Monthly Archives: May 2014

See the World in a…Flea?

 

From its inception of the principal goals of science education has been to cultivate students’ scientific habits of mind, develop their capability to engage in scientific inquiry, and teach them how to reason in a scientific context.–A Framework for K-12 Science Education

It is possible to mark the date when science became modern science.
The Royal Society in London, in the year 1660. The membership list of the Royal Society reads like a whose who from your science textbooks: Robert Boyle (Boyle’s Law), Robert Hooke (cell theory), Isaac Newton (physics). The motto that the founders chose for the new society was Nullius in Verba, roughly translated as “Take no one’s word.”
“Take no one’s word” is another way of describing both “the scientific habits of mind” as well as the rationale for scientific inquiry.
What does it mean to take no one’s word? Robert Hooke’s 1665 book Micrographia: or Some Physiolgical Descriptions of Minute Bodies Made By Magnifying Glasses, shows how modern science would address the question.
Hooke’s research question is “What happens when we look at ordinary, everyday things in a new way? In Micrographia, the new way is to use the newly available magnifying lens, rigged up by Hooke into a microscope.
In the course of the book, Hooke describes in detail with illustrations a progression of observations beginning with the tip of a steel needle and proceeding through a long list of objects (a razor, silk cloth) and eventually getting to various insects such as a blue fly and the flea illustrated here.
Along the way, Hooke builds the case that in order to understand the world, we need to improve our ability to observe. We can do this by two methods: first, build better instruments and use them, thermometers, hygrometers, telescopes and microscopes. Second, we can do it by developing habits of mind that will make our observations more reliable: be rigorous in deciding what observations to accept, be strict about how we compare the observations made of a natural phenomenon, and finally, to be very slow and deliberate about the conclusions we draw.
Now to the flea. image

Recall that the flea in Hooke’s day was a ubiquitous pest. There was no escaping its bite given the facts that the fleas lived in one’s clothes, including the bed clothes year around.
But under Hooke’s microscope, the flea is transformed. The flea is not a pest but a creature of “strength and beauty…[that] had it no other relation at all to man,would deserve a description.”
The flea is covered with curiously polished armor and its head is decorated with a beautiful eye. Behind the eye is an indentation filled with fluid and inhabited with hairs, “which may serve as [the flea’s] ear.
The microscope not only improves our ability to see smaller objects, it also transforms how we see those objects. The flea is no longer a human nuisance but becomes a strong and beautiful creature worthy of study for its own sake–for example, to understand how it is able to jump so powerfully based on the jointing of its legs.
Making the conscious effort to overcome the limitations of our senses also transforms our point of view. Instead of seeing the world in human terms (“fleas bite”) we try to see it in scientific terms; that is, as a part of nature and that is explicable in its own terms.
As you read Hooke, you can see across the span of time between his and ours, the work is much the same.

The Mystery of the Salt Marsh: An Anatomy of a Scientific Investigation

The work of science is to develop explanations of natural events. For students of science, this means learning to understand scientific explanations.

This is a bit tricky because scientific explanations are different from the usual kinds of explanations that students are asked to understand in other subjects.
A scientific explanation is really a kind of argument that is based on the construction of a model and the testing of the model with a carefully designed investigation that yields a body of data that can examined and used to make a case to support or refute the model.
In today’s blog, I have used a published investigation to follow the steps used by the scientists to develop a scientific explanation.
Salt Marsh Decline
Salt marshes are very important environments and many of them are dying because the plants such as cordgrass whose roots hold the soil together are rapidly and mysteriously disappearing. Because of the importance of salt marsh environments, finding the answer to why the cordgrasses and other vegetation are disappearing really matters. Instead of environments with abundant vegetation, providing support for lots of different forms of life, the shoreline is reduced to a lifeless mud flat.
This kind of die off has been observed all over the Western Atlantic region and investigators have posed a number of different possible reasons: eutrophication (that is, an overabundance of nitrates and phosphates that encourage algae blooms), pollution that changes the acid-basic balance, diseases that attack the vegetation, and even the mechanical wave action caused by outboard motors.
It is important to note that the work of any investigator is influenced by the work of all of the others investigating the given phenomenon. So for example, it has been suggested that in the specific area of Cape Cod, sport fishing and crabbing has reduced the top level predators (stripped bass, blue, and green crabs). The loss of the top level predators results in an increase in the numbers of the crabs that are herbivores. The now more numerous plant eating crabs destroy the cordgrasses and other plants that hold together the shoreline.
But so far, while this explanation is appealing, it has not been subjected to a test.
In a report published in Ecology Letters (March 2014), investigators conducted an experiment to see what would happen to the shoreline vegetation if top level predators (such as blue and green crabs) are excluded and herbivorous crabs are allowed to flourish.
The experiment was conducted by creating special predator exclusion pens that would be placed in eighteen randomly chosen locations around a particular salt marsh. A control set of cages that permitted entrance to the top level predator crabs was also established.
The investigators were able to quantify the amount of cordgrass in both the experimental and the control settings, the density of the herbivorous crab borrows, as well as the nutrients in the water and the water movement available at the beginning of the experiment. At the end of the experimental period (one growing season for the cordgrass), the amount of cordgrass was collected from the experimental and control settings, it was dried and weighed.
The experiment would then measure the what happened within each of these protected environments as compared with the control environments. The experimenters would know how much cordgrass was present when the experiment began as well as the size of the population of the herbivorous crabs at the outset and end of the experimental period.
At the end of the experimental period, it was found that in the predator exclusion pens, there was a great loss of cordgrass, and increase in the density of the herbivorous crab borrows.
The amount of cordgrass in the predator exclusion pens was reduced by greater that 60% when compared with the pens that permitted predator access.
The experimenters conclude that the experiment shows that removal of the top level predators can result in the rapid (that is, in a single season) destruction of the cordgrass population.
The experiment is part of a larger argument. The larger argument is that of the whole body of research findings about the relationships among organisms in an ecosystem. Another way to name the argument is to call it “scientific consensus” or “consilience.”
Thus, the experimenters point to other examples of what happens when top level predators are eliminated, allowing for the consumers (that is, in this case the herbivorous crabs) to run wild in the arctic and in the Southeastern United States Gulf coast.
The experimenters also argue that the solution to the “problem” is not simply one of preventing recreational fishing for stripped bass and blue crabs. The model of the ecosystem includes an understanding that impacts on one part of the will have predictable or non-predicable impacts elsewhere in the system.
Therefore, the experimenters argue that
While our results indicate that predator depletion can cause rapid, dramatic shifts in the biotic and abiotic condition of New England salt marshes, increasing population density and human activity in coastal areas suggests that multiple interacting threats are likely to become increasingly common, with the potential to fundamentally alter ecosystems worldwide.

With this conclusion they place their particular argument into the context of a larger argument about the interrelationships among organisms (including human beings, and their activities).

Source Material:

Carl Zimmer, When Predators Disappear So Does the Ecosystem. http://www.nytimes.com/2014/05/15/science/when-predators-vanish-so-does-the-ecosystem.html?_r=0

You can read about the complete experiment at
http://onlinelibrary.wiley.com/doi/10.1111/ele.12287/abstract

Testing and Expanding Models: The Example of Antibiotic Resistance

Antibiotic resistance has become a major medical problem.
A major report on the seriousness of the problem was in the news this morning (May 11, 2014).
[It is] a problem so serious that it threatens the achievements of modern medicine…. A post-antibiotic era, in which common infections and minor injuries can kill, far from being an apocalyptic fantasy, is instead a very real possibility for the 21st century. ( http://www.nytimes.com/2014/05/11/opinion/sunday/the-rise-of-antibiotic-resistance.html?hp&rref=opinion)

This blog provides an example of the importance of model building in science. Models are developed to help understand natural phenomena. When the model is constructed, it becomes a way to reveal new questions about the phenomena.
The conventional model for antibiotic resistance
The antibiotic action against the pathogen can be seen as an environmental pressure. Those pathogens within the population that possess a mutation that allows them to survive live to reproduce and will then pass this trait to their offspring, which leads to the evolution of a fully resistant colony of the pathogen.

Does the model account for all of the possibilities?
Is antibiotic resistance the result of using antibiotics to treat bacterial infections?
What if we able to go back in time to the time before the advent of penicillin (the first antibiotic) and test modern antibiotics on bacteria that have not experienced them?
In 2010 microbiologist Dr. Gerry Wright identified way to investigate the question when he discovered that the Lechugilla cave complex in New Mexico could serve as a kind of time machine because the 1,600 foot deep cave walls were covered with bacteria that had not been exposed to antibiotics over the four million year history of caves. (“http://www.nytimes.com/2014/05/08/science/antibiotic-resistant-germs-lying-in-wait.html)
Dr. Wright’s team found that there were many bacteria in the cave that were resistant to the rich cocktail of antibiotics used by the team. Further, it was found that the pre-antibiotic bacteria possessed many of genes that have evolved in the modern anti-resistant bacteria.
Using DNA databases filled with bacterial DNA from all over the world, those genes that made antibiotic resistance possible were ubiquitous.
Such investigations have uncovered additional mechanisms by which bacteria can become resistant. It is known that bacteria can borrow DNA from other bacteria. It was by this mechanism called “horizontal gene transfer” that a powerful antibiotic called vancomycin began acquiring resistance in the 1980s. It turns out that the resistance was acquired when the DNA of the bacterium that was the source of vancomycin was shared by way of horizontal gene transfer with certain disease causing bacteria.
This example illustrates that model building is a dynamic process in which the development of a model helps investigators to identify new questions that allow for the model to be both tested and expanded.
The idea for this blog came from Carl Zimmer’s May 8, 2014, “Matter” column (http://www.nytimes.com/2014/05/08/science/antibiotic-resistant-germs-lying-in-wait.html). It’s application to model building is mine.
You might be interested in looking for the following article in Nature.

D’Costa, Vanessa; King, Christine; Kalan, Lindsay; Morar, Mariya; Sung, Wilson; Schwarz, Carsten; Froese, Duane; Zazula, Grant; Calmels, Fabrice; Debruyne, Regis; Golding, G. Brian; Poinar, Hendrik N.; Wright, Gerard D. (September 2011). “Antibiotic resistance is ancient”. Nature 477 (7365): 457–461. Bibcode:2011Natur.477..457D. doi:10.1038/nature10388. PMID 21881561.

On Not Being Pre-Posterous

Another Discouraging Set of Test Results
The latest NAEP results are discouraging. It appears that American high school students have made little or no progress towards the goal that all students will graduate college and career ready.
This blog is not about the test results but instead about a word. The word is “preposterous”. I want to talk about “preposterous” because it suggests something about how we have constructed our accountability system.
Preposterous means “ridiculous”; literally, getting was is “post” ahead of what should come first, “pre”.
The way we have thought about accountability is literally “preposterous.” We have placed what is post before what should come first.
How can this be? Our accountability system measures the percentage of students who do well on the various accountability tests. So, only 38% of students are college and career ready.
But that is literally a preposterous way to do things. Think about it: “college and career ready” is really an outcome; it is a “post”; a result of good classroom practice. What is “pre” is the good classroom practice.
The argument is that if we took a sensible approach to accountability, we would put our accountability measures not on test results (the post) but on good classroom practice (the pre).
And there is some evidence in the NAEP results that validate this analysis.
Students who took more challenging classes (“interesting and engaging”) did better than those who took less demanding curriculum (less interesting and engaging?). Students who discussed what they read also did better than those who didn’t.
My point is that if we are truly serious about improving test scores, we go about our task by not being preposterous.
We do this by putting the “pre-” first: classes that are well-taught so as to be engaging, interesting, and challenging. The “post-” will likely take care of itself.
Getting our pre- and our post- in the proper order will make a big difference.