cosmos – on the nature of light


In this weekend’s Cosmos, a lot of attention was spent discussing the properties of light. For something so apparently simple, there is a lot beneath the surface.

I wanted to talk about two elements of this episode in particular and provide some examples to explain things a bit better.


The first idea is that white light (what we get from out sun) is composed of all the colors. What we see as colors is actually the various wavelengths of light. We see short wavelengths as colors toward the red end of the spectrum; longer wavelengths appear as colors toward the blue end.

We also know that shorted wavelengths carry more energy. I like to tell my students to imagine a shoreline where all the waves are exactly the same height. If the length of the wave is shorter (measure from the top of one wave to the top of the next), then more waves batter the shore per unit of time. Longer waves mean fewer waves hit the shore in a given period of time. So, is more energy transmitted to the shore from the longer or the shorter waves?

Another part of this ‘white light contains all wavelengths of light’ comes from the way a prism reflects and refracts light. Any wave will change its direction as it goes from one medium (like air) to another (like glass) – it actually changes speed, which suggests a good analogy that I’ll explain in a second. How much it bends depends on the wavelength of the light.

The analogy is that of a car driving on a street. Imagine the car veering of the street at an angle to the right. As it leaves the road, it hits mud. The right wheel hits the mud first and slows down pulling the car harder to the right until the left wheel hits the mud. When that happens, the car stops getting pulled to the right and goes off in a straight line again. (the moment when the car is getting pulled onto a new course I’ve drawn a dotted line) The important thing to note is that the car was pulled right by the icky mud clinging to the tires more than the road does.









We can bend light by passing it through a glass (prism). The result is depicted in this album cover for Pink Floyd’s Dark Side of the Moon.

ImageWe can even bring the colors back together to produce white light again by using a second prism.


All this gets us to the idea that light can be dissected into a spectrum using a prism. This is the first type of spectrum described below.


The three types of spectra:

  1. continuous spectrum – emitted by a dense hot object
  2. emission line spectrum – the precise wavelengths of light emitted from a hot gas   (we can ignore this type of spectrum for the purpose of this discussion)
  3. continuous spectrum with absorption lines – the inverse of the emission line spectrum. When a cooler gas absorbs wavelengths of light from a hot source.


In the example discussed in Cosmos this weekend, we learned about the third spectrum. This is what is produced when a hot star emits light in a continuous spectrum. The cooler atmosphere of the star then absorbs some wavelengths of the light as it passes through. This is how DeGrass Tyson was saying that we could determine the composition of a star’s atmosphere from its spectrum. All we need is to do some experiments in the lab and see what absorption lines we see from different elements’ gas.

As always, the theory is cleaner than the reality, but let’s take a look at the spectrum from the sun. This image highlights some major bands and indicates which elements they come from.

Below the solar spectrum are some of the spectra from the sun’s constituents with major bands that correspond to those seen in the solar spectrum marked with (*).



Again, I apologize for this not being very exact, but it does at least communicate the idea of what was discussed on Cosmos in a little more detail.


  1. for a good explanation of spectra
  2. for the periodic table of light
  3. for the composition of the sun


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Posted by on April 7, 2014 in Uncategorized


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RNA World and the Origin of Life

In 2011  Martin Hanczyc delivered a TED talk in London on the topic of the origin of life, “The Line Between Life and Not-Life” that discussed some of his work with proto-cells. I participated in some online commenting on the TED page including a conversation about the origin of genetic material.

I wanted to point to the talk itself and include some of the posts below.

ImageFrom Ted Mozer III: ” Two questions about life and the origin of same on earth:
Is all know life on earth related and DNA (or even RNA) based?
If life was created on earth (and not from a seed that either arrived via an comet or the like or from an alien visit), why is the creation process a not a contining process. Did the creation process occur and then stop once life awoke? If so, why??”

My Reply: “You’re asking a very good question, Ted.
Think of it this way, imagine that life first originated by self-replicating molecules (probably RNAs) that found a nice safe home in some protocells that were floating around in the neighborhood – it doesn’t matter if this is absolutely true or not, just consider the abstract idea. The ‘food’ that these cells need is more RNA and cell membrane material, right? So, the things that these cells will ‘eat’ are exactly the same stuff that they, themselves, once were. If our new cells are successful, they are probably gobbling up all the other pro to-life material around them.
This does not mean that life could not have happened more than once, but if it’s a rare enough event, then the first things to get there are going to probably stay at the top of the heap.

It would be really cool to find organisms that use different genetic material – this would support multiple origin events, but so far, the universality of DNA argues that it was a one-off thing.”

A Comment by an unknown person: “Self replicating RNA? RNA and its components are difficult to synthesize in a laboratory under the best of conditions, much less out in a primordial mud puddle. This is highly unlikely. Yes, this was a miraculous “one-off thing.””

My Reply: “Yes, I agree, it is difficult to conceive of RNA as a self-replicating genetic material that also acts as an enzyme. Although RNA does currently act as genetic material, this role is restricted to viruses while DNA plays the major role of genetic material in all other organisms (including some viruses). Also, much of the enzymatic work in biological systems is currently carried out by enzyme proteins. However, there are still some RNA enzymes (ribozymes) extant, one of note is the ribosome – a protein / ribozyme complex with deep phylogenetic roots.

The idea of an RNA world as life’s origin has been around for some time, with suggestions of such an origin being proposed by Francis Crick, Alexander Rich and Harold White (among others) in the 1960s and 1970s.

Over the years, data has emerged supporting such a possibility including:

“The system, created by Gerald Joyce and Tracey Lincoln at the Scripps research institute in La Jolla, California, involves a cross-replicating pair of ribozymes (RNA enzymes), each about 70 nucleotides long, which catalyse each other’s synthesis.  So the ‘left’ ribozyme templates the synthesis of the ‘right’, which in turn templates the ‘left’ and so on, building each other via Watson-Crick base pairing. “

discussed in “Chemists edge closer to recreating early life”, Royal Society of Chemistry 2009.


“Clemens Richert and colleagues at the University of Karlsruhe have now shown that, without the use of enzymes, an RNA strand bound to a longer template strand of RNA can grow more than one order of magnitude faster than previously believed. This growth occurs in single nucleotide steps according to the base pairing rules of Watson and Crick.”

-From “Accelerating non-enzymatic RNA replication“, Royal Society of Chemistry 2005.

However, support is not proof. There will never be proof of what actually happened, but, then again, I might just be a brain floating in a jar somewhere…

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Posted by on October 13, 2013 in Uncategorized


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All I know about is a bunch of damn gangs that live in a round neighborhood

Professor Venus schools Arnold on the Pros, the New Boys and the Elected Ones – the three gangs who rule the neighborhood.

Now, get back to school.

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Posted by on August 26, 2013 in Uncategorized


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Chemistry for Biology Students

Even though this post is from quite a while ago, I thought I would link to it because I could have just as easily written it today…

The letstalkaboutscience blog posted this great infographic illustrating the abundance of each of the elements in the universe, the oceans, etc. I’ve brought that here – click to enlarge and explore in greater detail.


This week, we talked about the various bonds that atoms engage in to satisfy the octet rule. I also found this great, simple illustration of Na and Cl forming ions and bonding through Imagetheir difference in charge.

 On Tuesday we’ll finish up discussing bonding and talk about the four basic molecules of life (proteins, nucleic acids, fats and carbohydrates). Then we’ll finish up with this brief overview of chemistry by talking about how it fits into the big picture.

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Posted by on August 24, 2013 in Uncategorized


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Limited Time Promotion – 100% off

Until Sunday, my iBooks, The Thirteenth Labor of Heracles, In Parts and The Curse of Sisyphus are free in the iTunes Store. Click the titles for more information.


Can I hez Brainz?!!!


Posted by on July 19, 2013 in Uncategorized


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More on Oxygen Binding

A reader brought up some interesting points and uncovered some details about Oxygen binding that I wanted to update. You can find the transcript of our discussion in the ‘Getting Oxygen Where It’s Needed’ post below.

What I wasn’t able to post there was a graph of an Oxygen dissociation curve comparing caucasians with Sherpas living at high altitude (+4000m) and those living at sea-level. Surprisingly, the advantage Sherpas have in binding Oxygen at low partial pressure is completely lost at sea level. (see below)


Oxygen dissociation curve of the blood of (A) Sherpa living at high altitude, (B) Caucasians, (C) Sherpas living at low altitudes.

Presumably,  caucasian blood came from those living at sea level. It would have been great to have data on caucasians (or anyone, else for that matter) living at both high and low altitudes.

For those unfamiliar with data presented in this way, the horizontal axis starts at very low Oxygen concentration on the left and increases to the right. The vertical axis shows the amount of the subjects’ blood binding oxygen at each particular concentration. If the curve rises quickly on the left side, it means that the blood is picking up Oxygen even when it is present at relatively low concentrations in the air.


Data from:

Sherpas living permanently at high altitutde: a new pattern of adaptation.


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Posted by on July 10, 2013 in Uncategorized


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