|Clickable Hierarchy of Biology|
Biology, just like an onion, has many layers presenting an organizational diversity of intriguing complexity. Today we shall look at Biology in a way that may seem backwards to some of you with experience...but shall be perhaps more natural than is normally presented in textbooks and classrooms.
This picture is a view of the earth from space. The photo was illuminated by the sun. You can tell from where the highlights are on the biosphere that it is summer in the Northern Hemisphere. You can make out North and Central America. You can see that even up into Canada, the surfaces are green with vegetation. This is definitely a summer photo.
The earth has become populated by a wide range of organisms that have diversified and spread to live in just about every place on this planet. And so the earth is a biological sphere. It is loaded with both terrestrial and aquatic (marine) areas that support many life forms. The earth provides geological surfaces, mineral deposits, water, weather and climate that create myriads of micro-habitats and micro-climates to support the various myriads of organisms that have specialized (speciated) to maximally use these resources.
Noticeable in this photo is the north polar ice cap, cloud formations including weather storms, sparsely vegetated desert and montane terrestrial areas, heavily forested terrestrial areas, and oceans brimming with life...especially at the edges of continents where the nutrient runoff supplies minerals for a vast marine food chain. Connecticut is covered by a huge summer storm system and so is not visible here.
The various areas of the biosphere are divided into:
As we zoom closer to the biosphere, it becomes obvious that there are areas of some similarity. As mentioned before there are desert areas, montane areas, forested areas, and marine areas.
In this view we are coming in over an area of the biosphere that is heavily forested. This kind of region and its ecological factors, such as cloud cover, rainfall, rivers, snow, altitude, and its living organisms are together called a biome.
This forest biome will vary with latitude, proximity to ocean, and so on. So there are deciduous forest biomes, montane forest biomes, rain forest biomes, and so on.
Here in Eastern Connecticut, we live in what is known as the Eastern Deciduous Forest biome. The trees of the Connecticut woods are mostly deciduous, meaning that they lose their leaves each autumn, are leafless through winter, and releaf in spring.
Our winters are mild, our summers are mild, we do get freezing winter temperatures and insulating snow, and in the spring the snow melt makes rivers run rapidly and provides the soil with good moisture for the spring leafing season. The summer productivity is high and the forest becomes dense.
The biome is subdivided into various...
As we move closer to the ground, we can see a prominent river ecosystem sweeping through the landscape. The river ecosystem receives organic nutrients from leaves that fall into the water. It receives minerals in runoff from the mineral soils of the land. These nutrients feed an aquatic ecosystem in the river made of phytoplankton and zooplankton that feed invertebrates that, in turn, feed fish. Fishing birds and shoreline bears feed upon the fish in the river. The sediments hold a range of decomposer organisms that help recycle waste organic and inorganic material back into the water.
Away from the river we can see forested regions in the light from the sun. In cleared areas we see grasses and other forbs covering disturbed areas. The forest ecosystem will have trees as the primary producers, herbivores as plentiful consumers, and a few predator species that feed upon the herbivores. In the leaf litter on the forest floor, decomposer fungi and bacteria will assist in the recycling of dead material back into the soil water for use by the trees.
The forest biome will also have pond ecosystems, although this photograph does not show a pond for our benefit.
The forest ecosystem is dominated by its forest....
This forest community is dominated by it trees:
It is often said that we sometimes miss the forest for the trees, however, in this view, I think we see the forest but not much about the individual trees. You might notice that the trees forming the canopy have the different colors of leaves and different overall shapes. And so the Eastern Deciduous forest has a wealth of tree species for which it is famous. Perhaps you are aware of the red oak, black oak, hickory, beech, birch, and red maples of our Connecticut woods.
But a forest community is more than its trees. As we get down to earth we will see other kinds of organisms making up the community too.
While a forest is dominated by its producers...the plants... we will also find herbivores (primary consumers feeding on the plants, and carnivores (secondary consumers) preying on the herbivores. So we have a food chain or, better, a food web of different organisms that interact with each other.
In this photo you see lots of tree trunks representing the producers. But there is also moss and lichen growing on their bark, and a range of forbs (small green plants) growing on the forest floor. In the right foreground, you can see some fern fronds, for example. The main subject of this photo was likely the black bear. This animal has been shredding the bark and outer wood layers from the tree behind it. This probably serves to sharpen and clean its claws, and provides bedding. Later the pile of debris will serve as fuel for the decomposers in the forest: invertebrate animals, fungi, and bacteria.
And so the forest community is rich with organisms for us to enjoy. It is my hope that you will enjoy a walk through the ECSU Arboretum to get first-hand experience with some of the many species of the forest community.
The individuals of each species in a community constitute a...
Virtually every picture of the forest actually shows a whole range of species, this photo shows lots of tree trunks of small diameter. It gives you an impression that each species, say red maple, is represented here by many individual trees. These trees constitute the population of red maples in the forest.
The population of red maples of course represents the species. The individuals of this population mate with each other each spring and produce propeller-like winged fruits that fall from the trees in the summer. Each fruit contains a seed, which in turn, contains an embryonic maple tree. In this way the population of maple trees expands in the forest. Individuals that die or fall down in a storm (notice in foreground) are replaced by other members of the population.
Over time this population will respond to changes in its ecosystem in differential reproductive success. This means that this scene might not be quite different in a million years, but left to nature, the genetics of the trees standing there could be very different indeed. It is at the level of population that evolution happens... because it is at this level of organization where differential reproductive success is a reality.
Put another way, in this population there is extreme competition between the members of this population. Some will be more successful in seed production because their genes are better suited for this competition in this place. They will survive genetically and play a larger role in the genetics of the future forest than the less-successful individuals. Survival of the fittest is about reproduction in a population.
Each member in a population is defined as a individual....
Here you see one individual tree...an organism. How is it different from one of those in the photo above?
It is clear that this individual is robust. It is loaded with leaves, its trunk is heavy. It is shading out the competition that might get a start beneath its canopy. It could be that this is a member of a great forest that happens to be a champion. But the lack of competitors in the foreground and the extreme shortness and high density of the vegetation on the forest floor leads us to decide that this tree may not be a champion, but has been championed by an animal. This animal keeps the vegetation low around this favored tree, waters it, fertilizes it, and prunes it for maximum effect. The animal is doubtless Homo sapiens.
This level of biological organization...the organism...is the focus for our semester. We will study how individual organisms cope with each other and with their environment, and to carry out all of the properties of life.
Each complex organism has a range of...
A tree has several organ systems. Vegetatively, it has a root system below ground to mine the soil of nutrients and transport water into the tree, and a shoot system of stem and leaves (shown here) to carry out photosynthesis and to evaporatively cool the tree in the heat of summer.
It is worthy to note that the tree cannot jump into a lake or hide in a cave when the temperature is hot and the sun is beating down intensely on it. And so its roots take in water, the stem conducts that water, and the leaves evaporate water into the air to cool the leaves. And so the shoot has two major functions: cooling and photosynthesis.
The shoot also supports later an organ system known as a flower, and another organ system known as a fruit.
A complex organ system consists of...
Here we show just one leaf from a maple shoot. This leaf is one organ of that organ system. It has a long petiole (lower right) and an expanded blade. This blade has a particular shape...a bit less blocky than the sugar maple leaf of the Canadian flag...this is the more delicate silver maple leaf. The margins of the blade are neatly but irregularly serrated. The blade is bright yellow-green, demonstrating chlorophyll a as the main photosynthetic pigment and xanthophylls as the main accessory or antenna pigments for photosynthesis. The blade of this leaf also shows yellowish veins. These contain conductive tissues for bringing water and dissolved soil minerals into the leaf, and for taking sugars and amino acids from photosynthesis (dissolved in water) out of the leaf.
The leaf has microscopic pores in its skin-like epidermis through which the water evaporates to cool the leaf. That water coats every cell in the inside of the leaf to maximize evaporation from those cells into the gas space inside the leaf. Thus each cell doing photosynthesis is also helping to cool the leaf.
As we have alluded to here, the leaf is composed of...
We have moved to a thin slice of the leaf blade above. This thin slice is viewed by microscope from the cut surface after staining the slice with artificial dyes.
At the top of the view is upper epidermis tissue. As its name indicates this is a skin-like tissue. It lets light pass through the cells and to the inside of the leaf. So the upper epidermis has window and lens-like functions.
The interior of the leaf is filled with two layers (labeled faintly A and B) of a tissue known as mesophyll (literally: middle of the leaf). The upper portion of the mesophyll (A) is called the palisade mesophyll because of the column-like shape of its cells. The cells each show an artificially red nucleus and pale lavender/brown chloroplasts. This portion does most of the photosynthesis of the leaf. The second layer of mesophyll (B) is shaded by the first and is called the spongy mesophyll, again, based on the rounder shape and the loose packing of the cells. The surfaces of these mesophyll cells are wetted with water from the soil and as it evaporates from their surface it cools them. So the spongy mesophyll functions more in cooling than in photosynthesis, though the cell have plenty of chloroplasts.
The lower epidermis shows two cells (labeled faintly C). These are guard cells and the opening between them is called the stoma. It is through this opening that water evaporates to cool the leaf. It is through this opening that carbon dioxide comes in for photosynthesis and oxygen comes out for us! The guard cells determine whether the opening is large or small, so the function of the lower epidermis tissue is regulating gas exchange.
Each tissue layer is made up of individual...
Our next photo here is a plant cell from the mesophyll of a leaf. This individual cell was isolated from a torn leaf by digesting away the pectin glue between the cells and the cellulose and hemicellulose of the cell walls. This was done enzymatically in an isotonic buffer so that what you see here is a plant cell without its cell wall. The boundary layer consists of cell membrane (plasma membrane) only. This kind of cell is sometimes called a protoplast.
You might notice the large green chloroplasts (organelles) inside the cell. Since this was a mesophyll cell, their presence for photosynthesis is not a surprise. This cell was not stained so you can see the natural color of chlorophyll-containing chloroplasts in this cell.
If you look closely inside the cell you might notice that the chloroplasts are, in three dimensions, located just under the cell membrane and that the majority of the interior space appears colorless. This is showing the large vacuole of typical plant cells. This fluid filled sac is the location of toxic waste processing.
What is not shown is the nucleus...it too is a clear sac containing DNA and information processing enzymes but lacks any natural pigments for color. In the previous photo it had been artificially stained with a red dye. But we shall see this nucleus stained another way below.
Each cell contains...
Here you are seeing part of a cell that was stained with heavy metals (Osmium and Uranium) and viewed in the transmission electron microscope. The image was made by electrons penetrating a thin slice of the cell and exposing the film. The dark areas have lots of heavy metal staining and so hold back the electrons so the print is dark. The clearer areas have less heavy metal staining and so look light because the electrons passed easily, exposed the film, turning it black, resulting in a light print area.
The large oval in the middle of this picture is the organelle known as a nucleus. The tiny letter A in the lower left quadrant is showing the two-layered nuclear membrane of this organelle. The lines inside the nucleus are pointing to portions of nucleic acid-protein chromosomes that stain heavily with the metals and look dark in the photo. Because the nucleus contains DNA condensed, at least partially, into a chromosome, we know this cell is probably approaching mitosis (or meiosis). But the presence of the membrane tells us it is still technically in early prophase. Some of the peripheral areas staining darkly are probably RNA that has been transcribed in the nucleus too.
Other organelles shown in this picture include the endoplasmic reticulum (ER) (perhaps shown by letter B in the upper right quadrant). There is a mitochondrion just below the letter A. To the left of letter A are parts of five lipid droplets (oleosomes).
Organelles are made of...
In our last photo is a model of a very small portion of a DNA molecule. In this image, the balls of various colors represent atoms found in the double helix of DNA. Here you can see the sugar-phosphate sides of the double helix ladder, and the interior nitrogenous bases. Phosphorus here is shown in yellow, oxygen in red, carbon in green, hydrogen in white, and nitrogen in blue. I'm sure you could have figured that out by checking out the structure.
DNA of course is but one molecule in Biology. And perhaps I should have continued this down to the subatomic particle. Indeed protons control the pH of the cellular compartments and are responsible for many processes in cells including the synthesis of ATP! Electrons are critically involved in the light reactions of photosynthesis.
Nevertheless, I hope you can see that the field of biology is very broad. Its many layers extend inward from the perspective of the whole planet down into biochemistry! There is much room for further study by generations of biologists. So indeed you have picked a field of study with much promise for future work!
I hope you won't mind that I chose to focus on a plant at the organismal level. Remember the producers out-weigh, and significantly out-number the other kinds of organisms in most ecosystems in our biosphere. It is for this reason that biomes are named by their plant communities. I know some will say I chose it because I am a plant physiologist. Well there could be a grain of truth in that too. Plus I like to do things differently that most people do. Almost every book uses humans or at least vertebrates for this topic...so I picked a plant...in part...just to be different! I also chose to start at the highest level of organization and work downwards to chemistry. Again, most textbooks and apparently teachers, choose to show you biology from chemistry and work upwards toward the planet. I'm just persuaded by years of contact with younger students that you relate better to the earth than to molecules. So I like to zoom in rather than zooming out...to start with the familiar and work toward the unknown. It seems natural to me.
This page © Ross E. Koning 1994.
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