Classification

Classification is not a scientific theory.  It is the effort of one species (us) to try and group organisms in such a way as to make sense to us.

The way in which we will classify is by using dichotomous keys.  These leave us with 2 choices. If structured well, it can be a simple yes/no choice.  A flow chart arrangement can be seen below.

Another option is where the choices are arranged in a table.  This example is shown below.



The advantages of keys are:

1. Allows for consistency when classifying
2. Can be used by a non expert

The disadvantages of keys are:

1. If not well written can cause confusion
2. If an organism is new to science, it may be difficult to assign or mistakenly classified

The father of classification is Linneaus. He named organisms using a binomial system, giving the genus name first, then the species name.  In the name, there should be some indication of the characterisics.  For example the name Panthera leo (for the lion) indicated "big cat, lion).

As time went on, and the number of plants and animals described increased, it became obvious that the system of 2 names was not going to be sufficient. The invention of the microscope also meant that the microscopic world was now open.  Eventually the groups of organisms were organised into 5 kingdoms according to their key features at the cell level.

However, the advance of technology and the uncovering of the Archaea has led to major revision of the classification system. Rather than having 5 kingdoms, its now proposed that 3 domains be placed at the top classification level.  4 of the 5 kingdoms are swept into one domain and the remaining one is divided into 2.

Archaea and Eubacteria

With the advent of better technology (particularly DNA sampling and sequencing), bacteria were being grouped into 2 large groupings.  These were the Archaea and the modern bacteria (referred to as Eubacteria).  Members of the Eubacteria were better known because they had grown on suitable mediums for nearly a century.  The link between bacteria and disease was one of the reasons this field was established.

The major features of Eubacteria are as follows:

1. Generally able to survive in the presence of oxygen
2. Generally they have two types of cell walls, that can be identified by certain staining techniques.
3. Widely distributed in a vast number of environments 
4. Essential in nutrient cycles as decomposers.


The major features of Archaea are as follows:

1. Often found in extreme environments
2. Many cannot grow in the presence of high oxygen levels
3. Cells walls are chemically very different from Eubacteria
4. DNA sequences very different from Eubacteria
5. A high proportion of these are autotrophic.  

Some of these bacteria live in environments thought to be like early Earth (hot, volcanic, chemical rich) it is possible that Archaea were the ancestors to many cell types found today. 

Technology and Understanding of Prokaryotes

One of the technologies that can be credited with a recent surge in understanding of bacterial cell types can be credited with the deep sea submersible ALVIN.  When it explored the hydrothermal vents along the mid-Atlantic ridge, it not only sampled larger organisms that were found but also bacterial mats that were on the surfaces on the surrounding rocks.

It was found that these bacteria were vastly different from those that were currently identified.  This led to scientists sampling bacteria in other extreme environments such as hot springs, acid pools and saline lakes.  Again, these bacteria are very different.

Other technologies that were utilised were DNA sequencing and the use of a technology called the Polymerase Chain Reaction.  Using this scientists have found varieties of bacteria that they haven't been able to grow in culture.  Amazingly a teaspoon of soil contains up to 10000 individual species of bacteria!

When the DNA sequences of the bacteria from extreme and often anaerobic conditions were compared to others that more was known about, it was found that they were vastly different.  

Given the incredible numbers and diversity of bacteria and the differences between them, this has led to a revision of the 5 kingdom system of classification.  More on this later.

Another piece of technology that should not be overlooked is the electron microscope.  It showed the internal workings of the cells, the structure of bacterial cell walls, and in some cases showed that bacterial cells formed tough resilient spores that could withstand tough environments.

The first cells, chemoautotrophs and photoautotrophs

The Urey Miller experiment caused a great deal of excitement and was partially responsible for launching a whole new branch of biology called exobiology.

Variations of the Urey-Miller experiment were soon trialed.  It was found that sugars could be produced, lipids that form bilayers could be formed, proteins could be assembled, and molecules that self replicate could be made.  However, how these were able to be aggregated into something resembling a cell is still a matter of conjecture.  However, it is agreed that first cells appeared on Earth between 3.5 to 3.8 billion years ago.  The first fossil evidence is dated to 3.45 billion years ago.

Bacterial specimens found in rocks from the Barbeton Mountains, South Africa.  The rocks are dated to over 3.4 billion years old.

  
It is thought that the first cells were likely to be heterotrophic. That is, they consumed the complex energy yielding chemicals that were in the environment.  This would have been limited and would have run out fairly quickly.  Varieties of bacteria that were able to have produced their own food (autotrophs) would have survived while most of the heterotrophs would have perished.  These bacteria are likely to be the ancestors of what we now call the Archaebacteria.  These are found in extreme environments such as submarine vents in the deep oceans, hot springs, salt lakes etc.

These bacteria utilise fairly simple chemical compounds to obtain their own energy and complex substances needed for growth and division.  Most of these Archaebacteria are anaerobic, supporting the idea that they had their origins in an oxygen free environment.

From this group of bacteria, a new type arose. Rather than being powered from the chemicals produced by volcanoes, they utilised the sun to power the processes need to grow and divide.  These were the cyanobacteria, and their activities would change the Earth and the path life would take.



The first fossil evidence of photosynthesis were the appearance of fossilised stromatolites in WA dated to 3.4 billion years old. The largest colony of stromatolites in the world is currently in Shark Bay, also in Western Australia.
These are colonies of photosynthetic bacteria which form columns as they grow.  A by-product of their metabolism is oxygen.  These organisms were largely responsible for the removal of iron from the oceans, and a for adding large portion of the atmospheric oxygen and ozone layer.  For over 2 billion years, these bacteria were the dominant fossil found in the fossil record.

From single cells to multicellular organisms

In the process leading up to multicellular organisms, eukaryotic cells had to form.  A suggested mechanism is below.  It is thought that a progenitor cell may have got larger than other cells.  To maintain SA:vol ratios it folded its membranes, some of which then enclosed the DNA (forming a nucleus) and the endoplasmic reticulum and Golgi apparatus.


From here we move into something called endosymbiosis (endocytosis - to engulf something, often for nutrients, symbiosis - a long term interaction between 2 things, often to the point where one can survive without the other).

It is thought that the progenitor cell engulfed a heterotrophic bacteria and over time it degenerated into a mitochondria.  These cells were to become heterotrophic eukaryotes.  One of these also engulfed a photosynthetic prokaryote.  This photosynthetic prokaryote degenerated into a chloroplast and the entire cell was the ancestral plant cell.

Evidence to support this idea includes:

1. The fact that mitochondria and chloroplast divide independently of each other
2. The DNA of mitochondria and chloroplasts is circular (like bacteria) and has many common bacterial sequences

A link to describe the process in more detail is here.


Now that we have cells that are structurally similar to modern ones the next step is to get them to work cooperatively.  The levels of cooperation were thought to be 

One example is colonial algae,  Volvox.  It is broken into 2 cell types; cells for swimming (outer shell) and ones for reproduction (small green spheres)



In the case of the Portuguese Man O War (bluebottles)there are a number of additional cell types which are working cooperatively to assist the survival or the organism.  Just to clarify the labelling here, the Gonozooids (reproductive structures) are the light blue ones near the polyp while the Gastrozooids are the red/brown ones just below.

From here it is possible to see further increases in cooperation between cells, and therefore increasing complexity of the organisms that possess them.

The Urey Miller Experiment

In 1953, Stanley Miller, a PhD student, proposed to his supervisor Harold Urey, an experiment to test if the chemosynthetic origins of life were possible under the conditions of what early Earth was like.

This would in part answer the chicken and the egg question about whether it was possible for the early Earth to produce the chemicals needed to sustain life, before life itself actually got going on Earth.

Energy source and some of the gases that Miller proposed to use.           Note NO OXYGEN.

Miller then set up his experiment as follows:



Over a number of days the apparatus showed orange brown materials sticking to the glass and in solution.  Chemical analysis showed the following:


The final group of materials include amino acids (used to make proteins). Other substances include metabolites that certain types of cells can get energy out of.  


The findings were significant for a number of reasons:

1. The early Earth could not have had oxygen present (supported by other geological evidence)
2. The early Earth had conditions that could have allowed for the generation of molecules that would sustain life
3. Other variations of the experiment showed that molecules that could be used in DNA and RNA could be produced.

So this experiment supports the chemosynthetic theory, but because we weren't there to observe it, it is NOT proven.

Chemosynthesis versus Panspermia

There are 2 theories that are proposed to try and explain the origings of life.  These are:

1. Chemosynthetic origins - The chemicals of life were made on Earth.  Once made, these eventually combined to make living organisms.
2. Panspermia - The chemicals of life and/or life was seeded from asteroids and meteorites from space.

Lets start with chemosynthesis.

Looking at the Earth 3.8 billion years ago, it was thought to be highly volcanic, anoxic and had liquid water.  Lightning storms were thought to be frequent around erupting volcanoes (as they are today).  The surface of the planet was being bombarded with radiation as there was no ozone layer formed. The atmosphere was thought to be made up of simple molecules.

It was proposed that the energy of any of the above sources could have been used to break and reform chemical bond, thus turning the simple molecules of the atmosphere into more complex ones.  There will be some description about the experiments involved in this later.

Panspermia describes the idea that complex molecules form in space.  Many dust clouds in space contain carbon, nitrogen and water (ice crystals) in them. In addition asteroids and comets contain these elements as well.  Energized by radiation from the stars the chemical bonds can be rearranged to form complex materials some of which are found on Earth.

The conditions thought to occur in deep space have been modeled in Earth labs and so this theory is plausible as well.  If we find life of a similar chemical make up on other Earth-like planets, it may be that Panspermia becomes the preferred model.  Given what we currently know, it appears that the chemosynthetic origins of life is still favoured. The experiment that got the ball rolling on this was the Urey-Miller experiment performed in 1953. This is the subject of the next post.