Organismal Biology

Terms and Concepts


Introduction:  The Basics


Human beings have an innate need to understand things, it's how we learn and how we teach - just try to teach something that you really don't understand!  In explaining things that are difficult to grasp, we have a long history of using what we do sort of know to explain what we really don't.

There are other ways to look at this, but one possible view of human history is that we see Nature in the terms that make the most sense at a given time.  Older societies, without the technology to strongly affect their worlds, saw their world in terms of the things that had the Power:  Nature Spirits, with motivations one might expect from a fusing of human consciousness but the limitations that come from being wind, or forests, or the sun.  Later, as humans gained the ability to manipulate their own environment, as power over Nature became something in their grasp, the forces of Nature they believed in became much more human, in form and personality, although much more powerful - the human-like gods controlled those larger aspects of the world in ways similar to the ways that humans controlled the small aspects of theirs, and nature spirits became more human and less powerful.  Today, these explanatory ideas occasionally slip out of the realm of explaining Nature and becomes something more concerned with Human Nature, with those aspects of Life and Afterlife that still seem unexplainable, and the forces conceived are less human and more forces of Consciousness itself.  Meanwhile, centuries of small successes in explaining this or that piece of the big Nature Puzzle has moved humanity, or a sizable fraction of it, from seeing Nature as something that can not really be understood, that must be explained in supernatural terms, to the conviction that everything can be broken down into tiny bits and all of the workings analyzed.  We like the feeling that this has moved us somehow closer to the Truth, and scientists probably feel some of the same sense of Specialness that used to be the province of priests, of being more In The Know than the rest.  Are we closer to some knowable Truth?


It's typical for a book to lead off by setting up its basic definitions and terms, and this will be no exception.  This is all about biology, the study of living things (the term organisms is a nice catch-all term that includes anything considered alive).  And generally, biology is thought of as more than just study, it's really the scientific study of living things.  We'll get to what makes a study scientific before long;  right now, let's deal with what makes a living thing alive.


When we look back from today to ancient times, there's no reason to think that human beings were any simpler or stupider as a group or as individuals than they are today.  They did have a much smaller pool of accumulated knowledge to build upon, so you might say that they were more ignorant than we are today.

But certain aspects of humanness were undoubtedly just as powerful then as now:  the need to know why things happen the way they do, and the need to break information down into manageable and useful bits, and the need to categorize and explain relationships.  Of all the abilities humans have in different amounts than other animals, it may be their greater sense of how cause relates to effect that most is the basis of science.

You can see aspects of human organization in how people have investigated Nature - we look for family, tribe, and nation types of relationships, in patterns that match patterns in human societies.  If Modern Science is a product of "Western Society" - which is arguable, of course - it may just be an outgrowth of the level of structure and coordination and planning needed for continental systems of connected cities and the support infrastructure to have them interact meaningfully with a globe of trade.

Historically, early biology was a mixture of a need to understand the practical - humans showed a practical grasp of genetics millennia before Mendel began to work out the details - and a compulsion to grasp the Big Picture.  From a simple level, as the concept that a dog, a wolf, and a fox were different types of animals but could be joined together in the larger but definable type of Canines, to a larger but understandable concept that living things with similar functions could be placed in groups together - the creatures of the water, the creatures of the air, the slithering legless things, the things that grow from the ground, et cetera.  It seems a simplistic way of grouping things together, but one suspects that it was convenient, and that the ancients who really used the system probably realized that it had some limitations, as users of today's systems do.


This is the first place that we get to deal with a recurring theme in this book:  biology is a practice, a set of behaviors, done by human beings, which means that some of the "rules and regulations" can be partly understood from the standpoint of general human compulsions.

First, humans like to name / label and categorize things, put them in neat little symbolic boxes, which helps us in our second endeavor:  humans also like (one could say that they need) to explain how things work.  The science of biology provides one way to explain the world, and what qualifies as a living thing falls into the area of labeling.  It's important to remember that human explanations are always limited by our knowledge at any given time, and that labels and categories are limited by how well real objects squeeze into the constraints we put on them.  Life goes on whether we understand it or not, and living things care not a whit whether they're in one or another of our little labeled boxes.  And, in biology, labels and explanations must be somewhat loose.  For example, a species description of dogs must be broad enough to include all dogs.

You may need to lose a tendency that most students, being human (or so they claim), bring to a biology course - they think that Life always works in the same patterns that you see in humans and other big fuzzy animals.  The sooner you come to the realization that there are lots of other ways of doing things than how it works in people, cats, and horses, the better off you'll be.

Although "life" may seem at first like "art" - "I know it when I see it" - it needs to be better defined for a science to be built around it.  We're going to develop a list of features that can be applied to living things everywhere.  Virtually every biology textbook in existence has a list like this, but if you were to check, you would find that the lists rarely match each other point-for-point;  some things are separated into distinct features, while others may be lumped together.  But if you look closely enough, the categories found here are all in those other lists somewhere.


"Oh, genetics, I've heard of that!"  Of course, that doesn't mean that the term really means anything to you.  What exactly is a genetic system?  In this instance, it means that living things are able to reproduce in a way that passes features, or at least information about making features, along from a parent to its offspring.  For living things on the planet Earth, this feature is usually based on information stored in Deoxyribonucleic Acid, or DNA.  Genes are made of the material DNA, and this is the basis of the term "genetic."  This molecule holds the sequential code by which sequence-of-amino-acids proteins are made - and proteins are the workhorse molecules of earthly organisms, producing directly or indirectly the "traits" people commonly connect to "genes."

But features can be passed along in non-DNA ways - some features found in your cells are there because they were in your mother's egg cell, and some of your traits and tendencies may be linked to the chemistry that surrounded you in the womb while you developed.   Another type of example would be this book, and all of the sorts of information that can be passed on through learning.  Inheritable traits that are not strictly in our DNA code are called memetic and epigenetic - later, when things like evolution are discussed in terms of passing on traits, this is something to remember:  all that we are, all that we pass on is not just in our genes.  This also opens the door for many of what we might call machines to have this aspect of life - is transferable computer code sort of genetic too?

This all connects to another aspect of Life - the ability to self-organize.  Those information systems allow living things to construct complexes of materials that all work together to produce themselves, using available energy (self-organization has to be an energy-using process).  All of the complexity in a cell is tied to the genetic system passed to it by the previous cell.

Embedded in this feature of Life is reproduction - its hard to pass traits on to offspring without reproducing. You could probably imagine a living thing that is immortal (and really lucky) and never reproduces, but no one has found such a thing.  In our world, living things reproduce, and reproduction falls mostly into two camps:  asexual reproduction, where offspring are genetic copies of the parent (they can be genetic copies yet not to be physical copies, because of how genes work), and sexual reproduction, where offspring are a mix of gene sets from two sources (and which may or may not involve two separate parents).  You might not think so by looking at these definitions, but there is a gray area between these types as well, where copying happens but some mixing is allowed.  As we'll see later, there are advantages to each and disadvantages to each (and, as a trend you'll eventually notice in many of these kinds of biology pairs, the advantage of one reflects upon the disadvantage of the other).

A side effect of reproduction is growth and development:  without growth, each generation would get progressively smaller beyond their ability to survive;  without development, the next reproduction phase could not be timed properly.  Growth is a fairly simple property, while development can be a simple switch in a cell that says, "Don't divide yet," or the many complicated stages that multicellular organisms go through between one zygote (the very first cell, usually created from the fusion of a sperm and an egg cell) and the next generations zygote-generating adult.

An old biology proverb states that, "An adult is just a zygote's way of making another zygote."  You might have heard a variation:  "A chicken is just an egg's way of making another egg."


Both parts of this term are important - dynamic refers to how living things are always changing, as their internal chemistries use resources, convert energies, and produce wastes (this energy-shifting chemistry is known as metabolism)units refers to how living things exist as individuals, separate entities with particular needs.

Internally, living things are a storm of interactive atoms and molecules, extremely tiny objects, not themselves considered alive, whose complex relationships, involving energy and particle transfers, make up the activity of life on its tiniest level.  This is the most modern area of biology, and a good example of science as reductionism:  the expectation that any large activity can be totally understood if you understand how all of its tiny pieces work.  Again, being human makes us feel in our guts that all of the little labeled components must add up to the whole, even though biology commonly exhibits what are called emergent properties that appear when several complex systems produce effects that don't seem to be simply a product of the pieces.   Anyone familiar with computers has seen examples in those complex systems as well - behaviors that can't easily be explained by knowing how each piece of software works by itself.  Of course, computer people and biologists are often sure that even emergent properties can be reduced to understandable components, and they may be right.

Just as a warning, when activity on an atomic / molecular level is covered later (mostly in the second semester), you may find it the most difficult section to grasp.  It is essential to have a good understanding of molecular issues as a foundation for most biological fields, but the basic mindset of budding biologists does not tend to match that of chemists, so that material may not settle in our brains as naturally as other concepts, and in fact may need to be learned by rote until later exposure and broader understanding brings it into better focus.

The units of life begin on the small level (much bigger than molecules, though) with cells, contained bags of many floating chemicals sealed inside an oily membrane that allows a large degree of control over what enters and leaves.  Organisms can be just one single cell (the vast majority of living individuals on Earth are unicellular, made up of only one cell), or they can be a collection of cells that divide up duties (multicellular organisms).  In keeping with the odd reality of the world, there are also unicellular colonial organisms made up of individuals that are technically "independent" cells but virtually cannot exist without others in the colony - the term "colonial" can apply to collections of unicellular organisms, but also to groups of multicellular species, such as ants, and even people.  Unicellular colonials are somewhat intermediate between unicellular and multicellular organisms.

Groupings exist on a larger level as well, all within (variable) defined systems - groups of individuals of the same species are populations;  groups of populations are communities;  taking in the non-biological aspects of a system makes it an ecosystem.


Living things, as stated before, are dynamic as their internal chemistries use resources, convert energies, and produce wastes.  These changes cannot be sustained in a locked chamber with no connection to the world around them.  Organisms must pick up materials, release materials, and try to avoid circumstances that would kill them, either from immediate threats (such as something trying to consume them, or a toxin, or a potentially-harmful germ) or long-term needs (examples would be finding needed resources, or preventing its own wastes from poisoning it).  These needs require the ability to pick up cues from the environment and respond to them, something that can be very simple, as some molecule-based "switches" are, or as complex as the information to absorb and process and the responses you produce every minute (Hello, you are responding, right...?).

The level of interaction depends upon the "size" of the environment being discussed ("environment" is a very flexible word).  Each cell exists in an immediate locale of atoms and molecules, usually in a water-based soup.  Individuals exist in microenvironments that are just their immediate surroundings and fit into ecosystems that include, in theory at least, all of the factors in the world that influence them and which they influence.  Not surprisingly, any practical discussion requires limits be imposed when studying any particular ecosystem - the boundaries of a discussed ecosystem must be defined

Ecosystems have niches, kind of like functional "slots" into which types of organisms fit - for example, most earthly ecosystems have a niche or niches for Top Predator(s), defined by factors including available prey but also territory and water availability.  This is another area where biology is reductionist, assuming that the workings of any ecosystem can be understood and predicted by a knowledge of all the "pertinent" niches;  this is also another area where emergent properties can be very inconvenient.

One niche absolutely needed in any ecosystem is that of producers: organisms that can move energy from the environment into the sort of molecular-bond energy that can be used as internal fuel.  These organisms form the "bottom of the food chain" - those energy-containing molecules then pass up the food chain to organisms, the consumers, that can't access energy directly from the environment.  One specialized consumer niche is called the decomposers:  these organisms specialize in breakdown of dead organisms and partial wastes, feeding raw materials back to the producers.  Fuel molecule energy is accessed by the process of respiration, which takes stable but hard-to-use molecules (often glucose, a sugar molecule) and moves the energy to easier-to-use molecules (often Adenosine Triphosphate, ATP).  Respiration processes can be done many ways - most multicellular organisms use the most efficient system, aerobic respiration, that consumes oxygen (the many non-oxygen-using respiration types are anaerobic). Energy moving through a living system is that system's metabolic processes, and every time energy transfers, only some of the energy moves through, the rest being lost in the random particle motion known as heat.  Thus, in ecosystems, most of the raw materials get continuously recycled, but the energy is almost all lost and needs to be picked up anew.

Producers on Earth use mostly photosynthesis to capture the energy of many light frequencies and move it into glucose bonds.  In some ecosystems, chemosynthesis relies on heat-energized molecules to supply the starting energy.  These ecosystems are mostly at hydrothermal vents, cracks in the ocean floor where the water and raw materials mix with heat from magma.


Evolution is a change in type over time.  It connects back to that human compulsion to label and categorize things, combined with a knowledge of how the world of the past was different than todays world.  All sorts of things can evolve, so this may be the feature of Life found most often in things that are not alive.  In living things, evolution happens to populations, groups of related organisms, over time - changes happen to the "average" until the definition of the group doesn't quite fit anymore.  That detail makes this feature somewhat different from all of the others, which can be applied to individuals;  individuals can't evolve.

The current best explanation for how evolution works is based upon the Theory of Evolution by Natural Selection, developed and written down originally by Charles Darwin and Alfred Russel Wallace in 1858, with many adjustments and additions, by many people, since.  Generally, "disagreement" in scientific circles with this theory involves a dispute about how much Natural Selection influences evolution compared to other factors, not whether the basic ideas are accurate.  A comparable theory might be the Theory of Gravity - scientists might disagree on the details of how gravity works, but no one suggests that gravity doesn't exist.

What is Evolution by Natural Selection?  Sometimes nicknamed "Survival of the Fittest," it would be more appropriate to call it "Reproduction by the Fittest."  Simply put, since more detail will appear later, in any given group of organisms, there will be some features that directly affect the chance that each individual has of living to reproductive age and then successfully reproducing - who manages to live long enough to make little ones?  As a general trend, each generation of offspring will, more and more, reflect those features the parents had that are advantageous to their current environment, which helped them to survive.  The important detail to include here is that environments change over time - what was a good feature in one environment may not be so good elsewhere or elsewhen - and these changes in environment (the "Nature" part of Natural Selection) influence (the "Selection" part) which individuals live long enough to reproduce and what features preferentially wind up in the offspring.  Over time, depending on an organism's suitability to the new environment, new features and combinations of features (called adaptations, a confusing term that does not always mean the same thing even to biologists) may spread through the population as a whole until the basic "type," or species (there will be a more particular definition of this term later) has changed significantly enough from the "type" of its ancestors that it needs to be relabeled.

Evolution is not an "ever upward movement toward perfection," although that is what it often is portrayed as;  species don't get better at anything other than fitting the environment of the day, which could change at any time.  There is no target, no progress, no ultimate peak at humans (our brand of intelligence may not even be a great adaptation, since it comes with a long list of self-extinction threats from our own meddling, including but not limited to making our own planet inhospitable to us), and not everything evolves at the same rate, partly because the rate at which environments change varies considerably from place to place (even pieces within environments vary), partly because some forms are more flexible and require little change for a new environment (think of humans - when faced with a new environment, we largely change the environment to suit us, a good thing on a small scale but a possible problem at larger scales), and partly due to how long generations last.  Organisms that reproduce quickly also can evolve quickly if need be.


Philosophical Musings on Science.

Viruses - are They Alive?

After defining the traits of living things, it should be made clear that there are things in this world that act alive but maybe don't hit the entire checklist of necessary features.  Modern computerized construction robots (especially ones used to build more robots) can present an interesting debate, but the question of viruses is an old one.

Viruses are extremely tiny things, usually well above molecular size, although the smallest ones get close to molecule-tiny, and well below the size of even the smallest cells.  The basic structure of viruses varies widely and often is not considered cellular - no membrane!  They float around the world, ejected from the last host cell, like set mousetraps, primed to become active only if they make contact with another potential host cell.  That is one of the problems:  free of a host, they seem completely inactive, with no metabolism of any kind, and minimal ability to interact with their environment.  Inside a host, their metabolism is then totally focused on turning the cell into a factory to make more viruses, which will eventually be released fully-formed and "set" to infect the next cell - there is no growth and development in a virus, only construction.  Viral diseases are hard to cure with drugs because viruses lack vulnerability - no working chemistry to interfere with when free, and when they are active, they use borrowed cell chemistry, where interference could kill regular uninfected cells.  Only the fact that, in some viruses, some of the construction or release chemistry is unlike what a normal cell uses, gives drug designers a possible target to poison.

Put these features together - no metabolism in the free form, no growth, no development, often no cell - and its not surprising that many biologists refuse to consider viruses as living things.  Some do consider them alive - after all, they do reproduce and evolve, and they do interact with the environment inside a cell in some ways (that's a gray area that can support either side in the debate).

It may be useful to remember one important fact - no virus in the world cares whether we put it on a "living" or "unliving" list.

Terms and Concepts

In the order they were covered.

  Genetic Systems  
Memetic and Epigenetic Features  
Asexual Reproduction  
Sexual Reproduction  
Growth and Development  
Emergent Properties  
Interaction with Surroundings  
Food Chains
Glucose - Intro
ATP - Intro
Energy in Food Chains
Aerobic Respiration
Anaerobic Respiration
Hydrothermal Vents
Theory of Evolution by Natural Selection  










Organismal Biology

Copyright 2003 - 2020, Michael McDarby.

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