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Monthly Archives: September 2012

An interesting look into why DNA and RNA might use different nucleic acids for what seems to be essentially the same purpose (namely Thymine and Uracil).

Earthling Nature

by Piter Kehoma Boll

ResearchBlogging.org About a year ago, while I was in my class of Techniques of Molecular Diagnosis, an interesting doubt sprouted: why does DNA use thymine instead of uracil as RNA does?

I hope everybody reading this knows about nucleic acids and the difference between DNA and RNA. As a very quick review:

RNA (ribonucleic acid) is a polymer made of ribonucleotides, compound molecules made of three parts, or smaller molecules: a nitrogenous base (adenine, uracil, cytosine or guanine), a ribose sugar and a phosphate group.

DNA (deoxyribonucleic acid) is similar, but instead of uracil it has thymine, and instead of a ribose sugar is has a deoxyribose, so that it is made of deoxyribonucleotides. Another difference is that DNA is a double chain twisted helicoidally, where two nitrogenous bases (each from one of the chains) are connected. Adenine is always connected to thymine and cytosine always to…

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Posted by on September 29, 2012 in Uncategorized

 

Nature’s hidden beauty – A tangent from Intro Bio

Photosynthesis is a way that nature observes the first law of thermodynamics.

As we all learn in school, the sun is the primary source of energy on Earth, but only a fraction of Earth’s residents can tap into that energy directly. The rest of us, the heterotrophs (from hetero- other and troph – food), get our energy indirectly. We either eat the plants (or other organisms) that produce their own food, or we eat the things that somewhere down the line got their energy from eating autotrophs (from auto- self).

But, because the first law of thermodynamics states that energy cannot be created or destroyed, but only converted from one form to another, these autotrophs could not make their food from nothing. Instead, they converted (solar) energy from the sun into chemical energy via photosynthesis.

Solar energy, which comes to Earth as photons, has characteristics of both particles and waves (as it turns out everything does). These waves have energy that is inversely proportional to the wavelength of the light- shorter wavelengths transfer more energy than longer ones. I like to think of it this way: Shorter wavelengths mean more waves per unit time. If you were one the beach watching waves come in to shore, if more waves crash on the beach in an hour on Saturday than on Sunday, then more energy was transferred per hour from the ocean waves to the shore on Saturday.

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Absorption spectrum of pigments

The visible light we can see only a small slice of the broader electromagnetic spectrum. Because we see only the light that bounces of things, if those things absorb some of that light (such as plants that use the light for photosynthesis), then we see only what they reflect back because it is not absorbed. This explains precisely why most leaves appear green – all but the green light is absorbed by pigment molecules that are collecting energy in the chloroplasts.

We can see this clearly by looking at an absorption spectrum of several pigments found in leaves.

What’s really interesting, is the beauty of flowers. These parts of the plant are not photosynthetic*, but they also contain pigment molecules. Why?

Of course we know this. Flowers are the reproductive organs of plants, and they often require assistance from insects or other animals for pollination. The way they attract pollinators is by giving a reward (nectar) and providing visual cues about where that reward can be found (the colorful flower).

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Visual spectrum comparison

But, it turns out that bees (a common pollinator) don’t see the same visual spectrum as we humans do. Instead, their spectrum is shifted slightly in the ultraviolet direction.

Naturally, this would have consequences. If bees can see UV light, it would be reasonable to expect that some flowers use pigments that make them visible at UV wavelengths. In fact, this is exactly what we see – well, what we would see if we could see UV. Here’s a representative flower shown as we see it and as a bee may see it – with a UV colored landing area right where the pollen and nectar are found.

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Natural Light / UV Light

*At least I think they aren’t. If anyone can provide an example of flower petals that photosynthesize, that would be greatly appreciated.

 
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Posted by on September 28, 2012 in Uncategorized

 

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The nature of truth

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The Valley of the Shadow of Death

There was an interesting podcast by RadioLab this week concerning the nature of truth that I wanted to comment on. There were a number of stories in the broadcast, as always. One on yellow rain is getting the lion’s share of attention on the RadioLab site for the treatment of one of the guests that many listeners objected to. However, that is not the one I would like to focus on. In fact, I really only wanted to mention the podcast because I thought it was a good introduction to a topic that I find troubles a lot of people.

First, the podcast. I would point you towards the short, “In the valley of the shadow of doubt,” about one of the earliest photographs taken during wartime. In fact, the episode is about two photographs by the same person, Errol Morris, who was documenting the Crimean War in 1855. The two photographs depict the same scene, titled ‘In the Valley of the Shadow of Death’ that depict a road in the Ukraine. In one, the road is littered with cannonballs. In the other, there are no cannonballs on the road, but there are many off on the side of the road in ditches an on the hills.

The question that the photographs bring up is, ‘Which one was taken first?’ That is, did the photographer come upon a road littered with cannonballs that were removed – or did he come across a road surrounded by cannonballs that he moved in order to catch a more interesting shot?

Of course, we can never know.

There are reasons that can lead us to believe one thing or another (personally, I think one argument is stronger) but there is no way to know absolutely one way or the other. This is the real question that the episode brings up, “Can we ever know truth?” This is a very basic question in science. Most scientists agree (I am presuming) that we can never know anything with certainty. We can only rule out unlikely answers and give support to one theory or another.

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Wielder of Occam’s Razor

We can blame Descartes for starting this with his Discourses on the Method published in 1637. He started the trouble by giving us the scientific method, a method for uncovering the way the world worked. In his pursuit of this, he also realized that we cannot really know anything. He admitted only one thing that we are sure of. Cogito ergo Sum. But from this modest beginning, he also built up a structure and assured us that we have to assume that we can trust in at least logic, and that, until there was reason to believe otherwise, we may as well proceed as if the world we see around us does exist – evidence that he read his William of Occam (1288-1348).

Natural Philosophers and scientists have been fairly comfortable with this state of affairs for years. Assume that the theory with the most data supporting it is true up until the point that new data demands a change in thinking. At this point, we are instructed to drop the old idea and embrace the new one until it inevitably is displaced.

But these words mean different things to different readers. Some may read this as, “See, they admit it, they know nothing. And even worse, the are certain that their ideas will be proven wrong sometime in the future.” Others think, “Yes, of course. How else could one perceive the world?” And they’re both right – in a manner of speaking. It is assumed that much of what we know will change over time. But we also have the security of knowing that our understanding of the world is getting better all the time and it is unlikely that with new ideas we will entirely abandon out old ways of thinking. Rather, we expect to tweak this ideas.

And this would all be fine. But there is another school of thought that comes mostly from the journalists. That is the idea that every position / point of view is equally valid. There are a lot of questions that come to mind where I do think opposing ideas have equal value. These are political questions mostly. However, when journalists come to interview scientists about some finding or idea, two (or more) sides often don’t have the same weight of evidence behind them.

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…hungry……

If I were to ask you where teeth go after they fall out and are placed under a pillow, you might say, “The parents take them and give the children money.” You might say, “the tooth fairy comes and leaves the money in exchange for the teeth.” I tell my son that the tooth fairy needs teeth because she eats them and couldn’t survive without nourishment.

Not all of these hypotheses are equally likely. I have to admit that I’ve never seen the tooth fairy, but someone must have left a camera out to get this picture…

Back to RadioLab. So, what’s true? Does the weight of evidence make something true? Does it make it more likely to be true? Does evidence mean nothing?

On a deep level, perhaps we never know anything. But I can also say this: data is nature’s voice and sometimes it pays to listen.

 
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Posted by on September 26, 2012 in Uncategorized

 

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Intro Biology – Photosynthesis

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A note on the order of my lectures:

So far we have discussed the cell itself and divided its several functions amongst organelles that carry them out. We have also discussed the properties of membranes and how diffusion operates across them as a passive event. As a consequence diffusion can be opposed, but requires energy input. Lastly, we covered energy and how it may be converted into various forms or used to do work. Within the cell this work is often guided by enzymes.

 

Where we are going:

In the next section we will address how energy is captured by living things from the environment and converted into a form that may be stored. In the chapter after that, we will consider how this captured energy can be brought out of storage and converted into a useful form for enzymes to use in getting specific jobs done.

 

Photosynthesis

 

As stated above, the purpose of photosynthesis is to convert energy from the environment (solar energy) into a new chemical form (glucose) that can be stored for later use by cells.  The process of photosynthesis is completed, in eukaryotic cells, entirely within organelles called chloroplasts. These are organelles that are theoretically descended from prokaryotic cells that engaged in symbiotic relationships with larger cells but are now inseparable parts of the larger cells. As such, we recognize that there are other cells that can carry out photosynthesis, but we will restrict our discussion to that carried out in plant cells.

 

The basic reaction occurs in two phases, the light reactions and the dark reactions. Despite their names, both occur at the same time, typically when it is light.

 

The light reactions are when photons from the sun transmit energy into pigment molecules in the chloroplast. From there, electrons carry the energy from one  molecule to the next in an electron transport chain that functions to pump protons (H+) across the membrane. In this way an electrochemical-, or proton-, gradient is established.  This gradient is a form of potential energy that can be released when protons diffuse back across the membrane passively, through ATP synthase proteins that form channels through the membrane. When H+ ions pass through this channel energy is captured to synthesize ATP through a process called chemiosmosis. This is very analogous to the way that dams capture the energy of water passing through. The high energy electron is finally passed off to form NADPH, a high energy electron shuttle. Because the reaction cannot repeat until the electron is replaced in the photosystem, one is taken from H2O, which splits to form O2 and more H+ ions. The end result of the light reactions is the formation of ATP and NADPH (and O2 as a waste product) from solar energy and H2O.

 

This summary does not include details reactions starting from Photosystems I and II specifically. Nor does it include the cyclic reaction.

 

The dark reactions will be covered in our next class a little more extensively, but basically, their function is to use the ATP and NADPH produced in the light reactions as power to synthesize glucose from CO2.

 

 

 

 
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Posted by on September 26, 2012 in Uncategorized

 

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An autotrophic animal

ImageHere’s the article that I stumbled upon today. It describes an animal (a sea slug) that ‘steals’ chloroplasts from the algae it eats and retains them in a functional way such that they can provide nourishment to the animal for many months.

This is not a true photosynthesizing animal – meaning that it can only temporarily harbor chloroplasts from its food, but it is still an amazing oddity.

http://www.independent.com/news/2010/jan/30/first-known-photosynthetic-animal/

 
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Posted by on September 25, 2012 in Uncategorized

 

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Diffusion Lab Rubric

For our diffusion lab using eggs, I would like each student to write up a short report following completion (approximately three weeks after starting). This report will be approximately one page (feel free to go over up to two pages) including the following:

Introduction / Background     5pts

Protocol Description             5pts

Data Reporting                     5pts

Conclusion / Discussion        5pts

+ 5 pts just for turning it in, for a total of 25 pts.

When you write this report,think about how this document should include all the information required for someone else to understand, what you did, why you did it, what results you saw and how you interpreted those results.

By the way, this is the greatest lab-themed video ever (This is what makes graduate students laugh and cry):

 
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Posted by on September 25, 2012 in Uncategorized

 

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A hint for my students

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Wow, does this man look powerful!

As I alluded to in an earlier post, there will be an extra credit question about some recent Presidential candidates. Nothing terribly hard. The one thing I will say is that I won’t ask anything as far back as Ford, who lost to Carter in 1976. 

By the way, isn’t it amazing that something so simple as one photograph could be plausibly considered a major contributing factor to losing a campaign?

 

 
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Posted by on September 24, 2012 in Uncategorized

 

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