Little Red

As always, my Microbiology class is reading Paul Offit’s Vaccinated this year. Recently, we have started into the chapters concerning Hilleman’s involvement in making vaccines against Measles, Mumps, and Rubella, each taking a chapter in the book.

 Rubella is often overlooked as an unimportant disease with milder symptoms than other vaccine-preventable illnesses such as Measles, Smallpox, or Polio. However, Rubella represents a different threat, less visible during the acute phase of infection.

From the Latin, Rubor, meaning red. Rubella (little red) was initially identified by its similarity to measles, resulting in a shorter-duration (aka 3-Day Measles) episode of red spots. Because of the similarity to Measles and being first described by a number of German scientists, Rubella took a third name, German Measles.

Although Rubella is not typically a dangerous disease for older children, it can be difficult for babies and is particularly destructive when contracted by women in the first trimester of pregnancy. Early in the pregnancy rubella infection can lead to serious problems in approximately 50% of babies. So common are these outcomes that they bear their own name, Congenital Rubella Syndrome (CRS). Effects include blindness, deafness, congenital heart disease, and intellectual disabilities.

During the course of the 1963-65 epidemic, “In the United States alone, about 11,000 babies died and 20,000 babies developed birth defects from rubella.” CDC

Following this epidemic, a vaccine against Rubella was approved for use in the US in 1969 and was followed by an abrupt decline in the number of cases as seen in this graph illustrating the number of rubella cases occurring in the US from 1966-1993. (taken from Centers for Disease Control and Prevention Summary of notifable diseases—United States, 1993 Published October 21, 1994 for Morbidity and Mortality Weekly Report 1993) Although not depicted in this graph, the resulting CRS incidence followed a similar pattern.


Until recently, the most common mechanism for vaccinating against Rubella was the Measles/Mumps/Rubella (MMR) combination vaccine. However, in 2004 a MMRV combination containing varicella (chickenpox virus) was approved adding additional protection to the single shot. Currently, the MMR/MMRV vaccine is recommended at age 12-14 months, with a booster at age 4-6.

 When the MMR vaccine came under suspicion following the 1998 publication of Andrew Wakefield’s notorious (and now retracted) article suggesting a link between vaccination and autism, Measles cases began to re-emerge.


Concurrently, Rubella cases have also rebounded in countries that had previously nearly eliminated the disease (see data below from Poland).

 Ultimately, the future for these viruses depends on how we, the public choose to use the information available to us – and where we choose to get that information, from talk show hosts and celebrities, or from the agencies we have built to protect the health of the country.


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Posted by on September 29, 2014 in Uncategorized


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Case Closed

I’ve been locked away in jury duty for the past 1.5 weeks. All the while falling behind in each of my classes and feeling like the case was never going to end. Today, however, after many hours of deliberating, we finally turned in a verdict and got released from our service.

Now it’s catch-up time.

In General Biology class we have several chapters of Your Inner Fish to talk about as a nice segue from this impromptu break back into study. In the text, we will tackle the flow of energy through biological systems. In the simplest terms, this asks the question, “How do biological systems capture energy from their environment and use it for their own purposes?” This includes two basic pathways, Photosynthesis and Cell Respiration. What’s amazing is how similar these two processes are – each involves a cycle of reactions and each involves an ‘electron transport chain’. The electron transport parts of these pathways tie together some of the topics we covered earlier this semester regarding membranes, enzymes and diffusion.

In Microbiology, we will consider a couple of chapters from Offit’s Vaccinated and hopefully tie this in to an introduction to Virology. Key to this is an understanding of how viruses are put together, how they operate in getting into cells and how they can then co-opt cellular processes. The simplest way this is done is to direct systems to creating more virus particles, however, some viruses, like HPV do more to affect cell cycle and thereby not just produce more virus, but also initiate a cascade of events that may lead to cancer of the infected cells.


It’s good to be back.

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Posted by on September 24, 2014 in Uncategorized


Two Things

crest-bda7b7a6e1b57bb9fb8ce9772b8faafb1. NaNoWriMo draws near. Pull yourself together and commit to writing a novel in 30 days along with thousands of others worldwide. There are still forty days to sign up, so head over to their site and check it out.

2. My wife has been away this week on business and our indoor cat is busy expressing his discontent under the piano. So far Penny has not joined in.

Day two:

William: 2

Penny: 0



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Posted by on September 18, 2014 in Uncategorized


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Today is the first day of the Coursera Cyrptography class taught by Stanford Professor, Dan Boneh. I follow courses like this every once in a while in order to learn a bit about topics that I would not otherwise get any exposure to. Boneh’s course is a little math-intense, but there is another more concept-driven course on the same topic being offered on Khan Academy. If you haven’t taken advantage of either of these two sites, you should look into them. Both are entirely free, and both are taught by excellent educators.

Here’s a video from the Khan Academy site introducing the Caesar Cipher, a simple cipher like those used on radio dramas of the past (get your secret decoder ring!).

If you want to crack a simple substitution cipher like this, you might want to start by using a frequency chart of letters used in the English language, like this one:

The Caesar cipher: Brit explains the Caesar cipher, the first popular substitution cipher, and shows how it was broken with “frequency analysis”





However, once you figure out the easiest letters (e,t,and a), things get a bit more difficult. At this point, you will probably have to start looking at letter pairings (Bigrams) to see if any useful patterns show up there. Here’s a listing of the most common Bigrams (again, in English).







It’s interesting that these kinds of codes might ever have been considered sophisticated enough to use in the real world. After all, it’s easy to find examples of these types of ciphers in daily newspapers around the world presented as cryptograms that people do for fun.




                                               -AVWQRAI IRCNVDJ

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Posted by on September 8, 2014 in Education


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Another hint

These are the men who were a heartbeat from the presidency  1989 – present.

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Posted by on September 3, 2014 in Uncategorized


Walk this way

for a hint on this week’s quiz…


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Posted by on September 1, 2014 in Uncategorized


New Life

Abiogenesis and Spontaneous Generation are two completely different things, even though they are the same thing.

This is not a pipe

This is not a pipe

The discovery of the microscopic world was to biology what Guttenberg’s printing press was to literature and widespread literacy.

But before the microscopic world was even conceived of, it had to be seen.

This brings in the curious personality of Zacharias Janssen. Although records of his time and life are sketchy – it isn’t even certain exactly when he was born, only that it occurred sometime between 1580 and 1588.

Janssen, who is widely regarded to be the inventor of both the microscope and telescope. Or at least he stole those ideas from those around him and copied them well in between his spectacle business and counterfeiting currency.

Janssen's microscope

Janssen’s microscope

It’s also important to recognize that these arguments were coming to a head following 1637, when Rene Descartes published his Discourse on the Method outlining the framework for the scientific method. This book would revolutionize the way the people looked at the world and represented critical change from a reliance on philosophy alone to describe the world to one where ideas were supported by evidence from the natural world.

Descartes argued that “animals, and the human body, are ‘automata’, mechanical devices differing from artificial devices only in their degree of complexity. Vitalism developed as a contrast to this mechanistic view. Over the next three centuries, numerous figures opposed the extension of Cartesian mechanism to biology, arguing that matter could not explain movement, perception, development or life.”

Spontaneous generation, abiogenesis, and vitalism all point to the generation of life from inorganic (unliving) material. Most people equate spontaneous generation with the appearance of flies on a sandwich left out overnight- “Where did these things come from?!” -saying that the generation of life out of nowhere can, and does, occur every day.  Abiogenesis is more commonly used to describe the single origin of life that set all living things in motion some 3.5 billion years ago (on this planet, at least). Both say life came from non-life at some point but differ on how frequently this occurs. Vitalism can be described almost as the magic within things that gives them the ability to create life.

The number of great minds that tackled this question is surprising. Today, it is easy to think that this these experiments are not worth doing. But, in fact, they were very worthwhile at the time. They answered the questions:  ‘What is life?’, ‘Where does life come from?’, and ‘What distinguishes living from non-living things?2005-09_Białowieski_Park_Narodowy_12

The spontaneous generation of life was most often recognized as occurring on decaying matter, a fallen tree trunk becoming covered with moss and fungi, a dead animal spawning flies, etc. This idea was summed up in a theory of vitalism which states that, “living organisms are fundamentally different from non-living entities because they contain some non-physical element or are governed by different principles than are inanimate things”

The spermist notion that women were nothing more than incubators required for humans to grow from men's sperm.

The spermist notion that women were nothing more than incubators required for humans to grow from men’s sperm.

Another explanation for the appearance of life was the theory of preformationism, which suggested that organisms arose from tiny, unseen versions of themselves. This idea was consistent with the notion that all life was created in one event, but that it was simply too small to be seen. The simplest illustration of this idea comes from Nicolaas Hartsoeker’s illustrations of human homunculi present inside of sperm that simply needed to grow up into larger (visible) forms. These ingenious ideas are reminiscent of the elaborate constructions imagined to maintain a geocentric universe and show how far the imagination is willing to stretch in order to maintain prior assumptions.

Epicycles within cycles

Epicycles within cycles

In 1665, Robert Hooke published his Micrographia thus establishing the publishing arm of the Royal Society. In it, Hooke presents beautiful images of natural and man-made objects as viewed through his microscope. These were among the first published images of such things and within its pages he coins the word ‘cell’ to describe the network of walls he observed in thinly sliced cork. He also presented other ideas and observations including observations of the planets and the wave theory of light.

In 1668, Francesco Redi put the idea to the test. He placed one piece of meat in an open jar and another in one closed off with cheesecloth. The open container represented what was commonly seen – flies appearing on the meat from nowhere. The covered jar represented an experimental condition in which pre-existing flies could not land on the meat and lay eggs on it. As he suspected, keeping flies away from the meat meant no new flies ‘appeared’ from nowhere on the meat.

“Life begets Life”

Redi’s experiment was adapted for examining whether micro-organisms arose spontaneously by John Needham in 1745 and Lazzaro Spallanzani in 1768. Both men boiled chicken broth (known already to kill any pre-existing organisms) and then kept the broth in sealed containers. Unfortunately, their results were mixed. Needham’s experiment was seen as open to contamination between boiling and sealing the containers, Lazzaro’s response used a vacuum to eliminate airborne agents, but many suggested that his work merely indicated the need for air for generation.

It wasn’t until Louis Pasteur took up the challenge in 1859 that the idea was challenged by an experiment that took these objections into consideration and demonstrated not only that spontaneous generation of life did not occur, but that what was previously seen as new life came – or preformed organisms, in fact came from airborne particles (organisms). Find a description of this experiment here and more on the direction of these ideas today here.

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Posted by on August 31, 2014 in Uncategorized


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