Looking forward to Robocop at KU Edwards



Win Me!

This Friday evening (October 21) the SciFlix film will be the 1987 cult classic, Robocop starring Peter Weller. The film will begin at 6:30pm and FREE to attend for the public. We will also have free light refreshments including Roasterie coffees and candy. After the show, there will be an open Q&A with a panel of experts in computer science, prosthetics, law enforcement, and psychology to answer your questions about Artificial Intelligence, Programming ethics, the idea of ‘self’, and the state of technology in prosthetics and augmentation. We will finish the evening with drawings for KU T-shirts (and whatever else I can rustle up), as well as a grand prize OmniCorp T-shirt.


If you’re in the Kansas City Metro area, come and enjoy a free date night with your brain. Join us on Meetup, see our future offerings at the KU Edwards website, or just send an RSVP and show up!

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Posted by on October 18, 2016 in Uncategorized


Martha Chase, Max Delbruck, and the American Phage Group

Martha Chase is a bit of an enigma. Her career started promisingly enough working in a productive field amongst productive scientists; but following her PhD, her health precipitated setbacks in both her career and her home life from which she did not recover.

She received her bachelor’s degree in 1950 from the College of Wooster. Later that same year, she joined the laboratory of Alfred Hershey in Cold Spring Harbor to work as his lone laboratory assistant asking questions about the mechanisms of life using a viral model system. The virus they used was the bacteriophage T2, a fascinating conglomeration of proteins and DNA that specifically infects bacteria. Through her work with Hershey, she became linked to the remarkable influence of a network of biologists nucleated around the German-American biologist, Max Delbrück, called the ‘American Phage Group.’

Delbrück, himself a Nobel Prizewinner, led a rich intellectual life amongst an elite group of academic luminaries. The Chemist, Karl Friedrich Bonhoeffer, was a close friend and mentor to him during his younger years steering him into the study of physics where he became associated with Wolfgang Pauli and Niels Bohr. It was Bohr’s influence that put him on the path to Biology through its relationship with Physics. Again, not to be on the outside looking in, he became assistant to Lise Meitner who had worked with Nobel Laureate Otto Hahn to discover fission of Uranium (Meitner is often regarded as missing out in the Nobel for anti-Semitic reasons), and with Otto Frisch, who recognized that fission must be accompanied by a massive energy release tying it to both the potential for energy production and a potential massive destructive power. Delbrück initially came to the States to study genetics in drosophila, but made a deeper mark studying viruses, eventually earning a Nobel Prize in 1969 for his work with Salvador Luria and Alfred Hershey, largely thanks to the diligent work of Martha Chase.

Many of the Phage Group’s members are credited with landmark advances in our understanding of molecular biology. Luria, working with Delbrück, demonstrated that mutation of bacteria occurred in a strictly Darwinian sense, i.e. that bacteria could mutate to resist viruses even without the virus being present. This is a fundamental distinction from Lamarck’s notion that evolution was driven by need, rather than by selection of completely random events. It was at this time that he took on and trained his first PhD student, James Watson (who also did something important – I forget what).

In 1949 Renato Dulbecco came to Caltech to join Delbrück’s group with the focus of understanding how some viruses would lead to tumors. Along with David Baltimore and Howard Temin, Dulbecco shared the 1975 Nobel Prize for discovering how these viruses would reverse transcribe their RNA genome into DNA and integrate it into the host’s chromosome.

Matthew Meselson and Franklin Stahl, also working with the phage group, demonstrated that DNA replication is a semi-conservative process retaining one strand from the ‘parent’ DNA and one ‘new’ strand synthesized as a complement to the ‘parent.’ This work did not earn them a Nobel Prize, although it provided early support for Watson and Crick’s DNA structure and remains a landmark experiment in biology that every student is taught.

As evidenced by the sheer number of Nobel Prizes shared by members of this group, the Phage Group and its associates dominated the fields of bacterial genetics and molecular biology. But before those experiments were performed and Prizes collected, the physical molecule carrying genetic material was yet to be discovered.


Frederick Griffith (see reference 1)

Frederick Griffith was the first to point the way to this molecule by showing bacteria’s mysterious ability to transfer new characteristics (Darwin’s Traits) between organisms. But, tragically, left his work incomplete due to his death in London during WWII. A number of stories exist regarding his whereabouts when he died. Regardless of its veracity, I personally like the one that suggests that he was working late in the lab when it was bombed by the Nazis.


Before his death, in the 1920s, Frederick Griffith demonstrated that some element of a bacterium, that is released upon its death, was sufficient to carry genetic information from one strain of bacteria to another. Specifically, he demonstrated that ‘smooth’ pneumococcus, which secreted a glycocalyx, could transfer this trait to ‘rough’ bacteria that lacked the glycocalyx. Clinically, this was very important because the rough type pneumococcus was easily handled by the immune system, while the smooth type colonized the heart and killed the host. He called this element the ‘Transforming Principle,’ but died before he could identify it specifically.2



see reference-2

Experiments showing that the transforming principle was probably DNA were performed by Avery, MacLeod, and McCarty at the Rockefeller Institute in 1944. Despite being both elegant and thorough, many thought these experiments lacked the appeal needed to be convincing.


Knowledge of Avery’s work supported the case for DNA as the genetic material, but Protein remained a persistent contender because, with its 20 physiological amino acids, its capacity to carry the information associated with genes seemed more reasonable. DNA, on the other hand, was an arrangement of only four bases, a simplicity that obfuscated its coding potential. One compromise hypothesis suggested that perhaps DNA served as a scaffold for the information-carrying proteins, although Avery’s experiments showing that protein-free DNA preps could transform bacteria strongly argued strongly against this model.

So, the issue remained to be effectively demonstrated denying Avery and his co-workers Nobel. A more satisfying answer, reaffirming Avery’s discovery, was to come from the ever-productive phage group in the hands of Martha Chase.


Martha Hershey and Alfred Chase (see reference 3)

Working together, as laboratory technician for Alfred Hershey, the two performed their eponymous experiment in 1952 with the purpose of identifying what served as the genetic material in phages.


Hershey intended to use the T2 bacteriophage to assess this question, in part because it contained no other molecules such as fats or sugars, making it an exceedingly simple model (See illustration of method, panel A) but also because electron micrographs already hinted of protein ‘ghost’ particles left outside of the cell while new phages were being assembled within. Indeed, by involving only DNA and unglycosylated proteins, it was possible to label the DNA and Protein elements individually using radioactive Phosphorous-32 to mark the DNA and radioactive Sulfur-35 to mark proteins. These isotopes worked well because they were trackable by following the radioactivity, while each was specific to its target due to the natural, exclusive distribution of Sulfur and Phosphorous in Protein and DNA, respectively.


images 7.01.06 PM.jpg

A bacterium with phages attached to its surface and phage capsids assembling within the cell. (attribution unknown)

The basic experiment was simple in theory. T2 bacteriophage was grown in media containing either nucleotides with Phosphorous-32 or amino acids with Sulfur-35. In the first condition, only the phage DNA was radiolabeled. In the second condition, only the protein was labelled (see illustration of method, panel B). Once the phage was prepared, it was allowed to attach to fresh bacteria for a time period known to allow for the passage of genetic material. At this time, the bacterial cultures were moved into a kitchen blender and pulsed to remove the material that did not enter the host cells (the ghosts). Centrifugation permits the separation of the ghosts and any other viruses in the supernatant from the (infected) bacterial cells. The only thing remaining was to check to see where the radioactive elements were: the supernatant fraction that did not enter the cell, or within the cell, where the genetic material was (see illustration of method, panel C). Like most experiments, much of the work invested in the project occurred prior to the actual experimentation in order to optimize each condition.4



Screen Shot 2016-10-03 at 10.31.09 PM.png

Illustration of Method for Hershey-Chase Experiment

The answer was clear, Radioactive Sulfur was never found inside of infected cells, only in the supernatant. Radioactive Phosphorus was overwhelmingly found within the cell. With this elegant experiment, the question was answered, and DNA was widely recognized as the genetic material setting up the next, obvious Nobel Prize: what is the structure of DNA? And does this structure reveal any of its properties?


At the University of Southern California, Martha continued to study phages under Giuseppe Bertani (Joe to his friends), ultimately following him to the Karolinska Institute in Stockholm, Sweden where she completed her PhD thesis on “Reactivation Of Phage-P2 Damaged By Ultraviolet Light” in 1964.5,6,7 Her obituary, which is one of only a few primary sources of information on Chase, describes life after earning her PhD as plagued with personal troubles arising from short-term memory loss that likely contributed to the end of her scientific career and possibly her marriage.

Despite the fact that this work represented the accomplishment of Hershey in the 1969 Nobel Prize along with Delbruck and Luria, Chase did not share in this honor. As a technician in the lab, it may be that her hands performed many (if not all) of the Hershey laboratory’s experiments, but technicians are rarely (if ever?) included in the Prize on the assumption that it is unlikely that they are major theoretical contributors to the work. Her name, however, will forever be associated with this experiment, serving as a lasting reminder of her contribution to molecular biology.


  1. Photograph of Frederick Griffith, photographer unknown
  2. “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Deoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III.” January 1944. Exp. Med., 79: 137-158.
  3. photo: Martha Chase and Alfred Hershey, 1953. Attribution unknown. I found both of these images at
  4. Link to Hershey and Chase’s J. Exp Med paper:
  8. See for a listing of Nobel Prizes, Biographies, Acceptance Speeches, and even games.
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Posted by on October 3, 2016 in Uncategorized


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The Book Scavenger

Screen Shot 2016-09-11 at 9.56.03 AM.png>Spoiler Alert! Or Trigger Warning, if you are emotionally tied to storytelling. This post will discuss some of the secret codes used in a book. If you haven’t yet read ‘The Book Scavenger,’ I suggest that you do so. Until that time, don’t read beyond the following paragraph!<

I picked up a copy of The Book Scavenger by Jennifer Chambliss Bertman from Denver’s Tattered Cover Book Store so that my wife would have something to read on the scant downtime she had during the AMVA Conference held there this past summer. It was advertised as the One Book One Denver selection for 2016.

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Posted by on September 11, 2016 in Uncategorized


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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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Lookin’ fit there buddy! *wink*

I want you to hear me out. I’m going to say something that you might find unbelievable.

It’s been a long slog to get here, but you’re a middle-aged businessman (possibly lawyer) making a solid mid-six figure salary (not counting investment returns, of course). You go to the gym –  your trainer says you’re really fit – and you just left your second wife, because (let’s be honest here) she was really cramping your style.

You haven’t had a clean shave for months now, but your secretary says the stubble looks hot despite (or because of?) the touch of grey. What you’re really needing now is to ‘complete the look.’  Screen Shot 2016-09-06 at 9.39.49 PM.png

But where do you go? And what’s it going to cost you?

Roll up your sleeves, tough guy. It’s time for some manly online shopping.

Ready for the unbelievable part?

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Posted by on September 6, 2016 in Uncategorized


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Link to my review of Kubo

See that on my other site: 100filmsin100days

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Posted by on August 24, 2016 in Uncategorized


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Understanding Exponential Decay



{              Special Intro Note:

OK, this post has been a pain to transfer from my original writing into WordPress. A lot of the complication originated from the use of super- and sub-scripts in the mathematics, it’s also meant that I got pretty irritated in reworking it so many times that now I haven’t gone back to ensure that the math is correct anymore.

I’m saying all this because I want to say, “don’t take my word for anything here if you believe I’ve made a mistake, let me know and I’ll check it out when I have less frustrated eyes.”}



Exponential decay is a concept integral to determining the age of natural substances when initial and final concentrations are known for a specific unstable radionuclide. There are largely stable ratios of individual elements and their isotopes in the environment. Some of these isotopes are stable, and some are not. Unstable isotopes will break down over time. Although one could never predict how long any given atom will exist before it breaks down, the extraordinary number of atoms in any sample and the predictability of their decay into new atoms allows us to compute how long a substance has existed since new atoms were being incorporated (i.e. the time of death). By looking at these ratios over time, we can make very accurate measures of the age of a sample.

Screen Shot 2016-08-12 at 10.56.05 PM.png

Different decay rates of various isotopes provide an array of measuring sticks for us to use.

Some examples:

32P has a short half-life of 14.29 days and therefore has to be made synthetically for lab use.

35S is formed from cosmic ray spallation of 40Ar in the atmosphere. It has a half-life of 87 days.

14C is formed cosmogenically by the reaction 14N + 1n → 14C + 1H. It has a half-life of 5,730 +/- 40 years.

40K It has a half-life of 1.248×109 years.

Some elements have a fairly straightforward decay path. For instance, Cosmic rays (high-energy protons and atomic nuclei) from outside of the solar system bombard the atmosphere striking atoms. When this occurs, the atoms are fractured into some Helium, some protons, and some neutrons. When these neutrons strike nitrogen 14N it displaces a proton and is converted to 14C. 14C then decays back to 14N by one neutron breaking down into a proton and electron which is emitted from the atom (beta decay) with a half-life of 5730 years (note that during formation, a neutron takes the place of a proton. Then in decay, the neutron breaks down resulting in a proton, which stays and the emission is an electron, which is why the atomic mass does not change from 14 in either direction).

n + 14N –> 14C + p+

14C –> 14N + e

Speaking Mathematically…

Exponential decay occurs in a general exponential function

Screen Shot 2016-08-12 at 11.03.16 PM.pngIn other words, as x increases, f(x) decreases and approaches zero. This is exactly the type of relation we want to describe half-life. In this case, we want a = ½, so that we have the relationship

Screen Shot 2016-08-12 at 11.02.24 PM.png

Rewrite in terms of half-life. Of course, our function does not depend on generic variable x, but time, t.

Screen Shot 2016-08-12 at 11.02.27 PM.png

    • Simply replacing the variable doesn’t tell us everything, though. We still have to account for the actual half-life, which is, for our purposes, a constant.
    • We could then add the half-life t1/2 into the exponent, but we need to be careful about how we do this. Another property of exponential functions in physics is that the exponent must be dimensionless. Since we know that the amount of substance depends on time, we must then divide by the half-life, which is measured in units of time as well, to obtain a dimensionless quantity.
    • Doing so also implies that t1/2 and t be measured in the same units as well. As such, we obtain the function below.

Screen Shot 2016-08-17 at 8.08.42 PM.png

Incorporate initial amount. Of course, our function f(t)f(t){\displaystyle f(t)} as it stands is only a relative function that measures the amount of substance left after a given time as a percentage of the initial amount. All we need to do is to add the initial quantity N0.{\displaystyle N_{0}.} N0. Now, we have the formula for the half-life of a substance.

Screen Shot 2016-08-17 at 8.10.43 PM.png

Solve for half-life. In principle, the above formula describes all the variables we need. But suppose we encountered an unknown radioactive substance. It is easy to directly measure the mass before and after an elapsed time, but not its half-life. So let’s express half-life in terms of the other measured (known) variables. Nothing new is being expressed by doing this; rather, it is a matter of convenience. Below, we walk through the process one step at a time.

Divide both sides by initial amount N0.

    • Take the logarithm, base 1/2 of both sides. This brings down the exponent.

Screen Shot 2016-08-17 at 8.13.53 PM.png

    • Multiply both sides by t1/2 and divide both sides by the entire left side to solve for half-life. Since there are logarithms in the final expression, you’ll probably need a calculator to solve half-life problems.



Example Problems

  1. If you start with a sample of 600 radioactive nuclei, how many would remain un-decayed after 3 half lives?
  1. What is meant by ‘decay constant’?



  1. Warm-up Problem. You receive a shipment of 32P in the lab on the first of the month. When it arrives, you perform an experiment using 10mL of this reagent. 57 days later, you wish to repeat this experiment using the same amount of radioactive P. About how many mL of your stock will you use (Don’t calculate this using the equations above, just work it out logically for an approximate answer)?




Worked Examples

  1. 300 g of an unknown radioactive substance decays to 112 g after 180 seconds. What is the half life of this substance?
    • Solution: we know the initial amount N0=300 g, final amount N=112 g,  and elapsed time t=180 s.
    • Recall the half-life formula

t1/2 = t / log1/2(N(t)/N0)

    • Half-life is already isolated, so simply substitute and evaluate.

t1/2=180s log1/2(112g / 300g)

= 127s

    • Check to see if the solution makes sense. Since 112 g is less than half of 300 g, at least one half-life must have elapsed. Our answer checks out.



2. A nuclear reactor produces 20 kg of uranium-232. If the half-life of uranium-232 is about 70 years, how long will it take to decay to 0.1 kg?

    • Solution: We know the initial amount N0=20 kg,
    • Rewrite the half-life formula to solve for time.


    • Substitute and evaluate.

t=(70 years)log1/2(0.1 kg20 kg)≈535 years


    • Remember to check your solution intuitively to see if it makes sense.



Of Note:

In sourcing this material (especially the maths), I came across something I did not expect. That is… a very good article explaining C14 dating in Answers In Genesis, a source that typically does not curate science in a remotely responsible manner. However, the article linked above does an excellent job in describing the steady-state production of C14 in the atmosphere and the process by which it is used to date carbon-containing remains.

In the end, Answers in Genesis quickly departs to an attack on a straw man, suggesting that only Carbon is used for dating the Earth, but this is (willfully?) mistaken in several ways.

“[B]ecause the half-life of carbon-14 is just 5,730 years, radiocarbon dating of materials containing carbon yields dates of only thousands of years, not the dates over millions of years that conflict with the framework of earth history provided by the Bible, God’s eyewitness account of history. ” (my emphasis)

First, C14 is only used to date materials in which Carbon was incorporated (e.g. organisms) during life – i.e., it is not the way non-living material is dated. Second, C14’s 5730-year half-life allows dating of materials to approximately 40,000 years, at which point there is so little C14 remaining, that this method’s accuracy is reached. Further, at such low levels, background contamination from other sources (e.g. bacteria) compromises accuracy.

I think if I were to use an analogous argument: ‘[memory] yields dates of only [dozens] of years, not the dates over [thousands] of years that conflict with [my notion of the universe beginning with my birth].’ one might see the fallacy.





>Taken in part from:





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Posted by on August 17, 2016 in Uncategorized