Tag Archives: physics

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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Finally: Basketball made interesting

I’ve never been much of a basketball fan. When I was in college I got behind my team (the Blue Hens) for two of their best seasons on record (1992 and 1993). It was easy to be a fan because I was going to UD at the time, which meant that we got free (?) or at least heavily discounted tickets – and all my friends were doing it, so …


However, youtube has actually turned me on to a couple brilliant uses for the sport. First, the simple one: Who doesn’t like watching what happens when you drop something mundane from a very high place?

I don’t actually know if this shot really merited a world record – although, really, how could it not? But it’s certainly fun to watch:

However, here’s where things get interesting. You’re all set to make the shot (drop, whatever) and you put a little spin on it. Natural enough. Enter the Magnus Effect:

Applying the Magnus effect to baseball demonstrates how the spin of a fastball affects its trajectory:

From Michael Richmond of, the horizontal flight path of a baseball with or without spin (in this case a 2200 RPM backspin)

Screen Shot 2015-08-29 at 12.00.47 PM

From the website of Michael Richmond: “The effect of air on baseball pitches”

Turning up the backspin to 3500RPM, the ball assumes a flat path ( actually rising in height as it approaches the plate.)

Screen Shot 2015-08-29 at 12.03.20 PM

Ahh. Physics.

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Posted by on August 29, 2015 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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History of the Solar System by Minute Physics

I’ve only recently discovered Minute Physics, a production of Embry-Riddle Aeronautical University. They state, quite correctly in my mind, that if you can’t explain it in a minute, you don’t understand it. This echoes a statement by Bob Doms, of the University of Pennsylvania, who once said to our class, “You need to always be able to explain your work in one sentence so your mother can understand.”

This is close enough, from Minute Physics, ‘Why is the Solar System Flat?”:

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Posted by on January 10, 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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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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A cute video about the beginning of time

From the Ted Ed site:

“How did the universe begin — and how is it expanding? CERN physicist Tom Whyntie shows how cosmologists and particle physicists explore these questions by replicating the heat, energy, and activity of the first few seconds of our universe, from right after the Big Bang.”

Lesson by Tom Whyntie, animation by Hornet Inc

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Posted by on June 24, 2013 in Uncategorized


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Release of ‘The Curse of Sisyphus’


The Curse of Sisyphus

The Curse of Sisyphus has been released and is available on the iTunes iBookstore. To celebrate the release, this, and its companion volume, The Thirteenth Labor of Heracles are both free until Sunday.

Zeus is not one to be trifled with. And Sisyphus has been a thorn in his side, defying him at every turn, yet escaping every punishment with uncanny cunning. But this time, the mortal has gone too far and Zeus has a special punishment befitting Sisyphus’ persistence.

The Curse of Sisyphus is the tale unlike others you may have heard about him before. Here you can find out exactly how Sisyphus defied Zeus yet again – and learn about the physics of motion, gravitation and orbit at the same time.

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Posted by on June 13, 2013 in Uncategorized


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The Bohr atom at 100


Bohr and Einstein having a smoke

One hundred years ago, in 1913, Niels Bohr published a trilogy of papers describing the atom in ways that we are still referring to today. These papers synthesized several previous ideas into one and presented the atom as a positive nucleus encircled by a cloud of electrons that stayed in very distinct orbits that were proportional to their energy (i.e.  electrons in low orbitals were lower energy than those that inhabited higher orbitals). 

This sounds like a simple concept, but it has some very important ideas nested in it. Probably most importantly is the idea that the orbitals are distinct. That is, there is no ‘between’ orbitals. Electrons are in one orbital or another, but never in between. Also, it takes energy input to raise an electron into a higher orbital and energy is released (as light) when an electron drops into a lower orbital. As a biologist, I find this most interesting and useful to think of when contemplating photosynthesis and considering how photons are absorbed by atoms in the reaction centers of chloroplasts. This is done by raising an electron to a higher … let’s say ‘energy level’. Once this happens, we have energy stored (at least for a while) in this electron. That energy can be used to do work, passed on to another atom or it can release the energy into the environment as light.


Bohr Model

Here’s a good representation of Bohr’s model with the different energy levels / orbitals indicated by the dotted lines labeled n=1, n=2 and n=3 .

Until now, this model has been a good, workable theory that seemed to fit  mathematically with what was observed indirectly. However, two really cool papers came out recently that have provided the first direct observations of atoms / molecules. In the first, Hydrogen atoms were observed using photoionization microscopy. This was done with a hydrogen at resting state (it’s lone electron in the lowest orbital), and in several higher energy states attained by providing energy to the atom using a laser. Below is a figure from the paper presented in Physical Review Letters 110, 213001 (2013). In each subsequent panel the electron can be seen in increasingly higher (distinct) orbitals.



Ok, I’m just going to come out and say it, ‘This is totally f’n cool.’ This means that Bohr’s totally theoretical model of a century ago has just been directly shown to be completely accurate.

But wait, there’s more. 

We’ve been using Bohr’s model and others’ ideas to model how multiple atoms come together to form molecules. Again, these structures have always been imagined from indirect observation. But, in the May 30 Science, this too has been directly observed using non-contact atomic force microscopy. Here we can see atoms in a molecule as well as the covalent bonds between them. 



Here’s to you Niels. Bang up work!! ImageNot to mention Dimas G. de Oteyza1,2,*,Patrick Gorman3,*Yen-Chia Chen1,4,*Sebastian Wickenburg1,4,Alexander Riss1Duncan J. Mowbray5,6Grisha Etkin3Zahra Pedramrazi1Hsin-Zon Tsai1,Angel Rubio2,5,6Michael F. Crommie1,4,,  and Felix R. Fischer3,4, for imaging the covalent bonds.

And A. S. Stodolna1,*A. Rouzée1,2F. Lépine3S. Cohen4F. Robicheaux5A. Gijsbertsen1J. H. Jungmann1C. Bordas3, and M. J. J. Vrakking for visualizing the orbitals of Hydrogen atoms.


Posted by on June 6, 2013 in Uncategorized


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The Curse of Sisyphus -Coming Soon to iTunes

ImageThe Curse of Sisyphus, from DownHouse Software is coming soon to iTunes.

Sisyphus’ is a tale of cleverness and cunning in which the malevolent King Sisyphus offends  and then repeatedly infuriates Zeus  until the King of the Gods is forced to personally curse Sisyphus to a punishment befitting his crimes: To slave beneath a stone, pushing it each day to the peak of a great mountain in the underworld and then have it come crashing down upon him, leaving him to repeat the task again … and again … and again, throughout eternity.

But Zeus has tried to hold Sisyphus captive before only to find that the clever human is not so easily trapped.

In this volume, Sisyphus taps into the vengeance of scorned brother, the wisdom of an oracle and the might of a demigod as he masters the rules governing gravitation and motion to escape his punishment.

Look for it in the iTunes book store this May.


Also, take a look at In Parts: A Tale of Fractional Zombies, free in the iTunes Bookstore now until Saturday!

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Posted by on April 23, 2013 in Uncategorized


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