Monthly Archives: August 2014

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.


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:


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.


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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Earthquakes and Fracking

Of course I’ve heard of Fracking and even have a reasonable idea of how the process works, but when Science magazine published an article on Injection-Induced Earthquakes, I thought I would look into it just a bit more.

The idea behind Hydraulic fracturing, or ‘Fracking’, is old – dating back to the 1860s, yet it only came into large scale industrial use in the late 1940s when Halliburton became the first company to use this technique to improve their harvest of natural gas.


Link to Wiki article on Fracking

The New York Times defines Fracking as “… horizontal drilling [that] has enabled engineers to inject millions of gallons of high-pressure water directly into layers of shale to create the fractures that release the gas. Chemicals added to the water dissolve minerals, kill bacteria that might plug up the well, and insert sand to prop open the fractures.”

In 1974, congress passed the Safe Water Drinking Act, which required permits for injecting fluid into the ground (42 U.S.C. , Chapter 6A, Subsection XII, Part C) in order to – obviously – protect underground waters from contamination before they are harvested for drinking. This didn’t stop fracking, but it did temper the method’s growth and put the Environmental Protection Agency, charged with upholding this law, against the Department of Energy, that was (in 1986) exploring unconventional methods of drilling, including horizontal drilling techniques.

1999 saw the use of high pressure treatments characteristic of today’s Fracking methodology being used to harvest natural gas from previously inaccessible shale sources in Texas. However, the EPA issued a statement in 2004 pointing out that Fracking fluids are toxic and are left behind in the soil following the process, but that it appeared to pose little risk to contaminating ground water.

[The] EPA retained the right, however, to conduct additional studies in the future. As a precautionary measure, the Agency also entered into a Memorandum of Agreement in 2003 (PDF) (9 pp., 331 K, about PDF) with companies that conduct hydraulic fracturing of CBM wells to eliminate use of diesel fuel in fracturing fluids. 

                                                                           – website

The next year (2005) Congress moved to “amended the SDWA definition of “underground injection” to exclude underground injection of fluids or propping agents, other than diesel fuels, in hydraulic fracturing activities related to oil, gas, or geothermal production activities.” This effectively removed the risk that the EPA could intervene in commercial Fracking and the business boomed. Since that time a number of efforts have been made to slow the expansion of Fracking or to revisit the technique’s environmental impact.

I did not want to get into the discussion of environmental effects of Fracking that are central to the EPA discussion above. Instead, I thought it would be a good opportunity to simply present the data from the Science article on the increased number of moderate earthquakes since the deregulation of 2005. 

The dotted line shows a steady number of earthquakes occurring prior to 2000. The red line shows the actual number of (cumulatively) earthquakes occuring since about 1970.

Science 12 July 2013:  Vol. 341 no. 6142  "Injection-Induced Earthquakes" William L. Ellsworth

Science 12 July 2013:
Vol. 341 no. 6142
“Injection-Induced Earthquakes”
William L. Ellsworth

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Posted by on August 12, 2014 in Uncategorized


Working Overtime to Prevent Sudden Death

Do you have Ebola? If you're reading this, then probably not.

Do you have Ebola?
If you’re reading this, then probably not.

My cousin, in Philadelphia, tipped me off that I should write a blog article about the current Ebola outbreak that has occurred this year in Western Africa. One of the reasons that this interested him was that the story of the outbreak was being shadowed by another story of a ‘secret’ serum that was being used to treat some of the American victims of the disease. I think ‘Secret’ was the operative word. I had definitely heard about the outbreak, but this was actually the first time that I heard about this serum – and it immediately tipped of my BS / Conspiracy theory detector because of the suggestion that America actually had a secret ‘cure’ for Ebola. It almost begs for allegations by people wearing tinfoil anti-alien hats that America was engineering some Apocalypse Bringing Disease a la I am Legend or Dawn of the Planet of the Apes.

So, I was interested to hear that there actually is a serum to treat Ebola – it’s just not secret, and it’s not an approved treatment, but an experimental one. Ebola VirusFirst, something about the virus…

There is currently no vaccine available for Ebola virus infection and the standard of care remains supportive therapy aimed at maintaining the body’s electrolytes, blood pressure and to prevent / treat additional infections that may otherwise complicate care(1). Coupled with an extraordinarily high fatality rate (up to 90%) and horrifying symptoms including internal and external bleeding, fever and

Western Africa

Western Africa

intense weakness, it remains one of the most feared diseases in the world (2). Ebola is so debilitating and deadly, in fact, that its severity has actually functioned to keep it contained within a relatively small area of western Africa. Most cases tend to occur in and around poor, unsanitary hospitals where virus spreads from a contaminated individual or cadaver to a person (often serving as a healthcare worker). Often cases present with symptoms similar to more common, less lethal diseases and are not quarantined away from other patients leading to a rapid accumulation of nosocomial infections (3). One reason for the high mortality rate associated with Ebola infections may be due to a curious condition in which antibodies against the virus may, ironically, worsen the infection. The mechanism of this behavior appears to operate through the binding of antibody to viral glycoproteins, followed by antibody-mediated phagocytosis of virus by immune cells. This is confounding because it is this process that is utilized by immune cells to destroy viruses and may further impair the ability of researchers to develop an effective vaccine as most vaccines work by promoting antibody development (4). With Ebola, the interaction of a protein on the virus’ surface is bound by antibody, which is then bound by an immune cell that internalizes the virus, but instead of destroying the virus, it manages to escape destruction and infect the cell.

Rather than making you better, antibodies against Ebola may make you worse off.

Rather than making you better, antibodies against Ebola may make you worse off.

To make matters worse, this time around many more people are contracting the disease, so concern is elevated around the world, even some US Congressmen have been making hay about the possibility that undocumented immigrants from Central America may introduce Ebola into the US. Which brings me back to the conspiracy angle. What’s this about a secret serum again?

The serum is actually just an experimental treatment – one that is extremely early in the development process, called ZMapp. This is a product produced by Mapp Biopharmaceutical Inc. that is a combination of three monoclonal antibodies made in tobacco plants (this is a more common method than you might think). The idea being that these antibodies will provide passive protection against Ebola, much like the antibodies produced by a typical vaccine, but -hopefully – without the adverse effects associated with the antibodies that enhance infectivity. Reading the article describing the manufacture of these antibodies does not provide an explanation of how the antibody-mediated enhancement of infection will be evaded, but one may imagine the construction of neutralizing antibodies that lack the constant regions associated with FcR or C1q binding as the binding of these two proteins have been proposed as causing the adverse effect. As this drug lends passive immunity, it may (if effective) prevent infection of an exposed person – or at least lesson the severity of the infection, however it will NOT lead to the accumulation of antibodies by the patient as would a vaccine. Rather, this form of immunity is more akin to treatment with an anti-serum following a snake bite. With luck, a silver lining to this major outbreak may be the opportunity to test an early-stage treatment, possibly resulting in the first ray of hope in improving Ebola survival.

Can I catch this?

Can I catch this?



Posted by on August 7, 2014 in Uncategorized


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imagesThe Fall Semester is starting soon and I have to say: ‘what a relief’. Going all summer without teaching is difficult, yet I always avoid summer classes because I’m worried that I will get myself into trouble with vacation plans or childcare responsibilities. But all that ends soon and I can get back in the classroom, start thinking (and writing) about science, and stop writing so much about movies and TV.

I’ve nearly finished one of my two iBook- format handbooks that I need to have ready for when classes begin. This year’s book is much more interactive, with review questions at the end of each chapter, keynote presentations of my lectures and some video animations. In writing it, I got a bit hung up on my day 1 material. Namely, the scientific method. This is the method developed by Descartes and others to help us figure out the difference from what is true about the world and what isn’t – although saying it that way makes it sound more clear and 100% accurate than it actually is. In reality, the scientific method is a way of thinking that is based on ‘verity and validity.’ What it is best at is determining what is NOT true. However, over time, that steps us ever so slightly closer to an accurate understanding of the way the universe works.

On the one hand, the scientific method is a very precious thing. It comes from the realization that our senses and our minds often fool us. We evolved in a world rife with danger and it made a lot of sense for us to see connections in the world – even when they were not really there. Because, as many evolutionary biologists will explain, the person who assumes there is a lion behind every bush tends to live longer than someone who does not – especially when there are occasionally lions lurking behind the bushes.

Once we escaped that world, created civilization and put an end to the lion problem, we started to wonder, “How does the world work?”

VariableTo answer that question, we could make up ideas and just cling to them so long as they appear to be at least make a consistent story (I’m thinking Aristotle), or, we could test our ideas and see what we get.Which brings us back to the scientific method.

For the most part, however, most scientists don’t really frame their ideas in the form of this method, but have internalized the method and just apply the principles. What I mean by this is, every introductory science book talks about independent and dependent variables, etc. but I have never actually heard anyone describe their experiments in these terms. Instead, we talk about conditions, controls, data and conclusions. Despite working in science my whole adult life, I still have to look up the difference between independent and dependent variables – and I don’t use these terms in my class unless someone asks about them. Instead, I spend much more time focused on setting up an experiment and thinking about what controls would be needed and how someone may interpret the data. I also spend a lot of time early on asking what data really tells us. What’s the difference between correlation and causation, are we reading too much into our data? Can there be other explanations for the same results?

But, having though about this a bit today, I wanted to ask (although I see that my readership has really died off over the summer) what people thought about these terms?

Do any of you actually think these terms are important to teach students? Do you regularly use them in your work? 

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Posted by on August 3, 2014 in Education