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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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Cryptography

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”

frequencies

 

 

 

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).

bigrams

 

 

 

 

 

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.

 

KT RPP EXRDJ PXZ’J KX BOXD EVDIXI,

KSZ DBZ JB BOXD EVDIXI ZQRZ BSA KARVDJ YRPP BSZ.

                                               -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…

klu_saigen10

 
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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

 

Sample Size

F1.mediumIn class last week, we talked about the scientific method and how one might put together an experiment to ask a simple question. Students selected one of a group of about a dozen superstitions and imagined that no one ha ever done any experimentation to determine whether these superstitions were true or not.

The exercise mimicked to things that scientists have to do in the real world. One is writing (and reviewing) grants. Because much of what scientists study requires a significant amount of resources to perform, it is common to write a grant for money to do the work. A fairly efficient system has been worked out to administrate how these awards are made where grants are submitted to an agency, where other scientists evaluate the proposition and rank them with a score that politicians use to determine a cutoff for funding (the F word!)

This type of review is fairly similar to the way that publications are evaluated to determine what merits (or does not merit) publication. In the case of publication reviews, reviewers write up their responses which can be returned to the scientists seeking to publish. These comments can be used to improve the publication prior to acceptance (unfortunately, for the applicant, this step does not occur in grant application).

In order to combine these two experiences, my students wrote up their proposals, submitted them to other students for review, and then rewrote their work in the light of these suggestions. One thing I brought up, but did not answer in any way was sample size determination. (I was relieved when no one asked for clarification about this in class because I wanted them to think about it themselves). The real answer to this question is more within the realm of statistics than science, so with respect to my class, I don’t want to actually answer it (phew!) so much as point to places where more info can be found. One good page on this topic can be found at  the concept stew website or at wikipedia.

New penny. Doesn't it look fake? maybe we should test it to make sure it's reliable.

New penny. Doesn’t it look fake? maybe we should test it to make sure it’s reliable.

Perhaps students might also think about these questions:

1. How many coin flips are required to determine fairness?

           good one! would you believe that you need about 10,000 tosses to get an answer with reasonable reliability?

2. How much soup do you need to sample in order to know whether it needs salt?

3. How many subjects should be examined to determine if a new drug is safe?

 

Just something to think about. I have a love/hate relationship with statistics myself. I love it, but I also hate how deep you have to go in order to get a good answer. That’s life, I guess.

 
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Posted by on August 25, 2014 in Uncategorized

 

Back to School: Zombies, Ebola and some cool tunes

Ebola is in the news a lot right now.

Could this be The Coming Plague that Laurie Garret warned us about in 1994?

By the late 1980s, with the world shaken by the strangest and deadliest arrival of all – HIV and AIDS – Garrett traveled widely in search of understanding: Why did new viruses and bacteria appear, seemingly out of nowhere? Why couldn’t modern medicine vanquish HIV and other newly emerging microbes? How were scientists battling these diseases? Had hubris put the arrogant biomedical world of the late 20th Century at peril?

- from her website

A recent depiction (below) of the rise of Ebola cases and deaths (cumulative numbers) appears on the wikipedia site.

Diseased_Ebola_2014

The CDC is probably the most reliable source of information on the virus today. They provide a wealth of information about the virus, including that infection does not spread through the air, water or food (with the possible exception of some bushmeat – likely bats acting as a reservoir for the virus). And further, although Ebola does have a frighteningly long incubation period (of about 21 days), there is no evidence that asymptomatic persons can spread the disease.

When an infection does occur in humans, the virus can be spread in several ways to others. The virus is spread through direct contact (through broken skin or mucous membranes) with

  • a sick person’s blood or body fluids (urine, saliva, feces, vomit, and semen)

  • objects (such as needles) that have been contaminated with infected body fluids

  • infected animals

In recent news, two items sound eerily similar to those scrolling across the newswire in the game Pandemic 2:

August 8, 2014 – Experts at the World Health Organization declare the Ebola epidemic ravaging West Africa an international health emergency that requires a coordinated global approach, describing it as the worst outbreak in the four-decade history of tracking the disease.

August 19, 2014 – Liberia’s President Ellen Johnson Sirleaf declares a nationwide curfew beginning August 20 and orders two communities to be completely quarantined, with no movement in or out of the areas.

With all this in mind, maybe it’s a good time to pack up your emergency preparedness kit. And, while you’re at it, check out this comic from the CDC to help determine what you need to include:

Zombie_GN_Final

Imagine a ven diagram illustrating preparedness. How prepared should you be for flooding? fire? tornado? active shooter? zombies?? If you’re prepared for the apocalypse, surely you can handle a flood.

prepared

While you’re huddled in the basement waiting for the threat to pass, enjoy some music to keep your spirits up.

 
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Posted by on August 20, 2014 in Education, Uncategorized

 

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