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I Think… but I do not Know

Darwin, wrote in his ‘B’ notebook in 1837,

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And in one instant transformed the way that we all think about life on earth. This simple diagram unified science. It captured Linnaeus’ nomenclature and married it to the fossil progressions that geologist the world over were seeing in the rocks. It redefined how we understand species and laid the framework for a new view of life as being all related at some level, with some organisms sharing more characteristics with their closer relatives and less with those more distant. It allowed scientists more than a hundred years later to recognize that the biochemical foundations of bacteria and yeast and drosophila and humans were all the same. Because we are fundamentally one family. There was no need to identify a genetic code for each species. Instead, we share a common (universal) code of DNA triplets each calling for an Amino Acid in building proteins.

However, there has been a lot of thought about what it really does mean to be a species. Darwin’s book, The Origin of Species, addresses just this point. I raise this question on the first day of my general biology class and my microbiology class. In general biology we eventually rest on the idea that, at least in the larger plants and animals we are used to encountering – and will discuss in the course of our class, the ability to mate with, and produce fertile offspring from is necessary and sufficient to group two animals into the same species. Of course the mule comes up as a near exception necessitating the ‘produce fertile offspring’ clause, but this is a definition we can accept. In microbiology, we are forced, by the nature of the organisms we study, to discard that convenient description. Many micro-organisms replicate asexually and are capable of transferring genes horizontally.

thrashing fish
knowing they’re in a bucket
and not knowing

          -Issa 1819

In the November 1 issue of The Scientist, Axel G. Rossberg, Tim Rogers, and Alan J. McKane tackle the very existence of ‘species.’ Therein, they acknowledge the fact that we use the concept of ‘species’ for our own convenience and consider the possibility (or rater, probability) that the very idea of species delineation may be artificial. The article looks into the variety of life and how the definition must change depending upon the organisms in question and makes us face the assumptions we often take for granted. Click on ‘The Scientist’ below to see the full article.

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                Link to the article in The Scientist

 
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Posted by on November 27, 2013 in Uncategorized

 

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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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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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