Introduction to Biology

Molecules and Cells




Chapter One - What is Life?






Biology is the study of living things.  Living things are also know as organisms.  What makes something "living"?  Here is a list of attributes for what is considered Life on Earth.  Some of these attributes would be necessary for any sort of Life, and some might be variable:  somewhere else in the universe, there may be things we would recognize as alive but which don't have cells, or have a different basic chemistry.

Organisms are internally organized. 

Many complex functional bits work together to produce the functions of living things.  On Earth, part of that complexity is a combination of chemistry based on protein activity and a reproducible coding system for that chemistry based upon DNA.  DNA contains genes, which are the "recipes" for all of those proteins.

Organisms on Earth are also based upon a basic living unit, a cell.  A cell is a contained chamber with its own internal complexity, even its own chambers, but it is the smallest unit considered to be alive.  Many organisms (most, in fact) are just a single cell (unicellular organisms), although the larger ones we see around us are made up of many cells (multicellular organisms).  There are even organisms that are kind of both:  single-celled, capable of living that way, but found in collections where different cells do different activities, as cells in multi-celled systems would behave.  These are one type of colonial organisms.

Complexity levels are very common in living things:  cells have organelles inside them;  cells in multi-celled systems can form specialized tissues;  tissues can organize into organs or structures;  organs and structures organize around basic functions in organ systems, which work with each other.

There is organization beyond the individual organism as well.  Organisms of the same type in an area form populations;  all of the populations in an area form a community;  add in the rest of the area, even the non-living parts, and it's an ecosystem. 

Internal complexity of a bacterial cell, considered "simple."

Internal complexity of a plant cell.

Internal complexity of an animal cell.

Some examples of unicellular colonial organisms.

Organisms transform and use energy.

Internal organization requires energy:  things must be built, activity must be supported.  Energy is available from the environment, but it isn't in exactly the needed form, so it must be taken in and changed into a usable form.  The form cells use for their own energy is the energy used to hold chemicals together;  these chemicals transfer energy to the ongoing chemistry of the cell.

Ultimately, the energy originates from the environment.  It could come from energetic but unstable environmental chemicals, but these are not common.  Using this kind of energy is called chemosynthesis, and can be found in ecosystems around deep-ocean cracks where water and chemicals are heated by lava just under the surface.  These areas are called hydrothermal vents.  Vents like them, but probably in much shallower water, are very likely where Life first developed on the planet from an ocean full of early organic chemicals, a process called abiogenesis.

The most common form of environmental energy used to make proper chemical energy is light, and the process of converting light energy to the energy holding chemicals together is called photosynthesis.  Usually, small non-living chemicals, carbon dioxide and water, are bound together using captured light energy into sugar molecules.  Much more on photosynthesis in later chapters.

Respiration is a chemical process that moves energy from basic energy-holding chemicals (usually sugar) to chemicals that can be actively used in the energy processes of a cell.  The most common active fuel is called ATP, for adenosine triphosphate.  Respiration comes in many forms, and does not necessarily use oxygen in the process.  Much more on respiration in later chapters.

In ecosystems, environmental energy is captured and stored in chemicals by producers.  Most producers are photosynthetic.  That chemical energy can be used by organisms that can't capture environmental energy and must get it from producers:  these are consumers.  One special class of consumers are called decomposers:  these process dead and waste materials so that almost all living material is recycled to the raw materials later organisms need to build themselves from.  The energy, meanwhile, is lost in bits at every transformation as random bursts of heat, which can't be recycled.  Ecosystems can recycle materials, but require constant inputs of energy to continue.  Most of Earth's Life energy comes from the Sun.

Metabolism is the name given to all of the energy-using chemistry in a system.  It sets up the ability of organisms to be self-organizing,  as discussed above.

More on deep-sea chemosynthesis.


The chemistry of deep-sea chemosynthesis.


Video of hydrothermal vents, with surrounding  ecosystem.


Basics of photosynthesis (video).


Some non-oxygen respiration types, with products.


Energy in ecosystems.


A food chain.

Organisms interact with their environments.

Since every activity in a cell loses a bit of energy in the process, an outside source of energy is needed.  Chemicals break down to bits that can no longer be needed, and more chemicals must be taken in.  There might be consumers out there looking to consume you.  For these and many more reasons, living things have to exist in a give-and-take relationship with the world around them.  They need to be able to sense important aspects of the world and respond to them.

Organisms make more organisms like them.

It might have occurred to you, when trying to imagine what makes something alive, that "Living things die."  That turns out not to be useful, since death is just the absence of Life, and it's not even always true.  Organisms can die, but some may not ever do so.

 It was mentioned that living things on Earth have a coding system based on DNA.  That coding system directs and controls the protein-based chemistry of living things, but it is also a way of passing on all of the information needed to make another individual.  This is called a genetic system, and it factors into an important ability of living things:  reproduction.

Since organisms can die, any population would most likely eventually die out without replacements, and reproduction provides those replacements.

There are two basic types of reproduction, and students often find this confusing because they think they know the differences when they really don't. 

In sexual reproduction, there are two sets of the coding instructions that may be different;  these two sets get mixed up and recombined in offspring.  Offspring are a genetic mixture different from the parent or parents.  Single individuals can, and often do, reproduce sexually all by themselves, just by changing the code mixtures - reproducing alone does not imply asexual reproduction.  Sexual reproduction also does not always involves genders, although male and female roles (based on how the cells work) are common.

In asexual reproduction, a complete set of coding instructions, just like the parent's, are sent on to offspring.  The offspring may use those codes differently (all of the cells in your body have the same codes, but they use different bits to do different jobs), but they still have the same ones.  In a very real way, this is the only type that is really reproduction, since only asexual reproduction makes copies of individuals.

Each reproduction type has advantages over the other.  The advantage of asexual reproduction has already been mentioned:  it actually can make copies.  The disadvantage to this is that populations of asexual reproducers tend to be very much alike;  something that will hurt or kill one is likely to hurt or kill them all.  Asexual reproducers counteract this disadvantage by making huge numbers of offspring:  this spreads offspring out so that some may avoid that bad thing, and it increases the odds that some "bad copies" might actually be "good," with a change that makes them able to survive the factor that's killing the rest.  Most asexual reproducers are single-celled or tiny, which makes them able to produce large numbers of offspring fairly quickly.

Sexual reproduction can't make actual copies, and that's a definite reproductive disadvantage, but the offspring have a lot of variation, which makes a new danger less likely to be equally dangerous to all.  Most multicelled organisms, especially those big enough to be visible without a microscope, are sexual reproducers.

Connected to reproduction, most organisms also go through growth and development between their "birth" and the age at which they themselves can reproduce.

The coding system, really simplified.


Many individual plants sexually reproduce by themselves.


Types of asexual reproduction (how old is an individual produced by binary fission?).

Populations of organisms can change over time - they evolve.

This one is different, because it can't be applied to individuals but only general types, kind of the "average" individual in a population.  An individual dog is enough like the "average" dog to be clearly a dog, but a fox is not a dog, because an "average" fox is too different.  Foxes and dogs are clearly similar, obviously related, and that relationship implies that if you go back along their family tree far enough, you'll find a past relative they share, which belonged to a group with a different "average" definition - not a dog, not a fox, probably not even "in between," but a group that eventually led to both groups of today.  The changes that have happened to the average individual between that past group and today is evolution.

It was the discovery and analysis of fossils that led folks to realize that the world has not always been the same, that organisms, related to those of today but obviously different existed in the past.  They recognized that evolution had happened and sought to explain how one type could change to another.  One man came up with a particularly satisfying explanation:  Charles Darwin developed his Theory of Evolution by Natural Selection.  This will get discussed more later, but here are the basics:

In a population, there is variation among the individuals.  The features of the environment (Nature) at any given time affect different individuals differently.  The individuals with traits that help them survive current conditions (or help them to be particularly successful at reproduction) are more likely to make more offspring, many of which will genetically inherit those helpful traits.  Traits suited to an environment will become more common, and over time (especially in circumstances where the environment is changing) the "average individual" will be quite different from its ancestor.  Descendant populations in different places, or working different parts of one environment, can split off until their genetic systems aren't compatible any more.

A related process is sexual selection, where the features that change over time relate to success at reproduction (and can apply to asexual reproducers as well as sexual ones).  Since evolution is heavily based on passing feature variations to offspring that become more common or rare in the population over time, it makes sense that these types of features also change.  There sometimes is a sort of conflict between the two types - think of a peacock tail, which can increase the odds of getting mates but also the odds of getting caught by predators.

Evidence for this can be seen in the genetic systems themselves, in fossils, in observations of it actually happening in quick-turnover populations and/or populations under environmental stress.  There is more to modern evolutionary theory than just natural selection, but it is still thought to be a major driving force in the changes that have been seen over and over again.

One somewhat strange piece of evidence for evolution by natural selection is found in some types of organisms that seem to have not changed from their fossil relatives.  How could they not evolve?  First, the fossil just gives you some basic anatomical parts to compare, and the ancestors could have changed greatly in their basic chemistry.  But maybe they didn't.  These organisms have one thing in common:  they live in parts of the environment that don't really change over even long periods of time:  deep open oceans (where large quick sharks have swum for a very long time), or surf zones (where horseshoe crabs have scrambled for hundreds of millions of years).  These types of organisms have been found to actually resist the mutations that add variation to others.





Fossils - Strengths and Weaknesses.

A specimen between fish and land vertebrates (Video).

Back the other way:  fossils showing ancestry of whales.

A bit about Darwin.

Evolution observed in modern Galapagos finches.

Evolution and environmental change - seen.

How natural selection led to the evolution of human "childhood diseases."

Darwin rap-? (video)

What exactly are fossils?  These are parts of living things that have managed to stick around for very long times.  Fossils are usually hard parts, such as bones, shells, and teeth, that are difficult to eat, and fossils are usually the remains of organisms that have been buried in some way before their hard parts could be broken down by natural processes.  The most common fossils are animal remains (plant remains, even trees, tend to get broken down fairly quickly) that have sunken to the bottom of a large body of water and been covered with sediment.   Sediment builds on sediment, layer after layer, compressing and picking up minerals, becoming sedimentary rock (this is oversimplifying it).  Tectonic plates, huge rafts of earth crust that float past, over, and under each other, drive former ocean bottom up out of the water and make it part of the continents, where people can see it, layer upon layer of fossil organisms.  Deeper layers tend to be older, and layers of ocean organisms from the same time periods have similar species in them, allowing a master list of layers to be developed from fossil beds in different places.

Some fossils form when small animals or plants are covered in special sap, which traps the organisms, protects them from any breakdown, and mineralizes into amber.  Bacteria millions of years old have been isolated from amber fossils and reawakened.  Organisms may be buried in mudslides, or sandstorms, or in tar pits, to become fossils.  Ash from volcanic eruptions can bury organisms (or quickly dry and bury footprints), although lava tend to incinerate everything.  Some of the best fossils come from special bodies of water that had lost most of their oxygen:  there were few things to eat the soft parts of the bodies that sank to the bottom, and the sediments were particularly soft and sludgy, often molding parts like skin surfaces and feathers.

A website all about fossils.

Many pictures of fossils.

Fossil feathers may even give evidence of color.

Fossils that include soft-body parts.

A bit on fossil footprints of human ancestors.




Applying the Rules - What About Viruses?

We have to wonder how many of the rules that define Life on this planet would apply to legitimately living things that evolved somewhere else.  However, there are even things on this planet that don't quite fit the rules, and so are thought to be alive by some people but not so by others.  These are the viruses.

Viruses may be descendants of pre-cellular molecular collections from the very earliest abiogenesis.  They invade "regular" cells, particular viruses limited to particular types of hosts and cells, and make more viruses to infect more cells.


They definitely reproduce, but they use the genetic expression chemistry of the host cell to do it.  Often, all that enters the host cell is viral DNA, and the cell taps into that code the same way it would do an abnormal code of its own, making the proteins of new viruses from the gene codes and making more viral DNA.   Eventually, new viruses are packaged, either in their protein structures or with protein-enhanced bits of the cell's own membrane, and the viruses are freed to infect more cells.

They evolve.  Reproduction is asexual, but the making of new virus DNA tends to be sloppy (cells have ways to check the process and correct mistakes that the viruses can't use), so the codes often change, producing altered virus "copies."  They may even pick up and integrate codes from the host, carrying them to new hosts.  Most alteration of offspring would be sub-standard, but among the millions of copies will be viruses with useful changes.


Going through the rules covered here, in order -

Although viruses are internally organized, the method of organization depends totally on processes stolen from the host cell.  Some people think this breaks the rule, but many clearly living organisms do the same thing - an adult tapeworm, for example, is totally dependent on the digestive processes of the host to gain the nutrients it needs.  A virus' complexity is very limited:  outside, it has a few proteins that help it get to, recognize, and enter the next host cell;  inside, it has its DNA and maybe a protein or two to get its processes started in the next host.

Viruses are not truly cellular.  Many have no cellular structures at all, and the ones that have membranes generally just steal them from the host cell, adding some proteins in the process.

Inside a host, a virus totally depends on the metabolic fuels and processes of the host to construct new viruses.  Between hosts, a virus is kind of like a trap, pre-set to react when the proper host cell is contacted, but there are no internal metabolic processes going on.  Viruses of important disease are very difficult to develop effective treatments for partly for this reason:  treatments often interfere with a disease organism's particular chemistry, but viruses generally use the chemistry of the host cell, which you don't want to poison, and have no active chemistry when they are out and about.  Our body defenses are limited to attacking recognizably altered host cells (and they may not be altered enough to be recognized) and gobbling up free viruses.

Interaction with the environment for a virus is limited to the response it gives from bumping into the right chemicals on the appropriate host cell.  It doesn't respond to anything else, really.

So, are viruses really Life?  It's just a definition, of course, and the viruses don't seem to care too much.

Introduction to viruses.




Are virus-like entities our distant ancestors?




The Big Picture Book of Viruses.




Introduction to coronaviruses.




History of Virus Studies.




Animation of Virus Activity.




Animation of HIV (AIDS) Virus Activity with Technical Narration.





Go On to Next Chapter - Science 






Introduction to Biology - Molecules & Cells.
For SCI-135.

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