Tag Archives: theory

Matting down the grass

ImageI put on a stern voice every morning as I try to get my dog, Penny, to ‘go poop’ after her breakfast. She wanders about, obviously taking in something more than I can perceive. She circles a spot and smells intently making a slight move as if – no. That was the wrong place. She bounces away and starts mimicking a tracker again, following some invisible trail.

“Go Poop!”

I imagine that I am helping her.

Despite my frustration with the dog this morning, I start doing exactly the same thing later in the day. I just arrived at the library to do a bit of quick studying (for the Chem Praxis Exam), do some research (regarding a product I am consulting on), and check email before I head over to the Enterprise Center of Johnson County (ECJC) for a lunch seminar. Because I arrived just at opening, there is nothing but space here and only a very few people. Like my dog – or like Dr. Sheldon Cooper trying to find a good movie seat, I go through the same antics.

I’ve wandered around for a while looking, then tried a few possibilities, and even now I’m sitting at what is decidedly NOT the right place.

I need to get something (other than this) done, so I think I’ll try just one more place and get to work.



Posted by on June 12, 2014 in Personal Life, Uncategorized


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Evolution Animated

I just stumbled upon this cartoon for the first time today and I’m totally blown away. Sure, there are some things that could be explained better. There are a couple of moments when the illustrations could be a bit more accurate. But, overall, it’s a very good summary of the basic elements of evolution and pretty funny. (I wish I had made this!)

Have a watch and enjoy.

also, check out Kurzgesagt’s other animations on the Big Bang Theory, et al.

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Posted by on March 6, 2014 in Uncategorized


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Bill Nye, Popular Guy

Bill Nye was on The Bill Maher Show tonight.He’s been very popular the past week or two, appearing in a debate on evolution and the viability of intelligent design, he spoke about climate science with Marsha Blackburn on Sunday’s Meet the Press, and now Bill Maher.


Teddy Roosevelt and party at the tree, General Sherman.

On Maher’s show Nye was asked how it is that we know the world is older than 6000 years. Or to rephrase, “How could we know if a tree is older than 6800 years old?”

It’s actually a good question.  It’s a good question that gets to the crux of what Bill Nye was engaging Ken Ham on: how do we know things?

To address that big question, let’s talk about how we would answer the smaller one about the tree and see if that gives us any insight into how we gain knowledge…

Every kid has heard that the rings in a tree stump correspond to years that that tree lived. But how do we know? tells us that, “The new, large cells that are produced the following spring are easily distinguished from the previous year’s tree growth as a distinctive ring. A ring composed of a light part (spring growth) and a dark part (late summer/fall growth) represents each year’s growth.”

If you want to test this method for dating trees, the best place to start is to find a tree that you know was planted at a certain date. Perhaps in a housing development, something you planted yourself, something your parents planted, or better yet… get some trees to plant this year and come back in a decade or so. 

ImageOver the course of a decade or so, cut one of your trees or use an increment borer to take a sample that includes the pith (the centermost section of the tree). Now count the rings. While you’re at it, consult some records that can tell you the weather patterns over the time that this particular tree lived. With this information, you can now cross-reference your tree ring data with weather data. If you have bores from your trees over successive years, you can line your samples up and compare. Do the older trees have more rings? Do all of your trees have numbers of rings corresponding to their known age? Do you see any weather-related patterns in your ring spacing? Do all the trees have the same weather patterns for the same years?

What I’m proposing is, you can adopt the hypothesis that trees make a ring every year and then test it just as we described above.

If you do this, you’re doing science. You can see the data yourself, see how the data supports or refutes the hypothesis you made. You don’t need any outside help, you just need time and access to some trees (and perhaps the equipment that enables you to get your data).

Now ask yourself, ‘do you believe your data? Do you think it supports your idea? What experiment would give you the best opportunity to change your mind about this?’

Now do that experiment.

And call yourself a scientist while you’re at it.

You aren’t just answering the question that started this column. You are seeing how scientific method works and getting a glimpse into the way that we learn from the world around us.

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Posted by on February 18, 2014 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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Theory, Hypothesis, Fact

A conversation with one of my students got me to thinking about how science is done and the distinction of the ‘Theory’. Time and again this idea comes into question because the layman’s definition of a theory is very different from the one used in science.

There are a large number of deifinitions of ‘Theory’, but I think that the one that most people have in their heads is this: “an unproved assumption.” I tend to favor one more like this: “a working hypothesis that is considered probable based on experimental evidence or factual or conceptual analysis and is accepted as a basis for experimentation,” however, even this suggests much less conviction than a scientist would mean when they used the word. Personally, I think the inclusion of the word ‘hypothesis’ reveals this because this is something altogether different in the vocabulary of a scientist.

Webster again: Hypothesis – “a proposition tentatively assumed in order to draw out its logical or empirical consequences and test its consistency with facts that are known or may be determined.”

A working example of how these two terms relate…

ImageThe Germ Theory states that some micro-organisms cause some diseases. Someone working on Germ Theory may have a hypothesis that some microorganism ‘X’ causes disease ‘Y’. Germ theory is the overarching idea of organisms causing disease (fairly well established), the hypothesis is that ‘X’ causes ‘Y’.

This is a nice example, because there is a well-known series of experiments that outline what steps to take to test if this hypothesis is supported. Robert Koch ( outlines these in the 19th century and they keep his name, Koch’s postulates.

These postulates state that to establish that an organism is the cause of a disease, it must be:

  • found in all cases of the disease examined, while absent in healthy organisms
  • prepared and maintained in a pure culture
  • capable of producing the original infection, even after several generations in culture
  • retrievable from an inoculated animal and cultured again.

If all of these hold, then we say that this hypothesis has support.

Another hypothesis that has been under investigation lately is how the existence of the Higgs Boson could provide more support for the Standard Model (part of The Atomic Theory).  Recent News of this has been reported on BBC at : The AAAS provides this chart (you can think of it as the Periodic Table for elementary particles):Image


How does this ‘test’ anything? Basically, the Higgs Boson is required in order for the standard model to be correct, i.e. it predicts the existence of this particle. 

The hypothesis is that this particle exists as predicted, the Theory is the larger structure that encapsulates this hypothesis.

Altogether, the workings of the Higgs Boson/ Higgs Field underlies our conception of why atoms have mass. Although there is more to it, this also leads to a somewhat better idea of why there is gravity (another Theory).

Oh, and ‘Fact’. That doesn’t really exist. Maybe mathematics…?

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Posted by on March 14, 2013 in Uncategorized


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