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Monthly Archives: April 2014

Your Inner Fish Crawls off the Page

ImageI’ve been assigning Neil Shubin’s Your Inner Fish as a reading and discussion assignment in my General Biology classes for several years now. I believe that it’s a good introduction to understanding how the process of science works in the real world, it does a good job communicating the methods and findings of a number of complex experiments, and it also walks through the history of ideas and how new information changed these ideas over time.

If I can get students to think about all these things and perhaps do a little extra digging (into the research), then I’ve down my job.

Episode I of the adaptation of this book  just aired this week and I was very impressed by the way the material was put together- refining the story from the book a little- and coming up with a standard documentary supported by computer graphics that really add to the story rather than looking tacky of fake. In fact, I think the graphics really transform the material into a living experience.

The story is told in two converging arcs. In one, we follow Shubin’s field work, where he decided that he was interested in finding the remains of one of the earliest organisms to crawl out of the water and establish terrestrial life. Prior work suggested that the earliest tetrapod ancestor on land emerged from the Devonian Seas about 370 Million Years Ago. Shubin and colleagues identified an ancient river delta of about this age in the Canadian Arctic and set out to locate some fossils.

ImageThe other story walks us through the idea of relationship with other life on Earth. What suggests this relationship? What evidence is there for it? How long does it go back?

As I said above, I have liked this adaptation very much so far and I am already planning to bring at least parts of this video into my classroom to supplement our discussions.

More on this later…

 
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Posted by on April 10, 2014 in Uncategorized

 

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Fifty

ImageThe fifty word story challenge.

Thanks for the inspiration, Regina.

It Came From Under the Bed

His breath held painfully as fretful fingers climbed the bedstand lamp for the switch. Below, old homework papers crunched slowly. Ominously.

“Skipper…?” The dog’s name was little more than a slow exhale.

“Please be Skipper.”

Pffffffffft

He gagged on the warm, unlikely relief of dog fart.

 
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Posted by on April 8, 2014 in Uncategorized

 

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Cosmos – on the nature of light

Spectroscopy

In this weekend’s Cosmos, a lot of attention was spent discussing the properties of light. For something so apparently simple, there is a lot beneath the surface.

I wanted to talk about two elements of this episode in particular and provide some examples to explain things a bit better.


 

The first idea is that white light (what we get from out sun) is composed of all the colors. What we see as colors is actually the various wavelengths of light. We see short wavelengths as colors toward the red end of the spectrum; longer wavelengths appear as colors toward the blue end.

We also know that shorted wavelengths carry more energy. I like to tell my students to imagine a shoreline where all the waves are exactly the same height. If the length of the wave is shorter (measure from the top of one wave to the top of the next), then more waves batter the shore per unit of time. Longer waves mean fewer waves hit the shore in a given period of time. So, is more energy transmitted to the shore from the longer or the shorter waves?

Another part of this ‘white light contains all wavelengths of light’ comes from the way a prism reflects and refracts light. Any wave will change its direction as it goes from one medium (like air) to another (like glass) – it actually changes speed, which suggests a good analogy that I’ll explain in a second. How much it bends depends on the wavelength of the light.

The analogy is that of a car driving on a street. Imagine the car veering of the street at an angle to the right. As it leaves the road, it hits mud. The right wheel hits the mud first and slows down pulling the car harder to the right until the left wheel hits the mud. When that happens, the car stops getting pulled to the right and goes off in a straight line again. (the moment when the car is getting pulled onto a new course I’ve drawn a dotted line) The important thing to note is that the car was pulled right by the icky mud clinging to the tires more than the road does.

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We can bend light by passing it through a glass (prism). The result is depicted in this album cover for Pink Floyd’s Dark Side of the Moon.

ImageWe can even bring the colors back together to produce white light again by using a second prism.

 

All this gets us to the idea that light can be dissected into a spectrum using a prism. This is the first type of spectrum described below.


 

The three types of spectra:

  1. continuous spectrum – emitted by a dense hot object
  2. emission line spectrum – the precise wavelengths of light emitted from a hot gas   (we can ignore this type of spectrum for the purpose of this discussion)
  3. continuous spectrum with absorption lines – the inverse of the emission line spectrum. When a cooler gas absorbs wavelengths of light from a hot source.

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In the example discussed in Cosmos this weekend, we learned about the third spectrum. This is what is produced when a hot star emits light in a continuous spectrum. The cooler atmosphere of the star then absorbs some wavelengths of the light as it passes through. This is how DeGrass Tyson was saying that we could determine the composition of a star’s atmosphere from its spectrum. All we need is to do some experiments in the lab and see what absorption lines we see from different elements’ gas.

As always, the theory is cleaner than the reality, but let’s take a look at the spectrum from the sun. This image highlights some major bands and indicates which elements they come from.

Below the solar spectrum are some of the spectra from the sun’s constituents with major bands that correspond to those seen in the solar spectrum marked with (*).

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Again, I apologize for this not being very exact, but it does at least communicate the idea of what was discussed on Cosmos in a little more detail.

References:

  1. for a good explanation of spectra http://www.astro.washington.edu/users/anamunn/Astro101/Project1/stellar_spectroscopy_introduction.html
  2. for the periodic table of light http://www.alexpetty.com/index.php/2011/07/20/the-periodic-table-of-the-light/
  3. for the composition of the sun http://chemistry.about.com/gi/o.htm?zi=1/XJ&zTi=1&sdn=chemistry&cdn=education&tm=41&f=10&su=p284.13.342.ip_&tt=65&bt=0&bts=0&zu=http%3A//imagine.gsfc.nasa.gov/docs/ask_astro/answers/961112a.html

 

 
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Posted by on April 7, 2014 in Uncategorized

 

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A game for cramming micro students

Exam II in Microbiology happens this Tuesday. If only there was some less stressful way of studying for the exam. Perhaps a puzzle to kick back and contemplate …?

(As an aside, I really don’t like the way this puzzle turned out – for a crossword puzzle, there are very few words that cross. I may attempt to redo this later, but there’s an exam to write first)

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Clues:

Oh No!

Autocorrect strikes again – 1 Across = the DESTRUCTION of all microbial life.

I do apologize for my poor clue-writing. I’m only a recent adopter of crosswords and I’m not yet very good at writing them the way they should appear.

(I can only solve NYTimes’ Monday puzzles)

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Posted by on April 6, 2014 in Uncategorized

 

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A quick look at mRNA Splice Variants

-Beadle and Tatum Redux

-Beadle and Tatum Redux

In my microbiology class this past week, we were discussing how prokaryotes and eukaryotes differ in their handling of DNA, RNA and gene regulation. Mostly, we focused on how the presence of the nuclear membrane in eukaryotes separates the processes of transcription and translation and what this results in. Briefly, bacteria are prokaryotic life forms that lack a defined nucleus (among other differences). Because of this, when bacteria transcribe mRNA, it is immediately available for translation – the DNA, RNA polymerase and Ribosome all exist in shared space. Below is a classic image of a strand of DNA(stretching left to right) in E. coli being transcribed into RNA. The RNA molecules extend away from the DNA and appear to travel up or down away from the DNA in this micrograph. Along the length of the RNA, we see dense ribosomes which are busy synthesizing proteins.

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In Eukaryotes, the nucleus encases the DNA, the RNA polymerases and mRNA. mRNA can be completely synthesized and modified in a number of ways before they are exported from the nucleus to the cytoplasm, where ribosomes will translate the message into protein.

One of the modifications of Eukaryotic mRNA we spoke about was splicing. Splicing is a means of snipping segments of non-coding introns out of the mRNA leaving a mature mRNA with a continuous strand of exons. One interesting possibility this enables is the production of alternative sequences made from differential splicing of the immature mRNA. These alternative mRNAs are known as splice variants. At this point, I was asked for an example of a gene that is handled in this way and was caught flat-footed.

Hmm. Perhaps this is something that I’d heard so much about in classes but never in the ‘real world’. I’ll have to look.

One of the first things I found was this discussion of splice variants suggesting that this was not a biologically significant event. i.e., the RNA may be alternatively spliced, but do these splice variants actually result in functional proteins with different properties. The author poses a challenge to find examples of splice variants that are ‘real’. The ensuing discussion is a good one.

What would this looks like?

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Regardless, I found a paper with some good figures that may help students understand how this phenomenon (at least putatively) occurs.  Here’s the best figure presenting a diagram of the different mRNAs created and gels and sequence data indicating that these exist.

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The above Figure shows the presence of distinct RNA species, although that, alone, does not mean that these RNA are ever made into protein. To do that, western blots of protein extracted from various tissues is shown below.

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What is left to find is whether each of these two proteins actually does something. Are both forms required? Are their functions distinguishable?
My quick look through the literature did not uncover any evidence for this last question. If anyone out there knows the literature on this, I would love a push in the right direction. It doesn’t matter what gene we’re looking at, just that it is an example of alternative splicing and that each of the splice variants is actually made and has some identifiable and distinct function.
 
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Posted by on April 4, 2014 in Uncategorized

 

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The Returned is wickedly good

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I’ve fallen under the spell of the Sundance Channel’s ‘The Returned’ (Fr. Les Revanants).

What started as a slow-paced introduction to a small city in the mountains of France dominated by a large dam on the outskirts of town that provides power to the city and appears to be hiding some secrets.

What separates The Returned from other thrillers like it is that it introduces us to the Living Dead in a way that is entirely new, these aren’t horrors that are out to sate their appetite for human flesh, instead, they are just like the rest of us. Perhaps a little more confused and alienated, but really just trying to find meaning.

Why am I here?

The Returned don’t seem to know any more than we do. They once lived in the city, they died and now – they’ve returned. In the first episode we are introduced to Camille, a girl who died when her bus swerved to miss a little boy and left the road to plunge off a precipice killing all aboard. Camille walks back into town remembering nothing of the accident and thinking that it just happened, when in fact she had been dead seven years.

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Why Can’t I Leave?

I expected the rest of the bus’ occupants to make up the remainder of the returned, but I was mistaken. The rest come from a number of walks of life and they’ve died at various times. None seem connected at first, but some similarities do appear as the season progresses.

I’ve watched all but the finale, which I look forward to eagerly. Recently, the last several episodes have altered my expectations and given hints of a variety of influences. Apparently no one can leave, and a horde is amassing…

 
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Posted by on April 2, 2014 in Uncategorized

 

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